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Sample records for target linkage assay-identified

  1. Kinase profiling of liposarcomas using RNAi and drug screening assays identified druggable targets

    Directory of Open Access Journals (Sweden)

    Deepika Kanojia

    2017-11-01

    Full Text Available Abstract Background Liposarcoma, the most common soft tissue tumor, is understudied cancer, and limited progress has been made in the treatment of metastatic disease. The Achilles heel of cancer often is their kinases that are excellent therapeutic targets. However, very limited knowledge exists of therapeutic critical kinase targets in liposarcoma that could be potentially used in disease management. Methods Large RNAi and small-molecule tyrosine kinase inhibitor screens were performed against the proliferative capacity of liposarcoma cell lines of different subtypes. Each small molecule inhibitor was either FDA approved or in a clinical trial. Results Screening assays identified several previously unrecognized targets including PTK2 and KIT in liposarcoma. We also observed that ponatinib, multi-targeted tyrosine kinase inhibitor, was the most effective drug with anti-growth effects against all cell lines. In vitro assays showed that ponatinib inhibited the clonogenic proliferation of liposarcoma, and this anti-growth effect was associated with apoptosis and cell cycle arrest at the G0/G1 phase as well as a decrease in the KIT signaling pathway. In addition, ponatinib inhibited in vivo growth of liposarcoma in a xenograft model. Conclusions Two large-scale kinase screenings identified novel liposarcoma targets and a FDA-approved inhibitor, ponatinib with clear anti-liposarcoma activity highlighting its potential therapy for treatment of this deadly tumor.

  2. High-throughput screening in niche-based assay identifies compounds to target preleukemic stem cells

    Science.gov (United States)

    Gerby, Bastien; Veiga, Diogo F.T.; Krosl, Jana; Nourreddine, Sami; Ouellette, Julianne; Haman, André; Lavoie, Geneviève; Fares, Iman; Tremblay, Mathieu; Litalien, Véronique; Ottoni, Elizabeth; Geoffrion, Dominique; Maddox, Paul S.; Chagraoui, Jalila; Hébert, Josée; Sauvageau, Guy; Kwok, Benjamin H.; Roux, Philippe P.

    2016-01-01

    Current chemotherapies for T cell acute lymphoblastic leukemia (T-ALL) efficiently reduce tumor mass. Nonetheless, disease relapse attributed to survival of preleukemic stem cells (pre-LSCs) is associated with poor prognosis. Herein, we provide direct evidence that pre-LSCs are much less chemosensitive to existing chemotherapy drugs than leukemic blasts because of a distinctive lower proliferative state. Improving therapies for T-ALL requires the development of strategies to target pre-LSCs that are absolutely dependent on their microenvironment. Therefore, we designed a robust protocol for high-throughput screening of compounds that target primary pre-LSCs maintained in a niche-like environment, on stromal cells that were engineered for optimal NOTCH1 activation. The multiparametric readout takes into account the intrinsic complexity of primary cells in order to specifically monitor pre-LSCs, which were induced here by the SCL/TAL1 and LMO1 oncogenes. We screened a targeted library of compounds and determined that the estrogen derivative 2-methoxyestradiol (2-ME2) disrupted both cell-autonomous and non–cell-autonomous pathways. Specifically, 2-ME2 abrogated pre-LSC viability and self-renewal activity in vivo by inhibiting translation of MYC, a downstream effector of NOTCH1, and preventing SCL/TAL1 activity. In contrast, normal hematopoietic stem/progenitor cells remained functional. These results illustrate how recapitulating tissue-like properties of primary cells in high-throughput screening is a promising avenue for innovation in cancer chemotherapy. PMID:27797342

  3. A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

    Science.gov (United States)

    Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

    2017-07-05

    The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

  4. Active targeted HIV testing and linkage to care among men who have sex with men attending a gay sauna in Thailand.

    Science.gov (United States)

    Khawcharoenporn, Thana; Apisarnthanarak, Anucha; Phanuphak, Nittaya

    2017-03-01

    Existing data on the feasibility of human immunodeficiency virus (HIV) testing and counseling (HTC) and linkage to care among men who have sex with men (MSM) in hotspots are currently limited. A prospective study on active targeted HTC and linkage to care among MSM (≥18 years old) was conducted at a gay sauna in Thailand from November 2013 to October 2015. HIV risks and risk perception were evaluated through an anonymous survey. HIV testing with result notification and care appointment arrangement were provided on-site. Of the 358 participants; median age was 30 years; 206/358(58%) were at high risk for HIV acquisition; 148/358(41%) accepted HTC, all of whom either had prior negative HIV tests [98/148 (66%)] or had not known their HIV status [50/148 (34%)]. The three most common reasons for declining HTC were prior HIV testing within 6 months (48%), not ready (19%) and perceiving self as no risk (11%). Of the 262 moderate- and high-risk participants, 172 (66%) had false perception of low HIV risk which was significantly associated with declining HTC. Among the 148 participants undergoing HTC, 25 (17%) were HIV-infected. Having false perception of low risk (P = 0.004) and age antiretroviral therapy. The active targeted HTC and facilitating care establishment was feasible among MSM attending the gay sauna but required strategies to improve accuracy of HIV-risk perception and linkage to care.

  5. [Linkage analysis of susceptibility loci in 2 target chromosomes in pedigrees with paranoid schizophrenia and undifferentiated schizophrenia].

    Science.gov (United States)

    Zeng, Li-ping; Hu, Zheng-mao; Mu, Li-li; Mei, Gui-sen; Lu, Xiu-ling; Zheng, Yong-jun; Li, Pei-jian; Zhang, Ying-xue; Pan, Qian; Long, Zhi-gao; Dai, He-ping; Zhang, Zhuo-hua; Xia, Jia-hui; Zhao, Jing-ping; Xia, Kun

    2011-06-01

    To investigate the relationship of susceptibility loci in chromosomes 1q21-25 and 6p21-25 and schizophrenia subtypes in Chinese population. A genomic scan and parametric and non-parametric analyses were performed on 242 individuals from 36 schizophrenia pedigrees, including 19 paranoid schizophrenia and 17 undifferentiated schizophrenia pedigrees, from Henan province of China using 5 microsatellite markers in the chromosome region 1q21-25 and 8 microsatellite markers in the chromosome region 6p21-25, which were the candidates of previous studies. All affected subjects were diagnosed and typed according to the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revised (DSM-IV-TR; American Psychiatric Association, 2000). All subjects signed informed consent. In chromosome 1, parametric analysis under the dominant inheritance mode of all 36 pedigrees showed that the maximum multi-point heterogeneity Log of odds score method (HLOD) score was 1.33 (α = 0.38). The non-parametric analysis and the single point and multi-point nonparametric linkage (NPL) scores suggested linkage at D1S484, D1S2878, and D1S196. In the 19 paranoid schizophrenias pedigrees, linkage was not observed for any of the 5 markers. In the 17 undifferentiated schizophrenia pedigrees, the multi-point NPL score was 1.60 (P= 0.0367) at D1S484. The single point NPL score was 1.95(P= 0.0145) and the multi-point NPL score was 2.39 (P= 0.0041) at D1S2878. Additionally, the multi-point NPL score was 1.74 (P= 0.0255) at D1S196. These same three loci showed suggestive linkage during the integrative analysis of all 36 pedigrees. In chromosome 6, parametric linkage analysis under the dominant and recessive inheritance and the non-parametric linkage analysis of all 36 pedigrees and the 17 undifferentiated schizophrenia pedigrees, linkage was not observed for any of the 8 markers. In the 19 paranoid schizophrenias pedigrees, parametric analysis showed that under recessive

  6. A sensitive HIV-1 envelope induced fusion assay identifies fusion enhancement of thrombin

    International Nuclear Information System (INIS)

    Cheng, De-Chun; Zhong, Guo-Cai; Su, Ju-Xiang; Liu, Yan-Hong; Li, Yan; Wang, Jia-Ye; Hattori, Toshio; Ling, Hong; Zhang, Feng-Min

    2010-01-01

    To evaluate the interaction between HIV-1 envelope glycoprotein (Env) and target cell receptors, various cell-cell-fusion assays have been developed. In the present study, we established a novel fusion system. In this system, the expression of the sensitive reporter gene, firefly luciferase (FL) gene, in the target cells was used to evaluate cell fusion event. Simultaneously, constitutively expressed Renilla luciferase (RL) gene was used to monitor effector cell number and viability. FL gave a wider dynamic range than other known reporters and the introduction of RL made the assay accurate and reproducible. This system is especially beneficial for investigation of potential entry-influencing agents, for its power of ruling out the false inhibition or enhancement caused by the artificial cell-number variation. As a case study, we applied this fusion system to observe the effect of a serine protease, thrombin, on HIV Env-mediated cell-cell fusion and have found the fusion enhancement activity of thrombin over two R5-tropic HIV strains.

  7. Dimeric DNA Aptamer Complexes for High-capacity–targeted Drug Delivery Using pH-sensitive Covalent Linkages

    Directory of Open Access Journals (Sweden)

    Olcay Boyacioglu

    2013-01-01

    Full Text Available Treatment with doxorubicin (Dox results in serious systemic toxicities that limit effectiveness for cancer treatment and cause long-term health issues for cancer patients. We identified a new DNA aptamer to prostate-specific membrane antigen (PSMA using fixed sequences to promote Dox binding and developed dimeric aptamer complexes (DACs for specific delivery of Dox to PSMA+ cancer cells. DACs are stable under physiological conditions and are internalized specifically into PSMA+ C4-2 cells with minimal uptake into PSMA-null PC3 cells. Cellular internalization of DAC was demonstrated by confocal microscopy and flow cytometry. Covalent modification of DAC with Dox (DAC-D resulted in a complex with stoichiometry ~4:1. Dox was covalently bound in DAC-D using a reversible linker that promotes covalent attachment of Dox to genomic DNA following cell internalization. Dox was released from the DAC-D under physiological conditions with a half-life of 8 hours, sufficient for in vivo targeting. DAC-D was used to selectively deliver Dox to C4-2 cells with endosomal release and nuclear localization of Dox. DAC-D was selectively cytotoxic to C4-2 cells with similar cytotoxicity as the molar equivalent of free-Dox. In contrast, DAC-D displayed minimal cytotoxicity to PC3 cells, demonstrating the complex displays a high degree of selectivity for PSMA+ cells. DAC-D displays specificity and stability features that may be useful for improved delivery of Dox selectively to malignant tissue in vivo.

  8. Care Cascade for targeted tuberculosis testing and linkage to Care in Homeless Populations in the United States: a meta-analysis.

    Science.gov (United States)

    Parriott, Andrea; Malekinejad, Mohsen; Miller, Amanda P; Marks, Suzanne M; Horvath, Hacsi; Kahn, James G

    2018-04-12

    Homelessness increases the risk of tuberculosis (TB) disease and latent TB infection (LTBI), but persons experiencing homelessness often lack access to testing and treatment. We assessed the yield of TB testing and linkage to care for programs targeting homeless populations in the United States. We conducted a comprehensive search of peer-reviewed and grey literature, adapting Cochrane systematic review methods. Two reviewers independently assessed study eligibility and abstracted key data on the testing to care cascade: number of persons reached, recruited for testing, tested for LTBI, with valid test results, referred to follow-up care, and initiating care. We used random effects to calculate pooled proportions and 95% confidence intervals (CI) of persons retained in each step via inverse-variance weighted meta-analysis, and cumulative proportions as products of adjacent step proportions. We identified 23 studies published between 1986 and 2014, conducted in 12 states and 15 cities. Among studies using tuberculin skin tests (TST) we found that 93.7% (CI 72.4-100%) of persons reached were recruited, 97.9% (89.3-100%) of those recruited had tests placed, 85.5% (78.6-91.3%) of those with tests placed returned for reading, 99.9% (99.6-100%) of those with tests read had valid results, and 24.7% (21.0-28.5%) with valid results tested positive. All persons testing positive were referred to follow-up care, and 99.8% attended at least one session of follow-up care. Heterogeneity was high for most pooled proportions. For a hypothetical cohort of 1000 persons experiencing homelessness reached by a targeted testing program using TST, an estimated 917 were tested, 194 were positive, and all of these initiated follow-up care. Targeted TB testing of persons experiencing homelessness appears effective in detecting LTBI and connecting persons to care and potential treatment. Future evaluations should assess diagnostic use of interferon gamma release assays and completion of

  9. VT Wildlife Linkage Habitat

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The Wildlife Linkage Habitat Analysis uses landscape scale data to identify or predict the location of potentially significant wildlife linkage...

  10. Subsidiary Linkage Patterns

    DEFF Research Database (Denmark)

    Andersson, Ulf; Perri, Alessandra; Nell, Phillip C.

    2012-01-01

    channels for spillovers to competitors. We find a curvilinear relationship between the extent of competitive pressure and the quality of a subsidiary's set of local linkages. Furthermore, the extent to which a subsidiary possesses capabilities moderates this relationship: Very capable subsidiaries...... in strongly competitive environments tend to shy away from high quality linkages. We discuss our findings in light of the literature on spillovers and inter-organizational linkages.......This paper investigates the pattern of subsidiaries' local vertical linkages under varying levels of competition and subsidiary capabilities. Contrary to most previous literature, we explicitly account for the double role of such linkages as conduits of learning prospects as well as potential...

  11. Probabilistic record linkage.

    Science.gov (United States)

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-06-01

    Studies involving the use of probabilistic record linkage are becoming increasingly common. However, the methods underpinning probabilistic record linkage are not widely taught or understood, and therefore these studies can appear to be a 'black box' research tool. In this article, we aim to describe the process of probabilistic record linkage through a simple exemplar. We first introduce the concept of deterministic linkage and contrast this with probabilistic linkage. We illustrate each step of the process using a simple exemplar and describe the data structure required to perform a probabilistic linkage. We describe the process of calculating and interpreting matched weights and how to convert matched weights into posterior probabilities of a match using Bayes theorem. We conclude this article with a brief discussion of some of the computational demands of record linkage, how you might assess the quality of your linkage algorithm, and how epidemiologists can maximize the value of their record-linked research using robust record linkage methods. © The Author 2015; Published by Oxford University Press on behalf of the International Epidemiological Association.

  12. A yeast-based assay identifies drugs that interfere with immune evasion of the Epstein-Barr virus

    Directory of Open Access Journals (Sweden)

    Cécile Voisset

    2014-04-01

    Full Text Available Epstein-Barr virus (EBV is tightly associated with certain human cancers, but there is as yet no specific treatment against EBV-related diseases. The EBV-encoded EBNA1 protein is essential to maintain viral episomes and for viral persistence. As such, EBNA1 is expressed in all EBV-infected cells, and is highly antigenic. All infected individuals, including individuals with cancer, have CD8+ T cells directed towards EBNA1 epitopes, yet the immune system fails to detect and destroy cells harboring the virus. EBV immune evasion depends on the capacity of the Gly-Ala repeat (GAr domain of EBNA1 to inhibit the translation of its own mRNA in cis, thereby limiting the production of EBNA1-derived antigenic peptides presented by the major histocompatibility complex (MHC class I pathway. Here we establish a yeast-based assay for monitoring GAr-dependent inhibition of translation. Using this assay we identify doxorubicin (DXR as a compound that specifically interferes with the GAr effect on translation in yeast. DXR targets the topoisomerase-II–DNA complexes and thereby causes genomic damage. We show, however, that the genotoxic effect of DXR and various analogs thereof is uncoupled from the effect on GAr-mediated translation control. This is further supported by the observation that etoposide and teniposide, representing another class of topoisomerase-II–DNA targeting drugs, have no effect on GAr-mediated translation control. DXR and active analogs stimulate, in a GAr-dependent manner, EBNA1 expression in mammalian cells and overcome GAr-dependent restriction of MHC class I antigen presentation. These results validate our approach as an effective high-throughput screening assay to identify drugs that interfere with EBV immune evasion and, thus, constitute candidates for treating EBV-related diseases, in particular EBV-associated cancers.

  13. A yeast-based assay identifies drugs that interfere with immune evasion of the Epstein-Barr virus.

    Science.gov (United States)

    Voisset, Cécile; Daskalogianni, Chrysoula; Contesse, Marie-Astrid; Mazars, Anne; Arbach, Hratch; Le Cann, Marie; Soubigou, Flavie; Apcher, Sébastien; Fåhraeus, Robin; Blondel, Marc

    2014-04-01

    Epstein-Barr virus (EBV) is tightly associated with certain human cancers, but there is as yet no specific treatment against EBV-related diseases. The EBV-encoded EBNA1 protein is essential to maintain viral episomes and for viral persistence. As such, EBNA1 is expressed in all EBV-infected cells, and is highly antigenic. All infected individuals, including individuals with cancer, have CD8(+) T cells directed towards EBNA1 epitopes, yet the immune system fails to detect and destroy cells harboring the virus. EBV immune evasion depends on the capacity of the Gly-Ala repeat (GAr) domain of EBNA1 to inhibit the translation of its own mRNA in cis, thereby limiting the production of EBNA1-derived antigenic peptides presented by the major histocompatibility complex (MHC) class I pathway. Here we establish a yeast-based assay for monitoring GAr-dependent inhibition of translation. Using this assay we identify doxorubicin (DXR) as a compound that specifically interferes with the GAr effect on translation in yeast. DXR targets the topoisomerase-II-DNA complexes and thereby causes genomic damage. We show, however, that the genotoxic effect of DXR and various analogs thereof is uncoupled from the effect on GAr-mediated translation control. This is further supported by the observation that etoposide and teniposide, representing another class of topoisomerase-II-DNA targeting drugs, have no effect on GAr-mediated translation control. DXR and active analogs stimulate, in a GAr-dependent manner, EBNA1 expression in mammalian cells and overcome GAr-dependent restriction of MHC class I antigen presentation. These results validate our approach as an effective high-throughput screening assay to identify drugs that interfere with EBV immune evasion and, thus, constitute candidates for treating EBV-related diseases, in particular EBV-associated cancers.

  14. A pantograph linkage

    International Nuclear Information System (INIS)

    Cole, G.V.

    1982-01-01

    A pantograph linkage is actuated by two linear actuators, pivotally connected together at the linkage. The displacement of the actuators is monitored by rectilinear potentiometers to provide feedback signals to a microprocessor which also receives input signals related to a required movement of a slave end of the linkage. In response to these signals, the microprocessor provides signals to control the displacement of the linear actuators to effect the required movement of the slave end. The movement of the slave end might be straightline in a substantially horizontal or vertical direction. (author)

  15. A high throughput Cre–lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry

    Energy Technology Data Exchange (ETDEWEB)

    Esposito, Anthony M. [Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, Immunology Institute, New York, NY (United States); Cheung, Pamela [Integrated Screening Core, Icahn School of Medicine at Mount Sinai, New York, NY (United States); Swartz, Talia H.; Li, Hongru [Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, Immunology Institute, New York, NY (United States); Tsibane, Tshidi [Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY (United States); Durham, Natasha D. [Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, Immunology Institute, New York, NY (United States); Basler, Christopher F. [Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY (United States); Felsenfeld, Dan P. [Integrated Screening Core, Icahn School of Medicine at Mount Sinai, New York, NY (United States); Chen, Benjamin K., E-mail: benjamin.chen@mssm.edu [Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, Immunology Institute, New York, NY (United States)

    2016-03-15

    Enveloped virus entry occurs when viral and cellular membranes fuse releasing particle contents into the target cell. Human immunodeficiency virus (HIV) entry occurs by cell-free virus or virus transferred between infected and uninfected cells through structures called virological synapses. We developed a high-throughput cell-based assay to identify small molecule inhibitors of cell-free or virological synapse-mediated entry. An HIV clone carrying Cre recombinase as a Gag-internal gene fusion releases active Cre into cells upon viral entry activating a recombinatorial gene switch changing dsRed to GFP-expression. A screen of a 1998 known-biological profile small molecule library identified pharmacological HIV entry inhibitors that block both cell-free and cell-to-cell infection. Many top hits were noted as HIV inhibitors in prior studies, but not previously recognized as entry antagonists. Modest therapeutic indices for simvastatin and nigericin were observed in confirmatory HIV infection assays. This robust assay is adaptable to study HIV and heterologous viral pseudotypes. - Highlights: • Cre recombinase viral fusion assay screens cell-free or cell–cell entry inhibitors. • This Gag-iCre based assay is specific for the entry step of HIV replication. • Screened a library of known pharmacologic compounds for HIV fusion antagonists. • Many top hits were previously noted as HIV inhibitors, but here are classified as entry antagonists. Many top hits were previously noted as HIV inhibitors, but not as entry antagonists. • The assay is compatible with pseudotyping with HIV and heterologous viruses.

  16. A high throughput Cre–lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry

    International Nuclear Information System (INIS)

    Esposito, Anthony M.; Cheung, Pamela; Swartz, Talia H.; Li, Hongru; Tsibane, Tshidi; Durham, Natasha D.; Basler, Christopher F.; Felsenfeld, Dan P.; Chen, Benjamin K.

    2016-01-01

    Enveloped virus entry occurs when viral and cellular membranes fuse releasing particle contents into the target cell. Human immunodeficiency virus (HIV) entry occurs by cell-free virus or virus transferred between infected and uninfected cells through structures called virological synapses. We developed a high-throughput cell-based assay to identify small molecule inhibitors of cell-free or virological synapse-mediated entry. An HIV clone carrying Cre recombinase as a Gag-internal gene fusion releases active Cre into cells upon viral entry activating a recombinatorial gene switch changing dsRed to GFP-expression. A screen of a 1998 known-biological profile small molecule library identified pharmacological HIV entry inhibitors that block both cell-free and cell-to-cell infection. Many top hits were noted as HIV inhibitors in prior studies, but not previously recognized as entry antagonists. Modest therapeutic indices for simvastatin and nigericin were observed in confirmatory HIV infection assays. This robust assay is adaptable to study HIV and heterologous viral pseudotypes. - Highlights: • Cre recombinase viral fusion assay screens cell-free or cell–cell entry inhibitors. • This Gag-iCre based assay is specific for the entry step of HIV replication. • Screened a library of known pharmacologic compounds for HIV fusion antagonists. • Many top hits were previously noted as HIV inhibitors, but here are classified as entry antagonists. Many top hits were previously noted as HIV inhibitors, but not as entry antagonists. • The assay is compatible with pseudotyping with HIV and heterologous viruses.

  17. Thermally actuated linkage arrangement

    International Nuclear Information System (INIS)

    Anderson, P.M.

    1981-01-01

    A reusable thermally actuated linkage arrangement includes a first link member having a longitudinal bore therein adapted to receive at least a portion of a second link member therein, the first and second members being sized to effect an interference fit preventing relative movement there-between at a temperature below a predetermined temperature. The link members have different coefficients of thermal expansion so that when the linkage is selectively heated by heating element to a temperature above the predetermined temperature, relative longitudinal and/or rotational movement between the first and second link members is enabled. Two embodiments of a thermally activated linkage are disclosed which find particular application in actuators for a grapple head positioning arm in a nuclear reactor fuel handling mechanism to facilitate back-up safety retraction of the grapple head independently from the primary fuel handling mechanism drive system. (author)

  18. Clause linkage in Ket

    NARCIS (Netherlands)

    Nefedov, Andrey

    2015-01-01

    This work provides a typologically oriented description of clause linkage strategies in Ket, a highly endangered language spoken in Central Siberia. It is now the only surviving member of the Yeniseian language family with the last remaining speakers residing in the north of Russia’s Krasnoyarsk

  19. Design of special planar linkages

    CERN Document Server

    Zhao, Jing-Shan; Ma, Ning; Chu, Fulei

    2013-01-01

    Planar linkages play a very important role in mechanical engineering. As the simplest closed chain mechanisms, planar four-bar linkages are widely used in mechanical engineering, civil engineering and aerospace engineering.Design of Special Planar Linkages proposes a uniform design theory for planar four-bar linkages. The merit of the method proposed in this book is that it allows engineers to directly obtain accurate results when there are such solutions for the specified n precise positions; otherwise, the best approximate solutions will be found. This book discusses the kinematics and reach

  20. A Formalization of Linkage Analysis

    DEFF Research Database (Denmark)

    Ingolfsdottir, Anna; Christensen, A.I.; Hansen, Jens A.

    In this report a formalization of genetic linkage analysis is introduced. Linkage analysis is a computationally hard biomathematical method, which purpose is to locate genes on the human genome. It is rooted in the new area of bioinformatics and no formalization of the method has previously been ...

  1. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages.

    Science.gov (United States)

    Yang, Xianbin

    2017-09-18

    The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  2. North-South Business Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Kuada, John

    2006-01-01

    Based on empirical studies of linkages between TNCs and local firms in India, Malaysia, Vietnam, Ghana and South Africa, five themes are discussed and related to present theoretical perspectives. The themes are (1) Linakge Governance; (2) Globalisation and the dynamics in developing countries (the...... TNC-driven markets in developing countries); (3) The upgrading impact of FDI; (4) Non-equity linkages as a platform for business development, and (5) The learning perspective on international business linakges. The chapter offers at the end a three-dimanional model for impacts of business linkages....

  3. From Enclave to Linkage Economies?

    DEFF Research Database (Denmark)

    Hansen, Michael W.

    as the enclave economy par excellence, moving in with fully integrated value chains, extracting resources and exporting them as commodities having virtually no linkages to the local economy. However, new opportunities for promoting linkages are offered by changing business strategies of local African enterprises...... as well as foreign multinational corporations (MNCs). MNCs in extractives are increasingly seeking local linkages as part of their efficiency, risk, and asset-seeking strategies, and linkage programmes are becoming integral elements in many MNCs’ corporate social responsibility (CSR) activities....... At the same time, local African enterprises are eager to, and increasingly capable of, linking up to the foreign investors in order to expand their activities and acquire technology, skills and market access. The changing strategies of MNCs and the improving capabilities of African enterprises offer new...

  4. Profiling the HER3/PI3K Pathway in Breast Tumors Using Proximity-Directed Assays Identifies Correlations between Protein Complexes and Phosphoproteins

    Science.gov (United States)

    Mukherjee, Ali; Badal, Youssouf; Nguyen, Xuan-Thao; Miller, Johanna; Chenna, Ahmed; Tahir, Hasan; Newton, Alicia; Parry, Gordon; Williams, Stephen

    2011-01-01

    Background The identification of patients for targeted antineoplastic therapies requires accurate measurement of therapeutic targets and associated signaling complexes. HER3 signaling through heterodimerization is an important growth-promoting mechanism in several tumor types and may be a principal resistance mechanism by which EGFR and HER2 expressing tumors elude targeted therapies. Current methods that can study these interactions are inadequate for formalin-fixed, paraffin-embedded (FFPE) tumor samples. Methodology and Principal Findings Herein, we describe a panel of proximity-directed assays capable of measuring protein-interactions and phosphorylation in FFPE samples in the HER3/PI3K/Akt pathway and examine the capability of these assays to inform on the functional state of the pathway. We used FFPE breast cancer cell line and tumor models for this study. In breast cancer cell lines we observe both ligand-dependent and independent activation of the pathway and strong correlations between measured activation of key analytes. When selected cell lines are treated with HER2 inhibitors, we not only observe the expected molecular effects based on mechanism of action knowledge, but also novel effects of HER2 inhibition on key targets in the HER receptor pathway. Significantly, in a xenograft model of delayed tumor fixation, HER3 phosphorylation is unstable, while alternate measures of pathway activation, such as formation of the HER3PI3K complex is preserved. Measurements in breast tumor samples showed correlations between HER3 phosphorylation and receptor interactions, obviating the need to use phosphorylation as a surrogate for HER3 activation. Significance This assay system is capable of quantitatively measuring therapeutically relevant responses and enables molecular profiling of receptor networks in both preclinical and tumor models. PMID:21297994

  5. High-throughput screening using the differential radial capillary action of ligand assay identifies ebselen as an inhibitor of diguanylate cyclases.

    Science.gov (United States)

    Lieberman, Ori J; Orr, Mona W; Wang, Yan; Lee, Vincent T

    2014-01-17

    The rise of bacterial resistance to traditional antibiotics has motivated recent efforts to identify new drug candidates that target virulence factors or their regulatory pathways. One such antivirulence target is the cyclic-di-GMP (cdiGMP) signaling pathway, which regulates biofilm formation, motility, and pathogenesis. Pseudomonas aeruginosa is an important opportunistic pathogen that utilizes cdiGMP-regulated polysaccharides, including alginate and pellicle polysaccharide (PEL), to mediate virulence and antibiotic resistance. CdiGMP activates PEL and alginate biosynthesis by binding to specific receptors including PelD and Alg44. Mutations that abrogate cdiGMP binding to these receptors prevent polysaccharide production. Identification of small molecules that can inhibit cdiGMP binding to the allosteric sites on these proteins could mimic binding defective mutants and potentially reduce biofilm formation or alginate secretion. Here, we report the development of a rapid and quantitative high-throughput screen for inhibitors of protein-cdiGMP interactions based on the differential radial capillary action of ligand assay (DRaCALA). Using this approach, we identified ebselen as an inhibitor of cdiGMP binding to receptors containing an RxxD domain including PelD and diguanylate cyclases (DGC). Ebselen reduces diguanylate cyclase activity by covalently modifying cysteine residues. Ebselen oxide, the selenone analogue of ebselen, also inhibits cdiGMP binding through the same covalent mechanism. Ebselen and ebselen oxide inhibit cdiGMP regulation of biofilm formation and flagella-mediated motility in P. aeruginosa through inhibition of diguanylate cyclases. The identification of ebselen provides a proof-of-principle that a DRaCALA high-throughput screening approach can be used to identify bioactive agents that reverse regulation of cdiGMP signaling by targeting cdiGMP-binding domains.

  6. Genetic linkage map of cowpea ( Vigna unguiculata (L.) Walp) using ...

    African Journals Online (AJOL)

    Genetic linkage maps provide a genomic framework for quantitative trait loci identification applied in marker assisted selection breeding in crops with limited resources. It serves as a powerful tool to breeders for analysing the mode of inheritance of genes of interest and monitoring of the transmission of target genes from ...

  7. STAKEHOLDER LINKAGES FOR SUSTAINABLE LAND ...

    African Journals Online (AJOL)

    Osondu

    Key words: Stakeholders; farmer-expert linkages; resource management; Ethiopia. Introduction ... decentralized democratic decision making processes and thus ..... district offices within the given time limits. They were often .... -less willing and less ready to hearing weaker performance reports (expect more success with ...

  8. Exploitation of linkage learning in evolutionary algorithms

    CERN Document Server

    Chen, Ying-ping

    2010-01-01

    The exploitation of linkage learning is enhancing the performance of evolutionary algorithms. This monograph examines recent progress in linkage learning, with a series of focused technical chapters that cover developments and trends in the field.

  9. Efficient Record Linkage Algorithms Using Complete Linkage Clustering.

    Science.gov (United States)

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times.

  10. Privacy preserving interactive record linkage (PPIRL).

    Science.gov (United States)

    Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

    2014-01-01

    Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.

  11. When to conduct probabilistic linkage vs. deterministic linkage? A simulation study.

    Science.gov (United States)

    Zhu, Ying; Matsuyama, Yutaka; Ohashi, Yasuo; Setoguchi, Soko

    2015-08-01

    When unique identifiers are unavailable, successful record linkage depends greatly on data quality and types of variables available. While probabilistic linkage theoretically captures more true matches than deterministic linkage by allowing imperfection in identifiers, studies have shown inconclusive results likely due to variations in data quality, implementation of linkage methodology and validation method. The simulation study aimed to understand data characteristics that affect the performance of probabilistic vs. deterministic linkage. We created ninety-six scenarios that represent real-life situations using non-unique identifiers. We systematically introduced a range of discriminative power, rate of missing and error, and file size to increase linkage patterns and difficulties. We assessed the performance difference of linkage methods using standard validity measures and computation time. Across scenarios, deterministic linkage showed advantage in PPV while probabilistic linkage showed advantage in sensitivity. Probabilistic linkage uniformly outperformed deterministic linkage as the former generated linkages with better trade-off between sensitivity and PPV regardless of data quality. However, with low rate of missing and error in data, deterministic linkage performed not significantly worse. The implementation of deterministic linkage in SAS took less than 1min, and probabilistic linkage took 2min to 2h depending on file size. Our simulation study demonstrated that the intrinsic rate of missing and error of linkage variables was key to choosing between linkage methods. In general, probabilistic linkage was a better choice, but for exceptionally good quality data (<5% error), deterministic linkage was a more resource efficient choice. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Bayesian estimates of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Abad-Grau María M

    2007-06-01

    Full Text Available Abstract Background The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. Results This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNPs that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. Conclusion Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.

  13. Challenges in administrative data linkage for research

    Directory of Open Access Journals (Sweden)

    Katie Harron

    2017-12-01

    Full Text Available Linkage of population-based administrative data is a valuable tool for combining detailed individual-level information from different sources for research. While not a substitute for classical studies based on primary data collection, analyses of linked administrative data can answer questions that require large sample sizes or detailed data on hard-to-reach populations, and generate evidence with a high level of external validity and applicability for policy making. There are unique challenges in the appropriate research use of linked administrative data, for example with respect to bias from linkage errors where records cannot be linked or are linked together incorrectly. For confidentiality and other reasons, the separation of data linkage processes and analysis of linked data is generally regarded as best practice. However, the ‘black box’ of data linkage can make it difficult for researchers to judge the reliability of the resulting linked data for their required purposes. This article aims to provide an overview of challenges in linking administrative data for research. We aim to increase understanding of the implications of (i the data linkage environment and privacy preservation; (ii the linkage process itself (including data preparation, and deterministic and probabilistic linkage methods and (iii linkage quality and potential bias in linked data. We draw on examples from a number of countries to illustrate a range of approaches for data linkage in different contexts.

  14. Linkage disequilibrium and association mapping.

    Science.gov (United States)

    Weir, B S

    2008-01-01

    Linkage disequilibrium refers to the association between alleles at different loci. The standard definition applies to two alleles in the same gamete, and it can be regarded as the covariance of indicator variables for the states of those two alleles. The corresponding correlation coefficient rho is the parameter that arises naturally in discussions of tests of association between markers and genetic diseases. A general treatment of association tests makes use of the additive and nonadditive components of variance for the disease gene. In almost all expressions that describe the behavior of association tests, additive variance components are modified by the squared correlation coefficient rho2 and the nonadditive variance components by rho4, suggesting that nonadditive components have less influence than additive components on association tests.

  15. An estimating function approach to linkage heterogeneity

    Indian Academy of Sciences (India)

    Testing linkage heterogeneity between two loci is an important issue in genetics. Currently, there are ... on linkage heterogeneity can help people to better understand complex .... χ2(F − 2) + cχ2 (1), where c is a constant (see Appendix). Here, it can be ..... gin, ancestry, gender, age, etc., for purpose of dividing sub- groups to ...

  16. Linkage Behavior and Practices of Agencies in the Agricultural ...

    African Journals Online (AJOL)

    The study examined the linkage behaviour and practices of agencies in the ... institutes; while (61.5%,65.5%and 50.0%) indicated that linkages with universities of ... Existing institutional framework for linkages between research and extension ...

  17. Linkage disequilibrium in wild mice.

    Directory of Open Access Journals (Sweden)

    Cathy C Laurie

    2007-08-01

    Full Text Available Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1 Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2 they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3 LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits.

  18. Resource linkages and sustainable development

    Science.gov (United States)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  19. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Natural Resource Agency — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  20. Multiobjective optimization of a steering linkage

    Energy Technology Data Exchange (ETDEWEB)

    Sleesonsom, S.; Bureerat, S. [Sustainable and Infrastructure Research and Development Center, Dept. of Mechanical Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen (Thailand)

    2016-08-15

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria.

  1. EDITORIAL Development Linkages between Tree Breeding ...

    African Journals Online (AJOL)

    EDITORIAL Development Linkages between Tree Breeding Programmes and National/Regional Tree Seed Centres in Africa. ... Discovery and Innovation. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives.

  2. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Department of Resources — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  3. Multiobjective optimization of a steering linkage

    International Nuclear Information System (INIS)

    Sleesonsom, S.; Bureerat, S.

    2016-01-01

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria

  4. Asian Financial Linkages: The Case of Japan

    OpenAIRE

    Fialová, Anežka

    2014-01-01

    This work reviews the topic of international financial linkages, including theoretical definitions and the main methodological approaches of the empirical measurement based on vector autoregressive models. One of the approaches, the Spillover Index methodology based on Diebold & Yilmaz (2009), is then used to analyze the developments of financial linkages of the Japanese stock market in the period from 1995 to 2012. The attention is paid both to the relations with western developed economies ...

  5. Dimensional threshold for fracture linkage and hooking

    Science.gov (United States)

    Lamarche, Juliette; Chabani, Arezki; Gauthier, Bertrand D. M.

    2018-03-01

    Fracture connectivity in rocks depends on spatial properties of the pattern including length, abundance and orientation. When fractures form a single-strike set, they hardly cross-cut each other and the connectivity is limited. Linkage probability increases with increasing fracture abundance and length as small fractures connect to each other to form longer ones. A process for parallel fracture linkage is the "hooking", where two converging fracture tips mutually deviate and then converge to connect due to the interaction of their crack-tip stresses. Quantifying the processes and conditions for fracture linkage in single-strike fracture sets is crucial to better predicting fluid flow in Naturally Fractured Reservoirs. For 1734 fractures in Permian shales of the Lodève Basin, SE France, we measured geometrical parameters in 2D, characterizing three stages of the hooking process: underlapping, overlapping and linkage. We deciphered the threshold values, shape ratios and limiting conditions to switch from one stage to another one. The hook set up depends on the spacing (S) and fracture length (Lh) with the relation S ≈ 0.15 Lh. Once the hooking is initiated, with the fracture deviation length (L) L ≈ 0.4 Lh, the fractures reaches the linkage stage only when the spacing is reduced to S ≈ 0.02 Lh and the convergence (C) is < 0.1 L. These conditions apply to multi-scale fractures with a shape ratio L/S = 10 and for fracture curvature of 10°-20°.

  6. Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

    Science.gov (United States)

    Jiang, Y; Slager, S L; Huang, J

    2001-01-01

    We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

  7. Intragroup emotions: physiological linkage and social presence

    Directory of Open Access Journals (Sweden)

    Simo eJärvelä

    2016-02-01

    Full Text Available We investigated how technologically mediating two different components of emotion – communicative expression and physiological state – to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression and visualization of group level physiological heart rates and their dyadic linkage (physiology was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member’s physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  8. Intragroup Emotions: Physiological Linkage and Social Presence.

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion-communicative expression and physiological state-to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  9. A microsatellite linkage map of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Schully Sheri

    2004-05-01

    Full Text Available Abstract Background Drosophila mojavensis has been a model system for genetic studies of ecological adaptation and speciation. However, despite its use for over half a century, no linkage map has been produced for this species or its close relatives. Results We have developed and mapped 90 microsatellites in D. mojavensis, and we present a detailed recombinational linkage map of 34 of these microsatellites. A slight excess of repetitive sequence was observed on the X-chromosome relative to the autosomes, and the linkage groups have a greater recombinational length than the homologous D. melanogaster chromosome arms. We also confirmed the conservation of Muller's elements in 23 sequences between D. melanogaster and D. mojavensis. Conclusions The microsatellite primer sequences and localizations are presented here and made available to the public. This map will facilitate future quantitative trait locus mapping studies of phenotypes involved in adaptation or reproductive isolation using this species.

  10. Intragroup Emotions: Physiological Linkage and Social Presence

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion—communicative expression and physiological state—to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  11. The Linkage of Urban and Energy Planning for Sustainable Cities: The Case of Denmark and Germany

    DEFF Research Database (Denmark)

    Petersen, Jens-Phillip

    2016-01-01

    to increase society’s energy-efficiency; this has a high significance to reach GHG-reduction targets. In this paper the actual linkage of urban planning and energy planning in Denmark and Germany was assessed; substantive barriers preventing their integration and driving factors that lead to successful...

  12. Weak and or non-existent farmer-research-extension linkage ...

    African Journals Online (AJOL)

    extension-farmer linkages in Nyanga district of Zimbabwe. The target sample population was comprised of 150 communal farmers (N=150) from three clusters in Nyanga districts, as well as 12 extension officers (N=12) and six research officers ...

  13. Some methods for blindfolded record linkage

    Directory of Open Access Journals (Sweden)

    Christen Peter

    2004-06-01

    Full Text Available Abstract Background The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. Methods A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. Results The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Conclusion Although the protocols described in

  14. The Barley Chromosome 5 Linkage Map

    DEFF Research Database (Denmark)

    Jensen, J.; Jørgensen, Jørgen Helms

    1975-01-01

    The distances between nine loci on barley chromosome 5 have been studied in five two-point tests, three three-point tests, and one four-point test. Our previous chromosome 5 linkage map, which contained eleven loci mapped from literature data (Jensen and Jørgensen 1975), is extended with four loci......-position is fixed on the map by a locus (necl), which has a good marker gene located centrally in the linkage group. The positions of the other loci are their distances in centimorgans from the 0-position; loci in the direction of the short chromosome arm are assigned positive values and those...

  15. Linkage disequilibrium and association mapping of drought ...

    African Journals Online (AJOL)

    Drought stress is a major abiotic stress that limits crop production. Molecular association mapping techniques through linkage disequilibrium (LD) can be effectively used to tag genomic regions involved in drought stress tolerance. With the association mapping approach, 90 genotypes of cotton Gossypium hirsutum, from ...

  16. principles, realities and challenges regarding institutional linkages ...

    African Journals Online (AJOL)

    p2333147

    (2) Compromise between proximity to community and effective coordination. If organisational linkage structures are to facilitate effective participation and ownership, it stands to reason that they should be as close to the grassroots community as possible. Unless community members regard such organisational structures as.

  17. Availability of Insurance Linkage Programs in U.S. Emergency Departments

    Directory of Open Access Journals (Sweden)

    Mia Kanak

    2014-07-01

    Full Text Available Introduction: As millions of uninsured citizens who use emergency department (ED services are now eligible for health insurance under the Affordable Care Act, the ED is ideally situated to facilitate linkage to insurance. Forty percent of U.S. EDs report having an insurance linkage program. This is the first national study to examine the characteristics of EDs that offer or do not offer these programs. Methods: This was a secondary analysis of data from the National Survey for Preventive Health Services in U.S. EDs conducted in 2008-09. We compared EDs with and without insurance programs across demographic and operational factors using univariate analysis. We then tested our hypotheses using multivariable logistic regression. We also further examined program capacity and priority among the sub-group of EDs with no insurance linkage program. Results: After adjustment, ED-insurance linkage programs were more likely to be located in the West (RR= 2.06, 95% CI = 1.33 – 2.72. The proportion of uninsured patients in an ED, teaching hospital status, and public ownership status were not associated with insurance linkage availability. EDs with linkage programs also offer more preventive services (RR = 1.87, 95% CI = 1.37–2.35 and have greater social worker availability (RR = 1.71, 95% CI = 1.12–2.33 than those who do not. Four of five EDs with a patient mix of ≥25% uninsured and no insurance linkage program reported that they could not offer a program with existing staff and funding. Conclusion: Availability of insurance linkage programs in the ED is not associated with the proportion of uninsured patients served by an ED. Policy or hospital-based interventions to increase insurance linkage should first target the 27% of EDs with high rates of uninsured patients that lack adequate program capacity. Further research on barriers to implementation and cost effectiveness may help to facilitate increased adoption of insurance linkage programs. [West J

  18. Linkage of anthropogenic aerosol to clouds and climate

    International Nuclear Information System (INIS)

    Hudson, J.G.

    1992-01-01

    This progress report describes the monitoring being done to validate a linkage of anthropogenic aerosol to clouds and climate. Equipment and findings are reported. The equipment construction called for in the original proposal has now been competed. These instruments are the high temperature processor, the data acquisition system for the direct Royco optical particle counter (OPC), and modifications to the formvar replicator. The main field effort during the past year has been the shipboard experiment SEAHUNT (Shiptrail Evolution Above High Updraft Naval Targets). There were also some laboratory and local ambient particle measurements and a surface field program on and near the California coast. The shipboard project was not anticipated in the original proposal but the laboratory and surface measurements were along the lines suggested in the original proposal

  19. Kempe's Linkages and the Universality Theorem

    Indian Academy of Sciences (India)

    sriranga

    that between BO and OA (i.e., \\BOA). Let these two angles be denoted by µ. Thus, if link OA makes an angle. µ with link OB, OE makes the same angle on the other side of OB. Kempe therefore referred to this linkage as the (angle) reversor. This is true irrespective of how OA and OB are placed relative to each other. Also ...

  20. Methods for genetic linkage analysis using trisomies.

    OpenAIRE

    Feingold, E; Lamb, N E; Sherman, S L

    1995-01-01

    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of "susceptibility" ...

  1. Hidden linkages between urbanization and food systems.

    Science.gov (United States)

    Seto, Karen C; Ramankutty, Navin

    2016-05-20

    Global societies are becoming increasingly urban. This shift toward urban living is changing our relationship with food, including how we shop and what we buy, as well as ideas about sanitation and freshness. Achieving food security in an era of rapid urbanization will require considerably more understanding about how urban and food systems are intertwined. Here we discuss some potential understudied linkages that are ripe for further examination. Copyright © 2016, American Association for the Advancement of Science.

  2. 'Linkage' pharmaceutical evergreening in Canada and Australia

    Science.gov (United States)

    Faunce, Thomas A; Lexchin, Joel

    2007-01-01

    'Evergreening' is not a formal concept of patent law. It is best understood as a social idea used to refer to the myriad ways in which pharmaceutical patent owners utilise the law and related regulatory processes to extend their high rent-earning intellectual monopoly privileges, particularly over highly profitable (either in total sales volume or price per unit) 'blockbuster' drugs. Thus, while the courts are an instrument frequently used by pharmaceutical brand name manufacturers to prolong their patent royalties, 'evergreening' is rarely mentioned explicitly by judges in patent protection cases. The term usually refers to threats made to competitors about a brand-name manufacturer's tactical use of pharmaceutical patents (including over uses, delivery systems and even packaging), not to extension of any particular patent over an active product ingredient. This article focuses in particular on the 'evergreening' potential of so-called 'linkage' provisions, imposed on the regulatory (safety, quality and efficacy) approval systems for generic pharmaceuticals of Canada and Australia, by specific articles in trade agreements with the US. These 'linkage' provisions have also recently appeared in the Korea-US Free Trade Agreement (KORUSFTA). They require such drug regulators to facilitate notification of, or even prevent, any potential patent infringement by a generic pharmaceutical manufacturer. This article explores the regulatory lessons to be learnt from Canada's and Australia's shared experience in terms of minimizing potential adverse impacts of such 'linkage evergreening' provisions on drug costs and thereby potentially on citizen's access to affordable, essential medicines. PMID:17543113

  3. The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

    Science.gov (United States)

    Huang, J; Jiang, Y

    2001-01-01

    We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

  4. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  5. Probabilistic linkage to enhance deterministic algorithms and reduce data linkage errors in hospital administrative data.

    Science.gov (United States)

    Hagger-Johnson, Gareth; Harron, Katie; Goldstein, Harvey; Aldridge, Robert; Gilbert, Ruth

    2017-06-30

     BACKGROUND: The pseudonymisation algorithm used to link together episodes of care belonging to the same patients in England (HESID) has never undergone any formal evaluation, to determine the extent of data linkage error. To quantify improvements in linkage accuracy from adding probabilistic linkage to existing deterministic HESID algorithms. Inpatient admissions to NHS hospitals in England (Hospital Episode Statistics, HES) over 17 years (1998 to 2015) for a sample of patients (born 13/28th of months in 1992/1998/2005/2012). We compared the existing deterministic algorithm with one that included an additional probabilistic step, in relation to a reference standard created using enhanced probabilistic matching with additional clinical and demographic information. Missed and false matches were quantified and the impact on estimates of hospital readmission within one year were determined. HESID produced a high missed match rate, improving over time (8.6% in 1998 to 0.4% in 2015). Missed matches were more common for ethnic minorities, those living in areas of high socio-economic deprivation, foreign patients and those with 'no fixed abode'. Estimates of the readmission rate were biased for several patient groups owing to missed matches, which was reduced for nearly all groups. CONCLUSION: Probabilistic linkage of HES reduced missed matches and bias in estimated readmission rates, with clear implications for commissioning, service evaluation and performance monitoring of hospitals. The existing algorithm should be modified to address data linkage error, and a retrospective update of the existing data would address existing linkage errors and their implications.

  6. Ethnicity and the ethics of data linkage

    Directory of Open Access Journals (Sweden)

    Boyd Kenneth M

    2007-11-01

    Full Text Available Abstract Linking health data with census data on ethnicity has potential benefits for the health of ethnic minority groups. Ethical objections to linking these data however include concerns about informed consent and the possibility of the findings being misused against the interests of ethnic minority groups. While consent concerns may be allayed by procedures to safeguard anonymity and respect privacy, robust procedures to demonstrate public approval of data linkage also need to be devised. The possibility of findings being misused against the interests of ethnic minority groups may be diminished by informed and open public discussion in mature democracies, but remain a concern in the international context.

  7. Strike-slip tectonics during rift linkage

    Science.gov (United States)

    Pagli, C.; Yun, S. H.; Ebinger, C.; Keir, D.; Wang, H.

