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Sample records for disequilibrium test tdt

  1. Transmission/disequilibrium tests incorporating unaffected offspring.

    Directory of Open Access Journals (Sweden)

    Qinyu Wei

    Full Text Available We propose a new method for family-based tests of association and linkage called transmission/disequilibrium tests incorporating unaffected offspring (TDTU. This new approach, constructed based on transmission/disequilibrium tests for quantitative traits (QTDT, provides a natural extension of the transmission/disequilibrium test (TDT to utilize transmission information from heterozygous parents to their unaffected offspring as well as the affected offspring from ascertained nuclear families. TDTU can be used in various study designs and can accommodate all types of independent nuclear families with at least one affected offspring. When the study sample contains only case-parent trios, the TDTU is equivalent to TDT. Informative-transmission disequilibrium test (i-TDT and generalized disequilibrium test(GDT are another two methods that can use information of both unaffected offspring and affected offspring. In contract to i-TDT and GDT, the test statistic of TDTU is simpler and more explicit, and can be implemented more easily. Through computer simulations, we demonstrate that power of the TDTU is slightly higher compared to i-TDT and GDT. All the three methods are more powerful than method that uses affected offspring only, suggesting that unaffected siblings also provide information about linkage and association.

  2. A robust TDT-type association test under informative parental missingness.

    Science.gov (United States)

    Chen, J H; Cheng, K F

    2011-02-10

    Many family-based association tests rely on the random transmission of alleles from parents to offspring. Among them, the transmission/disequilibrium test (TDT) may be considered to be the most popular statistical test. The TDT statistic and its variations were proposed to evaluate nonrandom transmission of alleles from parents to the diseased children. However, in family studies, parental genotypes may be missing due to parental death, loss, divorce, or other reasons. Under some missingness conditions, nonrandom transmission of alleles may still occur even when the gene and disease are not associated. As a consequence, the usual TDT-type tests would produce excessive false positive conclusions in association studies. In this paper, we propose a novel TDT-type association test which is not only simple in computation but also robust to the joint effect of population stratification and informative parental missingness. Our test is model-free and allows for different mechanisms of parental missingness across subpopulations. We use a simulation study to compare the performance of the new test with TDT and point out the advantage of the new method. Copyright © 2010 John Wiley & Sons, Ltd.

  3. The Transmission Disequilibrium/Heterogeneity Test with Parental-Genotype Reconstruction for Refined Genetic Mapping of Complex Diseases

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    Jing Han

    2012-01-01

    Full Text Available In linkage analysis for mapping genetic diseases, the transmission/disequilibrium test (TDT uses the linkage disequilibrium (LD between some marker and trait loci for precise genetic mapping while avoiding confounding due to population stratification. The sib-TDT (S-TDT and combined-TDT (C-TDT proposed by Spielman and Ewens can combine data from families with and without parental marker genotypes (PMGs. For some families with missing PMG, the reconstruction-combined TDT (RC-TDT proposed by Knapp may be used to reconstruct missing parental genotypes from the genotypes of their offspring to increase power and to correct for potential bias. In this paper, we propose a further extension of the RC-TDT, called the reconstruction-combined transmission disequilibrium/heterogeneity (RC-TDH test, to take into account the identical-by-descent (IBD sharing information in addition to the LD information. It can effectively utilize families with missing or incomplete parental genetic marker information. An application of this proposed method to Genetic Analysis Workshop 14 (GAW14 data sets and extensive simulation studies suggest that this approach may further increase statistical power which is particularly valuable when LD is unknown and/or when some or all PMGs are not available.

  4. Handling missing data in transmission disequilibrium test in nuclear families with one affected offspring.

    Directory of Open Access Journals (Sweden)

    Gulhan Bourget

    Full Text Available The Transmission Disequilibrium Test (TDT compares frequencies of transmission of two alleles from heterozygote parents to an affected offspring. This test requires all genotypes to be known from all members of the nuclear families. However, obtaining all genotypes in a study might not be possible for some families, in which case, a data set results in missing genotypes. There are many techniques of handling missing genotypes in parents but only a few in offspring. The robust TDT (rTDT is one of the methods that handles missing genotypes for all members of nuclear families [with one affected offspring]. Even though all family members can be imputed, the rTDT is a conservative test with low power. We propose a new method, Mendelian Inheritance TDT (MITDT-ONE, that controls type I error and has high power. The MITDT-ONE uses Mendelian Inheritance properties, and takes population frequencies of the disease allele and marker allele into account in the rTDT method. One of the advantages of using the MITDT-ONE is that the MITDT-ONE can identify additional significant genes that are not found by the rTDT. We demonstrate the performances of both tests along with Sib-TDT (S-TDT in Monte Carlo simulation studies. Moreover, we apply our method to the type 1 diabetes data from the Warren families in the United Kingdom to identify significant genes that are related to type 1 diabetes.

  5. [The genotype-based haplotype relative risk and transmission disequilibrium test analyses of familial febrile convulsions].

    Science.gov (United States)

    Qi, Y; Wu, X; Guo, Z; Zhang, J; Pan, H; Li, M; Bao, X; Peng, J; Zou, L; Lin, Q

    1999-10-01

    To confirm the linkage of familial febrile convulsions to the short arm of chromosome 6(6p) or the long arm of chromosome 8(8q). The authors finished genotyping of Pst I locus on the coding region of heat shock protein (HSP) 70, 5'untranslated region of HSP70-1, 3' untranslated region of HSP70-2, D8S84 and D8S85. The data were processed by the genotype-based haplotype relative risk(GHRR) and transmission disequilibrium test(TDT) methods in PPAP. Some signs of association and disequilibrium between D8S85 and FC were shown by GHRR and TDT. A suspect linkage of familial febrile convulsions to the long arm of chromosome 8 has been proposed.

  6. Linkage disequilibrium between an allele at the dopamine D4 receptor locus and Tourette syndrome, by the transmission-disequilibrium test

    Energy Technology Data Exchange (ETDEWEB)

    Grice, D.E.; Gelernter, J. [Veterans Administration Connecticut Healthcare System, West Haven, CT (United States); Leckman, J.F.; Pauls, D.L. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

    1996-09-01

    Dopaminergic abnormalities are implicated in the pathogenesis of Tourette syndrome (TS) and chronic multiple tics. We used the transmission-disequilibrium test (TDT) method to test for linkage disequilibrium between a specific allele (the seven-repeat allele (DRD4*7R) of the exon 3 VNTR polymorphic site) at the D4 dopamine receptor locus (DRD4) and expression of chronic multiple tics and TS. This particular allele had been shown in functional studies to have different binding properties compared with the other common alleles in this DRD4 polymorphic system. We studied 64 family trios (consisting of an affected person and two parents, at least one heterozygous for DRD4*7R), including 12 nuclear family trios and 52 trios from four large TS kindreds. The DRD4*7R allele was transmitted significantly more frequently than expected ({chi}{sup 2}{sub TDT} ranging from 8.47 [P < .004] to 10.80 [P = .001], depending on breadth of disease definition and inclusion or exclusion of inferred genotypes). Confirmation of this finding will depend on either replication in other samples or the identification of a transmitted functional mutation within this sample. 56 refs., 2 figs., 3 tabs.

  7. 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

  8. Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

    DEFF Research Database (Denmark)

    2017-01-01

    The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients...... with IS or LGS. The contribution of autosomal recessive genetic variation, however, is less well understood. We implemented a rare variant transmission disequilibrium test (TDT) to search for autosomal recessive epileptic encephalopathy genes in a cohort of 320 outbred patient-parent trios that were generally...... not find evidence of a role for individual autosomal recessive genes, our current sample is insufficiently powered to assess the overall role of autosomal recessive genotypes in an outbred epileptic encephalopathy population....

  9. Transonic Dynamics Tunnel (TDT)

    Data.gov (United States)

    Federal Laboratory Consortium — The Transonic Dynamics Tunnel (TDT) is a continuous flow wind-tunnel facility capable of speeds up to Mach 1.2 at stagnation pressures up to one atmosphere. The TDT...

  10. TdT activity in acute myeloid leukemias defined by monoclonal antibodies.

    Science.gov (United States)

    San Miguel, J F; González, M; Cañizo, M C; Anta, J P; Portero, J A; López-Borrasca, A

    1986-09-01

    Blast cells from eight out of 71 patients diagnosed with acute myeloid leukemia (AML) by morphological, cytochemical, and immunological criteria showed TdT activity. Their distribution according to the FAB classification was one M1, one M2, one M4, two M5a, one M5b, one M6, and one undifferentiated case. The TdT+ AML cases did not show major clinical and hematological differences when compared with the classical TdT- AML patients. Other phenotypical aberrations in the expression of membrane antigens, apart from the presence of nuclear TdT, were not observed in these TdT+ cases after study with a large panel of monoclonal antibodies. A higher incidence of TdT+ cases was found among the monocytic variants of AML (M4 and M5)--four cases--than in the granulocytic variants (M1, M2, and M3)--2 cases. These TdT+ cases should be distinguished from mixed leukemias by double labeling techniques, assessing in the TdT+ AML the coexpression of TdT and myeloid markers in individual cells as shown in four of our cases.

  11. A novel approach for small sample size family-based association studies: sequential tests.

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    Ilk, Ozlem; Rajabli, Farid; Dungul, Dilay Ciglidag; Ozdag, Hilal; Ilk, Hakki Gokhan

    2011-08-01

    In this paper, we propose a sequential probability ratio test (SPRT) to overcome the problem of limited samples in studies related to complex genetic diseases. The results of this novel approach are compared with the ones obtained from the traditional transmission disequilibrium test (TDT) on simulated data. Although TDT classifies single-nucleotide polymorphisms (SNPs) to only two groups (SNPs associated with the disease and the others), SPRT has the flexibility of assigning SNPs to a third group, that is, those for which we do not have enough evidence and should keep sampling. It is shown that SPRT results in smaller ratios of false positives and negatives, as well as better accuracy and sensitivity values for classifying SNPs when compared with TDT. By using SPRT, data with small sample size become usable for an accurate association analysis.

  12. Activity of TDT 067 (Terbinafine in Transfersome) against Agents of Onychomycosis, as Determined by Minimum Inhibitory and Fungicidal Concentrations▿

    Science.gov (United States)

    Ghannoum, Mahmoud; Isham, Nancy; Herbert, Jacqueline; Henry, William; Yurdakul, Sam

    2011-01-01

    TDT 067 is a novel carrier-based dosage form (liquid spray) of 15 mg/ml of terbinafine in Transfersome that has been developed to deliver terbinafine to the nail bed to treat onychomycosis. In this study, we report the in vitro activities of TDT 067 against dermatophytes, compared with those of the Transfersome vehicle, naked terbinafine, and commercially available terbinafine (1%) spray. The MICs of TDT 067 and comparators against 25 clinical strains each of Trichophyton rubrum, T. mentagrophytes, and Epidermophyton floccosum were determined according to the CLSI M38–A2 susceptibility method (2008). Minimum fungicidal concentrations (MFCs) were determined by subculturing visibly clear wells from the MIC microtiter plates. TDT 067 demonstrated potent activity against the dermatophyte strains tested, with an MIC range of 0.00003 to 0.015 μg/ml. Overall, TDT 067 MIC50 values (defined as the lowest concentrations to inhibit 50% of the strains tested) were 8-fold and 60-fold lower than those of naked terbinafine and terbinafine spray, respectively. The Transfersome vehicle showed minimal inhibitory activity. TDT 067 demonstrated lower MFC values for T. rubrum and E. floccosum than naked terbinafine and terbinafine spray. TDT 067 has more potent antifungal activity against dermatophytes that cause nail infection than conventional terbinafine preparations. The Transfersome vehicle appears to potentiate the antifungal activity of terbinafine. Clinical investigation of TDT 067 for the topical treatment of onychomycosis is warranted. PMID:21411586

  13. Activity of TDT 067 (terbinafine in Transfersome) against agents of onychomycosis, as determined by minimum inhibitory and fungicidal concentrations.

    Science.gov (United States)

    Ghannoum, Mahmoud; Isham, Nancy; Herbert, Jacqueline; Henry, William; Yurdakul, Sam

    2011-05-01

    TDT 067 is a novel carrier-based dosage form (liquid spray) of 15 mg/ml of terbinafine in Transfersome that has been developed to deliver terbinafine to the nail bed to treat onychomycosis. In this study, we report the in vitro activities of TDT 067 against dermatophytes, compared with those of the Transfersome vehicle, naked terbinafine, and commercially available terbinafine (1%) spray. The MICs of TDT 067 and comparators against 25 clinical strains each of Trichophyton rubrum, T. mentagrophytes, and Epidermophyton floccosum were determined according to the CLSI M38-A2 susceptibility method (2008). Minimum fungicidal concentrations (MFCs) were determined by subculturing visibly clear wells from the MIC microtiter plates. TDT 067 demonstrated potent activity against the dermatophyte strains tested, with an MIC range of 0.00003 to 0.015 μg/ml. Overall, TDT 067 MIC(50) values (defined as the lowest concentrations to inhibit 50% of the strains tested) were 8-fold and 60-fold lower than those of naked terbinafine and terbinafine spray, respectively. The Transfersome vehicle showed minimal inhibitory activity. TDT 067 demonstrated lower MFC values for T. rubrum and E. floccosum than naked terbinafine and terbinafine spray. TDT 067 has more potent antifungal activity against dermatophytes that cause nail infection than conventional terbinafine preparations. The Transfersome vehicle appears to potentiate the antifungal activity of terbinafine. Clinical investigation of TDT 067 for the topical treatment of onychomycosis is warranted.

  14. A Bibliography of Transonic Dynamics Tunnel (TDT) Publications

    Science.gov (United States)

    Doggett, Robert V.

    2016-01-01

    The Transonic Dynamics Tunnel (TDT) at the National Aeronautics and Space Administration's (NASA) Langley Research Center began research operations in early 1960. Since that time, over 600 tests have been conducted, primarily in the discipline of aeroelasticity. This paper presents a bibliography of the publications that contain data from these tests along with other reports that describe the facility, its capabilities, testing techniques, and associated research equipment. The bibliography is divided by subject matter into a number of categories. An index by author's last name is provided.

  15. Generation of Active Bovine Terminal Deoxynucleotidyl Transferase (TdT in E.coli

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    Wee Liang Kuan

    2010-08-01

    Full Text Available A synthetic gene encoding bovine terminal deoxynucleotidyl transferase (TdT was generated, cloned into an expression vector and expressed in E.coli. The effects of altering culture and induction conditions on the nature of recombinant protein production were investigated. This led to the expression of active recombinant bovine TdT in E.coli. After purification and characterisation, the activity of the enzyme was assessed in a biological assay for apoptosis. The process described in this report enables the economical production of TdT for high throughput applications.

  16. Generation of Active Bovine Terminal Deoxynucleotidyl Transferase (TdT in E.coli

    Directory of Open Access Journals (Sweden)

    Wee Liang Kuan

    2010-01-01

    Full Text Available A synthetic gene encoding bovine terminal deoxynucleotidyl transferase (TdT was generated, cloned into an expression vector and expressed in E.coli. The effects of altering culture and induction conditions on the nature of recombinant protein production were investigated. This led to the expression of active recombinant bovine TdT in E.coli. After purification and characterisation, the activity of the enzyme was assessed in a biological assay for apoptosis. The process described in this report enables the economical production of TdT for high throughput applications.

  17. Support of positive association in family-based genetic analysis between COL27A1 and Tourette syndrome.

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    Liu, Shiguo; Yu, Xiaoxia; Xu, Quanchen; Cui, Jiajia; Yi, Mingji; Zhang, Xinhua; Ge, Yinlin; Ma, Xu

    2015-08-03

    Recently, a genome-wide association study has indicated associations between single nucleotide polymorphisms in the Collagen Type XXVII Alpha 1 gene (COL27A1) and Tourette syndrome in several ethnic populations. To clarify the global relevance of the previously identified SNPs in the development of Tourette syndrome, the associations between polymorphisms in COL27A1 and Tourette syndrome were assessed in Chinese trios. PCR-directed sequencing was used to evaluate the genetic contributions of three SNPs in COL27A1(rs4979356, rs4979357 and rs7868992) using haplotype relative risk (HRR) and transmission disequilibrium tests (TDT) with a total of 260 Tourette syndrome trios. The family-based association was significant between Tourette syndrome and rs4979356 (TDT: χ2 = 4.804, P = 0.033; HRR = 1.75, P = 0.002; HHRR = 1.32, P = 0.027), and transmission disequilibrium was suspected for rs4979357 (TDT: χ2 = 3.969, P = 0.053; HRR = 1.84, P = 0.001; HHRR = 1.29, P = 0.044). No statistically significant allele transfer was found for rs7868992 (TDT: χ2 = 2.177, P = 0.158). Although the TDT results did not remain significant after applying the conservative Bonferroni correction (p = 0.005), the significant positive HRR analysis confirmed the possibility of showing transmission disequilibrium, which provides evidence for an involvement of COL27A1in the development of TS. However, these results need to be verified with larger datasets from different populations.

  18. A theoretical treatment of interval mapping of a disease gene using ...

    Indian Academy of Sciences (India)

    The genetic basis of the transmission disequilibrium test (TDT) for two-marker loci is explored from first principles. In this case, parents doubly heterozygous for a given haplotype at the pair of marker loci that are each in linkage disequilibrium with the disease gene with the further possibility of a second-order linkage ...

  19. Evaluation of the morphological effects of TDT 067 (terbinafine in Transfersome) and conventional terbinafine on dermatophyte hyphae in vitro and in vivo.

    Science.gov (United States)

    Ghannoum, M; Isham, N; Henry, W; Kroon, H-A; Yurdakul, S

    2012-05-01

    TDT 067 is a novel, carrier-based dosage form of terbinafine in Transfersome (1.5%) formulated for topical delivery of terbinafine to the nail, nail bed, and surrounding tissue. We examined the effects of TDT 067 and conventional terbinafine on the morphology of dermatophytes. Trichophyton rubrum hyphae were exposed to TDT 067 or terbinafine (15 mg/ml) and examined under white light, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Subungual debris from patients treated with TDT 067 in a clinical trial was also examined. Exposure of T. rubrum hyphae to TDT 067 led to rapid and extensive ultrastructural changes. Hyphal distortion was evident as early as 4 h after exposure to TDT 067. After 24 h, there was complete disruption of hyphal structure with few intact hyphae remaining. Exposure to terbinafine resulted in morphological alterations similar to those seen with TDT 067; however, the effects of TDT 067 were more extensive, whereas a portion of hyphae remained intact after 24 h of exposure to terbinafine. Lipid droplets were observed under TEM following 30 min of exposure to TDT 067, which after 24 h had filled the intracellular space. These effects were confirmed in vivo in subungual debris from patients with onychomycosis who received topical treatment with TDT 067. The Transfersome in TDT 067 may potentiate the action of terbinafine by delivering terbinafine more effectively to its site of action inside the fungus. Our in vivo data confirm that TDT 067 can enter fungus in the nail bed of patients with onychomycosis and exert its antifungal effects.

  20. Therapeutic potential of TDT 067 (terbinafine in Transfersome): a carrier-based dosage form of terbinafine for onychomycosis.

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    Sigurgeirsson, Bárdur; Ghannoum, Mahmoud

    2012-10-01

    Current topical treatments for onychomycosis are unsatisfactory. New topical agents that offer efficacy without the potential adverse effects of oral antifungal therapy would benefit patients with this condition and encourage a greater treatment rate. Currently available topical therapies are reviewed, and new approaches for enhancing delivery of the established antifungal terbinafine through the nail are summarized. We focus on the use of ultra-deformable lipid vesicles to facilitate delivery of terbinafine to the nail and surrounding tissue. TDT 067 (terbinafine in Transfersome) is the only such therapy in development for onychomycosis, and we review published preclinical and clinical studies on this formulation. TDT 067 offers the use of new technology to deliver an established antifungal, terbinafine. Preclinical data suggest that the Transfersome accelerates entry of terbinafine released from TDT 067 into fungi and potentiates its antifungal effects, resulting in enhanced activity, compared with conventional terbinafine. This translated into high rates of mycological cure and evidence of clinical effect in a study of TDT 067 administered twice daily for 12 weeks in patients with onychomycosis. An ongoing Phase-III trial involving more than 700 patients treated for 48 weeks is investigating the efficacy and safety of TDT 067.

  1. The NASA Engineering and Safety Center (NESC) GN and C Technical Discipline Team (TDT): Its Purpose, Practices and Experiences

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    Dennehy, Cornelius J.

    2008-01-01

    This paper will briefly define the vision, mission, and purpose of the NESC organization. The role of the GN&C TDT will then be described in detail along with an overview of how this team operates and engages in its objective engineering and safety assessments of critical NASA projects. This paper will then describe key issues and findings from several of the recent GN&C-related independent assessments and consultations performed and/or supported by the NESC GN&C TDT. Among the examples of the GN&C TDT s work that will be addressed in this paper are the following: the Space Shuttle Orbiter Repair Maneuver (ORM) assessment, the ISS CMG failure root cause assessment, the Demonstration of Autonomous Rendezvous Technologies (DART) spacecraft mishap consultation, the Phoenix Mars lander thruster-based controllability consultation, the NASA in-house Crew Exploration Vehicle (CEV) Smart Buyer assessment and the assessment of key engineering considerations for the Design, Development, Test & Evaluation (DDT&E) of robust and reliable GN&C systems for human-rated spacecraft.

  2. Recent Experiences of the NASA Engineering and Safety Center (NESC) GN and C Technical Discipline Team (TDT)

    Science.gov (United States)

    Dennehy, Cornelius J.

    2010-01-01

    The NASA Engineering and Safety Center (NESC), initially formed in 2003, is an independently funded NASA Program whose dedicated team of technical experts provides objective engineering and safety assessments of critical, high risk projects. The GN&C Technical Discipline Team (TDT) is one of fifteen such discipline-focused teams within the NESC organization. The TDT membership is composed of GN&C specialists from across NASA and its partner organizations in other government agencies, industry, national laboratories, and universities. This paper will briefly define the vision, mission, and purpose of the NESC organization. The role of the GN&C TDT will then be described in detail along with an overview of how this team operates and engages in its objective engineering and safety assessments of critical NASA projects. This paper will then describe selected recent experiences, over the period 2007 to present, of the GN&C TDT in which they directly performed or supported a wide variety of NESC assessments and consultations.

  3. Tide-Dominated Tract (TDT) as a key sedimentary zone characterizing tide-dominated large-river delta and estuary systems

    Science.gov (United States)

    Saito, Y.

    2017-12-01

    Large rivers in continents have a characteristic of slow rise and fall in water levels during floods or the wet season due to a wide drainage basin. A gentle river gradient and large water discharge have relatively large tidal ranges at the river mouth, resulting in large backwater effects further upstream. The result of the Mekong River survey (386 riverbed sediments, river topography, CTD, and biofacies) shows that the distributary channels of the Mekong River delta in Vietnam are divided into two parts: the landward river-dominated tract (RDT) and seaward tide-dominated tract (TDT). The RDT is characterized by a highly variable and deepening trend in water depth and coarse-grained sediments with a fining trend downstream. The TDT is characterized by a shallowing trend in water depth with river-widening, smooth riverbeds, a straight shape, and heterolithic f- to vf-sand and mud alternation (tidal thythmite). The boundary of both tracts is sharply identified by sediment facies and river morphology. Sediment facies indicates that the dominant sedimentary process of bottom sediments is "bedload" in the RDT and "suspension" in the TDT. Daily tidal changes are observed through the year, while water-level changes during the flood/wet season are limited in the TDT. Saltwater intrusion is limited within the seaward part of the TDT alone ( 50 km), close to final bifurcation points. However, brackish-water biofacies is observed in the TDT mainly due to diluted brackish water and/or tolerance to the freshwater environment. These characteristics are also found in the Yangtze; the distance of the TDT/RDT boundary from the river mouth is ca. 100 km in the Mekong, and 200 km in the Yangtze. The preservation potential of sediments in a TDT is low in a progradational system, and high in abandoned channels. The early Holocene transgressive estuary system in the incised valley of the Yangtze formed during the Last Glacial Maximum was composed of 20 m-thick fine-grained heterolithic

  4. The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

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    Uleberg Eivind

    2011-05-01

    Full Text Available Abstract Background Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets. Methods The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5th, 10th and 50th highest TCLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively. Results In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001, where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001. In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05, i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position. Conclusions The CLD test can provide evidence for a causative SNP, but its power may be low in situations

  5. Interactividad, dividendo digital e información en la implementación de la TDT, estudio de Ecuador

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    A Suing

    2014-08-01

    Full Text Available Introducción. La investigación busca establecer por qué la interactividad no está presente en emisión de televisión digital terrestre (TDT en Ecuador, conocer el empleo del dividendo digital; y, determinar cuánto conoce la población sobre la implementación de TDT. Metodología. Revisión de documentación oficial, entrevistas a representantes de sectores involucrados y encuestas. Resultados. Aplicaciones interactivas vinculadas con servicios públicos están desarrollándose en universidades pero no son emitidas. El dividendo digital será empleado para banda ancha móvil. Falta promover conocimiento de TDT. Conclusiones. En Ecuador hay capacidades para crear aplicaciones interactivas; los beneficios de interactividad están limitados a la aceptación universal del lenguaje del middleware. La asignación del dividendo digital para su explotación por empresas privadas y el desarrollo de IPTV dejan al usuario ante un futuro incierto sobre formas de consumo. Faltan definir responsabilidades y mecanismos de cooperación entre Estado y empresas para promover transición a TDT entre la comunidad.

  6. Drug-free gel containing ultra-deformable phospholipid vesicles (TDT 064) as topical therapy for the treatment of pain associated with osteoarthritis: a review of clinical efficacy and safety.

    Science.gov (United States)

    Conaghan, Philip G; Bijlsma, Johannes W; Kneer, Werner; Wise, Elspeth; Kvien, Tore K; Rother, Matthias

    2014-04-01

    Many patients with osteoarthritis (OA) experience side effects with available systemic therapies, some of which can be life threatening. The widespread use of nonsteroidal anti-inflammatory drugs (NSAIDs), often without prescription, is concerning given their potential risks. New treatments for OA are therefore required. This review discusses evidence supporting the use of TDT 064, a drug-free, topical gel containing ultra-deformable phospholipid vesicles (Sequessome * vesicles), for OA-associated pain. Preclinical and clinical studies investigating TDT 064 in patients with OA-associated knee pain were identified in searches of PubMed and congress abstracts. The ultra-deformable phospholipid vesicles (sequessome vesicles) in TDT 064 pass through the skin intact to reach the synovial space within the joint. The mechanism of action is not yet certain, but the phospholipid-based structure of these ultra-deformable phospholipid vesicles, and the observation that they localize to the cartilage surface, support biolubrication as a possible mechanism of action of TDT 064. Data from randomized, phase III studies in OA knee pain in which TDT 064 was used as the drug-free vehicle control for IDEA-033 (ketoprofen in ultra-deformable phospholipid vesicles) demonstrate a marked and consistent response to TDT 064 in terms of pain, stiffness, and function. In a 12 week study of >1300 patients, the effects of TDT 064 on pain and function were statistically noninferior to those of oral celecoxib, and superior to oral placebo. TDT 064 was well tolerated in all studies, and adverse events were typically mild-to-moderate effects on the skin. Evidence from clinical studies supports the use of TDT 064 as a drug-free topical treatment for patients with OA. Further experience with TDT 064, particularly among patients with comorbidities or NSAID contraindications, will provide more information on its potential use.

  7. Performance evaluation of TDT soil water content and watermark soil water potential sensors

    Science.gov (United States)

    This study evaluated the performance of digitized Time Domain Transmissometry (TDT) soil water content sensors (Acclima, Inc., Meridian, ID) and resistance-based soil water potential sensors (Watermark 200, Irrometer Company, Inc., Riverside, CA) in two soils. The evaluation was performed by compar...

  8. 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.

  9. SILENE and TDT: A code for collision probability calculations in XY geometries

    International Nuclear Information System (INIS)

    Sanchez, R.; Stankovski, Z.

    1993-01-01

    Collision probability methods are routinely used for cell and assembly multigroup transport calculations in core design tasks. Collision probability methods use a specialized tracking routine to compute neutron trajectories within a given geometric object. These trajectories are then used to generate the appropriate collision matrices in as many groups as required. Traditional tracking routines are based on open-quotes globalclose quotes geometric descriptions (such as regular meshes) and are not able to cope with the geometric detail required in actual core calculations. Therefore, users have to modify their geometry in order to match the geometric model accepted by the tracking routine, introducing thus a modeling error whose evaluation requires the use of a open-quotes referenceclose quotes method. Recently, an effort has been made to develop more flexible tracking routines either by directly adopting tracking Monte Carlo techniques or by coding of complicated geometries. Among these, the SILENE and TDT package is being developed at the Commissariat a l' Energie Atomique to provide routine as well as reference calculations in arbitrarily shaped XY geometries. This package combines a direct graphical acquisition system (SILENE) together with a node-based collision probability code for XY geometries (TDT)

  10. Recent Experiences of the NASA Engineering and Safety Center (NESC) Guidance Navigation and Control (GN and C) Technical Discipline Team (TDT)

    Science.gov (United States)

    Dennehy, Cornelius J.

    2011-01-01

    The NASA Engineering and Safety Center (NESC) is an independently funded NASA Program whose dedicated team of technical experts provides objective engineering and safety assessments of critical, high risk projects. NESC's strength is rooted in the diverse perspectives and broad knowledge base that add value to its products, affording customers a responsive, alternate path for assessing and preventing technical problems while protecting vital human and national resources. The Guidance Navigation and Control (GN&C) Technical Discipline Team (TDT) is one of fifteen such discipline-focused teams within the NESC organization. The TDT membership is composed of GN&C specialists from across NASA and its partner organizations in other government agencies, industry, national laboratories, and universities. This paper will briefly define the vision, mission, and purpose of the NESC organization. The role of the GN&C TDT will then be described in detail along with an overview of how this team operates and engages in its objective engineering and safety assessments of critical NASA.

  11. 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.

  12. 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 ...

  13. 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...

  14. disequilibrium?

    Directory of Open Access Journals (Sweden)

    J. P. L. Johnson

    2016-08-01

    τc(qs* and increasing transport rates. Model parameters are calibrated based on laboratory flume experiments that explore transport disequilibrium. The τc(qs* equation is then incorporated into a simple morphodynamic model. The evolution of τc(qs* is a negative feedback on morphologic change, while also allowing reaches to equilibrate to sediment supply at different slopes. Finally, τc(qs* is interpreted to be an important but nonunique state variable for morphodynamics, in a manner consistent with state variables such as temperature in thermodynamics.

  15. Possible gene dosage effect of glutathione-S-transferases on atopic asthma: using real-time PCR for quantification of GSTM1 and GSTT1 gene copy numbers

    DEFF Research Database (Denmark)

    Brasch-Andersen, Charlotte; Christiansen, L; Tan, Q

    2004-01-01

    -S-transferase (GST) involved in the antioxidant defense were tested for association to asthma using 246 Danish atopic families in a family-based transmission disequilibrium test (TDT) design. A real-time PCR assay for relative quantification of gene copy number of GSTM1 and GSTT1 was developed. The assay made......Asthma is a complex genetic disorder characterized by chronic inflammation in the airways. As oxidative stress is a key component of inflammation, variations in genes involved in antioxidant defense could therefore be likely candidates for asthma. Three enzymes from the superfamily glutathione...

  16. Signal-on electrochemical assay for label-free detection of TdT and BamHI activity based on grown DNA nanowire-templated copper nanoclusters.

    Science.gov (United States)

    Hu, Yufang; Zhang, Qingqing; Xu, Lihua; Wang, Jiao; Rao, Jiajia; Guo, Zhiyong; Wang, Sui

    2017-11-01

    Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient "signal-on" electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3'-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to H 2 O 2 reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3'-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery. Graphical Abstract Extraordinary TdT-generated DNA-CuNCs are synthesized and act as a novel electrochemical sensing platform for sensitive detection of TdT and BamHI activity in biological environments.

  17. 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.

  18. 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.

  19. Two-sector disequilibrium growth

    NARCIS (Netherlands)

    J.G.M. van Marrewijk (Charles); J.B.L.M. Verbeek (Jos)

    1994-01-01

    textabstractWe investigate the effects of (i) profit distribution to either laborers or capital-owners, (ii) sector-specific or efficient rationing schemes, and (iii) government consumption in a two-sector disequilibrium growth model with sluggish real wage rate adjustment (which affects capital

  20. 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...

  1. Uranium and radium geochemistry. Radioactive disequilibrium in natural waters

    International Nuclear Information System (INIS)

    Beaucaire, C.

    1987-09-01

    Rock-water interactions play a primary part in uranium-series disequilibrium either by different chemical behavior or by recoiling alpha emitting nuclei in solution. Three series of thermal water containing CO 2 (Vichy, Vals and Cezallier) and one from Lodeve uranium deposit are studied to define parameters (pH, Eh, pCO 2 , T,...) controlling studied nuclei. For U complexation by carbonates is in competition with redox conditions. Ra is coprecipitated by barium. For thermal waters keeping their deep characteristics there is a low disequilibriums 234 U- 238 U between 1 and 2. On the contrary important disequilibrium (up to 12) in Vichy Saint Yorre water are due to secondary remobilization. In the same way for these waters 234 U and 226 Ra are correlated. Then leaching is essential for the radioactive disequilibrium but alpha recoil of 234 Th is of secondary importance in this case [fr

  2. 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

  3. Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

    Energy Technology Data Exchange (ETDEWEB)

    Purandare, S.M.; Viskochil, D.H.; Cawthon, R. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

    1996-07-01

    Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

  4. La crisis de la TDT local pública en España: el caso de Cataluña

    Directory of Open Access Journals (Sweden)

    Josep-Àngel Guimerá-i-Orts

    2011-01-01

    Full Text Available El artículo describe y analiza el estado de la televisión digital terrestre local (TDT-L pública en Cataluña justo después del apagón analógico de abril de 2010. Los resultados muestran que sólo 12 de los 37 canales públicos previstos estaban emitiendo y que sólo cinco más podían hacerlo a medio plazo. Estos datos indican que la televisión pública local vive una crisis en el contexto de la migración digital, ya que estos canales sufren graves limitaciones para nacer y el apagón implica la desaparición de emisoras analógicas históricas. El artículo se basa en una investigación cualitativa en el transcurso de la cual se ha entrevistado en profundidad a representantes de los 37 canales previstos. Los objetivos del artículo son, por una parte, describir el modelo de TDT-L vigente y su estado de implantación en Cataluña en mayo de 2010. Por otra parte, aportar elementos interpretativos que expliquen la situación de crisis identificada. Finalmente, aportar conocimiento que permita formular hipótesis sobre el estado del sector en el resto de España. Los resultados ponen de manifiesto que los problemas de la TDT-L pública tienen su origen en las políticas de implantación digital de los gobiernos español y catalán, que no han tenido en cuenta la realidad analógica preexistente –sobre todo el primero. En este sentido, el caso catalán aporta indicios sobre la situación en el conjunto de España.

  5. 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.

  6. Disequilibrium biosignatures over Earth history and implications for detecting exoplanet life.

    Science.gov (United States)

    Krissansen-Totton, Joshua; Olson, Stephanie; Catling, David C

    2018-01-01

    Chemical disequilibrium in planetary atmospheres has been proposed as a generalized method for detecting life on exoplanets through remote spectroscopy. Among solar system planets with substantial atmospheres, the modern Earth has the largest thermodynamic chemical disequilibrium due to the presence of life. However, how this disequilibrium changed over time and, in particular, the biogenic disequilibria maintained in the anoxic Archean or less oxic Proterozoic eons are unknown. We calculate the atmosphere-ocean disequilibrium in the Precambrian using conservative proxy- and model-based estimates of early atmospheric and oceanic compositions. We omit crustal solids because subsurface composition is not detectable on exoplanets, unlike above-surface volatiles. We find that (i) disequilibrium increased through time in step with the rise of oxygen; (ii) both the Proterozoic and Phanerozoic may have had remotely detectable biogenic disequilibria due to the coexistence of O 2 , N 2 , and liquid water; and (iii) the Archean had a biogenic disequilibrium caused by the coexistence of N 2 , CH 4 , CO 2 , and liquid water, which, for an exoplanet twin, may be remotely detectable. On the basis of this disequilibrium, we argue that the simultaneous detection of abundant CH 4 and CO 2 in a habitable exoplanet's atmosphere is a potential biosignature. Specifically, we show that methane mixing ratios greater than 10 -3 are potentially biogenic, whereas those exceeding 10 -2 are likely biogenic due to the difficulty in maintaining large abiotic methane fluxes to support high methane levels in anoxic atmospheres. Biogenicity would be strengthened by the absence of abundant CO, which should not coexist in a biological scenario.