    2017-12-01

    The kinematics of triple junction linkage and the initiation of transforms in magmatic rifts remain debated. Strain patterns from the Afar triple junction provide tests of current models of how rifts grow to link in area of incipient oceanic spreading. Here we present a combined analysis of seismicity, InSAR and GPS derived strain rate maps to reveal that the plate boundary deformation in Afar is accommodated primarily by extensional tectonics in the Red Sea and Gulf of Aden rifts, and does not require large rotations about vertical axes (bookshelf faulting). Additionally, models of stress changes and seismicity induced by recent dykes in one sector of the Afar triple junction provide poor fit to the observed strike-slip earthquakes. Instead we explain these patterns as rift-perpendicular shearing at the tips of spreading rifts where extensional strains terminate against less stretched lithosphere. Our results demonstrate that rift-perpendicular strike-slip faulting between rift segments achieves plate boundary linkage during incipient seafloor spreading.

  8. Effects of Worldwide Population Subdivision on ALDH2 Linkage Disequilibrium

    OpenAIRE

    Peterson, Raymond J.; Goldman, David; Long, Jeffrey C.

    1999-01-01

    The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations acros...

  9. Linkage of PRA models. Phase 1, Results

    Energy Technology Data Exchange (ETDEWEB)

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ``Linkage of PRA Models`` project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ``linking`` analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ``generic`` classification scheme to groups plants based upon a particular plant attribute.

  10. Linkage of PRA models. Phase 1, Results

    International Nuclear Information System (INIS)

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ''Linkage of PRA Models'' project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ''linking'' analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ''generic'' classification scheme to groups plants based upon a particular plant attribute

  11. Selective cleavage of the C(α)-C(β) linkage in lignin model compounds via Baeyer-Villiger oxidation.

    Science.gov (United States)

    Patil, Nikhil D; Yao, Soledad G; Meier, Mark S; Mobley, Justin K; Crocker, Mark

    2015-03-21

    Lignin is an amorphous aromatic polymer derived from plants and is a potential source of fuels and bulk chemicals. Herein, we present a survey of reagents for selective stepwise oxidation of lignin model compounds. Specifically, we have targeted the oxidative cleavage of Cα-Cβ bonds as a means to depolymerize lignin and obtain useful aromatic compounds. In this work, we prepared several lignin model compounds that possess structures, characteristic reactivity, and linkages closely related to the parent lignin polymer. We observed that selective oxidation of benzylic hydroxyl groups, followed by Baeyer-Villiger oxidation of the resulting ketones, successfully cleaves the Cα-Cβ linkage in these model compounds.

  12. Genome-wide linkage scan for colorectal cancer susceptibility genes supports linkage to chromosome 3q

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

    Full Text Available Abstract Background Colorectal cancer is one of the most common causes of cancer-related mortality. The disease is clinically and genetically heterogeneous though a strong hereditary component has been identified. However, only a small proportion of the inherited susceptibility can be ascribed to dominant syndromes, such as Hereditary Non-Polyposis Colorectal Cancer (HNPCC or Familial Adenomatous Polyposis (FAP. In an attempt to identify novel colorectal cancer predisposing genes, we have performed a genome-wide linkage analysis in 30 Swedish non-FAP/non-HNPCC families with a strong family history of colorectal cancer. Methods Statistical analysis was performed using multipoint parametric and nonparametric linkage. Results Parametric analysis under the assumption of locus homogeneity excluded any common susceptibility regions harbouring a predisposing gene for colorectal cancer. However, several loci on chromosomes 2q, 3q, 6q, and 7q with suggestive linkage were detected in the parametric analysis under the assumption of locus heterogeneity as well as in the nonparametric analysis. Among these loci, the locus on chromosome 3q21.1-q26.2 was the most consistent finding providing positive results in both parametric and nonparametric analyses Heterogeneity LOD score (HLOD = 1.90, alpha = 0.45, Non-Parametric LOD score (NPL = 2.1. Conclusion The strongest evidence of linkage was seen for the region on chromosome 3. Interestingly, the same region has recently been reported as the most significant finding in a genome-wide analysis performed with SNP arrays; thus our results independently support the finding on chromosome 3q.

  13. Genome-wide linkage analysis for human longevity

    DEFF Research Database (Denmark)

    Beekman, Marian; Blanché, Hélène; Perola, Markus

    2013-01-01

    Clear evidence exists for heritability of human longevity, and much interest is focused on identifying genes associated with longer lives. To identify such longevity alleles, we performed the largest genome-wide linkage scan thus far reported. Linkage analyses included 2118 nonagenarian Caucasian...

  14. Effects of aquaculture researchers' job characteristics on linkage ...

    African Journals Online (AJOL)

    The study examined the effects of researchers' job characteristics on linkage activities in Nigeria due to the fact that many fish farmers have not been properly reached with technologies and the problem of poor fish production has been attributed to the weak linkages existing between research, extension and fish farmers.

  15. Electrostatic microactuators with integrated gear linkages for mechanical power transmission

    NARCIS (Netherlands)

    Legtenberg, R.; Legtenberg, Rob; Berenschot, Johan W.; Elwenspoek, Michael Curt; Fluitman, J.H.J.

    1996-01-01

    In this paper a surface micromachining process is presented which has been used to fabricate electrostatic microactuators that are interconnected with each other and linked to other movable microstructures by integrated gear linkages. The gear linkages consist of rotational and linear gear

  16. Privacy-preserving record linkage on large real world datasets.

    Science.gov (United States)

    Randall, Sean M; Ferrante, Anna M; Boyd, James H; Bauer, Jacqueline K; Semmens, James B

    2014-08-01

    Record linkage typically involves the use of dedicated linkage units who are supplied with personally identifying information to determine individuals from within and across datasets. The personally identifying information supplied to linkage units is separated from clinical information prior to release by data custodians. While this substantially reduces the risk of disclosure of sensitive information, some residual risks still exist and remain a concern for some custodians. In this paper we trial a method of record linkage which reduces privacy risk still further on large real world administrative data. The method uses encrypted personal identifying information (bloom filters) in a probability-based linkage framework. The privacy preserving linkage method was tested on ten years of New South Wales (NSW) and Western Australian (WA) hospital admissions data, comprising in total over 26 million records. No difference in linkage quality was found when the results were compared to traditional probabilistic methods using full unencrypted personal identifiers. This presents as a possible means of reducing privacy risks related to record linkage in population level research studies. It is hoped that through adaptations of this method or similar privacy preserving methods, risks related to information disclosure can be reduced so that the benefits of linked research taking place can be fully realised. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Identifying and Mapping Linkages between Actors in the Climate ...

    African Journals Online (AJOL)

    Promoting innovations in climate change requires innovation partnerships and linkages and also creating an enabling environment for actors. The paper reviewed available information on the identification and mapping of linkages between actors in the climate change innovation system. The findings showed different ...

  18. Agriculture–Tourism Linkages in Botswana: Evidence from the ...

    African Journals Online (AJOL)

    Tourism researchers are increasingly recognising that strengthened linkages between the sectors of tourism and agriculture are significant for maximising local multipliers and especially for pro-poor impacts. This article examines the linkages between the tourism and agriculture sectors in Botswana using evidence ...

  19. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    Energy Technology Data Exchange (ETDEWEB)

    Field, L.L.; Nagatomi, J. [Univ. of Calgary, Alberta (Canada)

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  20. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    NARCIS (Netherlands)

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. In

  1. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    OpenAIRE

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. Inthisstudyweexploredlinkagedisequilibrium(LD)mappingof traits in a set of modernbarleycultivars. LDbetweenmolecularmarkerswasfoundup to a distance of 10 centimorgan,whichislargecomparedtootherspecies.Thelarge distancemightbeinducedb...

  2. [MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

    Science.gov (United States)

    Liu, Ren-Hu; Meng, Jin-Ling

    2003-05-01

    MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

  3. Potential Linkage Between Cerebrovascular Diseases and Metabolic Syndrome.

    Science.gov (United States)

    Jabir, Nasimudeen R; Firoz, Chelapram Kandy; Khan, Mohd Shahnawaz; Zaidi, Syed Kashif; Ashraf, Ghulam Md; Shakil, Shazi; Kamal, Mohammad Amjad; Tabrez, Shams

    2017-01-01

    Cerebrovascular disease (CD) and metabolic syndrome (MetS) are two devastating health dilemma that continues to be a potential contributor to disability and mortality in human population all across the world. Scientific data clearly shows several mechanistic similarities between these two co-existing and interlinked conditions. The linkage exacerbates ongoing patho-physiological condition towards more lethal events. In view of the presence of modifiable risk factors in both CD and MetS, their management holds potential therapeutic value. Hence, developing common treatment strategies for these diseases could involve common molecular agents. In this communication, we have summarized some of the common pathological conditions viz. abdominal obesity, insulin resistance, dyslipidemia, hypertension, and endothelial dysfunction that further deteriorate existing homeostasis in CD and MetS. Based on our article, it is advocated that substantial improvements in novel multi-targeted drug discovery could provide the effective treatment methods in order to avoid the fatal complications related with CD and MetS. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome.

    Science.gov (United States)

    Shearman, Jeremy R; Sangsrakru, Duangjai; Jomchai, Nukoon; Ruang-Areerate, Panthita; Sonthirod, Chutima; Naktang, Chaiwat; Theerawattanasuk, Kanikar; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.

  5. The Structure-Function Linkage Database.

    Science.gov (United States)

    Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E; Barber, Alan E; Custer, Ashley F; Hicks, Michael A; Huang, Conrad C; Lauck, Florian; Mashiyama, Susan T; Meng, Elaine C; Mischel, David; Morris, John H; Ojha, Sunil; Schnoes, Alexandra M; Stryke, Doug; Yunes, Jeffrey M; Ferrin, Thomas E; Holliday, Gemma L; Babbitt, Patricia C

    2014-01-01

    The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies 'look alike', making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

  6. The Structure–Function Linkage Database

    Science.gov (United States)

    Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E.; Barber, Alan E.; Custer, Ashley F.; Hicks, Michael A.; Huang, Conrad C.; Lauck, Florian; Mashiyama, Susan T.; Meng, Elaine C.; Mischel, David; Morris, John H.; Ojha, Sunil; Schnoes, Alexandra M.; Stryke, Doug; Yunes, Jeffrey M.; Ferrin, Thomas E.; Holliday, Gemma L.; Babbitt, Patricia C.

    2014-01-01

    The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. PMID:24271399

  7. Linkages at Tourism Destinations: Challenges in Zanzibar

    Directory of Open Access Journals (Sweden)

    Wineaster Anderson

    2011-06-01

    Full Text Available This study explores challenges facing the linkages between the tourism industry and local suppliers at the destinations. During 2010 surveys involving hotel and restaurant operators, local suppliers and tourists were conducted in Zanzibar. Qualitative analysis of the perspectives of the respondents reveals the multitude of constraints. From operators, the main constraints include poor quality of the locally supplied products, business informalities, high transaction costs and violation of agreements by local suppliers. Low production levels, low prices offered by hotels and restaurants coupled with late payments for the products delivered were the most serious problems cited by local suppliers. There is also a certain degree of mistrust between the local suppliers and the operators. However, the source of the tourism products consumed in the hotels or restaurants was not a point of concern, at least from the tourists’ perspective. Strategies to bridge the demandsupply gaps in order to maximize the benefits of tourism, among the tools for fighting the rampant poverty, have been recommended.

  8. ANALYSIS OF INTER SECTORAL LINKAGES IN SEMARANG REGENCY

    Directory of Open Access Journals (Sweden)

    Fafurida

    2014-03-01

    Full Text Available This research aims to analyze inter economic sectoral linkages and to arrange the Klassen typology of economic sectors in Semarang Regency. The Klassen typology is composed from the result of the linkage analysis. To construct the analysis, this paper also utulizes the input-output analysis. It finds that service sector has the highest backward linkage while farming sector has the highest forward linkage. Based on the Klassen typology analysis, sectors with the highest backward and forward linkages and potential to be the leading sector are farming sector, dan trade, hotel and restaurant sector.Keywords: Backward linkage,forward linkage, Klassen typologyJEL classification number: R15, O21AbstrakPenelitian ini bertujuan untuk mengkaji seberapa besar keterkaitan antar sektor ekonomi di Kabupaten Semarang dan memetakan tipologi Klassennya. Tipologi Klasen disusun berdasarkan hasil perhitungan analisis keterkaitannya. Untuk menyusun analisis tersebut, paper ini juga menggunakan analisis input-output. Hasil penelitian menunjukkan bahwa sektor jasa memiliki keterkaitan ke belakang tertinggi dibandingkan dengan sektor lainnya. Sementara itu, sektor pertanian merupakan sektor yang memiliki keterkaitan ke depan tertinggi. Berdasarkan hasil analisis tipologi Klassen, sektor yang memiliki keterkaitan ke depan dan ke belakang yang tinggi dan dapat menjadi sektor unggulan adalah sektor perdagangan, hotel dan sektor restoran.Kata kunci: Keterkaitan ke belakang, keterkaitan ke depan, tipologi KlassenJEL classification numbers: R15, O21

  9. Posterior probability of linkage and maximal lod score.

    Science.gov (United States)

    Génin, E; Martinez, M; Clerget-Darpoux, F

    1995-01-01

    To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction between 0 and 0.5 and the test is based on the maximum value of the lod score Zmax. The impact of this deviation of the test on the probability that in fact linkage does not exist, when linkage was concluded, is documented here. This posterior probability of no linkage can be derived by using Bayes' theorem. It is less than 5% when the lod score at a predetermined theta 1 is used for the test. But, for a Zmax of +3, we showed that it can reach 16.4%. Thus, considering a composite alternative hypothesis instead of a single one decreases the reliability of the test. The reliability decreases rapidly when Zmax is less than +3. Given a Zmax of +2.5, there is a 33% chance that linkage does not exist. Moreover, the posterior probability depends not only on the value of Zmax but also jointly on the family structures and on the genetic model. For a given Zmax, the chance that linkage exists may then vary.

  10. Distribution of lod scores in oligogenic linkage analysis.

    Science.gov (United States)

    Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

    2001-01-01

    In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

  11. Bayesian linkage and segregation analysis: factoring the problem.

    Science.gov (United States)

    Matthysse, S

    2000-01-01

    Complex segregation analysis and linkage methods are mathematical techniques for the genetic dissection of complex diseases. They are used to delineate complex modes of familial transmission and to localize putative disease susceptibility loci to specific chromosomal locations. The computational problem of Bayesian linkage and segregation analysis is one of integration in high-dimensional spaces. In this paper, three available techniques for Bayesian linkage and segregation analysis are discussed: Markov Chain Monte Carlo (MCMC), importance sampling, and exact calculation. The contribution of each to the overall integration will be explicitly discussed.

  12. Markov chain Monte Carlo linkage analysis: effect of bin width on the probability of linkage.

    Science.gov (United States)

    Slager, S L; Juo, S H; Durner, M; Hodge, S E

    2001-01-01

    We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

  13. Review of the Linkages between Gender Equity and Climate ...

    African Journals Online (AJOL)

    Review of the Linkages between Gender Equity and Climate Change Issues in ... thereby exacerbating inequalities in health status and access to adequate food, clean ... Again, in traditional societies, women are even more vulnerable to the ...

  14. Mapping organizational linkages in the agricultural innovation system of Azerbaijan

    NARCIS (Netherlands)

    Temel, T.

    2004-01-01

    This study describes the evolving context and organisational linkages in the agricultural innovation system of Azerbaijan and suggests ways to promote effective organisational ties for the development, distribution and use of new or improved information and knowledge related to agriculture.

  15. Strengthening industry-research linkage for small scale industrial ...

    African Journals Online (AJOL)

    Strengthening industry-research linkage for small scale industrial development in Ghana - the relevance of scientific and technological information. ... Journal of Applied Science and Technology. Journal Home · ABOUT · Advanced Search ...

  16. Underreporting of maternal mortality in Taiwan: A data linkage study

    Directory of Open Access Journals (Sweden)

    Tung-Pi Wu

    2015-12-01

    Conclusion: Approximately two-thirds of the maternal deaths in Taiwan were unreported in the officially published mortality data. Hence, routine nationwide data linkage is essential to monitor maternal mortality in Taiwan accurately.

  17. Estimating parameters for probabilistic linkage of privacy-preserved datasets.

    Science.gov (United States)

    Brown, Adrian P; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Boyd, James H

    2017-07-10

    Probabilistic record linkage is a process used to bring together person-based records from within the same dataset (de-duplication) or from disparate datasets using pairwise comparisons and matching probabilities. The linkage strategy and associated match probabilities are often estimated through investigations into data quality and manual inspection. However, as privacy-preserved datasets comprise encrypted data, such methods are not possible. In this paper, we present a method for estimating the probabilities and threshold values for probabilistic privacy-preserved record linkage using Bloom filters. Our method was tested through a simulation study using synthetic data, followed by an application using real-world administrative data. Synthetic datasets were generated with error rates from zero to 20% error. Our method was used to estimate parameters (probabilities and thresholds) for de-duplication linkages. Linkage quality was determined by F-measure. Each dataset was privacy-preserved using separate Bloom filters for each field. Match probabilities were estimated using the expectation-maximisation (EM) algorithm on the privacy-preserved data. Threshold cut-off values were determined by an extension to the EM algorithm allowing linkage quality to be estimated for each possible threshold. De-duplication linkages of each privacy-preserved dataset were performed using both estimated and calculated probabilities. Linkage quality using the F-measure at the estimated threshold values was also compared to the highest F-measure. Three large administrative datasets were used to demonstrate the applicability of the probability and threshold estimation technique on real-world data. Linkage of the synthetic datasets using the estimated probabilities produced an F-measure that was comparable to the F-measure using calculated probabilities, even with up to 20% error. Linkage of the administrative datasets using estimated probabilities produced an F-measure that was higher

  18. Learning Expressive Linkage Rules for Entity Matching using Genetic Programming

    OpenAIRE

    Isele, Robert

    2013-01-01

    A central problem in data integration and data cleansing is to identify pairs of entities in data sets that describe the same real-world object. Many existing methods for matching entities rely on explicit linkage rules, which specify how two entities are compared for equivalence. Unfortunately, writing accurate linkage rules by hand is a non-trivial problem that requires detailed knowledge of the involved data sets. Another important issue is the efficient execution of link...

  19. Data Linkage: A powerful research tool with potential problems

    Directory of Open Access Journals (Sweden)

    Scott Ian

    2010-12-01

    Full Text Available Abstract Background Policy makers, clinicians and researchers are demonstrating increasing interest in using data linked from multiple sources to support measurement of clinical performance and patient health outcomes. However, the utility of data linkage may be compromised by sub-optimal or incomplete linkage, leading to systematic bias. In this study, we synthesize the evidence identifying participant or population characteristics that can influence the validity and completeness of data linkage and may be associated with systematic bias in reported outcomes. Methods A narrative review, using structured search methods was undertaken. Key words "data linkage" and Mesh term "medical record linkage" were applied to Medline, EMBASE and CINAHL databases between 1991 and 2007. Abstract inclusion criteria were; the article attempted an empirical evaluation of methodological issues relating to data linkage and reported on patient characteristics, the study design included analysis of matched versus unmatched records, and the report was in English. Included articles were grouped thematically according to patient characteristics that were compared between matched and unmatched records. Results The search identified 1810 articles of which 33 (1.8% met inclusion criteria. There was marked heterogeneity in study methods and factors investigated. Characteristics that were unevenly distributed among matched and unmatched records were; age (72% of studies, sex (50% of studies, race (64% of studies, geographical/hospital site (93% of studies, socio-economic status (82% of studies and health status (72% of studies. Conclusion A number of relevant patient or population factors may be associated with incomplete data linkage resulting in systematic bias in reported clinical outcomes. Readers should consider these factors in interpreting the reported results of data linkage studies.

  20. Effective interventions to improve young adults' linkage to HIV care in Sub-Saharan Africa: a systematic review.

    Science.gov (United States)

    Mavegam, Bertille Octavie; Pharr, Jennifer R; Cruz, Patricia; Ezeanolue, Echezona E

    2017-10-01

    HIV/AIDS remains a major public health problem despite the efforts to prevent and decrease its spread. Sub-Saharan Africa (SSA) represents 70% of the global number of people living with HIV and 73% of all HIV/AIDS-related deaths. Young adults age 15-24 years are disproportionately impacted by HIV/AIDS in SSA with 34% of people living with HIV (PLWHIV) and 37% of newly diagnosed individuals being in this age group. It is important that PLWHIV be linked to care to facilitate antiretroviral therapy (ART) initiation and limit the spread of infection. We conducted a systematic literature review to identify effective interventions designed to improve linkage to care among HIV-infected young adults in SSA. One hundred and forty-six titles and abstracts were screened, 28 full-texts were reviewed, and 6 articles met the inclusion and exclusion criteria. Home-based HIV counseling and testing, home-based HIV self-testing, and mobile HIV counseling and testing followed by proper referral of HIV-positive patients to HIV care were effective for improving linkage of young adults to care. Other factors such as referral forms, transportation allowance, home initiation of HIV care, and volunteer escort to the HIV treatment clinic were effective in reducing time to linkage to care. There is a vast need for research and interventions that target HIV-positive young adults in SSA which aim to improve their linkage and access to HIV care. The results of this study illustrate effective interventions in improving linkage to care and reducing time to linkage to care of young adults in SSA.

  1. Using Bureaucratic and Cultural Linkages to Improve Instruction: The Principal's Contribution.

    Science.gov (United States)

    Firestone, William A.; Wilson, Bruce L.

    1985-01-01

    Principals can influence teachers and instructional behavior by working through linkage mechanisms within the organizational structure of the school. Two types of linkages are identified: bureaucratic and cultural. Principals have access to linkages of both kinds; using linkages effectively, they can generate a common purpose in their schools. (MD)

  2. RLT-S: A Web System for Record Linkage.

    Directory of Open Access Journals (Sweden)

    Abdullah-Al Mamun

    Full Text Available Record linkage integrates records across multiple related data sources identifying duplicates and accounting for possible errors. Real life applications require efficient algorithms to merge these voluminous data sources to find out all records belonging to same individuals. Our recently devised highly efficient record linkage algorithms provide best-known solutions to this challenging problem.We have developed RLT-S, a freely available web tool, which implements our single linkage clustering algorithm for record linkage. This tool requires input data sets and a small set of configuration settings about these files to work efficiently. RLT-S employs exact match clustering, blocking on a specified attribute and single linkage based hierarchical clustering among these blocks.RLT-S is an implementation package of our sequential record linkage algorithm. It outperforms previous best-known implementations by a large margin. The tool is at least two times faster for any dataset than the previous best-known tools.RLT-S tool implements our record linkage algorithm that outperforms previous best-known algorithms in this area. This website also contains necessary information such as instructions, submission history, feedback, publications and some other sections to facilitate the usage of the tool.RLT-S is integrated into http://www.rlatools.com, which is currently serving this tool only. The tool is freely available and can be used without login. All data files used in this paper have been stored in https://github.com/abdullah009/DataRLATools. For copies of the relevant programs please see https://github.com/abdullah009/RLATools.

  3. Nature–society linkages in the Aral Sea region

    Directory of Open Access Journals (Sweden)

    Kristopher D. White

    2013-01-01

    Full Text Available Central Asia's Aral Sea crisis represents a disaster of monumental proportions, a tragedy for both the region's ecology and its human inhabitants. While the human and natural environments had operated in a sustainable co-joined system for millennia, Tsarist Russian expansion into Central Asia, followed by Soviet expansion of both the cotton industry and unsustainable irrigation practices to anchor it spelled doom for the Aral Sea. Today, many of the political and economic stimuli for such misguided practices continue, as do the continued retreat of the Sea and the proliferation of poor human health. The Aral Sea crisis has received ample scholarly attention, though somewhat surprising is a relative dearth of research explicitly investigating the nature, variety, and directionality of nature–society linkages today within the region. The purpose of this paper is to elucidate the contemporary nature–society linkages operating within the Aral Sea region of Central Asia. Historical nexuses will provide necessary background, and the linkages operating currently within the spheres of regional economy, human health, and political considerations will be detailed. Couching the current crisis within the framework of coupled human–environment system contexts reveals a region in which these linkages are largely inextricable. This paper concludes with a call for a reconsideration of the nature-society linkages and a greater emphasis placed on the local region's ecological and social sustainability.

  4. Autosomal dominant distal myopathy: Linkage to chromosome 14

    Energy Technology Data Exchange (ETDEWEB)

    Laing, N.G.; Laing, B.A.; Wilton, S.D.; Dorosz, S.; Mastaglia, F.L.; Kakulas, B.A. [Australian Neuromuscular Research Institute, Perth (Australia); Robbins, P.; Meredith, C.; Honeyman, K.; Kozman, H.

    1995-02-01

    We have studied a family segregating a form of autosomal dominant distal myopathy (MIM 160500) and containing nine living affected individuals. The myopathy in this family is closest in clinical phenotype to that first described by Gowers in 1902. A search for linkage was conducted using microsatellite, VNTR, and RFLP markers. In total, 92 markers on all 22 autosomes were run. Positive linkage was obtained with 14 of 15 markers tested on chromosome 14, with little indication of linkage elsewhere in the genome. Maximum two-point LOD scores of 2.60 at recombination fraction .00 were obtained for the markers MYH7 and D14S64 - the family structure precludes a two-point LOD score {ge} 3. Recombinations with D14S72 and D14S49 indicate that this distal myopathy locus, MPD1, should lie between these markers. A multipoint analysis assuming 100% penetrance and using the markers D14S72, D14S50, MYH7, D14S64, D14S54, and D14S49 gave a LOD score of exactly 3 at MYH7. Analysis at a penetrance of 80% gave a LOD score of 2.8 at this marker. This probable localization of a gene for distal myopathy, MPD1, on chromosome 14 should allow other investigators studying distal myopathy families to test this region for linkage in other types of the disease, to confirm linkage or to demonstrate the likely genetic heterogeneity. 24 refs., 3 figs., 1 tab.

  5. Two-locus linkage analysis in multiple sclerosis (MS)

    Energy Technology Data Exchange (ETDEWEB)

    Tienari, P.J. (National Public Health Institute, Helsinki (Finland) Univ. of Helsinki (Finland)); Terwilliger, J.D.; Ott, J. (Columbia Univ., New York (United States)); Palo, J. (Univ. of Helsinki (Finland)); Peltonen, L. (National Public Health Institute, Helsinki (Finland))

    1994-01-15

    One of the major challenges in genetic linkage analyses is the study of complex diseases. The authors demonstrate here the use of two-locus linkage analysis in multiple sclerosis (MS), a multifactorial disease with a complex mode of inheritance. In a set of Finnish multiplex families, they have previously found evidence for linkage between MS susceptibility and two independent loci, the myelin basic protein gene (MBP) on chromosome 18 and the HLA complex on chromosome 6. This set of families provides a unique opportunity to perform linkage analysis conditional on two loci contributing to the disease. In the two-trait-locus/two-marker-locus analysis, the presence of another disease locus is parametrized and the analysis more appropriately treats information from the unaffected family member than single-disease-locus analysis. As exemplified here in MS, the two-locus analysis can be a powerful method for investigating susceptibility loci in complex traits, best suited for analysis of specific candidate genes, or for situations in which preliminary evidence for linkage already exists or is suggested. 41 refs., 6 tabs.

  6. Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve

    Science.gov (United States)

    Shi, Yaohua; Guo, Ximing; Gu, Zhifeng; Wang, Aimin; Wang, Yan

    2010-05-01

    Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio ( P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.

  7. Robust LOD scores for variance component-based linkage analysis.

    Science.gov (United States)

    Blangero, J; Williams, J T; Almasy, L

    2000-01-01

    The variance component method is now widely used for linkage analysis of quantitative traits. Although this approach offers many advantages, the importance of the underlying assumption of multivariate normality of the trait distribution within pedigrees has not been studied extensively. Simulation studies have shown that traits with leptokurtic distributions yield linkage test statistics that exhibit excessive Type I error when analyzed naively. We derive analytical formulae relating the deviation from the expected asymptotic distribution of the lod score to the kurtosis and total heritability of the quantitative trait. A simple correction constant yields a robust lod score for any deviation from normality and for any pedigree structure, and effectively eliminates the problem of inflated Type I error due to misspecification of the underlying probability model in variance component-based linkage analysis.

  8. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    Science.gov (United States)

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  9. Linkage of biomolecules to solid phases for immunoassay

    International Nuclear Information System (INIS)

    Chapman, R.S.

    1998-01-01

    Topics covered by this lecture include a brief review of the principal methods of linkage of biomolecules to solid phase matrices. Copies of the key self explanatory slides are presented as figures together with reprints of two publications by the author dealing with a preferred chemistry for the covalent linkage of antibodies to hydroxyl and amino functional groups and the effects of changes in solid phase matrix and antibody coupling chemistry on the performance of a typical excess reagent immunoassay for thyroid stimulating hormone

  10. An improved recommendation algorithm via weakening indirect linkage effect

    International Nuclear Information System (INIS)

    Chen Guang; Qiu Tian; Shen Xiao-Quan

    2015-01-01

    We propose an indirect-link-weakened mass diffusion method (IMD), by considering the indirect linkage and the source object heterogeneity effect in the mass diffusion (MD) recommendation method. Experimental results on the MovieLens, Netflix, and RYM datasets show that, the IMD method greatly improves both the recommendation accuracy and diversity, compared with a heterogeneity-weakened MD method (HMD), which only considers the source object heterogeneity. Moreover, the recommendation accuracy of the cold objects is also better elevated in the IMD than the HMD method. It suggests that eliminating the redundancy induced by the indirect linkages could have a prominent effect on the recommendation efficiency in the MD method. (paper)

  11. Mapping autism risk loci using genetic linkage and chromosomal rearrangements

    Science.gov (United States)

    Szatmari, Peter; Paterson, Andrew; Zwaigenbaum, Lonnie; Roberts, Wendy; Brian, Jessica; Liu, Xiao-Qing; Vincent, John; Skaug, Jennifer; Thompson, Ann; Senman, Lili; Feuk, Lars; Qian, Cheng; Bryson, Susan; Jones, Marshall; Marshall, Christian; Scherer, Stephen; Vieland, Veronica; Bartlett, Christopher; Mangin, La Vonne; Goedken, Rhinda; Segre, Alberto; Pericak-Vance, Margaret; Cuccaro, Michael; Gilbert, John; Wright, Harry; Abramson, Ruth; Betancur, Catalina; Bourgeron, Thomas; Gillberg, Christopher; Leboyer, Marion; Buxbaum, Joseph; Davis, Kenneth; Hollander, Eric; Silverman, Jeremy; Hallmayer, Joachim; Lotspeich, Linda; Sutcliffe, James; Haines, Jonathan; Folstein, Susan; Piven, Joseph; Wassink, Thomas; Sheffield, Val; Geschwind, Daniel; Bucan, Maja; Brown, Ted; Cantor, Rita; Constantino, John; Gilliam, Conrad; Herbert, Martha; Lajonchere, Clara; Ledbetter, David; Lese-Martin, Christa; Miller, Janet; Nelson, Stan; Samango-Sprouse, Carol; Spence, Sarah; State, Matthew; Tanzi, Rudolph; Coon, Hilary; Dawson, Geraldine; Devlin, Bernie; Estes, Annette; Flodman, Pamela; Klei, Lambertus; Mcmahon, William; Minshew, Nancy; Munson, Jeff; Korvatska, Elena; Rodier, Patricia; Schellenberg, Gerard; Smith, Moyra; Spence, Anne; Stodgell, Chris; Tepper, Ping Guo; Wijsman, Ellen; Yu, Chang-En; Rogé, Bernadette; Mantoulan, Carine; Wittemeyer, Kerstin; Poustka, Annemarie; Felder, Bärbel; Klauck, Sabine; Schuster, Claudia; Poustka, Fritz; Bölte, Sven; Feineis-Matthews, Sabine; Herbrecht, Evelyn; Schmötzer, Gabi; Tsiantis, John; Papanikolaou, Katerina; Maestrini, Elena; Bacchelli, Elena; Blasi, Francesca; Carone, Simona; Toma, Claudio; Van Engeland, Herman; De Jonge, Maretha; Kemner, Chantal; Koop, Frederieke; Langemeijer, Marjolein; Hijmans, Channa; Staal, Wouter; Baird, Gillian; Bolton, Patrick; Rutter, Michael; Weisblatt, Emma; Green, Jonathan; Aldred, Catherine; Wilkinson, Julie-Anne; Pickles, Andrew; Le Couteur, Ann; Berney, Tom; Mcconachie, Helen; Bailey, Anthony; Francis, Kostas; Honeyman, Gemma; Hutchinson, Aislinn; Parr, Jeremy; Wallace, Simon; Monaco, Anthony; Barnby, Gabrielle; Kobayashi, Kazuhiro; Lamb, Janine; Sousa, Ines; Sykes, Nuala; Cook, Edwin; Guter, Stephen; Leventhal, Bennett; Salt, Jeff; Lord, Catherine; Corsello, Christina; Hus, Vanessa; Weeks, Daniel; Volkmar, Fred; Tauber, Maïté; Fombonne, Eric; Shih, Andy; Meyer, Kacie

    2007-01-01

    Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with ≥ 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. PMID:17322880

  12. Allele-sharing models: LOD scores and accurate linkage tests.

    Science.gov (United States)

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  13. Record linkage for pharmacoepidemiological studies in cancer patients.

    Science.gov (United States)

    Herk-Sukel, Myrthe P P van; Lemmens, Valery E P P; Poll-Franse, Lonneke V van de; Herings, Ron M C; Coebergh, Jan Willem W

    2012-01-01

    An increasing need has developed for the post-approval surveillance of (new) anti-cancer drugs by means of pharmacoepidemiology and outcomes research in the area of oncology. To create an overview that makes researchers aware of the available database linkages in Northern America and Europe which facilitate pharmacoepidemiology and outcomes research in cancer patients. In addition to our own database, i.e. the Eindhoven Cancer Registry (ECR) linked to the PHARMO Record Linkage System, we considered database linkages between a population-based cancer registry and an administrative healthcare database that at least contains information on drug use and offers a longitudinal perspective on healthcare utilization. Eligible database linkages were limited to those that had been used in multiple published articles in English language included in Pubmed. The HMO Cancer Research Network (CRN) in the US was excluded from this review, as an overview of the linked databases participating in the CRN is already provided elsewhere. Researchers who had worked with the data resources included in our review were contacted for additional information and verification of the data presented in the overview. The following database linkages were included: the Surveillance, Epidemiology, and End-Results-Medicare; cancer registry data linked to Medicaid; Canadian cancer registries linked to population-based drug databases; the Scottish cancer registry linked to the Tayside drug dispensing data; linked databases in the Nordic Countries of Europe: Norway, Sweden, Finland and Denmark; and the ECR-PHARMO linkage in the Netherlands. Descriptives of the included database linkages comprise population size, generalizability of the population, year of first data availability, contents of the cancer registry, contents of the administrative healthcare database, the possibility to select a cancer-free control cohort, and linkage to other healthcare databases. The linked databases offer a longitudinal

  14. How policies affect international biofuel price linkages

    International Nuclear Information System (INIS)

    Rajcaniova, Miroslava; Drabik, Dusan; Ciaian, Pavel

    2013-01-01

    We estimate the role of biofuel policies in determining which country is the price leader in world biofuel markets using a cointegration analysis and a Vector Error Correction (VEC) model. Weekly prices are analyzed for the EU, US, and Brazilian ethanol and biodiesel markets in the 2002–2010 and 2005–2010 time periods, respectively. The US blender's tax credit and Brazil's consumer tax exemption are found to play a role in determining the ethanol prices in other countries. For biodiesel, our results demonstrate that EU policies – the consumer tax exemption and blending target – tend to determine the world biodiesel price. - Highlights: • We estimate the role of biofuel policies in determining biofuel prices. • We use a cointegration analysis and the Vector Error Correction (VEC) model. • The biofuel policies in US and Brazil determine the world ethanol prices. • EU biofuel policies tend to form the world biodiesel price

  15. Analyzing the Relative Linkages of Land Use and Hydrologic Variables with Urban Surface Water Quality using Multivariate Techniques

    Science.gov (United States)

    Ahmed, S.; Abdul-Aziz, O. I.

    2015-12-01

    We used a systematic data-analytics approach to analyze and quantify relative linkages of four stream water quality indicators (total nitrogen, TN; total phosphorus, TP; chlorophyll-a, Chla; and dissolved oxygen, DO) with six land use and four hydrologic variables, along with the potential external (upstream in-land and downstream coastal) controls in highly complex coastal urban watersheds of southeast Florida, U.S.A. Multivariate pattern recognition techniques of principle component and factor analyses, in concert with Pearson correlation analysis, were applied to map interrelations and identify latent patterns of the participatory variables. Relative linkages of the in-stream water quality variables with their associated drivers were then quantified by developing dimensionless partial least squares (PLS) regression model based on standardized data. Model fitting efficiency (R2=0.71-0.87) and accuracy (ratio of root-mean-square error to the standard deviation of the observations, RSR=0.35-0.53) suggested good predictions of the water quality variables in both wet and dry seasons. Agricultural land and groundwater exhibited substantial controls on surface water quality. In-stream TN concentration appeared to be mostly contributed by the upstream water entering from Everglades in both wet and dry seasons. In contrast, watershed land uses had stronger linkages with TP and Chla than that of the watershed hydrologic and upstream (Everglades) components for both seasons. Both land use and hydrologic components showed strong linkages with DO in wet season; however, the land use linkage appeared to be less in dry season. The data-analytics method provided a comprehensive empirical framework to achieve crucial mechanistic insights into the urban stream water quality processes. Our study quantitatively identified dominant drivers of water quality, indicating key management targets to maintain healthy stream ecosystems in complex urban-natural environments near the coast.

  16. The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.

    Science.gov (United States)

    Padala, Prasanth; Soudah, Nadine; Giladi, Moshe; Haitin, Yoni; Isupov, Michail N; Wiener, Reuven

    2017-12-08

    The ability of ubiquitin to function in a wide range of cellular processes is ascribed to its capacity to cause a diverse spectrum of modifications. While a target protein can be modified with monoubiquitin, it can also be modified with ubiquitin chains. The latter include seven types of homotypic chains as well as mixed ubiquitin chains. In a mixed chain, not all the isopeptide bonds are restricted to a specific lysine of ubiquitin, resulting in a chain possessing more than one type of linkage. While structural characterization of homotypic chains has been well elucidated, less is known about mixed chains. Here we present the crystal structure of a mixed tri-ubiquitin chain at 3.1-Å resolution. In the structure, the proximal ubiquitin is connected to the middle ubiquitin via K48 and these two ubiquitins adopt a compact structure as observed in K48 di-ubiquitin. The middle ubiquitin links to the distal ubiquitin via its K63 and these ubiquitins adopt two conformations, suggesting a flexible structure. Using small-angle X-ray scattering, we unexpectedly found differences between the conformational ensembles of the above tri-ubiquitin chains and chains possessing the same linkages but in the reverse order. In addition, cleavage of the K48 linkage by DUB is faster if this linkage is at the distal end. Taken together, our results suggest that in mixed chains, not only the type of the linkages but also their sequence determine the structural and functional properties of the chain. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Multivariate Stable Isotope Analysis to Determine Linkages between Benzocaine Seizures

    Science.gov (United States)

    Kemp, H. F.; Meier-Augenstein, W.; Collins, M.; Salouros, H.; Cunningham, A.; Harrison, M.

    2012-04-01

    In July 2010, a woman was jailed for nine years in the UK after the prosecution successfully argued that attempting to import a cutting agent was proof of involvement in a conspiracy to supply Cocaine. That landmark ruling provided law enforcement agencies with much greater scope to tackle those involved in this aspect of the drug trade, specifically targeting those importing the likes of benzocaine or lidocaine. Huge quantities of these compounds are imported into the UK and between May and August 2010, four shipments of Benzocaine amounting to more then 4 tons had been seized as part of Operation Kitley, a joint initiative between the UK Border Agency and the Serious Organised Crime Agency (SOCA). By diluting cocaine, traffickers can make it go a lot further for very little cost, leading to huge profits. In recent years, dealers have moved away from inert substances, like sugar and baby milk powder, in favour of active pharmaceutical ingredients (APIs), including anaesthetics like Benzocaine and Lidocaine. Both these mimic the numbing effect of cocaine, and resemble it closely in colour, texture and some chemical behaviours, making it easier to conceal the fact that the drug has been diluted. API cutting agents have helped traffickers to maintain steady supplies in the face of successful interdiction and even expand the market in the UK, particularly to young people aged from their mid teens to early twenties. From importation to street-level, the purity of the drug can be reduced up to a factor of 80 and street level cocaine can have a cocaine content as low as 1%. In view of the increasing use of Benzocaine as cutting agent for Cocaine, a study was carried out to investigate if 2H, 13C, 15N and 18O stable isotope signatures could be used in conjunction with multivariate chemometric data analysis to determine potential linkage between benzocaine exhibits seized from different locations or individuals to assist with investigation and prosecution of drug

  18. Modeling Resource Hotspots: Critical Linkages and Processes

    Science.gov (United States)

    Daher, B.; Mohtar, R.; Pistikopoulos, E.; McCarl, B. A.; Yang, Y.

    2017-12-01

    Growing demands for interconnected resources emerge in the form of hotspots of varying characteristics. The business as usual allocation model cannot address the current, let alone anticipated, complex and highly interconnected resource challenges we face. A new paradigm for resource allocation must be adopted: one that identifies cross-sectoral synergies and, that moves away from silos to recognition of the nexus and integration of it. Doing so will result in new opportunities for business growth, economic development, and improved social well-being. Solutions and interventions must be multi-faceted; opportunities should be identified with holistic trade-offs in mind. No single solution fits all: different hotspots will require distinct interventions. Hotspots have varying resource constraints, stakeholders, goals and targets. The San Antonio region represents a complex resource hotspot with promising potential: its rapidly growing population, the Eagle Ford shale play, and the major agricultural activity there makes it a hotspot with many competing demands. Stakeholders need tools to allow them to knowledgeably address impending resource challenges. This study will identify contemporary WEF nexus questions and critical system interlinkages that will inform the modeling of the tightly interconnected resource systems and stresses using the San Antonio Region as a base; it will conceptualize a WEF nexus modeling framework, and develop assessment criteria to inform integrative planning and decision making.

  19. Inherently balanced 4R four-bar based linkages

    NARCIS (Netherlands)

    van der Wijk, V.; Herder, Justus Laurens; Lenarcis, J.; Husty, M.

    2012-01-01

    Synthesis of mechanisms with their center of mass (CoM) at an invariant point on one of the elements is useful for the design of statically balanced and shaking-force balanced mechanisms and manipulators. For this purpose, a kinematic architecture based on a general 4R four-bar linkage is found by

  20. Linkages between biodiversity attributes and ecosystem services: A systematic review

    NARCIS (Netherlands)

    Harrison, P.A.; Berry, P.M.; Simpson, G.; Haslett, J.R.; Blicharska, M.; Bucur, M.; Dunford, R.; Egoh, B.; Garcia-llorente, M.; Geamănă, N.; Geertsema, W.; Lommelen, E.; Meiresonne, L.; Turkelboom, F.

    2014-01-01

    A systematic literature review was undertaken to analyse the linkages between different biodiversity attributes and 11 ecosystem services. The majority of relationships between attributes and ecosystem services cited in the 530 studies were positive. For example, the services of water quality

  1. Linkages between aggregate formation, porosity and soil chemical properties

    NARCIS (Netherlands)

    Regelink, I.C.; Stoof, C.R.; Rousseva, S.; Weng, L.; Lair, G.J.; Kram, P.; Nikolaidis, N.P.; Kercheva, M.; Banwart, S.; Comans, R.N.J.

    2015-01-01

    Linkages between soil structure and physical–chemical soil properties are still poorly understood due to the wide size-range at which aggregation occurs and the variety of aggregation factors involved. To improve understanding of these processes, we collected data on aggregate fractions, soil

  2. Analysis of Linkage Effects among Currency Networks Using REER Data

    Directory of Open Access Journals (Sweden)

    Haishu Qiao

    2015-01-01

    Full Text Available We modeled the currency networks through the use of REER (real effective exchange rate instead of a bilateral exchange rate in order to overcome the confusion in selecting base currencies. Based on the MST (minimum spanning tree approach and the rolling-window method, we constructed time-varying and correlation-based networks with which we investigate the linkage effects among different currencies. In particular, and as the source of empirical data, we chose the monthly REER data for a set of 61 major currencies during the period from 1994 to 2014. The study demonstrated that obvious linkage effects existed among currency networks and the euro (EUR was confirmed as the predominant world currency. Additionally, we used the rolling-window method to investigate the stability of linkage effects, doing so by calculating the mean correlations and mean distances as well as the normalized tree length and degrees of those currencies. The results showed that financial crises during the study period had a great effect on the currency network’s topology structure and led to more clustered currency networks. Our results suggested that it is more appropriate to estimate the linkage effects among currency networks through the use of REER data.

  3. insights from a linkage map of the damselfly Ischnura elegans

    Indian Academy of Sciences (India)

    tion of achiasmiatic meiosis. Biochem. Genet. 19, 1237–. 1245. Cooper G., Miller P. L. and Holland P. W. H. 1994 Molecular genetic analysis of sperm competition in the damselfly Ischnura elegans (Vander Linden). Proc. R. Soc. London, Ser. B 263,. 1343–1349. Huxley J. S. 1928 Sexual differences in linkage in Gammar-.

  4. Changing rural urban linkages in Africa in a globalizing economy ...

    African Journals Online (AJOL)

    The role of rural-urban linkages is critically vital for Africa‟s development in this era of rapid socio-economic transformation. A better understanding of cities and how they relate both to the rural and urban development is needed in view of the continuous changes in development. This paper argues that many of Africa‟s ...

  5. Creative arts linkages, historiography: means to global aesthetics ...

    African Journals Online (AJOL)

    This paper surveys linkages and historiography in creative arts and globalization. The appreciation and possession of other nations' creative art objects/artifacts links different cultures and nations together as they share common aesthetic experiences, history and knowledge which was unique to a particular nation.

  6. Recombination patterns reveal information about centromere location on linkage maps

    DEFF Research Database (Denmark)

    Limborg, Morten T.; McKinney, Garrett J.; Seeb, Lisa W.

    2016-01-01

    . mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  7. A study of inter linkage effects on Candu feeder piping

    International Nuclear Information System (INIS)

    Li, M.; Aggarwal, M.L.; Meysner, A.

    2005-01-01

    A CANDU (Canadian Deuterium Uranium) reactor core consists of a large number of fuel channels where heat is generated. Two feeder pipes are connected to each fuel channel to transport D 2 O coolant into and out of the reactor core. The feeder piping is designed to the requirements of Class 1 piping of Section III NB of the ASME Boiler and Pressure Vessel and CSA Codes. Feeder piping stress analysis is being performed to demonstrate the code compliance check and the fitness for service of feeders. In the past, stress analyses were conducted for each individual feeder without including interaction effects among connected feeders. Interaction effects occur as a result of linkages that exist between feeders to prevent fretting and impacting damage during normal, abnormal and accident conditions. In this paper, a 'combined' approach is adopted to include all feeders connected by inter linkages into one feeder piping model. MSC/NASTRAN finite element software was used in the stress simulation, which contains up to 127 feeder pipes. The ASME Class 1 piping analysis was conducted to investigate the effects of the linkages between feeders. Both seismic time history and broadened response spectra methods were used in the seismic stress calculation. The results show that the effect of linkages is significant in dynamic stresses for all feeder configurations, as well as in static stresses for certain feeder configurations. The single feeder analysis could either underestimate or overestimate feeder stresses depending on the pipe geometry and bend wall thickness. (authors)

  8. Linkages among Key Actors in the Climate Change and Food ...

    African Journals Online (AJOL)

    Sierra Leone and Liberia, but a low linkage index of less than 2 between farmers and policy making bodies for all the countries. Poor generation of innovations over the past ten years and poor domestic support for climate change adaptation and food security in the West African sub-region were identified. The study points to ...

  9. Economic Growth, Structural Change and Productive Employment Linkages in India

    DEFF Research Database (Denmark)

    Aggarwal, Aradhna

    2018-01-01

    This article presents a quantitative analysis of growth, structural change and employment linkages at the aggregate level and by sector under the state- and market-led regimes in India. The underlying objectives are: (a) to understand how economic liberalization has affected the economic and labour...... intervention to broad base structural change for generating productive employment, which is at the core of poverty reduction....

  10. Broad scan linkage analysis in a large Tourette family pedigree

    Energy Technology Data Exchange (ETDEWEB)

    Peiffer, A.; Leppert, M. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States); Wetering, B.J.M. van der [Univ. Hospital Rotterdam (Netherlands)

    1994-09-01

    Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.

  11. A consensus linkage map of the chicken genome

    NARCIS (Netherlands)

    Groenen, M.A.M.; Cheng, H.H.; Bumstead, N.; Benkel, B.; Briles, E.; Burt, D.W.; Burke, T.; Dodgson, J.; Hillel, J.; Lamont, S.; Ponce, de F.A.; Soller, M.

    2000-01-01

    A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal

  12. The western arctic linkage experiment (WALE): overview and synthesis

    Science.gov (United States)

    A.D. McGuire; J. Walsh; J.S. Kimball; J.S. Clein; S.E. Euskirdhen; S. Drobot; U.C. Herzfeld; J. Maslanik; R.B. Lammers; M.A. Rawlins; C.J. Vorosmarty; T.S. Rupp; W. Wu; M. Calef

    2008-01-01

    The primary goal of the Western Arctic Linkage Experiment (WALE) was to better understand uncertainties of simulated hydrologic and ecosystem dynamics of the western Arctic in the context of 1) uncertainties in the data available to drive the models and 2) different approaches to simulating regional hydrology and ecosystem dynamics. Analyses of datasets on climate...

  13. Human Capital Linkages to Labour Productivity: Implications from Thai Manufacturers

    Science.gov (United States)

    Rukumnuaykit, Pungpond; Pholphirul, Piriya

    2016-01-01

    Human capital investment is a necessary condition for improving labour market outcomes in most countries. Empirical studies to investigate human capital and its linkages on the labour demand side are, however, relatively scarce due to limitations of firm-level data-sets. Using firm-level data from the Thai manufacturing sector, this paper aims to…

  14. The Dynamics of Linkages and Innovativeness in Publicly and ...

    African Journals Online (AJOL)

    The study examined how linkages among actors in the cocoa and pineapple value chains relate to the innovativeness of actors in the chains. The study showed that a policy environment that promoted public sector leadership in value chain functions and service provision, tended to offer less incentives for smallholder ...

  15. Patient and provider perspectives on improving the linkage of HIV ...

    African Journals Online (AJOL)

    This study examined barriers and facilitators to the linkage of HIV-positive pregnant women from antenatal care (ANC) to long-term HIV care from patient and provider perspectives, following the implementation of a collaborative quality improvement project in Eastern Uganda. It also solicited recommendations for improving ...

  16. Innovation and inter-firm linkages : new implications for policy

    NARCIS (Netherlands)

    Nooteboom, B

    This article discusses the implications for competition, innovation and learning of different forms of inter-firm linkage, ways to govern them, different 'generic systems' of innovation, and government policy. It employs a transformed theory of transactions that can deal with innovation and

  17. Localizing genes using linkage disequilibrium in plants: integrating ...

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... Localizing genes using linkage disequilibrium in plants: integrating lessons ... reduce that association as a function of the marker distance from the QTL. ..... the gene locus enhanced the resolution power of asso- ciation tests .... agents, such as insects, birds, water and wind, so mating is determined by a ...

  18. Multiple operating models for data linkage: A privacy positive

    Directory of Open Access Journals (Sweden)

    Katrina Irvine

    2017-04-01

    Our data linkage centre will implement new operating models with cascading levels of data handling on behalf of custodians. Sharing or publication of empirical evidence on timeframes, efficiency and quality can provide useful inputs in the design of new operating models and assist with the development of stakeholder and public confidence.

  19. International Environmental Problems, Issue Linkage and the European Union

    NARCIS (Netherlands)

    Kroeze-Gil, J.

    2003-01-01

    This thesis explores the circumstances under which issue linkage can be applied to achieve cooperation on international environmental problems in general and on environmental problems in the European Union in particular. A major topic in this thesis is the development and analysis of cooperative and

  20. Linkages over Time between Adolescents' Relationships with Parents and Friends

    Science.gov (United States)

    De Goede, Irene H. A.; Branje, Susan J. T.; Delsing, Marc J. M. H.; Meeus, Wim H. J.

    2009-01-01

    This 5-wave longitudinal study examines linkages over time between adolescents' perceptions of relationships with parents and friends with respect to support, negative interaction, and power. A total of 575 early adolescents (54.1% boys) and 337 middle adolescents (43.3% boys) participated. Path analyses mainly showed bidirectional associations…

  1. Strengthening linkages of the financial services and real sectors of ...

    African Journals Online (AJOL)

    Strengthening linkages of the financial services and real sectors of the ... policy, financial sector credit and capital market activities have impacted on the real sector growth. ... sector as a result such financial crimes like misappropriation of funds. ... better results; more investment instruments such as derivatives, convertibles, ...

  2. Linkage Mechanisms among key Actors in Rice Innovation System ...

    African Journals Online (AJOL)

    In assessment of linkage mechanisms among key actors in rice innovation system in southeast Nigeria, actors were classified into six major groups according to their main activity in the system namely research agency, policy personnel, technology transfer agencies, farmers, marketers and consumers. These constituted the ...

  3. The first genetic linkage map of Primulina eburnea (Gesneriaceae)

    Indian Academy of Sciences (India)

    Primulina eburneais a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flow-ers. An F2population of 189 individuals was established for the construction of first-generation linkage maps based onexpressed sequence tags-derived single-nucleotide polymorphism markers ...

  4. Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

    Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

  5. Evaluation of Price Linkages within the Supply Chain of Rice ...

    African Journals Online (AJOL)

    This paper evaluates price linkages within the supply chain of rice markets in Cross River State using weekly prices in three urban markets located in major rice producing areas of the State. The Johansen cointegration test indicated one cointegrating vector both at the 1% and 5% level of significance. The results of the ...

  6. Whole genome study of linkage disequilibrium in Sahiwal cattle

    African Journals Online (AJOL)

    Esnart Mukumbo

    2017-12-30

    Dec 30, 2017 ... 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior ..... on a high density SNP panel. BMC Genom. ... Linkage disequilibrium and the mapping of complex human traits. Trend.

  7. Linkages between landscapes and human well-being

    DEFF Research Database (Denmark)

    Bieling, Claudia; Plieninger, Tobias; Pirker, Heidemarie

    2014-01-01

    in Germany and Austria by performing open, single-question interviews with 262 respondents. Data reveal an outstanding relevance of nonmaterial values. Linkages between landscapes and human well-being are tied to specific features of the material environment but, likewise, practices and experiences play...

  8. Entrepreneurship And Business Management - Exploring Linkages For Sustainable Development

    Directory of Open Access Journals (Sweden)

    Dr Serah K Mbetwa

    2015-08-01

    Full Text Available Entrepreneurs have emerged as market leaders in todays business world amidst the numerous economic turmoil constantly affecting economies on a global scale. This research paper is on entrepreneurship and business management and its linkages to other business stakeholders. The research paper therefore discusses entrepreneurship and business management exploring the linkages to available financing and potential institutions for startup capital by linking entrepreneurs to the government financiers and the public clientele. It is believed that this can bring about achievement of sustainable development goals translating into sustainable development and hence economic growth. The idea of funding is echoed by Robert Rice 2016 An entrepreneur without funding is like a musician with no instruments. Sustainability and entrepreneurship sustainopreneurship is made possible with availability of information on linkages between entrepreneurs and financial lending institutions as well as government policy. It is hoped that the research will add to the existing knowledge and help entrepreneurs with funding options for their business ideas to come to life. Findings show that the government financial lending institutions and the public are the major linkages between entrepreneurship and business management and are critical for attaining sustainable development goals and achieving economic growth.

  9. Intra-facility linkage of HIV-positive mothers and HIV-exposed babies into HIV chronic care: rural and urban experience in a resource limited setting.

    Directory of Open Access Journals (Sweden)

    Christine Mugasha

    Full Text Available INTRODUCTION: Linkage of HIV-infected pregnant women to HIV care remains critical for improvement of maternal and child outcomes through prevention of maternal-to-child transmission of HIV (PMTCT and subsequent chronic HIV care. This study determined proportions and factors associated with intra-facility linkage to HIV care and Early Infant Diagnosis care (EID to inform strategic scale up of PMTCT programs. METHODS: A cross-sectional review of records was done at 2 urban and 3 rural public health care facilities supported by the Infectious Diseases Institute (IDI. HIV-infected pregnant mothers, identified through routine antenatal care (ANC and HIV-exposed babies were evaluated for enrollment in HIV clinics by 6 weeks post-delivery. RESULTS: Overall, 1,025 HIV-infected pregnant mothers were identified during ANC between January and June, 2012; 267/1,025 (26% in rural and 743/1,025 (74% in urban facilities. Of these 375/1,025 (37% were linked to HIV clinics [67/267(25% rural and 308/758(41% urban]. Of 636 HIV-exposed babies, 193 (30% were linked to EID. Linkage of mother-baby pairs to HIV chronic care and EID was 16% (101/636; 8/179 (4.5%] in rural and 93/457(20.3% in urban health facilities. Within rural facilities, ANC registration <28 weeks-of-gestation was associated with mothers' linkage to HIV chronic care [AoR, 2.0 95% CI, 1.1-3.7, p = 0.019] and mothers' multi-parity was associated with baby's linkage to EID; AoR 4.4 (1.3-15.1, p = 0.023. Stigma, long distance to health facilities and vertical PMTCT services affected linkage in rural facilities, while peer mothers, infant feeding services, long patient queues and limited privacy hindered linkage to HIV care in urban settings. CONCLUSION: Post-natal linkage of HIV-infected mothers to chronic HIV care and HIV-exposed babies to EID programs was low. Barriers to linkage to HIV care vary in urban and rural settings. We recommend targeted interventions to rapidly improve linkage to

  10. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

    Full Text Available An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red, genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10. We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

  11. A novel syndrome of abnormal striatum and congenital cataract: evidence for linkage to chromosomes 11.

    Science.gov (United States)

    Al-Owain, M; Al-Zahrani, J; Al-Bakheet, A; Abudheim, N; Al-Younes, B; Aldhalaan, H; Al-Zaidan, H; Colak, D; Almohaileb, F; Abouzied, M E; Al-Fadhli, F; Meyer, B; Kaya, N

    2013-09-01

    We report a consanguineous family of three girls and one boy affected with a novel syndrome involving the lens and the basal ganglia. The phenotype is strikingly similar between affected siblings with cognitive impairment, attention deficit hyperactivity disorder (ADHD), microcephaly, growth retardation, congenital cataract, and dystonia. The magnetic resonance imaging showed unusual pattern of swelling of the caudate heads and thinning of the putamina with severe degree of hypometabolism on the [18F] deoxyglucose positron emission tomography. Furthermore, the clinical assessment provides the evidence that the neurological phenotype is very slowly progressive. We utilized the 10K single-nucleotide polymorphism (SNP) microarray genotyping for linkage analysis. Genome-wide scan indicated a 45.9-Mb region with a 4.2353 logarithm of the odds score on chromosome 11. Affymetrix genome-wide human SNP array 6.0 assay did not show any gross chromosomal abnormality. Targeted sequencing of two candidate genes within the linkage interval (PAX6 and B3GALTL) as well as mtDNA genome sequencing did not reveal any putative mutations. © 2012 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Background and elements of the linkage between the Brazilian school feeding program and family farming.

    Science.gov (United States)

    Schwartzman, Flavia; Mora, Claudia Andrea Rodriguez; Bogus, Claudia Maria; Villar, Betzabeth Slater

    2017-12-18

    Since 2009, legislation of the National School Feeding Program of Brazil (PNAE) institutionalizes its linkage with family farming as it establishes the requirement that at least 30% out of the total financial resources allocated by the federal government to the states and municipalities for school feeding must be used in the purchase of products directly from this sector. This study analyzes the process of drafting this legislation, focusing on the elements related to the procurement from family farming, through a historical contextualization, and it also presents a graphical representation with the main elements of this linkage: its objectives, target population, actions implemented and expected results. Actors involved with the drafting of the legislation were interviewed. The analyses show that the procurement from family farming is a far-reaching initiative in terms of the concept, execution and results. It has also showed that a strong articulation between the actors and institutions of the different sectors involved is critical to its success. The education, agriculture, planning, procurement and civil society sectors should work articulately at national, state and local level. The results of this study demonstrate that initiatives like this, of institutional procurement from family farming, which are currently being implemented in several countries, constitute as an important strategy of food and nutrition security, for the fulfillment of the human right to adequate food and the promotion of long-term sustainable development.

  13. Transnational linkages in sustainability experiments : A typology and the case of solar photovoltaic energy in India

    NARCIS (Netherlands)

    Wieczorek, A.J.; Raven, R.; Berkhout, F.

    2015-01-01

    This paper explores transnational linkages in sustainability experiments. Transnational linkages refer to diverse cross-border relationships and interactions that can complement local, regional and national capabilities enabling sustainability experiments. The paper develops a typology of

  14. Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo

    Directory of Open Access Journals (Sweden)

    J.-H. Lee

    2012-01-01

    Full Text Available The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA, and marbling score (Marb, respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp with the most significant evidence for linkage (p<10−5. Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

  15. Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

    Science.gov (United States)

    Olsen, Aaron M; Westneat, Mark W

    2016-12-01

    Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing

  16. A genetic linkage map for the saltwater crocodile (Crocodylus porosus

    Directory of Open Access Journals (Sweden)

    Lance Stacey L

    2009-07-01

    Full Text Available Abstract Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL, and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1. Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD. However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition

  17. Nance-Horan syndrome: linkage analysis in a family from The Netherlands

    NARCIS (Netherlands)

    Bergen, A. A.; ten Brink, J.; Schuurman, E. J.; Bleeker-Wagemakers, E. M.

    1994-01-01

    Linkage analysis was carried out in a Dutch family with Nance-Horan (NH) syndrome. Close linkage without recombination between NH and the Xp loci DXS207, DXS43, and DXS365 (zmax = 3.23) was observed. Multipoint linkage analysis and the analysis of recombinations in multiple informative meioses

  18. Data Linkage in VET Research: Opportunities, Challenges and Principles. Discussion Paper

    Science.gov (United States)

    Osborne, Kristen; Fowler, Craig; Circelli, Michelle

    2018-01-01

    This discussion paper explores the possibilities and risks that data linkage presents for the vocational education and training (VET) sector. Along with a broad overview of the nature of data linkage, it highlights possible applications for data linkage in the VET sector and examines the key challenges associated with its use. A number of case…

  19. Do we understand the linkages between economic growth, poverty targets and poverty reduction?

    DEFF Research Database (Denmark)

    Casse, Thorkil; Jensen, Stig Eduard Breitenstein

    2009-01-01

    This article contributes to the debate on poverty trends in Africa, looking at the argument for a correspondence between economic growth and poverty reduction. It questions whether a link between economic growth and poverty reduction can be established. We first look at the general picture...... appears more obvious, social and political unrest in 2009 casts doubt on the reliability of the data. Indeed, it is probable that an increase in poverty contributed to the crisis in Madagascar. Furthermore, there a signs that in both countries poverty strategies are increasingly giving way to Poverty...... Reduction Growth Facility programmes, closely related to former structural adjustment loans. We conclude, first, that analysing poverty strategies through Poverty Reduction Strategy Papers does not help in resolving the uncertainty, since these strategies assume a priori the existence of a link between...

  20. Design control and scientific investigations: Is there any linkage?

    International Nuclear Information System (INIS)

    Richards, R.R.

    1995-01-01

    The quality assurance requirements that apply to the effort to achieve safe transportation, storage, and disposal of high-level nuclear waste specify that ''design control'' be applied to design activities. That effort also involves extensive scientific investigation activities to, among other things, develop information that may be used in engineering design activities. Individuals who are charged with the implementation of such quality assurance requirements have come to a variety of conclusions about whether there is any firm linkage between design control and the conduct of scientific investigations. This paper contends that there is a reasonable and necessary linkage between ''design control'' and scientific activities, though not a connection that has traditionally been made and not one addressed in the QA standards for radioactive waste management programs

  1. Countering Islamic State Messaging Through “Linkage-Based” Analysis

    Directory of Open Access Journals (Sweden)

    J.M. Berger

    2017-08-01

    Full Text Available The Islamic State’s recent losses on the battlefield, including significant casualties within its media and propaganda division, offer a unique opportunity to inject competing and alternative messages into the information space. This paper proposes that the content of such messages should be guided by a linkage-based analysis of existing Islamic State messaging. A linkage-based analysis of a top-level 2017 audio message by Islamic State spokesperson Abu Hasan al Muhajir offers several potential insights into crafting effective content for competing and alternative messages. A comparison of the 2017 work to earlier Islamic State messaging also reveals specific opportunities to undermine the credibility of the organisation’s broader propaganda programme by highlighting the organisation’s repeated failure to follow through on its extravagantly promised commitment to achieving its stated goals.

  2. An improved recommendation algorithm via weakening indirect linkage effect

    Science.gov (United States)

    Chen, Guang; Qiu, Tian; Shen, Xiao-Quan

    2015-07-01

    We propose an indirect-link-weakened mass diffusion method (IMD), by considering the indirect linkage and the source object heterogeneity effect in the mass diffusion (MD) recommendation method. Experimental results on the MovieLens, Netflix, and RYM datasets show that, the IMD method greatly improves both the recommendation accuracy and diversity, compared with a heterogeneity-weakened MD method (HMD), which only considers the source object heterogeneity. Moreover, the recommendation accuracy of the cold objects is also better elevated in the IMD than the HMD method. It suggests that eliminating the redundancy induced by the indirect linkages could have a prominent effect on the recommendation efficiency in the MD method. Project supported by the National Natural Science Foundation of China (Grant No. 11175079) and the Young Scientist Training Project of Jiangxi Province, China (Grant No. 20133BCB23017).

  3. CERN: Fixed target targets

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1993-03-15

    Full text: While the immediate priority of CERN's research programme is to exploit to the full the world's largest accelerator, the LEP electron-positron collider and its concomitant LEP200 energy upgrade (January, page 1), CERN is also mindful of its long tradition of diversified research. Away from LEP and preparations for the LHC proton-proton collider to be built above LEP in the same 27-kilometre tunnel, CERN is also preparing for a new generation of heavy ion experiments using a new source, providing heavier ions (April 1992, page 8), with first physics expected next year. CERN's smallest accelerator, the LEAR Low Energy Antiproton Ring continues to cover a wide range of research topics, and saw a record number of hours of operation in 1992. The new ISOLDE on-line isotope separator was inaugurated last year (July, page 5) and physics is already underway. The remaining effort concentrates around fixed target experiments at the SPS synchrotron, which formed the main thrust of CERN's research during the late 1970s. With the SPS and LEAR now approaching middle age, their research future was extensively studied last year. Broadly, a vigorous SPS programme looks assured until at least the end of 1995. Decisions for the longer term future of the West Experimental Area of the SPS will have to take into account the heavy demand for test beams from work towards experiments at big colliders, both at CERN and elsewhere. The North Experimental Area is the scene of larger experiments with longer lead times. Several more years of LEAR exploitation are already in the pipeline, but for the longer term, the ambitious Superlear project for a superconducting ring (January 1992, page 7) did not catch on. Neutrino physics has a long tradition at CERN, and this continues with the preparations for two major projects, the Chorus and Nomad experiments (November 1991, page 7), to start next year in the West Area. Delicate neutrino oscillation effects could become visible for the first

  4. INDONESIAN COUNTRY PAPER MECHANISMS USED TO STRENGTHEN INFORMATION LINKAGES

    Directory of Open Access Journals (Sweden)

    Achmad Djuhamsa

    2011-12-01

    Full Text Available ENSICNET-Indonesia provides dissemination of information on the field of water supply and sanitation to potential users by using different methods which depend on their own function and duty. Linkage mechanisms are developed to make users aware of the sources, to identify and define user n~eds and to make the contact 'between the user need and the information sources. Several forms of communication which can link information resources to an individual or groups are disscussed.

  5. Nuclear hazard/fire hazard: an elusive and important linkage

    International Nuclear Information System (INIS)

    Mariani, L.P.

    1977-01-01

    The Brown's Ferry Fire signaled a yellow alert for nuclear safety related fire protection and showed that fire protection engineering must be regarded as a bona fide nuclear discipline. A single-failure design criteria violation resulted in fire damage to plant systems and plant instrumentation. Localized damage lead to significant consequences. Although the linkage between fire and nuclear hazard is termed subtle, effective standards and criteria development must be aimed to future plants. Combined fire protection and nuclear engineering inspections are planned

  6. The changing international linkages of Switzerland: An overview

    OpenAIRE

    Tille, Cédric

    2017-01-01

    Over the last decade, the economic linkages between Switzerland and the rest of the world have been transformed. First, merchanting and the chemical industry account for an increasing share of international trade, with chemicals exports expanding robustly in recent years despite the European crisis and the strong Swiss franc. Second, the nature of international financial integration has changed. While private investors drove Switzerland's financial flows and net foreign assets before the fina...

  7. Linkage for Education and Research in Nursing (LEARN), une ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Linkage for Education and Research in Nursing (LEARN), une initiative de TIC-D dans les Caraïbes. Les infirmières représentent le plus important groupe de professionnels de la santé pouvant influer sur la qualité des soins dans les services de santé. Les efforts pour faire en sorte que les infirmières des Caraïbes soient ...

  8. Linear models for joint association and linkage QTL mapping

    Directory of Open Access Journals (Sweden)

    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  9. Genome scan for linkage to Gilles de la Tourette syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Barr, C.L.; Livingston, J.; Williamson, R. [and others

    1994-09-01

    Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

  10. Backward linkages from foreign investors to domestic firms

    OpenAIRE

    Apostolov, Mico

    2016-01-01

    The analysis of how to design policies to promote backward linkages would not be complete without introducing sound discovery into the debate. Foreign investors would naturally prefer to avoid creating rivals to their market position, aiming at horizontal positioning. But workers and managers often leave foreign plants to start up their own; local firms learn from watching the operations of foreigners. In the vertical direction, in cont...

  11. Heritability and linkage analysis of personality in bipolar disorder.

    Science.gov (United States)

    Greenwood, Tiffany A; Badner, Judith A; Byerley, William; Keck, Paul E; McElroy, Susan L; Remick, Ronald A; Dessa Sadovnick, A; Kelsoe, John R

    2013-11-01

    The many attempts that have been made to identify genes for bipolar disorder (BD) have met with limited success, which may reflect an inadequacy of diagnosis as an informative and biologically relevant phenotype for genetic studies. Here we have explored aspects of personality as quantitative phenotypes for bipolar disorder through the use of the Temperament and Character Inventory (TCI), which assesses personality in seven dimensions. Four temperament dimensions are assessed: novelty seeking (NS), harm avoidance (HA), reward dependence (RD), and persistence (PS). Three character dimensions are also included: self-directedness (SD), cooperativeness (CO), and self-transcendence (ST). We compared personality scores between diagnostic groups and assessed heritability in a sample of 101 families collected for genetic studies of BD. A genome-wide SNP linkage analysis was then performed in the subset of 51 families for which genetic data was available. Significant group differences were observed between BD subjects, their first-degree relatives, and independent controls for all but RD and PS, and all but HA and RD were found to be significantly heritable in this sample. Linkage analysis of the heritable dimensions produced several suggestive linkage peaks for NS (chromosomes 7q21 and 10p15), PS (chromosomes 6q16, 12p13, and 19p13), and SD (chromosomes 4q35, 8q24, and 18q12). The relatively small size of our linkage sample likely limited our ability to reach genome-wide significance in this study. While not genome-wide significant, these results suggest that aspects of personality may prove useful in the identification of genes underlying BD susceptibility. © 2013 Elsevier B.V. All rights reserved.

  12. Linkage Disequilibrium between STRPs and SNPs across the Human Genome

    OpenAIRE

    Payseur, Bret A.; Place, Michael; Weber, James L.

    2008-01-01

    Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this i...

  13. Identifying causal linkages between environmental variables and African conflicts

    Science.gov (United States)

    Nguy-Robertson, A. L.; Dartevelle, S.

    2017-12-01

    Environmental variables that contribute to droughts, flooding, and other natural hazards are often identified as factors contributing to conflict; however, few studies attempt to quantify these causal linkages. Recent research has demonstrated that the environment operates within a dynamical system framework and the influence of variables can be identified from convergent cross mapping (CCM) between shadow manifolds. We propose to use CCM to identify causal linkages between environmental variables and incidences of conflict. This study utilizes time series data from Climate Forecast System ver. 2 and MODIS satellite sensors processed using Google Earth Engine to aggregate country and regional trends. These variables are then compared to Armed Conflict Location & Event Data Project observations at similar scales. Results provide relative rankings of variables and their linkage to conflict. Being able to identify which factors contributed more strongly to a conflict can allow policy makers to prepare solutions to mitigate future crises. Knowledge of the primary environmental factors can lead to the identification of other variables to examine in the causal network influencing conflict.

  14. Effect of Linkage Disequilibrium on the Identification of Functional Variants

    Science.gov (United States)

    Thomas, Alun; Abel, Haley J; Di, Yanming; Faye, Laura L; Jin, Jing; Liu, Jin; Wu, Zheyan; Paterson, Andrew D

    2011-01-01

    We summarize the contributions of Group 9 of Genetic Analysis Workshop 17. This group addressed the problems of linkage disequilibrium and other longer range forms of allelic association when evaluating the effects of genotypes on phenotypes. Issues raised by long-range associations, whether a result of selection, stratification, possible technical errors, or chance, were less expected but proved to be important. Most contributors focused on regression methods of various types to illustrate problematic issues or to develop adaptations for dealing with high-density genotype assays. Study design was also considered, as was graphical modeling. Although no method emerged as uniformly successful, most succeeded in reducing false-positive results either by considering clusters of loci within genes or by applying smoothing metrics that required results from adjacent loci to be similar. Two unexpected results that questioned our assumptions of what is required to model linkage disequilibrium were observed. The first was that correlations between loci separated by large genetic distances can greatly inflate single-locus test statistics, and, whether the result of selection, stratification, possible technical errors, or chance, these correlations seem overabundant. The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium. PMID:22128051

  15. Evolution of zygotic linkage disequilibrium in a finite local population.

    Directory of Open Access Journals (Sweden)

    Xin-Sheng Hu

    Full Text Available One crucial feature of zygotic linkage disequilibrium (LD analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level are more informative than gametic LD (haploid level in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.

  16. Arctic-midlatitude weather linkages in North America

    Science.gov (United States)

    Overland, James E.; Wang, Muyin

    2018-06-01

    There is intense public interest in whether major Arctic changes can and will impact midlatitude weather such as cold air outbreaks on the central and east side of continents. Although there is progress in linkage research for eastern Asia, a clear gap is conformation for North America. We show two stationary temperature/geopotential height patterns where warmer Arctic temperatures have reinforced existing tropospheric jet stream wave amplitudes over North America: a Greenland/Baffin Block pattern during December 2010 and an Alaska Ridge pattern during December 2017. Even with continuing Arctic warming over the past decade, other recent eastern US winter months were less susceptible for an Arctic linkage: the jet stream was represented by either zonal flow, progressive weather systems, or unfavorable phasing of the long wave pattern. The present analysis lays the scientific controversy over the validity of linkages to the inherent intermittency of jet stream dynamics, which provides only an occasional bridge between Arctic thermodynamic forcing and extended midlatitude weather events.

  17. A dynamic birth-death model via Intrinsic Linkage

    Directory of Open Access Journals (Sweden)

    Robert Schoen

    2013-05-01

    Full Text Available BACKGROUND Dynamic population models, or models with changing vital rates, are only beginning to receive serious attention from mathematical demographers. Despite considerable progress, there is still no general analytical solution for the size or composition of a population generated by an arbitrary sequence of vital rates. OBJECTIVE The paper introduces a new approach, Intrinsic Linkage, that in many cases can analytically determine the birth trajectory of a dynamic birth-death population. METHODS Intrinsic Linkage assumes a weighted linear relationship between (i the time trajectory of proportional increases in births in a population and (ii the trajectory of the intrinsic rates of growth of the projection matrices that move the population forward in time. Flexibility is provided through choice of the weighting parameter, w, that links these two trajectories. RESULTS New relationships are found linking implied intrinsic and observed population patterns of growth. Past experience is "forgotten" through a process of simple exponential decay. When the intrinsic growth rate trajectory follows a polynomial, exponential, or cyclical pattern, the population birth trajectory can be expressed analytically in closed form. Numerical illustrations provide population values and relationships in metastable and cyclically stable models. Plausible projection matrices are typically found for a broad range of values of w, although w appears to vary greatly over time in actual populations. CONCLUSIONS The Intrinsic Linkage approach extends current techniques for dynamic modeling, revealing new relationships between population structures and the changing vital rates that generate them.

  18. Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.

    Science.gov (United States)

    Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh

    2016-07-01

    Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

  19. Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea

    Directory of Open Access Journals (Sweden)

    Jingqun Ao

    2015-11-01

    Full Text Available High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs evenly distributed across the large yellow croaker (Larimichthys crocea genome were identified using restriction-site associated DNA sequencing (RAD-seq. Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs. The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04% of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus and medaka (Oryzias latipes. Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

  20. ANALISIS KEBIJAKAN LINKAGE PROGRAM LEMBAGA KEUANGAN SYARIAH DALAM RANGKA PEMBERDAYAAN UKM DI INDONESIA

    Directory of Open Access Journals (Sweden)

    Siti Hamidah

    2016-03-01

    Linkage program adalah program yang menghubungkan bank dengan pelaku usaha mikro kecil melalui lembaga keuangan mikro. Kelemahan dalam Linkage program adalah pada aspek peraturan yang tersebar dalam berbagai aturan, dan khusus bagi lembaga keuangan syariah terdapat pula kendala berkaitan dengan kesesuaian dengan ketentuan syariah. Dari penelitian dengan pendekatan perundang-undangan dan pendekatan konseptual ini diperoleh inventarisasi serta analisis kebijakan Linkage Program bagi Lembaga Keuangan Syariah dalam hukum positif Indonesia. Kebijakan terkait Linkage program, diklasifikasi dalam 2 kelompok, yaitu kebijakan substansi dan prosedural. Aturan inilah yang menjadi rujukan bagi lembaga keuangan syariah rangka pemberdayaan usaha kecil mikro di Indonesia. Kata kunci: Linkage program, lembaga keuangan syariah, usaha mikro kecil

  1. CERN: Fixed target targets

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Full text: While the immediate priority of CERN's research programme is to exploit to the full the world's largest accelerator, the LEP electron-positron collider and its concomitant LEP200 energy upgrade (January, page 1), CERN is also mindful of its long tradition of diversified research. Away from LEP and preparations for the LHC proton-proton collider to be built above LEP in the same 27-kilometre tunnel, CERN is also preparing for a new generation of heavy ion experiments using a new source, providing heavier ions (April 1992, page 8), with first physics expected next year. CERN's smallest accelerator, the LEAR Low Energy Antiproton Ring continues to cover a wide range of research topics, and saw a record number of hours of operation in 1992. The new ISOLDE on-line isotope separator was inaugurated last year (July, page 5) and physics is already underway. The remaining effort concentrates around fixed target experiments at the SPS synchrotron, which formed the main thrust of CERN's research during the late 1970s. With the SPS and LEAR now approaching middle age, their research future was extensively studied last year. Broadly, a vigorous SPS programme looks assured until at least the end of 1995. Decisions for the longer term future of the West Experimental Area of the SPS will have to take into account the heavy demand for test beams from work towards experiments at big colliders, both at CERN and elsewhere. The North Experimental Area is the scene of larger experiments with longer lead times. Several more years of LEAR exploitation are already in the pipeline, but for the longer term, the ambitious Superlear project for a superconducting ring (January 1992, page 7) did not catch on. Neutrino physics has a long tradition at CERN, and this continues with the preparations for two major projects, the Chorus and Nomad experiments (November 1991, page 7), to start next year in the West Area. Delicate neutrino oscillation effects could become

  2. A guide to evaluating linkage quality for the analysis of linked data.

    Science.gov (United States)

    Harron, Katie L; Doidge, James C; Knight, Hannah E; Gilbert, Ruth E; Goldstein, Harvey; Cromwell, David A; van der Meulen, Jan H

    2017-10-01

    Linked datasets are an important resource for epidemiological and clinical studies, but linkage error can lead to biased results. For data security reasons, linkage of personal identifiers is often performed by a third party, making it difficult for researchers to assess the quality of the linked dataset in the context of specific research questions. This is compounded by a lack of guidance on how to determine the potential impact of linkage error. We describe how linkage quality can be evaluated and provide widely applicable guidance for both data providers and researchers. Using an illustrative example of a linked dataset of maternal and baby hospital records, we demonstrate three approaches for evaluating linkage quality: applying the linkage algorithm to a subset of gold standard data to quantify linkage error; comparing characteristics of linked and unlinked data to identify potential sources of bias; and evaluating the sensitivity of results to changes in the linkage procedure. These approaches can inform our understanding of the potential impact of linkage error and provide an opportunity to select the most appropriate linkage procedure for a specific analysis. Evaluating linkage quality in this way will improve the quality and transparency of epidemiological and clinical research using linked data. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

  3. Targeting Epigenetics to Prevent Obesity Promoted Cancers.

    Science.gov (United States)

    Berger, Nathan A; Scacheri, Peter C

    2018-03-01

    Epigenetic changes in DNA and associated chromatin proteins are increasingly being considered as important mediators of the linkage between obesity and cancer. Although multiple agents, targeted at epigenetic changes, are being tested for therapy of established cancers, this issue of Cancer Prevention Research carries two articles demonstrating that the bromodomain inhibitor I-BET-762 can attenuate adipose tissue-promoted cancers. Although I-BET-762 significantly delayed, rather than completely prevented, the onset of adiposity-promoted transformation and malignancy, these experiments provide important proof of principle for the strategies of targeting epigenetic changes to disrupt the obesity-cancer linkage. Because bromodomain proteins represent only one of multiple epigenetic mediators, it is probable that targeting other epigenetic processes, alone or in combination, may serve to even more effectively disrupt the obesity promotion of cancer. Given the magnitude of the current obesity pandemic and its impact on cancer, preventive measures to disrupt this linkage are critically important. Cancer Prev Res; 11(3); 125-8. ©2018 AACR See related article by Chakraborty et al., p. 129 . ©2018 American Association for Cancer Research.

  4. Target laboratory

    International Nuclear Information System (INIS)

    Ephraim, D.C.; Pednekar, A.R.

    1993-01-01

    A target laboratory to make stripper foils for the accelerator and various targets for use in the experiments is set up in the pelletron accelerator facility. The facilities available in the laboratory are: (1) D.C. glow discharge setup, (2) carbon arc set up, and (3) vacuum evaporation set up (resistance heating), electron beam source, rolling mill - all for target preparation. They are described. Centrifugal deposition technique is used for target preparation. (author). 3 figs

  5. Ice targets

    International Nuclear Information System (INIS)

    Pacheco, C.; Stark, C.; Tanaka, N.; Hodgkins, D.; Barnhart, J.; Kosty, J.

    1979-12-01

    This report presents a description of ice targets that were constructed for research work at the High Resolution Spectrometer (HRS) and at the Energetic Pion Channel and Spectrometer (EPICS). Reasons for using these ice targets and the instructions for their construction are given. Results of research using ice targets will be published at a later date

  6. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Science.gov (United States)

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  7. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Directory of Open Access Journals (Sweden)

    Bibek Yumnam

    Full Text Available Even with global support for tiger (Panthera tigris conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2 of forest habitat was found to be only 21,290 km(2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST between populations were better explained by modeled linkage costs (r>0.5, p<0.05 compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should

  8. Testing association and linkage using affected-sib-parent study designs.

    Science.gov (United States)

    Millstein, Joshua; Siegmund, Kimberly D; Conti, David V; Gauderman, W James

    2005-11-01

    We have developed a method for jointly testing linkage and association using data from affected sib pairs and their parents. We specify a conditional logistic regression model with two covariates, one that quantifies association (either direct association or indirect association via linkage disequilibrium), and a second that quantifies linkage. The latter covariate is computed based on expected identity-by-descend (ibd) sharing of marker alleles between siblings. In addition to a joint test of linkage and association, our general framework can be used to obtain a linkage test comparable to the mean test (Blackwelder and Elston [1985] Genet. Epidemiol. 2:85-97), and an association test comparable to the Family-Based Association Test (FBAT; Rabinowitz and Laird [2000] Hum. Hered. 50:211-223). We present simulation results demonstrating that our joint test can be more powerful than some standard tests of linkage or association. For example, with a relative risk of 2.7 per variant allele at a disease locus, the estimated power to detect a nearby marker with a modest level of LD was 58.1% by the mean test (linkage only), 69.8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping. Copyright 2005 Wiley-Liss, Inc.

  9. Haplotype analysis and linkage disequilibrium for DGAT1

    OpenAIRE

    Strucken, Eva M.; Rahmatalla, Siham; De Koning, Dirk-Jan; Brockmann, Gudrun A.

    2010-01-01

    This study focused on haplotype effects and linkage disequilibrium (LD) for the K232A locus and the promoter VNTR in the DGAT1 gene. Analyses were carried out in three German Holstein Frisian populations (including 492, 305, and 518 animals) for milk yield, milk fat and protein yield, and milk fat and protein content. We found that effects of the promoter VNTR were not significant and explain only a small amount of the variation of the QTL on BTA14. Haplotype effects were less significant tha...

  10. Learning and Competence Building through Cross-cultural Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull

    2006-01-01

    The aim of the chapter is to study upgrading of companies in developing countries in a learning perspective. Both formal and experiential and tacit knowledge is discussed. Learning effects of different management modes, expatriates, linkages to customers and suppliers are discussed as are learning...... thorugh actual production as well as through explicit transfer of knowledge. The chapter in this way makes an attempt to provide an overview of the multiplicity og learning interfaces. It is concluded that the learning perspective need to be adressed more both by managers and scholars....

  11. IFPE/GBGI, Grain-Bubble Gas Inter-linkage

    International Nuclear Information System (INIS)

    2007-01-01

    Description: The fuel microstructure examination at the thermocouple tips in the lower and upper part of a steady-state irradiated experimental fuel rod with different as fabricated fuel-to-clad gaps in these two regions revealed on-set of grain boundary gas bubble precipitation in the fuel center of the small-gap/low-temperature region (lower part) and developed inter-linkage in the fuel center of the large-gap/high-temperature region (upper part). By use of a diffusion model and the measured temperatures, corresponding grain boundary gas 'concentrations' were calculated

  12. Monetary Policy with Sectoral Linkages and Durable Goods

    DEFF Research Database (Denmark)

    Petrella, Ivan; Rossi, Raffaele; Santoro, Emiliano

    We study the normative implications of a New Keynesian model featuring intersectoral trade of intermediate goods between two sectors that produce durables and non-durables. The interplay between durability and sectoral production linkages fundamentally alters the intersectoral stabilization trade....... Aggregating durable and non-durable inflation depending on the relative degrees of sectoral price stickiness may induce a severe bias. Input materials attenuate the response of sectoral inflations to movements in the real marginal costs, so that the effective slopes of the sectoral supply schedules...

  13. Association between cancer and contact allergy: a linkage study

    DEFF Research Database (Denmark)

    Engkilde, Kaare; Thyssen, Jacob P; Menné, Torkil

    2011-01-01

    by logistic regression analysis. Results An inverse association between contact allergy and non-melanoma skin- and breast cancer, respectively, was identified in both sexes, and an inverse trend for brain cancer was found in women with contact allergy. Additionally, a positive association between contact...... and cancer, few have looked into the association between cancer and contact allergy, a type IV allergy. By linking two clinical databases, the authors investigate the possible association between contact allergy and cancer. Methods Record linkage of two different registers was performed: (1) a tertiary...

  14. Gear-shaft linkage, especially for nuclear reactor coolant pumps

    International Nuclear Information System (INIS)

    Delaunois, T.; Lefevre, R.

    1990-01-01

    The pump comprises: - inlet and outlet channels for the pumped fluid - a rotating shaft - a gear wheel mounted on the shaft by an axial locking nut which can support the axial hydraulic force - a thermal barrier above the gear wheel. A hydrostatic bearing fitted to the exterior surround of the gear wheel, the gear shaft linkage is made by at least a centering and locating device having a cylindrical span and an axial stop and another independent device which can take up the torque [fr

  15. A genetic linkage map for the apicomplexan protozoan parasite Eimeria maxima and comparison with Eimeria tenella.

    Science.gov (United States)

    Blake, Damer P; Oakes, Richard; Smith, Adrian L

    2011-02-01

    Eimeria maxima is one of the seven Eimeria spp. that infect the chicken and cause the disease coccidiosis. The well characterised immunogenicity and genetic diversity associated with E. maxima promote its use in genetics-led studies on avian coccidiosis. The development of a genetic map for E. maxima, presented here based upon 647 amplified fragment length polymorphism markers typed from 22 clonal hybrid lines and assembled into 13 major linkage groups, is a major new resource for work with this parasite. Comparison with genetic maps produced for other coccidial parasites indicates relatively high levels of genetic recombination. Conversion of ∼14% of the markers representing the major linkage groups to sequence characterised amplified region markers can provide a scaffold for the assembly of future genomic sequences as well as providing a foundation for more detailed genetic maps. Comparison with the Eimeria tenella genetic map produced 10years ago has revealed a less biased marker distribution, with no more than nine markers mapped within any unresolved heritable unit. Nonetheless, preliminary bioinformatic characterisation of the three largest publicly available genomic E. maxima sequences suggest that the feature-poor/feature-rich structure which has previously been found to define the first sequenced E. tenella chromosome also defines the E. maxima genome. The significance of such a segmented genome and the apparent potential for variation in genetic recombination will be relevant to haplotype stability and the longevity of future anticoccidial strategies based upon multiple loci targeted by novel chemotherapeutic drugs or recombinant subunit vaccines. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  16. Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia.

    Science.gov (United States)

    Rosenthal, Elisabeth A; Ranchalis, Jane; Crosslin, David R; Burt, Amber; Brunzell, John D; Motulsky, Arno G; Nickerson, Deborah A; Wijsman, Ellen M; Jarvik, Gail P

    2013-12-05

    Hypertriglyceridemia (HTG) is a heritable risk factor for cardiovascular disease. Investigating the genetics of HTG may identify new drug targets. There are ~35 known single-nucleotide variants (SNVs) that explain only ~10% of variation in triglyceride (TG) level. Because of the genetic heterogeneity of HTG, a family study design is optimal for identification of rare genetic variants with large effect size because the same mutation can be observed in many relatives and cosegregation with TG can be tested. We considered HTG in a five-generation family of European American descent (n = 121), ascertained for familial combined hyperlipidemia. By using Bayesian Markov chain Monte Carlo joint oligogenic linkage and association analysis, we detected linkage to chromosomes 7 and 17. Whole-exome sequence data revealed shared, highly conserved, private missense SNVs in both SLC25A40 on chr7 and PLD2 on chr17. Jointly, these SNVs explained 49% of the genetic variance in TG; however, only the SLC25A40 SNV was significantly associated with TG (p = 0.0001). This SNV, c.374A>G, causes a highly disruptive p.Tyr125Cys substitution just outside the second helical transmembrane region of the SLC25A40 inner mitochondrial membrane transport protein. Whole-gene testing in subjects from the Exome Sequencing Project confirmed the association between TG and SLC25A40 rare, highly conserved, coding variants (p = 0.03). These results suggest a previously undescribed pathway for HTG and illustrate the power of large pedigrees in the search for rare, causal variants. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  17. Climate and development: enhancing impact through stronger linkages in the implementation of the Paris Agreement and the Sustainable Development Goals (SDGs).

    Science.gov (United States)

    Gomez-Echeverri, Luis

    2018-05-13

    One of the greatest achievements in the global negotiations of 2015 that delivered the 2030 Agenda for Sustainable Development or Sustainable Development Goals (SDGs) and the Paris Agreement on climate change is that, for the first time, the linkages between climate and development were enshrined in each of the documents. This was done in recognition that climate change and development need to be addressed together in order not only to avoid harmful trade-offs and high costs, particularly for poorer countries, but also to exploit the benefits that come from strengthening these linkages. This review presents some of the latest data that argue for stronger linkages as well as the challenges of implementation which are not only politically and economically related but also include issues such as knowledge gaps, finance and governance. Finally, the review also presents a glimpse at the pathways that will be required to reach the ambitious global temperature targets of the Paris Agreement of less than 2°C above pre-industrial levels with efforts to limit temperature rise even further to 1.5°C. This provides the context for some conclusions and recommendations for policy-makers, including on methodologies for assessing linkages and leveraging them for greater benefit.This article is part of the theme issue 'The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'. © 2018 The Authors.

  18. Climate and development: enhancing impact through stronger linkages in the implementation of the Paris Agreement and the Sustainable Development Goals (SDGs)

    Science.gov (United States)

    Gomez-Echeverri, Luis

    2018-05-01

    One of the greatest achievements in the global negotiations of 2015 that delivered the 2030 Agenda for Sustainable Development or Sustainable Development Goals (SDGs) and the Paris Agreement on climate change is that, for the first time, the linkages between climate and development were enshrined in each of the documents. This was done in recognition that climate change and development need to be addressed together in order not only to avoid harmful trade-offs and high costs, particularly for poorer countries, but also to exploit the benefits that come from strengthening these linkages. This review presents some of the latest data that argue for stronger linkages as well as the challenges of implementation which are not only politically and economically related but also include issues such as knowledge gaps, finance and governance. Finally, the review also presents a glimpse at the pathways that will be required to reach the ambitious global temperature targets of the Paris Agreement of less than 2°C above pre-industrial levels with efforts to limit temperature rise even further to 1.5°C. This provides the context for some conclusions and recommendations for policy-makers, including on methodologies for assessing linkages and leveraging them for greater benefit. This article is part of the theme issue `The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'.

  19. A node linkage approach for sequential pattern mining.

    Directory of Open Access Journals (Sweden)

    Osvaldo Navarro

    Full Text Available Sequential Pattern Mining is a widely addressed problem in data mining, with applications such as analyzing Web usage, examining purchase behavior, and text mining, among others. Nevertheless, with the dramatic increase in data volume, the current approaches prove inefficient when dealing with large input datasets, a large number of different symbols and low minimum supports. In this paper, we propose a new sequential pattern mining algorithm, which follows a pattern-growth scheme to discover sequential patterns. Unlike most pattern growth algorithms, our approach does not build a data structure to represent the input dataset, but instead accesses the required sequences through pseudo-projection databases, achieving better runtime and reducing memory requirements. Our algorithm traverses the search space in a depth-first fashion and only preserves in memory a pattern node linkage and the pseudo-projections required for the branch being explored at the time. Experimental results show that our new approach, the Node Linkage Depth-First Traversal algorithm (NLDFT, has better performance and scalability in comparison with state of the art algorithms.

  20. Optimizing Opt-Out Consent for Record Linkage

    Directory of Open Access Journals (Sweden)

    Das Marcel

    2014-09-01

    Full Text Available This article reports on a study testing the effects of different ways of administering an opt-out consent for record linkage in a probability-based Internet panel. First, we conducted cognitive interviews to explore reactions to a draft version of the opt-out consent text. Second, we conducted a two-factor experiment to test the effects of content manipulations and mode. The results indicate that the way in which respondents were informed did not have much effect on opting out. Results from a follow-up survey on attitudes regarding privacy, confidentiality, and trust, along with knowledge questions about the process of linking, showed no evidence that presenting the opt-out consent statement makes respondents more concerned about privacy. Knowledge about the aspects of record linkage is generally not high. When looking at long-term effects of sending an opt-out consent statement, we found no evidence that this leads to higher attrition or lower participation rates.

  1. HLA region excluded by linkage analyses of early onset periodontitis

    Energy Technology Data Exchange (ETDEWEB)

    Sun, C.; Wang, S.; Lopez, N.

    1994-09-01

    Previous studies suggested that HLA genes may influence susceptibility to early-onset periodontitis (EOP). Segregation analyses indicate that EOP may be due to a single major gene. We conducted linkage analyses to assess possible HLA effects on EOP. Fifty families with two or more close relatives affected by EOP were ascertained in Virginia and Chile. A microsatellite polymorphism within the HLA region (at the tumor necrosis factor beta locus) was typed using PCR. Linkage analyses used a donimant model most strongly supported by previous studies. Assuming locus homogeneity, our results exclude a susceptibility gene within 10 cM on either side of our marker locus. This encompasses all of the HLA region. Analyses assuming alternative models gave qualitatively similar results. Allowing for locus heterogeneity, our data still provide no support for HLA-region involvement. However, our data do not statistically exclude (LOD <-2.0) hypotheses of disease-locus heterogeneity, including models where up to half of our families could contain an EOP disease gene located in the HLA region. This is due to the limited power of even our relatively large collection of families and the inherent difficulties of mapping genes for disorders that have complex and heterogeneous etiologies. Additional statistical analyses, recruitment of families, and typing of flanking DNA markers are planned to more conclusively address these issues with respect to the HLA region and other candidate locations in the human genome. Additional results for markers covering most of the human genome will also be presented.

  2. A “Linkage-Based” Approach to Combating Militant Islamist Propaganda: A Two-Tiered Framework for Practitioners

    Directory of Open Access Journals (Sweden)

    Haroro J. Ingram

    2016-11-01

    Full Text Available This Policy Brief outlines a “linkage-based” approach to combating militant Islamist propaganda tailored for practitioners. It argues for a two-tiered approach to counter-terrorism strategic communications that addresses a spectrum of target audience motivations: antis, curious, engaged, tacit supporters and active supporters. The first tier undermines the key arguments at the heart of militant Islamist narratives and offers alternative narratives. This approach is designed to dismantle the “systems of meaning” at the heart of militant Islamist propaganda via the deployment of pragmatic- and identity-choice messages tailored to dissolve the linkages violent extremists draw between themselves and solutions and their enemies and crisis. The second tier uses strategies of network disruption and disengagement strategies to catalyse behavioural changes in target audiences away from joining or acting on behalf of violent extremist groups like al Qaeda or so-called Islamic State (IS. These tiers are mutually reinforcing: the first degrades the appeal of violent extremist messaging in an effort to constrict those who may become engaged in or even supporters of violent extremists while the second disturbs the trajectory of individuals from tacit to active supporters. The framework is designed to not only assist practitioners with synchronising campaign planning and message design but provides a way to categorise messaging and facilitate metric collection for better informed decision-making.

  3. A literature review of record linkage procedures focusing on infant health outcomes

    Directory of Open Access Journals (Sweden)

    Carla Jorge Machado

    Full Text Available Record linkage is a powerful tool in assembling information from different data sources and has been used by a number of public health researchers. In this review, we provide an overview of the record linkage methodologies, focusing particularly on probabilistic record linkage. We then stress the purposes and research applications of linking records by focusing on studies of infant health outcomes based on large data sets, and provide a critical review of the studies in Brazil.