  7. Uranium series disequilibrium measurements at Mol, Belgium

    International Nuclear Information System (INIS)

    Ivanovich, M.; Wilkins, M.A.

    1985-02-01

    The contract just completed has funded two parallel uranium series disequilibrium studies and the aims of and the progress to completion of these studies are given in this report. The larger study was concerned with the measurement of uranium series disequilibrium in ground waters derived from sand layers above and below the Boom Clay formation in North East Belgium. The disequilibrium data are analysed in terms of uranium, thorium and radium isotopic geochemistries and in terms of water types and their mixing in the regional groundwater system. It is concluded that most sampled waters are mixtures of younger and older waters. No true old water end-members have been sampled. Simple considerations of the uranium isotopic data indicate that the longest residence times of the sampled waters are not much in excess of 1 to 10 x 10 3 y. Detailed mixing patterns could not be established from this limited data set particularly in the absence of more detailed modelling in conjunction with groundwater hydraulic pressure and flow direction data. (author)

  8. Contributions of Transonic Dynamics Tunnel Testing to Airplane Flutter Clearance

    Science.gov (United States)

    Rivera, Jose A.; Florance, James R.

    2000-01-01

    The Transonic Dynamics Tunnel (TDT) became in operational in 1960, and since that time has achieved the status of the world's premier wind tunnel for testing large in aeroelastically scaled models at transonic speeds. The facility has many features that contribute to its uniqueness for aeroelastic testing. This paper will briefly describe these capabilities and features, and their relevance to aeroelastic testing. Contributions to specific airplane configurations and highlights from the flutter tests performed in the TDT aimed at investigating the aeroelastic characteristics of these configurations are presented.

  9. Tilt testing results are influenced by tilt protocol.

    Science.gov (United States)

    Zyśko, Dorota; Fedorowski, Artur; Nilsson, David; Rudnicki, Jerzy; Gajek, Jacek; Melander, Olle; Sutton, Richard

    2016-07-01

    It is unknown how the return to supine position influences duration of loss of consciousness (LOC) and cardioinhibition during tilt test. Retrospective analysis of two datasets containing records of patients who underwent tilt testing for unexplained syncope in two centres was performed. Patients, totalling 1232, were included in the study: 262 in a Swedish centre and 970 patients in a Polish centre. In Sweden, tilt table with tilt-down time (TDT) of 18 s was used (Group II). In Poland, two different tilt tables were used, one of them with TDT of 10 s (Group I, n = 325), and the other with TDT of 47 s (Group III, n = 645). Cardioinhibitory reflex occurred most frequently in Group III, whereas number of pauses >3 s, frequency of very long asystole ≥30 s, and the total duration of pauses >3 s demonstrated a trend to increase from Group I to III. Duration of LOC in Groups II and III was significantly longer compared with Group I (32.0 and 33.7 s vs. 16.4 s). In the multivariate-adjusted regression model, cardioinhibitory reflex was predicted by tilt-table model (odds ratio per model with increasing TDT: 1.40; 95% confidence interval, 1.19-1.64; P < 0.0001), whereas LOC duration was longer with increasing TDT (P < 0.0001) and age (P < 0.0001). Longer TDT during induced vasovagal syncope increases the prevalence of cardioinhibitory reflex and prolongs the duration of LOC. Tilt-down time does not affect asystolic pause duration but delay may lead to occurrence of multiple pauses, higher frequency of very long asystole, and longer total asystole duration. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

  10. Disequilibrium biosignatures over Earth history and implications for detecting exoplanet life

    Science.gov (United States)

    Krissansen-Totton, Joshua; Olson, Stephanie; Catling, David C.

    2018-01-01

    Chemical disequilibrium in planetary atmospheres has been proposed as a generalized method for detecting life on exoplanets through remote spectroscopy. Among solar system planets with substantial atmospheres, the modern Earth has the largest thermodynamic chemical disequilibrium due to the presence of life. However, how this disequilibrium changed over time and, in particular, the biogenic disequilibria maintained in the anoxic Archean or less oxic Proterozoic eons are unknown. We calculate the atmosphere-ocean disequilibrium in the Precambrian using conservative proxy- and model-based estimates of early atmospheric and oceanic compositions. We omit crustal solids because subsurface composition is not detectable on exoplanets, unlike above-surface volatiles. We find that (i) disequilibrium increased through time in step with the rise of oxygen; (ii) both the Proterozoic and Phanerozoic may have had remotely detectable biogenic disequilibria due to the coexistence of O2, N2, and liquid water; and (iii) the Archean had a biogenic disequilibrium caused by the coexistence of N2, CH4, CO2, and liquid water, which, for an exoplanet twin, may be remotely detectable. On the basis of this disequilibrium, we argue that the simultaneous detection of abundant CH4 and CO2 in a habitable exoplanet’s atmosphere is a potential biosignature. Specifically, we show that methane mixing ratios greater than 10−3 are potentially biogenic, whereas those exceeding 10−2 are likely biogenic due to the difficulty in maintaining large abiotic methane fluxes to support high methane levels in anoxic atmospheres. Biogenicity would be strengthened by the absence of abundant CO, which should not coexist in a biological scenario. PMID:29387792

  11. La TDT: El gran contenedor infantil del futuro

    Directory of Open Access Journals (Sweden)

    María Dolores MORENO RODRÍGUEZ

    2009-08-01

    Full Text Available RESUMEN: Los expertos en edu-comunicación apuestan por la tematización que favorece la proliferación de canales infantiles al amparo de las nuevas frecuencias disponibles a través de la TDT. Reconocen, asimismo, la interactividad como un valor añadido aplicable a la producción televisiva infantil en tanto que elemento clave en la estimulación de la creatividad y recepción participativa por parte del niño. En cambio, los especialistas rechazan los sistemas de control parental por resultar ineficaces y evidenciar la insuficiente implicación de las familias en la educación televisiva de sus hijos. Así lo revela la investigación de la que damos cuenta en este artículo y que ha sido desarrollada mediante la configuración de un panel de treinta expertos que se han pronunciado sobre la TDT, sus nuevos usos y servicios de aplicación en la programación infantil. La obtención de información se ha llevado a cabo mediante la aplicación del Método Delphi lo que ha permitido la aportación deslocalizada y asincrónica de expertos procedentes de distintas áreas geográficas y científicas. Siendo de este modo que hemos reunido la opinión de especialistas en pedagogía, didáctica, periodismo, televisión educativa y televisión infantil, así como de representantes de observatorios audiovisuales, consejos, revistas especializadas, y asociaciones de consumidores.ABSTRACT: Experts in edu-communication are in favour of the thematic specialization that encourages the proliferation of children’s channels under the protection of the new frequencies available through DTTV. They also recognize the interactivity available as a value added applicable to children’s television production as a key element in the stimulation of children’s creativity and participatory reception. However, the specialists reject the systems of parental control because they are ineffective and demonstrate the insufficient involvement of the families in the televised

  12. Influence of radon daughter exposure rate, unattachment fraction, and disequilibrium on occurrence of lung tumours

    International Nuclear Information System (INIS)

    Cross, F.T.; Palmer, R.F.; Dagle, G.E.; Busch, R.H.; Buschbom, R.L.

    1984-01-01

    Groups of male, specific-pathogen-free (SPF), Wistar rats were exposed to several concentrations of radon daughters and uranium ore dust to clarify the roles of exposure rate, unattached RaA daughters, and the degree of radon daughter disequilibrium, in the development of respiratory system disease. Modelled, human dosimetric data indicate that the dose to sensitive tissues of the respiratory tract increases with increasing radon daughter unattachment fraction and degree of disequilibrium. Data bearing on these developments as well as updated results of experiments designed to test the role of radon daughter exposure rate on lung tumour incidence are reported. (author)

  13. Detecting rare variants in case-parents association studies.

    Directory of Open Access Journals (Sweden)

    Kuang-Fu Cheng

    Full Text Available Despite the success of genome-wide association studies (GWASs in detecting common variants (minor allele frequency ≥0.05 many suggested that rare variants also contribute to the genetic architecture of diseases. Recently, researchers demonstrated that rare variants can show a strong stratification which may not be corrected by using existing methods. In this paper, we focus on a case-parents study and consider methods for testing group-wise association between multiple rare (and common variants in a gene region and a disease. All tests depend on the numbers of transmitted mutant alleles from parents to their diseased children across variants and hence they are robust to the effect of population stratification. We use extensive simulation studies to compare the performance of four competing tests: the largest single-variant transmission disequilibrium test (TDT, multivariable test, combined TDT, and a likelihood ratio test based on a random-effects model. We find that the likelihood ratio test is most powerful in a wide range of settings and there is no negative impact to its power performance when common variants are also included in the analysis. If deleterious and protective variants are simultaneously analyzed, the likelihood ratio test was generally insensitive to the effect directionality, unless the effects are extremely inconsistent in one direction.

  14. 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...

  15. Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.

    Science.gov (United States)

    Yoo, Yun Joo; Sun, Lei; Poirier, Julia G; Paterson, Andrew D; Bull, Shelley B

    2017-02-01

    By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive. It combines variant effects within the same cluster linearly, and aggregates cluster-specific effects in a quadratic sum of squares and cross-products, producing a test statistic with reduced degrees of freedom (df) equal to the number of clusters. By simulation studies of 1000 genes from across the genome, we demonstrate that MLC is a well-powered and robust choice among existing methods across a broad range of gene structures. Compared to minimum P-value, variance-component, and principal-component methods, the mean power of MLC is never much lower than that of other methods, and can be higher, particularly with multiple causal variants. Moreover, the variation in gene-specific MLC test size and power across 1000 genes is less than that of other methods, suggesting it is a complementary approach for discovery in genome-wide analysis. The cluster construction of the MLC test statistics helps reveal within-gene LD structure, allowing interpretation of clustered variants as haplotypic effects, while multiple regression helps to distinguish direct and indirect associations. © 2016 The Authors Genetic Epidemiology Published by Wiley Periodicals, Inc.

  16. [Study of genetic variants in the BDNF, COMT, DAT1 and SERT genes in Colombian children with attention deficit disorder].

    Science.gov (United States)

    Ortega-Rojas, Jenny; Arboleda-Bustos, Carlos E; Morales, Luis; Benítez, Bruno A; Beltrán, Diana; Izquierdo, Álvaro; Arboleda, Humberto; Vásquez, Rafael

    Attention deficit and hyperactive disorder (ADHD) is highly prevalent among children in Bogota City. Both genetic and environmental factors play a very important role in the etiology of ADHD. However, to date few studies have addressed the association of genetic variants and ADHD in the Colombian population. To test the genetic association between polymorphisms in the DAT1, HTTLPR, COMT and BDNF genes and ADHD in a sample from Bogota City. We genotyped the most common polymorphisms in DAT1, SERT, COMT and BDNF genes associated with ADHD using conventional PCR followed by restriction fragment length polymorphism (RFLP) in 97 trios recruited in a medical center in Bogota. The transmission disequilibrium test (TDT) was used to determine the association between such genetic variants and ADHD. The TDT analysis showed that no individual allele of any variant studied has a preferential transmission. Our results suggest that the etiology of the ADHD may be complex and involves several genetic factors. Further studies in other candidate polymorphisms in a larger sample size will improve our knowledge of the ADHD in Colombian population. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  17. 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 ...

  18. 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 ...

  19. Influence of random daughter exposure rate, unattachment fraction, and disequilibrium on occurrence of lung tumors

    International Nuclear Information System (INIS)

    Cross, F.T.; Palmer, R.F.; Dagle, G.E.; Busch, R.H.; Buschbom, R.L.

    1983-10-01

    Groups of male, specific-pathogen-free (SPF), Wistar rats were exposed to several concentrations of radon daughters and uranium ore dust to clarify the roles of exposure rate, unattached RaA daughters, and the degree of radon daughter disequilibrium, in the development of respiratory system disease. Modeled, human-dosimetric data indicate that the dose to sensitive tissues of the respiratory tract increases with increasing radon-daughter unattachment fraction and degree of disequilibrium. Experimental verification of these dose-effect relationships is needed to protect the health of workers and of the public exposed to radon-daughter environments. Data bearing on these relationships as well as updated results of experiments designed to test the role of radon-daughter exposure rate on lung-tumor incidence are reported. 13 references, 3 tables

  20. [Familial febrile convulsions is supposed to link to human chromosome 19p13.3].

    Science.gov (United States)

    Qi, Y; Lü, J; Wu, X

    2001-01-10

    To localize the familial febrile convulsion (FC) genes on human chromosomes. For 63 FC pedigrees, tetranucleotide repeat markers D19S253 D19S395 and D19S591 on the short arm of chromosome 19, as well as dinucleotide repeat markers D8S84 and D8S85 on the long arm of chromosome 8 were genotyped. Transmission disequilibrium test (TDT) and Lod score calculation were carried out. The data were processed by PPAP software package. All the alleles in every locus of FC probands and normal controls were in Hardy-Weinburg balance. Transmission disequilibrium was found on D8S84, D19S395 and D19S591 in FC families. chi(2) values were 4.0, 5.124 and 7.364 separately. Each P value was < 0.05, and significantly meaningful. The two-point Lod scores between D8S84 and FC, D8S85 and FC, D19S253 and FC, D19S395 and FC, D19S591 and FC are 0.00002, 0.000017, 0.58, 1.53 and 1.42 respectively. The multi-point Lod score among markers on chromosome 8q and FC was 0.88, while Lod score among markers on chromosome 19p and FC reached 2.78. The results by both the non-parameter (TDT) and parameter (Lod score) methods were consistant on a whole. FC is linked with chromosome region 19p13.3, but not with chromosome 8q.

  1. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

    Directory of Open Access Journals (Sweden)

    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. tavgM_3d_tdt_Cp: MERRA 3D IAU Tendency, Temperature, Monthly Mean 1.25 x 1.25 degree V5.2.0 (MATMCPTDT) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — The MATMCPTDT or tavgM_3d_tdt_Cp data product is the MERRA Data Assimilation System 3-Dimensional temperature tendencies that is time averaged on pressure levels at...

  3. Chemical evolution of the Earth: Equilibrium or disequilibrium process?

    Science.gov (United States)

    Sato, M.

    1985-01-01

    To explain the apparent chemical incompatibility of the Earth's core and mantle or the disequilibrium process, various core forming mechanisms have been proposed, i.e., rapid disequilibrium sinking of molten iron, an oxidized core or protocore materials, and meteorite contamination of the upper mantle after separation from the core. Adopting concepts used in steady state thermodynamics, a method is devised for evaluating how elements should distribute stable in the Earth's interior for the present gradients of temperature, pressure, and gravitational acceleration. Thermochemical modeling gives useful insights into the nature of chemical evolution of the Earth without overly speculative assumptions. Further work must be done to reconcile siderophile elements, rare gases, and possible light elements in the outer core.

  4. Uranium series disequilibrium: Concepts and applications

    International Nuclear Information System (INIS)

    Ivanovich, M.

    1994-01-01

    During the past four decades it has been recognized that natural disruption of the U and Th decay chains, resulting in the separation of parent and daughter nuclides, occurs as a consequence of geochemical processes acting in the near-surface environment. This realization has lead to a rapid growth in the application of the naturally occurring radioactive disequilibria diversifying broadly to touch upon a wide spectrum of problems in earth sciences. This paper is a brief review of the subject and addresses a number of issues concerning (1) physico-chemical processes responsible for fractionation of radionuclides in the decay series, (2) the range of observed radioactive disequilibrium in nature, (3) implications in terms of relative mobilities of U, Th, Ra and their daughters in the geosphere, and (4) examples of the application of these concepts to studies of paleoclimate, dating of old groundwaters, and rock/water interaction processes. This review concludes that the concept of radioactive disequilibrium in naturally occurring decay series is a powerful isotopic tool with applications in both terrestrial and marine environments over timescales of up to one million years. (orig.)

  5. Characterization of genetic diversity and linkage disequilibrium of ZmLOX4 and ZmLOX5 loci in maize.

    Directory of Open Access Journals (Sweden)

    Gerald N De La Fuente

    Full Text Available Maize (Zea mays L. lipoxygenases (ZmLOXs are well recognized as important players in plant defense against pathogens, especially in cross kingdom lipid communication with pathogenic fungi. This study is among the first to investigate genetic diversity at important gene paralogs ZmLOX4 and ZmLOX5. Sequencing of these genes in 400 diverse maize lines showed little genetic diversity and low linkage disequilibrium in the two genes. Importantly, we identified one inbred line in which ZmLOX5 has a disrupted open reading frame, a line missing ZmLOX5, and five lines with a duplication of ZmLOX5. Tajima's D test suggests that both ZmLOX4 and ZmLOX5 have been under neutral selection. Further investigation of haplotype data revealed that within the ZmLOX family members only ZmLOX12, a monocot specific ZmLOX, showed strong linkage disequilibrium that extends further than expected in maize. Linkage disequilibrium patterns at these loci of interest are crucial for future candidate gene association mapping studies. ZmLOX4 and ZmLOX5 mutations and copy number variants are under further investigation for crop improvement.

  6. Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses.

    Science.gov (United States)

    Machado, Filipe Brum; de Vasconcellos Machado, Luana; Bydlowski, Cynthia Rachid; Bydlowski, Sergio Paulo; Medina-Acosta, Enrique

    2012-02-01

    Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4 M/HMS3 P, D'(+) = 0.6274; and HTG4 K/HMS3 P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.

  7. Evidence, from family studies, for linkage disequilibrium between TGFA and a gene for nonsyndromic cleft lip with or without cleft palate

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Hongshu; Lee, A.; Gasser, D.L. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States); Sassani, R.; Bartlett, S.P. [Children`s Hospital of Philadelphia, PA (United States); Buetow, K.H. [Fox Chase Cancer Center, Philadelphia, PA (United States); Hecht, J.T. [Univ. of Texas Medical School, Houston, TX (United States); Malcolm, S.; Winter, R.M.; Vintiner, G.M. [Univ. of London (United Kingdom)

    1994-11-01

    The inheritance of alleles of the transforming growth factor alpha (TGFA) locus has been studied in families affected with cleft lip with or without cleft palate (CL/P), by using the transmission/disequilibrium test described by Spielman and colleagues. Only heterozygous parents with an affected child can be included in this test, but within such families a significantly greater frequency of C2 alleles were transmitted to affected children than would be expected by chance. There was no evidence that the total number of C2 alleles transmitted to affected and unaffected children differed significantly from random segregation. These data provide evidence from within families that a gene for susceptibility to CL/P is in significant linkage disequilibrium with the C2 allele of the TGFA locus. 30 refs., 1 fig., 2 tabs.

  8. 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.

  9. INS VNTR is not associated with childhood obesity in 1,023 families: a family-based study.

    Science.gov (United States)

    Bouatia-Naji, Nabila; De Graeve, Franck; Brönner, Günter; Lecoeur, Cécile; Vatin, Vincent; Durand, Emmanuelle; Lichtner, Peter; Nguyen, Thuy T; Heude, Barbara; Weill, Jacques; Lévy-Marchal, Claire; Hebebrand, Johannes; Froguel, Philippe; Meyre, David

    2008-06-01

    Previous studies have described genetic associations of the insulin gene variable number tandem repeat (INS VNTR) variant with childhood obesity and associated phenotypes. We aimed to assess the contribution of INS VNTR genotypes to childhood obesity and variance of insulin resistance, insulin secretion, and birth weight using family-based design. Participants were either French or German whites. We used transmission disequilibrium tests (TDTs) for assessing binary traits and quantitative pedigree disequilibrium tests for assessing continuous traits. In contrast to previous findings, we did not observe any familial association with childhood obesity (T = 50%, P = 0.77) in the 1,023 families tested. In French obese children, INS VNTR did not associate with fasting insulin levels (P = 0.23) and class I allele showed only borderline association with increased insulin secretion index at 30 min (P = 0.03). INS VNTR did not associate with birth weight in obese children (P = 0.98) and TDT analyses in 350 French families with history of low birth weight (LBW) showed no association with this condition (P = 0.92). In summary, our study, the largest performed so far, does not support the previously reported associations between INS VNTR and childhood obesity, insulin resistance, or birth weight, and does not suggest any major role for this variant in modulating these traits.

  10. Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

    OpenAIRE

    Carmichael, Gordon A.

    2008-01-01

    Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demogr...

  11. Dialysis Disequilibrium Syndrome-Induced Cerebral Edema in a Patient with Uremia Following Hemodialysis: A Case Report

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Min; Kim, Heung Cheol [Dept. of Radiology, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon (Korea, Republic of)

    2012-03-15

    Dialysis disequilibrium syndrome is a metabolic complication that can be caused by rapid removal of plasma urea during hemodialysis. Dialysis disequilibrium syndrome can lead to osmotic demyelinating syndrome. This case report describes one case of encephalopathy accompanied by dialysis disequilibrium syndrome with imaging findings acquired immediately after hemodialysis in a 55-year-old woman with chronic renal failure. The patient was observed to present repetitive seizures and sudden deterioration of consciousness immediately after hemodialysis. Shortly after the onset of symptoms, the patient underwent a CT scan. The imaging findings of the CT scan reveal symmetrical diffuse white matter edema of bilateral cerebral hemispheres that extends to the pons along the internal capsule. A follow-up MRI taken two years later shows that reversible changes without damage have occurred in the lesions. The patient can thus be seen to present symptoms characteristically associated with dialysis disequilibrium syndrome, while brain imaging reveals dif-fuse reversible brain edema.

  12. Postoperative changes in visual evoked potentials and cognitive function tests following sevoflurane anaesthesia.

    LENUS (Irish Health Repository)

    Iohom, G

    2012-02-03

    We tested the hypothesis that minor disturbance of the visual pathway persists following general anaesthesia even when clinical discharge criteria are met. To test this, we measured visual evoked potentials (VEPs) in 13 ASA I or II patients who did not receive any pre-anaesthetic medication and underwent sevoflurane anaesthesia. VEPs were recorded on four occasions, before anaesthesia and at 30, 60, and 90 min after emergence from anaesthesia. Patients completed visual analogue scales (VAS) for sedation and anxiety, a Trieger Dot Test (TDT) and a Digit Symbol Substitution Test (DSST) immediately before each VEP recording. These results were compared using Student\\'s t-test. P<0.05 was considered significant. VEP latency was prolonged (P<0.001) and amplitude diminished (P<0.05) at 30, 60, and 90 min after emergence from anaesthesia, when VAS scores for sedation and anxiety, TDT, and DSST had returned to pre-anaesthetic levels.

  13. Early Detection of Alzheimer's Disease Based on the Patient's Creative Drawing Process: First Results with a Novel Neuropsychological Testing Method.

    Science.gov (United States)

    Heymann, Petra; Gienger, Regine; Hett, Andreas; Müller, Stephan; Laske, Christoph; Robens, Sibylle; Ostermann, Thomas; Elbing, Ulrich

    2018-01-01

    Based on the knowledge of art therapy, we developed a new neuropsychological drawing test in order to identify individuals with mild cognitive impairment (MCI) as well as dementia patients and healthy controls (HC). By observing a variety of drawing characteristics of 92 participants with a mean age of 67.7, art therapy and dementia experts discriminate HC from MCI, early dementia of the Alzheimer-type (eDAT), and moderate dementia of the Alzheimer-type (mDAT) by the process analysis of tree drawings on a digitizing tablet. The art therapist's average categorical rating of healthy and MCI or demented individuals matched the clinical diagnosis by 88%. In a first small study, we analyzed interrater reliability, sensitivity, specificity, negative and positive predicted values of our tree drawing test (TDT) in comparison with the clock drawing test (CDT). Similar values of moderate interrater reliability were found for the TDT (0.56) as well as for the CDT (0.54). A significant high sensitivity of 0.9 within this binary impairment scale (HC versus impaired or demented) can be demonstrated. Substantial values for the specificity (0.67) could be obtained that however remain under a perfect value of the CDT (1.0). Considering 31 individuals that received the clinical diagnosis "impaired or demented" the TDT shows a higher recognition rate for the MCI group than the CDT. Furthermore in 8 of 12 borderline cases of clinical diagnosis, the outcome of the TDT diagnosis was consistent with the final clinical result.

  14. Psychological characteristics of eating disorders as evidenced by the combined administration of questionnaires and two projective methods: the Tree Drawing Test (Baum Test) and the Sentence Completion Test.

    Science.gov (United States)

    Mizuta, Ichiro; Inoue, Yoichi; Fukunaga, Tomoko; Ishi, Ryohei; Ogawa, Asao; Takeda, Masatoshi

    2002-02-01

    The objective of this study is to examine psychological/psychopathological characteristics of eating disorders and their subtypes through a combined administration of questionnaires and projective tests. Three questionnaires (Eating Disorder Inventory - 2, Social Adaptation Scale, Southern California University Eating Disorder Inventory - Revised) and two projective tests (the Tree Drawing Test [TDT, Baum Test], and the Sentence Completion Test [SCT]) were administered to 126 female patients between the ages of 15 and 30 years, with eating disorders according to DSM-IV criteria at our outpatient clinic, and to 54 sex- and age-matched control subjects. The purging subtypes of eating disorders (anorexia nervosa - binge-eating/purging type [ANBP] and bulimia nervosa - purging type [BNP]) were clearly differentiated from the controls, both by the questionnaires and the projective tests. Compared with the controls, ANBP/BNP showed more problematic profiles across the three questionnaires, drew smaller and poorer trees in TDT to a more left location on the drawing paper, and gave fewer positive, and more negative responses in SCT. In contrast, few significant differences were found between anorexia nervosa- restricting type (ANR) and the controls, and between ANBP and BNP. As a trend, however, ANR was consistently located between the controls and ANBP/BNP across the whole questionnaires and projective tests.

  15. DIRECTRICES PARA LA ELABORACIÓN DE UN PLAN PARA LA MIGRACIÓN A TELEVISIÓN DIGITAL TERRESTRE (TDT) EN VENEZUELA

    OpenAIRE

    José Rafael Uzcátegui; José Francisco Torres; Nelson Pérez García; Luís Duque; Zeldívar Bruzual

    2010-01-01

    En octubre 2009, la República Bolivariana de Venezuela adoptó el estándar ISDB-Tb (Integrated Services Digital Broadcasting – Terrestrial Built On), de origen japonés, y con las mejoras introducidas por Brasil, como base para el sistema de Televisión Digital Terrestre (TDT) en Venezuela. Con la elección del estándar se inicia el camino hacia la solución de transcendentales aspectos de carácter técnico y legal que permitan la prestación de un servicio de Televisión Digital Terrestre cónsono co...

  16. An Association Between Functional Polymorphisms of the Interleukin 1 Gene Complex and Schizophrenia Using Transmission Disequilibrium Test.

    Science.gov (United States)

    Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Pawlak, Joanna; Dmitrzak-Weglarz, Monika; Szczepankiewicz, Aleksandra; Zaremba, Dorota; Twarowska-Hauser, Joanna

    2016-12-01

    IL1 gene complex has been implicated in the etiology of schizophrenia. To assess whether IL1 gene complex is associated with susceptibility to schizophrenia in Polish population we conducted family-based study. Functional polymorphisms from IL1A (rs1800587, rs17561, rs11677416), IL1B (rs1143634, rs1143643, rs16944, rs4848306, rs1143623, rs1143633, rs1143627) and IL1RN (rs419598, rs315952, rs9005, rs4251961) genes were genotyped in 143 trio with schizophrenia. Statistical analysis was performed using transmission disequilibrium test. We have found a trend toward an association of rs1143627, rs16944, rs1143623 in IL1B gene with the risk of schizophrenia. Our results show a protective effect of allele T of rs4251961 in IL1RN against schizophrenia. We also performed haplotype analysis of IL1 gene complex and found a trend toward an association with schizophrenia of GAGG haplotype (rs1143627, rs16944, rs1143623, rs4848306) in IL1B gene, haplotypes: TG (rs315952, rs9005) and TT (rs4251961, rs419598) in IL1RN. Haplotype CT (rs4251961, rs419598) in IL1RN was found to be associated with schizophrenia. After correction for multiple testing associations did not reach significance level. Our results might support theory that polymorphisms of interleukin 1 complex genes (rs1143627, rs16944, rs1143623, rs4848306 in IL1B gene and rs4251961, rs419598, rs315952, rs9005 in IL1RN gene) are involved in the pathogenesis of schizophrenia, however, none of the results reach significance level after correction for multiple testing.

  17. Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes.

    Science.gov (United States)

    van Endert, P M; Lopez, M T; Patel, S D; Monaco, J J; McDevitt, H O

    1992-01-01

    Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes. Images PMID:1360671

  18. Acceso y participación en la era digital: caso TDT en Argentina

    Directory of Open Access Journals (Sweden)

    Ornela Carboni

    2011-03-01

    Full Text Available El proceso de implementación la Televisión Digital Terrestre (TDT en Argentina se inició en septiembre de 2009/ luego de la publicación del Decreto 1148/09 por el cual se creó el Sistema Argentino de Televisión Digital Terrestre (SATVD-T, basado en el estándar nipón-brasilero Integrated Services Digital Broadcasting Terrestrial (lSDB-TJ. La elección de la norma y las medidas adoptadas para la expansión de la tecnología digital se insertan dentro de un contexto socio-político particular del país caracterizado por un hiperdinamismo en materia de políticas de comunicación. El presente trabajo intentará repensar las nociones de acceso y participación enmarcándolo en la implantación de una nueva tecnología. En este sentido se definirán tres etapas históricas de análisis ligadas al desarrollo de los sistemas de medios, particularmente de la televisión que permitirán establecer las mutaciones de los ejes conceptuales del artículo.

  19. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

    OpenAIRE

    Zhao, Huiying; Nyholt, Dale R.; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

    2017-01-01

    Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous...

  20. Association study of functional genetic variants of innate immunity related genes in celiac disease

    Directory of Open Access Journals (Sweden)

    Martín J

    2005-08-01

    Full Text Available Abstract Background Recent evidence suggest that the innate immune system is implicated in the early events of celiac disease (CD pathogenesis. In this work for the first time we have assessed the relevance of different proinflammatory mediators typically related to innate immunity in CD predisposition. Methods We performed a familial study in which 105 celiac families characterized by the presence of an affected child with CD were genotyped for functional polymorphisms located at regulatory regions of IL-1α, IL-1β, IL-1RN, IL-18, RANTES and MCP-1 genes. Familial data was analysed with a transmission disequilibrium test (TDT that revealed no statistically significant differences in the transmission pattern of the different genetic markers considered. Results The TDT analysis for IL-1α, IL-1β, IL-1RN, IL-18, and MCP-1 genes genetic variants did not reveal biased transmission to the affected offspring. Only a borderline association of RANTES promoter genetic variants with CD predisposition was observed. Conclusion Our results suggest that the analysed polymorphisms of IL-1α, IL-1β, IL-1RN, IL-18, RANTES and MCP-1 genes do not seem to play a major role in CD genetic predisposition in our population.

  1. Novel use of disequilibrium ages in geothermal energy exploration

    International Nuclear Information System (INIS)

    Goles, G.G.; Seymour, R.S.

    1984-01-01

    Geothermal exploration commonly involves estimation of ages of young volcanic rocks. Few reliable techniques are available for this purpose, uranium-series disequilibrium being one. Several activity ratios may be used to estimate disequilibrium ages. Th-230/U-238 were used because of the convenient half-life of Th-230 and because excess Th-230 in volcanic rocks has been found and used to obtain reasonable ages. By analyzing mafic and felsic fractions of each rock studied, data were obtained to construct quasi-isochrons, assuming that minerals in each fraction had the same initial Th-230/Th-232 activity ratio. Analyses were done via epithermal instrumental activation analysis (Th-232, and U-238) and alpha spectrometry (Th-230 and Th-232), an approach that is simple, rapid and allows explicit estimation of chemical yields. Four rocks from the Oregon High Cascades yielded ages or a limit on age consistent with known geological relations. Several improvements in the method could be implemented without serious impact on its simplicity. 15 references, 1 figure, 1 table

  2. Disequilibrium macro model and catastrophe theory: the case of an oil shock

    Energy Technology Data Exchange (ETDEWEB)

    German, I.

    1983-01-01

    This study builds a simple disequilibrium macromodel of a small open economy that imports oil from an exogenous unit. The model is motivated by very slow adjustment of prices and wages to disequilibrium. Output on the other hand adjusts to its final level instantaneously. A rationing scheme is specified that explicitly takes into account the spillover effects and differentiates between notional, effective, and actual quantities. In a Solow-Stiglitz (1968) setting, a dynamic model is developed in which the dynamic forces depend on the economic environment specified by the Malinvandian regimes: Classical Unemployment, Keynesian Unemployment, Repressed Inflation, and the Walrasian Equilibrium. Given that dynamic system, the author seeks to identify the stationary points of the system (quasi-equilibria) and to find their stability properties. To the disequilibrium model an oil shock is introduced and its effects on employment, real output, real wage, and the stationary points of the system are investigated. A one-time increase (decrease) in the real price of oil and a continuous increase (decrease) in the real price of oil are considered. The path the economy takes and, in particular, the continuous and discontinuous behavior of the quasi-equilibria are investigated. Finally, the model government policy is incorporated and different policy alternatives are studied.

  3. MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients

    Directory of Open Access Journals (Sweden)

    Jingjing Zhang

    2017-10-01

    Full Text Available Background/Aim Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene. Methods From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT, TDT allowing for errors (TDTae, and linkage analysis under dominant and recessive inheritance. Results The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2, on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2, on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis. Conclusions This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.

  4. Linking environmental filtering and disequilibrium to biogeography with a community climate framework.

    Science.gov (United States)

    Blonder, Benjamin; Nogués-Bravo, David; Borregaard, Michael K; Donoghue, John C; Jørgensen, Peter M; Kraft, Nathan J B; Lessard, Jean-Philippe; Morueta-Holme, Naia; Sandel, Brody; Svenning, Jens-Christian; Violle, Cyrille; Rahbek, Carsten; Enquist, Brian J

    2015-04-01

    We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial-interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.

  5. Part 1: determination of radioactive disequilibrium in uranium ores by alpha-spectrometry

    International Nuclear Information System (INIS)

    Killeen, P.G.; Carmichael, C.M.

    1976-01-01

    An α-spectrometric method of detecting the presence of disequilibrium in the 238 U decay series has been developed. A silicon semi-conductor detector and a 1024 channel pulse height analyzer were used to obtain alpha particle energy spectra of uraniferous rocks and minerals. 'Infinitely thick' sources were used to avoid the problems involved in preparation of 'infinitely thin' sources. The method involves the generation of theoretical energy distributions for infinitely thick sources. Complete theoretical spectra were computed for comparison with experimentally obtained alpha particle energy spectra of rocks and minerals. The presence and extent of disequilibrium in the 238 U decay series in a rock is determined from the residual spectrum obtained by subtracting a fitted theoretical spectrum from the measured spectrum of a rock. (author)

  6. Role of syn-eruptive plagioclase disequilibrium crystallization in basaltic magma ascent dynamics.

    Science.gov (United States)

    La Spina, G; Burton, M; De' Michieli Vitturi, M; Arzilli, F

    2016-12-12

    Timescales of magma ascent in conduit models are typically assumed to be much longer than crystallization and gas exsolution for basaltic eruptions. However, it is now recognized that basaltic magmas may rise fast enough for disequilibrium processes to play a key role on the ascent dynamics. The quantification of the characteristic times for crystallization and exsolution processes are fundamental to our understanding of such disequilibria and ascent dynamics. Here we use observations from Mount Etna's 2001 eruption and a magma ascent model to constrain timescales for crystallization and exsolution processes. Our results show that plagioclase reaches equilibrium in 1-2 h, whereas ascent times were magma ascent rate and disequilibrium crystallization and exsolution plays a key role in controlling eruption dynamics in basaltic volcanism.