  4. Heritability and whole genome linkage of pulse pressure in Chinese twin pairs

    DEFF Research Database (Denmark)

    Jiang, Wengjie; Zhang, Dongfeng; Pang, Zengchang

    2012-01-01

    with a heritability estimate of 0.45. Genome-wide non-parametric linkage analysis identified three significant linkage peaks on chromosome 11 (lod score 4.06 at 30.5 cM), chromosome 12 (lod score 3.97 at 100.7 cM), and chromosome 18 (lod score 4.01 at 70.7 cM) with the last two peaks closely overlapping with linkage...

  5. Quantifying sources of bias in longitudinal data linkage studies of child abuse and neglect: measuring impact of outcome specification, linkage error, and partial cohort follow-up.

    Science.gov (United States)

    Parrish, Jared W; Shanahan, Meghan E; Schnitzer, Patricia G; Lanier, Paul; Daniels, Julie L; Marshall, Stephen W

    2017-12-01

    Health informatics projects combining statewide birth populations with child welfare records have emerged as a valuable approach to conducting longitudinal research of child maltreatment. The potential bias resulting from linkage misspecification, partial cohort follow-up, and outcome misclassification in these studies has been largely unexplored. This study integrated epidemiological survey and novel administrative data sources to establish the Alaska Longitudinal Child Abuse and Neglect Linkage (ALCANLink) project. Using these data we evaluated and quantified the impact of non-linkage misspecification and single source maltreatment ascertainment use on reported maltreatment risk and effect estimates. The ALCANLink project integrates the 2009-2011 Alaska Pregnancy Risk Assessment Monitoring System (PRAMS) sample with multiple administrative databases through 2014, including one novel administrative source to track out-of-state emigration. For this project we limited our analysis to the 2009 PRAMS sample. We report on the impact of linkage quality, cohort follow-up, and multisource outcome ascertainment on the incidence proportion of reported maltreatment before age 6 and hazard ratios of selected characteristics that are often available in birth cohort linkage studies of maltreatment. Failure to account for out-of-state emigration biased the incidence proportion by 12% (from 28.3% w to 25.2% w ), and the hazard ratio (HR) by as much as 33% for some risk factors. Overly restrictive linkage parameters biased the incidence proportion downwards by 43% and the HR by as much as 27% for some factors. Multi-source linkages, on the other hand, were of little benefit for improving reported maltreatment ascertainment. Using the ALCANLink data which included a novel administrative data source, we were able to observe and quantify bias to both the incidence proportion and HR in a birth cohort linkage study of reported child maltreatment. Failure to account for out

  6. Genomewide Linkage Screen for Waldenström Macroglobulinemia Susceptibility Loci in High-Risk Families

    Science.gov (United States)

    McMaster, Mary L.; Goldin, Lynn R.; Bai, Yan; Ter-Minassian, Monica; Boehringer, Stefan; Giambarresi, Therese R.; Vasquez, Linda G.; Tucker, Margaret A.

    2006-01-01

    Waldenström macroglobulinemia (WM), a distinctive subtype of non-Hodgkin lymphoma that features overproduction of immunoglobulin M (IgM), clearly has a familial component; however, no susceptibility genes have yet been identified. We performed a genomewide linkage analysis in 11 high-risk families with WM that were informative for linkage, for a total of 122 individuals with DNA samples, including 34 patients with WM and 10 patients with IgM monoclonal gammopathy of undetermined significance (IgM MGUS). We genotyped 1,058 microsatellite markers (average spacing 3.5 cM), performed both nonparametric and parametric linkage analysis, and computed both two-point and multipoint linkage statistics. The strongest evidence of linkage was found on chromosomes 1q and 4q when patients with WM and with IgM MGUS were both considered affected; nonparametric linkage scores were 2.5 (P=.0089) and 3.1 (P=.004), respectively. Other locations suggestive of linkage were found on chromosomes 3 and 6. Results of two-locus linkage analysis were consistent with independent effects. The findings from this first linkage analysis of families at high risk for WM represent important progress toward identifying gene(s) that modulate susceptibility to WM and toward understanding its complex etiology. PMID:16960805

  7. A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

    Science.gov (United States)

    Boyd, James H; Guiver, Tenniel; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Anderson, Phil; Dickinson, Teresa

    2016-05-17

    Record linkage techniques allow different data collections to be brought together to provide a wider picture of the health status of individuals. Ensuring high linkage quality is important to guarantee the quality and integrity of research. Current methods for measuring linkage quality typically focus on precision (the proportion of incorrect links), given the difficulty of measuring the proportion of false negatives. The aim of this work is to introduce and evaluate a sampling based method to estimate both precision and recall following record linkage. In the sampling based method, record-pairs from each threshold (including those below the identified cut-off for acceptance) are sampled and clerically reviewed. These results are then applied to the entire set of record-pairs, providing estimates of false positives and false negatives. This method was evaluated on a synthetically generated dataset, where the true match status (which records belonged to the same person) was known. The sampled estimates of linkage quality were relatively close to actual linkage quality metrics calculated for the whole synthetic dataset. The precision and recall measures for seven reviewers were very consistent with little variation in the clerical assessment results (overall agreement using the Fleiss Kappa statistics was 0.601). This method presents as a possible means of accurately estimating matching quality and refining linkages in population level linkage studies. The sampling approach is especially important for large project linkages where the number of record pairs produced may be very large often running into millions.

  8. The Importance of Geographical Proximity for New Product Development Activities within Inter-firm Linkages

    DEFF Research Database (Denmark)

    Dahlgren, Johan Henrich

    important as a resource and where collaboration partners are important. Hypotheses are tested by means of a quantitative analysis of a data set containing information about 4842 domestic and international inter-firm linkages of Danish firms in manufacturing industries. The findings in this analysis exhibit...... for international linkages. It is further suggested closer geographical distance for inter-firm linkages with medium and high level of interaction, suppliers or customers accounting for more than one third of total purchases or sales, and for linkages lasting for at least 10 years.Key words: capabilities, economics...

  9. Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus...

  10. Implementing inflation targeting regimes: The case of Poland

    OpenAIRE

    Gottschalk, Jan; Moore, David

    1999-01-01

    This paper assesses the prospects for the new Polish monetary policy strategy of inflation targeting. Regarding the general requirements for implementing an inflation targeting strategy it appears that Poland has made sufficient progress in reducing fiscal dominance and hardening budget constraints. The paper also finds that the exchange rate has played a dominant role as a policy instrument, with the linkages between the short-term interest rate and inflation remaining unclear. Given this un...

  11. Conservation of gene linkage in dispersed vertebrate NK homeobox clusters.

    Science.gov (United States)

    Wotton, Karl R; Weierud, Frida K; Juárez-Morales, José L; Alvares, Lúcia E; Dietrich, Susanne; Lewis, Katharine E

    2009-10-01

    Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes.

  12. Antiproton Target

    CERN Multimedia

    1980-01-01

    Antiproton target used for the AA (antiproton accumulator). The first type of antiproton production target used from 1980 to 1982 comprised a rod of copper 3mm diameter and 120mm long embedded in a graphite cylinder that was itself pressed into a finned aluminium container. This assembly was air-cooled and it was used in conjunction with the Van der Meer magnetic horn. In 1983 Fermilab provided us with lithium lenses to replace the horn with a view to increasing the antiproton yield by about 30%. These lenses needed a much shorter target made of heavy metal - iridium was chosen for this purpose. The 50 mm iridium rod was housed in an extension to the original finned target container so that it could be brought very close to the entrance to the lithium lens. Picture 1 shows this target assembly and Picture 2 shows it mounted together with the lithium lens. These target containers had a short lifetime due to a combination of beam heating and radiation damage. This led to the design of the water-cooled target in...

  13. Strategies for Sustainable Urban Development and Urban-Rural Linkages

    DEFF Research Database (Denmark)

    Nilsson, Kjell; Nielsen, Thomas Alexander Sick; Aalbers, Carmen

    2014-01-01

    , identified how land use conflicts and the pressure towards peri- urban areas can be strategically managed in different development and regulatory contexts. To summarise, the following strategies were identified as important steps towards more sustainable urban-rural futures: (i) better coordination...... of transport, land use and open space planning; (ii) urban containment and densification – development a green compact city; (iii) preservation of blue and green infrastructure; and (iv) preservation of agricultural land and the promotion of local production. The need also remains to strengthen governance...... at the regional level while at the pan-European level there is clearly a need for more policy attention to be given to urban-rural linkages....

  14. Exploiting linkage disequilibrium in statistical modelling in quantitative genomics

    DEFF Research Database (Denmark)

    Wang, Lei

    Alleles at two loci are said to be in linkage disequilibrium (LD) when they are correlated or statistically dependent. Genomic prediction and gene mapping rely on the existence of LD between gentic markers and causul variants of complex traits. In the first part of the thesis, a novel method...... to quantify and visualize local variation in LD along chromosomes in describet, and applied to characterize LD patters at the local and genome-wide scale in three Danish pig breeds. In the second part, different ways of taking LD into account in genomic prediction models are studied. One approach is to use...... the recently proposed antedependence models, which treat neighbouring marker effects as correlated; another approach involves use of haplotype block information derived using the program Beagle. The overall conclusion is that taking LD information into account in genomic prediction models potentially improves...

  15. Biosynthesis of riboflavin: mechanism of formation of the ribitylamino linkage

    International Nuclear Information System (INIS)

    Keller, P.J.; Van, Q.L.; Kim, S.U.; Bown, D.H.; Chen, H.C.; Kohnle, A.; Bacher, A.; Floss, H.G.

    1988-01-01

    Feeding experiments with Ashbya gossypii followed by NMR analysis of the resulting riboflavin showed incorporation of deuterium from D-[2- 2 H]ribose at C-2' and from D-[1- 2 H] ribose in the pro-R position at C-1' of the ribityl side chain. The results rule out an Amadori rearrangement mechanism for the reduction of the ribosylamino to the ribitylamino linkage and point to formation of a Schiff base that is reduced stereospecifically opposite to the face from which the oxygen has departed. As prerequisite for the analysis, the 1 H NMR signals for the pro-R and pro-S hydrogens at C-1' of 6,7-dimethyl-8-ribityllumazine and riboflavin and its tetraacetate were assigned with the aid of synthetic stereospecifically deuteriated samples

  16. X linked exudative vitreoretinopathy: clinical features and genetic linkage analysis.

    Science.gov (United States)

    Fullwood, P; Jones, J; Bundey, S; Dudgeon, J; Fielder, A R; Kilpatrick, M W

    1993-03-01

    A four generation family in which familial exudative vitreoretinopathy is inherited as an X linked condition is described. Essentially the condition is one of abnormal vascularisation and signs at birth are those of a retinopathy superficially resembling retinopathy of prematurity, retinal folds, or, in advanced cases, enophthalmos or even phthisis. Prognosis depends on the progression of the retinal changes. The family members, including seven affected males and five obligate carrier females, have been types for 20 DNA markers, and linkage analysis suggests a gene locus either at Xq21.3 or at Xp11. As the latter region includes the locus for the gene for Norrie disease, it is possible that this and X linked vitreoretinopathy are allelic. We can further speculate that the differences in severity of the clinical manifestations are dependent only upon the timing of the insult.

  17. Construction of functional linkage gene networks by data integration.

    Science.gov (United States)

    Linghu, Bolan; Franzosa, Eric A; Xia, Yu

    2013-01-01

    Networks of functional associations between genes have recently been successfully used for gene function and disease-related research. A typical approach for constructing such functional linkage gene networks (FLNs) is based on the integration of diverse high-throughput functional genomics datasets. Data integration is a nontrivial task due to the heterogeneous nature of the different data sources and their variable accuracy and completeness. The presence of correlations between data sources also adds another layer of complexity to the integration process. In this chapter we discuss an approach for constructing a human FLN from data integration and a subsequent application of the FLN to novel disease gene discovery. Similar approaches can be applied to nonhuman species and other discovery tasks.

  18. Linkage of management decision to shareholder's value: EVA concept

    Directory of Open Access Journals (Sweden)

    Shrikant Krupasindhu Panigrahi

    2014-02-01

    Full Text Available In this paper, the author investigated the influence of management decisions like capital structure, dividend policies, remunerations, credit policy decisions and investment decisions on shareholder wealth maximization. To achieve the objective, portfolio theory, capital asset pricing model and modern financial theory providing evidence on the linkage between management decisions to shareholder’s value. Shareholders are only concerned about the value of shares of the company and the amount of return in the form of dividend paid. Thus in order to meet the demands of the shareholders of the company, managers needs to increase their abilities and skills to overcome the organizational goals. Thus the main goal of this paper is to discuss on the role of management decisions towards increasing shareholder’s wealth and meet organizational goals.

  19. Spin Transfer in Polymer Degradation of Abnormal Linkage

    Science.gov (United States)

    Yu, Tianrong; Tian, Chuanjin; Liu, Xizhe; Wang, Jia; Gao, Yang; Wang, Zhigang

    2017-07-01

    The degradation of polymer materials plays an important role in production and life. In this work, the degradation mechanism of poly-α-methylstyrene (PAMS) tetramers with abnormal linkage was investigated by using density functional theory (DFT). Calculated results indicate that the head-to-head and the tail-to-tail reactions needed to overcome the energy barriers are about 0.15 eV and about 1.26 eV, respectively. The broken C-C bond at the unsaturated end of the chain leads to the dissociation of alpha-methylstyrene (AMS) monomers one by one. Furthermore, the analyses of bond characteristics are in good agreement with the results of energy barriers. In addition, the spin population analysis presents an interesting net spin transfer process in depolymerization reactions. We hope that the current theoretical results provide useful help to understand the degradation mechanism of polymers.

  20. Validation of an instrument to measure inter-organisational linkages in general practice.

    Science.gov (United States)

    Amoroso, Cheryl; Proudfoot, Judith; Bubner, Tanya; Jayasinghe, Upali W; Holton, Christine; Winstanley, Julie; Beilby, Justin; Harris, Mark F

    2007-12-03

    Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice's linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. An interview to measure surgery-level (rather than individual clinician-level) clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations). Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. The resulting General Practice Clinical Linkages Interview (GP-CLI) is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however, comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples exploring the impact, outcomes, and facilitators of high

  1. Validation of an instrument to measure inter-organisational linkages in general practice

    Directory of Open Access Journals (Sweden)

    Cheryl Amoroso

    2007-11-01

    Full Text Available Purpose: Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice’s linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. Methods: An interview to measure surgery-level (rather than individual clinician-level clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations. Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. Results: The resulting General Practice Clinical Linkages Interview (GP-CLI is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. Conclusions: The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples

  2. Extreme drought decouples silicon and carbon geochemical linkages in lakes.

    Science.gov (United States)

    Li, Tianyang; Li, Siyue; Bush, Richard T; Liang, Chuan

    2018-09-01

    Silicon and carbon geochemical linkages were usually regulated by chemical weathering and organism activity, but had not been investigated under the drought condition, and the magnitude and extent of drought effects remain poorly understood. We collected a comprehensive data set from a total of 13 sampling sites covering the main water body of the largest freshwater lake system in Australia, the Lower Lakes. Changes to water quality during drought (April 2008-September 2010) and post-drought (October 2010-October 2013) were compared to reveal the effects of drought on dissolved silica (DSi) and bicarbonate (HCO 3 - ) and other environmental factors, including sodium (Na + ), pH, electrical conductivity (EC), chlorophyll a (Chl-a), total dissolved solids (TDS), dissolved inorganic nitrogen (DIN), total nitrogen (TN), total phosphorus (TP) and water levels. Among the key observations, concentrations of DSi and DIN were markedly lower in drought than in post-drought period while pH, EC and concentrations of HCO 3 - , Na + , Chl-a, TDS, TN, TP and the ratio TN:TP had inverse trends. Stoichiometric ratios of DSi:HCO 3 - , DSi:Na + and HCO 3 - :Na + were significantly lower in the drought period. DSi exhibited significantly negative relationships with HCO 3 - , and DSi:Na + was strongly correlated with HCO 3 - :Na + in both drought and post-drought periods. The backward stepwise regression analysis that could avoid multicollinearity suggested that DSi:HCO 3 - ratio in drought period had significant relationships with fewer variables when compared to the post-drought, and was better predictable using nutrient variables during post-drought. Our results highlight the drought effects on variations of water constituents and point to the decoupling of silicon and carbon geochemical linkages in the Lower Lakes under drought conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Rethinking health sector procurement as developmental linkages in East Africa.

    Science.gov (United States)

    Mackintosh, Maureen; Tibandebage, Paula; Karimi Njeru, Mercy; Kariuki Kungu, Joan; Israel, Caroline; Mujinja, Phares G M

    2018-03-01

    Health care forms a large economic sector in all countries, and procurement of medicines and other essential commodities necessarily creates economic linkages between a country's health sector and local and international industrial development. These procurement processes may be positive or negative in their effects on populations' access to appropriate treatment and on local industrial development, yet procurement in low and middle income countries (LMICs) remains under-studied: generally analysed, when addressed at all, as a public sector technical and organisational challenge rather than a social and economic element of health system governance shaping its links to the wider economy. This article uses fieldwork in Tanzania and Kenya in 2012-15 to analyse procurement of essential medicines and supplies as a governance process for the health system and its industrial links, drawing on aspects of global value chain theory. We describe procurement work processes as experienced by front line staff in public, faith-based and private sectors, linking these experiences to wholesale funding sources and purchasing practices, and examining their implications for medicines access and for local industrial development within these East African countries. We show that in a context of poor access to reliable medicines, extensive reliance on private medicines purchase, and increasing globalisation of procurement systems, domestic linkages between health and industrial sectors have been weakened, especially in Tanzania. We argue in consequence for a more developmental perspective on health sector procurement design, including closer policy attention to strengthening vertical and horizontal relational working within local health-industry value chains, in the interests of both wider access to treatment and improved industrial development in Africa. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Efficient sequential and parallel algorithms for record linkage.

    Science.gov (United States)

    Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

    2014-01-01

    Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Our sequential and parallel algorithms have been tested on a real dataset of 1,083,878 records and synthetic datasets ranging in size from 50,000 to 9,000,000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm.

  5. Association and linkage analysis of aluminum tolerance genes in maize.

    Directory of Open Access Journals (Sweden)

    Allison M Krill

    Full Text Available BACKGROUND: Aluminum (Al toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. METHODOLOGY: An association panel of 282 diverse maize inbred lines and three F2 linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. CONCLUSIONS: Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays AltSB like (ZmASL, Zea mays aluminum-activated malate transporter2 (ALMT2, S-adenosyl-L-homocysteinase (SAHH, and Malic Enzyme (ME. These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.

  6. The linkage between geopotential height and monthly precipitation in Iran

    Science.gov (United States)

    Shirvani, Amin; Fadaei, Amir Sabetan; Landman, Willem A.

    2018-04-01

    This paper investigates the linkage between large-scale atmospheric circulation and monthly precipitation during November to April over Iran. Canonical correlation analysis (CCA) is used to set up the statistical linkage between the 850 hPa geopotential height large-scale circulation and monthly precipitation over Iran for the period 1968-2010. The monthly precipitation dataset for 50 synoptic stations distributed in different climate regions of Iran is considered as the response variable in the CCA. The monthly geopotential height reanalysis dataset over an area between 10° N and 60° N and from 20° E to 80° E is utilized as the explanatory variable in the CCA. Principal component analysis (PCA) as a pre-filter is used for data reduction for both explanatory and response variables before applying CCA. The optimal number of principal components and canonical variables to be retained in the CCA equations is determined using the highest average cross-validated Kendall's tau value. The 850 hPa geopotential height pattern over the Red Sea, Saudi Arabia, and Persian Gulf is found to be the major pattern related to Iranian monthly precipitation. The Pearson correlation between the area averaged of the observed and predicted precipitation over the study area for Jan, Feb, March, April, November, and December months are statistically significant at the 5% significance level and are 0.78, 0.80, 0.82, 0.74, 0.79, and 0.61, respectively. The relative operating characteristic (ROC) indicates that the highest scores for the above- and below-normal precipitation categories are, respectively, for February and April and the lowest scores found for December.

  7. Exploiting semantic linkages among multiple sources for semantic information retrieval

    Science.gov (United States)

    Li, JianQiang; Yang, Ji-Jiang; Liu, Chunchen; Zhao, Yu; Liu, Bo; Shi, Yuliang

    2014-07-01

    The vision of the Semantic Web is to build a global Web of machine-readable data to be consumed by intelligent applications. As the first step to make this vision come true, the initiative of linked open data has fostered many novel applications aimed at improving data accessibility in the public Web. Comparably, the enterprise environment is so different from the public Web that most potentially usable business information originates in an unstructured form (typically in free text), which poses a challenge for the adoption of semantic technologies in the enterprise environment. Considering that the business information in a company is highly specific and centred around a set of commonly used concepts, this paper describes a pilot study to migrate the concept of linked data into the development of a domain-specific application, i.e. the vehicle repair support system. The set of commonly used concepts, including the part name of a car and the phenomenon term on the car repairing, are employed to build the linkage between data and documents distributed among different sources, leading to the fusion of documents and data across source boundaries. Then, we describe the approaches of semantic information retrieval to consume these linkages for value creation for companies. The experiments on two real-world data sets show that the proposed approaches outperform the best baseline 6.3-10.8% and 6.4-11.1% in terms of top five and top 10 precisions, respectively. We believe that our pilot study can serve as an important reference for the development of similar semantic applications in an enterprise environment.

  8. Genome-wide linkage scan to identify loci associated with type 2 diabetes and blood lipid phenotypes in the Sikh Diabetes Study.

    Directory of Open Access Journals (Sweden)

    Dharambir K Sanghera

    Full Text Available In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL cholesterol, low-density lipoprotein (LDL cholesterol, very low-density lipoprotein (VLDL cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS. A total of 870 individuals (526 male/344 female from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using S(all statistics (implemented in Merlin did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p≤0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p = 0.0011 occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p = 0.0016 and 5p15.33 (p = 0.0031 and for LDL cholesterol at 10p11.23 (p = 0.0045. Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance.

  9. Replication of TCF4 through association and linkage studies in late-onset Fuchs endothelial corneal dystrophy.

    Directory of Open Access Journals (Sweden)

    Yi-Ju Li

    Full Text Available Fuchs endothelial corneal dystrophy (FECD is a common, late-onset disorder of the corneal endothelium. Although progress has been made in understanding the genetic basis of FECD by studying large families in which the phenotype is transmitted in an autosomal dominant fashion, a recently reported genome-wide association study identified common alleles at a locus on chromosome 18 near TCF4 which confer susceptibility to FECD. Here, we report the findings of our independent validation study for TCF4 using the largest FECD dataset to date (450 FECD cases and 340 normal controls. Logistic regression with sex as a covariate was performed for three genetic models: dominant (DOM, additive (ADD, and recessive (REC. We found significant association with rs613872, the target marker reported by Baratz et al.(2010, for all three genetic models (DOM: P = 9.33×10(-35; ADD: P = 7.48×10(-30; REC: P = 5.27×10(-6. To strengthen the association study, we also conducted a genome-wide linkage scan on 64 multiplex families, composed primarily of affected sibling pairs (ASPs, using both parametric and non-parametric two-point and multipoint analyses. The most significant linkage region localizes to chromosome 18 from 69.94cM to 85.29cM, with a peak multipoint HLOD = 2.5 at rs1145315 (75.58cM under the DOM model, mapping 1.5 Mb proximal to rs613872. In summary, our study presents evidence to support the role of the intronic TCF4 single nucleotide polymorphism rs613872 in late-onset FECD through both association and linkage studies.

  10. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

    NARCIS (Netherlands)

    Geest, van Geert; Bourke, Peter M.; Voorrips, Roeland E.; Marasek-Ciolakowska, Agnieszka; Liao, Yanlin; Post, Aike; Meeteren, van Uulke; Visser, Richard G.F.; Maliepaard, Chris; Arens, Paul

    2017-01-01

    Key message: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL.Abstract: Construction and use of linkage maps are challenging in hexaploids with polysomic

  11. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.; Ekholm, J.; Forabosco, P.; Franke, F.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenkel, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schäfer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.; Steinhausen, H.C.; van der Meulen, E.; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  12. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder.

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J.; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.P.; Ekholm, J.; Forabosco, P.; Franke, B.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenke, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schafer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.J.S.; Steinhausen, H.C.; Meulen, E. van der; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  13. Applying Topographic Classification, Based on the Hydrological Process, to Design Habitat Linkages for Climate Change

    Directory of Open Access Journals (Sweden)

    Yongwon Mo

    2017-11-01

    Full Text Available The use of biodiversity surrogates has been discussed in the context of designing habitat linkages to support the migration of species affected by climate change. Topography has been proposed as a useful surrogate in the coarse-filter approach, as the hydrological process caused by topography such as erosion and accumulation is the basis of ecological processes. However, some studies that have designed topographic linkages as habitat linkages, so far have focused much on the shape of the topography (morphometric topographic classification with little emphasis on the hydrological processes (generic topographic classification to find such topographic linkages. We aimed to understand whether generic classification was valid for designing these linkages. First, we evaluated whether topographic classification is more appropriate for describing actual (coniferous and deciduous and potential (mammals and amphibians habitat distributions. Second, we analyzed the difference in the linkages between the morphometric and generic topographic classifications. The results showed that the generic classification represented the actual distribution of the trees, but neither the morphometric nor the generic classification could represent the potential animal distributions adequately. Our study demonstrated that the topographic classes, according to the generic classification, were arranged successively according to the flow of water, nutrients, and sediment; therefore, it would be advantageous to secure linkages with a width of 1 km or more. In addition, the edge effect would be smaller than with the morphometric classification. Accordingly, we suggest that topographic characteristics, based on the hydrological process, are required to design topographic linkages for climate change.

  14. Multipoint linkage analysis and homogeneity tests in 15 Dutch X-linked retinitis pigmentosa families

    NARCIS (Netherlands)

    Bergen, A. A.; van den Born, L. I.; Schuurman, E. J.; Pinckers, A. J.; van Ommen, G. J.; Bleekers-Wagemakers, E. M.; Sandkuijl, L. A.

    1995-01-01

    Linkage analysis and homogeneity tests were carried out in 15 Dutch families segregating X-linked retinitis pigmentosa (X L R P). The study included segregation data for eight polymorphic DNA markers from the short arm of the human X chromosome. The results of both multipoint linkage analysis in

  15. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

    Science.gov (United States)

    S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

    2004-01-01

    Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

  16. Multipoint linkage analysis in X-linked ocular albinism of the Nettleship-Falls type

    NARCIS (Netherlands)

    Bergen, A. A.; Samanns, C.; Schuurman, E. J.; van Osch, L.; van Dorp, D. B.; Pinckers, A. J.; Bakker, E.; Gal, A.; van Ommen, G. J.; Bleeker-Wagemakers, E. M.

    1991-01-01

    An extensive linkage analysis was performed by studying ten Xp22 loci in ten families segregating for X-linked ocular albinism of the Nettleship-Falls type (XOA). Linkage was confirmed between the XOA locus (OA1) and both DXS16 (theta max = 0.10, zeta max = 4.09) and DXS237 (theta max = 0.12, zeta

  17. Sustaining innovations : schools, institutions and linkages in the Cuzco region, Peru

    NARCIS (Netherlands)

    ChavezTafur, J.

    1998-01-01

    This thesis is about linkages between the different institutions operating in the rural areas and the contributions these linkages provide. Numerous activities are found taking place in the rural areas of Peru. Many are the result of a specific intervention, designed and implemented towards

  18. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait

    Energy Technology Data Exchange (ETDEWEB)

    Dube, M.P.; Kibar, Z.; Rouleau, G.A. [McGill Univ., Quebec (Canada)] [and others

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity. 19 refs., 1 fig., 1 tab.

  19. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait.

    Science.gov (United States)

    Dubé, M P; Mlodzienski, M A; Kibar, Z; Farlow, M R; Ebers, G; Harper, P; Kolodny, E H; Rouleau, G A; Figlewicz, D A

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity.

  20. Point-of-Care HIV Testing and Linkage in an Urban Cohort in the Southern US

    Directory of Open Access Journals (Sweden)

    Anne Zinski

    2013-01-01

    Full Text Available The Southern states experience the highest rates of HIV and AIDS in the US, and point-of-care (POC testing outside of primary care may contribute to status awareness in medically underserved populations in this region. To evaluate POC screening and linkage to care at an urban south site, analyses were performed on a dataset of 3,651 individuals from an integrated rapid-result HIV testing and linkage program to describe this test-seeking cohort and determine trends associated with screening, results, and linkage to care. Four percent of the population had positive results. We observed significant differences by test result for age, race and gender, reported risk behaviors, test location, and motivation for screening. The overall linkage rate was 86%, and we found significant differences for clients who were linked to HIV care versus persons whose linkage could not be confirmed with respect to race and gender, location, and motivation. The linkage rate for POC testing that included a comprehensive intake visit and colocated primary care services for in-state residents was 97%. Additional research on integrated POC screening and linkage methodologies that provide intake services at time of testing is essential for increasing status awareness and improving linkage to HIV care in the US.

  1. Prospective Linkages between Peer Victimization and Externalizing Problems in Children: A Meta-Analysis

    NARCIS (Netherlands)

    Reijntjes, A.; Kamphuis, J.H.; Prinzie, P.; Boelen, P.A.; van der Schoot, M.; Telch, M.J.

    2011-01-01

    Previous meta-analytic research has shown both concurrent and prospective linkages between peer victimization and internalizing problems in youth. However, the linkages between peer victimization and externalizing problems over time have not been systematically examined, and it is therefore unknown

  2. Linkage disequilibrium and demographic history of the isolated population of the Faroe Islands

    DEFF Research Database (Denmark)

    Jorgensen, Tove H; Degn, Birte; Wang, August G

    2002-01-01

    The isolated population of the Faroe Islands has a history of recent expansion after being limited to a small size for centuries. Such an isolated population may be ideal for linkage disequilibrium mapping of disease genes if linkage disequilibrium (LD) extends over large regions. Analyses of 18 ...

  3. Health problems in childhood cancer survivors: Linkage studies and guideline development

    NARCIS (Netherlands)

    Font-Gonzalez, A.

    2016-01-01

    This thesis comprises two parts. The first part of this thesis aims to increase the evidence on the burden of disease in childhood cancer survivors and to define high-risk groups of survivors by using medical record linkage studies. A two-step record linkage methodology between Dutch national

  4. [Linkage to care among new human immunodeficiency virus diagnoses in Spain].

    Science.gov (United States)

    Oliva, Jesús; Malo, Carmen; Fernández, Ana; Izquierdo, Ana; Marcos, Henar; Cevallos, Carlos; Castilla, Jesús; García, Rocio; Díez, Mercedes

    2014-03-01

    To describe linkage to care among new HIV diagnoses in Spain; and to estimate factors associated to linkage to care within three months after diagnosis. The distribution of the time elapsing between the date of HIV diagnosis and the date of first determination of CD4 (considered to be the date of linkage to care) was calculated among new HIV diagnoses in 2010 in the seven Autonomous Regions participating, where data on date of CD4 count was available. Linkage to care was considered «correct» if done within three months after diagnosis. Factors associated to correct linkage to care were estimated using logistic regression. A total of 1769 new HIV diagnoses were included. Of them, 83.1% had evidence of linkage to care within a year, and 75.7% were linked within three months after diagnosis. Being an injectable drug user (IDU) was the only factor inversely associated with linkage to care within 3 months (OR = 0.3; 95% CI: 0.2-0.6). In Spain linkage to care after HIV diagnosis is good, but there is still room for improvement, especially among IDUs. Copyright © 2013 Elsevier España, S.L. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  5. Model reduction of detailed-balanced reaction networks by clustering linkage classes

    NARCIS (Netherlands)

    Rao, Shodhan; Jayawardhana, Bayu; van der Schaft, Abraham; Findeisen, Rolf; Bullinger, Eric; Balsa-Canto, Eva; Bernaerts, Kristel

    2016-01-01

    We propose a model reduction method that involves sequential application of clustering of linkage classes and Kron reduction. This approach is specifically useful for chemical reaction networks with each linkage class having less number of reactions. In case of detailed balanced chemical reaction

  6. The acceptability of conducting data linkage research without obtaining consent: lay people's views and justifications.

    Science.gov (United States)

    Xafis, Vicki

    2015-11-17

    A key ethical issue arising in data linkage research relates to consent requirements. Patients' consent preferences in the context of health research have been explored but their consent preferences regarding data linkage specifically have been under-explored. In addition, the views on data linkage are often those of patient groups. As a result, little is known about lay people's views and their preferences about consent requirements in the context of data linkage. This study explores lay people's views and justifications regarding the acceptability of conducting data linkage research without obtaining consent. A qualitative study explored lay people's views regarding consent requirements in data linkage via four hypothetical data linkage scenarios of increasing complexity. Prior to considering the scenarios, participants were provided with information regarding best practice data linkage processes via discussion and a diagrammatic representation of the process. Lay people were able to understand the intricate processes involved in data linkage and the key protections afforded within a short amount of time. They were supportive of data linkage research and, on the whole, believed it should be conducted without consent provided a data linkage organization de-identifies the data used so that researchers do not handle identifiable data. Many thought that de-identified data holds a different status to identifiable data and should be used without specific consent in research that aims to benefit society. In weighing up conflicting values and interests, participants shifted consent preferences before arriving at their final consent preference for each scenario and provided justifications for their choices. They considered the protection of people's information, societal benefits, and the nature and constraints of research and recognized that these need to be balanced. With some exposure to the features of data linkage, lay people have the capacity to understand the

  7. Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

    Science.gov (United States)

    Wright, Fred A.; Strug, Lisa J.; Doshi, Vishal K.; Commander, Clayton W.; Blackman, Scott M.; Sun, Lei; Berthiaume, Yves; Cutler, David; Cojocaru, Andreea; Collaco, J. Michael; Corey, Mary; Dorfman, Ruslan; Goddard, Katrina; Green, Deanna; Kent, Jack W.; Lange, Ethan M.; Lee, Seunggeun; Li, Weili; Luo, Jingchun; Mayhew, Gregory M.; Naughton, Kathleen M.; Pace, Rhonda G.; Paré, Peter; Rommens, Johanna M.; Sandford, Andrew; Stonebraker, Jaclyn R.; Sun, Wei; Taylor, Chelsea; Vanscoy, Lori L.; Zou, Fei; Blangero, John; Zielenski, Julian; O’Neal, Wanda K.; Drumm, Mitchell L.; Durie, Peter R.; Knowles, Michael R.; Cutting, Garry R.

    2012-01-01

    A combined genome-wide association and linkage study was used to identify loci causing variation in CF lung disease severity. A significant association (P=3. 34 × 10-8) near EHF and APIP (chr11p13) was identified in F508del homozygotes (n=1,978). The association replicated in F508del homozygotes (P=0.006) from a separate family-based study (n=557), with P=1.49 × 10-9 for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family-based study identified a significant QTL on chromosome 20q13.2 (LOD=5.03). Our findings provide insight into the causes of variation in lung disease severity in CF and suggest new therapeutic targets for this life-limiting disorder. PMID:21602797

  8. A new model of care collaboration for community-dwelling elders: findings and lessons learned from the NORC-health care linkage evaluation

    Directory of Open Access Journals (Sweden)

    Corinne Kyriacou

    2011-05-01

    Full Text Available Introduction and Background: Few financial incentives in the United States encourage coordination across the health and social care systems. Supportive Service Programs (SSPs, operating in Naturally Occurring Retirement Communities (NORCs, attempt to increase access to care and enhance care quality for aging residents.  This article presents findings from an evaluation conducted from 2004 to 2006 looking at the feasibility, quality and outcomes of linking health and social services through innovative NORC-SSP and health organization micro-collaborations.  Methods: Four NORC-SSPs participated in the study by finding a health care organization or community-based physicians to collaborate with on addressing health conditions that could benefit from a biopsychosocial approach. Each site focused on a specific population, addressed a specific condition or problem, and created different linkages to address the target problem.  Using a case study approach, incorporating both qualitative and quantitative methods, this evaluation sought to answer the following two primary questions: 1 Have the participating sites created viable linkages between their organizations that did not exist prior to the study; and, 2 To what extent have the linkages resulted in improvements in clinical and other health and social outcomes?    Results: Findings suggest that immediate outcomes were widely achieved across sites: knowledge of other sector providers’ capabilities and services increased; communication across providers increased; identification of target population increased; and, awareness of risks, symptoms and health seeking behaviors among clients/patients increased.  Furthermore, intermediate outcomes were also widely achieved: shared care planning increased across providers; continuity of care was enhanced; disease management improved; and self care among clients improved.  Finally, several linkage partnerships were also able to demonstrate improvements

  9. A genetic linkage map of hexaploid naked oat constructed with SSR markers

    Directory of Open Access Journals (Sweden)

    Gaoyuan Song

    2015-08-01

    Full Text Available Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 cM and including 208 simple sequence repeat (SSR markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. Thirty-six markers (17.3% showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

  10. Intracellular drug delivery nanocarriers of glutathione-responsive degradable block copolymers having pendant disulfide linkages.

    Science.gov (United States)

    Khorsand, Behnoush; Lapointe, Gabriel; Brett, Christopher; Oh, Jung Kwon

    2013-06-10

    Self-assembled micelles of amphiphilic block copolymers (ABPs) with stimuli-responsive degradation (SRD) properties have a great promise as nanotherapeutics exhibiting enhanced release of encapsulated therapeutics into targeted cells. Here, thiol-responsive degradable micelles based on a new ABP consisting of a pendant disulfide-labeled methacrylate polymer block (PHMssEt) and a hydrophilic poly(ethylene oxide) (PEO) block were investigated as effective intracellular nanocarriers of anticancer drugs. In response to glutathione (GSH) as a cellular trigger, the cleavage of pendant disulfide linkages in hydrophobic PHMssEt blocks of micellar cores caused the destabilization of self-assembled micelles due to change in hydrophobic/hydrophilic balance. Such GSH-triggered micellar destabilization changed their size distribution with an appearance of large aggregates and led to enhanced release of encapsulated anticancer drugs. Cell culture results from flow cytometry and confocal laser scanning microscopy for cellular uptake as well as cell viability measurements for high anticancer efficacy suggest that new GSH-responsive degradable PEO-b-PHMssEt micelles offer versatility in multifunctional drug delivery applications.

  11. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

    Science.gov (United States)

    Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

    2018-01-01

    The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

  12. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

    Science.gov (United States)

    Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

    2018-01-01

    The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

  13. A Linkage Model of Supply Chain Operation and Financial Performance for Economic Sustainability of Firm

    Directory of Open Access Journals (Sweden)

    Suk Ho Jin

    2017-01-01

    Full Text Available Although several studies have explored the relationship between the operation and performance of a supply chain (SC, a general SC model cannot deliver the expected financial results at a company-wide level. In this paper, we argue that this cannot guarantee the maximization of a firm’s overall value because short-term financial performance metrics do not reflect the risk to businesses and the invested capital. Owing to the varying natures of risk and the capital invested, firms with multiple divisions should assess each division separately, and the results can be compared for decisions concerning the allocation of the firm’s capital and resources to maximize the overall value of its businesses. We propose a linkage model to consider operational activities and financial performance simultaneously in a firm’s supply chain model. To exhibit the superiority of the proposed model that connects SC operation and financial indicators, we first compare the differences between models for maximizing profit and enterprise-wise economic value added (EVA as objective functions. To examine uncertainty in the operational and financial parameters of the SC, the results of sensitivity analyses are then reported. Experimental results showed that our model, using the EVA approach, is more effective and superior in terms of maximizing the firm’s overall value from the long-term perspective while satisfying the target values for financial ratios set by the firm’s executives and shareholders for all periods, unlike the results of the general model.

  14. Possible linkage of SP6 transcriptional activity with amelogenesis by protein stabilization.

    Science.gov (United States)

    Utami, Trianna W; Miyoshi, Keiko; Hagita, Hiroko; Yanuaryska, Ryna Dwi; Horiguchi, Taigo; Noma, Takafumi

    2011-01-01

    Ameloblasts produce enamel matrix proteins such as amelogenin, ameloblastin, and amelotin during tooth development. The molecular mechanisms of ameloblast differentiation (amelogenesis) are currently not well understood. SP6 is a transcription factor of the Sp/KLF family that was recently found to regulate cell proliferation in a cell-type-specific manner. Sp6-deficient mice demonstrate characteristic tooth anomalies such as delayed eruption of the incisors and supernumerary teeth with disorganized amelogenesis. However, it remains unclear how Sp6 controls amelogenesis. In this study, we used SP6 high producer cells to identify SP6 target genes. Based on the observations that long-term culture of SP6 high producer cells reduced SP6 protein expression but not Sp6 mRNA expression, we found that SP6 is short lived and specifically degraded through a proteasome pathway. We established an in vitro inducible SP6 expression system coupled with siRNA knockdown and found a possible linkage between SP6 and amelogenesis through the regulation of amelotin and Rock1 gene expression by microarray analysis. Our findings suggest that the regulation of SP6 protein stability is one of the crucial steps in amelogenesis.

  15. Possible Linkage of SP6 Transcriptional Activity with Amelogenesis by Protein Stabilization

    Directory of Open Access Journals (Sweden)

    Trianna W. Utami

    2011-01-01

    Full Text Available Ameloblasts produce enamel matrix proteins such as amelogenin, ameloblastin, and amelotin during tooth development. The molecular mechanisms of ameloblast differentiation (amelogenesis are currently not well understood. SP6 is a transcription factor of the Sp/KLF family that was recently found to regulate cell proliferation in a cell-type-specific manner. Sp6-deficient mice demonstrate characteristic tooth anomalies such as delayed eruption of the incisors and supernumerary teeth with disorganized amelogenesis. However, it remains unclear how Sp6 controls amelogenesis. In this study, we used SP6 high producer cells to identify SP6 target genes. Based on the observations that long-term culture of SP6 high producer cells reduced SP6 protein expression but not Sp6 mRNA expression, we found that SP6 is short lived and specifically degraded through a proteasome pathway. We established an in vitro inducible SP6 expression system coupled with siRNA knockdown and found a possible linkage between SP6 and amelogenesis through the regulation of amelotin and Rock1 gene expression by microarray analysis. Our findings suggest that the regulation of SP6 protein stability is one of the crucial steps in amelogenesis.

  16. HealthNavigator: a mobile application for chronic disease screening and linkage to services at an urban Primary Health Network.

    Science.gov (United States)

    Seneviratne, Martin G; Hersch, Fred; Peiris, David P

    2018-03-26

    Mobile applications (apps) are promising tools to support chronic disease screening and linkage to health services. They have the potential to increase healthcare access for vulnerable populations. The HealthNavigator app was developed to provide chronic disease risk assessments, linkage to local general practitioners (GPs) and lifestyle programs, and a personalised health report for discussion with a GP. Assessments were either self-administered or facilitated by community health workers through a Primary Health Network (PHN) initiative targeting ethnically diverse communities. In total, 1492 assessments (80.4% self-administered, 19.6% facilitated) were conducted over a 12-month period in Queensland, Australia. Of these, 26% of people screened came from postcodes representing the lowest quartile of socioeconomic disadvantage. When compared against self-administered assessments, subjects screened by the facilitated program were more likely to be born outside Australia (80.5 v. 33.2%, P<0.001), and to fall within a high risk category based on cardiovascular risk scores (19.8 v. 13.7%, P<0.01) and type 2 diabetes mellitus risk scores (58.0 v. 40.1%, P<0.001). Mobile apps embedded into PHN programs may be a useful adjunct for the implementation of community screening programs. Further research is needed to determine their effect on health service access and health outcomes.

  17. Wearing weighted backpack dilates subjective visual duration: The role of functional linkage between weight experience and visual timing

    Directory of Open Access Journals (Sweden)

    Lina eJia

    2015-09-01

    Full Text Available Bodily state plays a critical role in our perception. In the present study, we asked the question whether and how bodily experience of weights influences time perception. Participants judged durations of a picture (a backpack or a trolley bag presented on the screen, while wearing different weight backpacks or without backpack. The results showed that the subjective dura-tion of the backpack picture was dilated when participants wore a medium weighted backpack relative to an empty backpack or without backpack, regardless of identity (e.g., color of the visual backpack. However, the duration dilation was not manifested for the picture of trolley bag. These findings suggest that weight experience modulates visual duration estimation through the linkage between the wore backpack and to-be-estimated visual target. The con-gruent action affordance between the wore backpack and visual inputs plays a critical role in the functional linkage between inner experience and time perception. We interpreted our findings within the framework of embodied time perception.

  18. Targeted Learning

    CERN Document Server

    van der Laan, Mark J

    2011-01-01

    The statistics profession is at a unique point in history. The need for valid statistical tools is greater than ever; data sets are massive, often measuring hundreds of thousands of measurements for a single subject. The field is ready to move towards clear objective benchmarks under which tools can be evaluated. Targeted learning allows (1) the full generalization and utilization of cross-validation as an estimator selection tool so that the subjective choices made by humans are now made by the machine, and (2) targeting the fitting of the probability distribution of the data toward the targe

  19. Target preparation

    International Nuclear Information System (INIS)

    Hinn, G.M.

    1984-01-01

    A few of the more interesting of the 210 targets prepared in the Laboratory last year are listed. In addition the author continues to use powdered silver mixed with /sup 9,10/BeO to produce sources for accelerator radio dating of Alaskan and South Polar snow. Currently, he is trying to increase production by multiple sample processing. Also the author routinely makes 3 μg/cm 2 cracked slacked carbon stripper foils and is continuing research with some degree of success in making enriched 28 Si targets starting with the oxide

  20. Primordial linkage of β2-microglobulin to the MHC.

    Science.gov (United States)

    Ohta, Yuko; Shiina, Takashi; Lohr, Rebecca L; Hosomichi, Kazuyoshi; Pollin, Toni I; Heist, Edward J; Suzuki, Shingo; Inoko, Hidetoshi; Flajnik, Martin F

    2011-03-15

    β2-Microglobulin (β2M) is believed to have arisen in a basal jawed vertebrate (gnathostome) and is the essential L chain that associates with most MHC class I molecules. It contains a distinctive molecular structure called a constant-1 Ig superfamily domain, which is shared with other adaptive immune molecules including MHC class I and class II. Despite its structural similarity to class I and class II and its conserved function, β2M is encoded outside the MHC in all examined species from bony fish to mammals, but it is assumed to have translocated from its original location within the MHC early in gnathostome evolution. We screened a nurse shark bacterial artificial chromosome library and isolated clones containing β2M genes. A gene present in the MHC of all other vertebrates (ring3) was found in the bacterial artificial chromosome clone, and the close linkage of ring3 and β2M to MHC class I and class II genes was determined by single-strand conformational polymorphism and allele-specific PCR. This study satisfies the long-held conjecture that β2M was linked to the primordial MHC (Ur MHC); furthermore, the apparent stability of the shark genome may yield other genes predicted to have had a primordial association with the MHC specifically and with immunity in general.

  1. Spatial Linkage and Urban Expansion: AN Urban Agglomeration View

    Science.gov (United States)

    Jiao, L. M.; Tang, X.; Liu, X. P.

    2017-09-01

    Urban expansion displays different characteristics in each period. From the perspective of the urban agglomeration, studying the spatial and temporal characteristics of urban expansion plays an important role in understanding the complex relationship between urban expansion and network structure of urban agglomeration. We analyze urban expansion in the Yangtze River Delta Urban Agglomeration (YRD) through accessibility to and spatial interaction intensity from core cities as well as accessibility of road network. Results show that: (1) Correlation between urban expansion intensity and spatial indicators such as location and space syntax variables is remarkable and positive, while it decreases after rapid expansion. (2) Urban expansion velocity displays a positive correlation with spatial indicators mentioned above in the first (1980-1990) and second (1990-2000) period. However, it exhibits a negative relationship in the third period (2000-2010), i.e., cities located in the periphery of urban agglomeration developing more quickly. Consequently, the hypothesis of convergence of urban expansion in rapid expansion stage is put forward. (3) Results of Zipf's law and Gibrat's law show urban expansion in YRD displays a convergent trend in rapid expansion stage, small and medium-sized cities growing faster. This study shows that spatial linkage plays an important but evolving role in urban expansion within the urban agglomeration. In addition, it serves as a reference to the planning of Yangtze River Delta Urban Agglomeration and regulation of urban expansion of other urban agglomerations.

  2. A genetic linkage map of the chromosome 4 short arm

    Energy Technology Data Exchange (ETDEWEB)

    Locke, P.A.; MacDonald, M.E.; Srinidhi, J.; Tanzi, R.E.; Haines, J.L. (Massachusetts General Hospital, Boston (United States)); Gilliam, T.C. (Columbia Univ., New York, NY (United States)); Conneally, P.M. (Indiana Univ. Medical Center, Indianapolis (United States)); Wexler, N.S. (Columbia Univ., New York, NY (United States) Hereditary Disease Foundation, Santa Monica, CA (United States)); Gusella, J.F. (Massachusetts General Hospital, Boston (United States) Harvard Univ., Boston, MA (United States))

    1993-01-01

    The authors have generated an 18-interval contiguous genetic linkage map of human chromosome 4 spanning the entire short arm and proximal long arm. Fifty-seven polymorphisms, representing 42 loci, were analyzed in the Venezuelan reference pedigree. The markers included seven genes (ADRA2C, ALB, GABRB1, GC, HOX7, IDUA, QDPR), one pseudogene (RAF1P1), and 34 anonymous DNA loci. Four loci were represented by microsatellite polymorphisms and one (GC) was expressed as a protein polymorphism. The remainder were genotyped based on restriction fragment length polymorphism. The sex-averaged map covered 123 cM. Significant differences in sex-specific rates of recombination were observed only in the pericentromeric and proximal long arm regions, but these contributed to different overall map lengths of 115 cM in males and 138 cM in females. This map provides 19 reference points along chromosome 4 that will be particularly useful in anchoring and seeding physical mapping studies and in aiding in disease studies. 26 refs., 1 fig., 1 tab.