  7. Characteristics of depression in community-dwelling elderly people as indicated by the tree-drawing test.

    Science.gov (United States)

    Murayama, Norio; Endo, Tadashi; Inaki, Koichiro; Sasaki, Shinsai; Fukase, Yuko; Ota, Kazumi; Iseki, Eizo; Tagaya, Hirokuni

    2016-07-01

    The tree-drawing test (TDT) is a typical projective method, but previous studies have paid little attention to it for elderly people. We investigated the characteristics of depression in community-dwelling elderly people as indicated by the TDT. This study was a complete enumeration survey of elderly people conducted through home visits. The contents of the survey included gender, age, presence or absence of housemates, frequency of going out, the 15-item Geriatric Depression Scale, and TDT. The subjects were divided into three groups (normal, depressed tendency, and depressed) according to the total 15-item Geriatric Depression Scale score. In TDT, no significant difference was observed in drooping crown, shadow of the whole tree, or shadow near the base, which have been regarded as indices of depression in younger people. However, the values concerning the size of the tree, such as the height and width of the whole tree, height and width of the crown, and number of occupied areas (of the paper), were significantly lower in the depressed group than in the other groups. In addition, the width of the trunk was significantly smaller in the depressed group than in the normal group. Subjects were classified as being in a 'depressed state' if they used 40 or fewer areas for drawing (i.e. occupied areas) and a 'non-depressed state' if they used 41 or more areas. This enabled depression to be detected (sensitivity: 71.4%; specificity: 79.9%). The size of the tree in TDT is suggested to reflect characteristics of depression in elderly people, such as introversion, reserve, antisocial attitude, a feeling of inferiority, weakness of ego, and lack of vigour. Furthermore, the numbers of occupied areas were found to be relatively useful in detecting depression in elderly people. © 2015 The Authors. Psychogeriatrics © 2015 Japanese Psychogeriatric Society.

  8. Uranium disequilibrium dating of phosphate deposits from the Lau Group, Fiji

    International Nuclear Information System (INIS)

    Roe, K.K.; Burnett, W.C.

    1983-01-01

    A determination of the absolute age of two phosphate deposits in the Lau Group, Fiji by uranium-series disequilibrium techniques is reported. These measurements were undertaken in order to assist in the evaluation of their origin in terms of known palaeoclimatic information. (U.K.)

  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. Government deficits, private investment and the current account: an intertemporal disequilibrium analysis

    NARCIS (Netherlands)

    van Wijnbergen, S.J.G.

    1987-01-01

    An analysis of the fiscal policy in the account of a model with intertemporal optimisation underlying private behaviour. Besides is incorporated explicitly the possibility of (short-run) labour and goods market disequilibrium caused by Fischer (1977)--Gray (1978) type contract-based real-wage

  11. 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.

  12. Disequilibrium dynamics in a Keynesian model with time delays

    Science.gov (United States)

    Gori, Luca; Guerrini, Luca; Sodini, Mauro

    2018-05-01

    The aim of this research is to analyse a Keynesian goods market closed economy by considering a continuous-time setup with fixed delays. The work compares dynamic results based on linear and nonlinear adjustment mechanisms through which the aggregate supply (production) reacts to a disequilibrium in the goods market and consumption depends on income at a preceding date. Both analytical and geometrical (stability switching curves) techniques are used to characterise the stability properties of the stationary equilibrium.

  13. Managerial responses to transaction cost disequilibrium in food supply chains and networks

    NARCIS (Netherlands)

    Bremmers, H.J.; Meulen, van der B.M.J.; Poppe, K.J.; Wijnands, J.H.M.

    2010-01-01

    Differences in transaction costs (i.e. costs of information processing, monitoring and control) between firms in local supply chains as well as in an international setting may have a negative impact on competitiveness and on creation of value added. Transaction cost disequilibrium is defined as a

  14. Comparing endophenotypes in adult-onset primary torsion dystonia.

    LENUS (Irish Health Repository)

    Bradley, David

    2012-02-01

    Adult-onset primary torsion dystonia (AOPTD) has an autosomal dominant pattern of inheritance with markedly reduced penetrance; the genetic causes of most forms of AOPTD remain unknown. Endophenotypes, markers of sub-clinical gene carriage, may be of use detecting non-manifesting gene carriers in relatives of AOPTD patients. The aim of this study was to compare the utility of the spatial discrimination threshold (SDT) and temporal discrimination threshold (TDT) as potential endophenotypes in AOPTD. Data on other published candidate endophenotypes are also considered. Both SDT and TDT testing were performed in 24 AOPTD patients and 34 of their unaffected first degree relatives; results were compared with normal values from a control population. Of the 24 AOPTD patients 5 (21%) had abnormal SDTs and 20 (83%) had abnormal TDTs. Of the 34 first degree relatives 17 (50%) had abnormal SDTs and 14 (41%) had abnormal TDTs. Discordant results on SDT and TDT testing were found in 16 (67%) AOPTD patients and 21 (62%) first degree relatives. TDT testing has superior sensitivity compared to SDT testing in AOPTD patients; although false positive TDTs are recognised, the specificity of TDT testing in unaffected relatives is not determinable. The high level of discordance between the two tests probably relates methodological difficulties with SDT testing. The SDT is an unreliable AOPTD endophenotype; TDT testing fulfils criteria for a reliable endophenotype with a high sensitivity.

  15. Data on genotypic distribution and linkage disequilibrium of several ANRIL polymorphisms in hemodialysis patients

    Directory of Open Access Journals (Sweden)

    A. Arbiol-Roca

    2017-04-01

    Full Text Available A long non-coding RNA called ANRIL located on chromosome 9p21.3 has been identified as a novel genetic factor associated with cardiovascular disease. Investigation of several single nucleotide polymorphisms (SNPs of Noncoding Antisense RNA in the INK4 Locus (ANRIL gene are of particular interest. This article reports data related to the research article entitled: “Association of ANRIL gene polymorphisms with major adverse cardiovascular events in hemodialysis patients” (Arbiol-Roca et al. [1]. Data presented show the genotypic distribution of four selected ANRIL SNPs: rs10757278, rs4977574, rs10757274 and rs6475606 in a cohort constituted by 284 hemodialysis patients. This article analyzes the Hardy-Weinberg disequilibrium of each studied SNP, and the linkage disequilibrium between them.

  16. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.

    Science.gov (United States)

    Dapper, Amy L; Payseur, Bret A

    2018-02-01

    In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees.

    Science.gov (United States)

    Crous, Casparus J; Burgess, Treena I; Le Roux, Johannes J; Richardson, David M; Slippers, Bernard; Wingfield, Michael J

    2016-12-23

    Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards, and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilise these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies, and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. Published by Oxford University Press on

  18. Disequilibrium implications on dose assessment in the use of NORM as building material

    International Nuclear Information System (INIS)

    Rosa, R.; Amaral, E.C.S.

    2002-01-01

    The need of reusing industrial wastes to avoid environmental impact resulting from their deposition and to reduce the management costs, indicates the building industry as an important user of large quantities of industrial wastes, mainly those generated in the ore milling. The industry of phosphate fertilizers is a typical example of this situation. The phosphate rock contains radionuclides of the U and Th decay series. During the chemical attack these radionuclides are distributed in different proportions between the phosphoric acid and the phosphogypsum, depending on the process. Several countries adopt a methodology based on the Ra-226, Th-232 and K-40 content in order to allow the use of materials with natural radionuclides. Dose assessment for the use of phosphogypsum as building material have shown that methodology is not adequate when disequilibrium exists. This paper will present some implications on dose assessment and on the use of that methodology when disequilibrium exists, using two phosphogypsum radionuclides distribution patterns obtained through different milling processes in Brazil. (author)

  19. Unconsciously Indigenous Leadership: The Role of Cognitive Disequilibrium in Preparing Democratic Educational Leaders

    Science.gov (United States)

    Farmer, Tod Allen

    2008-01-01

    This paper focuses on the role of cognitive disequilibrium in preparing democratic educational leaders. Followers emerge into leaders with what are many times unconsciously socialized norms and values indigenous to their local culture. One of the roles of a democratic leadership preparation program is to challenge these unconsciously accepted…

  20. 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...

  1. 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...

  2. Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

    Science.gov (United States)

    Carmichael, Gordon A

    2008-07-17

    Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demographic transition theory postulates initially high birth and death rates, this equilibrium eventually being broken by falling mortality. In Thailand, however, there is likely to have been both significant mortality decline and appreciable fertility increase after 1850, as the virtual elimination of indigenous warfare, rapid growth of the export rice economy and the demise of slavery and corvée labour created a new domestic environment. Characterized by more dispersed, often frontier, settlement, this environment was unprecedentedly sedate and settled, afforded ordinary households a previously unknown level of control over their resources of labour, and generated optimism about prospects for the next generation.

  3. 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.

  4. Equilibrium and disequilibrium chemistry of adiabatic, solar-composition planetary atmospheres

    Science.gov (United States)

    Lewis, J. S.

    1976-01-01

    The impact of atmospheric and cloud-structure models on the nonequilibrium chemical behavior of the atmospheres of the Jovian planets is discussed. Quantitative constraints on photochemical, lightning, and charged-particle production of organic matter and chromophores are emphasized whenever available. These considerations imply that inorganic chromophore production is far more important than that of organic chromophores, and that lightning is probably a negligibly significant process relative to photochemistry on Jupiter. Production of complex molecules by gas-phase disequilibrium processes on Saturn, Uranus, and Neptune is severely limited by condensation of even simple intermediates.

  5. Uranium series disequilibrium in the coastal surface sediments and sea water of the Arabian sea

    Digital Repository Service at National Institute of Oceanography (India)

    Joshi, L.U.; Zingde, M.D.

    activity ratios in leachates, and residues after removal of surface organic matter from the sediment particles by treatment with hydrogen peroxide and 0.05M HCl, revealed disequilibrium between sup(238) U and sup(234) U only in the surface organic matter...

  6. The Lu-Hf isotope composition of cratonic lithosphere: disequilibrium between garnet and clinopyroxene in kimberlite xenoliths

    NARCIS (Netherlands)

    Simon, N.S.C.; Carlson, R.W.; Pearson, D.G.; Davies, G.R.

    2002-01-01

    12th Annual V.M. Goldschmidt Conference Davos Switzerland, The Lu-Hf isotope composition of cratonic lithosphere: disequilibrium between garnet and clinopyroxene in kimberlite xenoliths (DTM, Carnegie Institution of Washington), Pearson, D.G. (University of Durham)

  7. 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...

  8. Employment in Disequilibrium: a Disaggregated Approach on a Panel of French Firms

    OpenAIRE

    Brigitte Dormont

    1989-01-01

    The purpose of this paper is to understand disequilibrium phenomena at a disaggregated level. By using data on French firms, we carry out the estimation of labor demand model with two regimes, which correspond to the Keynesian and classical hypotheses. The results enable us to characterize classical firms as being particularly good performers: they have more rapid growth, younger productive plant and higher productivity gains and profitability. Classical firms stand out, with respect to their...

  9. Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

    Science.gov (United States)

    Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

    2008-02-01

    The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

  10. 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

  11. 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...

  12. The Isotopologue Record of Repeat Vital Effect Offenders: Tracking (Dis)equilibrium Effects in Sea Urchins and Nannofossil Using Clumped Isotopes

    Science.gov (United States)

    John, C. M.; Davies, A.; Drury, A. J.

    2016-12-01

    Vital effects vary between species and affect various isotopic systems in unequal proportion. The magnitude of the response of different isotopic systems might thus be key in understanding biologically-mediated disequilibrium, especially in groups that show a tendency to be "repeat offenders" with regards to vital effects. Here we present carbon, oxygen, and clumped isotope data from echinoderm calcite and nannofossil ooze, both of which exhibit strong vital effects in bulk isotopes. Our study is the first to investigate the clumped isotope (dis)equilibrium of echinoids. Results from two echinoids, three marine gastropods and a bivalve mollusk from modern beach deposits of Bali, Indonesia, highlight a significant offset in clumped isotopes of a regular echinoid test from expected values, interpreted as evidence of a similar "vital effect" as observed in surface corals. This is in contrast to the test of an irregular "sand dollar" echinoid, with clumped isotope values within error of expected sea surface temperature. Furthermore, data on the inter-skeletal variability in the clumped isotopic composition of two regular echinoid species shows that the spines of the echinoids are in equilibrium with seawater with respect to clumped isotopes, but the test is not. For the nannofossil material, no clumped isotope vital effects are observed, consistent with previously published studies but at odds with strong vital effects in carbon and oxygen isotopes, often correlated with cell-size. In addition, we reveal that the <63 micron fraction of deep-sea ooze could constitute useful material for clumped isotope studies. An intriguing result of our study is that vital effects are mostly absent in clumped isotopes, even in phylums known for important isotopic effects. It remains to be explained why some parts of the echinoids show clear vital effects, notably enrichment in clumped isotopes of urchin tests. Mechanisms that could explain this include pH effects during calcification

  13. Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

    Science.gov (United States)

    Houle, David; Márquez, Eladio J

    2015-06-10

    We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r(2) ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines. Copyright © 2015 Houle and Márquez.

  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. 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

  16. 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.

  17. MICA diversity and linkage disequilibrium with HLA-B alleles in renal-transplant candidates in southern Brazil.

    Science.gov (United States)

    Yamakawa, Roger Haruki; Saito, Patrícia Keiko; Gelmini, Geórgia Fernanda; da Silva, José Samuel; Bicalho, Maria da Graça; Borelli, Sueli Donizete

    2017-01-01

    The major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located centromerically to the human leukocyte antigen (HLA)-B. The short distance between these loci in the MHC indicates the presence of linkage disequilibrium (LD). Similarly to the HLA, the MICA is highly polymorphic, and this polymorphism has not been well documented in different populations. In this study, we estimated the allelic frequencies of MICA and the linkage disequilibrium with HLA-B alleles in 346 renal-transplant candidates in southern Brazil. MICA and HLA were typed using the polymerase chain reaction-sequence-specific primer method (PCR-SSO), combined with the Luminex technology. A total of 19 MICA allele groups were identified. The most frequent allele groups were MICA*008 (21.6%), MICA*002 (17.0%) and MICA*004 (14.8%). The most common haplotypes were MICA*009-B*51 (7.8%), MICA*004-B*44 (6.06%) and MICA*002-B*35 (5.63%). As expected from the proximity of the MICA and HLA-B loci, most haplotypes showed strong LD. Renal patients and healthy subjects in the same region of Brazil showed statistically significant differences in their MICA polymorphisms. The MICA*027 allele group was more frequent in renal patients (Pc = 0.018, OR: 3.421, 95% CI: 1.516-7.722), while the MICA*019 allele group was more frequent in healthy subjects (Pc = 0.001, OR: 0.027, 95% CI: 0.002-0.469). This study provided information on the distribution of MICA polymorphisms and linkage disequilibrium with HLA-B alleles in Brazilian renal-transplant candidates. This information should help to determine the mechanisms of susceptibility to different diseases in patients with chronic kidney disease, and to elucidate the mechanisms involved in allograft rejection associated with MICA polymorphisms in a Brazilian population.

  18. Uranium isotopic disequilibrium in ground water as an indicator of anomalies

    International Nuclear Information System (INIS)

    Osmond, J.K.; Cowart, J.B.; Ivanovich, M.

    1983-01-01

    Because of the unique elemental and isotopic properties of uranium, ground water surveys are a most appropriate approach to prospecting for surficial and secondary uranium deposits. Uranium4+ is generally immobile, but in oxidising and carbonate bearing waters U 6 + is mobile and conservative. Uranium 234 is the radiogenic daughter of 238 U. The intervening α-decay event causes recoil displacements and radioactive disequilibrium between the two isotopes in open systems such as surficial aquifers. Extreme variations in dissolved uranium composition of ground waters combined with significant variations in the ratio 234 U/ 238 U are indicative of the proximity and stage of evolution of secondary deposits. (author)

  19. Aspects of uranium/thorium series disequilibrium applications to radionuclide migration studies

    International Nuclear Information System (INIS)

    Ivanovich, M.

    1989-11-01

    The aim of this paper is to consider the contribution which the uranium/thorium series disequilibrium concept can make to understanding the retardation and transport of radionuclides in the far-field of a radioactive waste repository. In principle, naturally occurring isotopes of uranium, thorium and radium can be regarded as geochemical analogues of the divalent radionuclides and multivalent actinides expected to be present in the radioactive waste inventory. The study of their retardation and/or transport in real rock/water systems which have taken place over geological timescales, can make an important contribution to establishing a rational basis for long-term predictive modelling of radionuclide transport required for safety assessments. (author)

  20. 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...

  1. Dynamics of a durable commodity market involving trade at disequilibrium

    Science.gov (United States)

    Panchuk, A.; Puu, T.

    2018-05-01

    The present work considers a simple model of a durable commodity market involving two agents who trade stocks of two different types. Stock commodities, in contrast to flow commodities, remain on the market from period to period and, consequently, there is neither unique demand function nor unique supply function exists. We also set up exact conditions for trade at disequilibrium, the issue being usually neglected, though a fact of reality. The induced iterative system has infinite number of fixed points and path dependent dynamics. We show that a typical orbit is either attracted to one of the fixed points or eventually sticks at a no-trade point. For the latter the stock distribution always remains the same while the price displays periodic or chaotic oscillations.

  2. DISEQUILIBRIUM CARBON, OXYGEN, AND NITROGEN CHEMISTRY IN THE ATMOSPHERES OF HD 189733b AND HD 209458b

    International Nuclear Information System (INIS)

    Moses, Julianne I.; Visscher, C.; Fortney, J. J.; Showman, A. P.; Lewis, N. K.; Griffith, C. A.; Klippenstein, S. J.; Shabram, M.; Friedson, A. J.; Marley, M. S.; Freedman, R. S.

    2011-01-01

    We have developed a one-dimensional photochemical and thermochemical kinetics and diffusion model to study the effects of disequilibrium chemistry on the atmospheric composition of 'hot-Jupiter' exoplanets. Here we investigate the coupled chemistry of neutral carbon, hydrogen, oxygen, and nitrogen species on HD 189733b and HD 209458b and we compare the model results with existing transit and eclipse observations. We find that the vertical profiles of molecular constituents are significantly affected by transport-induced quenching and photochemistry, particularly on the cooler HD 189733b; however, the warmer stratospheric temperatures on HD 209458b help maintain thermochemical equilibrium and reduce the effects of disequilibrium chemistry. For both planets, the methane and ammonia mole fractions are found to be enhanced over their equilibrium values at pressures of a few bar to less than an mbar due to transport-induced quenching, but CH 4 and NH 3 are photochemically removed at higher altitudes. Disequilibrium chemistry also enhances atomic species, unsaturated hydrocarbons (particularly C 2 H 2 ), some nitriles (particularly HCN), and radicals like OH, CH 3 , and NH 2 . In contrast, CO, H 2 O, N 2 , and CO 2 more closely follow their equilibrium profiles, except at pressures ∼ 2 O, and N 2 are photochemically destroyed and CO 2 is produced before its eventual high-altitude destruction. The enhanced abundances of CH 4 , NH 3 , and HCN are expected to affect the spectral signatures and thermal profiles of HD 189733b and other relatively cool, transiting exoplanets. We examine the sensitivity of our results to the assumed temperature structure and eddy diffusion coefficients and discuss further observational consequences of these models.

  3. Linkage disequilibrium in the insulin gene region: Size variation at the 5{prime} flanking polymorphism and bimodality among {open_quotes}Class I{close_quotes} alleles

    Energy Technology Data Exchange (ETDEWEB)

    McGinnis, R.E.; Spielman, R.S. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1994-09-01

    The 5{prime} flanking polymorphism (5{prime}FP), a hypervariable region at the 5{prime} end of the insulin gene, has {open_quotes}class 1{close_quotes} alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). The authors report that precise sizing of the 5{prime}FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. They also examined 5{prime}FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5{prime}FP, they found that one allele exhibits near-total association with the upper component of the 5FP class 1 distribution. Such associations represent a little-known but potentially wide-spread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. 22 refs., 5 figs., 6 tabs.

  4. Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

    Science.gov (United States)

    Greenberg, David A; Zhang, Junying; Shmulewitz, Dvora; Strug, Lisa J; Zimmerman, Regina; Singh, Veena; Marathe, Sudhir

    2005-12-30

    The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. 2) To observe the effect on genetic analysis and gene discovery of a complex set of gene x gene interactions. 3) To allow comparison of microsatellite vs. large-scale single-nucleotide polymorphism (SNP) data. 4) To allow testing of association to identify the disease gene and the effect of moderate marker x marker linkage disequilibrium. 5) To observe the effect of different ascertainment/disease definition schemes on the analysis. Data was distributed in two forms. Data distributed to participants contained about 1,000 SNPs and 400 microsatellite markers. Internet-obtainable data consisted of a finer 10,000 SNP map, which also contained data on controls. While disease characteristics and parameters were constant, four "studies" used varying ascertainment schemes based on differing beliefs about disease characteristics. One of the studies contained multiplex two- and three-generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different phenotypes, which were themselves heterogeneous. The population parameters were calibrated so that the major genes could be discovered by linkage analysis in most datasets. The association evidence was more difficult to calibrate but was designed to find statistically significant association in 50% of datasets. We also

  5. 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.

  6. Maternal Transmission Effect of a PDGF-C SNP on Nonsyndromic Cleft Lip with or without Palate from a Chinese Population

    Science.gov (United States)

    Wang, Xingang; Yin, Ningbei; Song, Tao; Li, Haidong; Zhang, Feng; Zhang, Yongbiao; Ye, Zhenqing; Yu, Jun; Wang, Duen-Mei; Zhao, Zhenmin

    2012-01-01

    Cleft lip with or without palate (CL/P) is a common congenital anomaly with a high birth prevalence in China. Based on a previous linkage signal of nonsyndromic CL/P (NSCL/P) on the chromosomal region 4q31–q32 from the Chinese populations, we screened the 4q31–q32 region for susceptibility genes in 214 trios of Han Chinese. PDGF-C, an important developmental factor, resides in the region and has been implicated in NSCL/P. However, in our family-based association test (transmission disequilibrium test; TDT), we could not conclude an association between PDGF-C and NSCL/P as previously suggested. Instead, we found strong evidence for parent-of-origin effect at a PDGF-C SNP, rs17035464, by a likelihood ratio test (unadjusted p-value = 0.0018; Im = 2.46). The location of rs17035464 is 13 kb downstream of a previously reported, NSCL/P-associated SNP, rs28999109. Furthermore, a patient from our sample trios was observed with a maternal segmental uniparental isodisomy (UPD) in a region containing rs17035464. Our findings support the involvement of PDGF-C in the development of oral clefts; moreover, the UPD case report contributes to the collective knowledge of rare variants in the human genome. PMID:23029525

  7. 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.

  8. Linkage disequilibrium between human leukocyte antigen (HLA) class II and HLA-G--possible implications for human reproduction and autoimmune disease

    DEFF Research Database (Denmark)

    Hviid, Thomas Vauvert F; Christiansen, Ole B

    2005-01-01

    ). We found a significant linkage disequilibrium between HLA-DR3 and HLA-G*010102 in both the RSA and control populations. For all four studied HLA loci, the alleles in the haplotype HLA-DRB1*03.DQA1*05.DQB1*02.G*010102 was in clear linkage disequilibrium. This HLA haplotype has repeatedly been...... associated with different autoimmune diseases but also with RSA. The G*010102 allele includes a 14-bp sequence polymorphism in the 3' untranslated region of the gene, which has been associated with differences in HLA-G mRNA alternative splicing and stability. This 14-bp polymorphism has also been associated...... with RSA, pre-eclampsia, and outcome of in vitro fertilization. Implications of HLA polymorphism--and other polymorphic genes in the MHC for pregnancy outcome--and for autoimmune diseases during pregnancy are discussed....

  9. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    Science.gov (United States)

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-07-29

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

  10. HLA class II linkage disequilibrium and haplotype evolution in the Cayapa Indians of Ecuador

    Energy Technology Data Exchange (ETDEWEB)

    Trachtenberg, E.A.; Erlich, H.A. [Roche Molecular Systems, Alameda, CA (United States); Klitz, W. [Univ. of California, Berkeley, CA (United States)] [and others

    1995-08-01

    DNA-based typing of the HLA class II loci in a sample of the Cayapa Indians of Ecuador reveals several lines of evidence that selection has operated to maintain and to diversify the existing level of polymorphism in the class II region. As has been noticed for other Native American groups, the overall level of polymorphism at the DRB1, DQA1, DQB1, and DPB1 loci is reduced relative to that found in other human populations. Nonetheless, the relative eveness in the distribution of allele frequencies at each of the four loci points to the role of balancing selection in the maintenance of the polymorphism. The DQA1 and DQB1 loci, in particular, have near-maximum departures from the neutrality model, which suggests that balancing selection has been especially strong in these cases. Several novel DQA1-DQB1 haplotypes and the discovery of a new DRB1 allele demonstrate an evolutionary tendency favoring the diversification of class II alleles and haplotypes. The recombination interval between the centromeric DPB1 locus and the other class II loci will, in the absence of other forces such as selection, reduce disequilibrium across this region. However, nearly all common alleles were found to be part of DR-DP haplotypes in strong disequilibrium, consistent with the recent action of selection acting on these haplotypes in the Cayapa. 50 refs., 3 figs., 3 tabs.

  11. 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.

  12. U-series disequilibrium constraints on magma generation at the Jan Mayen hotspot

    Science.gov (United States)

    Rivers, E. R.; Chernow, R.; Elkins, L. J.; Sims, K. W.; Blichert-Toft, J.; Devey, C. W.

    2013-12-01

    The incompatible element-enriched magma source beneath the Jan Mayen Island hotspot influences melt generation on the adjacent northern Mid-Atlantic Ridge system and likely derives from either a small, local mantle plume, ancient Icelandic plume material emplaced in the mantle source, and/or sub-continental lithospheric mantle remnants emplaced locally by rifting of Greenland. The slow spreading Northern Kolbeinsey and Southern Mohns Ridges are immediately adjacent to Jan Mayen Island. Both have relatively shallow ridge axes, particularly the extremely shallow Eggvin Bank region of the Northern Kolbeinsey Ridge, which host anomalously large central volcanic edifices. We are currently collecting U-series disequilibrium and long-lived radiogenic isotope data for fresh, glassy mid-ocean ridge basalts from the Northern Kolbeinsey and Southern Mohns Ridge segments to better constrain source composition, depth of melting in the garnet peridotite stability field, solid mantle upwelling rates, and the nature of melt extraction beneath those segments. In particular, we are measuring isotopic data for geographically well-located samples collected from hummocky pillow basalt flows within the axial valley of the Northern Kolbeinsey Ridge segment as well as from the large volcanoes on both ridge segments, to further determine the role of the Jan Mayen hotspot in crustal construction on the Mid-Atlantic Ridge. Recently collected data show particularly high strontium isotope ratios consistent with trace element patterns that suggest a distinct local plume located beneath the Jan Mayen hotspot. A plume model for Jan Mayen is supported by new bathymetric imaging of adjacent ridge segments that reveals excess volcanism beneath the large axial volcanoes and a radial distribution of enrichment surrounding Jan Mayen Island. We predict that age-constrained U-series disequilibrium measurements will support active mantle upwelling focused beneath both Jan Mayen Island and the large axial

  13. 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.

  14. Association between the polymorphism of C861G (rs6296) in the serotonin 1B receptor gene and Tourette syndrome in Han Chinese people.

    Science.gov (United States)

    Yi, Mingji; Zhang, Ying; Wang, Yujie; Su, Nailun; Liu, Shiguo

    2017-06-01

    Clinical, neuroimaging and other studies provided evidence that the dysfunction of the serotonin neurotransmitter system were found in Tourette syndrome (TS). This study is to explore the association between the polymorphism of C861G (rs6296) in HTR1B and TS in Han Chinese people. Two hundred ninety-nine TS patients (260 TS trios and 39 TS patients) and 388 healthy controls were collected. The genotype of HTR1B C861G was detected using Taqman probes. The case-control study and family-based study was used separately to study association between HTR1B C861G and TS in Han Chinese people. In case-control study, no statistically significant difference was found in the distribution of HTR1B C861G polymorphism between TS patients and controls (for genotype: χ 2  = 3.408, P = 0.182; for allele: χ 2  = 0.395, P = 0.530, OR = 0.934, 95%CI: 0.754-1.156). In family-based study, we observed nonsignificant over-transmission of the G861 allele in HTR1B to TS offspring using the transmission disequilibrium test (TDT), haplotype relative risk (HRR) and haplotype-based HRR (HHRR) (TDT χ 2  = 0.410, P = 0.560; HRR = 1.151, χ 2  = 0.421, P = 0.517, 95% CI: 0.753-1.759; HHRR = 0.919, χ 2  = 0.467, P = 0.495, 95%CI: 0.720-1.172). Our study suggested that the polymorphism of HTR1B C861G is not a risk factor for TS in Han Chinese population. However, the result should be replicated in larger sample and different population. © 2015 Wiley Publishing Asia Pty Ltd.

  15. A statistical procedure for testing financial contagion

    Directory of Open Access Journals (Sweden)

    Attilio Gardini

    2013-05-01

    Full Text Available The aim of the paper is to provide an analysis of contagion through the measurement of the risk premia disequilibria dynamics. In order to discriminate among several disequilibrium situations we propose to test contagion on the basis of a two-step procedure: in the first step we estimate the preference parameters of the consumption-based asset pricing model (CCAPM to control for fundamentals and to measure the equilibrium risk premia in different countries; in the second step we measure the differences among empirical risk premia and equilibrium risk premia in order to test cross-country disequilibrium situations due to contagion. Disequilibrium risk premium measures are modelled by the multivariate DCC-GARCH model including a deterministic crisis variable. The model describes simultaneously the risk premia dynamics due to endogenous amplifications of volatility and to exogenous idiosyncratic shocks (contagion, having controlled for fundamentals effects in the first step. Our approach allows us to achieve two goals: (i to identify the disequilibria generated by irrational behaviours of the agents, which cause increasing in volatility that is not explained by the economic fundamentals but is endogenous to financial markets, and (ii to assess the existence of contagion effect defined by exogenous shift in cross-country return correlations during crisis periods. Our results show evidence of contagion from the United States to United Kingdom, Japan, France, and Italy during the financial crisis which started in 2007-08.

  16. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

    Science.gov (United States)

    2014-01-01

    Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

  17. Equilibrium and Disequilibrium of River Basins: Effects on Stream Captures in Serra do Mar and Serra da Mantiqueira, Brazil

    Science.gov (United States)

    DA Silva, L. M.

    2015-12-01

    Landscapes are mainly driven by river processes that control the dynamic reorganization of networks. Discovering and identifying whether river basins are in geometric equilibrium or disequilibrium requires an analysis of water divides, channels that shift laterally or expand upstream and river captures. Issues specifically discussed include the variation of drainage area change and erosion rates of the basins. In southeastern Brazil there are two main escarpments with extensive geomorphic surfaces: Serra do Mar and Serra da Mantiqueira Mountains. These landscapes are constituted of Neoproterozoic and early Paleozoic rocks, presenting steep escarpments with low-elevation coastal plains and higher elevation interior plateaus. To identify whether river basins and river profiles are in equilibrium or disequilibrium in Serra do Mar and Serra da Mantiqueira Mountains, we used the proxy (χ), evaluating the effect of drainage area change and erosion rates. We selected basins that drain both sides of these two main escarpments (oceanic and continental sides) and have denudation rates derived from pre-existing cosmogenic isotopes data (Rio de Janeiro, Paraná and Minas Gerais). Despite being an ancient and tectonically stable landscape, part of the coastal plain of Serra do Mar Mountain in Rio de Janeiro and Paraná is in geometric disequilibrium, with water divides moving in the direction of higher χ values. To achieve equilibrium, some basins located in the continental side are retracting and disappearing, losing area to the coastal basins. On the contrary, there are some adjacent sub-basins that are close to equilibrium, without strong contrasts in χ values. The same pattern was observed in Serra da Mantiqueira (Minas Gerais state), with stream captures and river network reorganization in its main rivers. The initial results suggest a strong contrast between erosion rates in the continental and the oceanic portions of the escarpments.

  18. Pharmacogenetic testing through the direct-to-consumer genetic testing company 23andMe.

    Science.gov (United States)

    Lu, Mengfei; Lewis, Cathryn M; Traylor, Matthew

    2017-06-19

    Rapid advances in scientific research have led to an increase in public awareness of genetic testing and pharmacogenetics. Direct-to-consumer (DTC) genetic testing companies, such as 23andMe, allow consumers to access their genetic information directly through an online service without the involvement of healthcare professionals. Here, we evaluate the clinical relevance of pharmacogenetic tests reported by 23andMe in their UK tests. The research papers listed under each 23andMe report were evaluated, extracting information on effect size, sample size and ethnicity. A wider literature search was performed to provide a fuller assessment of the pharmacogenetic test and variants were matched to FDA recommendations. Additional evidence from CPIC guidelines, PharmGKB, and Dutch Pharmacogenetics Working Group was reviewed to determine current clinical practice. The value of the tests across ethnic groups was determined, including information on linkage disequilibrium between the tested SNP and causal pharmacogenetic variant, where relevant. 23andMe offers 12 pharmacogenetic tests to their UK customers, some of which are in standard clinical practice, and others which are less widely applied. The clinical validity and clinical utility varies extensively between tests. The variants tested are likely to have different degrees of sensitivity due to different risk allele frequencies and linkage disequilibrium patterns across populations. The clinical relevance depends on the ethnicity of the individual and variability of pharmacogenetic markers. Further research is required to determine causal variants and provide more complete assessment of drug response and side effects. 23andMe reports provide some useful pharmacogenetics information, mirroring clinical tests that are in standard use. Other tests are unspecific, providing limited guidance and may not be useful for patients without professional interpretation. Nevertheless, DTC companies like 23andMe act as a powerful

  19. Association study between a polymorphism at the 3'-untranslated region of CLOCK gene and attention deficit hyperactivity disorder

    Directory of Open Access Journals (Sweden)

    Xu Xiaohui

    2010-08-01

    Full Text Available Abstract Background The circadian locomotor output cycles kaput (CLOCK gene encodes protein regulation circadian rhythm and also plays some roles in neural transmitter systems including the dopamine system. Several lines of evidence implicate a relationship between attention-deficit hyperactivity disorder (ADHD, circadian rythmicity and sleeping disturbances. A recent study has reported that a polymorphism (rs1801260 at the 3'-untranslated region of the CLOCK gene is associated with adult ADHD. Methods To investigate the association between the polymorphism (rs1801260 in ADHD, two samples of ADHD probands from the United Kingdom (n = 180 and Taiwan (n = 212 were genotyped and analysed using within-family transmission disequilibrium test (TDT. Bonferroni correction procedures were used to just for multiple comparisons. Results We found evidence of increased transmission of the T allele of the rs1801260 polymorphism in Taiwanese samples (P = 0.010. There was also evidence of preferential transmission of the T allele of the rs1801260 polymorphism in combined samples from the Taiwan and UK (P = 0.008. Conclusion This study provides evidence for the possible involvement of CLOCK in susceptibility to ADHD.

  20. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

    Science.gov (United States)

    Fariello, María Inés; Boitard, Simon; Mercier, Sabine; Robelin, David; Faraut, Thomas; Arnould, Cécile; Recoquillay, Julien; Bouchez, Olivier; Salin, Gérald; Dehais, Patrice; Gourichon, David; Leroux, Sophie; Pitel, Frédérique; Leterrier, Christine; SanCristobal, Magali

    2017-07-01

    Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single-marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS. © 2017 John Wiley & Sons Ltd.

  1. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers.

    Science.gov (United States)

    Zhang, Yu; Yan, Haidong; Jiang, Xiaomei; Wang, Xiaoli; Huang, Linkai; Xu, Bin; Zhang, Xinquan; Zhang, Lexin

    2016-01-01

    To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass ( Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei's gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r 2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 ( P  < 0.01). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

  2. A reliability design method for a lithium-ion battery pack considering the thermal disequilibrium in electric vehicles

    Science.gov (United States)

    Xia, Quan; Wang, Zili; Ren, Yi; Sun, Bo; Yang, Dezhen; Feng, Qiang

    2018-05-01

    With the rapid development of lithium-ion battery technology in the electric vehicle (EV) industry, the lifetime of the battery cell increases substantially; however, the reliability of the battery pack is still inadequate. Because of the complexity of the battery pack, a reliability design method for a lithium-ion battery pack considering the thermal disequilibrium is proposed in this paper based on cell redundancy. Based on this method, a three-dimensional electric-thermal-flow-coupled model, a stochastic degradation model of cells under field dynamic conditions and a multi-state system reliability model of a battery pack are established. The relationships between the multi-physics coupling model, the degradation model and the system reliability model are first constructed to analyze the reliability of the battery pack and followed by analysis examples with different redundancy strategies. By comparing the reliability of battery packs of different redundant cell numbers and configurations, several conclusions for the redundancy strategy are obtained. More notably, the reliability does not monotonically increase with the number of redundant cells for the thermal disequilibrium effects. In this work, the reliability of a 6 × 5 parallel-series configuration is the optimal system structure. In addition, the effect of the cell arrangement and cooling conditions are investigated.

  3. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs

    Directory of Open Access Journals (Sweden)

    Cheng Yu-Huei

    2009-06-01

    Full Text Available Abstract Background Linkage disequilibrium (LD mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping. Results We developed a freeware called LD2SNPing, which provides a complete package of mining tools for genotyping and LD analysis environments. The software provides SNP ID- and gene-centric online retrievals for SNP information and tag SNP selection from dbSNP/NCBI and HapMap, respectively. Restriction fragment length polymorphism (RFLP enzyme information for SNP genotype is available to all SNP IDs and tag SNPs. Single and multiple SNP inputs are possible in order to perform LD analysis by online retrieval from HapMap and NCBI. An LD statistics section provides D, D', r2, δQ, ρ, and the P values of the Hardy-Weinberg Equilibrium for each SNP marker, and Chi-square and likelihood-ratio tests for the pair-wise association of two SNPs in LD calculation. Finally, 2D and 3D plots, as well as plain-text output of the results, can be selected. Conclusion LD2SNPing thus provides a novel visualization environment for multiple SNP input, which facilitates SNP association studies. The software, user manual, and tutorial are freely available at http://bio.kuas.edu.tw/LD2NPing.

  4. 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

  5. A dynamic general disequilibrium model of a sequential monetary production economy

    International Nuclear Information System (INIS)

    Raberto, Marco; Teglio, Andrea; Cincotti, Silvano

    2006-01-01

    A discrete, deterministic, economic model, based on the framework of non-Walrasian or disequilibrium economics, is presented. The main feature of this approach is the presence of non-clearing markets, where not all demands and supplies are satisfied and some agents may be rationed. The model is characterized by three agents (i.e., a representative firm, a representative consumer, and a central bank), three commodities (i.e., goods, labour and money, each homogeneous) and three markets for their exchange. The imbalance between demand and supply in each market determines the dynamics of price, nominal wage and nominal interest rate. The central bank provides the money supply according to an operating target interest rate that is fixed accordingly to Taylor's rule. The model has been studied by means of computer simulations. Results pointed out the presence of business cycles that can be controlled by proper policies of the central bank

  6. 'Signs of disequilibrium chemistry in extrasolar hot-Jupiter type planets?'

    Science.gov (United States)

    Rocha, Graca; Swain, Mark; Line, Michael; West, Robert

    2018-01-01

    In the recent years Infrared spectroscopy of hot exoplanets has been revealing their atmospheric composition. For example the spectra of the planet HD189733b exhibits signatures of CH4, CO2, CO and H2O molecules (Swain et al 2008, 2009, etc.). The original 2008 detection of CH4 was a surprise because it is not thermochemically favored at the relatively high temperature (~1300 K) of the atmosphere of HD 189733b. More recent analysis of HD 189733b measurements (Swain, Line, Deroo 2014) implied a CH4 enhancement of ~1000x greater than has been assumed. Significantly more data has recently become available from WFC3 observations (Mccullah et al. 2014, Crozet at al. 2015) of this planet. In the meantime theoretical models by Moses et al. 2011 showed that large enhancement of quenched methane is possible due to transport if vertical eddy diffusion is significant.In this talk we will present results from a new study of CH4 enhancement in the atmosphere of HD189733b. We analysise the transit spectra of this planet obtained with the Hubble Space Telescope, combining the shorter wavelength 1.1-1.6 μm data from WFC3 measurements with the 1.5-2.4 μm data from NICMOS measurements. We also introduce a new methodology, implemented within a Bayesian framework, where hypothesis testing is conducted via evidence based model selection. Our analysis indicates, for the first time, that the observed excess of Methane in HD189733b’s atmosphere requires disequilibrium chemistry. However the Evidence has a modest discriminatory power amongst a subset of models. Furthermore our constraints confirm Swain et al. 2014 results with an excess of Methane with a mixing ratio of 10 2.26 ppm with EvidencelogZ=-58.602 +/- 0.109.

  7. 238 series isotopes at different soil depths and disequilibrium over various geology and soil classifications along transects in selected parts of Ireland

    International Nuclear Information System (INIS)

    McAulay, I.R.; Hayes, A.

    1996-01-01

    Sampling of soils was carried out along linear transects in selected regions of the country, a technique known as Transect Sampling. This was a controlled rather than a random sampling technique. The transects were located in regions which were previously known to contain high levels of the 226 Ra isotope, from the 238 U series. The soil sampling was carried out at selected sites along these transects. At each transect site, two different soil depths were examined and the soil samples collected were identified as the top and bottom soil samples. This transect data set, consisting of the isotope activity levels and the influencing variables transect geology and soil types, provided a data base for investigation. Comparisons were made between the soil isotope activity levels measured at different soil depths. An examination of the 238 U decay series showed the existence of disequilibrium. Relationships between the disequilibrium data and the associated geology and soil types were investigated. (author)

  8. Disequilibrium Chemistry in the Solar Nebula and Early Solar System: Implications for the Chemistry of Comets

    Science.gov (United States)

    Fegley, Bruce, Jr.

    1997-12-01

    A growing body of observations demonstrates that comets, like the chondritic meteorites, are disequilibrium assemblages, whose chemistry and molecular composition cannot be explained solely on the basis of models of equilibrium condensation in the solar nebula. These observations include: (1) The coexistence of reduced (e.g., CH4 and organics) and oxidized (e.g., CO, CO2, and H2CO) carbon compounds observed in the gas and dust emitted by comet P/Halley; (2) The coexistence of reduced (e.g., NH3) and oxidized (e.g., N2) nitrogen compounds in the gas emitted by comet P/Halley; (3) The observation of large amounts of formaldehyde in the gas emitted by comet P/Halley (H2CO/H2O approx. 1.5 - 4%) and by comet Machholz (1988j). Formaldehyde would be rapidly destroyed by thermal processing in the solar nebula and must be formed by some disequilibrating process either in the solar nebula or in some presolar environment. (4) The observation of large amounts of the oxidized carbon gases CO and CO2 in comet P/Halley at levels far exceeding those predicted by chemical equilibrium models of solar nebula carbon chemistry. In fact, oxidized carbon gases (CO+ C02 + H2CO) are the most abundant volatile (after water vapor) emitted by comet P/Halley. (5) The observation of HCN, which is not a predicted low temperature condensate in the solar nebula (e.g., Lewis 1972), in comet P/Halley (e.g., Schloerb et al. 1987) and in comet Kohoutek. (6) The observation of S2, which is argued to be a parent molecule vaporized from the nucleus, in comet IRAS-Araki-Alcock (1983d) by A'Hearn et aL (1983) and Feldman et al. (1984). This molecule is not an equilibrium condensate in the solar nebula and must result from disequilibrium chemistry. (7) The deduction that organic grains (C-H-O-N particles) comprise about 30% of the dust emitted by comet P/Halley and that about 75% of the total carbon inventory of Halley is in these grains also implies substantial disequilibrium chemistry. (8) The deductions

  9. Mechanical sensitivity and psychological factors in patients with burning mouth syndrome.

    Science.gov (United States)

    Honda, Mika; Iida, Takashi; Kamiyama, Hirona; Masuda, Manabu; Kawara, Misao; Svensson, Peter; Komiyama, Osamu

    2018-05-18

    The aim of this study was to compare mechanical sensitivity on the tongue using quantitative sensory testing (QST) and psychological factors using the General Health Questionnaire (GHQ) between burning mouth syndrome (BMS) patients and healthy participants. Participants comprised 20 female BMS patients (68.1 ± 7.4 years) and 20 healthy females (65.4 ± 4.6 years). Psychological factors were evaluated with GHQ. Tactile detection thresholds (TDT) and filament-prick pain detection thresholds (FPT) were used to evaluate mechanical sensitivity on the tongue in all participants. TDT and FPT were measured on the tongue within both the painful area and the non-painful area in BMS patients, and on the tongue on both sides in healthy participants. As controls, TDT and FPT were measured with Semmes-Weinstein monofilaments on the skin of the mentum and palm in all participants. GHQ scores were significantly higher in BMS patients than in healthy participants (P = 0.024). No significant differences in TDT or FPT on the tongue, mentum, or palm were seen between BMS patients and healthy participants (P > 0.05). BMS patients showed no significant differences in TDT or FPT between the painful and non-painful areas on the tongue (P > 0.05). There were no significant correlations among TDT/FPT and GHQ score in BMS patients (P > 0.05). These findings could indicate a more important role for psychological factors than mechanical sensitivity in BMS pathophysiology. Pain on the tongue in elderly female patients with BMS may be more related to psychological factors.

  10. Frequent video game players resist perceptual interference.

    Directory of Open Access Journals (Sweden)

    Aaron V Berard

    Full Text Available Playing certain types of video games for a long time can improve a wide range of mental processes, from visual acuity to cognitive control. Frequent gamers have also displayed generalized improvements in perceptual learning. In the Texture Discrimination Task (TDT, a widely used perceptual learning paradigm, participants report the orientation of a target embedded in a field of lines and demonstrate robust over-night improvement. However, changing the orientation of the background lines midway through TDT training interferes with overnight improvements in overall performance on TDT. Interestingly, prior research has suggested that this effect will not occur if a one-hour break is allowed in between the changes. These results have suggested that after training is over, it may take some time for learning to become stabilized and resilient against interference. Here, we tested whether frequent gamers have faster stabilization of perceptual learning compared to non-gamers and examined the effect of daily video game playing on interference of training of TDT with one background orientation on perceptual learning of TDT with a different background orientation. As a result, we found that non-gamers showed overnight performance improvement only on one background orientation, replicating previous results with the interference in TDT. In contrast, frequent gamers demonstrated overnight improvements in performance with both background orientations, suggesting that they are better able to overcome interference in perceptual learning. This resistance to interference suggests that video game playing not only enhances the amplitude and speed of perceptual learning but also leads to faster and/or more robust stabilization of perceptual learning.

  11. Frequent video game players resist perceptual interference.

    Science.gov (United States)

    Berard, Aaron V; Cain, Matthew S; Watanabe, Takeo; Sasaki, Yuka

    2015-01-01

    Playing certain types of video games for a long time can improve a wide range of mental processes, from visual acuity to cognitive control. Frequent gamers have also displayed generalized improvements in perceptual learning. In the Texture Discrimination Task (TDT), a widely used perceptual learning paradigm, participants report the orientation of a target embedded in a field of lines and demonstrate robust over-night improvement. However, changing the orientation of the background lines midway through TDT training interferes with overnight improvements in overall performance on TDT. Interestingly, prior research has suggested that this effect will not occur if a one-hour break is allowed in between the changes. These results have suggested that after training is over, it may take some time for learning to become stabilized and resilient against interference. Here, we tested whether frequent gamers have faster stabilization of perceptual learning compared to non-gamers and examined the effect of daily video game playing on interference of training of TDT with one background orientation on perceptual learning of TDT with a different background orientation. As a result, we found that non-gamers showed overnight performance improvement only on one background orientation, replicating previous results with the interference in TDT. In contrast, frequent gamers demonstrated overnight improvements in performance with both background orientations, suggesting that they are better able to overcome interference in perceptual learning. This resistance to interference suggests that video game playing not only enhances the amplitude and speed of perceptual learning but also leads to faster and/or more robust stabilization of perceptual learning.

  12. Family-based transmission disequilibrium test (TDT) and case-control association studies reveal surfactant protein A (SP-A) susceptibility alleles for respiratory distress syndrome (RDS) and possible race differences

    NARCIS (Netherlands)

    Floros, J.; Fan, R.; Matthews, A.; DiAngelo, S.; Luo, J.; Nielsen, H.; Dunn, M.; Gewolb, I. H.; Koppe, J.; Van Sonderen, L.; Farri-Kostopoulos, L.; Tzaki, M.; Rämet, M.; Merrill, J.

    2001-01-01

    A key cause of respiratory distress syndrome (RDS) in the prematurely born infant is deficiency of pulmonary surfactant, a lipoprotein complex. Both low levels of surfactant protein A (SP-A) and SP-A alleles have been associated with RDS. Using the candidate gene approach, we performed family-based

  13. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks.

    Science.gov (United States)

    Zhao, Huiying; Nyholt, Dale R; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

    2017-06-14

    Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path .

  14. Identification and Functional Characterization of a Tonoplast Dicarboxylate Transporter in Tomato (Solanum lycopersicum).

    Science.gov (United States)

    Liu, Ruiling; Li, Boqiang; Qin, Guozheng; Zhang, Zhanquan; Tian, Shiping

    2017-01-01

    Acidity plays an important role in flavor and overall organoleptic quality of fruit and is mainly due to the presence of organic acids. Understanding the molecular basis of organic acid metabolism is thus of primary importance for fruit quality improvement. Here, we cloned a putative tonoplast dicarboxylate transporter gene ( SlTDT ) from tomato, and submitted it to the NCBI database (GenBank accession number: KC733165). SlTDT protein contained 13 putative transmembrane domains in silico analysis. Confocal microscopic study using green fluorescent fusion proteins revealed that SlTDT was localized on tonoplast. The expression patterns of SlTDT in tomato were analyzed by RT-qPCR. The results indicated that SlTDT expressed in leaves, roots, flowers and fruits at different ripening stages, suggesting SlTDT may be associated with the development of different tissues. To further explore the function of SlTDT , we constructed both overexpression and RNAi vectors and obtained transgenic tomato plants by agrobacterium-mediated method. Gas chromatography-mass spectrometer (GC-MS) analysis showed that overexpression of SlTDT significantly increased malate content, and reduced citrate content in tomato fruit. By contrast, repression of SlTDT in tomato reduced malate content of and increased citrate content. These results indicated that SlTDT played an important role in remobilization of malate and citrate in fruit vacuoles.

  15. GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs

    Directory of Open Access Journals (Sweden)

    Broxholme John

    2009-10-01

    Full Text Available Abstract Background A number of tools for the examination of linkage disequilibrium (LD patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb. We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search engine that enables the retrieval of pairwise associations with r2 ≥ 0.3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers. Description GLIDERS is an easy to use web tool that only requires the user to enter rs numbers of SNPs they want to retrieve genome-wide LD for (both nearby and long-range. The intuitive web interface handles both manual entry of SNP IDs as well as allowing users to upload files of SNP IDs. The user can limit the resulting inter SNP associations with easy to use menu options. These include MAF limit (5-45%, distance limits between SNPs (minimum and maximum, r2 (0.3 to 1, HapMap population sample (CEU, YRI and JPT+CHB combined and HapMap build/release. All resulting genome-wide inter-SNP associations are displayed on a single output page, which has a link to a downloadable tab delimited text file. Conclusion GLIDERS is a quick and easy way to retrieve genome-wide inter-SNP associations and to explore LD patterns for any number of SNPs of interest. GLIDERS can be useful in identifying SNPs with long-range LD. This can highlight mis-mapping or other potential association signal localisation problems.

  16. Inorganic carbon uptake during photosynthesis. II. Uptake by isolated Asparagus mesophyll cells during isotopic disequilibrium

    International Nuclear Information System (INIS)

    Espie, G.S.; Owttrim, G.W.; Colman, B.

    1986-01-01

    The species of inorganic carbon (CO 2 or HCO 3 - ) taken up as a source of substrate for photosynthetic fixation by isolated Asparagus sprengeri mesophyll cells is investigated. Discrimination between CO 2 or HCO 3 - transport, during steady state photosynthesis, is achieved by monitoring the changes (by 14 C fixation) which occur in the specific activity of the intracellular pool of inorganic carbon when the inorganic carbon present in the suspending medium is in a state of isotopic disequilibrium. Quantitative comparisons between theoretical (CO 2 or HCO 3 - transport) and experimental time-courses of 14 C incorporation, over the pH range of 5.2 to 7.5, indicate that the specific activity of extracellular CO 2 , rather than HCO 3 - , is the appropriate predictor of the intracellular specific activity. It is concluded, therefore, that CO 2 is the major source of exogenous inorganic carbon taken up by Asparagus cells. However, at high pH (8.5), a component of net DIC uptake may be attributable to HCO 3 - transport, as the incorporation of 14 C during isotopic disequilibrium exceeds the maximum possible incorporation predicted on the basis of CO 2 uptake alone. The contribution of HCO 3 - to net inorganic carbon uptake (pH 8.5) is variable, ranging from 5 to 16%, but is independent of the extracellular HCO 3 - concentration. The evidence for direct HCO 3 - transport is subject to alternative explanations and must, therefore, be regarded as equivocal. Nonlinear regression analysis of the rate of 14 C incorporation as a function of time indicates the presence of a small extracellular resistance to the diffusion of CO 2 , which is partially alleviated by a high extracellular concentration of HCO 3 -

  17. Genotyping of a tri-allelic polymorphism by a novel melting curve assay in MTHFD1L: an association study of nonsyndromic Cleft in Ireland

    LENUS (Irish Health Repository)

    Minguzzi, Stefano

    2012-04-20

    AbstractBackgroundPolymorphisms within the MTHFD1L gene were previously associated with risk of neural tube defects in Ireland. We sought to test the most significant MTHFD1L polymorphisms for an association with risk of cleft in an Irish cohort. This required the development of a new melting curve assay to genotype the technically challenging MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406).MethodsMelting curve analysis was used to genotype the MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406) and a Single Nucleotide Polymorphism rs17080476 in an Irish cohort consisting of 981 Irish case-parent trios and 1,008 controls. Tests for association with nonsyndromic cleft lip with or without cleft palate and cleft palate included case\\/control analysis, mother\\/control analysis and Transmission Disequilibrium Tests of case-parent trios.ResultsA successful melting curve genotyping assay was developed for the deletion\\/insertion polymorphism (rs3832406). The TDT analysis initially showed that the rs3832406 polymorphism was associated with isolated cleft lip with or without cleft palate. However, corrected p-values indicated that this association was not significant.ConclusionsMelting Curve Analysis can be employed to successfully genotype challenging polymorphisms such as the MTHFD1L triallelic deletion\\/insertion polymorphism (DIP) reported here (rs3832406) and is a viable alternative to capillary electrophoresis. Corrected p-values indicate no association between MTHFD1L and risk of cleft in an Irish cohort.

  18. Lack of concordance and linkage disequilibrium among brothers for androgenetic alopecia and CAG/GGC haplotypes of the androgen receptor gene in Mexican families.

    Science.gov (United States)

    Arteaga-Vázquez, Jazmín; López-Hernández, María A; Svyryd, Yevgeniya; Mutchinick, Osvaldo M

    2015-12-01

    Androgenetic alopecia (AGA) or common baldness is the most prevalent form of hair loss in males. Familial predisposition has been recognized, and heritability estimated in monozygotic twins suggests an important genetic predisposition. Several studies indicate that the numbers of CAG/GGC repeats in exon 1 of the androgen receptor gene (AR) maybe associated with AGA susceptibility. To investigate a possible correlation between AR CAG/GGC haplotypes and the presence or not of alopecia in sibships with two or more brothers among them at least one of them has AGA. Thirty-two trios including an alopecic man, one brother alopecic or not, and their mother were enrolled. Sanger sequencing of the exon 1 of the AR gene was conducted to ascertain the number of CAG/GGC repeats in each individual. Heterozygous mother for the CAG/GGC haplotypes was an inclusion criterion to analyze the segregation haplotype patterns in the family. Concordance for the number of repeats and AGA among brothers was evaluated using kappa coefficient and the probability of association in the presence of genetic linkage between CAG and GGC repeats and AGA estimated by means of the family-based association test (FBAT). The median for the CAG and GGC repeats in the AR is similar to that reported in other populations. The CAG/GGC haplotypes were less polymorphic than that reported in other studies, especially due to the GGC number of repeats found. Kappa coefficient resulted in a concordance of 37.3% (IC 95%, 5.0-69.0%) for the AGA phenotype and identical CAG/GGC haplotypes. There was no evidence of linkage disequilibrium. Our results do not confirm a possible correlation or linkage disequilibrium between the CAG/GGC haplotypes of the AR gene and androgenetic alopecia in Mexican brothers. © 2015 Wiley Periodicals, Inc.

  19. Soiled-based uranium disequilibrium and mixed uranium-thorium series radionuclide reference materials

    International Nuclear Information System (INIS)

    Donivan, S.; Chessmore, R.

    1988-12-01

    The US Department of Energy (DOE) Office of Remedial Action and Waste Technology has assigned the Technical Measurements Center (TMC), located at the DOE Grand Junction Colorado, Projects Office and operated by UNC Geotech (UNC), the task of supporting ongoing remedial action programs by providing both technical guidance and assistance in making the various measurements required in all phases of remedial action work. Pursuant to this task, the Technical Measurements Center prepared two sets of radionuclide reference materials for use by remedial action contractors and cognizant federal and state agencies. A total of six reference materials, two sets comprising three reference materials each, were prepared with varying concentrations of radionuclides using mill tailings materials, ores, and a river-bottom soil diluent. One set (disequilibrium set) contains varying amounts of uranium with nominal amounts of radium-226. The other set (mixed-nuclide set) contains varying amounts of uranium-238 and thorium-232 decay series nuclides. 14 refs., 10 tabs

  20. Myeloblastic and lymphoblastic markers in acute undifferentiated leukemia and chronic myelogenous leukemia in blast crisis.

    Science.gov (United States)

    Shumak, K H; Baker, M A; Taub, R N; Coleman, M S

    1980-11-01

    Blast cells were obtained from 17 patients with acute undifferentiated leukemia and 13 patients with chronic myelogenous leukemia in blast crisis. The blasts were tested with anti-i serum in cytotoxicity tests and with antisera to myeloblastic leukemia-associated antigens in immunofluorescence tests. The terminal deoxynucleotidyl transferase (TDT) content of the blasts was also measured. Lymphoblasts react strongly with anti-i, do not react with anti-myeloblast serum, and have high levels of TDT; myeloblasts react weakly with anti-i, do not react with anti-myeloblast serum, and have very low levels of TDT. Of the 17 patients with acute undifferentiated leukemia, there were six with blasts which reacted like lymphoblasts, six with blasts which reacted like myeloblasts, and five with blasts bearing different combinations of these lymphoblastic and myeloblastic markers. Eight of the 11 patients with lymphoblastic or mixed lymphoblastic-myeloblastic markers, but only one of the six with myeloblastic markers, achieved complete or partial remission in response to therapy. Thus, in acute undifferentiated leukemia, classification of blasts with these markers may be of prognostic value. Of the 13 patients with chronic myelogenous leukemia in blast crises, the markers were concordant (for myeloblasts) in only two cases. Three of the 13 patients had TDT-positive blasts, but the reactions of these cells with anti-i and with anti-myeloblast serum differed from those seen with lymphoblasts from patients with acute lymphoblastic leukemia. Although the cell involved in "lymphoid" blast crisis of chronic myelogenous leukemia is similar in many respects to that involved in acute lymphoblastic leukemia, these cells are not identical.

  1. U isotopes distribution in the Lower Rhone River and its implication on radionuclides disequilibrium within the decay series.

    Science.gov (United States)

    Zebracki, Mathilde; Cagnat, Xavier; Gairoard, Stéphanie; Cariou, Nicolas; Eyrolle-Boyer, Frédérique; Boulet, Béatrice; Antonelli, Christelle

    2017-11-01

    The large rivers are main pathways for the delivery of suspended sediments into coastal environments, affecting the biogeochemical fluxes and the ecosystem functioning. The radionuclides from 238 U and 232 Th-series can be used to understand the dynamic processes affecting both catchment soil erosion and sediment delivery to oceans. Based on annual water discharge the Rhone River represents the largest river of the Mediterranean Sea. The Rhone valley also represents the largest concentration in nuclear power plants in Europe. A radioactive disequilibrium between particulate 226 Ra (p) and 238 U (p) was observed in the suspended sediment discharged by the Lower Rhone River (Eyrolle et al. 2012), and a fraction of particulate 234 Th was shown to derive from dissolved 238 U (d) (Zebracki et al. 2013). This extensive study has investigated the dissolved U isotopes distribution in the Lower Rhone River and its implication on particulate radionuclides disequilibrium within the decay series. The suspended sediment and filtered river waters were collected at low and high water discharges. During the 4-months of the study, two flood events generated by the Rhone southern tributaries were monitored. In river waters, the total U (d) concentration and U isotopes distribution were obtained through Q-ICP-MS measurements. The Lower Rhone River has displayed non-conservative U-behavior, and the variations in U (d) concentration between southern tributaries were related to the differences in bedrock lithology. The artificially occurring 236 U was detected in the Rhone River at low water discharges, and was attributed to the liquid releases from nuclear industries located along the river. The ( 235 U/ 238 U) (d) activity ratio (=AR) in river waters was representative of the 235 U natural abundance on Earth. The ( 226 Ra/ 238 U) (p) AR in suspended sediment has indicated a radioactive disequilibrium (average 1.3 ± 0.1). The excess of 234 Th in suspended sediment =( 234 Th xs

  2. Lack of association of genetic variants in genes of the endocannabinoid system with anorexia nervosa

    Directory of Open Access Journals (Sweden)

    Herpertz-Dahlmann Beate

    2008-11-01

    Full Text Available Abstract Background Several lines of evidence indicate that the central cannabinoid receptor 1 (CNR1 as well as the major endocannabinoid degrading enzymes fatty acid amide hydrolase (FAAH, N-acylethanolamine-hydrolyzing acid amidase (NAAA and monoglyceride lipase (MGLL are implicated in mediating the orexigenic effects of cannabinoids. The aim of this study was to analyse whether nucleotide sequence variations in the CNR1, FAAH, NAAA and MGLL genes are associated with anorexia nervosa (AN. Methods We analysed the association of a previously described (AATn repeat in the 3' flanking region of CNR1 as well as a total of 15 single nucleotide polymorphisms (SNPs representative of regions with restricted haplotype diversity in CNR1, FAAH, NAAA or MGLL in up to 91 German AN trios (patient with AN and both biological parents using the transmission-disequilibrium-test (TDT. One SNP was additionally analysed in an independent case-control study comprising 113 patients with AN and 178 normal weight controls. Genotyping was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ARMS-PCR or using 3730xl capillary sequencers. Results The TDT revealed no evidence for association for any of the SNPs or the (AATn repeat with AN (all two-sided uncorrected p-values > 0.05. The lowest p-value of 0.11 was detected for the A-allele of the CNR1 SNP rs1049353 for which the transmission rate was 59% (95% confidence interval 47%...70%. Further genotyping of rs1049353 in 113 additional independent patients with AN and 178 normal weight controls could not substantiate the initial trend for association (p = 1.00. Conclusion As we found no evidence for an association of genetic variation in CNR1, FAAH, NAAA and MGLL with AN, we conclude that genetic variations in these genes do not play a major role in the etiology of AN in our study groups.

  3. Uranium-thorium disequilibrium in north-east Atlantic waters

    International Nuclear Information System (INIS)

    Smith, K.J.; Leon Vintro, L.; Mitchell, P.I.; Bally de Bois, P.; Boust, D.

    2004-01-01

    In this paper we report and compare the concentrations of 234 Th and 238 U measured in surface and subsurface waters collected in the course of a sampling campaign in the north east Atlantic in June-July 1998. Dissolved 234 Th concentrations in surface waters ranged from 5 to 20 Bq m -3 , showing a large deficiency relative to 238 U concentrations (typically 42 Bq m -3 ). This disequilibrium is indicative of active 234 Th scavenging from surface waters. Observed 234 Th/ 238 U activity ratios, together with corresponding 234 Th particulate concentrations, were used to calculate mean residence times for 234 Th with respect to scavenging onto particles (τ diss ) and subsequent removal from surface waters (τ part ). Residence times in the range 5-30 days were determined for τ diss and 4-18 days for τ part (n=14). In addition, ultrafiltration experiments at six stations in the course of the same expedition revealed that in north-east Atlantic surface waters a significant fraction (46±17%; n=6) of the thorium in the (operationally-defined) dissolved phase ( 234 Th is rapidly absorbed by colloidal particles, which then aggregate, albeit at a slower rate, into larger filterable particles. In essence, colloids act as intermediaries in the transition from the fully dissolved to the filter-retained (>0.45 μm) phase. Thus, the time (τ c ) for fully dissolved 234 Th to appear in the filter-retained fraction is dependent on the rate of colloidal aggregation. Here, we determined τ c values in the range 3-17 days

  4. ALDH1A2 (RALDH2 genetic variation in human congenital heart disease

    Directory of Open Access Journals (Sweden)

    Mesquita Sonia MF

    2009-11-01

    Full Text Available Abstract Background Signaling by the vitamin A-derived morphogen retinoic acid (RA is required at multiple steps of cardiac development. Since conversion of retinaldehyde to RA by retinaldehyde dehydrogenase type II (ALDH1A2, a.k.a RALDH2 is critical for cardiac development, we screened patients with congenital heart disease (CHDs for genetic variation at the ALDH1A2 locus. Methods One-hundred and thirty-three CHD patients were screened for genetic variation at the ALDH1A2 locus through bi-directional sequencing. In addition, six SNPs (rs2704188, rs1441815, rs3784259, rs1530293, rs1899430 at the same locus were studied using a TDT-based association approach in 101 CHD trios. Observed mutations were modeled through molecular mechanics (MM simulations using the AMBER 9 package, Sander and Pmemd programs. Sequence conservation of observed mutations was evaluated through phylogenetic tree construction from ungapped alignments containing ALDH8 s, ALDH1Ls, ALDH1 s and ALDH2 s. Trees were generated by the Neighbor Joining method. Variations potentially affecting splicing mechanisms were cloned and functional assays were designed to test splicing alterations using the pSPL3 splicing assay. Results We describe in Tetralogy of Fallot (TOF the mutations Ala151Ser and Ile157Thr that change non-polar to polar residues at exon 4. Exon 4 encodes part of the highly-conserved tetramerization domain, a structural motif required for ALDH oligomerization. Molecular mechanics simulation studies of the two mutations indicate that they hinder tetramerization. We determined that the SNP rs16939660, previously associated with spina bifida and observed in patients with TOF, does not affect splicing. Moreover, association studies performed with classical models and with the transmission disequilibrium test (TDT design using single marker genotype, or haplotype information do not show differences between cases and controls. Conclusion In summary, our screen indicates that

  5. Post-irradiation regeneration of early B-lymphocyte precursor cells in mouse bone marrow

    International Nuclear Information System (INIS)

    Park, Y.-H.; Osmond, D.G.

    1989-01-01

    To examine the sequential development of early B-cell precursors in mouse bone marrow, B-lineage cells have been examined during a wave of post-irradiation regeneration. Cell phenotypes have been defined for (i) terminal deoxynucleotidyl transferase (TdT); (ii) B220 glycoprotein, (iii) μ heavy chains in the cytoplasm (cμ) and at the cell surface (sμ). Three populations of μ - cells (TdT + 14.8 - ; TdT + 14.8 + ; TdT - 14.8 + ) have been proposed to be early B-cell precursors which would give rise to cμ + sμ - pre-B cells and to sμ + B lymphocytes. The timing, cell-size shifts and progressive amplification of the waves of regeneration accord with a dynamic model in which the TdT + 14.8 - , TdT + 14.8 + and TdT - 14.8 + cells form three successive stages in B-cell differentiation before the expression of μ chains, presumptively including the stage of μ chain gene rearrangement. In addition, the results provide an experimental system for the enrichment of early B-cell precursors in mouse bone marrow. (author)

  6. RSW

    Data.gov (United States)

    National Aeronautics and Space Administration — Documentation of tests conducted at NASA TDT of Rectangular Supercritical wing test in the 1980's and documented in RTO Report 26. More results are also published in...

  7. Divergência genética e subcoleção representativa de populações da traça-do-tomateiro Genetic divergence and representative tomato pinworm populations subcollection

    Directory of Open Access Journals (Sweden)

    Gisele Rodrigues Moreira

    2004-05-01

    Full Text Available O objetivo deste trabalho foi estudar a divergência genética e propor uma subcoleção representativa da traça-do-tomateiro, Tuta absoluta (TDT. O experimento foi conduzido com quatro populações do inseto procedentes de Uberlândia, MG, Viçosa, MG, Camocim de São Félix, PE, e Santa Teresa, ES, e cinco acessos de tomateiro, 'Santa Clara', 'Moneymaker', TOM-601, PI 126445 (Lycopersicon hirsutum f. typicum e PI 134417 (L. hirsutum f. glabratum. Foi realizada análise de agrupamento (método de Tocher, usando a distância de Mahalanobis como medida de dissimilaridade e verificada a importância relativa dos caracteres da TDT para a divergência genética entre populações por meio do método de Singh. As populações de cada grupo obtido pela análise de agrupamento foram combinadas e, para cada caráter, foi realizado o teste t de Student para uma média. Existe variabilidade genética entre populações da TDT provenientes de diferentes localidades do Brasil, quando estão infestando Lycopersicon spp. A mortalidade larval teve maior contribuição para a divergência genética entre as populações, com exceção de PI 134417, cujo caráter de maior contribuição foi o número de pupas fêmeas. Propõe-se uma subcoleção da TDT tomando-se por base a combinação das populações de Santa Teresa e Uberlândia.This work aimed to study the genetic diversity and to propose a representative tomato pinworm, Tuta absoluta (TDT, subcollection. Populations of insect originally from Uberlândia, MG, Viçosa (MG, Camocim de São Félix, PE, and Santa Teresa, ES, Brazil, and five tomato accessions, 'Santa Clara', 'Moneymaker', TOM-601, PI 126445 (Lycopersicon hirsutum f. typicum and PI 134417 (L. hirsutum f. glabratum were used. Grouping analysis (Tocher method, using the Mahalanobis distance as dissimilarity measurement was performed and the relative importance of TDT characters to the genetic divergence among populations was evaluated by Singh

  8. Learning about the X from our parents

    Directory of Open Access Journals (Sweden)

    Alison S. Wise

    2015-02-01

    Full Text Available The X chromosome is generally understudied in association studies, in part because the analyst has had limited methodological options. For nuclear-family-based association studies, most current methods extend the transmission disequilibrium test (TDT to the X chromosome. We present a new method to study association in case-parent triads: the parent-informed likelihood ratio test for the X chromosome (PIX-LRT. Our method enables estimation of relative risks and takes advantage of parental genotype information and the sex of the affected offspring to increase statistical power to detect an effect. Under a parental exchangeability assumption for the X, if case-parent triads are complete, the parents of affected offspring provide an independent replication sample for estimates based on transmission distortion to their affected offspring. For each offspring sex we combine the parent-level and the offspring-level information to form a likelihood ratio test statistic; we then combine the two to form a composite test statistic. Our method can estimate relative risks under different modes of inheritance or a more general co-dominant model. In triads with missing parental genotypes, the method accounts for missingness with the Expectation-Maximization algorithm. We calculate non-centrality parameters to assess the power gain and robustness of our method compared to alternative methods. We apply PIX-LRT to publically available data from an international consortium of genotyped families affected by the birth defect oral cleft and find a strong, internally-replicated signal for a SNP marker related to cleft lip with or without cleft palate.