  3. Plankton of Southern Chilean fjords: trends and linkages

    Directory of Open Access Journals (Sweden)

    Tarcisio Antezana

    1999-12-01

    Full Text Available The present paper compiles and reviews past and recent results from Magellan and Fuegian fjords for an overview of the planktonic assemblage there. It first examines linkages to local, adjacent and remote environments. The plankton assemblage presents deviations from the biota of the Magellan biogeographic Province, where the occasional presence of Antarctic species is related to oceanographic phenomena at the Polar Front. Complex bathymetric and hydrographic features within the fjords suggest that the plankton is rather isolated. Adaptations and constraints for population survival, and the role of diel migrators and gregarious zooplankters with regard to bentho-pelagic coupling are discussed. Results on seasonal differences in the plankton of the largest and most isolated basin of the Strait of Magellan are compiled. In spring the plankton was dominated by large diatoms suggesting a short food chain where most of the phytoplankton bloom goes to the bottom, to the meroplankton and to a few dominant holoplankters. In summer, the phytoplankton was dominated by pico- and nanophytoplankton suggesting a more complex food web mediated by a bacterial loop. High abundance of holo- and meroplanktonic larvae coincided with spring blooming conditions.

  4. Heavy ion mutagenesis: linear energy transfer effects and genetic linkage

    Science.gov (United States)

    Kronenberg, A.; Gauny, S.; Criddle, K.; Vannais, D.; Ueno, A.; Kraemer, S.; Waldren, C. A.; Chatterjee, A. (Principal Investigator)

    1995-01-01

    We have characterized a series of 69 independent mutants at the endogenous hprt locus of human TK6 lymphoblasts and over 200 independent S1-deficient mutants of the human x hamster hybrid cell line AL arising spontaneously or following low-fluence exposures to densely ionizing Fe ions (600 MeV/amu, linear energy transfer = 190 keV/microns). We find that large deletions are common. The entire hprt gene (> 44 kb) was missing in 19/39 Fe-induced mutants, while only 2/30 spontaneous mutants lost the entire hprt coding sequence. When the gene of interest (S1 locus = M1C1 gene) is located on a nonessential human chromosome 11, multilocus deletions of several million base pairs are observed frequently. The S1 mutation frequency is more than 50-fold greater than the frequency of hprt mutants in the same cells. Taken together, these results suggest that low-fluence exposures to Fe ions are often cytotoxic due to their ability to create multilocus deletions that may often include the loss of essential genes. In addition, the tumorigenic potential of these HZE heavy ions may be due to the high potential for loss of tumor suppressor genes. The relative insensitivity of the hprt locus to mutation is likely due to tight linkage to a gene that is required for viability.

  5. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

    Science.gov (United States)

    Wall, Jeffrey D; Stevison, Laurie S

    2016-08-09

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. Copyright © 2016 Wall and Stevison.

  6. A statistical design for testing apomictic diversification through linkage analysis.

    Science.gov (United States)

    Zeng, Yanru; Hou, Wei; Song, Shuang; Feng, Sisi; Shen, Lin; Xia, Guohua; Wu, Rongling

    2014-03-01

    The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory (Carya cathayensis) and pecan (C. illinoensis) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

  7. Climate change and its linkages with development, equity and sustainability

    International Nuclear Information System (INIS)

    Munasinghe, M.; Swart, R.

    2000-01-01

    The IPCC Working Groups 2 and 3 (on impacts and adaptation, and on mitigation, respectively) have taken the initiative to organise a number of expert meetings. The main goals of the meetings are: (a) to increase co-ordination among, and inform lead authors about development, equity and sustainability (DES) issues and climate change; and (b) to better place the IPCC Third Assessment Report in the context of DES, through enhanced access to the best available scientific, technical economic and social information from across the world. The rapidly growing economies of Asia will play a key role in determining future climate change policy. Thus, the organisation of the first expert meeting in Colombo, Sri Lanka, under the able guidance of Professor Mohan Munasinghe, is very appropriate. The conference has provided a crucial first step towards broadening the scope of the IPCC reports, by integrating DES issues into climate change response strategies. This Proceedings volume is also important as a key policy-relevant (but not policy-prescriptive) vehicle that will better inform worldwide networks of scientists from different regional, cultural and disciplinary backgrounds, in their pursuit of the best scientific information on the linkages between climate change and sustainable development. refs

  8. The Thai-Canadian nuclear human resources development linkage project

    International Nuclear Information System (INIS)

    Sumitra, Tatchai; Chankow, Nares; Bradley, K.; Bereznai, G.

    1998-01-01

    The Thai-Canadian Nuclear Human Resources Development Linkage Project (the P roject ) was initiated in 1994 in order to develop the engineering and scientific expertise needed for Thailand to decide whether and how the country can best benefit from the establishment of a nuclear power program. The Project was designed to upgrade current academics and people in industry, and to develop an adequate supply of new technical personnel for academic, industry, utility, regulatory and other government institutions. The key Project objectives included the establishment of a Chair in Nuclear Engineering at Chulalongkorn University, the upgrading of the current Masters level curriculum, the establishment of undergraduate and doctorate level curricula, development and delivery of an industrial training program for people in industry and government, exchanges of Thai and Canadian academics and industry experts to establish common research programs and teaching interests, and a public education program that was to test in Thailand some of the techniques that have been successfully used in Canada. (author)

  9. THE NATIONAL SECURITY - MEDIA POWER LINKAGE. A THEORETICAL FRAMEWORK

    Directory of Open Access Journals (Sweden)

    KARIN MEGHEŞAN

    2013-05-01

    Full Text Available The mechanism of national security policy is an issue of increasing interests in post cold war era. But what is the impact of the media upon national security policy decision making? New world wide events show us that more than ever national policy is often at the mercy of the media. The Wiki leaks, the Murdoch inquiry, the impact of new social media on Arab democratic movements are just some examples regarding the effect of nearly simultaneous presentation of information around the world. The world is changing, and the processes by which national policy is developed may also be changing especially in the security domain. The essence of this study, as the title suggests is the idea of a „dual use” media in the national security issues. This study employs a relatively narrow definition of national security issues as only those which are concerned with national survival and preservation of our society. The media affects us as individuals and as a collective body so we will like to focus on a realistic understanding of the media-secrecy-security linkage, noting that we will do nothing else but advance and underline the main points of view from the public and scientific discourse.

  10. Linkage disequilibrium in HLA cannot be explained by selective recombination.

    Science.gov (United States)

    Termijtelen, A; D'Amaro, J; van Rood, J J; Schreuder, G M

    1995-11-01

    Some combinations of HLA-A, -B and -DR antigens occur more frequently than would be expected from their gene frequencies in the population. This phenomenon, referred to as Linkage Disequilibrium (LD) has been the origin of many speculations. One hypothesis to explain LD is that some haplotypes are protected from recombination. A second hypothesis is that these HLA antigens preferentially recombine after cross-over to create an LD haplotype. We tested these 2 hypotheses: from a pool of over 10,000 families typed in our department, we analyzed 126 families in which HLA-A:B or B:DR recombinant offspring was documented. To overcome a possible bias in our material, we used the non-recombined haplotypes from the same 126 families as a control group. Our results show that the number of cross-overs through LD haplotypes is not significantly lower then would be expected if recombination occurred randomly. Also the number of LD haplotypes created upon recombination was not significantly increased.

  11. Linkage disequilibrium between STRPs and SNPs across the human genome.

    Science.gov (United States)

    Payseur, Bret A; Place, Michael; Weber, James L

    2008-05-01

    Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this idea, we measured associations between short-tandem-repeat polymorphisms (STRPs), which can mutate rapidly and recurrently, and SNPs in 721 regions across the human genome. We directly compared STRP-SNP LD with SNP-SNP LD from the same genomic regions in the human HapMap populations. The intensity of STRP-SNP LD, measured by the average of D', was reduced, consistent with the action of recurrent mutation. Nevertheless, a higher fraction of STRP-SNP pairs than SNP-SNP pairs showed significant LD, on both short (up to 50 kb) and long (cM) scales. These results reveal the substantial effects of mutational processes on LD at STRPs and provide important measures of the potential of STRPs for association mapping of disease genes.

  12. Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus

    Directory of Open Access Journals (Sweden)

    Matthew C. Hale

    2017-11-01

    Full Text Available Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq to generate a marker-dense genetic map for Brook Trout (Salvelinus fontinalis. The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.

  13. Phase-Division-Based Dynamic Optimization of Linkages for Drawing Servo Presses

    Science.gov (United States)

    Zhang, Zhi-Gang; Wang, Li-Ping; Cao, Yan-Ke

    2017-11-01

    Existing linkage-optimization methods are designed for mechanical presses; few can be directly used for servo presses, so development of the servo press is limited. Based on the complementarity of linkage optimization and motion planning, a phase-division-based linkage-optimization model for a drawing servo press is established. Considering the motion-planning principles of a drawing servo press, and taking account of work rating and efficiency, the constraints of the optimization model are constructed. Linkage is optimized in two modes: use of either constant eccentric speed or constant slide speed in the work segments. The performances of optimized linkages are compared with those of a mature linkage SL4-2000A, which is optimized by a traditional method. The results show that the work rating of a drawing servo press equipped with linkages optimized by this new method improved and the root-mean-square torque of the servo motors is reduced by more than 10%. This research provides a promising method for designing energy-saving drawing servo presses with high work ratings.

  14. A new method for assessing how sensitivity and specificity of linkage studies affects estimation.

    Directory of Open Access Journals (Sweden)

    Cecilia L Moore

    Full Text Available While the importance of record linkage is widely recognised, few studies have attempted to quantify how linkage errors may have impacted on their own findings and outcomes. Even where authors of linkage studies have attempted to estimate sensitivity and specificity based on subjects with known status, the effects of false negatives and positives on event rates and estimates of effect are not often described.We present quantification of the effect of sensitivity and specificity of the linkage process on event rates and incidence, as well as the resultant effect on relative risks. Formulae to estimate the true number of events and estimated relative risk adjusted for given linkage sensitivity and specificity are then derived and applied to data from a prisoner mortality study. The implications of false positive and false negative matches are also discussed.Comparisons of the effect of sensitivity and specificity on incidence and relative risks indicate that it is more important for linkages to be highly specific than sensitive, particularly if true incidence rates are low. We would recommend that, where possible, some quantitative estimates of the sensitivity and specificity of the linkage process be performed, allowing the effect of these quantities on observed results to be assessed.

  15. A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16.

    Science.gov (United States)

    Asherson, P; Zhou, K; Anney, R J L; Franke, B; Buitelaar, J; Ebstein, R; Gill, M; Altink, M; Arnold, R; Boer, F; Brookes, K; Buschgens, C; Butler, L; Cambell, D; Chen, W; Christiansen, H; Feldman, L; Fleischman, K; Fliers, E; Howe-Forbes, R; Goldfarb, A; Heise, A; Gabriëls, I; Johansson, L; Lubetzki, I; Marco, R; Medad, S; Minderaa, R; Mulas, F; Müller, U; Mulligan, A; Neale, B; Rijsdijk, F; Rabin, K; Rommelse, N; Sethna, V; Sorohan, J; Uebel, H; Psychogiou, L; Weeks, A; Barrett, R; Xu, X; Banaschewski, T; Sonuga-Barke, E; Eisenberg, J; Manor, I; Miranda, A; Oades, R D; Roeyers, H; Rothenberger, A; Sergeant, J; Steinhausen, H-C; Taylor, E; Thompson, M; Faraone, S V

    2008-05-01

    As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage was observed on the most established ADHD-linked genomic regions of 5p and 17p. We found suggestive linkage signals on chromosomes 9 and 16, respectively, with the highest multipoint nonparametric linkage signal on chromosome 16q23 at 99 cM (log of the odds, LOD=3.1) overlapping data published from the previous UCLA (University of California, Los Angeles) (LOD>1, approximately 95 cM) and Dutch (LOD>1, approximately 100 cM) studies. The second highest peak in this study was on chromosome 9q22 at 90 cM (LOD=2.13); both the previous UCLA and German studies also found some evidence of linkage at almost the same location (UCLA LOD=1.45 at 93 cM; German LOD=0.68 at 100 cM). The overlap of these two main peaks with previous findings suggests that loci linked to ADHD may lie within these regions. Meta-analysis or reanalysis of the raw data of all the available ADHD linkage scan data may help to clarify whether these represent true linked loci.

  16. Nance-Horan syndrome: linkage analysis in a family from The Netherlands.

    Science.gov (United States)

    Bergen, A A; ten Brink, J; Schuurman, E J; Bleeker-Wagemakers, E M

    1994-05-01

    Linkage analysis was carried out in a Dutch family with Nance-Horan (NH) syndrome. Close linkage without recombination between NH and the Xp loci DXS207, DXS43, and DXS365 (zmax = 3.23) was observed. Multipoint linkage analysis and the analysis of recombinations in multiple informative meioses suggest the genetic order Xcen-DMD (exon 49)-DXS451-(NH, DXS207, DXS365, DXS43)-(STS, DXF30)-Xpter. These data refine the localization of the NH locus on the distal Xp.

  17. INTERACTION OF TRADE AND FINANCIAL LINKAGES IN THE FREE TRADE ZONES

    Directory of Open Access Journals (Sweden)

    V. Shevchenko

    2014-09-01

    Full Text Available Different models of free trade agreements (FTA and free trade zones (FTZ are considered in the article, argued the complex approach to their structures and results under unstable global economic environment. The typology of the free trade zones models and financial linkages types between countries have been developed. Approaches to the results of the free trade zones have been argued. It has been discovered that for the free trade zones of transitional countries the prevailing are tarde flows concentration whereas financial and investment linkages are acting with developed countries. The main directions of increasing of the financial linkages results in the free trade zones have been discovered.

  18. Dimensional Anxiety Mediates Linkage of GABRA2 Haplotypes With Alcoholism

    Science.gov (United States)

    Enoch, Mary-Anne; Schwartz, Lori; Albaugh, Bernard; Virkkunen, Matti; Goldman, David

    2015-01-01

    The GABAAα2 receptor gene (GABRA2) modulates anxiety and stress response. Three recent association studies implicate GABRA2 in alcoholism, however in these papers both common, opposite-configuration haplotypes in the region distal to intron3 predict risk. We have now replicated the GABRA2 association with alcoholism in 331 Plains Indian men and women and 461 Finnish Caucasian men. Using a dimensional measure of anxiety, harm avoidance (HA), we also found that the association with alcoholism is mediated, or moderated, by anxiety. Nine SNPs were genotyped revealing two haplotype blocks. Within the previously implicated block 2 region, we identified the two common, opposite-configuration risk haplotypes, A and B. Their frequencies differed markedly in Finns and Plains Indians. In both populations, most block 2 SNPs were significantly associated with alcoholism. The associations were due to increased frequencies of both homozygotes in alcoholics, indicating the possibility of alcoholic subtypes with opposite genotypes. Congruently, there was no significant haplotype association. Using HA as an indicator variable for anxiety, we found haplotype linkage to alcoholism with high and low dimensional anxiety, and to HA itself, in both populations. High HA alcoholics had the highest frequency of the more abundant haplotype (A in Finns, B in Plains Indians); low HA alcoholics had the highest frequency of the less abundant haplotype (B in Finns, A in Plains Indians) (Finns: P α0.007, OR α2.1, Plains Indians: P α0.040, OR α1.9). Non-alcoholics had intermediate frequencies. Our results suggest that within the distal GABRA2 region is a functional locus or loci that may differ between populations but that alters risk for alcoholism via the mediating action of anxiety. PMID:16874763

  19. Linkage disequilibrium of evolutionarily conserved regions in the human genome

    Directory of Open Access Journals (Sweden)

    Johnson Todd A

    2006-12-01

    Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

  20. Linkage between forest-based mitigation and GHG markets

    International Nuclear Information System (INIS)

    Loisel, C.

    2008-01-01

    According to the latest assessment report of the Intergovernmental Panel on Climate Change, deforestation and forest degradation contributed to 23% of global carbon dioxide emissions and 17% of global emissions of all greenhouse gases in 2004 (IPCC AR4 SPM, 2007). Despite significant uncertainties, these figures stress the relevance of addressing deforestation into the new global climate governance regime. Deforestation is primarily a concern for tropical regions nowadays and FAO's Forest resource assessments (2005) highlight significant national disparities as a consequence of history, soil and climate conditions and current policies and socio-economic conditions. The Stern Review (2006) pointed to deforestation abatement as a must-seize opportunity to cut global greenhouse emissions with good cost/efficiency and numerous co-benefits. Under the framework of the 2007 Bali Action Plan, the UNFCCC is now considering policy approaches to promote the reduction of emissions from deforestation and forest degradation, and also forest conservation, sustainable forest management and forestation ('REDD+'). At the same time, the European Union is engaged in a major review of its climate and energy legislation. The EU climate/energy package has entered into the final stages of negotiation and the outcome should provide funding for REDD+ actions on the long run through some sort of connection to carbon markets. These are moments of historic significance both for world forests and climate protection, but significant challenges remain. This workshop focuses on one of these challenges: while mechanisms are being designed to connect greenhouse gas emission trading schemes and REDD+ actions, we must ensure that they enable broad and far-reaching actions while safeguarding against various sorts of unintended consequences. This background paper intends to provide a rapid initial overview on three aspects of the linkage between forest-based mitigation and emission trading schemes: (i

  1. Hypoxia Impacts on Food Web Linkages in a Pelagic Ecosystem

    Science.gov (United States)

    Sato, M.; Horne, J. K.; Parker-Stetter, S. L.; Essington, T.; Keister, J. E.; Moriarty, P.; Li, L.

    2016-02-01

    Low dissolved oxygen (DO), or hypoxia, causes significant disturbances on aquatic organisms, but the consequences for key food web linkages is not well understood. Here, we tested how the intensity of low DO events governs the degree of spatial overlap between pelagic zooplanktivorous fish and their zooplankton prey, fish feeding rates, and community compositions of zooplankton. We hypothesized that the greater sensitivity of fish to DO compared to zooplankton would lead to diminished spatial overlap at moderate DO and reduced feeding rates of fish, while severe hypoxia would amplify spatial overlap by preventing zooplankton from using deep refuge habitats leading to increased fish feeding rates. We also hypothesized shifts in zooplankton community composition towards less energetically profitable taxa such as small copepods and gelatinous species. We used a combination of multifrequency acoustic and net sampling for detecting distributions and abundance of zooplankton and pelagic fish in Hood Canal, WA, a seasonally hypoxic fjord. We employed a sampling design which paired hypoxic regions of Hood Canal with normoxic regions sampled prior to, during, and after the onset of hypoxia in two years. Contrary to our hypotheses, we found that fish and zooplankton did not change their horizontal and vertical distributions during periods and in locations with low DO levels. Consequently, the vertical overlap between fish and zooplankton did not change with DO. Fish feeding rates and the dominant zooplankton prey did not change with hypoxia events. The apparent resilience of fish to low DO in our system may be explained by decreased metabolic oxygen demand due to cool temperatures, increased availability and accessibility to their prey in low DO waters, or potential increase in predation risk at shallower depth. This study highlights the importance of both temperature and DO, instead of hypoxia threshold alone, in evaluating the impacts of hypoxia on pelagic communities.

  2. K-Anonymity Based Privacy Risk Budgeting System for Interactive Record Linkage

    Directory of Open Access Journals (Sweden)

    Hye-Chung Kum

    2017-04-01

    The k-anonymity based privacy risk budgeting system provides a mechanism where we can concretely reason about the tradeoff between the privacy risks due to information disclosed, accuracy gained, and biases reduced during interactive record linkage.

  3. Linkage and mapping analyses of the no glue egg gene Ng in the ...

    African Journals Online (AJOL)

    Jane

    2011-08-24

    Aug 24, 2011 ... The Ng gene was mapped at 28.0 of the silkworm classical genetic linkage group 12. (Xiang, 1995). In recent years, molecular biology has made consider- able progress ..... project (08080703017), China agriculture research.

  4. ECOTOXICOGENOMICS: LINKAGES BETWEEN EXPOSURE AND EFFECTS IN ASSESSING RISKS OF AQUATIC CONTAMINANTS TO FISH (JOURNAL ARTICLE)

    Science.gov (United States)

    Understanding the biological effects of exposures to chemicals in the environment relies on classical methods and emerging technologies in the areas of genomics, proteomics, and metabonomics. Linkages between the historical and newer toxicological tools are currently being devel...

  5. ECOTOXICOGENOMICS: LINKAGES BETWEEN EXPOSURE AND EFFECTS IN ASSESSING RISKS OF AQUATIC CONTAMINANTS TO FISH

    Science.gov (United States)

    Understanding the biological effects of exposures to chemicals in the environment relies on classical and emerging technologies in the areas of genomics, proteomics, and metabonomics. Linkages between the historical and newer toxicological tools are currently being developed in o...

  6. Balancing of linkages and robot manipulators advanced methods with illustrative examples

    CERN Document Server

    Arakelian, Vigen

    2015-01-01

    In this book advanced balancing methods for planar and spatial linkages, hand operated and automatic robot manipulators are presented. It is organized into three main parts and eight chapters. The main parts are the introduction to balancing, the balancing of linkages and the balancing of robot manipulators. The review of state-of-the-art literature including more than 500 references discloses particularities of shaking force/moment balancing and gravity compensation methods. Then new methods for balancing of linkages are considered. Methods provided in the second part of the book deal with the partial and complete shaking force/moment balancing of various linkages. A new field for balancing methods applications is the design of mechanical systems for fast manipulation. Special attention is given to the shaking force/moment balancing of robot manipulators. Gravity balancing methods are also discussed. The suggested balancing methods are illustrated by numerous examples.

  7. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...... represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

  8. Epidemiological Studies Persian Gulf War Illnesses Persian Gulf Women's Health Linkage Study

    National Research Council Canada - National Science Library

    Klemm, Rebecca

    1997-01-01

    The Persian Gulf Women's Health Linkage Study will provide baseline health and risk factor information to estimate the prevalence of selected health conditions, with an emphasis on reproductive health...

  9. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

  10. Managing the trade-public health linkage in defence of trade ...

    African Journals Online (AJOL)

    Managing the trade-public health linkage in defence of trade liberalisation and ... of United States-measures affecting the production and sale of clove cigarettes. ... Potchefstroom Electronic Law Journal/Potchefstroomse Elektroniese Regsblad.

  11. Male-biased recombination in odonates: insights from a linkage map ...

    Indian Academy of Sciences (India)

    2013-04-05

    Apr 5, 2013 ... Male-biased recombination in odonates: insights from a linkage map of the damselfly ... particular, odonates are emerging model systems for biotic effects of .... sex with highest variance in reproductive success (Trivers. 1988).

  12. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...

  13. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

    Science.gov (United States)

    Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

    2013-10-26

    Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed

  14. Linkage of the National Health Interview Survey to air quality data

    OpenAIRE

    Parker, JD; Kravets, N; Woodruff, TJ

    2012-01-01

    Objective This report describes the linkage between the National Health Interview Survey (NHIS) and air monitoring data from the U.S. Environmental Protection Agency (EPA). There have been few linkages of these data sources, partly because of restrictions on releasing geographic detail from NHIS on public-use files in order to protect participant confidentiality. Methods Pollution exposures for NHIS respondents were calculated by averaging the annual average exposure estimates from EPA air mo...

  15. Bronx Teens Connection's Clinic Linkage Model: Connecting Youth to Quality Sexual and Reproductive Health Care.

    Science.gov (United States)

    O'Uhuru, Deborah J; Santiago, Vivian; Murray, Lauren E; Travers, Madeline; Bedell, Jane F

    2017-03-01

    Teen pregnancy and birth rates in the Bronx have been higher than in New York City, representing a longstanding health disparity. The New York City Department of Health and Mental Hygiene implemented a community-wide, multicomponent intervention to reduce unintended teen pregnancy, the Bronx Teens Connection. The Bronx Teens Connection Clinic Linkage Model sought to increase teens' access to and use of sexual and reproductive health care by increasing community partner capacity to link neighborhood clinics to youth-serving organizations, including schools. The Bronx Teens Connection Clinic Linkage Model used needs assessments, delineated the criteria for linkages, clarified roles and responsibilities of partners and staff, established trainings to support the staff engaged in linkage activities, and developed and used process evaluation methods. Early results demonstrated the strength and feasibility of the model over a 4-year period, with 31 linkages developed and maintained, over 11,300 contacts between clinic health educators and teens completed, and increasing adherence to the Centers for Disease Control and Prevention-defined clinical best practices for adolescent reproductive health. For those eight clinics that were able to provide data, there was a 25% increase in the number of teen clients seen over 4 years. There are many factors that relate to an increase in clinic utilization; some of this increase may have been a result of the linkages between schools and clinics. The Bronx Teens Connection Clinic Linkage Model is an explicit framework for clinical and youth-serving organizations seeking to establish formal linkage relationships that may be useful for other municipalities or organizations. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  16. Using the Bootstrap to Account for Linkage Errors when Analysing Probabilistically Linked Categorical Data

    Directory of Open Access Journals (Sweden)

    Chipperfield James O.

    2015-09-01

    Full Text Available Record linkage is the act of bringing together records that are believed to belong to the same unit (e.g., person or business from two or more files. Record linkage is not an error-free process and can lead to linking a pair of records that do not belong to the same unit. This occurs because linking fields on the files, which ideally would uniquely identify each unit, are often imperfect. There has been an explosion of record linkage applications, particularly involving government agencies and in the field of health, yet there has been little work on making correct inference using such linked files. Naively treating a linked file as if it were linked without errors can lead to biased inferences. This article develops a method of making inferences for cross tabulated variables when record linkage is not an error-free process. In particular, it develops a parametric bootstrap approach to estimation which can accommodate the sophisticated probabilistic record linkage techniques that are widely used in practice (e.g., 1-1 linkage. The article demonstrates the effectiveness of this method in a simulation and in a real application.

  17. Quality of record linkage in a highly automated cancer registry that relies on encrypted identity data

    Directory of Open Access Journals (Sweden)

    Schmidtmann, Irene

    2016-06-01

    Full Text Available Objectives: In the absence of unique ID numbers, cancer and other registries in Germany and elsewhere rely on identity data to link records pertaining to the same patient. These data are often encrypted to ensure privacy. Some record linkage errors unavoidably occur. These errors were quantified for the cancer registry of North Rhine Westphalia which uses encrypted identity data. Methods: A sample of records was drawn from the registry, record linkage information was included. In parallel, plain text data for these records were retrieved to generate a gold standard. Record linkage error frequencies in the cancer registry were determined by comparison of the results of the routine linkage with the gold standard. Error rates were projected to larger registries.Results: In the sample studied, the homonym error rate was 0.015%; the synonym error rate was 0.2%. The F-measure was 0.9921. Projection to larger databases indicated that for a realistic development the homonym error rate will be around 1%, the synonym error rate around 2%.Conclusion: Observed error rates are low. This shows that effective methods to standardize and improve the quality of the input data have been implemented. This is crucial to keep error rates low when the registry’s database grows. The planned inclusion of unique health insurance numbers is likely to further improve record linkage quality. Cancer registration entirely based on electronic notification of records can process large amounts of data with high quality of record linkage.

  18. Mobile assemblies of Bennett linkages from four-crease origami patterns

    Science.gov (United States)

    Zhang, Xiao; Chen, Yan

    2018-02-01

    This paper deals with constructing mobile assemblies of Bennett linkages inspired by four-crease origami patterns. A transition technique has been proposed by taking the thick-panel form of an origami pattern as an intermediate bridge. A zero-thickness rigid origami pattern and its thick-panel form share the same sector angles and folding behaviours, while the thick-panel origami and the mobile assembly of linkages are kinematically equivalent with differences only in link profiles. Applying this transition technique to typical four-crease origami patterns, we have found that the Miura-ori and graded Miura-ori patterns lead to assemblies of Bennett linkages with identical link lengths. The supplementary-type origami patterns with different mountain-valley crease assignments correspond to different types of Bennett linkage assemblies with negative link lengths. And the identical linkage-type origami pattern generates a new mobile assembly. Hence, the transition technique offers a novel approach to constructing mobile assemblies of spatial linkages from origami patterns.

  19. Evidence for an asthma risk locus on chromosome Xp: a replication linkage study

    DEFF Research Database (Denmark)

    Brasch-Andersen, C; Møller, M U; Haagerup, A

    2008-01-01

    replication sample as used in the present study. The aim of the study was to replicate linkage to candidate regions for asthma in an independent Danish sample. METHODS: We performed a replication study investigating linkage to candidate regions for asthma on chromosomes 1p36.31-p36.21, 5q15-q23.2, 6p24.3-p22...... studies have been carried out the results are still conflicting and call for replication experiments. A Danish genome-wide scan has prior reported evidence for candidate regions for asthma susceptibility genes on chromosomes 1p, 5q, 6p, 12q and Xp. Linkage to chromosome 12q was later confirmed in the same.......3, and Xp22.31-p11.4 using additional markers in an independent set of 136 Danish asthmatic sib pair families. RESULTS: Nonparametric multipoint linkage analyses yielded suggestive evidence for linkage to asthma to chromosome Xp21.2 (MLS 2.92) but failed to replicate linkage to chromosomes 1p36.31-p36.21, 5...

  20. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

    Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

  1. Pulses, linkages, and boundaries of coupled aquatic-terrestrial ecosystems

    Science.gov (United States)

    Tockner, K.

    2009-04-01

    Riverine floodplains are linked ecosystems where terrestrial and aquatic habitats overlap, creating a zone where they interact, the aquatic-terrestrial interface. The interface or boundary between aquatic and terrestrial habitats is an area of transition, contact or separation; and connectivity between these habitats may be defined as the ease with which organisms, matter or energy traverse these boundaries. Coupling of aquatic and terrestrial systems generates intertwining food webs, and we may predict that coupled systems are more productive than separated ones. For example, riparian consumers (aquatic and terrestrial) have alternative prey items external to their respective habitats. Such subsidized assemblages occupy a significant higher trophic position than assemblages in unsubsidized areas. Further, cross-habitat linkages are often pulsed; and even small pulses of a driver (e.g. short-term increases in flow) can cause major resource pulses (i.e. emerging aquatic insects) that control the recipient community. For example, short-term additions of resources, simulating pulsed inputs of aquatic food to terrestrial systems, suggest that due to resource partitioning and temporal separation among riparian arthropod taxa the resource flux from the river to the riparian zone increases with increasing riparian consumer diversity. I will discuss the multiple transfer and transformation processes of matter and organisms across aquatic-terrestrial habitats. Key landscape elements along river corridors are vegetated islands that function as instream riparian areas. Results from Central European rivers demonstrate that islands are in general more natural than fringing riparian areas, contribute substantially to total ecotone length, and create diverse habitats in the aquatic and terrestrial realm. In braided rivers, vegetated islands are highly productive landscape elements compared to the adjacent aquatic area. However, aquatic habitats exhibit a much higher decomposition

  2. A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16

    NARCIS (Netherlands)

    Asherson, P.; Zhou, K.; Anney, R. J. L.; Franke, B.; Buitelaar, J.; Ebstein, R.; Gill, M.; Altink, M.; Arnold, R.; Boer, F.; Brookes, K.; Buschgens, C.; Butler, L.; Cambell, D.; Chen, W.; Christiansen, H.; Feldman, L.; Fleischman, K.; Fliers, E.; Howe-Forbes, R.; Goldfarb, A.; Heise, A.; Gabrieels, I.; Johansson, L.; Lubetzki, I.; Marco, R.; Medad, S.; Minderaa, R.; Mulas, F.; Müller, U.; Mulligan, A.; Neale, B.; Rijsdijk, F.; Rabin, K.; Rommelse, N.; Sethna, V.; Sorohan, J.; Uebel, H.; Psychogiou, L.; Weeks, A.; Barrett, R.; Xu, X.; Banaschewski, T.; Sonuga-Barke, E.; Eisenberg, J.; Manor, I.; Miranda, A.; Oades, R. D.; Roeyers, H.; Rothenberger, A.; Sergeant, J.; Steinhausen, H-C; Taylor, E.; Thompson, M.; Faraone, S. V.

    As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage

  3. A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16

    NARCIS (Netherlands)

    Asherson, P.; Zhou, K.; Anney, R. J. L.; Franke, B.; Buitelaar, J.; Ebstein, R.; Gill, M.; Altink, M.; Arnold, R.; Boer, F.; Brookes, K.; Buschgens, C.; Butler, L.; Cambell, D.; Chen, W.; Christiansen, H.; Feldman, L.; Fleischman, K.; Fliers, E.; Howe-Forbes, R.; Goldfarb, A.; Heise, A.; Gabriëls, I.; Johansson, L.; Lubetzki, I.; Marco, R.; Medad, S.; Minderaa, R.; Mulas, F.; Müller, U.; Mulligan, A.; Neale, B.; Rijsdijk, F.; Rabin, K.; Rommelse, N.; Sethna, V.; Sorohan, J.; Uebel, H.; Psychogiou, L.; Weeks, A.; Barrett, R.; Xu, X.; Banaschewski, T.; Sonuga-Barke, E.; Eisenberg, J.; Manor, I.; Miranda, A.; Oades, R. D.; Roeyers, H.; Rothenberger, A.; Sergeant, J.; Steinhausen, H.-C.; Taylor, E.; Thompson, M.; Faraone, S. V.

    2008-01-01

    As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage

  4. A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16.

    NARCIS (Netherlands)

    Asherson, P.; Zhou, K.; Anney, R.; Franke, B.; Buitelaar, J.K.; Ebstein, R.P.; Gill, M.; Altink, M.E.; Arnold, R.; Boer, F.; Brookes, K.; Buschgens, C.J.M.; Butler, L.; Cambell, D.; Chen, W.; Christiansen, H.; Feldman, L.B.; Fleischman, K.; Fliers, E.A.; Howe-Forbes, R.; Goldfarb, A.; Heise, A.; Gabriels, I.; Johansson, L.; Lubetzki, I.; Marco, R.; Medad, S.; Minderaa, R.B.; Mulas, F.; Muller, U.; Mulligan, A.; Neale, B.; Rijsdijk, F.; Rabin, K.; Lambregts-Rommelse, N.N.J.; Sethna, V.; Sorohan, J.; Uebel, H.; Psychogiou, L.; Weeks, A.; Barrett, R.; Xu, X.; Banaschewski, T.; Sonuga-Barke, E.J.S.; Eisenberg, J.; Manor, I.; Miranda, A.; Oades, R.D.; Roeyers, H.; Rothenberger, A.; Sergeant, J.A.; Steinhausen, H.C.; Taylor, E.; Thompson, M.; Faraone, S.V.

    2008-01-01

    As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage

  5. Perceived Barriers and Opportunities to the Linkage of Research ...

    African Journals Online (AJOL)

    Unknown User

    depression treatment: A Rumination Focused Cognitive ... Improvement in PTSD is a function of the improvement in rumination, social sharing and loneliness. ... Therapy (RFCBT) targeting rumination as key psychological process governing .... assess how beneficial is the disclosure of negative experience and emotions.

  6. Impact of the Hepatitis Testing and Linkage to Care (HepTLC) Initiative on Linkage to Care for Minnesota Refugees with Hepatitis B, 2012-2014.

    Science.gov (United States)

    Linde, Ann C; Sweet, Kristin A; Nelson, Kailey; Mamo, Blain; Chute, Sara M

    2016-01-01

    The Hepatitis Testing and Linkage to Care (HepTLC) initiative promoted viral hepatitis B and hepatitis C screening, posttest counseling, and linkage to care at 34 U.S. sites from 2012 to 2014. Through the HepTLC initiative, the Minnesota Department of Health (MDH) and clinic partners began conducting linkage-to-care activities with hepatitis B-positive refugees in October 2012. This intervention provided culturally appropriate support to link refugees to follow-up care for hepatitis B. MDH refugee health and viral hepatitis surveillance programs, along with clinics that screened newly arrived refugees in Hennepin and Ramsey counties in Minnesota, collaborated on the project, which took place from October 1, 2012, through September 30, 2014. Bilingual care navigators contacted refugees to provide education, make appointments, and arrange transportation. We compared the linkage-to-care rate for participants with the rates for refugees screened the year before project launch using a two-sample test of proportions. In the year preceding the project (October 2011 through September 2012), 87 newly arrived refugees had a positive hepatitis B surface antigen (HBsAg) test. Fifty-six (64%) refugees received follow-up care, 12 (14%) refugees did not receive follow-up care, and 19 (22%) refugees could not be located and had no record of follow-up care. During the project, 174 HBsAg-positive, newly arrived refugees were screened. Of those 174 refugees, 162 (93%) received follow-up care, seven (4%) did not receive follow-up care, and five (3%) could not be located and had no record of follow-up care. The one-year linkage-to-care rate for project participants (93%) was significantly higher than the rate for refugees screened the previous year (64%) (prefugees.

  7. Impact of the Hepatitis Testing and Linkage to Care (HepTLC) Initiative on Linkage to Care for Minnesota Refugees with Hepatitis B, 2012–2014

    Science.gov (United States)

    Sweet, Kristin A.; Nelson, Kailey; Mamo, Blain; Chute, Sara M.

    2016-01-01

    Objective The Hepatitis Testing and Linkage to Care (HepTLC) initiative promoted viral hepatitis B and hepatitis C screening, posttest counseling, and linkage to care at 34 U.S. sites from 2012 to 2014. Through the HepTLC initiative, the Minnesota Department of Health (MDH) and clinic partners began conducting linkage-to-care activities with hepatitis B-positive refugees in October 2012. This intervention provided culturally appropriate support to link refugees to follow-up care for hepatitis B. Methods MDH refugee health and viral hepatitis surveillance programs, along with clinics that screened newly arrived refugees in Hennepin and Ramsey counties in Minnesota, collaborated on the project, which took place from October 1, 2012, through September 30, 2014. Bilingual care navigators contacted refugees to provide education, make appointments, and arrange transportation. We compared the linkage-to-care rate for participants with the rates for refugees screened the year before project launch using a two-sample test of proportions. Results In the year preceding the project (October 2011 through September 2012), 87 newly arrived refugees had a positive hepatitis B surface antigen (HBsAg) test. Fifty-six (64%) refugees received follow-up care, 12 (14%) refugees did not receive follow-up care, and 19 (22%) refugees could not be located and had no record of follow-up care. During the project, 174 HBsAg-positive, newly arrived refugees were screened. Of those 174 refugees, 162 (93%) received follow-up care, seven (4%) did not receive follow-up care, and five (3%) could not be located and had no record of follow-up care. The one-year linkage-to-care rate for project participants (93%) was significantly higher than the rate for refugees screened the previous year (64%) (prefugees. PMID:27168670

  8. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  9. Production Cells in Construction: Considering Time, Space and Information Linkages to Seek Broader Implementations

    Directory of Open Access Journals (Sweden)

    Renato Nunes Mariz

    2013-01-01

    Full Text Available The use of production cells in manufacturing has achieved many benefits, motivating researchers to apply them in the construction environment. The aim of this research is to identify time, space, and information linkages in construction’s production cells applications, seeking opportunities for broader implementations. We adopted a literature review approach focusing on cases in the Brazilian construction sector that addressed cell applications. Subsequently, comparative tables of these publications were prepared, analyzing the consideration of time, space, and information linkages, as well as identified results. The article pointed out that there is a gap in publications that address the application of a production cell in almost all construction flows, except the job site flow, reflecting the tendency of most companies of applying lean concepts firstly in physical flows. By analyzing these aspects (group of features that enhance the use of the cell, it was found that “material flow and pull systems” and “operators interaction” were the aspects most often considered, but mostly partially. Few cases reported the use of “flexibility” and “equipment maintenance”. No case reported comprehensive considerations of the three important linkages of time, space, and information. Space was the linkage better considered compared to time and information linkages. Lead time reduction, cost savings and increased productivity were among the greatest benefits reported from the applications of production cells. There is also a positive correlation between the linkages coverage and the number of benefits obtained. Further research is suggested in order to investigate the results of a more comprehensive application considering all linkages.

  10. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    Science.gov (United States)

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  11. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae

    Directory of Open Access Journals (Sweden)

    Kakioka Ryo

    2013-01-01

    Full Text Available Abstract Background The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus Gnathopogon (Cyprinidae for comparative genomics with the zebrafish Danio rerio (a member of the same family as gudgeons and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of Gnathopogon. Results We constructed the first genetic linkage map of Gnathopogon using a 198 F2 interspecific cross between two closely related species in Japan: river-dwelling Gnathopogon elongatus and lake-dwelling Gnathopogon caerulescens. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD. Synteny and collinearity were extensively conserved between Gnathopogon and zebrafish. Conclusions The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.

  12. Energy for sustainable development in India: Linkages and strategic direction

    International Nuclear Information System (INIS)

    Srivastava, Leena; Rehman, I.H.

    2006-01-01

    In recent times the two major international endorsements of the elements of sustainable development the Millennium Development Goals (Mags) and the World Summit on Sustainable Development (Wsso), have recognized universal access to energy as an important goal. In India, with a population of over a 1000 million people, it is estimated that a mere 43.5% of the households have access to electricity. The choices that the country makes towards energizing the remaining population will have a significant impact on other Sustainable Development parameters such as agriculture, water, health, and even biodiversity. India has set itself a target, going beyond the Mags, of energizing all households by the year 2012. In view of the differentiated responsibilities of the various ministries to the Government of India, the strategy for reaching this target may not address itself to the larger development goals

  13. Large-scale linkage analysis of 1302 affected relative pairs with rheumatoid arthritis

    Science.gov (United States)

    Hamshere, Marian L; Segurado, Ricardo; Moskvina, Valentina; Nikolov, Ivan; Glaser, Beate; Holmans, Peter A

    2007-01-01

    Rheumatoid arthritis is the most common systematic autoimmune disease and its etiology is believed to have both strong genetic and environmental components. We demonstrate the utility of including genetic and clinical phenotypes as covariates within a linkage analysis framework to search for rheumatoid arthritis susceptibility loci. The raw genotypes of 1302 affected relative pairs were combined from four large family-based samples (North American Rheumatoid Arthritis Consortium, United Kingdom, European Consortium on Rheumatoid Arthritis Families, and Canada). The familiality of the clinical phenotypes was assessed. The affected relative pairs were subjected to autosomal multipoint affected relative-pair linkage analysis. Covariates were included in the linkage analysis to take account of heterogeneity within the sample. Evidence of familiality was observed with age at onset (p << 0.001) and rheumatoid factor (RF) IgM (p << 0.001), but not definite erosions (p = 0.21). Genome-wide significant evidence for linkage was observed on chromosome 6. Genome-wide suggestive evidence for linkage was observed on chromosomes 13 and 20 when conditioning on age at onset, chromosome 15 conditional on gender, and chromosome 19 conditional on RF IgM after allowing for multiple testing of covariates. PMID:18466440

  14. Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus).

    Science.gov (United States)

    Portis, E; Mauromicale, G; Mauro, R; Acquadro, A; Scaglione, D; Lanteri, S

    2009-12-01

    The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.

  15. Video-conferencing Telehealth Linkage attempts to Schools to Facilitate Mental Health Consultation.

    Science.gov (United States)

    McLennan, John D

    2018-04-01

    Telehealth to schools may be a strategic approach to expand child mental health service delivery, however, there are only a few published examples. This report describes video-conferencing telehealth linkage attempts to schools to facilitate mental health consultation. A series of synchronous video-conferencing linkage strategies were attempted to connect a mental health consultation service to multiple schools in a Canadian setting. Consultation to support the implementation of the Daily Report Card, for students with attentional and behavioural problems, was the core content of this pilot linkage attempt. Synchronous video conference consultations were successfully delivered to six elementary schools across three school districts. Two of three linkage strategies were functional. One used existing health centre-based telehealth units to connect to school-based dedicated tablets with a video collaboration app and reliance on existing school Wi-Fi. A second used existing laptops in both the health and school system linked through a communication platform. A third connection, using 3G/4G hotspots to obviate the need to access school Wi-Fi, was deemed too expensive in this setting. The potential to use existing computer hardware to connect mental health providers and schools could facilitate scale-up. However, it is unknown whether mental health systems and school sectors will invest in such linkages and reorganize core mental health services to be delivered in this way.

  16. African American church-based HIV testing and linkage to care: assets, challenges and needs.

    Science.gov (United States)

    Stewart, Jennifer M; Thompson, Keitra; Rogers, Christopher

    2016-01-01

    The US National HIV AIDS strategy promotes the use of faith communities to lessen the burden of HIV in African American communities. One specific strategy presented is the use of these non-traditional venues for HIV testing and co-location of services. African American churches can be at the forefront of this endeavour through the provision of HIV testing and linkage to care. However, there are few interventions to promote the churches' involvement in both HIV testing and linkage to care. We conducted 4 focus groups (n = 39 participants), 4 interviews and 116 surveys in a mixed-methods study to examine the feasibility of a church-based HIV testing and linkage to care intervention in Philadelphia, PA, USA. Our objectives were to examine: (1) available assets, (2) challenges and barriers and (3) needs associated with church-based HIV testing and linkage to care. Analyses revealed several factors of importance, including the role of the church as an access point for testing in low-income neighbourhoods, challenges in openly discussing the relationship between sexuality and HIV, and buy-in among church leadership. These findings can support intervention development and necessitate situating African American church-based HIV testing and linkage to care interventions within a multi-level framework.

  17. Linkage studies on Gilles de la Tourette syndrome: What is the strategy of choice?

    Energy Technology Data Exchange (ETDEWEB)

    Heutink, P.; Wetering, J.M. van de; Oostra, B.A. [Erasmus Univ. Rotterdam (Netherlands)] [and others

    1995-08-01

    For a linkage study it is important to ascertain family material that is sufficiently informative. The statistical power of linkage sample can be determined via computer simulation. For complex traits uncertain parameters such as incomplete penetrance, frequency of phenocopies, gene frequency and variable expression have to be taken into account. One can either include only the most severe phenotype in the analysis or apply multiple linkage tests for a gradually broadened disease phenotype. Gilles de la Tourette syndrome (GTS) is a chronic neurological disorder characterized by multiple, intermittent motor and vocal tics. Segregation analyses suggests that GTS and milder phenotypes are caused by a single dominant gene. We report here the results of an extensive simulation study on a large set of families. We compared the effectiveness of linkage tests with only the GTS phenotype versus multiple tests that included various milder phenotypes and different gene frequencies. The scenario of multiple tests yielded superior power. Our results show that computer simulation can indicate the strategy of choice in linkage studies of multiple, complex phenotypes. 33 refs., 2 figs., 3 tabs.

  18. Genomewide Linkage Scan for Diabetic Renal Failure and Albuminuria: The FIND Study

    Science.gov (United States)

    Igo, Robert P.; Iyengar, Sudha K.; Nicholas, Susanne B.; Goddard, Katrina A.B.; Langefeld, Carl D.; Hanson, Robert L.; Duggirala, Ravindranath; Divers, Jasmin; Abboud, Hanna; Adler, Sharon G.; Arar, Nedal H.; Horvath, Amanda; Elston, Robert C.; Bowden, Donald W.; Guo, Xiuqing; Ipp, Eli; Kao, W.H. Linda; Kimmel, Paul L.; Knowler, William C.; Meoni, Lucy A.; Molineros, Julio; Nelson, Robert G.; Pahl, Madeline V.; Parekh, Rulan S.; Rasooly, Rebekah S.; Schelling, Jeffrey R.; Shah, Vallabh O.; Smith, Michael W.; Winkler, Cheryl A.; Zager, Philip G.; Sedor, John R.; Freedman, Barry I.

    2011-01-01

    Background Diabetic nephropathy (DN) is a leading cause of mortality and morbidity in patients with type 1 and type 2 diabetes. The multicenter FIND consortium aims to identify genes for DN and its associated quantitative traits, e.g. the urine albumin:creatinine ratio (ACR). Herein, the results of whole-genome linkage analysis and a sparse association scan for ACR and a dichotomous DN phenotype are reported in diabetic individuals. Methods A genomewide scan comprising more than 5,500 autosomal single nucleotide polymorphism markers (average spacing of 0.6 cM) was performed on 1,235 nuclear and extended pedigrees (3,972 diabetic participants) ascertained for DN from African-American (AA), American-Indian (AI), European-American (EA) and Mexican-American (MA) populations. Results Strong evidence for linkage to DN was detected on chromosome 6p (p = 8.0 × 10−5, LOD = 3.09) in EA families as well as suggestive evidence for linkage to chromosome 7p in AI families. Regions on chromosomes 3p in AA, 7q in EA, 16q in AA and 22q in MA displayed suggestive evidence of linkage for urine ACR. The linkage peak on chromosome 22q overlaps the MYH9/APOL1 gene region, previously implicated in AA diabetic and nondiabetic nephropathies. Conclusion These results strengthen the evidence for previously identified genomic regions and implicate several novel loci potentially involved in the pathogenesis of DN. PMID:21454968

  19. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  20. Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation

    Directory of Open Access Journals (Sweden)

    Marta Niedzicka

    2017-07-01

    Full Text Available Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker. It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

  1. Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond-Paul

    2000-07-01

    Full Text Available Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57. This study allowed us, (i, to anchor all linkage groups on sheep chromosomes, (ii, to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii, to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

  2. Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

    Directory of Open Access Journals (Sweden)

    Shashi N. Goonetilleke

    2018-01-01

    Full Text Available In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb, application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

  3. Irish study of high-density Schizophrenia families: Field methods and power to detect linkage

    Energy Technology Data Exchange (ETDEWEB)

    Kendler, K.S.; Straub, R.E.; MacLean, C.J. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

    1996-04-09

    Large samples of multiplex pedigrees will probably be needed to detect susceptibility loci for schizophrenia by linkage analysis. Standardized ascertainment of such pedigrees from culturally and ethnically homogeneous populations may improve the probability of detection and replication of linkage. The Irish Study of High-Density Schizophrenia Families (ISHDSF) was formed from standardized ascertainment of multiplex schizophrenia families in 39 psychiatric facilities covering over 90% of the population in Ireland and Northern Ireland. We here describe a phenotypic sample and a subset thereof, the linkage sample. Individuals were included in the phenotypic sample if adequate diagnostic information, based on personal interview and/or hospital record, was available. Only individuals with available DNA were included in the linkage sample. Inclusion of a pedigree into the phenotypic sample required at least two first, second, or third degree relatives with non-affective psychosis (NAP), one of whom had schizophrenia (S) or poor-outcome schizoaffective disorder (PO-SAD). Entry into the linkage sample required DNA samples on at least two individuals with NAP, of whom at least one had S or PO-SAD. Affection was defined by narrow, intermediate, and broad criteria. 75 refs., 6 tabs.