  9. The impact of therapeutic delay time on acute scintigraphic lesion and ultimate scar formation in children with first febrile UTI.

    Science.gov (United States)

    Oh, Mi Mi; Kim, Jin Wook; Park, Min Gu; Kim, Je Jong; Yoo, Kee Hwan; Moon, Du Geon

    2012-03-01

    We assessed the role of therapeutic delay time (TDT) in acute renal cortical scintigraphic lesion (ASL) and ultimate scar formation (USF) in children with first febrile UTI and whether it is affected by the presence of vesico-ureteral reflux (VUR). 230 children, 90 girls and 140 boys with first febrile UTI were included. Radiologic (USG, DMSA, and VCUG), clinical (age, gender, peak fever, therapeutic delay time) and laboratory (CBC with differential count, ANC (absolute neutrophil count), BUN, Creatinine, urine analysis, gram stain, culture, CRP and ESR) variables were analysed. DMSA was performed within 5 days and after six months. VCUG was performed after acute phase of UTI. The differences in TDT according to the presence of ASL, USF and VUR were assessed. And the correlation between ASL or USF with the duration of TDT was assessed. Of 230 patients enrolled, 142 patients had refluxing UTI and 88 patients had non-refluxing UTI. TDT was the risk factor associated with ASL and USF along with presence of VUR. TDT was longer in ASL positive group compared with the ASL negative group. Also USF group showed longer TDT compared with those without USF in both refluxing UTI and non refluxing UTI. The TDT was significantly shorter in USF group with the presence of VUR. Positive linear association was noted between prevalence of ASL and USF and duration of TDT. In conclusion, the impact of UTI on formation of USF may be enhanced by the presence of VUR with shorter duration of TDT.

  10. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L. Improved by Accounting for Linkage Disequilibrium

    Directory of Open Access Journals (Sweden)

    Guillaume P. Ramstein

    2016-04-01

    Full Text Available Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.

  11. Application of radiometric core data in developing correlation index for insitu gamma log and disequilibrium status across exploratory boreholes: a case study in Wahkut Block of West Khasi Hills District, Meghalaya, India

    International Nuclear Information System (INIS)

    Kukreti, B.M.; Kumar, Pramod

    2011-01-01

    With the objective to affirm apparent Uranium ore zone grade/thickness with good confidence for non-coring and coring boreholes with poor core recovery, a systematic study in the mineralised coring boreholes between insitu measured gamma ray log and laboratory measured core assay has been carried out, in the sedimentary environment of Wahkut block, West Khasi Hills district of Meghalaya. This also helps in quantifying correlation index and U disequilibrium status across the drilled boreholes and to convert apparent eU 3 O 8 grade to ore reserve (U 3 O 8 ). Study area consist of 2 sq km having 33 coring and 39 non coring boreholes with cumulative drilled depth of about 11,000 mts. On this available database, grade thickness continuity of uranium ore zone, in coring boreholes was evaluated with the criteria of minimal ore zone thickness of 1.0 mts at 100 ppm eU 3 O 8 cut-off grade. The same criteria were also extended to the core assay of drilled core. A population of 19 such simultaneous qualifying zone (borehole log and core assay) meeting the set criteria from 17 coring boreholes (average core recovery > 90%) was drawn. Study results gave grade thickness continuity index of 0.93 between radiometric core assay and borehole log with moderately strong relationship. Disequilibrium status of apparent eU 3 O 8 grade in the borehole was examined using chemically checked U 3 O 8 (β/γ) (Having high degree uranium data confidence 91%) and Ra (e) plot, after getting complete core samples radiometric and spectral gamma analysed for 14 such boreholes. Equilibrium status on this population indicates, disequilibrium in favour of parent (0.90-1.78 range) having log normal distribution and skewed to the higher side of mean 1.37 disequilibrium factor. (author)

  12. Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

    DEFF Research Database (Denmark)

    Brazauskas, Gintaras; Lenk, Ingo; Pedersen, Morten Greve

    2011-01-01

    Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent...... of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers...... and occurred within 0.4 cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6 cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials...

  13. Temperature and precipitation records from stalagmites grown under disequilibrium conditions: A model approach.

    Science.gov (United States)

    Mühlinghaus, C.; Scholz, D.; Mangini, A.

    2009-04-01

    To reconstruct past variations in Earth's climate, a variety of climate archives are studied. During the last decades stalagmites came into focus due to their long, continuous growth and absolute dating techniques. In this study a numerical model was developed, which calculates variations in temperature and precipitation during the growth period of stalagmites grown under isotopic disequilibrium conditions using the isotope profiles both along the growth axis and individual growth layers as well as the growth depth relation. The model is based on the inversion and combination of existing models (Dreybrodt 1999, Kaufmann et al. 2004, Mühlinghaus et al. 2007, Scholz et al. 2008, Mühlinghaus et al. 2008b) and incorporates important parameters describing the cave and the overlying soil. Beside the dependence on temperature and water supply it depends on the isotopic composition of the drip water, the pCO2 pressure of the soil and the cave atmosphere as well as on the mixing coefficient, which describes mixing between the impinging drop and the existing solution layer. To determine the characteristics of temperature and precipitation, in a first step all other parameters are assumed to remain constant over the whole growth period to simplify calculations. This allows to run the model with only two input variables: the isotopic composition ^13C of the drip water and a temperature information at any point of time during the growth period of the stalagmite (e.g. the recent cave temperature). All other parameters are determined by the model. The CSM (Combined Stalagmite Model, Mühlinghaus et al. 2008a) was applied to three stalagmites from the Marcelo Arévalo cave in Southern Patagonia, Chile (Schimpf 2005, Kilian et al. 2006, Schimpf et al. in prep). These stalagmites grew in a small cave next to each other during the last 4500 years. However, their isotopic profiles along the growth axis show different kinetic influences. Despite these conditions, the temperature

  14. Combustion and environmental performance of clean coal end products

    Energy Technology Data Exchange (ETDEWEB)

    Skodras, G.; Sakellaropoulos, G. [Centre for Research and Technology, Hellas, Ptolemaidas-Kozanis, Ptolemaida (Greece). Inst. for Solid Fuel Technolgy and Applications]|[Aristotle Univ. of Thessaloniki, Thessaloniki (Greece). Dept. of Chemical Engineering, Chemical Process Engineering Lab]|[Chemical Process Engineering Research Inst., Thessaloniki (Greece). Lab. of Solid Fuels and Environment; Someus, E. [Thermal Desorption Technology Group (Greece); Grammelis, P.; Amarantos, P.S. [Centre for Research and Technology, Hellas, Ptolemaidas-Kozanis, Ptolemaida (Greece). Inst. for Solid Fuel Technolgy and Applications; Palladas, A.; Basinas, P.; Natas, P.; Prokopidou, M.; Diamantopoulou, I.; Sakellaropoulos, G. [Aristotle Univ. of Thessaloniki, Thessaloniki (Greece). Dept. of Chemical Engineering, Chemical Process Engineering Lab

    2006-07-01

    Clean and affordable power production is needed in order to achieve sustainable economic development. This paper focused on clean coal technologies in which coal-fired power plants are used in conjunction with large amounts of renewable energy sources to offer a high level of process safety and long term management of all residual operation streams. Thermal Desorption Recycle-Reduce-Reuse Technology (TDT-3R) was described as being a promising solid fuel pretreatment process for clean energy production up to 300 MWe capacities. TDT-3R is based on low temperature carbonisation fuel pre-treatment principles, which produce cleansed anthracite type fuels from coal and other carbonaceous material such as biomass and organic wastes. The combustion efficiency of such clean coals and the environmental performance of the TDT-3R process were investigated in this study via pilot scale tests of clean fuel production. Tests included flue gas emissions monitoring, raw fuel and product characterisation and thermogravimetric tests, polychlorinated dibenzo-p-dioxins and dibenzo-furans, and heavy metals analyses, and toxicity tests. Raw material included coal and biomass, such as willow, straw and demolition wood. The fuels were heated in a rotary kiln operating at 550 degrees C under slightly vacuum conditions. Clean coals were tested either alone or in conjunction with biomass fuels in a pilot scale combustion facility at Dresden, Germany. The clean coal samples were shown to have higher fixed carbon and ash content and lower volatiles compared to the respective raw coal samples. The major advantage of the TDT-3R process is the production of fuels with much lower pollutants content. Low nitrogen, sulphur, chlorine and heavy metal contents result in produced fuels that have excellent environmental performance, allow boiler operation in higher temperatures and overall better efficiency. Moreover, the use of clean fuels reduces deposition problems in the combustion chamber due to the

  15. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

    Directory of Open Access Journals (Sweden)

    John A Sved

    Full Text Available There is a substantial literature on the use of linkage disequilibrium (LD to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-12, rather than the usual factor 1+1/(2S-1 for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

  16. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

    Science.gov (United States)

    Sved, John A; Cameron, Emilie C; Gilchrist, A Stuart

    2013-01-01

    There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-1)2, rather than the usual factor 1+1/(2S-1) for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

  17. Uranium and thorium series disequilibrium in quaternary carbonate deposits from the Serra da Bodoquena and Pantanal do Miranda, Mato Grosso do Sul State, central Brazil

    International Nuclear Information System (INIS)

    Ribeiro, Fernando Brenha; Roque, Arnaldo; Boggiani, Paulo Cesar; Flexor, J.-M.

    2001-01-01

    Activities of gamma-ray emitting members of the uranium ( 238 U) and thorium ( 232 Th) series were measured in a quaternary limestone deposit that outcrops in the southeastern Pantanal Matogrossense Basin and in quaternary tufas deposited at the drainage of the Serra da Bodoquena. It is a first step in a study of the mobilization of uranium and thorium series and its relation to surface hydrology, in a region where carbonate deposits are being continuously dissolved and reprecipitated. The obtained results show that all these deposits are characterized by very low concentrations of uranium and thorium. The 238 U/ 226 Ra and 228 Th/ 228 Ra activity ratios are significantly different than 1.0, indicating that both series are in radioactive disequilibrium. Although the Serra da Bodoquena deposits seem to be very recent, their very fine granulation and high porosity suggest that they behave as open systems for geochemical exchanges of uranium and thorium series members. The Pantanal do Miranda limestone has a radiocarbon age of 3900 yr BP. Since the thorium series is in disequilibrium it is also concluded that this deposit behaves as an open system for geochemical exchanges

  18. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica.

    Directory of Open Access Journals (Sweden)

    Shui-Lian He

    Full Text Available Foxtail millet (Setaria italica (L. Beauv is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1 in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

  19. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

    Science.gov (United States)

    He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

    2015-01-01

    Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

  20. Preliminary U-series disequilibrium and thermoluminescence ages of surficial deposits and paleosols associated with Quaternary fault, Eastern Yucca Mountain

    International Nuclear Information System (INIS)

    Paces, J.B.; Menges, C.M.; Bush, C.A.; Futa, K.; Millard, H.T.; Maat, P.B.; Whitney, J.W.; Widmann, B.; Wesling, J.R.

    1994-01-01

    Geochronological control is an essential component of paleoseismic evaluation of faults in the Yucca Mountain region. New U-series disequilibrium and thermoluminescence age estimates for pedogenic deposits that bracket surface-rupture events are presented from four sites exposing the Paintbrush Canyon, Bow Ridge and Stagecoach Road faults. Ages show an internal consistency with stratigraphic relationships as well as an overall concordancy between the two independent geochronometers. Age estimates are therefore interpreted to date depositional events or episodes of pedogenic carbonate mobility that can be used to establish a paleoseismic fault chronology. Ultimately, this type of chronological information will be used to evaluate seismic hazards at Yucca Mountain

  1. Terminal deoxynucleotidyl transferase in the diagnosis of leukemia and malignant lymphoma.

    Science.gov (United States)

    Kung, P C; Long, J C; McCaffrey, R P; Ratliff, R L; Harrison, T A; Baltimore, D

    1978-05-01

    Neoplastic cells from 253 patients with leukemia and 46 patients with malignant lymphoma were studied for the presence of terminal deoxynucleotidyl transferase (TdT) by biochemical and fluorescent antibody technics. TdT was detected in circulating blast cells from 73 of 77 patients with acute lymphoblastic leukemia, 24 of 72 patients with chronic myelogenous leukemia examined during the blastic phase of the disorder and in cell suspensions of lymph nodes from nine of nine patients with diffuse lymphoblastic lymphoma. Blast cells from six of 10 patients with acute undifferentiated leukemia were TdT positive, but the enzyme was found in only two of 55 patients with acute myeloblastic leukemia. TdT was not detected in other lymphocytic or granulocytic leukemias or in other types of malignant lymphomas. The fluorescent antibody assay for TdT permits rapid and specific identification of the enzyme in single cells. The TdT assay is clinically useful in confirming the diagnosis of acute lymphoblastic leukemia, evaluating patients with blastic chronic myelogenous leukemia, and distinguishing patients with lymphoblastic lymphoma, whose natural history includes rapid extranodal dissemination, from patients with other poorly differentiated malignant lymphomas.

  2. Money demand elasticity, effective money supply and money market disequilibrium: ¡°China¡¯s Puzzle¡± and long-term excessive liquidity

    OpenAIRE

    LI Zhiguo

    2008-01-01

    Chinese excessive liquidity problems are more serious than other main countries. The upgrading industrial structure and the increasing opening degree lead to the excessive money demand and higher money demand elasticity. Bad credits weaken money supply effectiveness and lead to illusive increasing money. We set up the money market disequilibrium model under the condition of the excessive liquidity. The imbalance between money demand and money supply is the key of Chinese excessive liquidity p...

  3. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    Science.gov (United States)

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of 100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations. © 2016 Stichting International Foundation for Animal Genetics.

  4. 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.

  5. Targeted scan of fifteen regions for nonsyndromic cleft lip and palate in Filipino families.

    Science.gov (United States)

    Schultz, R E; Cooper, M E; Daack-Hirsch, S; Shi, M; Nepomucena, B; Graf, K A; O'Brien, E K; O'Brien, S E; Marazita, M L; Murray, J C

    2004-02-15

    Cleft lip with or without cleft palate (CL/P) is a congenital anomaly with variable birth prevalence based on geographic origins, with the highest rates commonly found in Asian populations. About 70% of cases are nonsyndromic (NS), in which the affected individual has no other abnormalities. NS CL/P is a complex disorder with genetic and environmental effects and no specific genetic loci yet confirmed. Fifteen candidate regions were examined for linkage to NS CL/P. Regions were chosen based on previous suggestive linkage and/or association in human families, or suggestive animal model data. Polymorphic markers in these regions were genotyped for analysis on 36 Filipino families comprised of 126 affected and 218 unaffected individuals. An additional 70 families with 149 affecteds were used for replication of suggestive results. Parametric (LOD score) and nonparametric (SIMIBD) linkage analyses were performed as well as transmission disequilibrium test (TDT) analysis. Five markers yielded suggestive results from the 36 families. The parametric LOD scores for the MSX1-CA and D4S1629 were >1.0 and the SIMIBD P values for D6S1029 and RFC1 are suggestive (value of 0.01 for TGFA was significant. Since the Msx1 mouse knockout has cleft palate and MSX1 mutations have been found in rare cases of syndromic CL/P, this locus is especially plausible for linkage. Previous studies have also found linkage of NS CL/P to 4q31 and 6p23. These regions contain several candidate genes, including AP2 at 6p23 and FGF2, BMPR1B, and MADH1 at 4q31. TGFA has both linkage and linkage disequilibrium data supporting it as a candidate gene for NS CL/P. While no region was definitively confirmed for linkage to NS CL/P, the data do support further investigation using larger sample sizes and candidate gene studies at 2p13.2, 4p16.2, 4q31, 6p23, and 16q22-24. Copyright 2003 Wiley-Liss, Inc.

  6. Fatal dialysis disequilibrium syndrome: A tale of two patients

    Directory of Open Access Journals (Sweden)

    Shaikh Nissar

    2010-01-01

    Full Text Available Dialysis disequilibrium syndrome (DDS is a central nervous system disorder, which occurs during hemodialysis (HD or within 24 h following the first HD. DDS commonly occurs in patients suffering from end-stage renal failure undergoing HD for the first time. In a critically ill patient suffering from severe sepsis or septic shock, the combined effects of post-HD brain edema and changes in the brain due to septic encephalopathy, may become amplified leading to DDS. Here we report 2 cases with acute renal failure (ARF, undergoing HD for more than a week and being ventilated and who developed DDS. DDS might have contributed to the sudden deterioration and death in these septic patients. The first case was a 31-year-old male, involved in a motor vehicle accident and had a severe abdominal injury. Underwent laparotomy and hemostasis was achieved. On day 4, the patient developed hemorrhagic shock associated with ARF, which prompted daily HD. On day 8, he went into septic shock. On day 16, 1 h after his daily HD, he became unresponsive and his pupils became dilated and fixed and he expired 2 days later. The second case was a young male who suffered severe abdominal and chest injury after a fall from a height. He developed ARF on day 3 and required HD. On day 9, he had septic shock. Three days later, during his daily HD, he became unconscious and his pupils were not reacting to light and the patient died on day 12. Conclusion: In patients with severe sepsis/septic shock, DDS may occur even after repeated sessions of HD. The acute care physicians, intensivists, and nephrologists should be aware of the risks of DDS.

  7. The disequilibrium between {sup 210}Po and {sup 210}Pb in raw and drinking waters

    Energy Technology Data Exchange (ETDEWEB)

    Idoeta, R. [Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Escuela Tecnica Superior de Ingenieria de Bilbao, Alameda Urquijo s/n, 48013 Bilbao (Spain); Herranz, M., E-mail: m.herranz@ehu.e [Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Escuela Tecnica Superior de Ingenieria de Bilbao, Alameda Urquijo s/n, 48013 Bilbao (Spain); Legarda, F. [Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Escuela Tecnica Superior de Ingenieria de Bilbao, Alameda Urquijo s/n, 48013 Bilbao (Spain)

    2011-01-15

    Many countries have to monitor and control the radioactivity in drinking waters in order to ensure compliance with the requirements of their respective regulations. Among radionuclides responsible for this radioactivity there are {sup 210}Po and {sup 210}Pb, which are usually not in radioactive equilibrium in waters. This paper deals with the analysis of this disequilibrium and the way that the water treatment plants affect it. To do this, {sup 210}Po and {sup 210}Pb activity concentrations were measured in raw and drinking water. The measurements were performed by alpha-particle spectrometry and gas flow proportional counting and the corresponding formulae for uncertainties and detection limits are presented. The values obtained show that the Po/Pb ratio is lower in surface than in ground waters. Regarding water treatment, this ratio adopts values lower in drinking water than in raw waters. In any case, for the waters analysed in this work the committed effective doses due to these radionuclides, are negligible.

  8. 234Th/238U disequilibrium in near-shore sediment: particle reworking and diagenetic time scales

    International Nuclear Information System (INIS)

    Aller, R.C.; Cochran, J.K.

    1976-01-01

    The distribution of 234 Th (tsub(1.2)=24.1 days) in excess of its parent 238 U in the upper layers of near-shore sediment makes possible the evaluation of short-term sediment reworking and diagenetic rates. 234 Th has a maximum residence time in Long Island Sound water of 1.4 days. Seasonal measurement of 234 Th/ 238 U disequilibrium in sediment at a single station in central Long Island Sound demonstrates rapid particle reworking and high 234 Thsub(XS)(>1 dpm/g) in the upper 4 cm of sediment with slower, irregular reworking and low 234 Thsub(XS) to at least 12 cm. The rate of rapid particle reworking varies seasonally and is highest in the fall. The rapidly mixed zone is characterized by steep gradients in sediment chemistry implying fast reactions spanned by 234 Th decay time scales. 238 U is depleted in the upper mixed zone and shows addition in reducing sediment at depth. (Auth.)

  9. SU-E-T-554: Comparison of Electron Disequilibrium Factor in External Photon Beams for Different Models of Linear Accelerators

    International Nuclear Information System (INIS)

    LIU, B; Zhu, T

    2014-01-01

    Purpose: The dose in the buildup region of a photon beam is usually determined by the transport of the primary secondary electrons and the contaminating electrons from accelerator head. This can be quantified by the electron disequilibrium factor, E, defined as the ratio between total dose and equilibrium dose (proportional to total kerma), E = 1 in regions beyond buildup region. Ecan be different among accelerators of different models and/or manufactures of the same machine. This study compares E in photon beams from different machine models/ Methods: Photon beam data such as fractional depth dose curve (FDD) and phantom scatter factors as a function of field size and phantom depth were measured for different Linac machines. E was extrapolated from these fractional depth dose data while taking into account inverse-square law. The ranges of secondary electron were chosen as 3 and 6 cm for 6 and 15 MV photon beams, respectively. The field sizes range from 2x2 to 40x40 cm 2 . Results: The comparison indicates the standard deviations of electron contamination among different machines are about 2.4 - 3.3% at 5 mm depth for 6 MV and 1.2 - 3.9% at 1 cm depth for 15 MV for the same field size. The corresponding maximum deviations are 3.0 - 4.6% and 2 - 4% for 6 and 15 MV, respectively. Both standard and maximum deviations are independent of field sizes in the buildup region for 6 MV photons, and slightly decreasing with increasing field size at depths up to 1 cm for 15 MV photons. Conclusion: The deviations of electron disequilibrium factor for all studied Linacs are less than 3% beyond the depth of 0.5 cm for the photon beams for the full range of field sizes (2-40 cm) so long as they are from the same manufacturer

  10. Preconditioning Strategies for Solving Elliptic Difference Equations on a Multiprocessor.

    Science.gov (United States)

    1982-01-01

    CALLING MA31C. C TD - TIME REQUIRED BY MA31C TO PERFORM THE C FACTORIZATION. 160 C TDT - TOTAL TIME REQUIRED BY SUBROUTINE FACTOR. C TDT-T IM3-T IMI...TPD-TIM2-TIM1 TD -TIM3-TIM2 165 C WRITE(LP,70) TDT,TPD, TD 70 FORMAT(7H TDT - ,F6.3,7H TPD " F6.3,6H TD ,F6.3) C WRITE(LP, 85) NTYPE,NVERN 170 85 FORMAT...INTEGER INI(IAI) ,INJ(IAJ) ,IK(NN,4) INTEGER NU(3000) C COMMON/EA 4BD /PRVT(4),IPRVT(6) 15 COMMON/MA31I/DD,LP,MP COMMON/MA31J/LROW,LCOL,NCP,ND, IPD

  11. Rapakivi texture formation via disequilibrium melting in a contact partial melt zone, Antarctica

    Science.gov (United States)

    Currier, R. M.

    2017-12-01

    In the McMurdo Dry Valleys of Antarctica, a Jurassic aged dolerite sill induced partial melting of granite in the shallow crust. The melt zone can be traced in full, from high degrees of melting (>60%) along the dolerite contact, to no apparent signs of melting, 10s of meters above the contact. Within this melt zone, the well-known rapakivi texture is found, arrested in various stages of development. High above the contact, and at low degrees of melting, K-feldspar crystals are slightly rounded and unmantled. In the lower half of the melt zone, mantles of cellular textured plagioclase appear on K-feldspar, and thicken towards the contact heat source. At the highest degrees of melting, cellular-textured plagioclase completely replaces restitic K-feldspar. Because of the complete exposure and intact context, the leading models of rapakivi texture formation can be tested against this system. The previously proposed mechanisms of subisothermal decompression, magma-mixing, and hydrothermal exsolution all fail to adequately describe rapakivi generation in this melt zone. Preferred here is a closed system model that invokes the production of a heterogeneous, disequilibrium melt through rapid heating, followed by calcium and sodium rich melt reacting in a peritectic fashion with restitic K-feldspar crystals. This peritectic reaction results in the production of plagioclase of andesine-oligoclase composition—which is consistent with not just mantles in the melt zone, but globally as well. The thickness of the mantle is diffusion limited, and thus a measure of the diffusive length scale of sodium and calcium over the time scale of melting. Thermal modeling provides a time scale of melting that is consistent with the thickness of observed mantles. Lastly, the distribution of mantled feldspars is highly ordered in this melt zone, but if it were mobilized and homogenized—mixing together cellular plagioclase, mantled feldspars, and unmantled feldspars—the result would be

  12. Genetic Variants of Surfactant Proteins A, B, C, and D in Bronchopulmonary Dysplasia

    Directory of Open Access Journals (Sweden)

    J. Pavlovic

    2006-01-01

    Full Text Available BPD_28D (O2 dependency at 28 days of life and BPD_36W (O2 dependency at 36 wks post-menstrual age are diseases of prematurely born infants exposed to mechanical ventilation and/or oxygen supplementation. In order to determine whether genetic variants of surfactant proteins (SPs-A, B, C, and D and SP-B-linked microsatellite markers are risk factors in BPD, we performed a family based association study using a Greek study group of 71 neonates (<30 wks gestational age from 60 families with, 52 BPD_28D and 19 BPD_36W, affected infants. Genotyping was performed using newly designed pyrosequencing assays and previously published methods. Associations between genetic variants of SPs and BPD subgroups were determined using Transmission Disequilibrium Test (TDT and Family Based Association Test (FBAT. Significant associations (p ≤ 0.01 were observed for alleles of SP-B and SP-B-linked microsatellite markers, and haplotypes of SP-A, SP-D, and SP-B. Specifically, allele B-18_C associated with susceptibility in BPD_36W. Microsatellite marker AAGG_6 associated with susceptibility in BPD_28D/36W group. Haplotype analysis revealed ten susceptibility and one protective haplotypes for SP-B and SP-B-linked microsatellite markers and two SP-A-SP-D protective haplotypes. The data indicate that SP loci are linked to BPD. Studies in different study groups and/or of larger sample size are warranted to confirm these observations and delineate genetic background of BPD subgroups.

  13. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes.

    Science.gov (United States)

    Long, Ji-Rong; Zhao, Lan-Juan; Liu, Peng-Yuan; Lu, Yan; Dvornyk, Volodymyr; Shen, Hui; Liu, Yong-Jun; Zhang, Yuan-Yuan; Xiong, Dong-Hai; Xiao, Peng; Deng, Hong-Wen

    2004-05-24

    The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. We examined the patterns of LD and haplotype distribution in eight candidate genes for osteoporosis and/or obesity using 31 SNPs in 1,873 subjects. These eight genes are apolipoprotein E (APOE), type I collagen alpha1 (COL1A1), estrogen receptor-alpha (ER-alpha), leptin receptor (LEPR), parathyroid hormone (PTH)/PTH-related peptide receptor type 1 (PTHR1), transforming growth factor-beta1 (TGF-beta1), uncoupling protein 3 (UCP3), and vitamin D (1,25-dihydroxyvitamin D3) receptor (VDR). Yin yang haplotypes, two high-frequency haplotypes composed of completely mismatching SNP alleles, were examined. To quantify LD patterns, two common measures of LD, D' and r2, were calculated for the SNPs within the genes. The haplotype distribution varied in the different genes. Yin yang haplotypes were observed only in PTHR1 and UCP3. D' ranged from 0.020 to 1.000 with the average of 0.475, whereas the average r2 was 0.158 (ranging from 0.000 to 0.883). A decay of LD was observed as the intermarker distance increased, however, there was a great difference in LD characteristics of different genes or even in different regions within gene. The differences in haplotype distributions and LD patterns among the genes underscore the importance of characterizing genomic regions of interest prior to association studies.

  14. Hover Testing of the NASA/Army/MIT Active Twist Rotor Prototype Blade

    Science.gov (United States)

    Wilbur, Matthew L.; Yeager, William T., Jr.; Wilkie, W. Keats; Cesnik, Carlos E. S.; Shin, Sangloon

    2000-01-01

    Helicopter rotor individual blade control promises to provide a mechanism for increased rotor performance and reduced rotorcraft vibrations and noise. Active material methods, such as piezoelectrically actuated trailing-edge flaps and strain-induced rotor blade twisting, provide a means of accomplishing individual blade control without the need for hydraulic power in the rotating system. Recent studies have indicated that controlled strain induced blade twisting can be attained using piezoelectric active fiber composite technology. In order to validate these findings experimentally, a cooperative effort between NASA Langley Research Center, the Army Research Laboratory, and the MIT Active Materials and Structures Laboratory has been developed. As a result of this collaboration an aeroelastically-scaled active-twist model rotor blade has been designed and fabricated for testing in the heavy gas environment of the Langley Transonic Dynamics Tunnel (TDT). The results of hover tests of the active-twist prototype blade are presented in this paper. Comparisons with applicable analytical predictions of active-twist frequency response in hovering flight are also presented.

  15. 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.

  16. Titanates of the lindsleyite-mathiasite (LIMA) group reveal isotope disequilibrium associated with metasomatism in the mantle beneath Kimberley (South Africa)

    Science.gov (United States)

    Giuliani, Andrea; Woodhead, Jon D.; Phillips, David; Maas, Roland; Davies, Gareth R.; Griffin, William L.

    2018-01-01

    Radiogenic isotope variations unrelated to radiogenic ingrowth are common between minerals found in metasomatised mantle xenoliths entrained in kimberlite, basalts and related magmas. As the metasomatic minerals are assumed to have been in isotopic equilibrium originally, such variations are typically attributed to contamination by the magma host and/or interaction with mantle fluids during or before xenolith transport to surface. However, the increasing evidence of metasomatism by multiple, compositionally distinct fluids permeating the lithospheric mantle, coeval with specific magmatic events, suggests that isotopic disequilibrium might be a consequence of discrete, though complex, metasomatic events. Here we provide clear evidence of elemental and Sr isotope heterogeneity between coeval Ti-rich LIMA (lindsleyite-mathiasite) minerals at the time of their formation in the mantle. LIMA minerals occur in close textural association with clinopyroxene and phlogopite in low-temperature (∼800-900 °C), strongly metasomatised mantle xenoliths from the ∼84 Ma Bultfontein kimberlite (South Africa). Previous U/Pb dating of the LIMA phases was used to argue that each xenolith recorded a single event of LIMA crystallisation at ∼180-190 Ma, coeval with the emplacement of Karoo magmas. SEM imaging reveals that up to four types of LIMA phases coexist in each xenolith, and occasionally in a single LIMA grain. Major element and in situ Sr isotope analyses of the different LIMA types show that each phase has a distinct elemental composition and initial 87Sr/86Sr ratio (e.g., 0.7068-0.7086 and 0.7115-0.7129 for two LIMA types in a single xenolith; 0.7053-0.7131 across the entire sample suite). These combined age and isotopic constraints require that multiple fluids metasomatised these rocks at broadly the same time (i.e. within a few thousands to millions of years), and produced similar mineralogical features. Elemental and isotopic variations between different LIMA types

  17. Characterization of Linkage Disequilibrium and Population Structure in a Mungbean Diversity Panel

    Directory of Open Access Journals (Sweden)

    Thomas J. Noble

    2018-01-01

    Full Text Available Mungbean [Vigna radiata (L. R. Wilczek var. radiata] is an important grain legume globally, providing a high-quality plant protein source largely produced and consumed in South and East Asia. This study aimed to characterize a mungbean diversity panel consisting of 466 cultivated accessions and demonstrate its utility by conducting a pilot genome-wide association study of seed coat color. In addition 16 wild accessions were genotyped for comparison and in total over 22,000 polymorphic genome-wide SNPs were identified and used to analyze the genetic diversity, population structure, linkage disequilibrium (LD of mungbean. Polymorphism was lower in the cultivated accessions in comparison to the wild accessions, with average polymorphism information content values 0.174, versus 0.305 in wild mungbean. LD decayed in ∼100 kb in cultivated lines, a distance higher than the linkage decay of ∼60 kb estimated in wild mungbean. Four distinct subgroups were identified within the cultivated lines, which broadly corresponded to geographic origin and seed characteristics. In a pilot genome-wide association mapping study of seed coat color, five genomic regions associated were identified, two of which were close to seed coat color genes in other species. This mungbean diversity panel constitutes a valuable resource for genetic dissection of important agronomical traits to accelerate mungbean breeding.

  18. The membrane stress response buffers lethal effects of lipid disequilibrium by reprogramming the protein homeostasis network.

    Science.gov (United States)

    Thibault, Guillaume; Shui, Guanghou; Kim, Woong; McAlister, Graeme C; Ismail, Nurzian; Gygi, Steven P; Wenk, Markus R; Ng, Davis T W

    2012-10-12

    Lipid composition can differ widely among organelles and even between leaflets of a membrane. Lipid homeostasis is critical because disequilibrium can have disease outcomes. Despite their importance, mechanisms maintaining lipid homeostasis remain poorly understood. Here, we establish a model system to study the global effects of lipid imbalance. Quantitative lipid profiling was integral to monitor changes to lipid composition and for system validation. Applying global transcriptional and proteomic analyses, a dramatically altered biochemical landscape was revealed from adaptive cells. The resulting composite regulation we term the "membrane stress response" (MSR) confers compensation, not through restoration of lipid composition, but by remodeling the protein homeostasis network. To validate its physiological significance, we analyzed the unfolded protein response (UPR), one facet of the MSR and a key regulator of protein homeostasis. We demonstrate that the UPR maintains protein biogenesis, quality control, and membrane integrity-functions otherwise lethally compromised in lipid dysregulated cells. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. A tetranucleotide repeat (D4S1652) is linked to facioscapulohumeral dystrophy and shows no linkage disequilibrium with the disease

    Energy Technology Data Exchange (ETDEWEB)

    Mathews, K.D.; Bailey, H.L.; Mills, K.A. [and others

    1994-09-01

    Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant dystrophy which is associated with a deletion in a subtelomeric repeat element on 4q35. The gene has not yet been identified. The probe detecting this deletion (D4F104S1) is not chromosome 4-specific, and at least one large family has been identified which is not linked to chromosome 4. Thus, persymptomatic/prenatal diagnosis can only be provided to families that are proven to be chromosome 4-linked or where a new mutation is demonstrated. The markers available to demonstrate linkage to chromosome 4, D4S139, D4S163, and D4F35S1, are VNTRs. We have used D4S1652, a tetranucleotide repeat recently identified by the Cooperative Human Linkage Center, in our FSHD families. We found it is completely linked to the 4q35 VNTRs and to the disease phenotype. Physical mapping, using radiation hybrids and somatic cell hybrids, places D4S1652 between D4S139, an interval of approximately 1 Mb. We have used D4S1652 to look for linkage disequilibrium in our FSHD patient population. This result is of interest because of our hypothesis that the deletion in the subtelomeric repeat element alters transcription of a more proximal gene through a position effect. Previously available markers have been unsatisfactory for this experiment because of difficulty comparing numerous VNTR alleles across families. We observed 4, easily distinguished, D4S1652 alleles in our families. We studied 14 chromosomes associated with disease phenotype and 55 chromosomes from nontransmitting parents. We found no evidence for linkage disequilibrium ({chi}{sup 2}=1.313, nonsignificant). This result will need confirmation with a larger patient population, but is consistent with the clinical observation that there is a high rate of a new mutation in this disorder.

  20. 226Ra/238U disequilibrium in an upland organic soil exhibiting elevated natural radioactivity

    International Nuclear Information System (INIS)

    Dowdall, M.; O'Dea, J.

    2002-01-01

    This paper presents the results of a study into the anomalous 226 Ra/ 238 U disequilibrium ( 226 Ra/ 238 U of 0.5-9) exhibited by an upland organic soil in Co. Donegal, Ireland. Radiochemical speciation of 226 Ra, 238 U and 228 Ra indicates that in this organic soil the high 226 Ra/ 238 U ratio is due to loss of 238 U relative to 226 Ra via oxidation and mobilisation of 238 U in the upper layers of the soil and subsequent loss in solution. At the lower, more reducing depths of the soil profile, 238 U and 226 Ra are essentially in equilibrium. Loss of 238 U appears to occur primarily from the easily oxidised organic and iron oxide fractions of the soil, samples exhibiting high 226 Ra/ 238 U ratios displaying significantly lower 238 U levels in these fractions than samples whose ratio is below the average value for the soil of the valley. Selective enrichment of 226 Ra by plants or preferential leaching of 226 Ra from the underlying rock is not supported by the results of this study

  1. Titin is a candidate gene for stroke volume response to endurance training: the HERITAGE Family Study.

    Science.gov (United States)

    Rankinen, Tuomo; Rice, Treva; Boudreau, Anik; Leon, Arthur S; Skinner, James S; Wilmore, Jack H; Rao, D C; Bouchard, Claude

    2003-09-29

    A genome-wide linkage scan for endurance training-induced changes in submaximal exercise stroke volume (DeltaSV50) in the HERITAGE Family Study revealed two chromosomal regions (2q31-q32 and 10p11.2) with at least suggestive evidence of linkage among white families. Here we report a further characterization of the quantitative trait locus (QTL) in chromosome 2q31 and provide evidence that titin (TTN) is likely a candidate gene involved. The original linkage was detected with two markers (D2S335 and D2S1391), and the QTL covered approximately 25 million base pairs (Mb). We added 12 microsatellite markers resulting in an average marker density of one marker per 2.3 Mb. The evidence of linkage increased from P = 0.006 to P = 0.0002 and 0.00002 in the multi- and single-point analyses, respectively. The strongest evidence of linkage was seen with two markers in and near the TTN gene. Transmission/disequilibrium test (TDT) with the same marker set provided evidence for association with one of the TTN markers (D2S385; P = 0.004). TTN is a major contributor to the elasticity of cardiomyocytes and a key regulator of the Frank-Starling mechanism. Since TTN is the largest gene in the human genome, the challenge is to identify the DNA sequence variants contributing to the interindividual differences in cardiac adaptation to endurance training.

  2. Improved long-term survival after intra-operative single high-dose ATG-Fresenius induction in renal transplantation: a single centre experience.

    Science.gov (United States)

    Kaden, Jürgen; May, Gottfried; Völp, Andreas; Wesslau, Claus

    2009-01-01

    In organ grafts donor-specific sensitization is initiated immediately after revascularization. Therefore, in 1990 we introduced the intra-operative single high-dose ATG-Fresenius (ATG-F) induction in addition to standard triple drug therapy (TDT) consisting of steroids, azathioprine and cyclosporin. A total of 778 first renal transplantations from deceased donors, performed between 1987 and 1998, were included in this evaluation. This retrospective analysis of clinic records and electronic databases presents data of all recipients of first kidney grafts who received two different ATG-F inductions (1(st) group: 9 mg/kg body weight as single high-dose intra-operatively, n=484; 2(nd) group: 3 mg/kg body weight on 7 or 8 consecutive days as multiple-dose starting also intra-operatively, n=78) and standard TDT alone (3(rd) group: TDT alone, n=216). The 10-year patient survival rates were 72.6+/-2.6% (TDT + ATG-F single high-dose), 79.5+/-5.1% (TDT + ATG-F multiple-dose) and 67.2+/-3.7%% (TDT alone; Kaplan-Meier estimates with standard errors; ATG-F vs TDT alone, p=0.001). The 10-year graft survival rates with censoring of patients that died with a functioning graft were 73.8+/-2.4%, 57.7+/-5.8% and 58.4+/-3.6% (Kaplan-Meier estimates with standard errors; 1(st) vs 2(nd )and 3(rd) group, respectively, p<0.001) and the 10-year graft survival rates with patient death counted as graft failure were 58.3+/-2.7%, 55.7+/-5.8% and 48.2+/-3.5% (Kaplan-Meier estimates with standard errors; ATG-F single high-dose vs TDT, p=0.023). In pre-sensitized recipients there were also significant differences in favour of ATG-F, more notably in the single high-dose ATG-F induction. A total of 69% of the patients in the two cohorts receiving ATG-F did not experience any transplant rejections compared to 56% in patients undergoing TDT alone (p=0.018). The incidence of infectious complications was comparable across all groups. According to evidence obtained from the routine documentation of 778

  3. 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

  4. 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.

  5. Extent and distribution of linkage disequilibrium in the Old Order Amish.

    Science.gov (United States)

    Van Hout, Cristopher V; Levin, Albert M; Rampersaud, Evadnie; Shen, Haiqing; O'Connell, Jeffrey R; Mitchell, Braxton D; Shuldiner, Alan R; Douglas, Julie A

    2010-02-01

    Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02-0.09, and for autosomal SNPs 10-20 kb apart with common alleles (minor allele frequency > or =0.05), the LD measure r(2) was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA ( approximately 88%) at r(2) > or =0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations. 2009 Wiley-Liss, Inc.

  6. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Statistical ... Keywords. family-based genetic association; logistic regression; linkage disequilibrium. ... Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we ...

  7. Uranium series disequilibrium: application to studies of the groundwater regime of the Harwell region

    International Nuclear Information System (INIS)

    Ivanovich, M.; Alexander, J.

    1985-03-01

    Regional groundwater systems incorporating argillaceous formations beneath the Harwell site have been studied as part of a national research programme of investigation into the feasibility of disposal of low and intermediate radioactive wastes into argillaceous rocks. The principal aim of the programme is to establish the groundwater flow patterns using hydrogeological and geochemical methods in association with isotope contents and uranium series disequilibrium and thus provide an independent approach to the study of effective permeabilities of clay lithologies in a sedimentary sequence. Thirty four groundwater samples derived from the high permeability formations in the Harwell region have been analysed for uranium and thorium content and 234 U/ 238 U, 230 Th/ 234 U and 230 Th/ 232 Th activity ratios. The uranium isotopic signatures have been interpreted in terms of the regional groundwater circulation and mixing patterns. The most significant zones of groundwater mixing determined from uranium isotopic data are situated just beneath the edge of the confined strata. These zones coincide with the locations of hydraulic lows in the Great Oolite and the Corallian formations towards which the regional groundwaters move. It is concluded that the uranium isotopic signatures can be used to identify water masses and to evaluate mixing of groundwaters in a sedimentary sequence on a regional scale. (author)

  8. Uranium-series disequilibrium studies in phosphorite nodules from the west coast of South America

    International Nuclear Information System (INIS)

    Burnett, W.C.; Veeh, H.H.

    1977-01-01

    Sedimentary phosphorites occurring on the sea floor off Peru and Chile have been analyzed for U and Th isotopes, to establish their ages and hence obtain clues for their mode of formation. Fission-track distribution studies indicate that the U is primarily associated with the apatite fraction. Uranium-series disequilibrium methods, therefore, should be applicable, if the U incorporation is syngenetic with the apatite. The fractionation of U isotopes between oxidation states in the relatively young phosphorites from South America is low compared to that in older deposits. This supports the contention of Kolodny et al., (Geochim.Cosmochim.Acta;34:3 (1970)) that the major mechanism of 234 U/ 238 U fractionation is displacement of 234 U atoms into sites where they are more 'oxidizable' than the 238 U parent. Age estimates based on 234 U(IV) and 230 Th contents are internally consistent and range from late Pleistocene to Recent. The results indicate that marine phosphorites are currently forming in this area of intense oceanic upwelling. The age pattern during the last 150,000 yr suggests a correlation with eustatic high sea level stands and implies that conditions were more favourable for apatite genesis in this area during interglacials rather than during glacial times. (author)

  9. HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703

    DEFF Research Database (Denmark)

    Matthews, Philippa C; Adland, Emily; Listgarten, Jennifer

    2011-01-01

    -clade-infected subjects. We present evidence that HLA-A*7401 operates an effect that is independent of HLA-B*5703, with which it is in linkage disequilibrium in some populations, to mediate lowered viremia. We describe a novel statistical approach to detecting additive effects between class I alleles in control of HIV-1...... epitopes appear immunodominant. We identify eight novel putative HLA-A*7401-restricted epitopes, of which three have been defined to the optimal epitope. In common with HLA-B alleles linked with slow progression, viremic control through an HLA-A*7401-restricted response appears to be associated...... with the selection of escape mutants within Gag epitopes that reduce viral replicative capacity. These studies highlight the potentially important contribution of an HLA-A allele to immune control of HIV infection, which may have been concealed by a stronger effect mediated by an HLA-B allele with which...

  10. Chromosome abnormalities in the acute phase of CML

    Energy Technology Data Exchange (ETDEWEB)

    Rowley, J D

    1978-01-01

    Additional chromosome changes are superimposed on the Ph/sup 1/ positive cell line in approximately 80% of patients in the acute phase of chronic myelogenous leukemia (CML). These changes may precede the onset of blast crisis by several months. They are nonrandom and frequently involve an extra No. 8, an isochromosome for the long arm of No. 17, an extra No. 19, and a second Ph/sup 1/ chromosome. Since such changes may occur in combination, modal numbers frequently range between 47 and 57 chromosomes. Although present evidence suggests that abnormal clones originate, or at least proliferate, in the spleen, similar changes have been observed in patients who underwent splenectomy during the chronic phase of their disease. The question of particular clinical-chromosomal correlations has been discussed in only one study. It appeared that patients whose karyotype did not change might have a longer median survival than those whose karyotype showed additional abnormalities. Tests for levels of terminal deoxynucleotidyl transferase (TDT) and response to anti-acute lymphoblastic leukemia (ALL) serum suggest that some, but not all patients react as do patients with ALL. Those who are similar to ALL have high levels of TDT and are anti-ALL serum-positive; the others have low levels of TDT and are anti-ALL serum-negative. In the future, correlations of these more sophisticated tests with the blast morphology, clinical course, and karyotype pattern should provide significant new insights into the acute phase of CML.

  11. Statistical equivalent of the classical TDT for quantitative traits and ...

    Indian Academy of Sciences (India)

    sion model to test the association for quantitative traits based on a trio design. We show that the method ... from the analyses and only one transmission is considered. Keywords. .... use the sample mean or median of Y, as an estimator of c in.

  12. The effect of the freezing curve type on bull spermatozoa motility after thawing

    Directory of Open Access Journals (Sweden)

    Martina Doležalová

    2015-01-01

    Full Text Available The objective of this work was to determine the effect of selected freezing curves on spermatozoa survivability after thawing, defined by its motility. The ejaculates of nine selected sires of the same age, breed, and frequency of collecting, bred under the same breeding conditions including handling, stabling, feeding system and feeding ratio composition, were repeatedly collected and evaluated. Sperm samples of each sire were diluted using only one extender and divided into four parts. Selected four freezing curves – the standard, commercially recommended three-phase curve; a two-phase curve; a slow three-phase curve; and a fast three-phase curve, differing in the course of temperature vs time, were applied. The percentage rate of progressive motile spermatozoa above head was determined immediately after thawing, and after 30, 60, 90, and 120 min of the thermodynamic test (TDT. Moreover, average spermatozoa motility (AMOT and spermatozoa motility decrease (MODE throughout the entire TDT were evaluated. Insemination doses frozen using the simpler two-phase curve demonstrated the highest motility values (+2.97% to +10.37%; P < 0.05–0.01 immediately after thawing and during the entire TDT. Concurrently, the highest AMOT (+4.37% to +8.82%; P < 0.01 was determined. The highest spermatozoa motility values were detected after thawing doses frozen by the two-phase freezing curve in eight out of nine sires. Simultaneously, a significant effect of sire individuality was clearly confirmed. Inter-sire differences of spermatozoa motility during TDT as well as AMOT and MODE were significant (P < 0.01. The findings describing both factors of interaction indicate the necessity of individual cryopreservation of the ejaculate to increase its fertilization capability after thawing.

  13. The broad utility of Trizac diamond tile

    Science.gov (United States)

    Gagliardi, John I.; Romero, Vincent D.; Sventek, Bruce; Zu, Lijun

    2017-10-01

    Sample finishing data from a broad range of materials — glasses, sapphire, silicon carbide, silicon, zirconium oxide, lithium tantalate, and flooring materials — are shown effectively processed with Trizact™ Diamond Tile (TDT). This data should provide the reader with an understanding of what to expect when using TDT on hard to grind or brittle materials. Keys to maintaining effective TDT pad wear rates, and therefore cost effect and stable processes, are described as managing 1) the proper lubricant flow rate for glasses and silicon-type materials and 2) the conditioning particle concentration for harder-to-grind materials

  14. Terminal deoxynucleotidyl transferase activity in the regenerating thymus of X-irradiated mice

    International Nuclear Information System (INIS)

    Daculsi, R.; Astier, T.; Legrand, E.; Duplan, J.F.

    1982-01-01

    The distribution of terminal deoyxnucleotidyl transferase (TdT) enzyme activity (EU per 10 8 cells) between peaks I and II was followed for a period of 42 days in regenerating thymus of lethally irradiated (9 Gy) C3H mice restored with 10 6 (C3H x AKR) F1 bone marrow cells. The detection of Thy-1.1 and Thy-1.2 surface antigens allowed for the discrimination between host and donor cells, and the main subpopulations of thymic cells were characterized by their sensitivity to H-2sup(k) antiserum and to dexamethazone. Two peaks of TdT activity could be detected on phosphocellulose chromatographic separation. The distribution of TdT activity between these two peaks was followed during the two periods of thymic endo- and exoregeneration. Peak I TdT activity was closely correlated with the variation in the percentage of the high H-2 population. Peak II activity was mostly related to low H-2 cells. The per cell content of both peak I and peak II activities exceeded the norm in rapidly expanding populations. Finally between days 10 and 14 the TdT activity of the endoregenerating population was apparently not different from that of the exoregenerating population between days 14 and 22. (Auth.)

  15. Family-based association study of DRD4 gene in methylphenidate-responded Attention Deficit/Hyperactivity Disorder.

    Directory of Open Access Journals (Sweden)

    Patrick Wing-Leung Leung

    Full Text Available The 48-basepair (48-bp variable number tandem repeat (VNTR polymorphism in exon 3 of the dopamine receptor D4 gene (DRD4 is implicated in the etiology of attention-deficit/ hyperactivity disorder (ADHD. In particular, ADHD in European-ancestry population is associated with an increased prevalence of the 7-repeat (7R allele of the exon 3 VNTR. However, it is intriguing to note that the 7R allele has been found to be of very low prevalence in the Chinese general population. In a previous case-control study, our research team had found that the 7R allele was similarly absent in Chinese ADHD children in Hong Kong. Instead, there was an increased prevalence of the 2R allele in Chinese ADHD children. Interestingly, in Asian samples, the 2R allele had been found to be an evolutionary derivative of the 7R allele with equivalent biochemical functionality. So, the finding of an association between ADHD and 2R allele in Chinese population does not exactly contradict the original 7R allele finding in European-ancestry population. However, given the potential pitfall of population stratification in the previous case-control design, this current study tested the 2R allele and ADHD association using a methodologically more rigorous family-based approach on 33 Chinese ADHD probands who had favorable clinical responses to stimulant medication (methylphenidate. Haplotype Relative Risk (HRR analysis and Transmission Disequilibrium Test (TDT both showed a significant preferential transmission of the 2R allele from the biological parents to ADHD probands (pone-tailed = 0.038, OR = 2.04; pone-tailed = 0.048, OR = 2.29, respectively. A second hypothesis speculates that it is the deviation, including 7R and 2R alleles, from the conserved ancestral 4R allele which confers risk to ADHD. Thus, a preferential transmission of non-4R alleles, against the 4R allele, from biological parents to their ADHD probands is predicted. Both HRR analysis and TDT confirmed such

  16. Response transforms from comparative study of commercial pulsed-neutron-capture logging systems

    International Nuclear Information System (INIS)

    Salaita, G.N.

    1992-01-01

    This paper reports that three generations of Schlumberger's Thermal Decay Time (TDT SM ) logging devices - viz., TDT-K, TDT-M, and TDT-P - along with an Atlas Wireline PDK-100 SM system were run in a Saudi Aramco well. The wellbore (8 1/2 in. with 7-in. casing) penetrated a sequence of clean sand, shaly sand, and shale streaks as exhibited by the openhole natural gamma ray log. The initial wellbore fluid was diesel. The fluid was then changed to brines of 42,000 and 176,000 ppm NaCl, respectively. Three repeat passes at a logging speed of 900 ft/hr were obtained by each device for each borehole liquid. As a result of this extensive comparative study, a set of departure curves and mathematical transforms was developed primarily for standardizing the various Schlumberger tools to a common reference logging system and/or borehole environment. The transforms were used beneficially to determine residual oil saturation (ROS) from time-lapse logs in a Saudi Aramco reservoir

  17. Advancing Tobacco Dependence Treatment Services in the Eastern Mediterranean Region: International collaboration for training and capacity-building

    Directory of Open Access Journals (Sweden)

    Feras I. Hawari

    2014-10-01

    Full Text Available Tobacco use negatively affects health and is a major risk factor for non-communicable diseases (NCDs. Today, tobacco use ranks third among risk factors in North Africa and the Middle East in terms of disease burden. Despite the established need for these services, tobacco dependence treatment (TDT services are still inadequate in the Eastern Mediterranean region (EMR. Among the main challenges hindering their expansion is the current lack of training opportunities. The provision of training and capacity-building—a key enabler of TDT—offers an excellent catalyst to launch TDT services in the region. This review discusses the need for TDT training in the EMR and describes a model for providing regional evidence-based training in line with international standards. The King Hussein Cancer Center in Amman, Jordan, is the regional host for Global Bridges, a worldwide TDT initiative. Using this model, they have trained 1,500 professionals and advocates from the EMR over the past three years.

  18. Characteristics of Control Laws Tested on the Semi-Span Super-Sonic Transport (S4T) Wind-Tunnel Model

    Science.gov (United States)

    Christhilf, David M.; Moulin, Boris; Ritz, Erich; Chen, P. C.; Roughen, Kevin M.; Perry, Boyd

    2012-01-01

    The Semi-Span Supersonic Transport (S4T) is an aeroelastically scaled wind-tunnel model built to test active controls concepts for large flexible supersonic aircraft in the transonic flight regime. It is one of several models constructed in the 1990's as part of the High Speed Research (HSR) Program. Control laws were developed for the S4T by M4 Engineering, Inc. and by Zona Technologies, Inc. under NASA Research Announcement (NRA) contracts. The model was tested in the NASA-Langley Transonic Dynamics Tunnel (TDT) four times from 2007 to 2010. The first two tests were primarily for plant identification. The third entry was used for testing control laws for Ride Quality Enhancement, Gust Load Alleviation, and Flutter Suppression. Whereas the third entry only tested FS subcritically, the fourth test demonstrated closed-loop operation above the open-loop flutter boundary. The results of the third entry are reported elsewhere. This paper reports on flutter suppression results from the fourth wind-tunnel test. Flutter suppression is seen as a way to provide stability margins while flying at transonic flight conditions without penalizing the primary supersonic cruise design condition. An account is given for how Controller Performance Evaluation (CPE) singular value plots were interpreted with regard to progressing open- or closed-loop to higher dynamic pressures during testing.

  19. Tuning the Stability of Organic Active Materials for Nonaqueous Redox Flow Batteries via Reversible, Electrochemically Mediated Li + Coordination

    Energy Technology Data Exchange (ETDEWEB)

    Carino, Emily V.; Staszak-Jirkovsky, Jakub; Assary, Rajeev S.; Curtiss, Larry A.; Markovic, Nenad M.; Brushett, Fikile R.

    2016-03-24

    We describe an electrochemically mediated interaction between Li+ and a promising active material for nonaqueous redox flow batteries (RFBs), 1,2,3,4-tetrahydro-6,7-dimethoxy-1,1,4,4-tetramethylnaphthalene (TDT), and the impact of this structural interaction on material stability during voltammetric cycling. TDT could be an advantageous organic positive electrolyte material for nonaqueous RFBs due to its high oxidation potential, 4.21 V vs Li/Li+, and solubility of at least 1.0 M in select electrolytes. Although results from voltammetry suggest TDT displays Nernstian reversibility in many nonaqueous electrolyte solutions, bulk electrolysis reveals significant degradation in all electrolytes studied, the extent of which depends on the electrolyte solution composition. Results of subtractively normalized in situ Fourier transform infrared spectroscopy (SNIFTIRS) confirm that TDT undergoes reversible structural changes during cyclic voltammetry in propylene carbonate and 1,2-dimethoxyethane solutions containing Li+ electrolytes, but irreversible degradation occurs when tetrabutylammonium (TBA+) replaces Li+ as the electrolyte cation in these solutions. By combining the results from SNIFTIRS experiments with calculations from density functional theory, solution-phase active species structure and potential-dependent interactions can be determined. We find that Li+ coordinates to the Lewis basic methoxy groups of neutral TDT and, upon electrochemical oxidation, this complex dissociates into the radical cation TDT•+ and Li+. The improved cycling stability in the presence of Li+ relative to TBA+ suggests that the structural interaction reported herein may be advantageous to the design of energy storage materials based on organic molecules.

  20. Analysis of Limit Cycle Oscillation Data from the Aeroelastic Test of the SUGAR Truss-Braced Wing Model

    Science.gov (United States)

    Bartels, Robert E.; Funk, Christie; Scott, Robert C.

    2015-01-01

    Research focus in recent years has been given to the design of aircraft that provide significant reductions in emissions, noise and fuel usage. Increases in fuel efficiency have also generally been attended by overall increased wing flexibility. The truss-braced wing (TBW) configuration has been forwarded as one that increases fuel efficiency. The Boeing company recently tested the Subsonic Ultra Green Aircraft Research (SUGAR) Truss-Braced Wing (TBW) wind-tunnel model in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). This test resulted in a wealth of accelerometer data. Other publications have presented details of the construction of that model, the test itself, and a few of the results of the test. This paper aims to provide a much more detailed look at what the accelerometer data says about the onset of aeroelastic instability, usually known as flutter onset. Every flight vehicle has a location in the flight envelope of flutter onset, and the TBW vehicle is not different. For the TBW model test, the flutter onset generally occurred at the conditions that the Boeing company analysis said it should. What was not known until the test is that, over a large area of the Mach number dynamic pressure map, the model displayed wing/engine nacelle aeroelastic limit cycle oscillation (LCO). This paper dissects that LCO data in order to provide additional insights into the aeroelastic behavior of the model.

  1. Correlation Between Contrast Time-Density Time on Digital Subtraction Angiography and Flow: An in Vitro Study.

    Science.gov (United States)

    Brunozzi, Denise; Shakur, Sophia F; Ismail, Rahim; Linninger, Andreas; Hsu, Chih-Yang; Charbel, Fady T; Alaraj, Ali

    2018-02-01

    Digital subtraction angiography (DSA) provides an excellent anatomic characterization of cerebral vasculature, but hemodynamic assessment is often qualitative and subjective. Various clinical algorithms have been produced to semiquantify flow from the data obtained from DSA, but few have tested them against reliable flow values. An arched flow model was created and injected with contrast material. Seventeen injections were acquired in anterior-posterior and lateral DSA projections, and 4 injections were acquired in oblique projection. Image intensity change over the angiogram cycle of each DSA run was analyzed through a custom MATLAB code. Time-density plots obtained were divided into 3 components (time-density times, TDTs): TDT 10%-100% (time needed for contrast material to change image intensity from 10% to 100%), TDT 100%-10% (time needed for contrast material to change image intensity from 100% to 10%), and TDT 25%-25% (time needed for contrast material to change from 25% image intensity to 25%). Time-density index (TDI) was defined as model cross-sectional area to TDT ratio, and it was measured against different flow rates. TDI 10%-100% , TDI 100%-10% , and TDI 25%-25% all correlated significantly with flow (P < 0.001). TDI 10%-100% , TDI 100%-10% , and TDI 25%-25% showed, respectively, a correlation coefficient of 0.91, 0.91, and 0.97 in the anterior-posterior DSA projections (P < 0.001). In the lateral DSA projection, TDI 100%-10% showed a weaker correlation (r = 0.57; P = 0.03). Also in the oblique DSA projection, TDIs correlated significantly with flow. TDI on DSA correlates significantly with flow. Although in vitro studies might overlook conditions that occur in patients, this method appears to correlate with the flow and could offer a semiquantitative method to evaluate the cerebral blood flow. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Nicotine facilitates memory consolidation in perceptual learning.

    Science.gov (United States)

    Beer, Anton L; Vartak, Devavrat; Greenlee, Mark W

    2013-01-01

    Perceptual learning is a special type of non-declarative learning that involves experience-dependent plasticity in sensory cortices. The cholinergic system is known to modulate declarative learning. In particular, reduced levels or efficacy of the neurotransmitter acetylcholine were found to facilitate declarative memory consolidation. However, little is known about the role of the cholinergic system in memory consolidation of non-declarative learning. Here we compared two groups of non-smoking men who learned a visual texture discrimination task (TDT). One group received chewing tobacco containing nicotine for 1 h directly following the TDT training. The other group received a similar tasting control substance without nicotine. Electroencephalographic recordings during substance consumption showed reduced alpha activity and P300 latencies in the nicotine group compared to the control group. When re-tested on the TDT the following day, both groups responded more accurately and more rapidly than during training. These improvements were specific to the retinal location and orientation of the texture elements of the TDT suggesting that learning involved early visual cortex. A group comparison showed that learning effects were more pronounced in the nicotine group than in the control group. These findings suggest that oral consumption of nicotine enhances the efficacy of nicotinic acetylcholine receptors. Our findings further suggest that enhanced efficacy of the cholinergic system facilitates memory consolidation in perceptual learning (and possibly other types of non-declarative learning). In that regard acetylcholine seems to affect consolidation processes in perceptual learning in a different manner than in declarative learning. Alternatively, our findings might reflect dose-dependent cholinergic modulation of memory consolidation. This article is part of a Special Issue entitled 'Cognitive Enhancers'. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Collaborative Curriculum Design to Increase Science Teaching Self-Efficacy: A Case Study

    NARCIS (Netherlands)

    Velthuis, C.H.; Fisser, Petra; Pieters, Julius Marie

    2015-01-01

    The purpose of this study was to establish whether participation in a teacher design team (TDT) is an effective way to increase the science teaching self-efficacy of primary school teachers who vary in their levels of experience and interest in science. A TDT is a group of at least 2 teachers from

  4. Demographic disequilibrium in living nautiloids (Nautilus and Allonautilus: Canary in the coal mines?

    Directory of Open Access Journals (Sweden)

    W Bruce Saunders

    Full Text Available Averaged demographic data from previously unfished populations of Nautilus and Allonautilus (Cephalopoda provide a baseline to determine if a population is undisturbed and in "equilibrium" or is in "disequilibrium" as a result of fishery pressure. Data are available for previously undisturbed local nautiloid populations in Papua New Guinea, Australia, Indonesia, Fiji, Palau, American Samoa, New Caledonia and Vanuatu (total n = 2,669 live-caught, tagged and released animals. The data show that unfished populations average ~75% males and ~74% mature animals. By contrast, unpublished, anecdotal and historical records since 1900 from the heavily fished central Philippines have shown a persistent decline in trap yields and a change in demographics of N. pompilius. By 1979, a sample of fished live-caught animals (n = 353 comprised only ~28% males and ~27% mature animals. Continued uncontrolled trapping caused collapse of the fishery and the shell industry has moved elsewhere, including Indonesia. In addition, we show that estimated rates of population decline are offered by unpublished tag-release records in unfished Palau. These data show that patterns of trap yields and demographic differences between fished and unfished populations in relative age class and sex ratios can indicate disequilibria wrought by fisheries pressure that can render local populations inviable. Given adequate samples (n ≥100 live-caught animals, a threshold of <50% males and mature animals in fished populations should signal the need to initiate curative conservation initiatives. The current trajectory of uncontrolled nautiloid fisheries can only mean trouble and possibly extinction of local populations of this ancient, iconic molluscan lineage.

  5. Magmatic evolution of a volcano studied by 230Th-238U disequilibrium and trace elements systematics: the Etna case

    International Nuclear Information System (INIS)

    Condomines, M.; Allegre, C.J.; Tanguy, J.C.; Kieffer, G.

    1982-01-01

    Age determinations of several lava flows from Etna through 230 Th- 238 U disequilibrium (internal isochrons) yield a precise chronology of the volcano's history for the last 200,000 years, and emphasize the main episodes in the formation of this huge complex strato-volcano. Study of ( 230 Th/ 232 Th) 0 initial ratios of lavas together with their trace-element compositions yields a consistent model of magmatic evolution implying the existence, for 200,000 years, of a deep reservoir of alkalic magma periodically mixed with magmas of tholeiitic affinity. These short periods of mixing appear to be related to the formation of the large calderas of Etna. In addition to these processes affecting the deep reservoir, fractional crystallization also occurred in more superficial levels of the volcanic edifice, thereby yielding several series of differentiation of relatively short duration. As for its geochemistry, Etna's volcanism is of oceanic type but with its own characteristics and in a peculiar geodynamic context, at the edge of the African Plate. (author)

  6. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Ganal Martin W

    2006-01-01

    Full Text Available Abstract Background The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles, Principal Coordinate Analysis (PCoA, and analysis of genome-wide linkage disequilibrium. Results A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i geographical regions and (ii agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD was estimated as squared correlation of allele frequencies (r2. The values of LD for barley were comparable to other plant species (conifers, poplar, maize. The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P 0.80 provided higher LD values as compared to 19 low polymorphic loci (PIC Conclusion A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing

  7. 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.

  8. Los nuevos canales de Televisión Digital Terrestre en España. Reconfiguración de la oferta televisiva en abierto dos años después del encendido digital

    Directory of Open Access Journals (Sweden)

    Costa Sánchez, Carmen

    2012-12-01

    Full Text Available En español: La evolución del medio televisivo en nuestro país ha tenido como última etapa el apagón analógico y el consecuente nacimiento de múltiples programas que nutren la oferta de la Televisión Digital. En el presente artículo se analiza la reconfiguración de la oferta de Televisión Digital Terrestre (TDT en España después de la aprobación del Real-Decreto 365/2010 para asignar los múltiples de la TDT una vez finalizadas las emisiones analógicas In english: The evolution of television in our country has had like last stage the analogue switch off and the birth of multiple programs that nourish the offer of the Digital Television. In the present article we analyze the reconfiguration of the offer of Terrestrial Digital Television (TDT in our country, after the approval of the Real-Decree 365/2010 to assign the multiple of the TDT once finalized the analog broadcasts.

  9. Mind the gap: temporal discrimination and dystonia.

    Science.gov (United States)

    Sadnicka, A; Daum, C; Cordivari, C; Bhatia, K P; Rothwell, J C; Manohar, S; Edwards, M J

    2017-06-01

    One of the most widely studied perceptual measures of sensory dysfunction in dystonia is the temporal discrimination threshold (TDT) (the shortest interval at which subjects can perceive that there are two stimuli rather than one). However the elevated thresholds described may be due to a number of potential mechanisms as current paradigms test not only temporal discrimination but also extraneous sensory and decision-making parameters. In this study two paradigms designed to better quantify temporal processing are presented and a decision-making model is used to assess the influence of decision strategy. 22 patients with cervical dystonia and 22 age-matched controls completed two tasks (i) temporal resolution (a randomized, automated version of existing TDT paradigms) and (ii) interval discrimination (rating the length of two consecutive intervals). In the temporal resolution task patients had delayed (P = 0.021) and more variable (P = 0.013) response times but equivalent discrimination thresholds. Modelling these effects suggested this was due to an increased perceptual decision boundary in dystonia with patients requiring greater evidence before committing to decisions (P = 0.020). Patient performance on the interval discrimination task was normal. Our work suggests that previously observed abnormalities in TDT may not be due to a selective sensory deficit of temporal processing as decision-making itself is abnormal in cervical dystonia. © 2017 EAN.

  10. Intravenous sedation for implant surgery: midazolam, butorphanol, and dexmedetomidine versus midazolam, butorphanol, and propofol.

    Science.gov (United States)

    Kawaai, Hiroyoshi; Tomita, Shu; Nakaike, Yoshihiro; Ganzberg, Steven; Yamazaki, Shinya

    2014-02-01

    We compared the amnesic action, recovery process, and satisfaction of patients and surgeons after the use of 2 different sedation regimens for 40 patients undergoing scheduled implant surgery. Butorphanol, midazolam, dexmedetomidine (BMD) was administered to 20 patients who were maintained with continuous infusion of dexmedetomidine after the induction with butorphanol and midazolam, and butorphanol, midazolam, propofol (BMP) was administered to 20 patients who were maintained with continuous infusion of propofol after the induction with butorphanol and midazolam. To assess the amnesic action, the memory of local anesthesia, auditory memory, and visual memory were evaluated. The Trieger Dot Test (TDT) was applied during the recovery process. A questionnaire regarding the patient's feelings of the management of sedation was taken from each patient and was also filled out by the surgeon. The comparison between groups was analyzed by the Mann-Whitney U test. No significant differences in the amnesic action and the TDT were noted. Both methods also satisfied the patients and surgeons, as determined by the questionnaire results. In conclusion, both sedation regimens are appropriate for implant surgery.

  11. A DRD1 haplotype is associated with risk for autism spectrum disorders in male-only affected sib-pair families.

    Science.gov (United States)

    Hettinger, Joe A; Liu, Xudong; Schwartz, Charles E; Michaelis, Ron C; Holden, Jeanette J A

    2008-07-05

    Individuals with autism spectrum disorders (ASDs) have impairments in executive function and social cognition, with males generally being more severely affected in these areas than females. Because the dopamine D1 receptor (encoded by DRD1) is integral to the neural circuitry mediating these processes, we examined the DRD1 gene for its role in susceptibility to ASDs by performing single marker and haplotype case-control comparisons, family-based association tests, and genotype-phenotype assessments (quantitative transmission disequilibrium tests: QTDT) using three DRD1 polymorphisms, rs265981C/T, rs4532A/G, and rs686T/C. Our previous findings suggested that the dopaminergic system may be more integrally involved in families with affected males only than in other families. We therefore restricted our study to families with two or more affected males (N = 112). There was over-transmission of rs265981-C and rs4532-A in these families (P = 0.040, P = 0.038), with haplotype TDT analysis showing over-transmission of the C-A-T haplotype (P = 0.022) from mothers to affected sons (P = 0.013). In addition, haplotype case-control comparisons revealed an increase of this putative risk haplotype in affected individuals relative to a comparison group (P = 0.004). QTDT analyses showed associations of the rs265981-C, rs4532-A, rs686-T alleles, and the C-A-T haplotype with more severe problems in social interaction, greater difficulties with nonverbal communication and increased stereotypies compared to individuals with other haplotypes. Preferential haplotype transmission of markers at the DRD1 locus and an increased frequency of a specific haplotype support the DRD1 gene as a risk gene for core symptoms of ASD in families having only affected males. Copyright 2008 Wiley-Liss, Inc.

  12. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers.

    Science.gov (United States)

    Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

    2011-02-18

    Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (Pvarieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 ∼ 25 cM) compared to landraces (<5 ∼ 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.

  13. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  14. Sup(210)Pb and 210Po distributions and disequilibrium in the coastal and shelf waters of the southern North Sea

    International Nuclear Information System (INIS)

    Zhizheng, Zuo; Eisma, Doeke

    1993-01-01

    Concentration profiles of 210 Pb and 210 Po were measured at 10 stations in the coastal and shelf areas of the southern North Sea. Scavenging processes in this study area are revealed by 210 Po/ 210 Pb disequilibrium and their distributions in the water column. Results for 210 Po show strong excess, relative to 210 Pb, in both dissolved and particulate forms, indicating an additional flux of 210 Po from the coastal and shelf sediment. A significant maximum of the dissolved 210 Po and 210 Pb over the fine grained depositional area (Oyster Ground) was observed to correspond with resuspension of the underlying muddy sediments. A comparison of the data between the water and sediment columns shows that the excess of 210 Po found in the water body could be balanced by only a small amount of deficit of 210 Po in the sediment, due to the characteristics of this continental shelf area. (author)

  15. Collaborative Curriculum Design to Increase Science Teaching Self-Efficacy: A Case Study

    Science.gov (United States)

    Velthuis, Chantal; Fisser, Petra; Pieters, Jules

    2015-01-01

    The purpose of this study was to establish whether participation in a teacher design team (TDT) is an effective way to increase the science teaching self-efficacy of primary school teachers who vary in their levels of experience and interest in science. A TDT is a group of at least 2 teachers from the same or related subjects working together to…

  16. Measuring demand for flat water recreation using a two-stage/disequilibrium travel cost model with adjustment for overdispersion and self-selection

    Science.gov (United States)

    McKean, John R.; Johnson, Donn; Taylor, R. Garth

    2003-04-01

    An alternate travel cost model is applied to an on-site sample to estimate the value of flat water recreation on the impounded lower Snake River. Four contiguous reservoirs would be eliminated if the dams are breached to protect endangered Pacific salmon and steelhead trout. The empirical method applies truncated negative binomial regression with adjustment for endogenous stratification. The two-stage decision model assumes that recreationists allocate their time among work and leisure prior to deciding among consumer goods. The allocation of time and money among goods in the second stage is conditional on the predetermined work time and income. The second stage is a disequilibrium labor market which also applies if employers set work hours or if recreationists are not in the labor force. When work time is either predetermined, fixed by contract, or nonexistent, recreationists must consider separate prices and budgets for time and money.