  4. High-Resolution Genome-Wide Linkage Mapping Identifies Susceptibility Loci for BMI in the Chinese Population

    DEFF Research Database (Denmark)

    Zhang, Dong Feng; Pang, Zengchang; Li, Shuxia

    2012-01-01

    The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic...... linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis...... in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin...

  5. Cardiovascular disease treatment among patients with severe mental illness: a data linkage study between primary and secondary care.

    Science.gov (United States)

    Woodhead, Charlotte; Ashworth, Mark; Broadbent, Matthew; Callard, Felicity; Hotopf, Matthew; Schofield, Peter; Soncul, Murat; Stewart, Robert J; Henderson, Max J

    2016-06-01

    Suboptimal treatment of cardiovascular diseases (CVD) among patients with severe mental illness (SMI) may contribute to physical health disparities. To identify SMI characteristics associated with meeting CVD treatment and prevention guidelines. Population-based electronic health record database linkage between primary care and the sole provider of secondary mental health care services in south east London, UK. Cardiovascular disease prevalence, risk factor recording, and Quality and Outcomes Framework (QOF) clinical target achievement were compared among 4056 primary care patients with SMI whose records were linked to secondary healthcare records and 270 669 patients without SMI who were not known to secondary care psychiatric services, using multivariate logistic regression modelling. Data available from secondary care records were then used to identify SMI characteristics associated with QOF clinical target achievement. Patients with SMI and with coronary heart disease and heart failure experienced reduced prescribing of beta blockers and angiotensin-converting enzyme inhibitor/angiotensin receptor blockers (ACEI/ARB). A diagnosis of schizophrenia, being identified with any indicator of risk or illness severity, and being prescribed with depot injectable antipsychotic medication was associated with the lowest likelihood of prescribing. Linking primary and secondary care data allows the identification of patients with SMI most at risk of undertreatment for physical health problems. © British Journal of General Practice 2016.

  6. Linkage of anthropogenic aerosol to clouds and climate

    International Nuclear Information System (INIS)

    Hudson, J.G.

    1992-01-01

    During the first year of this project equipment was built to obtain direct droplet measurement data from a mobile platform in fog (or mountain impacted stratum) and to characterize CCN according to particle volatility (thermal processing). Since the start date, July 15, 1990, was during the California stratus season and it was necessary to complete the construction of equipment and allow time before a field project it was not possible to begin field work until the summer of 1991. This report discusses surface measurements made in 1991 and 1992 as well as the SEAHUNT (Shiptrail Evolution Above High Updraft Naval Targets) Project and the ASTEX (Atlantic Stratocumulus Transition Experiment) Project

  7. High-throughput respirometric assay identifies predictive toxicophore of mitochondrial injury

    Energy Technology Data Exchange (ETDEWEB)

    Wills, Lauren P. [MitoHealth Inc., Charleston, SC 29403 (United States); Beeson, Gyda C.; Trager, Richard E.; Lindsey, Christopher C. [Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425 (United States); Beeson, Craig C. [MitoHealth Inc., Charleston, SC 29403 (United States); Peterson, Yuri K. [Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425 (United States); Schnellmann, Rick G., E-mail: schnell@musc.edu [Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425 (United States); Ralph H. Johnson VA Medical Center, Charleston, SC 29401 (United States)

    2013-10-15

    Many environmental chemicals and drugs negatively affect human health through deleterious effects on mitochondrial function. Currently there is no chemical library of mitochondrial toxicants, and no reliable methods for predicting mitochondrial toxicity. We hypothesized that discrete toxicophores defined by distinct chemical entities can identify previously unidentified mitochondrial toxicants. We used a respirometric assay to screen 1760 compounds (5 μM) from the LOPAC and ChemBridge DIVERSet libraries. Thirty-one of the assayed compounds decreased uncoupled respiration, a stress test for mitochondrial dysfunction, prior to a decrease in cell viability and reduced the oxygen consumption rate in isolated mitochondria. The mitochondrial toxicants were grouped by chemical similarity and two clusters containing four compounds each were identified. Cheminformatic analysis of one of the clusters identified previously uncharacterized mitochondrial toxicants from the ChemBridge DIVERSet. This approach will enable the identification of mitochondrial toxicants and advance the prediction of mitochondrial toxicity for both drug discovery and risk assessment. - Highlights: • Respirometric assay conducted in RPTC to create mitochondrial toxicant database. • Chemically similar mitochondrial toxicants aligned as mitochondrial toxicophores • Mitochondrial toxicophore identifies five novel mitochondrial toxicants.

  8. High-throughput respirometric assay identifies predictive toxicophore of mitochondrial injury

    International Nuclear Information System (INIS)

    Wills, Lauren P.; Beeson, Gyda C.; Trager, Richard E.; Lindsey, Christopher C.; Beeson, Craig C.; Peterson, Yuri K.; Schnellmann, Rick G.

    2013-01-01

    Many environmental chemicals and drugs negatively affect human health through deleterious effects on mitochondrial function. Currently there is no chemical library of mitochondrial toxicants, and no reliable methods for predicting mitochondrial toxicity. We hypothesized that discrete toxicophores defined by distinct chemical entities can identify previously unidentified mitochondrial toxicants. We used a respirometric assay to screen 1760 compounds (5 μM) from the LOPAC and ChemBridge DIVERSet libraries. Thirty-one of the assayed compounds decreased uncoupled respiration, a stress test for mitochondrial dysfunction, prior to a decrease in cell viability and reduced the oxygen consumption rate in isolated mitochondria. The mitochondrial toxicants were grouped by chemical similarity and two clusters containing four compounds each were identified. Cheminformatic analysis of one of the clusters identified previously uncharacterized mitochondrial toxicants from the ChemBridge DIVERSet. This approach will enable the identification of mitochondrial toxicants and advance the prediction of mitochondrial toxicity for both drug discovery and risk assessment. - Highlights: • Respirometric assay conducted in RPTC to create mitochondrial toxicant database. • Chemically similar mitochondrial toxicants aligned as mitochondrial toxicophores • Mitochondrial toxicophore identifies five novel mitochondrial toxicants

  9. Is Theory Applied in Practice?A Stady of Linkage between Swedish MNC's Strategies and Húman Resource Staffing Policies

    OpenAIRE

    Ivinger, Linnea; Lindvetter, Lisa

    2006-01-01

    Theory suggests that there is a linkage between strategies and human resource staffing policies. Our aim with the dissertation was to test if such a linkage could be proven in Swedish MNCs. Also, indications spoke for ethnocentric tendencies in MNCs. We wanted to test if this was the reality for Swedish companies. In order to test the linkage we had to categorise the companies’ strategies and human resource staffing policies. By a survey we concluded that there was not full consistency in the...

  10. Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

    Science.gov (United States)

    Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

    2015-05-22

    Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

  11. Biomechanical design of escalading lower limb exoskeleton with novel linkage joints.

    Science.gov (United States)

    Zhang, Guoan; Liu, Gangfeng; Ma, Sun; Wang, Tianshuo; Zhao, Jie; Zhu, Yanhe

    2017-07-20

    In this paper, an obstacle-surmounting-enabled lower limb exoskeleton with novel linkage joints that perfectly mimicked human motions was proposed. Currently, most lower exoskeletons that use linear actuators have a direct connection between the wearer and the controlled part. Compared to the existing joints, the novel linkage joint not only fitted better into compact chasis, but also provided greater torque when the joint was at a large bend angle. As a result, it extended the angle range of joint peak torque output. With any given power, torque was prioritized over rotational speed, because instead of rotational speed, sufficiency of torque is the premise for most joint actions. With insufficient torque, the exoskeleton will be a burden instead of enhancement to its wearer. With optimized distribution of torque among the joints, the novel linkage method may contribute to easier exoskeleton movements.

  12. Definitive evidence for Ufd2-catalyzed elongation of the ubiquitin chain through Lys48 linkage

    International Nuclear Information System (INIS)

    Saeki, Yasushi; Tayama, Yoko; Toh-e, Akio; Yokosawa, Hideyoshi

    2004-01-01

    Saccharomyces cerevisiae Ufd2 is a ubiquitin chain elongation factor in the ubiquitin fusion degradation (UFD) pathway and functions in stress tolerance. A recent study has suggested that the mammalian Ufd2 homologue UFD2a catalyzes formation of Lys27- and Lys33-linked polyubiquitin chains rather than the Lys48-linked chain, but the linkage type of the polyubiquitin chain formed by yeast Ufd2 remains unclear. To determine the property of Ufd2, we reconstituted the UFD pathway using purified enzymes from yeast. Direct determination of the ubiquitin chain linkage type in polyubiquitinated UFD substrates by MALDI-TOF mass spectrometry revealed that Ufd2 catalyzes elongation of the ubiquitin chain through Lys48 linkage

  13. Revealing the fate of the phenylcoumaran linkage during lignin oxidation reactions.

    Science.gov (United States)

    Lahive, Ciaran W; Lancefield, Christopher S; Codina, Anna; Kamer, Paul C J; Westwood, Nicholas J

    2018-03-14

    The fate of most lignin linkages, other than the β-O-4, under selective oxidation conditions is largely unknown. In this work we use advanced β-5 lignin model compounds to identify the fate of phenylcoumaran units in a softwood lignin during oxidation with DDQ. By using model compounds combined with detailed characterisation of the oxidised lignin polymer using HSQC and HMBC NMR we show that phenylcoumarones are a major product, and therefore constitute a novel non-native β-5 linkage in oxidised lignins. Additionally, the reactivity of these units in lignin led us to further investigate their connectivity in lignin, showing that they are found as both phenolic and etherified units. The findings and approach developed here will help improve the efficiency of selective oxidative lignin depolymerisation processes, particularly those aimed at the upgrading of softwood lignin in which phenylcoumarans are a major linkage.

  14. The Water Framework Directive and the Strategic Environmental Assessment Directive: Exploring the linkages

    International Nuclear Information System (INIS)

    Carter, Jeremy; Howe, Joe

    2006-01-01

    This paper highlights, explores and reflects on the linkages between the Water Framework Directive (WFD) and the Strategic Environmental Assessment (SEA) Directive. The assessment of river basin management plans (RBMPs), the key procedural linkage between the two Directives, is addressed. The assessment of other actions affecting the water environment, particularly land use plans, could also aid the achievement of the aims of the Water Framework Directive. As water quality is related intimately to the development and use of land, this significant issue is considered. There are numerous potential benefits that could arise from exploring the linkages between these two pieces of EU environmental legislation. These are highlighted, and include encouraging resource savings, generating a holistic approach to water resource management and ultimately the promotion of more sustainable forms of development

  15. Name segmentation using hidden Markov models and its application in record linkage

    Directory of Open Access Journals (Sweden)

    Rita de Cassia Braga Gonçalves

    2014-10-01

    Full Text Available This study aimed to evaluate the use of hidden Markov models (HMM for the segmentation of person names and its influence on record linkage. A HMM was applied to the segmentation of patient’s and mother’s names in the databases of the Mortality Information System (SIM, Information Subsystem for High Complexity Procedures (APAC, and Hospital Information System (AIH. A sample of 200 patients from each database was segmented via HMM, and the results were compared to those from segmentation by the authors. The APAC-SIM and APAC-AIH databases were linked using three different segmentation strategies, one of which used HMM. Conformity of segmentation via HMM varied from 90.5% to 92.5%. The different segmentation strategies yielded similar results in the record linkage process. This study suggests that segmentation of Brazilian names via HMM is no more effective than traditional segmentation approaches in the linkage process.

  16. Genome-wide linkage scan for maximum and length-dependent knee muscle strength in young men: significant evidence for linkage at chromosome 14q24.3.

    Science.gov (United States)

    De Mars, G; Windelinckx, A; Huygens, W; Peeters, M W; Beunen, G P; Aerssens, J; Vlietinck, R; Thomis, M A I

    2008-05-01

    Maintenance of high muscular fitness is positively related to bone health, functionality in daily life and increasing insulin sensitivity, and negatively related to falls and fractures, morbidity and mortality. Heritability of muscle strength phenotypes ranges between 31% and 95%, but little is known about the identity of the genes underlying this complex trait. As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to muscle and bone cross-sectional area, isometric knee flexion and extension torque, and torque-length relationship for knee flexors and extensors. In total, 283 informative male siblings (17-36 years old), belonging to 105 families, were used to conduct a genome-wide SNP-based multipoint linkage analysis. The strongest evidence for linkage was found for the torque-length relationship of the knee flexors at 14q24.3 (LOD = 4.09; p<10(-5)). Suggestive evidence for linkage was found at 14q32.2 (LOD = 3.00; P = 0.005) for muscle and bone cross-sectional area, at 2p24.2 (LOD = 2.57; p = 0.01) for isometric knee torque at 30 degrees flexion, at 1q21.3, 2p23.3 and 18q11.2 (LOD = 2.33, 2.69 and 2.21; p<10(-4) for all) for the torque-length relationship of the knee extensors and at 18p11.31 (LOD = 2.39; p = 0.0004) for muscle-mass adjusted isometric knee extension torque. We conclude that many small contributing genes rather than a few important genes are involved in causing variation in different underlying phenotypes of muscle strength. Furthermore, some overlap in promising genomic regions were identified among different strength phenotypes.

  17. HIV-1 transmission linkage in an HIV-1 prevention clinical trial

    Energy Technology Data Exchange (ETDEWEB)

    Leitner, Thomas [Los Alamos National Laboratory; Campbell, Mary S [UNIV OF WASHINGTON; Mullins, James I [UNIV OF WASHINGTON; Hughes, James P [UNIV OF WASHINGTON; Wong, Kim G [UNIV OF WASHINGTON; Raugi, Dana N [UNIV OF WASHINGTON; Scrensen, Stefanie [UNIV OF WASHINGTON

    2009-01-01

    HIV-1 sequencing has been used extensively in epidemiologic and forensic studies to investigate patterns of HIV-1 transmission. However, the criteria for establishing genetic linkage between HIV-1 strains in HIV-1 prevention trials have not been formalized. The Partners in Prevention HSV/HIV Transmission Study (ClinicaITrials.gov NCT00194519) enrolled 3408 HIV-1 serodiscordant heterosexual African couples to determine the efficacy of genital herpes suppression with acyclovir in reducing HIV-1 transmission. The trial analysis required laboratory confirmation of HIV-1 linkage between enrolled partners in couples in which seroconversion occurred. Here we describe the process and results from HIV-1 sequencing studies used to perform transmission linkage determination in this clinical trial. Consensus Sanger sequencing of env (C2-V3-C3) and gag (p17-p24) genes was performed on plasma HIV-1 RNA from both partners within 3 months of seroconversion; env single molecule or pyrosequencing was also performed in some cases. For linkage, we required monophyletic clustering between HIV-1 sequences in the transmitting and seroconverting partners, and developed a Bayesian algorithm using genetic distances to evaluate the posterior probability of linkage of participants sequences. Adjudicators classified transmissions as linked, unlinked, or indeterminate. Among 151 seroconversion events, we found 108 (71.5%) linked, 40 (26.5%) unlinked, and 3 (2.0%) to have indeterminate transmissions. Nine (8.3%) were linked by consensus gag sequencing only and 8 (7.4%) required deep sequencing of env. In this first use of HIV-1 sequencing to establish endpoints in a large clinical trial, more than one-fourth of transmissions were unlinked to the enrolled partner, illustrating the relevance of these methods in the design of future HIV-1 prevention trials in serodiscordant couples. A hierarchy of sequencing techniques, analysis methods, and expert adjudication contributed to the linkage

  18. PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2014-07-01

    Full Text Available Ubiquitin (Ub can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

  19. PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

    Science.gov (United States)

    Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

    2014-07-01

    Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

  20. Meta-analysis of 32 genome-wide linkage studies of schizophrenia

    Science.gov (United States)

    Ng, MYM; Levinson, DF; Faraone, SV; Suarez, BK; DeLisi, LE; Arinami, T; Riley, B; Paunio, T; Pulver, AE; Irmansyah; Holmans, PA; Escamilla, M; Wildenauer, DB; Williams, NM; Laurent, C; Mowry, BJ; Brzustowicz, LM; Maziade, M; Sklar, P; Garver, DL; Abecasis, GR; Lerer, B; Fallin, MD; Gurling, HMD; Gejman, PV; Lindholm, E; Moises, HW; Byerley, W; Wijsman, EM; Forabosco, P; Tsuang, MT; Hwu, H-G; Okazaki, Y; Kendler, KS; Wormley, B; Fanous, A; Walsh, D; O’Neill, FA; Peltonen, L; Nestadt, G; Lasseter, VK; Liang, KY; Papadimitriou, GM; Dikeos, DG; Schwab, SG; Owen, MJ; O’Donovan, MC; Norton, N; Hare, E; Raventos, H; Nicolini, H; Albus, M; Maier, W; Nimgaonkar, VL; Terenius, L; Mallet, J; Jay, M; Godard, S; Nertney, D; Alexander, M; Crowe, RR; Silverman, JM; Bassett, AS; Roy, M-A; Mérette, C; Pato, CN; Pato, MT; Roos, J Louw; Kohn, Y; Amann-Zalcenstein, D; Kalsi, G; McQuillin, A; Curtis, D; Brynjolfson, J; Sigmundsson, T; Petursson, H; Sanders, AR; Duan, J; Jazin, E; Myles-Worsley, M; Karayiorgou, M; Lewis, CM

    2009-01-01

    A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (PSR) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for ‘aggregate’ genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies. PMID:19349958

  1. Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial.

    Directory of Open Access Journals (Sweden)

    Mary S Campbell

    2011-03-01

    Full Text Available Characterization of viruses in HIV-1 transmission pairs will help identify biological determinants of infectiousness and evaluate candidate interventions to reduce transmission. Although HIV-1 sequencing is frequently used to substantiate linkage between newly HIV-1 infected individuals and their sexual partners in epidemiologic and forensic studies, viral sequencing is seldom applied in HIV-1 prevention trials. The Partners in Prevention HSV/HIV Transmission Study (ClinicalTrials.gov #NCT00194519 was a prospective randomized placebo-controlled trial that enrolled serodiscordant heterosexual couples to determine the efficacy of genital herpes suppression in reducing HIV-1 transmission; as part of the study analysis, HIV-1 sequences were examined for genetic linkage between seroconverters and their enrolled partners.We obtained partial consensus HIV-1 env and gag sequences from blood plasma for 151 transmission pairs and performed deep sequencing of env in some cases. We analyzed sequences with phylogenetic techniques and developed a Bayesian algorithm to evaluate the probability of linkage. For linkage, we required monophyletic clustering between enrolled partners' sequences and a Bayesian posterior probability of ≥ 50%. Adjudicators classified each seroconversion, finding 108 (71.5% linked, 40 (26.5% unlinked, and 3 (2.0% indeterminate transmissions, with linkage determined by consensus env sequencing in 91 (84%. Male seroconverters had a higher frequency of unlinked transmissions than female seroconverters. The likelihood of transmission from the enrolled partner was related to time on study, with increasing numbers of unlinked transmissions occurring after longer observation periods. Finally, baseline viral load was found to be significantly higher among linked transmitters.In this first use of HIV-1 sequencing to establish endpoints in a large clinical trial, more than one-fourth of transmissions were unlinked to the enrolled partner

  2. Validation of de-identified record linkage to ascertain hospital admissions in a cohort study

    Directory of Open Access Journals (Sweden)

    English Dallas R

    2011-04-01

    Full Text Available Abstract Background Cohort studies can provide valuable evidence of cause and effect relationships but are subject to loss of participants over time, limiting the validity of findings. Computerised record linkage offers a passive and ongoing method of obtaining health outcomes from existing routinely collected data sources. However, the quality of record linkage is reliant upon the availability and accuracy of common identifying variables. We sought to develop and validate a method for linking a cohort study to a state-wide hospital admissions dataset with limited availability of unique identifying variables. Methods A sample of 2000 participants from a cohort study (n = 41 514 was linked to a state-wide hospitalisations dataset in Victoria, Australia using the national health insurance (Medicare number and demographic data as identifying variables. Availability of the health insurance number was limited in both datasets; therefore linkage was undertaken both with and without use of this number and agreement tested between both algorithms. Sensitivity was calculated for a sub-sample of 101 participants with a hospital admission confirmed by medical record review. Results Of the 2000 study participants, 85% were found to have a record in the hospitalisations dataset when the national health insurance number and sex were used as linkage variables and 92% when demographic details only were used. When agreement between the two methods was tested the disagreement fraction was 9%, mainly due to "false positive" links when demographic details only were used. A final algorithm that used multiple combinations of identifying variables resulted in a match proportion of 87%. Sensitivity of this final linkage was 95%. Conclusions High quality record linkage of cohort data with a hospitalisations dataset that has limited identifiers can be achieved using combinations of a national health insurance number and demographic data as identifying variables.

  3. Elite capture and the development of natural resource linkages in Mozambique

    DEFF Research Database (Denmark)

    Buur, Lars; Monjane, Celso Marcos

    2017-01-01

    for a more fair distribution of opportunities for local firms to gain from large-scale natural resource investments and for learning and spillover effects to other parts of the economy. In a longer term perspective, it is a potential key source of economic transformation towards higher value added activities......This chapter explores these broader processes from the perspective of linkage creation in Mozambique related to mega-projects in natural resource extraction and development from a political economy perspective. From a resource fairness perspective, linkage creation is essential as it allows...

  4. Corporate identity, customer orientation and performance of SMEs: Exploring the linkages

    Directory of Open Access Journals (Sweden)

    Upendra Kumar Maurya

    2015-09-01

    Full Text Available This research aims to explore the impact of corporate identity (CI on performance in B2C small and medium enterprises (SMEs in food processing, with varying degrees of customer orientation (CO. The research is embedded in the positivistic paradigm. Based on a literature review, a conceptual model (consisting of five hypotheses has been tested with 102 samples using PLS-SEM tool. This study establishes the mediating role of CO on the CI and performance linkage, it provides empirical evidence to CI and performance linkage, and makes an incremental contribution by extension of theory of CI and CO in the given context.

  5. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii

    Directory of Open Access Journals (Sweden)

    Patel Hardip R

    2011-08-01

    Full Text Available Abstract Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH, (b End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby

  6. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii).

    Science.gov (United States)

    Wang, Chenwei; Webley, Lee; Wei, Ke-jun; Wakefield, Matthew J; Patel, Hardip R; Deakin, Janine E; Alsop, Amber; Marshall Graves, Jennifer A; Cooper, Desmond W; Nicholas, Frank W; Zenger, Kyall R

    2011-08-19

    The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first

  7. Condition of the centers of linkage of serum albumin in cancer gynecological patients at beam therapy

    International Nuclear Information System (INIS)

    Malenchenko, A.F.; Belyakovskij, V.N.; Lukovskaya, N.D.; Prigozhaya, T.I.; Stasenkova, S.V.

    2009-01-01

    With the use of the method of fluorescent probes the condition of the centers of linkage of serum albumin in healthy women and in the cancer patients, passing a course of beam therapy, is analyzed at different modes. It is shown that general concentration of albumin in healthy persons and cancer patients are in the limits of normal values, however parameters of effective concentration of albumin, reserve of albumin linkage and toxicity index of patients statistically, for certain, differ in comparison with those in the control group. Carrying out the beam therapy course both split and not split promotes an increase of values of toxicity index. (authors)

  8. Entrepreneurship Processes and Small Farms Achievements: Empirical Analysis of Linkage

    Directory of Open Access Journals (Sweden)

    Temidayo Gabriel Apata

    2015-01-01

    Full Text Available Entrepreneurship process has been argued as opportunity-driven, creative, and resource-efficient, that could influence income generation of small farmers that adopted entrepreneurial skills and innovation into their farming operations. This study examines entrepreneurship process strategies employed to income increase by small farmers, evidence from southwest of Nigeria. The sampling procedures entail three stages of samples selection of 240 farmers but only 200 data was useful. Descriptive statistical and inferential statistics were used to analyze and describe the data. Respondents’ age ranges from 16 to 65 years old, mean age was 36.16 years. The study found out that 5 % of the samples had modest communication skills that aid adoption of effective entrepreneurial processes and about 83% have a strong belief in one’s self to succeed. Successful farmers had multiple sources of related income generation business ventures. Targeting the entrepreneurs for support could make them even more effective.

  9. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    Energy Technology Data Exchange (ETDEWEB)

    Urbanek, M.; Goldman, D.; Long, J.C. [Lab. of Neurogenetics, Rockville, MD (United States)

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  10. Structural features of Aspergillus niger β-galactosidase define its activity against glycoside linkages.

    Science.gov (United States)

    Rico-Díaz, Agustín; Ramírez-Escudero, Mercedes; Vizoso-Vázquez, Ángel; Cerdán, M Esperanza; Becerra, Manuel; Sanz-Aparicio, Julia

    2017-06-01

    β-Galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of β-galactosides. Among them, the Aspergillus niger β-galactosidase (AnβGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity which is used to degrade lactose. We present here its three-dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304, and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnβGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnβGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto-oligosaccharides production than the Aspergillus oryzae β-galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 β-galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design. Structural data are available in PDB database under the accession numbers 5IFP (native form), 5IHR (in complex with 6

  11. Insulin Resistance and Alzheimer’s Disease: Bioenergetic Linkages

    Directory of Open Access Journals (Sweden)

    Bryan J. Neth

    2017-10-01

    Full Text Available Metabolic dysfunction is a well-established feature of Alzheimer’s disease (AD, evidenced by brain glucose hypometabolism that can be observed potentially decades prior to the development of AD symptoms. Furthermore, there is mounting support for an association between metabolic disease and the development of AD and related dementias. Individuals with insulin resistance, type 2 diabetes mellitus (T2D, hyperlipidemia, obesity, or other metabolic disease may have increased risk for the development of AD and similar conditions, such as vascular dementia. This association may in part be due to the systemic mitochondrial dysfunction that is common to these pathologies. Accumulating evidence suggests that mitochondrial dysfunction is a significant feature of AD and may play a fundamental role in its pathogenesis. In fact, aging itself presents a unique challenge due to inherent mitochondrial dysfunction and prevalence of chronic metabolic disease. Despite the progress made in understanding the pathogenesis of AD and in the development of potential therapies, at present we remain without a disease-modifying treatment. In this review, we will discuss insulin resistance as a contributing factor to the pathogenesis of AD, as well as the metabolic and bioenergetic disruptions linking insulin resistance and AD. We will also focus on potential neuroimaging tools for the study of the metabolic dysfunction commonly seen in AD with hopes of developing therapeutic and preventative targets.

  12. Siblings versus Parents and Friends: Longitudinal Linkages to Adolescent Externalizing Problems

    Science.gov (United States)

    Defoe, Ivy N.; Keijsers, Loes; Hawk, Skyler T.; Branje, Susan; Dubas, Judith Semon; Buist, Kirsten; Frijns, Tom; van Aken, Marcel A. G.; Koot, Hans M.; van Lier, Pol A. C.; Meeus, Wim

    2013-01-01

    Background: It is well documented that friends' externalizing problems and negative parent-child interactions predict externalizing problems in adolescence, but relatively little is known about the role of siblings. This four-wave, multi-informant study investigated linkages of siblings' externalizing problems and sibling-adolescent negative…

  13. Siblings versus parents and friends : Longitudinal linkages to adolescent externalizing problems

    NARCIS (Netherlands)

    Defou, I.N.; Keijsers, L.; Hawk, S.T.; Branje, S.T.J.; Dubas, J.S.; Buist, K.L.; Frijns, T.; van Aken, M.A.G.; Koot, H.M.; van Lier, P.A.C.; Meeus, W.H.J.

    2013-01-01

    Background It is well documented that friends' externalizing problems and negative parent–child interactions predict externalizing problems in adolescence, but relatively little is known about the role of siblings. This four-wave, multi-informant study investigated linkages of siblings'

  14. The ties that bind: interorganizational linkages and physician-system alignment.

    Science.gov (United States)

    Alexander, J A; Waters, T M; Burns, L R; Shortell, S M; Gillies, R R; Budetti, P P; Zuckerman, H S

    2001-07-01

    To examine the association between the degree of alignment between physicians and health care systems, and interorganizational linkages between physician groups and health care systems. The study used a cross sectional, comparative analysis using a sample of 1,279 physicians practicing in loosely affiliated arrangements and 1,781 physicians in 61 groups closely affiliated with 14 vertically integrated health systems. Measures of physician alignment were based on multiitem scales validated in previous studies and derived from surveys sent to individual physicians. Measures of interorganizational linkages were specified at the institutional, administrative, and technical core levels of the physician group and were developed from surveys sent to the administrator of each of the 61 physician groups in the sample. Two stage Heckman models with fixed effects adjustments in the second stage were used to correct for sample selection and clustering respectively. After accounting for sample selection, fixed effects, and group and individual controls, physicians in groups with more valued practice service linkages display consistently higher alignment with systems than physicians in groups that have fewer such linkages. Results also suggest that centralized administrative control lowers physician-system alignment for selected measures of alignment. Governance interlocks exhibited only weak associations with alignment. Our findings suggest that alignment generally follows resource exchanges that promote value-added contributions to physicians and physician groups while preserving control and authority within the group.

  15. Productivity gains, intersectoral linkages, and trade : Indonesian manufacturing, 1980-1996

    NARCIS (Netherlands)

    Jacob, J.; Meister, H.C.

    2004-01-01

    The importance of R&D spillovers for productivity growth has been well-documented in the literature. While studies in the context of developed countries have extensively focused on sectoral linkages, research on North-South spillovers has been largely confined to the aggregate level. This paper

  16. Polarization-induced interference within electromagnetically induced transparency for atoms of double-V linkage

    Science.gov (United States)

    Sun, Yuan; Liu, Chang; Chen, Ping-Xing; Liu, Liang

    2018-02-01

    People have been paying attention to the role of atoms' complex internal level structures in the research of electromagnetically induced transparency (EIT) for a long time, where the various degenerate Zeeman levels usually generate complex linkage patterns for the atomic transitions. It turns out, with special choices of the atomic states and the atomic transitions' linkage structure, clear signatures of quantum interference induced by the probe and coupling light's polarizations can emerge from a typical EIT phenomena. We propose to study a four-state system with double-V linkage pattern for the transitions and analyze the polarization-induced interference under the EIT condition. We show that such interference arises naturally under mild conditions on the optical field and atom manipulation techniques. Moreover, we construct a variation form of double-M linkage pattern where the polarization-induced interference enables polarization-dependent cross modulation between incident weak lights that can be effective even at the few-photon level. The theme is to gain more insight into the essential question: how can we build a nontrivial optical medium where incident lights experience polarization-dependent nonlinear optical interactions, valid for a wide range of incidence intensities down to the few-photon level?

  17. Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot branching

    DEFF Research Database (Denmark)

    Brazauskas, Gintaras; Pašakinskienė, Izolda; Asp, Torben

    2010-01-01

    Knowledge on nucleotide diversity and linkage disequilibrium (LD) patterns is prerequisite for association analyses. However, little is known about the nucleotide diversity in the evolutionary important ryegrass shoot morphology genes. Five candidate genes, LpIAA1, LpRUB1, LpBRI1, LpSHOOT1 and Lp...

  18. Normalization Ridge Regression in Practice II: The Estimation of Multiple Feedback Linkages.

    Science.gov (United States)

    Bulcock, J. W.

    The use of the two-stage least squares (2 SLS) procedure for estimating nonrecursive social science models is often impractical when multiple feedback linkages are required. This is because 2 SLS is extremely sensitive to multicollinearity. The standard statistical solution to the multicollinearity problem is a biased, variance reduced procedure…

  19. Influence of Ti–O–Si hetero-linkages in the photocatalytic degradation of Rhodamine B

    NARCIS (Netherlands)

    Rasalingam, S; Kibombo, H.S.; Wu, C.M.; Budhi, S.; Peng, R.; Baltrusaitis, Jonas; Koodali, R.T.

    2013-01-01

    The influence of Ti–O–Si hetero-linkages in the degradation of Rhodamine B (RhB) dye over TiO2–SiO2 xerogels is exemplified by XPS analysis. We demonstrate a relationship between the percentage surface content of Ti–O–Si and the rate of photocatalytic degradation of RhB. Our detailed surface

  20. Upland Forest Linkages to Seasonal Wetlands: Litter Flux, Processing, and Food Quality

    Science.gov (United States)

    Brian J. Palik; Darold P. Batzer; Christel Kern

    2005-01-01

    The flux of materials across ecosystem boundaries has significant effects on recipient systems. Because of edge effects, seasonal wetlands in upland forest are good systems to explore these linkages. The purpose of this study was to examine flux of coarse particulate organic matter as litter fall into seasonal wetlands in Minnesota, and the relationship of this flux to...

  1. Revealing the Linkage Network Dynamic Structures of Chinese Maritime Ports through Automatic Information System Data

    Directory of Open Access Journals (Sweden)

    Hongchu Yu

    2017-10-01

    Full Text Available Marine economic cooperation has emerged as a major theme in this era of globalization; hence, maritime network connectivity and dynamics have attracted more and more attention. Port construction and maritime route improvements increase maritime trade and thus facilitate economic viability and resource sustainability. This paper reveals the regional dimension of inter-port linkage dynamic structure of Chinese maritime ports from a complex multilayer perspective that is meaningful for strategic forecasting and regional long-term economic development planning. In this research, Automatic Information System (AIS-derived traffic flows were used to construct a maritime network and subnetworks based on the geographical locations of ports. The linkage intensity between subnetworks, the linkage tightness within subnetworks, the spatial isolation between high-intensity backbones and tight skeleton networks, and a linkage concentration index for each port were calculated. The ports, in turn, were analyzed based on these network attributes. This study analyzed the external competitiveness and internal cohesion of each subnetwork. The results revealed problems in port management and planning, such as unclear divisions in port operations. More critically, weak complementary relationships between the backbone and skeleton networks among the ports reduce connectivity and must be strengthened. This research contributes to the body of work supporting strategic decision-making for future development.

  2. Suggestive linkage on chromosome 2, 8, and 17 for Lifetime Major Depression

    NARCIS (Netherlands)

    Middeldorp, C.M.; Sullivan, P.F.; Wray, N.R.; Hottenga, J.J.; de Geus, E.J.C.; van den Berg, M.; Montgomery, GW; Coventry, W.L.; Statham, D.J.; Andrews, G.; Slagboom, P.E.; Boomsma, D.I.; Martin, N.G.

    2009-01-01

    It is well established that major depressive disorder (MDD) is partly heritable. We present a genome-wide linkage study aiming to find regions on the genome that influence the vulnerability for MDD. Our sample consists of 110 Australian and 23 Dutch pedigrees with two or more siblings affected with

  3. Linkage and mapping analyses of the no glue egg gene Ng in the ...

    African Journals Online (AJOL)

    In the silkworm, Bombyx mori, no glue egg is mainly controlled by Ng (No glue) gene, which is located on the 12th chromosome. Owning to a lack of crossing over in females, reciprocal backcrossed F1 (BC1) progenies were used for linkage analysis and mapping of the Ng gene based on the simple sequence repeats ...

  4. Fine mapping analysis confirms and strengthens linkage of four chromosomal regions in familial hypospadias

    NARCIS (Netherlands)

    Soderhall, C.; Korberg, I.B.; Thai, H.T.; Cao, J.; Chen, Y; Zhang, X.; Shulu, Z.; Zanden, L.F.M. van der; Rooij, I.A.L.M. van; Frisen, L.; Roeleveld, N.; Markljung, E.; Kockum, I.; Nordenskjold, A.

    2015-01-01

    Hypospadias is a common male genital malformation and is regarded as a complex disease affected by multiple genetic as well as environmental factors. In a previous genome-wide scan for familial hypospadias, we reported suggestive linkage in nine chromosomal regions. We have extended this analysis by

  5. Transformational leadership climate : Performance linkages, mechanisms, and boundary conditions at the organizational level

    NARCIS (Netherlands)

    Menges, J.; Walter, F.; Vogel, B.; Bruch, H.

    2011-01-01

    Transformational leadership (TFL) climate describes the degree to which leaders throughout an organization engage in TFL behaviors. In this study, we investigate performance linkages, mechanisms, and boundary conditions of TFL climate at the organizational level of analysis. In a sample of 158

  6. Advancing the climate agenda: Exploiting material and institutional linkages to develop a menu of policy options

    NARCIS (Netherlands)

    van Asselt, H.D.; Gupta, J.; Biermann, F.

    2005-01-01

    The utilization of interlinkages of existing material and the strengthening and promotion of new institutional interlinkages can widen the climate change agenda through new and innovative policy and legal measures. Material linkages are inherent structural connections between policy domains that are

  7. Genetic linkage maps of Japanese and European pears aligned to the apple consensus map

    NARCIS (Netherlands)

    Yamamoto, T.; Kimura, T.; Saito, T.; Kotobuki, K.; Matsuta, N.; Liebhard, R.; Gessler, C.; Weg, van de W.E.; Hayashi, T.

    2004-01-01

    Genetic linkage maps of the Japanese pear (Pyrus pyrifolia Nakai) cultivar `Housui¿ and the European pear (Pyrus communis L.) cultivar `Bartlett¿ were constructed based on Amplified Fragment Length Polymorphism markers (AFLPs), Simple Sequence Repeat markers (SSRs) (from pear, apple and Prunus),

  8. Spatial linkages between coral proxies of terrestrial runoff across a large embayment in Madagascar

    NARCIS (Netherlands)

    Grove, C.A.; Zinke, J.; Scheufen, T.; Maina, J.; Epping, E.; Boer, W.; Randriamanantsoa, B.; Brummer, G.-J.A.

    2012-01-01

    Coral cores provide vital climate reconstructions for site-specific temporal variability in river flow and sediment load. Yet, their ability to record spatial differences across multiple catchments is relatively unknown. Here, we investigate spatial linkages between four coral proxies of terrestrial

  9. Can Network Linkage Effects Determine Return? Evidence from Chinese Stock Market.

    Science.gov (United States)

    Qiao, Haishu; Xia, Yue; Li, Ying

    2016-01-01

    This study used the dynamic conditional correlations (DCC) method to identify the linkage effects of Chinese stock market, and further detected the influence of network linkage effects on magnitude of security returns across different industries. Applying two physics-derived techniques, the minimum spanning tree and the hierarchical tree, we analyzed the stock interdependence within the network of the China Securities Index (CSI) industry index basket. We observed that that obvious linkage effects existed among stock networks. CII and CCE, CAG and ITH as well as COU, CHA and REI were confirmed as the core nodes in the three different networks respectively. We also investigated the stability of linkage effects by estimating the mean correlations and mean distances, as well as the normalized tree length of these indices. In addition, using the GMM model approach, we found inter-node influence within the stock network had a pronounced effect on stock returns. Our results generally suggested that there appeared to be greater clustering effect among the indexes belonging to related industrial sectors than those of diverse sectors, and network comovement was significantly affected by impactive financial events in the reality. Besides, stocks that were more central within the network of stock market usually had higher returns for compensation because they endured greater exposure to correlation risk.

  10. Candidate gene linkage approach to identify DNA variants that predispose to preterm birth

    DEFF Research Database (Denmark)

    Bream, Elise N A; Leppellere, Cara R; Cooper, Margaret E

    2013-01-01

    Background:The aim of this study was to identify genetic variants contributing to preterm birth (PTB) using a linkage candidate gene approach.Methods:We studied 99 single-nucleotide polymorphisms (SNPs) for 33 genes in 257 families with PTBs segregating. Nonparametric and parametric analyses were...... through the infant and/or the mother in the etiology of PTB....

  11. A Genetic Linkage Map of Mycosphaerella Fijiensis, using SSR and DArT Markers

    Science.gov (United States)

    Mycosphaerella fijiensis is the causal agent of black leaf streak or Black Sigatoka disease in bananas. This pathogen threatens global banana production as the main export Cavendish cultivars are highly susceptible. Previously a genetic linkage map was generated predominantly using anonymous AFLP ma...

  12. FDI, local sourcing and supportive linkages with domestic suppliers: The case of Monterrey, Mexico

    NARCIS (Netherlands)

    Jordaan, J.A.

    2011-01-01

    In this paper, we use unique data from firm level surveys among foreign-owned and domestic producer firms as well as domestic suppliers to obtain novel direct empirical evidence on the level, supportive nature, and impact of input-output linkages in Monterrey, Mexico. Our main empirical findings are

  13. Partial clonning cytogenetic and linkage mapping of the porcine resistin (RSTN) gene

    Czech Academy of Sciences Publication Activity Database

    Čepica, Stanislav; Rohrer, G. A.; Masopust, m.; Kubíčková, S.; Musilová, P.; Rubeš, J.

    2002-01-01

    Roč. 33, - (2002), s. 381-383 ISSN 0268-9146 R&D Projects: GA ČR GA523/99/0842; GA AV ČR KSK5052113 Keywords : cytogenetic and linkage mapping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.443, year: 2002

  14. Use of deterministic sampling for exploring likelihoods in linkage analysis for quantitative traits.

    NARCIS (Netherlands)

    Mackinnon, M.J.; Beek, van der S.; Kinghorn, B.P.

    1996-01-01

    Deterministic sampling was used to numerically evaluate the expected log-likelihood surfaces of QTL-marker linkage models in large pedigrees with simple structures. By calculating the expected values of likelihoods, questions of power of experimental designs, bias in parameter estimates, approximate

  15. Examining Linkages between Psychological Health Problems, Socio-Demographic Characteristics and Workplace Stressors in Pakistan's Academia

    Science.gov (United States)

    Khan, Anwar; Yusoff, Rosman Bin Md; Isa, Khairunesa Binti

    2016-01-01

    Scholarly work and research are globally known as stressful and challenging. Teachers may develop different psychological health problems once they are exposed to workplace stressors. Considering it as a serious issue of education sector, this study has examined the linkages between prevalent workplace stressors and psychological health problems…

  16. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, H.; Sorensen, A.P.; Antonise, R.; van de Wiel, C.; van der Linden, C.G.; van 't Westende, W.; Hooftman, D.A.P.; den Nijs, J.C.M.; Flavell, A.J.

    2006-01-01

    Abstract Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  17. Linkage of mike she to wetland-dndc for carbon budgeting and anaerobic biogeochemistry simulation

    Science.gov (United States)

    Jianbo Cui; Changsheng Li; Ge Sun; Carl Trettin

    2005-01-01

    This study reports the linkage between MIKE SHE and Wetland-DNDC for carbon dynamics and greenhouse gases (GHGs) emissions simulation in forested wetland.Wet1and-DNDC was modified by parameterizing management measures, refining anaerobic biogeochemical processes, and was linked to the hydrological model - MIKE SHE. As a preliminary application, we simulated the effect...

  18. Genome-Wide Association Study and Linkage Analysis of the Healthy Aging Index

    DEFF Research Database (Denmark)

    Minster, Ryan L; Sanders, Jason L; Singh, Jatinder

    2015-01-01

    BACKGROUND: The Healthy Aging Index (HAI) is a tool for measuring the extent of health and disease across multiple systems. METHODS: We conducted a genome-wide association study and a genome-wide linkage analysis to map quantitative trait loci associated with the HAI and a modified HAI weighted...

  19. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

    DEFF Research Database (Denmark)

    Mckinney, G. J.; Seeb, L. W.; Larson, W. A.

    2016-01-01

    Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged...

  20. Linkage mapping in a watermelon population segregating for fusarium wilt resistance

    Science.gov (United States)

    Leigh K. Hawkins; Fenny Dane; Thomas L. Kubisiak; Billy B. Rhodes; Robert L. Jarret

    2001-01-01

    Isozyme, randomly amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers were used to generate a linkage map in an F2 and F3 watermelon (Citrullus lanatus (Thumb.) Matsum. & Nakai) population derived from a cross between the fusarium wilt (Fusarium oxysporum f....

  1. Indian migrants in britain: mirror image of social linkages between Gujarat and London

    NARCIS (Netherlands)

    Rutten, M.; Patel, P.J.

    2003-01-01

    This article discusses the social linkages between Gujarati migrants in Britain and their family members in India. It considers the home and the migrant community in the same unit of analysis rather than as separate communities. It is based on fieldwork conducted in 1998 among members of the Patidar

  2. High-frequency stock linkage and multi-dimensional stationary processes

    Science.gov (United States)

    Wang, Xi; Bao, Si; Chen, Jingchao

    2017-02-01

    In recent years, China's stock market has experienced dramatic fluctuations; in particular, in the second half of 2014 and 2015, the market rose sharply and fell quickly. Many classical financial phenomena, such as stock plate linkage, appeared repeatedly during this period. In general, these phenomena have usually been studied using daily-level data or minute-level data. Our paper focuses on the linkage phenomenon in Chinese stock 5-second-level data during this extremely volatile period. The method used to select the linkage points and the arbitrage strategy are both based on multi-dimensional stationary processes. A new program method for testing the multi-dimensional stationary process is proposed in our paper, and the detailed program is presented in the paper's appendix. Because of the existence of the stationary process, the strategy's logarithmic cumulative average return will converge under the condition of the strong ergodic theorem, and this ensures the effectiveness of the stocks' linkage points and the more stable statistical arbitrage strategy.

  3. Linkages among Adolescent Girls' Romantic Relationships, Best Friendships, and Peer Networks

    Science.gov (United States)

    Kuttler, Ami Flam; La Greca, Annette M.

    2004-01-01

    This study examined the linkages among girls' best friendships and romantic relationships and accounted for the level of dating involvement as a moderating variable. Social exchange and Sullivan's socioemotional theories served as guides in this process. Questionnaires were administered to 446 girls aged 15-19 years. Results showed that: (a)…

  4. Across the divide: The impact of farmer-to-farmer linkages in the ...

    African Journals Online (AJOL)

    Across the divide: The impact of farmer-to-farmer linkages in the absence of extension services. ... South African Journal of Agricultural Extension ... The literature on recent trends in agricultural development emphasises the importance of extension and research practitioners participating with smallholder farmers in order to ...

  5. Linkages between Total Quality Management and the Outcomes-Based Approach in an Education Environment

    Science.gov (United States)

    de Jager, H. J.; Nieuwenhuis, F. J.

    2005-01-01

    South Africa has embarked on a process of education renewal by adopting outcomes-based education (OBE). This paper focuses on the linkages between total quality management (TQM) and the outcomes-based approach in an education context. Quality assurance in academic programmes in higher education in South Africa is, in some instances, based on the…

  6. Can Network Linkage Effects Determine Return? Evidence from Chinese Stock Market

    Science.gov (United States)

    Qiao, Haishu; Xia, Yue; Li, Ying

    2016-01-01

    This study used the dynamic conditional correlations (DCC) method to identify the linkage effects of Chinese stock market, and further detected the influence of network linkage effects on magnitude of security returns across different industries. Applying two physics-derived techniques, the minimum spanning tree and the hierarchical tree, we analyzed the stock interdependence within the network of the China Securities Index (CSI) industry index basket. We observed that that obvious linkage effects existed among stock networks. CII and CCE, CAG and ITH as well as COU, CHA and REI were confirmed as the core nodes in the three different networks respectively. We also investigated the stability of linkage effects by estimating the mean correlations and mean distances, as well as the normalized tree length of these indices. In addition, using the GMM model approach, we found inter-node influence within the stock network had a pronounced effect on stock returns. Our results generally suggested that there appeared to be greater clustering effect among the indexes belonging to related industrial sectors than those of diverse sectors, and network comovement was significantly affected by impactive financial events in the reality. Besides, stocks that were more central within the network of stock market usually had higher returns for compensation because they endured greater exposure to correlation risk. PMID:27257816

  7. Overview of surface study of fusion research in universities linkage organization, (2)

    International Nuclear Information System (INIS)

    Miyahara, Akira; Kamada, Kohji; Yamashina, Toshiro.