  17. Association of a functional 17beta-estradiol sensitive IL6-174G/C promoter polymorphism with early-onset type 1 diabetes in females

    DEFF Research Database (Denmark)

    Kristiansen, Ole P; Nolsøe, Runa L; Larsen, Lykke

    2003-01-01

    The type 1 diabetes mellitus (T1DM) candidate gene SNP IL6-174G/C was genotyped in 253 Danish T1DM families (1129 individuals). TDT analysis demonstrated linkage in the presence of association between the IL6-174C allele and T1DM in the 416 T1DM offspring, P(tdt)=0.04. Gender conditioned TDT......DM versus non-T1DM females) excluded preferential meiotic segregation in females, P=4.6 x 10(-3), and demonstrated differences in the transmission patterns between female and male T1DM offspring, P=5.1 x 10(-3). The IL6-174 CC genotype was associated with younger age at onset of T1DM in females (P=0...

  18. Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

    Science.gov (United States)

    Vitart, Veronique; Carothers, Andrew D; Hayward, Caroline; Teague, Peter; Hastie, Nicholas D; Campbell, Harry; Wright, Alan F

    2005-05-01

    Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

  19. Linkage disequilibrium with HLA-DRB1-DQB1 haplotypes explains the association of TNF-308G>A variant with type 1 diabetes in a Brazilian cohort.

    Science.gov (United States)

    Patente, Thiago A; Monteiro, Maria B; Vieira, Suzana M; Rossi da Silva, Maria E; Nery, Márcia; Queiroz, Márcia; Azevedo, Mirela J; Canani, Luis H; Parisi, Maria C; Pavin, Elizabeth J; Mainardi, Débora; Javor, Juraj; Velho, Gilberto; Coimbra, Cássio N; Corrêa-Giannella, Maria Lúcia

    2015-08-15

    A functional variant in the promoter region of the gene encoding tumor necrosis factor (TNF; rs1800629, -308G>A) showed to confer susceptibility to T1D. However, TNF rs1800629 was found, in several populations, to be in linkage disequilibrium with HLA susceptibility haplotypes to T1D. We evaluated the association of TNF rs1800629 with T1D in a cohort of Brazilian subjects, and assessed the impact of HLA susceptibility haplotypes in this association. 659 subjects with T1D and 539 control subjects were genotyped for TNF-308G>A variant. HLA-DRB1 and HLA-DQB1 genes were genotyped in a subset of 313 subjects with T1D and 139 control subjects. Associations with T1D were observed for the A-allele of rs1800629 (OR 1.69, 95% CI 1.33-2.15, p<0.0001, in a codominant model) and for 3 HLA haplotypes: DRB1*03:01-DQB1*02:01 (OR 5.37, 95% CI 3.23-8.59, p<0.0001), DRB1*04:01-DQB1*03:02 (OR 2.95, 95% CI 1.21-7.21, p=0.01) and DRB1*04:02-DQB1*03:02 (OR 2.14, 95% CI 1.02-4.50, p=0.04). Linkage disequilibrium was observed between TNF rs1800629 and HLA-DRB1 and HLA-DQB1 alleles. In a stepwise regression analysis HLA haplotypes, but not TNF rs1800629, remained independently associated with T1D. Our results do not support an independent effect of allelic variations of TNF in the genetic susceptibility to T1D. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Two types of adakites revealed by 238U-230Th disequilibrium from Daisen volcano, southwestern Japan

    International Nuclear Information System (INIS)

    Tokunaga, Saimi; Nakai, Shun'ichi; Orihashi, Yuji

    2010-01-01

    Daisen volcano is located on the Quaternary volcanic front in southwestern Japan. The volcano is composed mainly of andesite and dacite, which chemically resemble adakites, with high Al 2 O 3 and Sr/Y, steep REE patterns, and no negative Eu anomaly. ( 238 U/ 230 Th) disequilibrium (herein, a ratio in parentheses denotes the activity ratio) and trace element analyses of adakites from two volcanic domes, Karasugasen and Misen, indicate two adakite types. Adakite from Karasugasen is characterized by excess ( 230 Th) over ( 238 U), typical of most adakites, whereas adakite from Misen is characterized by excess ( 238 U) over ( 230 Th). The latter is consistent with enrichment in fluid-mobile elements relative to fluid immobile elements compared to rocks from Karasugasen. The values of ( 230 Th/ 232 Th) of adakites from Karasugasen and Misen are, respectively, around 0.75 and 0.81. These low ( 230 Th/ 232 Th) ratios result from the incorporation of subducted sedimentary material. The ratios, nevertheless, are higher than that for the estimate of lower crustal material suggesting significant incorporation of lower crust is unlikely. As adakites from Misen have ( 238 U) excess over ( 230 Th), adakite magma must have interacted with wedge mantle metasomatized by a slab-derived fluid, confirming the presence of a fluid-metasomatized mantle beneath Daisen volcano. (author)

  1. Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

    Directory of Open Access Journals (Sweden)

    Shanmugapriya Arumugasundaram

    Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

  2. Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road.

    Science.gov (United States)

    Branscomb, Elbert; Russell, Michael J

    2013-02-01

    The Submarine Hydrothermal Alkaline Spring Theory for the emergence of life holds that it is the ordered delivery of hydrogen and methane in alkaline hydrothermal solutions at a spontaneously precipitated inorganic osmotic and catalytic membrane to the carbon dioxide and other electron acceptors in the earliest acidulous cool ocean that, through these gradients, drove life into being. That such interactions between hydrothermal fuels and potential oxidants have so far not been accomplished in the lab is because some steps along the necessary metabolic pathways are endergonic and must therefore be driven by being coupled to thermodynamically larger exergonic processes. But coupling of this kind is far from automatic and it is not enough to merely sum the ΔGs of two supposedly coupled reactions and show their combined thermodynamic viability. An exergonic reaction will not drive an endergonic one unless 'forced' to do so by being tied to it mechanistically via an organized "engine" of "Free Energy Conversion" (FEC). Here we discuss the thermodynamics of FEC and advance proposals regarding the nature and roles of the FEC devices that could, in principle, have arisen spontaneously in the alkaline hydrothermal context and have forced the onset of a protometabolism. The key challenge is to divine what these initial engines of life were in physicochemical terms and as part of that, what structures provided the first "turnstile-like" mechanisms needed to couple the partner processes in free energy conversion; in particular to couple the dissipation of geochemically given gradients to, say, the reduction of CO(2) to formate and the generation of a pyrophosphate disequilibrium. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Evaluation of high-energy brachytherapy source electronic disequilibrium and dose from emitted electrons.

    Science.gov (United States)

    Ballester, Facundo; Granero, Domingo; Pérez-Calatayud, José; Melhus, Christopher S; Rivard, Mark J

    2009-09-01

    The region of electronic disequilibrium near photon-emitting brachytherapy sources of high-energy radionuclides (60Co, 137CS, 192Ir, and 169Yb) and contributions to total dose from emitted electrons were studied using the GEANT4 and PENELOPE Monte Carlo codes. Hypothetical sources with active and capsule materials mimicking those of actual sources but with spherical shape were examined. Dose contributions due to source photons, x rays, and bremsstrahlung; source beta-, Auger electrons, and internal conversion electrons; and water collisional kerma were scored. To determine if conclusions obtained for electronic equilibrium conditions and electron dose contribution to total dose for the representative spherical sources could be applied to actual sources, the 192Ir mHDR-v2 source model (Nucletron B.V., Veenendaal, The Netherlands) was simulated for comparison to spherical source results and to published data. Electronic equilibrium within 1% is reached for 60Co, 137CS, 192Ir, and 169Yb at distances greater than 7, 3.5, 2, and 1 mm from the source center, respectively, in agreement with other published studies. At 1 mm from the source center, the electron contributions to total dose are 1.9% and 9.4% for 60Co and 192Ir, respectively. Electron emissions become important (i.e., > 0.5%) within 3.3 mm of 60Co and 1.7 mm of 192Ir sources, yet are negligible over all distances for 137Cs and 169Yb. Electronic equilibrium conditions along the transversal source axis for the mHDR-v2 source are comparable to those of the spherical sources while electron dose to total dose contribution are quite different. Electronic equilibrium conditions obtained for spherical sources could be generalized to actual sources while electron contribution to total dose depends strongly on source dimensions, material composition, and electron spectra.

  4. Disequilibrium dihedral angles in layered intrusions: the microstructural record of fractionation

    Science.gov (United States)

    Holness, Marian; Namur, Olivier; Cawthorn, Grant

    2013-04-01

    The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only rarely in textural equilibrium in gabbros from km-scale crustal layered intrusions. The median of a population of these disequilibrium angles, Θcpp, varies systematically within individual layered intrusions, remaining constant over large stretches of stratigraphy with significant increases or decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The step-wise changes in Θcpp are present in Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard Intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of Θcpp, dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the step-wise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the interstitial liquid inferred to be present in the crystal mush. Step-wise changes in the rate of change in enthalpy with temperature (ΔH) of the cooling and crystallizing magma correspond to the observed variation of Θcpp, with increases of both ΔH and Θcpp associated with the addition of another liquidus phase, and decreases of both associated with the removal of a liquidus phase. The replacement of one phase by another (e.g. olivine ⇔ orthpyroxene) has little effect on ΔH and no discernible effect on Θcpp. An increase of ΔH is manifest by an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also results in an increase in the amount crystallized in each incremental temperature drop (the crystal productivity). An increased fractional latent heat and crystal productivity result in an increased rate of plagioclase growth compared to that of augite during the final stages of solidification

  5. Creación de contenidos interactivos de deporte para televisión digital terrestre en Ecuador

    Directory of Open Access Journals (Sweden)

    Abel Suing

    2016-08-01

    Full Text Available Ecuador, al igual que otros países latinoamericanos, implementa el sistema ISDB-T para Televisión Digital Terrestre (TDT que permite la emisión de interactividad a través del middleware Ginga. La TDT puede implicar un cambio en la calidad de los contenidos pero sobre todo una oportunidad de acceso a la sociedad del conocimiento. La investigación describe una dinámica de trabajo y la integración de equipos multidisciplinarios en la producción de dos programas de deportes “Aventura-T”, empleando metodología cualitativa, los instrumentos usados son observación, entrevistas semiestructuradas y grupos focales. Se concluye que las aplicaciones en Ginga NCL generadas cumplen con estándares de calidad para emisiones de TDT.

  6. Striatal FP-CIT uptake differs in the subtypes of early Parkinson's disease

    International Nuclear Information System (INIS)

    Spiegel, J.; Fassbender, K.; Dillmann, U.; Hellwig, D.; Samnick, S.; Moellers, M.-O.; Kirsch, C.-M.; Jost, W.

    2007-01-01

    In idiopathic Parkinson's disease (PD), a tremor-dominant type (TDT), an akinetic-rigid type (ART), and a mixed type (MT) are distinguished. We compared cerebral [I- 123 ]FP-CIT SPECT in the PD subtypes (67 patients Hoehn and Yahr stage 1:26 with ART, 19 with MT, 22 with TDT). We measured the ratios putamen/occipital lobe binding and caudate nucleus/occipital lobe binding. Parkinsonian motor symptoms were quantified by UPDRS motor scale. In both putamen and caudate nucleus contralateral to the clinically affected body side TDT patients showed a significantly higher FP-CIT uptake than ART or MT patients (ANOVA; p 0.05). The missing correlation between striatal FP-CIT uptake and tremor suggests, that further systems besides the nigrostriatal dopaminergic system may contribute to generation of parkinsonian tremor. (author)

  7. A study of uranium series disequilibrium in core profiles and mineral separates from the samples of Lac du Bonnet granite from the URL site, Pinawa, Manitoba, Canada

    International Nuclear Information System (INIS)

    Ivanovich, M.; Longworth, G.; Wilkins, M.A.; Hasler, S.E.

    1987-12-01

    Uranium series disequilibrium measurements of actinide activities and activity ratios have been used to study the geochemical history of Lac du Bonnet granite, from the URL site, Pinawa, Canada. Measurements on core profiles between fractured surfaces and the parent rock show that the granite underwent high temperature events several million years ago, followed by more recent low temperature events within the last million years. The main locations for the rock/water interaction and exchange of actinides are the fracture surfaces. The results of similar measurements on separated mineral phases show that the 'soft' minerals such as biotite and feldspar are more vulnerable to weathering than the 'hard' accessory minerals such as zircon. (author)

  8. Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges.

    Science.gov (United States)

    Jensen, Michael A; Davis, Ronald W

    2018-03-27

    There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single-stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template-free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis.

  9. Development of response transforms from comparative study of commercial pulsed neutron capture logging systems

    International Nuclear Information System (INIS)

    Salaita, G.N.; Youngblood, W.E.

    1991-01-01

    This paper reports that the absence of a common calibration facility to ascertain the accuracy of commercial pulsed neutron capture logging systems, coupled with the desire for more accurate saturation determination from time-lapse logs, prompted Saudi Aramco to carry out this comparative study. Three generations of Schlumberger's Thermal Decay Time (TDT) logging devices, viz., TDT-K, TDT-M, and TDT-P along with Atlas Wireline PDK-100 system were run in an Aramco well. The wellbore 8-1/2 inch with 7-inch casing-penetrated clean sand, shaly sand, and shale streaks sequence as exhibited by the open hole natural gamma ray log. initially, the wellbore fluid was diesel. The fluid was then changed to brines of 42-kppm and 176-kppm NACl, respectively. Three repeat passes at a logging speed of 900 ft/hr were obtained by each device for each of the three borehole liquids. In the case of PDK-100, a second set of log runs was obtained at 1800 ft/hr. The results of this extensive comparative study have increased the author's understanding of the borehole liquid and the diffusion effects on the response of pulsed neutron capture logging systems and also on the relative accuracy and precision of measured formation thermal neutron capture cross section by each system

  10. Complications of Transfusion-Dependent β-Thalassemia Patients in Sistan and Baluchistan, South-East of Iran

    Science.gov (United States)

    Yaghobi, Maryam; Miri-Moghaddam, Ebrahim; Majid, Naderi; Bazi, Ali; Navidian, Ali; Kalkali, Asiyeh

    2017-01-01

    Background: Thalassemia syndromes are among prevalent hereditary disorders imposing high expenses on health-care system worldwide and in Iran. Organ failure represents a life-threatening challenge in transfusion- dependent β-thalassemia (TDT) patients. The purpose of the present study was to determine the frequency of organ dysfunctions among TDT patients in Sistan and Baluchistan province in South-East of Iran. Materials and Methods: Laboratory and clinical data were extracted from medical records as well as by interviews. Standard criteria were applied to recognize cardiac, gonadal, endocrine and renal dysfunctions. The collected data were analyzed using the SPSS statistics software (Ver.19). Results: A total of 613 TDT patients (54.3% males and 45.7% females) were included in this study. The mean age of patients was 13.3 ±7.7 years old. Cardiac events comprised the most encountered complications (76.4%), following by hypogonadism (46.8%), parathyroid dysfunction (22%), thyroid abnormalities (8.3%), diabetes (7.8%) and renal disease (1.8%). Hypogonadism comprised the most identified complication in patient 15 years old (P<0.01). Conclusion: As cardiac events are significantly more common among TDT patients, close monitoring of the heart function is recommended for identifying patients with cardiac problems. PMID:29340121

  11. The new Digital Television channels in Spain. The changes of the free TV offer two years after the switch on

    Directory of Open Access Journals (Sweden)

    José Juan VIDELA RODRÍGUEZ

    2014-10-01

    Full Text Available The evolution of television in our country has had like last stage the analogue switch off and the birth of multiple programs that nourish the offer of the Digital Television. In the present article we analyze the reconfiguration of the offer of Terrestrial Digital Television (TDT in our country, after the approval of the Real-Decree 365/2010 to assign the multiple of the TDT once finalized the analog broadcasts.

  12. Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

    Science.gov (United States)

    Song, Bao-Hua; Windsor, Aaron J.; Schmid, Karl J.; Ramos-Onsins, Sebastian; Schranz, M. Eric; Heidel, Andrew J.; Mitchell-Olds, Thomas

    2009-01-01

    Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ∼45% higher recombination per kilobase than outcrossing A. lyrata. PMID:19104077

  13. Linkage disequilibrium analysis in young populations: Pseudo-vitamin D-deficiency rickets and the founder effect in French Canadians

    Energy Technology Data Exchange (ETDEWEB)

    Labuda, M.; Glorieux, F.H. [McGill Univ., Montreal (Canada); Labuda, D.; Korab-Laskowska, M. [Universite de Montreal (Canada)] [and others

    1996-09-01

    Pseudo-vitamin D-deficiency rickets (PDDR) was mapped close to D12S90 and between proximal D12S312 and distal (D12S305, D12S104) microsatellites that were subsequently found on a single YAC clone. Analysis of a complex haplotype in linkage disequilibrium (LD) with the disease discriminated among distinct founder effects in French Canadian populations in Acadia and in Charlevoix-Saguenay-Lac-Saint-Jean (Ch-SLSJ), as well as an earlier one in precolonial Europe. A simple demographic model suggested the historical age of the founder effect in Ch-SLSJ to be {approximately}12 generations. The corresponding LD data are consistent with this figure when they are analyzed within the framework of Luria-Delbruck model, which takes into account the population growth. Population sampling due to a limited number of first settlers and the rapid demographic expansion appear to have played a major role in the founding of PDDR in Ch-SLSJ and, presumably, other genetic disorders endemic to French Canada. Similarly, the founder effect in Ashkenazim, coinciding with their early settlement in medieval Poland and subsequent expansion eastward, could explain the origin of frequent genetic diseases in this population. 48 refs., 5 figs., 2 tabs.

  14. The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

    Science.gov (United States)

    Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

    2012-01-01

    The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

  15. 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.

  16. Correction for ‘artificial’ electron disequilibrium due to cone-beam CT density errors: implications for on-line adaptive stereotactic body radiation therapy of lung

    International Nuclear Information System (INIS)

    Disher, Brandon; Hajdok, George; Craig, Jeff; Gaede, Stewart; Battista, Jerry J; Wang, An

    2013-01-01

    Cone-beam computed tomography (CBCT) has rapidly become a clinically useful imaging modality for image-guided radiation therapy. Unfortunately, CBCT images of the thorax are susceptible to artefacts due to scattered photons, beam hardening, lag in data acquisition, and respiratory motion during a slow scan. These limitations cause dose errors when CBCT image data are used directly in dose computations for on-line, dose adaptive radiation therapy (DART). The purpose of this work is to assess the magnitude of errors in CBCT numbers (HU), and determine the resultant effects on derived tissue density and computed dose accuracy for stereotactic body radiation therapy (SBRT) of lung cancer. Planning CT (PCT) images of three lung patients were acquired using a Philips multi-slice helical CT simulator, while CBCT images were obtained with a Varian On-Board Imaging system. To account for erroneous CBCT data, three practical correction techniques were tested: (1) conversion of CBCT numbers to electron density using phantoms, (2) replacement of individual CBCT pixel values with bulk CT numbers, averaged from PCT images for tissue regions, and (3) limited replacement of CBCT lung pixels values (LCT) likely to produce artificial lateral electron disequilibrium. For each corrected CBCT data set, lung SBRT dose distributions were computed for a 6 MV volume modulated arc therapy (VMAT) technique within the Philips Pinnacle treatment planning system. The reference prescription dose was set such that 95% of the planning target volume (PTV) received at least 54 Gy (i.e. D95). Further, we used the relative depth dose factor as an a priori index to predict the effects of incorrect low tissue density on computed lung dose in regions of severe electron disequilibrium. CT number profiles from co-registered CBCT and PCT patient lung images revealed many reduced lung pixel values in CBCT data, with some pixels corresponding to vacuum (−1000 HU). Similarly, CBCT data in a plastic lung

  17. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

    Directory of Open Access Journals (Sweden)

    Hasan Alhaddad

    Full Text Available Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2 was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

  18. Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

    Directory of Open Access Journals (Sweden)

    Yang Ming

    2012-07-01

    Full Text Available Abstract Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have

  19. Akkumulation von L-Malat und D-Lactat in Arabidopsis thaliana und Laccase/HBT-vermittelte Delignifizierung von Spartina alterniflora und Phragmites australis

    OpenAIRE

    Heil, Alexander

    2016-01-01

    The current work contains two projects "Accumulation of L-malate and D-lactate in Arabidopsis thaliana" (A) "Laccase/HBT mediated delignification of Spartina alterniflora and Phragmites australis" (B). In project A, L-malate and D-lactate accumulated in A. thaliana plants. The accumulation of L-malate is carried out by modification of the plant metabolism with the enzymes PEPC, MDH and the tonoplast dicarboxylate transporter (TDT). Gene pepci2 (Hydrilla verticillata), mdh5 (Zea mays) and tdt ...

  20. Identification and Functional Characterization of a Tonoplast Dicarboxylate Transporter in Tomato (Solanum lycopersicum)

    OpenAIRE

    Liu, Ruiling; Li, Boqiang; Qin, Guozheng; Zhang, Zhanquan; Tian, Shiping

    2017-01-01

    Acidity plays an important role in flavor and overall organoleptic quality of fruit and is mainly due to the presence of organic acids. Understanding the molecular basis of organic acid metabolism is thus of primary importance for fruit quality improvement. Here, we cloned a putative tonoplast dicarboxylate transporter gene (SlTDT) from tomato, and submitted it to the NCBI database (GenBank accession number: KC733165). SlTDT protein contained 13 putative transmembrane domains in silico analys...

  1. A G protein-coupled receptor (GPCR) in red: live cell imaging of the kappa opioid receptor-tdTomato fusion protein (KOPR-tdT) in neuronal cells

    Science.gov (United States)

    Huang, Peng; Chiu, Yi-Ting; Chen, Chongguang; Wang, Yujun; Liu-Chen, Lee-Yuan

    2013-01-01

    Introduction In contrast to green fluorescent protein and variants (GFPs), red fluorescent proteins (RFPs) have rarely been employed for generation of GPCR fusion proteins, likely because of formation of aggregates and cell toxicity of some RFPs. Among all the RFPs available, tdTomato (tdT), one of the non-aggregating RFP, has the highest brightness score (about 3 times that of eGFP) and unsurpassed photostability. Methods We fused tdT to the KOPR C-terminus. The KOPR-tdT cDNA construct was transfected into Neuro2A mouse neuroblastoma cell line (Neuro2A cells) and rat cortical primary neurons for characterization of pharmacological properties and imaging studies on KOPR trafficking. Results KOPR-tdT retained KOPR properties (cell surface expression, ligand binding, agonist-induced signaling and internalization) when expressed in Neuro2A cells and rat primary cortical neurons. Live cell imaging of KOPR-tdT enables visualization of time course of agonist-induced internalization of KOPR in real time for 60 min, without photobleaching and apparent cell toxicity. U50,488H-induced KOPR internalization occurred as early as 4 min and plateaued at about 30 min. A unique pattern of internalized KOPR in processes of primary neurons was induced by U50,488H. Discussion tdT is an alternative to, or even a better tool than, GFPs for fusing to GPCR for trafficking studies, because tdT has higher brightness and thus better resolution and less photobleaching problems due to reduced laser power used. It also has advantages associated with its longer-wavelength emission including spectral separation from autofluorescence and GFPs, reduced cell toxicity the laser may impose, and greater tissue penetration. These advantages of tdT over GPFs may be critical for live cell imaging studies of GPCRs in vitro and for studying GPCRs in vivo because of their low abundance. PMID:23856011

  2. Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22

    Directory of Open Access Journals (Sweden)

    González-Neira Anna

    2004-11-01

    Full Text Available Abstract Recent studies of haplotype diversity in a number of genomic regions have suggested that long stretches of DNA are preserved in the same chromosome, with little evidence of recombination events. The knowledge of the extent and strength of these haplotypes could become a powerful tool for future genetic analysis of complex traits. Different patterns of linkage disequilibrium (LD have been found when comparing individuals of African and European descent, but there is scarce knowledge about the worldwide population stratification. Thus, the study of haplotype composition and the pattern of LD from a global perspective are relevant for elucidating their geographical stratification, as it may have implications in the future analysis of complex traits. We have typed 12 single nucleotide polymorphisms in a chromosome 22 region--previously described as having high LD levels in European populations -- in 39 different world populations. Haplotype structure has a clear continental structure with marked heterogeneity within some continents (Africa, America. The pattern of LD among neighbouring markers exhibits a strong clustering of all East Asian populations on the one hand and of Western Eurasian populations (including Europe on the other, revealing only two major LD patterns, but with some very specific outliers due to specific demographic histories. Moreover, it should be taken into account that African populations are highly heterogeneous. The present results support the existence of a wide (but not total communality in LD patterns in human populations from different continental regions, despite differences in their demographic histories, as population factors seem to be less relevant compared with genomic forces in shaping the patterns of LD.

  3. Impaired Malate and Fumarate Accumulation Due to the Mutation of the Tonoplast Dicarboxylate Transporter Has Little Effects on Stomatal Behavior.

    Science.gov (United States)

    Medeiros, David B; Barros, Kallyne A; Barros, Jessica Aline S; Omena-Garcia, Rebeca P; Arrivault, Stéphanie; Sanglard, Lílian M V P; Detmann, Kelly C; Silva, Willian Batista; Daloso, Danilo M; DaMatta, Fábio M; Nunes-Nesi, Adriano; Fernie, Alisdair R; Araújo, Wagner L

    2017-11-01

    Malate is a central metabolite involved in a multiplicity of plant metabolic pathways, being associated with mitochondrial metabolism and playing significant roles in stomatal movements. Vacuolar malate transport has been characterized at the molecular level and is performed by at least one carrier protein and two channels in Arabidopsis ( Arabidopsis thaliana ) vacuoles. The absence of the Arabidopsis tonoplast Dicarboxylate Transporter (tDT) in the tdt knockout mutant was associated previously with an impaired accumulation of malate and fumarate in leaves. Here, we investigated the consequences of this lower accumulation on stomatal behavior and photosynthetic capacity as well as its putative metabolic impacts. Neither the stomatal conductance nor the kinetic responses to dark, light, or high CO 2 were highly affected in tdt plants. In addition, we did not observe any impact on stomatal aperture following incubation with abscisic acid, malate, or citrate. Furthermore, an effect on photosynthetic capacity was not observed in the mutant lines. However, leaf mitochondrial metabolism was affected in the tdt plants. Levels of the intermediates of the tricarboxylic acid cycle were altered, and increases in both light and dark respiration were observed. We conclude that manipulation of the tonoplastic organic acid transporter impacted mitochondrial metabolism, while the overall stomatal and photosynthetic capacity were unaffected. © 2017 American Society of Plant Biologists. All Rights Reserved.

  4. Sexual antagonism and meiotic drive cause stable linkage disequilibrium and favour reduced recombination on the X chromosome.

    Science.gov (United States)

    Rydzewski, W T; Carioscia, S A; Liévano, G; Lynch, V D; Patten, M M

    2016-06-01

    Sexual antagonism and meiotic drive are sex-specific evolutionary forces with the potential to shape genomic architecture. Previous theory has found that pairing two sexually antagonistic loci or combining sexual antagonism with meiotic drive at linked autosomal loci augments genetic variation, produces stable linkage disequilibrium (LD) and favours reduced recombination. However, the influence of these two forces has not been examined on the X chromosome, which is thought to be enriched for sexual antagonism and meiotic drive. We investigate the evolution of the X chromosome under both sexual antagonism and meiotic drive with two models: in one, both loci experience sexual antagonism; in the other, we pair a meiotic drive locus with a sexually antagonistic locus. We find that LD arises between the two loci in both models, even when the two loci freely recombine in females and that driving haplotypes will be enriched for male-beneficial alleles, further skewing sex ratios in these populations. We introduce a new measure of LD, Dz', which accounts for population allele frequencies and is appropriate for instances where these are sex specific. Both models demonstrate that natural selection favours modifiers that reduce the recombination rate. These results inform observed patterns of congealment found on driving X chromosomes and have implications for patterns of natural variation and the evolution of recombination rates on the X chromosome. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  5. Affected sib pair tests in inbred populations.

    Science.gov (United States)

    Liu, W; Weir, B S

    2004-11-01

    The affected-sib-pair (ASP) method for detecting linkage between a disease locus and marker loci was first established 50 years ago, and since then numerous modifications have been made. We modify two identity-by-state (IBS) test statistics of Lange (Lange, 1986a, 1986b) to allow for inbreeding in the population. We evaluate the power and false positive rates of the modified tests under three disease models, using simulated data. Before estimating false positive rates, we demonstrate that IBS tests are tests of both linkage and linkage disequilibrium between marker and disease loci. Therefore, the null hypothesis of IBS tests should be no linkage and no LD. When the population inbreeding coefficient is large, the false positive rates of Lange's tests become much larger than the nominal value, while those of our modified tests remain close to the nominal value. To estimate power with a controlled false positive rate, we choose the cutoff values based on simulated datasets under the null hypothesis, so that both Lange's tests and the modified tests generate same false positive rate. The powers of Lange's z-test and our modified z-test are very close and do not change much with increasing inbreeding. The power of the modified chi-square test also stays stable when the inbreeding coefficient increases. However, the power of Lange's chi-square test increases with increasing inbreeding, and is larger than that of our modified chi-square test for large inbreeding coefficients. The power is high under a recessive disease model for both Lange's tests and the modified tests, though the power is low for additive and dominant disease models. Allowing for inbreeding is therefore appropriate, at least for diseases known to be recessive.

  6. Genetic polymorphisms and asthma: findings from a case-control study in the Madeira island population.

    Science.gov (United States)

    Berenguer, Anabela Gonçalves; Fernandes, Ana Teresa; Oliveira, Susana; Rodrigues, Mariana; Ornelas, Pedro; Romeira, Diogo; Serrão, Tânia; Rosa, Alexandra; Câmara, Rita

    2014-09-04

    Asthma is a complex disease influenced by multiple genetic and environmental factors. While Madeira has the highest prevalence of asthma in Portugal (14.6%), the effect of both genetic and environmental factors in this population has never been assessed. We categorized 98 asthma patients according to the Global Initiative for Asthma (GINA) guidelines, established their sensitization profile, and measured their forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) indexes. Selected single nucleotide polymorphisms (SNPs) were analysed as potential markers for asthma susceptibility and severity in the interleukin 4 (IL4), interleukin 13 (IL13), beta-2-adrenergic receptor (ADRB2), a disintegrin and metalloprotease 33 (ADAM33), gasdermin-like (GSDML) and the signal transducer and activator of transcription 6 (STAT6) genes comparatively to a population reference set. Although mites are the major source of allergic sensitization, no significant difference was found amongst asthma severity categories. IL4-590*CT/TT and IL4-RP2*253183/183183 were found to predict the risk (2-fold) and severity (3 to 4-fold) of asthma and were associated with a lower FEV1 index. ADRB2-c.16*AG is a risk factor (3.5-fold), while genotype GSDML-236*TT was protective (4-fold) for moderate-severe asthma. ADAM33-V4*C was associated to asthma and mild asthma by the transmission disequilibrium test (TDT). Finally, ADAM33-V4*CC and STAT6-21*TT were associated with higher sensitization (mean wheal size ≥10 mm) to house dust (1.4-fold) and storage mite (7.8-fold). In Madeira, IL4-590C/T, IL4-RP2 253/183, GSDML-236C/T and ADAM33-V4C/G SNPs are important risk factors for asthma susceptibility and severity, with implications for asthma healthcare management.

  7. Extent of linkage disequilibrium and effective population size in four South African Sanga cattle breeds

    Directory of Open Access Journals (Sweden)

    Sithembile Olga Makina

    2015-12-01

    Full Text Available Knowledge on the extent of linkage disequilibrium (LD in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies. This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne for four Sanga cattle breeds in South Africa including the Afrikaner (n=44, Nguni (n=54, Drakensberger (n=47 and Bonsmara breeds (n=46, using Angus (n=31 and Holstein (n=29 as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21 and Holstein (0.21 and up to 100 kb in Afrikaner (0.20. This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2 ≥ 0.20 would require about 30,000 -50,000 SNPs. However, r2 ≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for genome-wide association studies in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne=95 (Nguni, Ne=87 (Drakensberger, Ne=77 (Bonsmara and Ne=41 (Afrikaner. Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

  8. Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

    Science.gov (United States)

    Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

    2009-02-01

    The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.

  9. A versatile omnibus test for detecting mean and variance heterogeneity.

    Science.gov (United States)

    Cao, Ying; Wei, Peng; Bailey, Matthew; Kauwe, John S K; Maxwell, Taylor J

    2014-01-01

    Recent research has revealed loci that display variance heterogeneity through various means such as biological disruption, linkage disequilibrium (LD), gene-by-gene (G × G), or gene-by-environment interaction. We propose a versatile likelihood ratio test that allows joint testing for mean and variance heterogeneity (LRT(MV)) or either effect alone (LRT(M) or LRT(V)) in the presence of covariates. Using extensive simulations for our method and others, we found that all parametric tests were sensitive to nonnormality regardless of any trait transformations. Coupling our test with the parametric bootstrap solves this issue. Using simulations and empirical data from a known mean-only functional variant, we demonstrate how LD can produce variance-heterogeneity loci (vQTL) in a predictable fashion based on differential allele frequencies, high D', and relatively low r² values. We propose that a joint test for mean and variance heterogeneity is more powerful than a variance-only test for detecting vQTL. This takes advantage of loci that also have mean effects without sacrificing much power to detect variance only effects. We discuss using vQTL as an approach to detect G × G interactions and also how vQTL are related to relationship loci, and how both can create prior hypothesis for each other and reveal the relationships between traits and possibly between components of a composite trait.

  10. Further Delineation of the Clinical Phenotype of Cerebellar Ataxia, Mental Retardation, and Disequilibrium Syndrome Type 4

    Directory of Open Access Journals (Sweden)

    Saud Alsahli

    2018-02-01

    Full Text Available Background: Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ is a heterogeneous group of genetic disorders that have been grouped by shared clinical features; all of these features are transmitted via an autosomal recessive mechanism. Four variants of this syndrome have been identified so far, and each one differs in terms of both clinical and genotypical features. CAMRQ4 is a rare genetic disorder characterized by mental retardation, ataxia or an inability to walk, dysarthria and, in some patients, quadrupedal gait. Methods: We investigated three Saudi families with CAMRQ4. Blood samples were collected from the affected patients, their parents, and healthy siblings. DNA was extracted from whole blood, and whole-exome sequencing was performed. Findings were confirmed by segregation analysis, which was performed on other family members. Results: Thus far, 17 patients have been affected by CAMRQ4. Genetic analysis of all patients, including our current patients, showed a mutation in the aminophospholipid transporter, class I, type 8A, member 2 gene ( ATP8A2 . A series of common phenotypical features have been reported in these patients, with few exceptions. Ataxia, mental retardation, and hypotonia were present in all patients, consanguinity in 90% and abnormal movements in 50%. Moreover, 40% achieved ambulation at least once in their lifetime, 40% had microcephaly, whereas 30% were mute. Magnetic resonance imaging (MRI of the brain was normal in 60% of patients. Conclusions: We described the largest cohort of patients with CAMRQ4 syndrome and identified three novel mutations. CAMRQ4 syndrome should be suspected in patients presenting with ataxia, intellectual disability, hypotonia, microcephaly, choreoathetoid movements, ophthalmoplegia, and global developmental delay, even if brain MRI appears normal.

  11. Further Delineation of the Clinical Phenotype of Cerebellar Ataxia, Mental Retardation, and Disequilibrium Syndrome Type 4.