    1981-02-01

    Overview of surface material developments for fusion devices in university linkage organization has been described. Including subjects are surface properties investigations, surface diagnostics, coating technologies tritium related surface problems and permeation studies. Because surface material investigations are wide spread subjects, necessities of problem definitions from plasma physics side were recognized. (author)

  8. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

    Science.gov (United States)

    The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

  9. Method to eliminate flux linkage DC component in load transformer for static transfer switch.

    Science.gov (United States)

    He, Yu; Mao, Chengxiong; Lu, Jiming; Wang, Dan; Tian, Bing

    2014-01-01

    Many industrial and commercial sensitive loads are subject to the voltage sags and interruptions. The static transfer switch (STS) based on the thyristors is applied to improve the power quality and reliability. However, the transfer will result in severe inrush current in the load transformer, because of the DC component in the magnetic flux generated in the transfer process. The inrush current which is always 2 ~ 30 p.u. can cause the disoperation of relay protective devices and bring potential damage to the transformer. The way to eliminate the DC component is to transfer the related phases when the residual flux linkage of the load transformer and the prospective flux linkage of the alternate source are equal. This paper analyzes how the flux linkage of each winding in the load transformer changes in the transfer process. Based on the residual flux linkage when the preferred source is completely disconnected, the method to calculate the proper time point to close each phase of the alternate source is developed. Simulation and laboratory experiments results are presented to show the effectiveness of the transfer method.

  10. Sustainability inter-linkages in reporting vindeicated: a study of European companies

    NARCIS (Netherlands)

    Lozano, R.

    2013-01-01

    Recently, there has been a rapid growth in company sustainability reporting, as well as an improvement in quality of reports. A number of guidelines have been instrumental in this process; however, they still do not consider the importance of the inter-linkages and synergies among the different

  11. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

    Science.gov (United States)

    Signatures of selection are regions in the genome that have been preferentially maintained because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium patterns. The varLD methodol...

  12. Productivity in Academia: An Assessment of Causal Linkages between Output and Outcome Indicators

    Science.gov (United States)

    Wamala, Robert; Ssembatya, Vincent A.

    2015-01-01

    Purpose: The purpose of this paper is to investigate causal linkages between output and outcome indicators of productivity in academia. Design/methodology/approach: The duration of teaching service and the number of graduate students supervised to completion were adopted as output indicators of productivity. Equivalent outcome indicators were the…

  13. Meta-analysis of genome-wide linkage studies in BMI and obesity

    NARCIS (Netherlands)

    Saunders, Catherine L.; Chiodini, Benedetta D.; Sham, Pak; Lewis, Cathryn M.; Abkevich, Victor; Adeyemo, Adebowale A.; de Andrade, Mariza; Arya, Rector; Berenson, Gerald S.; Blangero, John; Boehnke, Michael; Borecki, Ingrid B.; Chagnon, Yvon C.; Chen, Wei; Comuzzie, Anthony G.; Deng, Hong-Wen; Duggirala, Ravindranath; Feitosa, Mary F.; Froguel, Philippe; Hanson, Robert L.; Hebebrand, Johannes; Huezo-Dias, Patricia; Kissebah, Ahmed H.; Li, Weidong; Luke, Amy; Martin, Lisa J.; Nash, Matthew; Ohman, Muena; Palmer, Lyle J.; Peltonen, Leena; Perola, Markus; Price, R. Arlen; Redline, Susan; Srinivasan, Sathanur R.; Stern, Michael P.; Stone, Steven; Stringham, Heather; Turner, Stephen; Wijmenga, Cisca; Collier, David A.

    Objective: The objective was to provide an overall assessment of genetic linkage data of BMI and BMI-defined obesity using a nonparametric genome scan meta-analysis. Research Methods and Procedures: We identified 37 published studies containing data on over 31,000 individuals from more than >10,000

  14. Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.

    Science.gov (United States)

    Mutisya, Daniel; Selvam, Chelliah; Lunstad, Benjamin D; Pallan, Pradeep S; Haas, Amanda; Leake, Devin; Egli, Martin; Rozners, Eriks

    2014-06-01

    RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3'-CH2-CO-NH-5' amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P-OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5'-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Industry-academe linkages in the Philippines: Embedding foreign investors, capturing institutions?

    NARCIS (Netherlands)

    Kleibert, J.M.

    2015-01-01

    The global sourcing of services from developing countries has made human capital a key local asset for attracting foreign direct investment. This paper analyses to what extent individual companies engage in linkages and collaborations with universities and how the education sector responds to the

  16. Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage.

    Science.gov (United States)

    Králíková, Sárka; Buděšínský, Miloš; Barvík, Ivan; Masojídková, Milena; Točík, Zdeněk; Rosenberg, Ivan

    2011-01-01

    A complete series of the 2 '-5 ' and 3 '-5 ' regioisomeric types of r(ApA) and 2 '-d(ApA) analogues with the α-hydroxy-phosphonate C3 '-O-P-CH(OH)-C4 ″ internucleotide linkage, isopolar but non-isosteric with the phosphodiester one, were synthesized and their hybridization properties with polyU studied. Due to the chirality on the 5 '-carbon atom of the modified internucleotide linkage bearing phosphorus and hydroxy moieties, each regioisomeric type of ApA dimer is split into epimeric pairs. To examine the role of the 5 '-hydroxyl of the α-hydroxy-phosphonate moiety during hybridization, the appropriate r(ApA) analogues with 3 '(2 ')-O-P-CH(2)-C4 ″ linkage lacking the 5 '-hydroxyl were synthesized. Nuclear magnetic resonance (NMR) spectroscopy study on the conformation of the modified sugar-phosphate backbone, along with the hybridization measurements, revealed remarkable differences in the stability of complexes with polyU, depending on the 5 '-carbon atom configuration. Potential usefulness of the α-hydroxy-phosphonate linkage in modified oligoribonucleotides is discussed.

  17. Romantic Relationship Commitment and Its Linkages with Commitment to Parents and Friends during Adolescence

    Science.gov (United States)

    De Goede, Irene H. A.; Branje, Susan; van Duin, Jet; VanderValk, Inge E.; Meeus, Wim

    2012-01-01

    This five-wave longitudinal study examines linkages between adolescents' perceptions of romantic relationship commitment and the development of adolescents' perceptions of commitment to parents and friends. A total of 218 early-to-middle adolescents (39.0 percent boys) and 185 middle-to-late adolescents (30.8 percent boys) participated.…

  18. Linkage of a Physically Based Distributed Watershed Model and a Dynamic Plant Growth Model

    Science.gov (United States)

    2006-12-01

    i.e., Universal Soil Loss Equation ( USLE ) factors, K, C, and P). The K, C, and P factors are empiri- cal coefficients with the same conceptual...with general ecosystem models designed to make long-term projections of ecosystem dynamics. This development effort investigated the linkage of soil ...20 EDYS soil module

  19. Untied Efforts: The Challenges for Improved Research, Extension and Education Linkages

    Science.gov (United States)

    Eneyew, Adugna

    2013-01-01

    Ethiopian agriculture is characterized by smallholders farming whose access to modern technology and basic education is very limited. Research, extension, education and farmers are the main pillars of agricultural knowledge systems and their effectiveness largely depends on strong linkage among each other. However, the existing…

  20. Foreign Direct Investment, Linkage Formation and Supplier Development in Thailand during the 1990s

    DEFF Research Database (Denmark)

    Lauridsen, Laurids Sandager

    2004-01-01

    in Thailand. This led in turn to the formulation of TNC-SME linkage policies as well as a set of broader SME and supporting industry policies to supplement unfolding liberalisation of trade- and investment policies. The article is concerned with the extent to which the Thai government was able to formulate...

  1. Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs

    Science.gov (United States)

    Mutisya, Daniel; Selvam, Chelliah; Lunstad, Benjamin D.; Pallan, Pradeep S.; Haas, Amanda; Leake, Devin; Egli, Martin; Rozners, Eriks

    2014-01-01

    RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3′-CH2-CO-NH-5′ amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P–OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5′-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications. PMID:24813446

  2. High-density Integrated Linkage Map Based on SSR Markers in Soybean

    Science.gov (United States)

    Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

    2009-01-01

    A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

  3. Linkage isomerism in trimeric and polymeric 2,3-cis-procyanindins

    Science.gov (United States)

    Richard W. Hemingway; Lai Yeap Foo; Lawrence J. Porter

    1982-01-01

    Procyanindins polymers consist of chains of 5,7,3',4'-tetrahydroxyflavan-3-ol units linked by C(4)-C(6) or C(4)-C(8) bonds.1 Whereas the procyanidin-B group of dimers are known to exist as pairs of isomers with common flavan-3-ol units, but different interflavanoid linkages,2,3 the extent of such isomerism in...

  4. Polymeric proanthocyanidins: Interflavanoid linkage isomerism in (epicatechin-4)-(epicatechin-4)-catechin procyanidins

    Science.gov (United States)

    Richard W. Hemingway; L. Yeap Foo; L. J. Porter

    1981-01-01

    Procyanidin trimers have been isolated from a variety of plants,1-3 but their structures remain unresolved. We have now isolated three configurational isomers of (epicatechin-4)-(epicatechin-4)-catechin from Pinus taeda L. (loblolly pine) phloem which exhibit isomerism of the interflavanoid linkages.

  5. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars

    NARCIS (Netherlands)

    Kraakman, A.T.W.; Martinez, F.; Mussiraliev, B.; Eeuwijk, van F.A.; Niks, R.E.

    2006-01-01

    A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus

  6. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

    Science.gov (United States)

    A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

  7. Linkage studies and mutation analysis of the PDEB gene in 23 families with Leber congenital amaurosis

    DEFF Research Database (Denmark)

    Riess, O; Weber, B; Nørremølle, Anne

    1992-01-01

    as to whether mutations in the human PDEB gene might cause LCA. We have previously cloned and characterized the human homologue of the mouse Pdeb gene and have mapped it to chromosome 4p16.3. In this study, a total of 23 LCA families of various ethnic backgrounds have been investigated. Linkage analysis using...

  8. Linkage to chromosome 1p36 for attention-deficit/ hyperactivity disorder traits in school and home settings

    NARCIS (Netherlands)

    Zhou, K.; Asherson, P.; Sham, P.; Franke, B.; Anney, R.J.; Buitelaar, J.K.; Ebstein, R.; Gill, M.; Brookes, K; Buschgens, C.J.M.; Campbell, D.; Chen, W.; Christiansen, H.; Fliers, E.; Gabriëls, I.; Johansson, L.; Marco, R.; Mulas, F.; Müller, U.; Mulligan, A.; Neale, B.; Rijsdijk, F.; Rommelse, N.N.J.; Uebel, H.; Psychogiou, L.; Xu, X.; Banaschewski, T.; Sonuga-Barke, E.; Eisenberg, J.; Manor, I.; Miranda, A.; Oades, R.D.; Roeyers, H.; Rothenberger, A.; Sergeant, J.A.; Steinhausen, H.C.; Taylor, E.; Thompson, M.; Faraone, S.V.

    2008-01-01

    Background: Limited success has been achieved through previous attention-deficit/hyperactivity disorder (ADHD) linkage scans, which were all designed to map genes underlying the dichotomous phenotype. The International Multi-centre ADHD Genetics (IMAGE) project performed a whole genome linkage scan

  9. Young people’s views about consenting to data linkage: findings from the PEARL qualitative study

    Directory of Open Access Journals (Sweden)

    Suzanne Audrey

    2016-03-01

    Full Text Available Abstract Background Electronic administrative data exist in several domains which, if linked, are potentially useful for research. However, benefits from data linkage should be considered alongside risks such as the threat to privacy. Avon Longitudinal Study of Parents and Children (ALSPAC is a birth cohort study. The Project to Enhance ALSPAC through Record Linkage (PEARL was established to enrich the ALSPAC resource through linkage between ALSPAC participants and routine sources of health and social data. Qualitative research was incorporated in the PEARL study to examine participants’ views about data linkage and inform approaches to information sharing. This paper focusses on issues of consent. Methods Digitally recorded interviews were conducted with 55 participants aged 17–19 years. Terms and processes relating to consent, anonymization and data linkage were explained to interviewees. Scenarios were used to prompt consideration of linking different sources of data, and whether consent should be requested. Interview recordings were fully transcribed. Thematic analysis was undertaken using the Framework approach. Results Participant views on data linkage appeared to be most influenced by: considerations around the social sensitivity of the research question, and; the possibility of tangible health benefits in the public interest. Some participants appeared unsure about the effectiveness of anonymization, or did not always view effective anonymization as making consent unnecessary. This was related to notions of ownership of personal information and etiquette around asking permission for secondary use. Despite different consent procedures being explained, participants tended to equate consent with ‘opt-in’ consent through which participants are ‘asked’ if their data can be used for a specific study. Participants raising similar concerns came to differing conclusions about whether consent was needed. Views changed when presented

  10. Linkage to HIV care and antiretroviral therapy in Cape Town, South Africa.

    Directory of Open Access Journals (Sweden)

    Katharina Kranzer

    2010-11-01

    Full Text Available Antiretroviral therapy (ART has been scaled-up rapidly in Africa. Programme reports typically focus on loss to follow-up and mortality among patients receiving ART. However, little is known about linkage and retention in care of individuals prior to starting ART.Data on adult residents from a periurban community in Cape Town were collected at a primary care clinic and hospital. HIV testing registers, CD4 count results provided by the National Health Laboratory System and ART registers were linked. A random sample (n = 885 was drawn from adults testing HIV positive through antenatal care, sexual transmitted disease and voluntary testing and counseling services between January 2004 and March 2009. All adults (n = 103 testing HIV positive through TB services during the same time period were also included in the study. Linkage to HIV care was defined as attending for a CD4 count measurement within 6 months of HIV diagnosis. Linkage to ART care was defined as initiating ART within 6 months of HIV diagnosis in individuals with a CD4 count ≤200 cells/µl taken within 6 months of HIV diagnosis.Only 62.6% of individuals attended for a CD4 count measurement within 6 months of testing HIV positive. Individuals testing through sexually transmitted infection services had the best (84.1% and individuals testing on their own initiative (53.5% the worst linkage to HIV care. One third of individuals with timely CD4 counts were eligible for ART and 66.7% of those were successfully linked to ART care. Linkage to ART care was highest among antenatal care clients. Among individuals not yet eligible for ART only 46.3% had a repeat CD4 count. Linkage to HIV care improved in patients tested in more recent calendar period.Linkage to HIV and ART care was low in this poor peri-urban community despite free services available within close proximity. More efforts are needed to link VCT scale-up to subsequent care.

  11. Young people's views about consenting to data linkage: findings from the PEARL qualitative study.

    Science.gov (United States)

    Audrey, Suzanne; Brown, Lindsey; Campbell, Rona; Boyd, Andy; Macleod, John

    2016-03-21

    Electronic administrative data exist in several domains which, if linked, are potentially useful for research. However, benefits from data linkage should be considered alongside risks such as the threat to privacy. Avon Longitudinal Study of Parents and Children (ALSPAC) is a birth cohort study. The Project to Enhance ALSPAC through Record Linkage (PEARL) was established to enrich the ALSPAC resource through linkage between ALSPAC participants and routine sources of health and social data. Qualitative research was incorporated in the PEARL study to examine participants' views about data linkage and inform approaches to information sharing. This paper focusses on issues of consent. Digitally recorded interviews were conducted with 55 participants aged 17-19 years. Terms and processes relating to consent, anonymization and data linkage were explained to interviewees. Scenarios were used to prompt consideration of linking different sources of data, and whether consent should be requested. Interview recordings were fully transcribed. Thematic analysis was undertaken using the Framework approach. Participant views on data linkage appeared to be most influenced by: considerations around the social sensitivity of the research question, and; the possibility of tangible health benefits in the public interest. Some participants appeared unsure about the effectiveness of anonymization, or did not always view effective anonymization as making consent unnecessary. This was related to notions of ownership of personal information and etiquette around asking permission for secondary use. Despite different consent procedures being explained, participants tended to equate consent with 'opt-in' consent through which participants are 'asked' if their data can be used for a specific study. Participants raising similar concerns came to differing conclusions about whether consent was needed. Views changed when presented with different scenarios, and were sometimes inconsistent. Findings

  12. Accuracy of Probabilistic Linkage Using the Enhanced Matching System for Public Health and Epidemiological Studies.

    Science.gov (United States)

    Aldridge, Robert W; Shaji, Kunju; Hayward, Andrew C; Abubakar, Ibrahim

    2015-01-01

    The Enhanced Matching System (EMS) is a probabilistic record linkage program developed by the tuberculosis section at Public Health England to match data for individuals across two datasets. This paper outlines how EMS works and investigates its accuracy for linkage across public health datasets. EMS is a configurable Microsoft SQL Server database program. To examine the accuracy of EMS, two public health databases were matched using National Health Service (NHS) numbers as a gold standard unique identifier. Probabilistic linkage was then performed on the same two datasets without inclusion of NHS number. Sensitivity analyses were carried out to examine the effect of varying matching process parameters. Exact matching using NHS number between two datasets (containing 5931 and 1759 records) identified 1071 matched pairs. EMS probabilistic linkage identified 1068 record pairs. The sensitivity of probabilistic linkage was calculated as 99.5% (95%CI: 98.9, 99.8), specificity 100.0% (95%CI: 99.9, 100.0), positive predictive value 99.8% (95%CI: 99.3, 100.0), and negative predictive value 99.9% (95%CI: 99.8, 100.0). Probabilistic matching was most accurate when including address variables and using the automatically generated threshold for determining links with manual review. With the establishment of national electronic datasets across health and social care, EMS enables previously unanswerable research questions to be tackled with confidence in the accuracy of the linkage process. In scenarios where a small sample is being matched into a very large database (such as national records of hospital attendance) then, compared to results presented in this analysis, the positive predictive value or sensitivity may drop according to the prevalence of matches between databases. Despite this possible limitation, probabilistic linkage has great potential to be used where exact matching using a common identifier is not possible, including in low-income settings, and for vulnerable

  13. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

    Directory of Open Access Journals (Sweden)

    Matsumoto Takashi

    2010-04-01

    Full Text Available Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin. Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7% deviated (p Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker

  14. Photoactive Zn(II)Porphyrin–multi-walled carbon nanotubes nanohybrids through covalent β-linkages

    International Nuclear Information System (INIS)

    Lipińska, Monika E.; Rebelo, Susana L.H.; Pereira, M. Fernando R.; Figueiredo, José L.; Freire, Cristina

    2013-01-01

    Donor–acceptor nanohybrids by a covalent linkage between the β-position of a Zn(II)Porphyrin and multi-walled carbon nanotubes are reported for the first time, in a closer analogy to the natural light harvesting systems, which are based on β-substituted porphyrinoid structures, the chlorophylls. An unique and direct connection was established through the immobilization of the Zn(II)(β-NH 2 -tetraphenylporphyrin), using diazonium chemistry, in order to afford i) a short and conjugated linkage between the two aromatic systems and ii) an amide bond resulting from a three-step functionalization synthesis. Electronic and steady-state fluorescence spectroscopies confirmed high photoinduced electron communication through the β-linkage when compared to analogous meso-phenyl linkers, stating its positive effect. The procedure involving the amide linkage allowed higher chromophore loadings; however, the direct conjugated bond showed improved photoinduced activity and a different emission pattern that can be associated with intense communication within the expanded π-system MWCNT–metalloporphyrin. - Graphical abstract: Preparation and photo-induced activity of two donor–acceptor nanohybrids is reported based on different linkages through β-position of porphyrin core to MWCNT, direct conjugation and amide bond. - Highlights: • β-linked Zn(II)Porphyrin–MWCNT nanohybrids were prepared through direct or amide bond. • Efficient and mild functionalizations were achieved using diazonium chemistry. • Good nanohybrid dispersibility was obtained in low boiling point solvent. • Nanohybrids showed strong photoinduced electronic transfer. • The emission quenching was higher for the π-expanded system

  15. A consensus linkage map of the grass carp (Ctenopharyngodon idella based on microsatellites and SNPs

    Directory of Open Access Journals (Sweden)

    Li Jiale

    2010-02-01

    Full Text Available Abstract Background Grass carp (Ctenopharyngodon idella belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards understanding genome evolution. The aim of this study is to construct a first generation genetic map of grass carp using microsatellites and SNPs to generate a new resource for mapping QTL for economically important traits and to conduct a comparative mapping analysis to shed new insights into the evolution of fish genomes. Results We constructed a first generation linkage map of grass carp with a mapping panel containing two F1 families including 192 progenies. Sixteen SNPs in genes and 263 microsatellite markers were mapped to twenty-four linkage groups (LGs. The number of LGs was corresponding to the haploid chromosome number of grass carp. The sex-specific map was 1149.4 and 888.8 cM long in females and males respectively whereas the sex-averaged map spanned 1176.1 cM. The average resolution of the map was 4.2 cM/locus. BLAST searches of sequences of mapped markers of grass carp against the whole genome sequence of zebrafish revealed substantial macrosynteny relationship and extensive colinearity of markers between grass carp and zebrafish. Conclusions The linkage map of grass carp presented here is the first linkage map of a food fish species based on co-dominant markers in the family Cyprinidae. This map provides a valuable resource for mapping phenotypic variations and serves as a reference to approach comparative genomics and understand the evolution of fish genomes and could be complementary to grass carp genome sequencing project.

  16. Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

    Science.gov (United States)

    Arya, Rector; Lehman, Donna; Hunt, Kelly J; Schneider, Jennifer; Almasy, Laura; Blangero, John; Stern, Michael P; Duggirala, Ravindranath

    2003-12-31

    Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecting obesity and dyslipidemia is very limited. To address this issue, we first conducted univariate multipoint linkage analysis for body mass index (BMI) and HDL-C to identify loci influencing variation in these phenotypes using Framingham Heart Study data relating to 1702 subjects distributed across 330 pedigrees. Subsequently, we performed bivariate multipoint linkage analysis to detect common loci influencing covariation between these two traits. We scanned the genome and identified a major locus near marker D6S1009 influencing variation in BMI (LOD = 3.9) using the program SOLAR. We also identified a major locus for HDL-C near marker D2S1334 on chromosome 2 (LOD = 3.5) and another region near marker D6S1009 on chromosome 6 with suggestive evidence for linkage (LOD = 2.7). Since these two phenotypes have been independently mapped to the same region on chromosome 6q, we used the bivariate multipoint linkage approach using SOLAR. The bivariate linkage analysis of BMI and HDL-C implicated the genetic region near marker D6S1009 as harboring a major gene commonly influencing these phenotypes (bivariate LOD = 6.2; LODeq = 5.5) and appears to improve power to map the correlated traits to a region, precisely. We found substantial evidence for a quantitative trait locus with pleiotropic effects, which appears to influence both BMI and HDL-C phenotypes in the Framingham data.

  17. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

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    Foley Brad R

    2011-11-01

    Full Text Available Abstract Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are

  18. Photoactive Zn(II)Porphyrin–multi-walled carbon nanotubes nanohybrids through covalent β-linkages

    Energy Technology Data Exchange (ETDEWEB)

    Lipińska, Monika E., E-mail: m.e.lipinska@gmail.com [REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto (Portugal); Rebelo, Susana L.H., E-mail: susana.rebelo@fc.up.pt [REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto (Portugal); Pereira, M. Fernando R., E-mail: fpereira@fe.up.pt [Laboratório de Catálise e Materiais (LCM), Laboratório Associado LSRE/LCM, Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto (Portugal); Figueiredo, José L., E-mail: jlfig@fe.up.pt [Laboratório de Catálise e Materiais (LCM), Laboratório Associado LSRE/LCM, Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto (Portugal); Freire, Cristina, E-mail: acfreire@fc.up.pt [REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto (Portugal)

    2013-12-16

    Donor–acceptor nanohybrids by a covalent linkage between the β-position of a Zn(II)Porphyrin and multi-walled carbon nanotubes are reported for the first time, in a closer analogy to the natural light harvesting systems, which are based on β-substituted porphyrinoid structures, the chlorophylls. An unique and direct connection was established through the immobilization of the Zn(II)(β-NH{sub 2}-tetraphenylporphyrin), using diazonium chemistry, in order to afford i) a short and conjugated linkage between the two aromatic systems and ii) an amide bond resulting from a three-step functionalization synthesis. Electronic and steady-state fluorescence spectroscopies confirmed high photoinduced electron communication through the β-linkage when compared to analogous meso-phenyl linkers, stating its positive effect. The procedure involving the amide linkage allowed higher chromophore loadings; however, the direct conjugated bond showed improved photoinduced activity and a different emission pattern that can be associated with intense communication within the expanded π-system MWCNT–metalloporphyrin. - Graphical abstract: Preparation and photo-induced activity of two donor–acceptor nanohybrids is reported based on different linkages through β-position of porphyrin core to MWCNT, direct conjugation and amide bond. - Highlights: • β-linked Zn(II)Porphyrin–MWCNT nanohybrids were prepared through direct or amide bond. • Efficient and mild functionalizations were achieved using diazonium chemistry. • Good nanohybrid dispersibility was obtained in low boiling point solvent. • Nanohybrids showed strong photoinduced electronic transfer. • The emission quenching was higher for the π-expanded system.

  19. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

    Science.gov (United States)

    2011-01-01

    Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development

  20. Meta-analysis of genome-wide linkage studies in BMI and obesity.

    Science.gov (United States)

    Saunders, Catherine L; Chiodini, Benedetta D; Sham, Pak; Lewis, Cathryn M; Abkevich, Victor; Adeyemo, Adebowale A; de Andrade, Mariza; Arya, Rector; Berenson, Gerald S; Blangero, John; Boehnke, Michael; Borecki, Ingrid B; Chagnon, Yvon C; Chen, Wei; Comuzzie, Anthony G; Deng, Hong-Wen; Duggirala, Ravindranath; Feitosa, Mary F; Froguel, Philippe; Hanson, Robert L; Hebebrand, Johannes; Huezo-Dias, Patricia; Kissebah, Ahmed H; Li, Weidong; Luke, Amy; Martin, Lisa J; Nash, Matthew; Ohman, Miina; Palmer, Lyle J; Peltonen, Leena; Perola, Markus; Price, R Arlen; Redline, Susan; Srinivasan, Sathanur R; Stern, Michael P; Stone, Steven; Stringham, Heather; Turner, Stephen; Wijmenga, Cisca; Collier, David A

    2007-09-01

    The objective was to provide an overall assessment of genetic linkage data of BMI and BMI-defined obesity using a nonparametric genome scan meta-analysis. We identified 37 published studies containing data on over 31,000 individuals from more than >10,000 families and obtained genome-wide logarithm of the odds (LOD) scores, non-parametric linkage (NPL) scores, or maximum likelihood scores (MLS). BMI was analyzed in a pooled set of all studies, as a subgroup of 10 studies that used BMI-defined obesity, and for subgroups ascertained through type 2 diabetes, hypertension, or subjects of European ancestry. Bins at chromosome 13q13.2- q33.1, 12q23-q24.3 achieved suggestive evidence of linkage to BMI in the pooled analysis and samples ascertained for hypertension. Nominal evidence of linkage to these regions and suggestive evidence for 11q13.3-22.3 were also observed for BMI-defined obesity. The FTO obesity gene locus at 16q12.2 also showed nominal evidence for linkage. However, overall distribution of summed rank p values <0.05 is not different from that expected by chance. The strongest evidence was obtained in the families ascertained for hypertension at 9q31.1-qter and 12p11.21-q23 (p < 0.01). Despite having substantial statistical power, we did not unequivocally implicate specific loci for BMI or obesity. This may be because genes influencing adiposity are of very small effect, with substantial genetic heterogeneity and variable dependence on environmental factors. However, the observation that the FTO gene maps to one of the highest ranking bins for obesity is interesting and, while not a validation of this approach, indicates that other potential loci identified in this study should be investigated further.

  1. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

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    Smith Oscar

    2002-10-01

    Full Text Available Abstract Background Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. Results We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp, but rare in coding regions. A small number (2–8 of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. Conclusions No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

  2. Genetic counseling in Usher syndrome: linkage and mutational analysis of 10 Colombian families.

    Science.gov (United States)

    Tamayo, M L; Lopez, G; Gelvez, N; Medina, D; Kimberling, W J; Rodríguez, V; Tamayo, G E; Bernal, J E

    2008-01-01

    Usher Syndrome (US), an autosomal recessive disease, is characterized by retinitis pigmentosa (RP), vestibular dysfunction, and congenital sensorineural deafness. There are three recognized clinical types of the disorder. In order to improve genetic counseling for affected families, we conducted linkage analysis and DNA sequencing in 10 Colombian families with confirmed diagnosis of US (4 type I and 6 type II). Seventy-five percent of the US1 families showed linkage to locus USH1B, while the remaining 25% showed linkage to loci USH1B and USH1C. Among families showing linkage to USH1B we found two different mutations in the MYO7A gene: IVS42-26insTTGAG in exon 43 (heterozygous state) and R634X (CGA-TGA) in exon 16 (homozygous state). All six US2 families showed linkage to locus USH2A. Of them, 4 had c.2299delG mutation (1 homozygote state and 3 heterozygous); in the remaining 2 we did not identify any pathologic DNA variant. USH2A individuals with a 2299delG mutation presented a typical and homogeneous retinal phenotype with bilateral severe hearing loss, except for one individual with a heterozygous 2299delG mutation, whose hearing loss was asymmetric, but more profound than in the other cases. The study of these families adds to the genotype-phenotype characterization of the different types and subtypes of US and facilitates genetic counseling in these families. We would like to emphasize the need to perform DNA studies as a prerequisite for genetic counseling in affected families.

  3. Heavy-ion targets

    International Nuclear Information System (INIS)

    Adair, H.L.; Kobisk, E.H.

    1985-01-01

    This chapter examines the characteristics of targets required in heavy-ion accelerator physics experiments. The effects of target parameters on heavy-ion experimental results are reviewed. The target fabrication and characterization techniques used to minimize experimental problems during heavy-ion bombardment are described. Topics considered include target thickness and uniformity, target lifetime, target purity, substrate materials, Doppler shift effects, metal preparations, and target preparation methods

  4. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

    Science.gov (United States)

    de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

    2012-10-04

    Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  5. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    Directory of Open Access Journals (Sweden)

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  6. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

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    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  7. Identifying the catalytic components of cellulose synthase and the maize mixed-linkage beta-glucan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Nicholas C Carpita

    2009-04-20

    Five specific objectives of this project are to develop strategies to identify the genes that encode the catalytic components of "mixed-linkage" (1→3),(1→4)-beta-D-glucans in grasses, to determine the protein components of the synthase complex, and determine the biochemical mechanism of synthesis. We have used proteomic approaches to define intrinsic and extrinsic polypeptides of Golgi membranes that are associated with polysaccharide synthesis and trafficking. We were successful in producing recombinant catalytic domains of cellulose synthase genes and discovered that they dimerize upon concentration, indicating that two CesA proteins form the catalytic unit. We characterized a brittle stalk2 mutant as a defect in a COBRA-like protein that results in compromised lignin-cellulose interactions that decrease tissue flexibility. We used virus-induced gene silencing of barley cell wall polysaccharide synthesis by BSMV in an attempt to silence specific members of the cellulose synthase-like gene family. However, we unexpectedly found that regardless of the specificity of the target gene, whole gene interaction networks were silenced. We discovered the cause to be an antisense transcript of the cellulose synthase gene initiated small interfering RNAs that spread silencing to related genes.

  8. The relationship between CO2 emission, energy consumption and economic growth in Malaysia: a three-way linkage approach.

    Science.gov (United States)

    Sulaiman, Chindo; Abdul-Rahim, A S

    2017-11-01

    This study examines the three-way linkage relationships between CO 2 emission, energy consumption and economic growth in Malaysia, covering the 1975-2015 period. An autoregressive distributed lag approach was employed to achieve the objective of the study and gauged by dynamic ordinary least squares. Additionally, vector error correction model, variance decompositions and impulse response functions were employed to further examine the relationship between the interest variables. The findings show that economic growth is neither influenced by energy consumption nor by CO 2 emission. Energy consumption is revealed to be an increasing function of CO 2 emission. Whereas, CO 2 emission positively and significantly depends on energy consumption and economic growth. This implies that CO 2 emission increases with an increase in both energy consumption and economic growth. Conclusively, the main drivers of CO 2 emission in Malaysia are proven to be energy consumption and economic growth. Therefore, renewable energy sources ought to be considered by policy makers to curb emission from the current non-renewable sources. Wind and biomass can be explored as they are viable sources. Energy efficiency and savings should equally be emphasised and encouraged by policy makers. Lastly, growth-related policies that target emission reduction are also recommended.

  9. Knowledge, perceptions and practices of farming communities on linkages between malaria and agriculture in Mvomero District, Tanzania.

    Science.gov (United States)

    Mboera, Leonard E G; Shayo, Elizabeth H; Senkoro, Kesheni P; Rumisha, Susan F; Mlozi, Malongo R S; Mayala, Benjamin K

    2010-02-01

    This study was carried out to determine knowledge, perceptions and practices of farming communities on linkages between agriculture and malaria in Mvomero District in Tanzania. A total of 661 adult males and females were interviewed using a structured questionnaire. Most respondents (85.6%) were engaged in crop production. Significantly, a larger proportion (55.2%) of the respondents had primary school education (Pfarming was significantly associated with malaria transmission compared to either maize or sugarcane farming (Pgoats were the domestic animals most frequently incriminated to create aquatic habitats for mosquito breeding. Householders with formal education (OR: 4.6, CI: 1.33-15.89, P-value=0.016) and higher knowledge (OR: 1.7, CI: 1.15-2.55, P-value=0.008) reported to incur large losses when having a malaria case than those without education/low knowledge. Majority (60.2%) of the respondent owned at least an insecticide treated mosquito net (ITN). Respondents with higher knowledge of malaria were likely to own at least an ITN than those with low knowledge (Pfarming communities in Mvomero District is low. Malaria is a complex health problem and its control approach needs understanding of the environmental factors associated with agricultural practices. It therefore is important that education and communication messages on malaria targeting farming communities take into consideration local agricultural practices. Copyright 2009 Elsevier B.V. All rights reserved.

  10. HTLV-1 Tax Functions as a Ubiquitin E3 Ligase for Direct IKK Activation via Synthesis of Mixed-Linkage Polyubiquitin Chains.

    Science.gov (United States)

    Wang, Chong; Long, Wenying; Peng, Chao; Hu, Lin; Zhang, Qiong; Wu, Ailing; Zhang, Xiaoqing; Duan, Xiaotao; Wong, Catherine C L; Tanaka, Yuetsu; Xia, Zongping

    2016-04-01

    The HTLV-1 oncoprotein Tax plays a key role in CD4+ T cell transformation by promoting cell proliferation and survival, mainly through permanent activation of the NK-κB pathway and induction of many NF-κB target genes. Elucidating the underlying molecular mechanism is therefore critical in understanding HTLV-1-mediated transformation. Current studies have suggested multiple but controversial mechanisms regarding Tax-induced IKK activation mainly due to blending of primary Tax-induced IKK activation events and secondary IKK activation events induced by cytokines secreted by the primary Tax-induced IKK-NF-κB activation events. We reconstituted Tax-stimulated IKK activation in a cell-free system to dissect the essential cellular components for primary IKK activation by Tax and studied the underlying biochemical mechanism. We found that Tax is a putative E3 ubiquitin ligase, which, together with UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of free mixed-linkage polyubiquitin chains. These free mixed-linkage polyubiquitin chains are then responsible for direct IKK activation by binding to the NEMO subunit of IKK. Our studies revealed the biochemical function of Tax in the process of IKK activation, which utilizes the minimal cellular ubiquitination components for NF-κB activation.

  11. HTLV-1 Tax Functions as a Ubiquitin E3 Ligase for Direct IKK Activation via Synthesis of Mixed-Linkage Polyubiquitin Chains.

    Directory of Open Access Journals (Sweden)

    Chong Wang

    2016-04-01

    Full Text Available The HTLV-1 oncoprotein Tax plays a key role in CD4+ T cell transformation by promoting cell proliferation and survival, mainly through permanent activation of the NK-κB pathway and induction of many NF-κB target genes. Elucidating the underlying molecular mechanism is therefore critical in understanding HTLV-1-mediated transformation. Current studies have suggested multiple but controversial mechanisms regarding Tax-induced IKK activation mainly due to blending of primary Tax-induced IKK activation events and secondary IKK activation events induced by cytokines secreted by the primary Tax-induced IKK-NF-κB activation events. We reconstituted Tax-stimulated IKK activation in a cell-free system to dissect the essential cellular components for primary IKK activation by Tax and studied the underlying biochemical mechanism. We found that Tax is a putative E3 ubiquitin ligase, which, together with UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of free mixed-linkage polyubiquitin chains. These free mixed-linkage polyubiquitin chains are then responsible for direct IKK activation by binding to the NEMO subunit of IKK. Our studies revealed the biochemical function of Tax in the process of IKK activation, which utilizes the minimal cellular ubiquitination components for NF-κB activation.

  12. A combination intervention strategy to improve linkage to and retention in HIV care following diagnosis in Mozambique: A cluster-randomized study.

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    Batya Elul

    2017-11-01

    Full Text Available Concerning gaps in the HIV care continuum compromise individual and population health. We evaluated a combination intervention strategy (CIS targeting prevalent barriers to timely linkage and sustained retention in HIV care in Mozambique.In this cluster-randomized trial, 10 primary health facilities in the city of Maputo and Inhambane Province were randomly assigned to provide the CIS or the standard of care (SOC. The CIS included point-of-care CD4 testing at the time of diagnosis, accelerated ART initiation, and short message service (SMS health messages and appointment reminders. A pre-post intervention 2-sample design was nested within the CIS arm to assess the effectiveness of CIS+, an enhanced version of the CIS that additionally included conditional non-cash financial incentives for linkage and retention. The primary outcome was a combined outcome of linkage to care within 1 month and retention at 12 months after diagnosis. From April 22, 2013, to June 30, 2015, we enrolled 2,004 out of 5,327 adults ≥18 years of age diagnosed with HIV in the voluntary counseling and testing clinics of participating health facilities: 744 (37% in the CIS group, 493 (25% in the CIS+ group, and 767 (38% in the SOC group. Fifty-seven percent of the CIS group achieved the primary outcome versus 35% in the SOC group (relative risk [RR]CIS vs SOC = 1.58, 95% CI 1.05-2.39. Eighty-nine percent of the CIS group linked to care on the day of diagnosis versus 16% of the SOC group (RRCIS vs SOC = 9.13, 95% CI 1.65-50.40. There was no significant benefit of adding financial incentives to the CIS in terms of the combined outcome (55% of the CIS+ group achieved the primary outcome, RRCIS+ vs CIS = 0.96, 95% CI 0.81-1.16. Key limitations include the use of existing medical records to assess outcomes, the inability to isolate the effect of each component of the CIS, non-concurrent enrollment of the CIS+ group, and exclusion of many patients newly diagnosed with HIV.The CIS

  13. Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

    Science.gov (United States)

    Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

    2012-01-01

    Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference

  14. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

    Directory of Open Access Journals (Sweden)

    César D Petroli

    Full Text Available Diversity Arrays Technology (DArT provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for

  15. Linkage to HIV care after home-based HIV counselling and testing in sub-Saharan Africa: a systematic review.

    Science.gov (United States)

    Ruzagira, Eugene; Baisley, Kathy; Kamali, Anatoli; Biraro, Samuel; Grosskurth, Heiner

    2017-07-01

    Home-based HIV counselling and testing (HBHCT) has the potential to increase HIV testing uptake in sub-Saharan Africa (SSA), but data on linkage to HIV care after HBHCT are scarce. We conducted a systematic review of linkage to care after HBHCT in SSA. Five databases were searched for studies published between 1st January 2000 and 19th August 2016 that reported on linkage to care among adults newly identified with HIV infection through HBHCT. Eligible studies were reviewed, assessed for risk of bias and findings summarised using the PRISMA guidelines. A total of 14 studies from six countries met the eligibility criteria; nine used specific strategies (point-of-care CD4 count testing, follow-up counselling, provision of transport funds to clinic and counsellor facilitation of HIV clinic visit) in addition to routine referral to facilitate linkage to care. Time intervals for ascertaining linkage ranged from 1 week to 12 months post-HBHCT. Linkage ranged from 8.2% [95% confidence interval (CI), 6.8-9.8%] to 99.1% (95% CI, 96.9-99.9%). Linkage was generally lower (80%) if additional strategies were used. Only one study assessed linkage by means of a randomised trial. Five studies had data on cotrimoxazole (CTX) prophylaxis and 12 on ART eligibility and initiation. CTX uptake among those eligible ranged from 0% to 100%. The proportion of persons eligible for ART ranged from 16.5% (95% CI, 12.1-21.8) to 77.8% (95% CI, 40.0-97.2). ART initiation among those eligible ranged from 14.3% (95% CI, 0.36-57.9%) to 94.9% (95% CI, 91.3-97.4%). Additional linkage strategies, whilst seeming to increase linkage, were not associated with higher uptake of CTX and/or ART. Most of the studies were susceptible to risk of outcome ascertainment bias. A pooled analysis was not performed because of heterogeneity across studies with regard to design, setting and the key variable definitions. Only few studies from SSA investigated linkage to care among adults newly diagnosed with HIV through

  16. Effectiveness of a combination strategy for linkage and retention in adult HIV care in Swaziland: The Link4Health cluster randomized trial.

    Directory of Open Access Journals (Sweden)

    Margaret L McNairy

    2017-11-01

    Full Text Available Gaps in the HIV care continuum contribute to poor health outcomes and increase HIV transmission. A combination of interventions targeting multiple steps in the continuum is needed to achieve the full beneficial impact of HIV treatment.Link4Health, a cluster-randomized controlled trial, evaluated the effectiveness of a combination intervention strategy (CIS versus the standard of care (SOC on the primary outcome of linkage to care within 1 month plus retention in care at 12 months after HIV-positive testing. Ten clusters of HIV clinics in Swaziland were randomized 1:1 to CIS versus SOC. The CIS included point-of-care CD4+ testing at the time of an HIV-positive test, accelerated antiretroviral therapy (ART initiation for treatment-eligible participants, mobile phone appointment reminders, health educational packages, and noncash financial incentives. Secondary outcomes included each component of the primary outcome, mean time to linkage, assessment for ART eligibility, ART initiation and time to ART initiation, viral suppression defined as HIV-1 RNA < 1,000 copies/mL at 12 months after HIV testing among patients on ART ≥6 months, and loss to follow-up and death at 12 months after HIV testing. A total of 2,197 adults aged ≥18 years, newly tested HIV positive, were enrolled from 19 August 2013 to 21 November 2014 (1,096 CIS arm; 1,101 SOC arm and followed for 12 months. The median participant age was 31 years (IQR 26-39, and 59% were women. In an intention-to-treat analysis, 64% (705/1,096 of participants at the CIS sites achieved the primary outcome versus 43% (477/1,101 at the SOC sites (adjusted relative risk [RR] 1.52, 95% CI 1.19-1.96, p = 0.002. Participants in the CIS arm versus the SOC arm had the following secondary outcomes: linkage to care regardless of retention at 12 months (RR 1.08, 95% CI 0.97-1.21, p = 0.13, mean time to linkage (2.5 days versus 7.5 days, p = 0.189, retention in care at 12 months regardless of time to linkage (RR

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

    Science.gov (United States)

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

    2017-10-31

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

  18. Reclink: aplicativo para o relacionamento de bases de dados, implementando o método probabilistic record linkage Reclink: an application for database linkage implementing the probabilistic record linkage method

    Directory of Open Access Journals (Sweden)

    Kenneth R. de Camargo Jr.

    2000-06-01

    Full Text Available Apresenta-se um sistema de relacionamento de bases de dados fundamentado na técnica de relacionamento probabilístico de registros, desenvolvido na linguagem C++ com o ambiente de programação Borland C++ Builder versão 3.0. O sistema foi testado a partir de fontes de dados de diferentes tamanhos, tendo sido avaliado em tempo de processamento e sensibilidade para a identificação de pares verdadeiros. O tempo gasto com o processamento dos registros foi menor quando se empregou o programa do que ao ser realizado manualmente, em especial, quando envolveram bases de maior tamanho. As sensibilidades do processo manual e do processo automático foram equivalentes quando utilizaram bases com menor número de registros; entretanto, à medida que as bases aumentaram, percebeu-se tendência de diminuição na sensibilidade apenas no processo manual. Ainda que em fase inicial de desenvolvimento, o sistema apresentou boa performance tanto em velocidade quanto em sensibilidade. Embora a performance dos algoritmos utilizados tenha sido satisfatória, o objetivo é avaliar outras rotinas, buscando aprimorar o desempenho do sistema.This paper presents a system for database linkage based on the probabilistic record linkage technique, developed in the C++ language with the Borland C++ Builder version 3.0 programming environment. The system was tested in the linkage of data sources of different sizes, evaluated both in terms of processing time and sensitivity for identifying true record pairs. Significantly less time was spent in record processing when the program was used, as compared to manual processing, especially in situations where larger databases were used. Manual and automatic processes had equivalent sensitivities in situations where we used databases with fewer records. However, as the number of records grew we noticed a clear reduction in the sensitivity of the manual process, but not in the automatic one. Although in its initial stage of

  19. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

  20. Analysis of sulfidic linkages formed in natural rubber latex medical gloves by using X-ray absorption near edge structure

    Science.gov (United States)

    Chankrachang, M.; Limphirat, W.; Yongyingsakthavorn, P.; Nontakaew, U.; Tohsan, A.

    2017-09-01

    A study of sulfidic linkages formed in natural rubber (NR) latex medical gloves by using X-ray Absorption Near Edge Structure (XANES) is presented in this paper. The NR latex compound was prepared by using prevulcanization method, that is, it was prevulcanized at room temperature for 24 hrs before utilization. After the 24 hrs of prevulcanization, the latex film samples were obtained by dipping process. The dipped films were subjected to vulcanize at 110°C for 5 to 25 min. It was observed that after the compound was prevulcanized for 24 hrs, polysulfidic linkages were mainly formed in the sample. It was however found that after curing at 110°C for 5-25 min, the polysulfidic linkages are tended to change into disulfide linkages. Especially, in the case of 25 minutes cured sample, disulfide linkages are found to be the main linkages. In term of tensile strength, it was observed that when cure time increased from 5 - 10 min, tensile strengths were also increased. But when the cure time of the film is 25 minutes, tensile strength was slightly dropped. The dropped of tensile strength when cure time is longer than 10 minutes can be ascribed to a degradation of polysulfidic and disulfidic linkages during curing. Therefore, by using XANES analysis, it was found to be very useful to understand the cure characteristic, thus it can be very helpful to optimize cure time and tensile properties of the product.

  1. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

    Directory of Open Access Journals (Sweden)

    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  2. Initial Reactivity of Linkages and Monomer Rings in Lignin Pyrolysis Revealed by ReaxFF Molecular Dynamics.

    Science.gov (United States)

    Zhang, Tingting; Li, Xiaoxia; Guo, Li

    2017-10-24

    The initial conversion pathways of linkages and their linked monomer units in lignin pyrolysis were investigated comprehensively by ReaxFF MD simulations facilitated by the unique VARxMD for reaction analysis. The simulated molecular model contains 15 920 atoms and was constructed on the basis of Adler's softwood lignin model. The simulations uncover the initial conversion ratio of various linkages and their linked aryl monomers. For linkages and their linked monomer aryl rings of α-O-4, β-O-4 and α-O-4 & β-5, the C α /C β ether bond cracking dominates the initial pathway accounting for at least up to 80% of their consumption. For the linkage of β-β & γ-O-α, both the C α -O ether bond cracking and its linked monomer aryl ring opening are equally important. Ring-opening reactions dominate the initial consumption of other 4-O-5, 5-5, β-1, β-2, and β-5 linkages and their linked monomers. The ether bond cracking of C α -O and C β -O occurs at low temperature, and the aryl ring-opening reactions take place at relatively high temperature. The important intermediates leading to the stable aryl ring opening are the phenoxy radicals, the bridged five-membered and three-membered rings and the bridged six-membered and three-membered rings. In addition, the reactivity of a linkage and its monomer aryl ring may be affected by other linkages. The ether bond cracking of α-O-4 and β-O-4 linkages can activate its neighboring linkage or monomer ring through the formed phenoxy radicals as intermediates. The important intermediates revealed in this article should be of help in deepening the understanding of the controlling mechanism for producing aromatic chemicals from lignin pyrolysis.

  3. A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer

    International Nuclear Information System (INIS)

    Middeldorp, Anneke; Wijnen, Juul T; Wezel, Tom van; Jagmohan-Changur, Shantie; Helmer, Quinta; Klift, Heleen M van der; Tops, Carli MJ; Vasen, Hans FA; Devilee, Peter; Morreau, Hans; Houwing-Duistermaat, Jeanine J

    2007-01-01

    The apparent dominant model of colorectal cancer (CRC) inheritance in several large families, without mutations in known CRC susceptibility genes, suggests the presence of so far unidentified genes with strong or moderate effect on the development of CRC. Linkage analysis could lead to identification of susceptibility genes in such families. In comparison to classical linkage analysis with multi-allelic markers, single nucleotide polymorphism (SNP) arrays have increased information content and can be processed with higher throughput. Therefore, SNP arrays can be excellent tools for linkage analysis. However, the vast number of SNPs on the SNP arrays, combined with large informative pedigrees (e.g. >35–40 bits), presents us with a computational complexity that is challenging for existing statistical packages or even exceeds their capacity. We therefore setup a procedure for linkage analysis in large pedigrees and validated the method by genotyping using SNP arrays of a colorectal cancer family with a known MLH1 germ line mutation. Quality control of the genotype data was performed in Alohomora, Mega2 and SimWalk2, with removal of uninformative SNPs, Mendelian inconsistencies and Mendelian consistent errors, respectively. Linkage disequilibrium was measured by SNPLINK and Merlin. Parametric linkage analysis using two flanking markers was performed using MENDEL. For multipoint parametric linkage analysis and haplotype analysis, SimWalk2 was used. On chromosome 3, in the MLH1-region, a LOD score of 1.9 was found by parametric linkage analysis using two flanking markers. On chromosome 11 a small region with LOD 1.1 was also detected. Upon linkage disequilibrium removal, multipoint linkage analysis yielded a LOD score of 2.1 in the MLH1 region, whereas the LOD score dropped to negative values in the region on chromosome 11. Subsequent haplotype analysis in the MLH1 region perfectly matched the mutation status of the family members. We developed a workflow for linkage

  4. Construction of the All-region Linkage System for Emergency Management of Agricultural Product Quality and Safety in West China

    Institute of Scientific and Technical Information of China (English)

    Hua; YU; Yanbin; QI; Yubao; YAN

    2013-01-01

    Quality and safety of agricultural products are significant for national socioeconomic development,sustainable development,and vital interests of people.To safeguard quality and safety of agricultural products in west China is to safeguard economic safety and ecological safety of the country,public health and social stability,of which an important task is to properly handle emergencies concerning quality and safety of agricultural products.Considering actual conditions of west China,suggestions are given to construct the all-region linkage system for emergency management of agricultural product quality and safety in the local area,enhance the all-region linkage,and improve the linkage efficiency.

  5. Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

    Science.gov (United States)

    Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

    2002-01-01

    Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

  6. Nonsyndromic cleft lip and palate: No evidence of linkage to HLA or factor 13A

    Energy Technology Data Exchange (ETDEWEB)

    Hecht, J.T.; Yaping Wang; Connor, B.; Daiger, S.P. (Univ. of Texas, Houston (United States)); Blanton, S.H. (Univ. of Texas, Houston (United States) Univ. of Virginia, Charlottesville (United States))

    1993-06-01

    Nonsyndromic cleft lip with or without cleft palate (CLP) is a common craniofacial anomaly, the etiology of which is not known. Population studies have shown that a large proportion of cases occur sporadically. Recently, segregation analyses applied to CLP families have demonstrated that an autosomal dominant/codominant gene(s) may cause clefting in cases. Associations of autosomal dominant CLP and nonsyndromic cleft palate (CP) with HLA and F13A genes on chromosome 6p have been suggested previously. Linkage to these two areas on chromosome 6p were tested in 12 autosomal dominant families with CLP. With a LOD score of [minus]2 or less for exclusion, no evidence of linkage was found to four chromosome 6p markers. Multipoint analysis showed no evidence of a clefting locus in this region spanning 54 cM on chromosome 6p in these CLP families. 30 refs., 2 figs., 1 tab.

  7. A genome-wide linkage study of bipolar disorder and co-morbid migraine

    DEFF Research Database (Denmark)

    Oedegaard, K. J.; Greenwood, T. A.; Lunde, Asger

    2010-01-01

    Migraine and Bipolar Disorder (BPAD) are clinically heterogeneous disorders of the brain with a significant, but complex, genetic component. Epidemiological and clinical studies have demonstrated a high degree of co-morbidity between migraine and BPAD. Several genomewide linkage studies in BPAD...... that using migraine comorbidity to look at subsets of BPAD families in a genetic linkage analysis would prove useful in identifying genetic susceptibility regions in both of these disorders. We used BPAD with comorbid migraine as an alternative phenotype definition in a re-analysis of the NIMH Bipolar...... osome 4 (not co-segregating with BPAD) in a sample of BPAD families with comorbid migraine, and suggest a susceptibility locus on chromosome 20, harboring a gene for the migraine/BPAD phenotype. Together these data suggest that some genes may predispose to both bipolar disorder and migraine....

  8. Pronounced photosensitivity of molecular [Ru(bpy)2(OSO)]+ solutions based on two photoinduced linkage isomers.

    Science.gov (United States)

    Dieckmann, Volker; Eicke, Sebastian; Rack, Jeffrey J; Woike, Theo; Imlau, Mirco

    2009-08-17

    Photosensitive properties of [Ru(bpy)(2)(OSO)] PF(6) dissolved in propylene carbonate originating from photoinduced linkage isomerism have been studied by temperature and exposure dependent transmission and UV/Vis absorption spectroscopy. An exceeding photochromic photosensitivity of S = (63 +/- 10) x 10(3) cm l J(-1) mol(-1) is determined. It is attributed to a maximum population of 100% molecules in the photoinduced isomers, a unique absorption cross section per molecule and a very low light exposure of Q(0) = (0.25 +/- 0.03) Ws cm(-2) for isomerism. Relaxation studies of O-bonded to S-bonded isomers at different temperatures verify the existence of two distinct structures of linkage isomers determined by the activation energies of E(A,1) = (0.76 +/- 0.08) eV and E(A,2) = (1.00 +/- 0.14) eV.

  9. Design, modeling and optimization of an underwater manipulator with four-bar mechanism and compliant linkage

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Sang Ok; Kim, Ji Hoon; Bae, Jang Ho; Kim, Jong Won [School of Mechanical and Aerospace Engineering, Seoul National University, Seoul (Korea, Republic of); Seo, Tae Won [School of Mechanical Engineering, Yeungnam University, Gyeongsan (Korea, Republic of)

    2016-09-15

    Underwater manipulators are very important for a robot to perform a specific operation in water. Conventional robot arm manipulators have been suggested for various operations but have not been suitable for repeated motion in gathering something. This paper presents a new underwater manipulator design for gathering things such as starfish on the sea floor. The manipulator is composed of a four-bar linkage to achieve repeated motion along a loop and compliant linkages to enhance the efficiency of the gathering work. Kinematic and quasi-static analyses were performed to calculate the loop path and the reaction force at the actuation point. Based on the analysis, optimal design was performed to maximize the working distance with the height difference and the reaction moments considered as constraints. A prototype was assembled to test the performance of the manipulator, and the empirical loop path was compared to simulation results.

  10. Design, modeling and optimization of an underwater manipulator with four-bar mechanism and compliant linkage

    International Nuclear Information System (INIS)

    Jin, Sang Ok; Kim, Ji Hoon; Bae, Jang Ho; Kim, Jong Won; Seo, Tae Won

    2016-01-01

    Underwater manipulators are very important for a robot to perform a specific operation in water. Conventional robot arm manipulators have been suggested for various operations but have not been suitable for repeated motion in gathering something. This paper presents a new underwater manipulator design for gathering things such as starfish on the sea floor. The manipulator is composed of a four-bar linkage to achieve repeated motion along a loop and compliant linkages to enhance the efficiency of the gathering work. Kinematic and quasi-static analyses were performed to calculate the loop path and the reaction force at the actuation point. Based on the analysis, optimal design was performed to maximize the working distance with the height difference and the reaction moments considered as constraints. A prototype was assembled to test the performance of the manipulator, and the empirical loop path was compared to simulation results

  11. Optimal Monetary Policy with Durable Consumption Goods and Factor Demand Linkages

    DEFF Research Database (Denmark)

    Petrella, Ivan; Santoro, Emiliano

    of production in both sectors, according to an input-output matrix calibrated on the US economy. As shown in a number of recent contributions, this roundabout technology allows us to reconcile standard two-sector New Keynesian models with the empirical evidence showing co-movement between durable and non......-durable spending in response to a monetary policy shock. A main result of our monetary policy analysis is that strategic complementarities generated by factor demand linkages amplify social welfare loss. As the degree of interconnection between sectors increases, the cost of misperceiving the correct production......This paper deals with the implications of factor demand linkages for monetary policy design. We develop a dynamic general equilibrium model with two sectors that produce durable and non-durable goods, respectively. Part of the output produced in each sector is used as an intermediate input...

  12. New heparin–indomethacin conjugate with an ester linkage: Synthesis, self aggregation and drug delivery behavior

    Energy Technology Data Exchange (ETDEWEB)

    Li, Nan-Nan; Zheng, Bing-Na [DSAPM Lab and PCFM Lab, Institute of Polymer Science, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Lin, Jian-Tao [DSAPM Lab and PCFM Lab, Institute of Polymer Science, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Guangdong Medical College, Dongguan 523808 (China); Zhang, Li-Ming, E-mail: ceszhlm@mail.sysu.edu.cn [DSAPM Lab and PCFM Lab, Institute of Polymer Science, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China)

    2014-01-01

    New heparin–indomethacin conjugate with an ester linkage was prepared by the carbodiimide-mediated condensation reaction, and then characterized by FTIR and {sup 1}HNMR analyses. Due to its amphiphilic character, such a conjugate could self-aggregate into spherical nanoparticles in aqueous system, as confirmed by fluorescence spectroscopy, dynamic light scattering and transmission electron microscopy. By the in vitro drug release tests, the resultant conjugate nanoparticles were found to have a sustained and esterase-sensitive release behavior for conjugated indomethacin. In addition, the uptake of these conjugate nanoparticles into human nasopharyngeal carcinoma CNE1 cells was confirmed by fluorescence microscopy. - Highlights: • New heparin–indomethacin conjugate with an ester linkage was prepared. • Such a conjugate could self-aggregate into spherical nanoparticles in aqueous system. • The resultant conjugate nanoparticles exhibited an esterase-sensitive drug release behavior. • The resultant conjugate nanoparticles showed the cellular uptake ability in CNE1 cells.

  13. PSMA-targeted bispecific Fab conjugates that engage T cells.

    Science.gov (United States)

    Patterson, James T; Isaacson, Jason; Kerwin, Lisa; Atassi, Ghazi; Duggal, Rohit; Bresson, Damien; Zhu, Tong; Zhou, Heyue; Fu, Yanwen; Kaufmann, Gunnar F

    2017-12-15

    Bioconjugate formats provide alternative strategies for antigen targeting with bispecific antibodies. Here, PSMA-targeted Fab conjugates were generated using different bispecific formats. Interchain disulfide bridging of an αCD3 Fab enabled installation of either the PSMA-targeting small molecule DUPA (SynFab) or the attachment of an αPSMA Fab (BisFab) by covalent linkage. Optimization of the reducing conditions was critical for selective interchain disulfide reduction and good bioconjugate yield. Activity of αPSMA/CD3 Fab conjugates was tested by in vitro cytotoxicity assays using prostate cancer cell lines. Both bispecific formats demonstrated excellent potency and antigen selectivity. Copyright © 2017. Published by Elsevier Ltd.

  14. Trait Emotional Intelligence and Personality: Gender-Invariant Linkages Across Different Measures of the Big Five.

    OpenAIRE

    Siegling, A. B.; Furnham, A.; Petrides, K. V.

    2015-01-01

    This study investigated if the linkages between trait emotional intelligence (trait EI) and the Five-Factor Model of personality were invariant between men and women. Five English-speaking samples (N = 307-685) of mostly undergraduate students each completed a different measure of the Big Five personality traits and either the full form or short form of the Trait Emotional Intelligence Questionnaire (TEIQue). Across samples, models predicting global TEIQue scores from the Big Five were invari...

  15. Young people’s views about consenting to data linkage: Findings from the PEARL qualitative study

    Directory of Open Access Journals (Sweden)

    Suzanne Audrey

    2017-04-01

    Findings from this study question the validity of ‘informed consent’ as a cornerstone of good governance, and the extent to which potential research participants understand different types of consent and what they are consenting, or not consenting, to. Pragmatic, imaginative and flexible approaches are needed if research using data linkage is to successfully realise its potential for public good without undermining public trust in the research process.

  16. The prune belly anomaly: heterogeneity and superficial X-linkage mimicry.

    Science.gov (United States)

    Riccardi, V M; Grum, C M

    1977-01-01

    The genetic, clinical, and necropsy findings of 2 brothers with the prune belly anomaly are presented and the literature reviewed. The combined data emphasise the clinical and genetic heterogeneity of the disorder and show that in at least some instances a heritable component may be the primary insult. The most likely heritable explanation involves a two-step autosomal dominant mutation with sex-limited expression that partially mimics X-linkage. PMID:144797

  17. A Multipoint Method for Detecting Genotyping Errors and Mutations in Sibling-Pair Linkage Data

    OpenAIRE

    Douglas, Julie A.; Boehnke, Michael; Lange, Kenneth

    2000-01-01

    The identification of genes contributing to complex diseases and quantitative traits requires genetic data of high fidelity, because undetected errors and mutations can profoundly affect linkage information. The recent emphasis on the use of the sibling-pair design eliminates or decreases the likelihood of detection of genotyping errors and marker mutations through apparent Mendelian incompatibilities or close double recombinants. In this article, we describe a hidden Markov method for detect...

  18. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd

    OpenAIRE

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 9...

  19. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas.

    Science.gov (United States)

    Hippolyte, Isabelle; Bakry, Frederic; Seguin, Marc; Gardes, Laetitia; Rivallan, Ronan; Risterucci, Ange-Marie; Jenny, Christophe; Perrier, Xavier; Carreel, Françoise; Argout, Xavier; Piffanelli, Pietro; Khan, Imtiaz A; Miller, Robert N G; Pappas, Georgios J; Mbéguié-A-Mbéguié, Didier; Matsumoto, Takashi; De Bernardinis, Veronique; Huttner, Eric; Kilian, Andrzej; Baurens, Franc-Christophe; D'Hont, Angélique; Cote, François; Courtois, Brigitte; Glaszmann, Jean-Christophe

    2010-04-13

    The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.

  20. Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage

    Czech Academy of Sciences Publication Activity Database

    Králíková, Šárka; Buděšínský, Miloš; Barvík, I.; Masojídková, Milena; Točík, Zdeněk; Rosenberg, Ivan

    2011-01-01

    Roč. 30, 7/9 (2011), s. 524-543 ISSN 1525-7770 R&D Projects: GA ČR GA202/09/0193; GA AV ČR KAN200520801; GA MŠk(CZ) LC06061 Institutional research plan: CEZ:AV0Z40550506 Keywords : alpha-hydroxy-phosphonate linkage * ApA analogues * phosphonate internucleotide bond * NMR conformational study Subject RIV: CC - Organic Chemistry Impact factor: 0.899, year: 2011

  1. Combined segregation and linkage analysis of genetic hemochromatosis using affection status, serum iron, and HLA.

    OpenAIRE

    Borecki, I B; Lathrop, G M; Bonney, G E; Yaouanq, J; Rao, D C

    1990-01-01

    Characterizing the distribution of parameters of iron metabolism by hemochromatosis genotype remains an important goal vis-à-vis potential screening strategies to identify individuals at genetic risk, since a specific marker to detect the abnormal gene has not been identified as yet. In the present investigation, we analyze serum iron values in ascertained families using a method which incorporates both segregation of the clinical affection status and the HLA linkage information to identify t...

  2. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae

    Directory of Open Access Journals (Sweden)

    Nakatsuka Takashi

    2012-11-01

    Full Text Available Abstract Background Japanese gentians (Gentiana triflora and Gentiana scabra are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR sequences using the recently developed inter-primer binding site (iPBS method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP markers combining retrotransposon and inter-simple sequence repeat (ISSR markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP and random amplification polymorphic DNA (RAPD markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers. One phenotypic trait (stem color and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map

  3. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae)

    OpenAIRE

    Nakatsuka, Takashi; Yamada, Eri; Saito, Misa; Hikage, Takashi; Ushiku, Yuka; Nishihara, Masahiro

    2012-01-01

    Abstract Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enr...

  4. Hybrid scaffold bearing polymer-siloxane Schiff base linkage for bone tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Nair, Bindu P., E-mail: bindumelekkuttu@gmail.com; Gangadharan, Dhanya; Mohan, Neethu; Sumathi, Babitha; Nair, Prabha D., E-mail: pdnair49@gmail.com

    2015-07-01

    Scaffolds that can provide the requisite biological cues for the fast regeneration of bone are highly relevant to the advances in tissue engineering and regenerative medicine. In the present article, we report the fabrication of a chitosan–gelatin–siloxane scaffold bearing interpolymer-siloxane Schiff base linkage, through a single-step dialdehyde cross-linking and freeze-drying method using 3-aminopropyltriethoxysilane as the siloxane precursor. Swelling of the scaffolds in phosphate buffered saline indicates enhancement with increase in siloxane concentration, whereas compressive moduli of the wet scaffolds reveal inverse dependence, owing to the presence of siloxane, rich in silanol groups. It is suggested that through the strategy of dialdehyde cross-linking, a limiting siloxane loading of 20 wt.% into a chitosan-gelatin matrix should be considered ideal for bone tissue engineering, because the scaffold made with 30 wt.% siloxane loading degrades by 48 wt.%, in 21 days. The hybrid scaffolds bearing Schiff base linkage between the polymer and siloxane, unlike the stable linkages in earlier reports, are expected to give a faster release of siloxanes and enhancement in osteogenesis. This is verified by the in vitro evaluation of the hybrid scaffolds using rabbit adipose mesenchymal stem cells, which revealed osteogenic cell-clusters on a polymer-siloxane scaffold, enhanced alkaline phosphatase activity and the expression of bone-specific genes, whereas the control scaffold without siloxane supported more of cell-proliferation than differentiation. A siloxane concentration dependent enhancement in osteogenic differentiation is also observed. - Highlights: • A hybrid scaffold bearing interpolymer-siloxane Schiff base linkage • A limiting siloxane loading of 20 wt.% into chitosan–gelatin matrix • A siloxane concentration dependent enhancement in osteogenic differentiation.

  5. PLAB and UK graduates' performance on MRCP(UK) and MRCGP examinations: data linkage study

    OpenAIRE

    McManus, I. C.; Wakeford, R.

    2014-01-01

    OBJECTIVES: To assess whether international medical graduates passing the two examinations set by the Professional and Linguistic Assessments Board (PLAB1 and PLAB2) of the General Medical Council (GMC) are equivalent to UK graduates at the end of the first foundation year of medical training (F1), as the GMC requires, and if not, to assess what changes in the PLAB pass marks might produce equivalence. DESIGN: Data linkage of GMC PLAB performance data with data from the Royal Colleges of Phys...

  6. Historical measures of social context in life course studies: retrospective linkage of addresses to decennial censuses

    Directory of Open Access Journals (Sweden)

    Whitsel Eric A

    2004-11-01

    Full Text Available Abstract Background There is evidence of a contribution of early life socioeconomic exposures to the risk of chronic diseases in adulthood. However, extant studies investigating the impact of the neighborhood social environment on health tend to characterize only the current social environment. This in part may be due to complexities involved in obtaining and geocoding historical addresses. The Life Course Socioeconomic Status, Social Context, and Cardiovascular Disease Study collected information on childhood (1930–1950 and early adulthood (1960–1980 place of residence from 12,681 black and white middle-aged and older men and women from four U.S. communities to link participants with census-based socioeconomic indicators over the life course. Results Most (99% participants were linked to 1930–50 county level socioeconomic census data (the smallest level of aggregation universally available during this time period corresponding to childhood place of residence. Linkage did not vary by race, gender, birth cohort, or level of educational attainment. A commercial geocoding vendor processed participants' self-reported street addresses for ages 30, 40, and 50. For 1970 and 1980 censuses, spatial coordinates were overlaid onto shape files containing census tract boundaries; for 1960 no shape files existed and comparability files were used. Several methods were tested for accuracy and to increase linkage. Successful linkage to historical census tracts varied by census (66% for 1960, 76% for 1970, 85% for 1980. This compares to linkage rates of 94% for current addresses provided by participants over the course of the ARIC examinations. Conclusion There are complexities and limitations in characterizing the past social context. However, our results suggest that it is feasible to characterize the earlier social environment with known levels of measurement error and that such an approach should be considered in future studies.

  7. Industrial CO2 emissions in China based on the hypothetical extraction method: Linkage analysis

    International Nuclear Information System (INIS)

    Wang, Yuan; Wang, Wenqin; Mao, Guozhu; Cai, Hua; Zuo, Jian; Wang, Lili; Zhao, Peng

    2013-01-01

    Fossil fuel-related CO 2 emissions are regarded as the primary sources of global climate change. Unlike direct CO 2 emissions for each sector, CO 2 emissions associated with complex linkages among sectors are usually ignored. We integrated the input–output analysis with the hypothetical extraction method to uncover the in-depth characteristics of the inter-sectoral linkages of CO 2 emissions. Based on China's 2007 data, this paper compared the output and demand emissions of CO 2 among eight blocks. The difference between the demand and output emissions of a block indicates that CO 2 is transferred from one block to another. Among the sectors analyzed in this study, the Energy industry block has the greatest CO 2 emissions with the Technology industry, Construction and Service blocks as its emission's primary destinations. Low-carbon industries that have lower direct CO 2 emissions are deeply anchored to high-carbon ones. If no effective measures are taken to limit final demand emissions or adjust energy structure, shifting to an economy that is low-carbon industries oriented would entail a decrease in CO 2 emission intensity per unit GDP but an increase in overall CO 2 emissions in absolute terms. The results are discussed in the context of climate-change policy. - Highlights: • Quantitatively analyze the characteristics of inter-industrial CO 2 emission linkages. • Propose the linkage measuring method of CO 2 emissions based on the modified HEM. • Detect the energy industry is a key sector on the output of embodied carbon. • Conclude that low-carbon industries are deeply anchored to high-carbon industries

  8. Macro-Financial Linkages in Egypt; A Panel Analysis of Economic Shocks and Loan Portfolio Quality

    OpenAIRE

    Inessa Love; Rima Turk-Ariss

    2013-01-01

    This paper investigates macro-financial linkages in Egypt using two complementary methods, assessing the interaction between different macroeconomic aggregates and loan portfolio quality in a multivariate framework as well as through a panel vector autoregressive method that controls for bank-level characteristics. Using a panel of banks over 1993-2010, the authors find that a positive shock to capital inflows and growth in gross domestic product improves banks’ loan portfolio quality, and ...

  9. Academic elite in accounting: linkages among top-ranked graduate programs.

    Science.gov (United States)

    Bair, Jeffrey H

    2002-06-01

    The 10 top-ranked graduate programs in accounting, based on a national survey of deans and top administrators, were linked to one another by hiring in the programs one another's graduates. Almost one-half (45.9%) of the faculty members in these 10 programs (N = 172) had graduated from one of these 10 programs. It is suggested that this linkage helps these programs to maintain and enhance their prestige.

  10. Factors That Influence Linkages to HIV Continuum of Care Services: Implications for Multi-Level Interventions

    Directory of Open Access Journals (Sweden)

    Rogério M. Pinto

    2017-11-01

    Full Text Available Worldwide, the human immunodeficiency virus (HIV continuum of care involves health promotion providers (e.g., social workers and health educators linking patients to medical personnel who provide HIV testing, primary care, and antiretroviral treatments. Regrettably, these life-saving linkages are not always made consistently and many patients are not retained in care. To design, test and implement effective interventions, we need to first identify key factors that may improve linkage-making. To help close this gap, we used in-depth interviews with 20 providers selected from a sample of 250 participants in a mixed-method longitudinal study conducted in New York City (2012–2017 in order to examine the implementation of HIV services for at-risk populations. Following a sociomedical framework, we identified provider-, interpersonal- and environmental-level factors that influence how providers engage patients in the care continuum by linking them to HIV testing, HIV care, and other support services. These factors occurred in four domains of reference: Providers’ Professional Knowledge Base; Providers’ Interprofessional Collaboration; Providers’ Work-Related Changes; and Best Practices in a Competitive Environment. Of particular importance, our findings show that a competitive environment and a fear of losing patients to other agencies may inhibit providers from engaging in linkage-making. Our results suggest relationships between factors within and across all four domains; we recommend interventions to modify factors in all domains for maximum effect toward improving care continuum linkage-making. Our findings may be applicable in different areas of the globe with high HIV prevalence.

  11. A meiotic linkage map of the silver fox, aligned and compared to the canine genome

    OpenAIRE

    Kukekova, Anna V.; Trut, Lyudmila N.; Oskina, Irina N.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Kharlamova, Anastasiya V.; Shepeleva, Darya V.; Gulievich, Rimma G.; Shikhevich, Svetlana G.; Graphodatsky, Alexander S.; Aguirre, Gustavo D.; Acland, Gregory M.

    2007-01-01

    A meiotic linkage map is essential for mapping traits of interest and is often the first step toward understanding a cryptic genome. Specific strains of silver fox (a variant of the red fox, Vulpes vulpes), which segregate behavioral and morphological phenotypes, create a need for such a map. One such strain, selected for docility, exhibits friendly dog-like responses to humans, in contrast to another strain selected for aggression. Development of a fox map is facilitated by the known cytogen...

  12. Decomposition of Domestic and International Linkages of the Korean Financial Markets

    Directory of Open Access Journals (Sweden)

    Taiki Lee

    2009-12-01

    Full Text Available A large degree of co-movements across financial markets within and between countries has been frequently observed worldwide and these co-movements intensify in times of financial crisis such as the recent financial turmoil triggered by the US sub-prime mortgage crisis. The aim of this paper is to analyze the degrees of financial linkages between four major markets of the US and Korea: money markets, bond markets, equity markets and foreign exchange markets. To break down the structures of these linkages, we fully identify a structural VAR without any ad-hoc restrictions using the methodology of Rigobon (2003. In addition to confirming that there are significant contemporaneous linkages across US asset prices and across Korean asset prices, we quantify and analyze the channels of international cross-market transmission of shocks between the US and Korea, comparing them with the Japanese cases. The main results are as follows. First, there are no significant substitution effects between bond and equity markets in Korea. Second, the US equity market shocks have a substantial effect on the Korean stock market while the US bond and equity market shocks don't on the Korean interest rates. Third, the Korea stock market shocks have a significant impact on the won-dollar exchange rate while the Korean bond market shocks don't. Fourth, Japan shows the similar international linkages as Korea even though it is a large open economy. However, the yen-dollar exchange rate responses to the Japanese bond market shocks, not the Japanese stock market shocks.

  13. The power to detect linkage in complex disease by means of simple LOD-score analyses.

    Science.gov (United States)

    Greenberg, D A; Abreu, P; Hodge, S E

    1998-09-01

    Maximum-likelihood analysis (via LOD score) provides the most powerful method for finding linkage when the mode of inheritance (MOI) is known. However, because one must assume an MOI, the application of LOD-score analysis to complex disease has been questioned. Although it is known that one can legitimately maximize the maximum LOD score with respect to genetic parameters, this approach raises three concerns: (1) multiple testing, (2) effect on power to detect linkage, and (3) adequacy of the approximate MOI for the true MOI. We evaluated the power of LOD scores to detect linkage when the true MOI was complex but a LOD score analysis assumed simple models. We simulated data from 14 different genetic models, including dominant and recessive at high (80%) and low (20%) penetrances, intermediate models, and several additive two-locus models. We calculated LOD scores by assuming two simple models, dominant and recessive, each with 50% penetrance, then took the higher of the two LOD scores as the raw test statistic and corrected for multiple tests. We call this test statistic "MMLS-C." We found that the ELODs for MMLS-C are >=80% of the ELOD under the true model when the ELOD for the true model is >=3. Similarly, the power to reach a given LOD score was usually >=80% that of the true model, when the power under the true model was >=60%. These results underscore that a critical factor in LOD-score analysis is the MOI at the linked locus, not that of the disease or trait per se. Thus, a limited set of simple genetic models in LOD-score analysis can work well in testing for linkage.

  14. Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex diseases.

    Science.gov (United States)

    Abreu, P C; Greenberg, D A; Hodge, S E

    1999-09-01

    Several methods have been proposed for linkage analysis of complex traits with unknown mode of inheritance. These methods include the LOD score maximized over disease models (MMLS) and the "nonparametric" linkage (NPL) statistic. In previous work, we evaluated the increase of type I error when maximizing over two or more genetic models, and we compared the power of MMLS to detect linkage, in a number of complex modes of inheritance, with analysis assuming the true model. In the present study, we compare MMLS and NPL directly. We simulated 100 data sets with 20 families each, using 26 generating models: (1) 4 intermediate models (penetrance of heterozygote between that of the two homozygotes); (2) 6 two-locus additive models; and (3) 16 two-locus heterogeneity models (admixture alpha = 1.0,.7,.5, and.3; alpha = 1.0 replicates simple Mendelian models). For LOD scores, we assumed dominant and recessive inheritance with 50% penetrance. We took the higher of the two maximum LOD scores and subtracted 0.3 to correct for multiple tests (MMLS-C). We compared expected maximum LOD scores and power, using MMLS-C and NPL as well as the true model. Since NPL uses only the affected family members, we also performed an affecteds-only analysis using MMLS-C. The MMLS-C was both uniformly more powerful than NPL for most cases we examined, except when linkage information was low, and close to the results for the true model under locus heterogeneity. We still found better power for the MMLS-C compared with NPL in affecteds-only analysis. The results show that use of two simple modes of inheritance at a fixed penetrance can have more power than NPL when the trait mode of inheritance is complex and when there is heterogeneity in the data set.

  15. Evaluation of linkages between equity indices : evidence from İstanbul Stock Exchange and Dow Jones

    OpenAIRE

    Ertan, Aytekin

    2009-01-01

    Ankara : The Department of Management, Bilkent Univiversity, 2009. Thesis (Master's) -- Bilkent University, 2009. Includes bibliographical references leaves 30-33. This study investigates the linkage between the major stock market indices of Turkey (ISE National 100) and USA (Dow Jones Industrial Average). Main purpose of this research is to measure the interdependence and cointegration between these indices and figure out the significance and the direction of short run r...

  16. An evaluation of a data linkage training workshop for research ethics committees.

    Science.gov (United States)

    Tan, Kate M; Flack, Felicity S; Bear, Natasha L; Allen, Judy A

    2015-03-04

    In Australia research projects proposing the use of linked data require approval by a Human Research Ethics Committee (HREC). A sound evaluation of the ethical issues involved requires understanding of the basic mechanics of data linkage, the associated benefits and risks, and the legal context in which it occurs. The rapidly increasing number of research projects utilising linked data in Australia has led to an urgent need for enhanced capacity of HRECs to review research applications involving this emerging research methodology. The training described in this article was designed to respond to an identified need among the data linkage units in the Australian Population Health Research Network (PHRN) and HREC members in Australia. Five one-day face to face workshops were delivered in the study period to a total of 98 participants. Participants in the workshops represented all six categories of HREC membership composition listed in the National Health and Medical Research Centres' (NHMRC) National Statement on Ethical Conduct in Human Research. Participants were assessed at three time points, prior to the training (T1), immediately after the training (T2) and 8 to 17 months after the training (T3). Ninety participants completed the pre and post questionnaires; 58 of them completed the deferred questionnaire. Participants reported significant improvements in levels of knowledge, understanding and skills in each of the eight areas evaluated. The training was beneficial for those with prior experience in the area of ethics and data linkage as well as those with no prior exposure. Our preliminary work in this area demonstrates that the provision of intensive face to face ethics training in data linkage is feasible and has a significant impact on participant's confidence in reviewing HREC applications.

  17. ROLE OF AGRO-INDUSTRY IN BANGLADESH ECONOMY: AN EMPIRICAL ANALYSIS OF LINKAGES AND MULTIPLIERS

    OpenAIRE

    Quddus, Md. Abdul

    2009-01-01

    The study was undertaken to evaluate the contribution of agro-industry in the Bangladesh economy. The latest two input-output tables of the year 1993-94 and 2001-2002 in Bangladesh were used to calculate inter-industry linkage indices and multiplier effects. Agroindustry contributes a significant portion of national income and the prospect of employment generation is increasing at the higher extent for the sectors food processing, tanning and leather finishing, leather industry, saw milling a...

  18. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  19. A Record Linkage Protocol for a Diabetes Registry at Ethnically Diverse Community Health Centers

    OpenAIRE

    Maizlish, Neil A.; Herrera, Linda

    2005-01-01

    Community health centers serve ethnically diverse populations that may pose challenges for record linkage based on name and date of birth. The objective was to identify an optimal deterministic algorithm to link patient encounters and laboratory results for hemoglobin A1c testing and examine its variability by health center site, patient ethnicity, and other variables. Based on data elements of last name, first name, date of birth, gender, and health center site, matches with ≥50% to < 100% o...

  20. Linkages between Income Inequality, International Remittances and Economic Growth in Pakistan

    OpenAIRE

    Shahbaz, Muhammad; Ur Rehman, Ijaz; Ahmad Mahdzan, Nurul Shahnaz

    2013-01-01

    This paper explores the dynamic linkages between income inequality, international remittances and economic growth using time series data over the period of 1976-2006 in case of Pakistan. The cointegration analysis based on the bounds test confirms the existence of a long-run relationship between income inequality, international remittances and economic growth. Our results reveal that income inequality and international remittances enhance economic growth. The causality analysis based on innov...

  1. Dynamic and Long-term Linkages among Growth, Inequality and Poverty in Developing Countries

    OpenAIRE

    Katsushi S. Imai; Raghav Gaiha

    2014-01-01

    Abstract Drawing upon a cross-country panel data for developing countries, the present study sheds new empirical light on dynamic and long-term linkages among growth, inequality and poverty. First, agricultural sector growth is found to be consistently the most important factor in reducing inequality and poverty not only through its direct effects but also through its indirect effects. Second, there is a significant and negative association between inequality and GDP per capita, with macro in...

  2. International financial linkages of Latin American banks: the effects of political risk and deposit dollarisation

    OpenAIRE

    Ramon-Ballester, Francisco; Wezel, Torsten

    2007-01-01

    This paper empirically investigates the extent to which the financial linkages of Latin American banks with the exterior are influenced by political risk and deposit dollarisation. We find that the sum of banks’ foreign assets and liabilities is a function of risk-return considerations and excess domestic credit demand. An increase in political risk is shown to be associated with a build-up of foreign positions by the banking sector, but this adverse effect on the banking system is mitigated ...

  3. Resource use, dependence and vulnerability: community-resource linkages on Alaska's Tongass National Forest

    Science.gov (United States)

    E.T. Mekbeb; R.J. Lilieholm; D.J. Blahna; L.E. Kruger

    2009-01-01

    Understanding how rural communities use and depend upon local natural resources is a critical factor in developing policies to sustain the long-term viability of human and natural systems. Such “community-resource” linkages are particularly important in Alaska, where rural communities – many of them comprised of indigenous Alaskan Natives – are highly dependent upon...

  4. Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

    Czech Academy of Sciences Publication Activity Database

    Wang, L.; Luzynski, K.; Pool, J. E.; Janoušek, V.; Dufková, Petra; Vyskočilová, Martina; Teeter, K. C.; Nachman, M. W.; Munclinger, P.; Macholán, Miloš; Piálek, Jaroslav; Tucker, P. K.

    2011-01-01

    Roč. 20, č. 14 (2011), s. 2985-3000 ISSN 0962-1083 R&D Projects: GA ČR GA206/08/0640 Grant - others:NSF(US) DEB0746560 Institutional research plan: CEZ:AV0Z60930519; CEZ:AV0Z50450515 Keywords : house mouse * hybrid zones * linkage disequilibrium * SNP markers Subject RIV: EG - Zoology Impact factor: 5.522, year: 2011

  5. Genetic mapping of the gene for Usher syndrome: Linkage analysis in a large Samaritan kindred

    Energy Technology Data Exchange (ETDEWEB)

    Bonne-Tamir, B.; Korostishevsky, M.; Kalinsky, H.; Seroussi, E.; Beker, R.; Weiss, S. (Sackler Faculty of Medicine, Ramat-Aviv (Israel)); Godel, V. (Ichilov Hospital, Tel-Aviv (Israel))

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed. 35 refs., 2 figs., 6 tabs.

  6. Community-engaged strategies to promote hepatitis B testing and linkage to care in immigrants

    Directory of Open Access Journals (Sweden)

    Jevetta Stanford

    2016-12-01

    Full Text Available To improve early identification and linkage to treatment and preventive services for hepatitis B virus (HBV in persons born in countries with intermediate or high (>2% HBV prevalence, the University of Florida Center for HIV/AIDS Research, Education, and Services (UF CARES employed community-engaged strategies to implement the Hepatitis B Awareness and Service Linkage (HBASL program. In this brief report, we present a summary of program components, challenges, and successes. Faith and community-based networks were established to improve HBV testing and screening and to increase foreign born nationals (FBNs access to HBV care. A total of 1516 FBNs were tested and screened for hepatitis B. The majority were females (50.4%, Asians (62.8%, non-Hispanic (87.2%, and they also received post-test counseling (54.8%. Noted program advantages included the development of community networks and outreach to a large population of FBNs. The major challenges were institutional delays, pressures related to meeting program deliverables, and diversity within FBNs populations. Community health workers in the United States can replicate this program in their respective communities and ensure success by maintaining a strong community presence, establishing partnerships and linkage processes, developing a sustainability plan, and ensuring the presence of dedicated program staff.

  7. Health services research and data linkages: issues, methods, and directions for the future.

    Science.gov (United States)

    Bradley, Cathy J; Penberthy, Lynne; Devers, Kelly J; Holden, Debra J

    2010-10-01

    Research on pressing health services and policy issues requires access to complete, accurate, and timely patient and organizational data. This paper describes how administrative and health records (including electronic medical records) can be linked for comparative effectiveness and health services research. We categorize the major agents (i.e., who owns and controls data and who carries out the data linkage) into three areas: (1) individual investigators; (2) government sponsored linked data bases; and (3) public-private partnerships that facilitate linkage of data owned by private organizations. We describe challenges that may be encountered in the linkage process, and the benefits of combining secondary databases with primary qualitative and quantitative sources. We use cancer care research to illustrate our points. To fill the gaps in the existing data infrastructure, additional steps are required to foster collaboration among institutions, researchers, and public and private components of the health care sector. Without such effort, independent researchers, governmental agencies, and nonprofit organizations are likely to continue building upon a fragmented and costly system with limited access. Discussion. Without the development and support for emerging information technologies across multiple health care settings, the potential for data collected for clinical and transactional purposes to benefit the research community and, ultimately, the patient population may go unrealized. The current environment is characterized by budget and technical challenges, but investments in data infrastructure are arguably cost-effective given the need to reform our health care system and to monitor the impact of health reform initiatives. © Health Research and Educational Trust.

  8. Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

    Directory of Open Access Journals (Sweden)

    Shubhada R Hegde

    2008-11-01

    Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.

  9. Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.

    Science.gov (United States)

    Balliu, Brunilda; Uh, Hae-Won; Tsonaka, Roula; Boehringer, Stefan; Helmer, Quinta; Houwing-Duistermaat, Jeanine J

    2014-01-01

    In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and without linkage disequilibrium for the first part and the impact of imputation in testing for association by using imputed genome-wide association studies or raw sequence markers for the second part. We apply the method to next-generation sequencing longitudinal family data from Genetic Association Workshop 18 and identify a significant region at chromosome 3: 40249244-41025167 (p-value = 2.3 × 10(-3)).

  10. The linkage among ambulance transports, death and climate parameters in Asahikawa City, Japan.

    Science.gov (United States)

    Kataoka, Hiroaki; Mochimasu, Kazumi Dokai; Katayama, Akihiko; Kanda, Kanae Oda; Sakano, Noriko; Tanaka, Keiko; Miyatake, Nobuyuki

    2015-01-01

    The aim of this study was to investigate the linkage among climate parameters, total ambulance transports and the number of deaths in Asahikawa City in northern Japan. Monthly data on total ambulance transports and the number of deaths from January 2004 to December 2011 were obtained from Asahikawa City Fire Department and the Asahikawa City official website. Climate parameters for the required period were also obtained from the Japan Meteorological Agency, Japan. To adjust for the population, we also used monthly population data on Asahikawa City. The linkage among climate parameters, total ambulance transports and the number of deaths was evaluated by ecological analysis. The mean air temperature in the Asahikawa area was 7.3 ± 10.1 °C. Total ambulance transports (/a hundred thousand people/day) and the number of deaths (/a hundred thousand people/day) were 10.0 ± 0.6 and 2.6 ± 0.3, respectively. Using quadratic curves, total ambulance transports and the number of deaths were weakly correlated with some climate parameters. The number of deaths was weakly and positively correlated with total ambulance transports. A weak linkage among climate parameters, total ambulance transports and the number of deaths was noted in Asahikawa City, Japan. However, these associations were not as high as expected.

  11. Genetic linkage of autosomal dominant progressive supranuclear palsy to 1q31.1.

    Science.gov (United States)

    Ros, Raquel; Gómez Garre, Pilar; Hirano, Michio; Tai, Yen F; Ampuero, Israel; Vidal, Lídice; Rojo, Ana; Fontan, Aurora; Vazquez, Ana; Fanjul, Samira; Hernandez, Jaime; Cantarero, Susana; Hoenicka, Janet; Jones, Alison; Ahsan, R Laila; Pavese, Nicola; Piccini, Paola; Brooks, David J; Perez-Tur, Jordi; Nyggard, Torbjorn; de Yébenes, Justo G

    2005-05-01

    Progressive supranuclear palsy (PSP) is a disorder of unknown pathogenesis. Familial clusters of PSP have been reported related to mutations of protein tau. We report the linkage of a large Spanish family with typical autosomal dominant PSP to a new locus in chromosome 1. Four members of this family had typical PSP, confirmed by neuropathology in one case. At least five ancestors had similar disease. Other members of the family have incomplete phenotypes. The power of the linkage analysis was increased by detecting presymptomatic individuals with 18F-fluoro-dopa and 18F-deoxyglucose positron emission tomography. We screened the human genome with 340 polymorphic markers and we enriched the areas of interest with additional markers. The disease status was defined according to the clinical and positron emission tomography data. We excluded linkage to the tau gene in chromosome 17. PSP was linked, in this family, to one area of 3.4 cM in chromosome 1q31.1, with a maximal multipoint < OD score of +3.53. This area contains at least three genes, whose relevance in PSP is unknown. We expect to further define the gene responsible for PSP, which could help to understand the pathogenesis of this disease and to design effective treatment.

  12. Clinical and linkage study of a large family with simple ectopia lentis linked to FBN1

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, M.J.; Roberts, J.; Partington, M.W. [Newcastle and Northern New South Wales Genetics Service (Australia); Colley, P.W. [John Hunter Hospital, Newcastle (Australia); Hollway, G.E.; Kozman, H.M.; Mulley, J.C. [Adelaide Children`s Hospital, North Adelaide (Australia)

    1994-10-15

    Simple ectopia lentis (EL) was studied in a large family, by clinical examination and analysis of linkage to markers in the region of FBN1, the gene for fibrillin which causes Marfan syndrome on chromosome 15. No patient had clinical or echocardiographic evidence of Marfan syndrome, although there was a trend towards relatively longer measurements of height; lower segment; arm span; middle finger, hand, and foot length in the affected members of the family, compared with unaffected sibs of the same sex. Analysis of linkage to intragenic FBN1 markers was inconclusive because they were relatively uninformative. Construction of a multipoint background map from the CEPH reference families identified microsatellite markers linked closely to FBN1 which could demonstrate linkage of EL in this family to the FBN1 region. LINKMAP analysis detected a multipoint lod score of 5.68 at D15S119, a marker approximately 6 cM distal to FBN1, and a multipoint lod score of 5.04 at FBN1. The EL gene in this family is likely to be allelic to Marfan syndrome, and molecular characterization of the FBN1 mutation should now be possible. 25 refs., 6 figs., 2 tabs.

  13. Pendred syndrome: evidence for genetic homogeneity and further refinement of linkage.

    Science.gov (United States)

    Gausden, E; Coyle, B; Armour, J A; Coffey, R; Grossman, A; Fraser, G R; Winter, R M; Pembrey, M E; Kendall-Taylor, P; Stephens, D; Luxon, L M; Phelps, P D; Reardon, W; Trembath, R

    1997-02-01

    Pendred syndrome is the association between congenital sensorineural deafness and goitre. The disorder is characterised by the incomplete discharge of radioiodide from a primed thyroid following perchlorate challenge. However, the molecular basis of the association between hearing loss and a defect in organification of iodide remains unclear. Pendred syndrome is inherited as an autosomal recessive trait and has recently been mapped to 7q31 coincident with the non-syndromic deafness locus DFNB4. To define the critical linkage interval for Pendred syndrome we have studied five kindreds, each with members affected by Pendred syndrome. All families support linkage to the chromosome 7 region, defined by the microsatellite markers D7S501-D7S523. Detailed haplotype analysis refines the Pendred syndrome linkage interval to a region flanked by the marker loci D7S501 and D7S525, separated by a genetic distance estimated to be 2.5 cM. As potential candidate genes have as yet not been mapped to this interval, these data will contribute to a positional cloning approach for the identification of the Pendred syndrome gene.

  14. Optimal synthesis of a four-bar linkage by method of controlled deviation

    Directory of Open Access Journals (Sweden)

    Bulatović Radovan R.

    2004-01-01

    Full Text Available This paper considers optimal synthesis of a four-bar linkage by method of controlled deviations. The advantage of this approximate method is that it allows control of motion of the coupler in the four-bar linkage so that the path of the coupler is in the prescribed environment around the given path on the segment observed. The Hooke-Jeeves’s optimization algorithm has been used in the optimization process. Calculation expressions are not used as the method of direct searching, i.e. individual comparison of the calculated value of the objective function is made in each iteration and the moving is done in the direction of decreasing the value of the objective function. This algorithm does not depend on the initial selection of the projected variables. All this is illustrated on an example of synthesis of a four-bar linkage whose coupler point traces a straight line, i.e. passes through sixteen prescribed points lying on one straight line. .

  15. Macro economic linkages and impacts. Technical and fiscal options in GHG abatement

    International Nuclear Information System (INIS)

    Backus, G.; Barker, T.

    1995-01-01

    This paper discusses some of the main macro economic linkages and feedbacks associated with policies for GHG abatement. The linkages in a global model are described when OECD carbon taxes or alternatively OECD/OPEC joint action raises world oil prices with a smaller OECD carbon tax. The results give a world perspective on the GHG abatement problem. The paper continues with a discussion of the linkages and feedbacks associated with three options: demand-side management (DSM), mainly to improve end-use energy efficiency, reductions in subsidies of fossil fuel production and use, and investment in renewable energy supplies, specifically in energy forestry and associated infrastructure. It concludes that DSM and investment in renewables are unlikely on their own to bring about reduction in GHG emissions, and that new supplies may even lead to increased emissions by driving down the price of energy. However, reductions in emissions may be compatible with increased efficiency and development, as well as with improvements in the quality of the local environment and in rural living, with the new supplies replacing fossil fuel supplies, provided that real fossil fuel prices are increased via removal of subsidies and if required carbon taxes. (au) 15 refs

  16. Replication of linkage to quantitative trait loci: variation in location and magnitude of the lod score.

    Science.gov (United States)

    Hsueh, W C; Göring, H H; Blangero, J; Mitchell, B D

    2001-01-01

    Replication of linkage signals from independent samples is considered an important step toward verifying the significance of linkage signals in studies of complex traits. The purpose of this empirical investigation was to examine the variability in the precision of localizing a quantitative trait locus (QTL) by analyzing multiple replicates of a simulated data set with the use of variance components-based methods. Specifically, we evaluated across replicates the variation in both the magnitude and the location of the peak lod scores. We analyzed QTLs whose effects accounted for 10-37% of the phenotypic variance in the quantitative traits. Our analyses revealed that the precision of QTL localization was directly related to the magnitude of the QTL effect. For a QTL with effect accounting for > 20% of total phenotypic variation, > 90% of the linkage peaks fall within 10 cM from the true gene location. We found no evidence that, for a given magnitude of the lod score, the presence of interaction influenced the precision of QTL localization.

  17. Feasibility of motion laws for planar one degree of freedom linkage mechanisms at dead point configurations

    Science.gov (United States)

    Lores García, E.; Veciana Fontanet, J. M.; Jordi Nebot, L.

    2018-01-01

    This paper proposes an analytical solution of the Inverse Kinematics (IK) problem at dead point configurations for any planar one degree of freedom linkage mechanism, with regard to the continuity Cn of the motion law. The systems analyzed are those whose elements are linked with lower pairs and do not present redundancies. The study aims to provide the user with some rules to facilitate the design of feasible motion profiles to be reproduced by conventional electrical actuators at these configurations. During the last decades, several methods and techniques have been developed to study this specific configuration. However, these techniques are mainly focused on solving numerically the IK indeterminacy, rather than analyzing the motion laws that the mechanisms are able to perform at these particular configurations. The analysis presented in this paper has been carried out differentiating and applying l'Hôpital's rule to the system of constraint equations ϕ (q) of the mechanism. The study also considers the feasibility of the time-domain profiles to be reproduced with conventional electrical actuators (i.e. AC/DC motors, linear actuators, etc.). To show the usefulness and effectiveness of the method, the development includes the analytical application and numerical simulations for two common one degree of freedom systems: a slider-crank and a four linkage mechanisms. Finally, experimental results are presented on a four linkage mechanism test bed.

  18. The California Linkages Program: Doorway to Housing Support for Child Welfare-Involved Parents.

    Science.gov (United States)

    D'Andrade, Amy; Simon, James David; Fabella, Danna; Castillo, Lolita; Mejia, Cesar; Shuster, David

    2017-09-01

    Housing instability can complicate parents' efforts to provide for their children. Child welfare service agencies have had difficulty adequately serving parents' housing needs due to limited and constrained funding streams. This article integrates the voices of four important stakeholders to illuminate how an innovative model of service system coordination called Linkages addresses housing needs for child welfare-involved parents eligible for public assistance. Facilitated by Linkages, these parents can receive supportive housing services through programs affiliated with the California public assistance program CalWORKs. Personal narratives reflecting the diverse perspectives of stakeholders in the Linkages collaboration-the statewide program director, a child welfare services coordinator, a CalWORKs caseworker, and a parent program participant-shed light on how the collaboration assists parents in attaining case plan goals, and highlights some of the factors facilitating and hindering effective collaboration between the agencies involved. Stakeholders emphasized the value of flexible service approaches, the intensity of the efforts required, the role of advocacy, and the importance of a shared vision between agencies working together to provide housing supports. © Society for Community Research and Action 2016.

  19. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  20. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

    Science.gov (United States)

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

    2004-12-28

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.