    Science.gov (United States)

    Alsahli, Saud; Alrifai, Muhammad Talal; Al Tala, Saeed; Mutairi, Fuad Al; Alfadhel, Majid

    2018-01-01

    Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) is a heterogeneous group of genetic disorders that have been grouped by shared clinical features; all of these features are transmitted via an autosomal recessive mechanism. Four variants of this syndrome have been identified so far, and each one differs in terms of both clinical and genotypical features. CAMRQ4 is a rare genetic disorder characterized by mental retardation, ataxia or an inability to walk, dysarthria and, in some patients, quadrupedal gait. We investigated three Saudi families with CAMRQ4. Blood samples were collected from the affected patients, their parents, and healthy siblings. DNA was extracted from whole blood, and whole-exome sequencing was performed. Findings were confirmed by segregation analysis, which was performed on other family members. Thus far, 17 patients have been affected by CAMRQ4. Genetic analysis of all patients, including our current patients, showed a mutation in the aminophospholipid transporter, class I, type 8A, member 2 gene ( ATP8A2 ). A series of common phenotypical features have been reported in these patients, with few exceptions. Ataxia, mental retardation, and hypotonia were present in all patients, consanguinity in 90% and abnormal movements in 50%. Moreover, 40% achieved ambulation at least once in their lifetime, 40% had microcephaly, whereas 30% were mute. Magnetic resonance imaging (MRI) of the brain was normal in 60% of patients. We described the largest cohort of patients with CAMRQ4 syndrome and identified three novel mutations. CAMRQ4 syndrome should be suspected in patients presenting with ataxia, intellectual disability, hypotonia, microcephaly, choreoathetoid movements, ophthalmoplegia, and global developmental delay, even if brain MRI appears normal.

  12. Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Horvath, Aniko; Didier, Audrey; Koenig, Jean; Exbrayat, Florence; Charmet, Gilles; Balfourier, François

    2009-11-01

    A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT-ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920-1959), modern varieties (1960-2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT-ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0-5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.

  13. Temporal discrimination thresholds in adult-onset primary torsion dystonia: an analysis by task type and by dystonia phenotype.

    LENUS (Irish Health Repository)

    Bradley, D

    2012-01-01

    Adult-onset primary torsion dystonia (AOPTD) is an autosomal dominant disorder with markedly reduced penetrance. Sensory abnormalities are present in AOPTD and also in unaffected relatives, possibly indicating non-manifesting gene carriage (acting as an endophenotype). The temporal discrimination threshold (TDT) is the shortest time interval at which two stimuli are detected to be asynchronous. We aimed to compare the sensitivity and specificity of three different TDT tasks (visual, tactile and mixed\\/visual-tactile). We also aimed to examine the sensitivity of TDTs in different AOPTD phenotypes. To examine tasks, we tested TDT in 41 patients and 51 controls using visual (2 lights), tactile (non-painful electrical stimulation) and mixed (1 light, 1 electrical) stimuli. To investigate phenotypes, we examined 71 AOPTD patients (37 cervical dystonia, 14 writer\\'s cramp, 9 blepharospasm, 11 spasmodic dysphonia) and 8 musician\\'s dystonia patients. The upper limit of normal was defined as control mean +2.5 SD. In dystonia patients, the visual task detected abnormalities in 35\\/41 (85%), the tactile task in 35\\/41 (85%) and the mixed task in 26\\/41 (63%); the mixed task was less sensitive than the other two (p = 0.04). Specificity was 100% for the visual and tactile tasks. Abnormal TDTs were found in 36 of 37 (97.3%) cervical dystonia, 12 of 14 (85.7%) writer\\'s cramp, 8 of 9 (88.8%) blepharospasm, 10 of 11 (90.1%) spasmodic dysphonia patients and 5 of 8 (62.5%) musicians. The visual and tactile tasks were found to be more sensitive than the mixed task. Temporal discrimination threshold results were comparable across common adult-onset primary torsion dystonia phenotypes, with lower sensitivity in the musicians.

  14. 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.

  15. Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes

    International Nuclear Information System (INIS)

    Allen-Brady, Kristina; Camp, Nicola J

    2005-01-01

    Characterization of the linkage disequilibrium (LD) structure of candidate genes is the basis for an effective association study of complex diseases such as cancer. In this study, we report the LD and haplotype architecture and tagging-single nucleotide polymorphisms (tSNPs) for five DNA repair genes: ATM, MRE11A, XRCC4, NBS1 and RAD50. The genes ATM, MRE11A, and XRCC4 were characterized using a panel of 94 unrelated female subjects (47 breast cancer cases, 47 controls) obtained from high-risk breast cancer families. A similar LD structure and tSNP analysis was performed for NBS1 and RAD50, using publicly available genotyping data. We studied a total of 61 SNPs at an average marker density of 10 kb. Using a matrix decomposition algorithm, based on principal component analysis, we captured >90% of the intragenetic variation for each gene. Our results revealed that three of the five genes did not conform to a haplotype block structure (MRE11A, RAD50 and XRCC4). Instead, the data fit a more flexible LD group paradigm, where SNPs in high LD are not required to be contiguous. Traditional haplotype blocks assume recombination is the only dynamic at work. For ATM, MRE11A and XRCC4 we repeated the analysis in cases and controls separately to determine whether LD structure was consistent across breast cancer cases and controls. No substantial difference in LD structures was found. This study suggests that appropriate SNP selection for an association study involving candidate genes should allow for both mutation and recombination, which shape the population-level genomic structure. Furthermore, LD structure characterization in either breast cancer cases or controls appears to be sufficient for future cancer studies utilizing these genes

  16. Solution of the neutron transport equation by the collision probability for 3D geometries; Resolution de l`equation du transport pour les neutrons par la methode des probabilites de collision dans le geometries 3D

    Energy Technology Data Exchange (ETDEWEB)

    Oujidi, B.

    1996-09-19

    The TDT code solves the multigroup transport equation by the interface current method for unstructured 2D geometries. This works presents the extension of TDT to the treatment of 3D geometries obtained by axial displacement of unstructured 2D geometries. Three-dimensional trajectories are obtained by lifting the 2D trajectories. The code allows for the definition of macro-domains in the axial direction to be used in the interface-current method. Specular and isotropic reflection or translations boundary conditions can be applied to the horizontal boundaries of the domain. Numerical studies have shown the need for longer trajectory cutoffs for trajectories intersecting horizontal boundaries. Numerical applications to the calculation of local power peaks are given in a second part for: the local destruction of a Pyrex absorbent and inter-assembly (UO{sub 2}-MOX) power distortion due to pellet collapsing at the top of the core. Calculations with 16 groups were performed by coupling TDT to the spectral code APOLLO2. One-group comparisons with the Monte Carlo code TRIMARAN2 are also given. (author). 30 refs.

  17. Solution of the neutron transport equation by the collision probability method for 3D geometries; Resolution de l`equation du transport par les neutrons par la methode des probabilites de collision dans les geometries 3D

    Energy Technology Data Exchange (ETDEWEB)

    Oujidi, B

    1996-09-19

    The TDT code solves the multigroup transport equation by the interface-current method for unstructured 2D geometries. This works presents the extension of TDT to the treatment of 3D geometries obtained by axial displacement of unstructured 2D geometries. Three-dimensional trajectories are obtained by lifting the 2D trajectories. The code allows for the definition of macro-domains in the axial direction to be used in interface-current method. Specular and isotropic reflection or translations boundary conditions can be applied to the horizontal boundaries of the domain. Numerical studies have shown the need for longer trajectory cutoffs for trajectories intersecting horizontal boundaries. Numerical applications to the calculation of local power peaks are given in a second part for: the local destruction of a Pyrex absorbent, inter-assembly (U02-MOX) power distortion due to pellet collapsing at the top of the core. Calculations with 16 groups were performed by coupling TDT to the spectral code APOLLO2. One-group comparisons with the Monte Carlo code TRIMARAN2 are also given. (author) 30 refs.

  18. 230Th-238U disequilibrium systematics in oceanic tholeiites from 210N on the East Pacific Rise

    International Nuclear Information System (INIS)

    Newman, S.; Finkel, R.C.; MacDougall, J.D.

    1983-01-01

    Significant disequilibrium occurs between 230 Th and its parent, 238 U, in a suite of fresh basalt glasses from the RISE Project study area at 21 0 N on the East Pacific Rise. The ( 230 Th/ 232 Th) activity ratios observed for eight of nine samples from the crest of the axis at this site are constant within analytical uncertainty, with a value of 1.22. This observed homogeneity of ( 230 Th/ 232 Th) has two possible interpretations. First, the measured ( 230 Th/ 232 Th) can be considered to indicate a mantle-source for the RISE basalts with Th/U of 2.5. This interpretation, however, conflicts with the proposed correlation between ( 230 Th/ 232 Th) and 87 Sr/ 86 Sr which predicts that ( 230 Th/ 232 Th) should equal 1.33 at the RISE site. A second possible interpretation is that radioactive decay of 230 Th, in the basalts themselves or in a magma chamber, has decreased ( 230 Th/ 232 Th) from 1.33 to the observed values. The required time span is 11,000 to > 100,000 years. However, petrologic arguments rule against long residence time in a magma chamber, and the spreading rate of this section of the East Pacific Rise (6 cm/yr) predicts that the maximum age for axis basalts is 27,000 years. Both interpretations of the measured ( 230 Th/ 232 Th) imply a low Th/U ratio for the RISE basalt source and suggest that the MORB source at this location is depleted in Th with respect to U relative to primitive mantle or bulk earth. (orig./WL)

  19. What Happens When a Teacher's Science Belief Structure Is in Disequilibrium? Entangled Nature of Beliefs and Practice

    Science.gov (United States)

    Martin, Anita; Park, Soonhye; Hand, Brian

    2017-08-01

    This qualitative case study examined the process of change in an experienced elementary teacher's belief structure during implementation of an inquiry-based science program. Difficulties generally associated with ascertaining beliefs were minimized by using Leatham's (Journal of Mathematics Teacher Education, 9, 91-102 (2006) Sensible System Framework, enabling researchers to obtain rich descriptions of the teacher's belief structure by focusing on words (professed beliefs), intentions (intended beliefs), and actions (enacted beliefs). Models were constructed of the teacher's belief structure before and after implementation of the Science Writing Heuristic (SWH) approach (Hand et al. International Journal of Science Education, 26(2), 131-149, 2004), an inquiry-based approach to teaching science. Key beliefs for this teacher were related to how students learn, goals for teaching science, focus of instruction, and roles of teacher and student. Ultimately, the teacher shifted her professed, intended, and enacted beliefs resulting in a shift from a teacher-centered to a student-centered classroom. Findings support Thagard's Coherence Theory of Justification (2002), positing that change in one belief creates a state of disequilibrium that must be alleviated by changing/realigning other beliefs in order to re-establish coherence in the overall belief structure. This research focus is distinct from the general trend in teacher beliefs research in important ways. Most significant is that this study was not focused on the traditional two lists—those beliefs that were consistent with practice and those that were inconsistent with practice—but instead focused on the entwined nature of beliefs and practice and have shown that a teacher's practice can be viewed as their enacted beliefs, an integral part of the teacher's overall belief structure.

  20. Dialysis Disequilibrium Syndrome: Brain death following hemodialysis for metabolic acidosis and acute renal failure – A case report

    Directory of Open Access Journals (Sweden)

    Bagshaw Sean M

    2004-08-01

    Full Text Available Abstract Background Dialysis disequilibrium syndrome (DDS is the clinical phenomenon of acute neurologic symptoms attributed to cerebral edema that occurs during or following intermittent hemodialysis (HD. We describe a case of DDS-induced cerebral edema that resulted in irreversible brain injury and death following acute HD and review the relevant literature of the association of DDS and HD. Case Presentation A 22-year-old male with obstructive uropathy presented to hospital with severe sepsis syndrome secondary to pneumonia. Laboratory investigations included a pH of 6.95, PaCO2 10 mmHg, HCO3 2 mmol/L, serum sodium 132 mmol/L, serum osmolality 330 mosmol/kg, and urea 130 mg/dL (46.7 mmol/L. Diagnostic imaging demonstrated multifocal pneumonia, bilateral hydronephrosis and bladder wall thickening. During HD the patient became progressively obtunded. Repeat laboratory investigations showed pH 7.36, HCO3 19 mmol/L, potassium 1.8 mmol/L, and urea 38.4 mg/dL (13.7 mmol/L (urea-reduction-ratio 71%. Following HD, spontaneous movements were absent with no pupillary or brainstem reflexes. Head CT-scan showed diffuse cerebral edema with effacement of basal cisterns and generalized loss of gray-white differentiation. Brain death was declared. Conclusions Death is a rare consequence of DDS in adults following HD. Several features may have predisposed this patient to DDS including: central nervous system adaptations from chronic kidney disease with efficient serum urea removal and correction of serum hyperosmolality; severe cerebral intracellular acidosis; relative hypercapnea; and post-HD hemodynamic instability with compounded cerebral ischemia.

  1. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L. germplasm

    Directory of Open Access Journals (Sweden)

    Fricano Agostino

    2012-03-01

    Full Text Available Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD in seven genomic regions using simple sequence repeat (SSR markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2. The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

  2. Effects of stimulus-driven synchronization on sensory perception

    Directory of Open Access Journals (Sweden)

    Holden Jameson K

    2007-12-01

    Full Text Available Abstract Background A subject's ability to differentiate the loci of two points on the skin depends on the stimulus-evoked pericolumnar lateral inhibitory interactions which increase the spatial contrast between regions of SI cortex that are activated by stimulus-evoked afferent drive. Nevertheless, there is very little known about the impact that neuronal interactions – such as those evoked by mechanical skin stimuli that project to and coordinate synchronized activity in adjacent and/or near-adjacent cortical columns – could have on sensory information processing. Methods The temporal order judgment (TOJ and temporal discriminative threshold (TDT of 20 healthy adult subjects were assessed both in the absence and presence of concurrent conditions of tactile stimulation. These measures were obtained across a number of paired sites – two unilateral and one bilateral – and several conditions of adapting stimuli were delivered both prior to and concurrently with the TOJ and TDT tasks. The pairs of conditioning stimuli were synchronized and periodic, synchronized and non-periodic, or asynchronous and non-periodic. Results In the absence of any additional stimuli, TOJ and TDT results obtained from the study were comparable across a number of pairs of stimulus sites – unilateral as well as bilateral. In the presence of a 25 Hz conditioning sinusoidal stimulus which was delivered both before, concurrently and after the TOJ task, there was a significant change in the TOJ measured when the two stimuli were located unilaterally on digits 2 and 3. However, in the presence of the same 25 Hz conditioning stimulus, the TOJ obtained when the two stimuli were delivered bilaterally was not impacted. TDT measures were not impacted to the same degree by the concurrent stimuli that were delivered to the unilateral or bilateral stimulus sites. This led to the speculation that the impact that the conditioning stimuli – which were sinusoidal, periodic and

  3. Factors impacting short and long-term kidney graft survival: modification by single intra-operative -high-dose induction with ATG-Fresenius.

    Science.gov (United States)

    Kaden, Jürgen; May, Gottfried; Völp, Andreas; Wesslau, Claus

    2011-01-01

    A majority of recipients benefited from the intra-operative single high-dose induction (HDI) with ATG-Fresenius (ATG-F) still leaving a group of recipients who did not profit from this kind of induction. Therefore the aim of this retrospective analysis was 1st to identify the risk factors impacting short and long-term graft survival, and 2nd to assess the efficacy of this type of induction in kidney graft recipients with or without these risk factors. A total of 606 recipients receiving two different immunosuppressive treatment regimens (1st: Triple drug therapy [TDT, n=196] consisting mainly of steroids, azathioprine and cyclosporine; 2nd: TDT + 9 mg/kg ATG-F intra-operatively [HDI, n=410]) were included in this analysis and grouped according to their kidney graft survival time (short GST: ≤1 yr, n=100 and long GST: >5 yrs, n=506). The main risk factors associated with a shortened graft survival were pre-transplant sensitization, re-transplantation, rejections (in particular vascular or mixed ones) and the necessity of a long-term anti-rejection therapy. Adding ATG-F single high dose induction to TDT was more efficient in prolonging kidney graft survival than TDT alone not only in recipients without any risk factors (p<0.005) but also in recipients with at least one risk factor (p<0.021). Only in 4.6% of recipients having two or more risk factors this effect could not be demonstrated. The intra-operative single high-dose induction with ATG-F significantly improves the kidney graft survival in recipients with or without risk factors and can therefore be recommended.

  4. Gender differences in locomotor and stereotypic behavior associated with l-carnitine treatment in mice.

    Science.gov (United States)

    Benvenga, Salvatore; Itri, Elenora; Hauser, Peter; De Tolla, Louis; Yu, Sui-Foh; Testa, Giuseppe; Pappalardo, Maria Angela; Trimarchi, Francesco; Amato, Antonino

    2011-02-01

    The carnitines exert neuroprotective and neuromodulatory actions, and carnitine supplementation increases locomotor activity (LMA) in experimental animals. We measured 13 indexes of LMA and 3 indexes of stereotypic activity (STA) in adult male and female caged mice. In a randomized 4-week trial, 10 males and 10 females received 50 mg/kg body weight PO l-carnitine, and another 10 males and 10 females received placebo. Compared with placebo-treated females, placebo-treated males had a greater number of stereotypies (NSTs), stereotypy counts (STCs), stereotypy time (STT), and right front time (RFT), but smaller total distance traveled (TDT), margin distance (MD), number of vertical movements (NVMs), and left rear time (LRT). Compared with placebo-treated males, carnitine-treated males had greater horizontal activity (HA), movement time (MT), NVM, STT, TDT, STC, MD, LRT, and clockwise revolutions (CRs), but smaller left front time (LFT) and RFT. Compared with placebo-treated females, carnitine-treated females had greater NST, STC, STT, LFT, and RFT, but smaller NM, HA, NVM, VA, MT, anticlockwise revolutions (ACRs), CR, TDT, and MD; right rear time (RRT) remained statistically insignificant across all comparisons. In summary, l-carnitine caused gender differences to persist for STC, diminish for NST and STT, disappear for LRT and NVM, change in the opposite direction for TDT and MD, appear de novo for HA, VA, NM, MT, and LFT, and remain absent for RRT and ACR. Some indexes of LMA and STA are sexually dimorphic in adult mice, and l-carnitine differentially maintains, diminishes/cancels, inverts, or creates the sexual dimorphism of particular indexes. Copyright © 2011 Elsevier HS Journals, Inc. All rights reserved.

  5. Significance testing in ridge regression for genetic data

    Directory of Open Access Journals (Sweden)

    De Iorio Maria

    2011-09-01

    Full Text Available Abstract Background Technological developments have increased the feasibility of large scale genetic association studies. Densely typed genetic markers are obtained using SNP arrays, next-generation sequencing technologies and imputation. However, SNPs typed using these methods can be highly correlated due to linkage disequilibrium among them, and standard multiple regression techniques fail with these data sets due to their high dimensionality and correlation structure. There has been increasing interest in using penalised regression in the analysis of high dimensional data. Ridge regression is one such penalised regression technique which does not perform variable selection, instead estimating a regression coefficient for each predictor variable. It is therefore desirable to obtain an estimate of the significance of each ridge regression coefficient. Results We develop and evaluate a test of significance for ridge regression coefficients. Using simulation studies, we demonstrate that the performance of the test is comparable to that of a permutation test, with the advantage of a much-reduced computational cost. We introduce the p-value trace, a plot of the negative logarithm of the p-values of ridge regression coefficients with increasing shrinkage parameter, which enables the visualisation of the change in p-value of the regression coefficients with increasing penalisation. We apply the proposed method to a lung cancer case-control data set from EPIC, the European Prospective Investigation into Cancer and Nutrition. Conclusions The proposed test is a useful alternative to a permutation test for the estimation of the significance of ridge regression coefficients, at a much-reduced computational cost. The p-value trace is an informative graphical tool for evaluating the results of a test of significance of ridge regression coefficients as the shrinkage parameter increases, and the proposed test makes its production computationally feasible.

  6. Gene-based testing of interactions in association studies of quantitative traits.

    Directory of Open Access Journals (Sweden)

    Li Ma

    Full Text Available Various methods have been developed for identifying gene-gene interactions in genome-wide association studies (GWAS. However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene-gene interaction (GGG tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein-protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies.

  7. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

    Science.gov (United States)

    Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

    2012-08-01

    White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

  8. Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Blair, Matthew W; Prieto, Sergio; Díaz, Lucy M; Buendía, Héctor F; Cardona, César

    2010-04-29

    An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome. Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004. We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for

  9. Association test based on SNP set: logistic kernel machine based test vs. principal component analysis.

    Directory of Open Access Journals (Sweden)

    Yang Zhao

    Full Text Available GWAS has facilitated greatly the discovery of risk SNPs associated with complex diseases. Traditional methods analyze SNP individually and are limited by low power and reproducibility since correction for multiple comparisons is necessary. Several methods have been proposed based on grouping SNPs into SNP sets using biological knowledge and/or genomic features. In this article, we compare the linear kernel machine based test (LKM and principal components analysis based approach (PCA using simulated datasets under the scenarios of 0 to 3 causal SNPs, as well as simple and complex linkage disequilibrium (LD structures of the simulated regions. Our simulation study demonstrates that both LKM and PCA can control the type I error at the significance level of 0.05. If the causal SNP is in strong LD with the genotyped SNPs, both the PCA with a small number of principal components (PCs and the LKM with kernel of linear or identical-by-state function are valid tests. However, if the LD structure is complex, such as several LD blocks in the SNP set, or when the causal SNP is not in the LD block in which most of the genotyped SNPs reside, more PCs should be included to capture the information of the causal SNP. Simulation studies also demonstrate the ability of LKM and PCA to combine information from multiple causal SNPs and to provide increased power over individual SNP analysis. We also apply LKM and PCA to analyze two SNP sets extracted from an actual GWAS dataset on non-small cell lung cancer.

  10. CYP21A2 polymorphisms in patients with autoimmune Addison's disease, and linkage disequilibrium to HLA risk alleles.

    Science.gov (United States)

    Brønstad, Ingeborg; Skinningsrud, Beate; Bratland, Eirik; Løvås, Kristian; Undlien, Dag; Sverre Husebye, Eystein; Wolff, Anette Susanne Bøe

    2014-12-01

    Steroid 21-hydroxylase, encoded by CYP21A2, is the major autoantigen in autoimmune Addison's disease (AAD). CYP21A2 is located in the region of the HLA complex on chromosome 6p21.3, which harbours several risk alleles for AAD. The objective was to investigate whether CYP21A2 gene variants confer risk of AAD independently of other risk alleles in the HLA loci. DNA samples from 381 Norwegian patients with AAD and 340 healthy controls (HC) previously genotyped for the HLA-A, -B, -DRB1, and -DQB1 and MICA loci were used for genotyping of CYP21A2. Genotyping of CYP21A2 was carried out by direct sequencing. Linkage of CYP21A2 to the HLA loci was assessed using UNPHASED version 3.0.10 and PHASE version 2.1. Heterozygotes of the single-nucleotide polymorphisms (SNPs) rs397515394, rs6467, rs6474, rs76565726 and rs6473 were detected significantly more frequently in AAD patients compared with HC (P<0.005), but all SNPs were in a linkage disequilibrium (LD) with high-risk HLA-DRB1 haplotypes. rs6472C protected against AAD (odds ratio=0.15, 95% CI (0.08-0.30), P=3.8×10(-10)). This SNP was not in an LD with HLA loci (P=0.02), but did not increase protection when considering the effect of HLA-DRB1 alleles. Mutations causing congenital adrenal hyperplasia were found in heterozygosity in <1.5% of the cases in both groups. Genetic variants of CYP21A2 associated to AAD are in LD with the main AAD risk locus HLA-DRB1, and CYP21A2 does not constitute an independent susceptibility locus. © 2014 European Society of Endocrinology.

  11. Perisoreus infaustus

    Indian Academy of Sciences (India)

    avian genome evolution from cross-species amplification tests. MENG-HUA LI* ..... We tested for Hardy-. Weinberg equilibrium and linkage disequilibrium (LD) using ... 12 loci, two loci (Ase50 and Phtr3) were assigned to the Z- chromosome by ...

  12. NASA Space Environments Technical Discipline Team Space Weather Activities

    Science.gov (United States)

    Minow, J. I.; Nicholas, A. C.; Parker, L. N.; Xapsos, M.; Walker, P. W.; Stauffer, C.

    2017-12-01

    The Space Environment Technical Discipline Team (TDT) is a technical organization led by NASA's Technical Fellow for Space Environments that supports NASA's Office of the Chief Engineer through the NASA Engineering and Safety Center. The Space Environments TDT conducts independent technical assessments related to the space environment and space weather impacts on spacecraft for NASA programs and provides technical expertise to NASA management and programs where required. This presentation will highlight the status of applied space weather activities within the Space Environment TDT that support development of operational space weather applications and a better understanding of the impacts of space weather on space systems. We will first discuss a tool that has been developed for evaluating space weather launch constraints that are used to protect launch vehicles from hazardous space weather. We then describe an effort to better characterize three-dimensional radiation transport for CubeSat spacecraft and processing of micro-dosimeter data from the International Space Station which the team plans to make available to the space science community. Finally, we will conclude with a quick description of an effort to maintain access to the real-time solar wind data provided by the Advanced Composition Explorer satellite at the Sun-Earth L1 point.

  13. Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations.

    Science.gov (United States)

    Martin, Eden R; Tunc, Ilker; Liu, Zhi; Slifer, Susan H; Beecham, Ashley H; Beecham, Gary W

    2018-03-01

    Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations. We show that admixture does not lead to confounding when the trait locus is tested directly in a single admixed population. However, if there is more complex population structure or a marker locus in linkage disequilibrium (LD) with the trait locus is tested, both global and local ancestry can be confounders. Additionally, we show the genotype parameters of adjusted and unadjusted models all provide tests for LD between the marker and trait locus, but in different contexts. The local ancestry adjusted model tests for LD in the ancestral populations, while tests using the unadjusted and the global ancestry adjusted models depend on LD in the admixed population(s), which may be enriched due to different ancestral allele frequencies. Practically, this implies that global-ancestry adjustment should be used for screening, but local-ancestry adjustment may better inform fine mapping and provide better effect estimates at trait loci. © 2017 WILEY PERIODICALS, INC.

  14. The Generalized Higher Criticism for Testing SNP-Set Effects in Genetic Association Studies

    Science.gov (United States)

    Barnett, Ian; Mukherjee, Rajarshi; Lin, Xihong

    2017-01-01

    It is of substantial interest to study the effects of genes, genetic pathways, and networks on the risk of complex diseases. These genetic constructs each contain multiple SNPs, which are often correlated and function jointly, and might be large in number. However, only a sparse subset of SNPs in a genetic construct is generally associated with the disease of interest. In this article, we propose the generalized higher criticism (GHC) to test for the association between an SNP set and a disease outcome. The higher criticism is a test traditionally used in high-dimensional signal detection settings when marginal test statistics are independent and the number of parameters is very large. However, these assumptions do not always hold in genetic association studies, due to linkage disequilibrium among SNPs and the finite number of SNPs in an SNP set in each genetic construct. The proposed GHC overcomes the limitations of the higher criticism by allowing for arbitrary correlation structures among the SNPs in an SNP-set, while performing accurate analytic p-value calculations for any finite number of SNPs in the SNP-set. We obtain the detection boundary of the GHC test. We compared empirically using simulations the power of the GHC method with existing SNP-set tests over a range of genetic regions with varied correlation structures and signal sparsity. We apply the proposed methods to analyze the CGEM breast cancer genome-wide association study. Supplementary materials for this article are available online. PMID:28736464

  15. Desarrollo de aplicaciones para TDT con GINGA-J

    Directory of Open Access Journals (Sweden)

    D. Alulema

    2012-11-01

    Full Text Available This article is an introduction to the events that led to Ecuador to the adoption of ISDB-Tb standard for digital terrestrial television, and is considered an analysis of the Ginga middleware, and especially Ginga-J for developing interactive applications and finally presents an application developed using Netbeans.

  16. Using incomplete trios to boost confidence in family based association studies

    Directory of Open Access Journals (Sweden)

    Varsha eDhankani

    2016-03-01

    Full Text Available Most currently available family based association tests are designed to account only for nuclear families with complete genotypes for parents as well as offspring. Due to the availability of increasingly less expensive generation of whole genome sequencing information, genetic studies are able to collect data for more families and from large family cohorts with the goal of improving statistical power. However, due to missing genotypes, many families are not included in the family based association tests, negating the benefits of large scale sequencing data. Here, we present the CIFBAT method to use incomplete families in Family Based Association Test (FBAT to evaluate robustness against missing data. CIFBAT uses quantile intervals of the FBAT statistic by randomly choosing valid completions of incomplete family genotypes based on Mendelian inheritance rules. By considering all valid completions equally likely and computing quantile intervals over several randomized iterations, CIFBAT avoids assumption of a homogeneous population structure or any particular missingness pattern in the data. Using simulated data, we show that the quantile intervals computed by CIFBAT are useful in validating robustness of the FBAT statistic against missing data and in identifying genomic markers with higher precision. We also propose a novel set of candidate genomic markers for uterine related abnormalities from analysis of familial whole genome sequences, and provide validation for a previously established set of candidate markers for Type 1 diabetes. We have provided a software package that incorporates TDT, robustTDT, FBAT and CIFBAT. The data format proposed for the software uses half the memory space that the standard FBAT format (PED files use, making it efficient for large scale genome wide association studies.

  17. Frequencies of HID-ion ampliseq ancestry panel markers among greenlanders

    DEFF Research Database (Denmark)

    Espregueira Themudo, Gonçalo; Smidt Mogensen, Helle; Børsting, Claus

    2016-01-01

    set of 89 individuals and a test set of 15 individuals. All loci showed genotype distributions consistent with Hardy-Weinberg expectations. Linkage disequilibrium tests indicated that 14 pairs of loci were in association in Greenlanders. Population assignment of the training set to populations...

  18. Study of two new methods of geochronometry: dating method of carbonaceous formations by U-series disequilibrium gamma spectrometry; ESR dating method of rich U-content fossil dental enamel

    International Nuclear Information System (INIS)

    Ma, Jean-Luc

    1984-01-01

    First, the U-series disequilibrium dating method was re-examined using non-destructive γ-spectrometry. A new low-background (≤ 10 ppb U- equivalent) Ge-HP γ-spectrometer has been used to date travertine with small U-content (∼ 0.1 ppm) and low (≤ 5%) Th/U , content, by comparison with old-limestone γ-spectra. Second, a new ESR dating method has been developed using fossil dental enamel which is rich in U-content (10 - 100 ppm). Both methods were applied to Arago Cave (Tautavel, France): - with an ionium-age of 120 ka (10%), the upper travertine seems to have been set up during the Riss-deglaciation period. - the high (∼ 50%) Th/U-content samples of the intermediate travertine are un-datable. - the ESR-age of EQUUS mosbachensis enamel is 400 ka (10%) for the G-soil of Arago. XXI H. erectus, and 600 ka (10%) for the Q-soil above (- 1 m) of the lower travertine of which Io-age is older than 350 ka. (author)

  19. Properties of permutation-based gene tests and controlling type 1 error using a summary statistic based gene test.

    Science.gov (United States)

    Swanson, David M; Blacker, Deborah; Alchawa, Taofik; Ludwig, Kerstin U; Mangold, Elisabeth; Lange, Christoph

    2013-11-07

    The advent of genome-wide association studies has led to many novel disease-SNP associations, opening the door to focused study on their biological underpinnings. Because of the importance of analyzing these associations, numerous statistical methods have been devoted to them. However, fewer methods have attempted to associate entire genes or genomic regions with outcomes, which is potentially more useful knowledge from a biological perspective and those methods currently implemented are often permutation-based. One property of some permutation-based tests is that their power varies as a function of whether significant markers are in regions of linkage disequilibrium (LD) or not, which we show from a theoretical perspective. We therefore develop two methods for quantifying the degree of association between a genomic region and outcome, both of whose power does not vary as a function of LD structure. One method uses dimension reduction to "filter" redundant information when significant LD exists in the region, while the other, called the summary-statistic test, controls for LD by scaling marker Z-statistics using knowledge of the correlation matrix of markers. An advantage of this latter test is that it does not require the original data, but only their Z-statistics from univariate regressions and an estimate of the correlation structure of markers, and we show how to modify the test to protect the type 1 error rate when the correlation structure of markers is misspecified. We apply these methods to sequence data of oral cleft and compare our results to previously proposed gene tests, in particular permutation-based ones. We evaluate the versatility of the modification of the summary-statistic test since the specification of correlation structure between markers can be inaccurate. We find a significant association in the sequence data between the 8q24 region and oral cleft using our dimension reduction approach and a borderline significant association using the

  20. Disequilibrium of flavonol synthase and dihydroflavonol-4-reductase expression associated tightly to white versus red color flower formation in plants

    Directory of Open Access Journals (Sweden)

    Ping eLuo

    2016-01-01

    Full Text Available Flower colour is the main character throughout the plant kingdom. Though substantial information exists regarding the structural and regulatory genes involved in anthocyanin and flavonol biosynthesis, little is known that what make a diverse white versus red color flower in natural species. Here, the contents of pigments in seven species from varied phylogenetic location in plants with red and white flowers.were determined. Flavonols could be detected in red and white flowers, but anthocyanins were almost undetectable in the white cultivar. Comparisons of expression patterns of gene related to the flavonoid biosynthesis indicated that disequilibrium expression of flavonol synthase (FLS and dihydroflavonol-4-reductase (DFR genes determined the accumulation of flavonols and anothcyanins in both red and white flowers of seven species. To further investigate the role of such common regulatory patterns in determining flower color, FLS genes were isolated from Rosa rugosa (RrFLS1, Prunus persica (PpFLS and Petunia hybrida (PhFLS, and DFR genes were isolated from Rosa rugosa (RrDFR1 and Petunia hybrida (PhDFR. Heterologous expression of the FLS genes within tobacco host plants demonstrated conservation of function, with the transgenes promoting flavonol biosynthesis and inhibiting anthocyanin accumulation, so resulting in white flowers. Conversely, overexpression of DFR genes in tobacco displayed down-regulation of the endogenous NtFLS gene, and the promotion of anthocyanin synthesis. On this basis, we propose a model in which FLS and DFR gene-products compete for common substrates in order to direct the biosynthesis of flavonols and anthocyanins, respectively, thereby determining white versus red coloration of flowers.

  1. Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

    Science.gov (United States)

    Schopp, Pascal; Müller, Dominik; Technow, Frank; Melchinger, Albrecht E

    2017-01-01

    Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ([Formula: see text] and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from [Formula: see text]2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios differing in relatedness of the training and prediction sets and in the types of data used to calculate the relationship matrix (QTL, SNPs, tag markers, and pedigree), we investigated the prediction accuracy (PA) of Genomic best linear unbiased prediction (GBLUP) and analyzed contributions from pedigree relationships captured by SNP markers, as well as from cosegregation and ancestral LD between QTL and SNPs. The effects of training set size [Formula: see text] and marker density were also studied. Sampling few parents ([Formula: see text]) generates substantial sample LD that carries over into synthetics through cosegregation of alleles at linked loci. For fixed [Formula: see text], [Formula: see text] influences PA most strongly. If the training and prediction set are related, using [Formula: see text] parents yields high PA regardless of ancestral LD because SNPs capture pedigree relationships and Mendelian sampling through cosegregation. As [Formula: see text] increases, ancestral LD contributes more information, while other factors contribute less due to lower frequencies of closely related individuals. For unrelated prediction sets, only ancestral LD contributes information and accuracies were poor and highly variable for [Formula: see text] due to large sample LD. For large [Formula: see text], achieving moderate accuracy requires

  2. Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

    NARCIS (Netherlands)

    Allen, Andrew S.; Berkovic, Samuel F.; Bridgers, Joshua; Cossette, Patrick; Dlugos, Dennis; Epstein, Michael P.; Glauser, Tracy; Goldstein, David B.; Heinzen, Erin L.; Jiang, Yu; Johnson, Michael R.; Kuzniecky, Ruben; Lowenstein, Daniel H.; Marson, Anthony G.; Mefford, Heather C.; O'Brien, Terence J.; Ottman, Ruth; Petrou, Steven; Petrovski, Slavé; Poduri, Annapurna; Ren, Zhong; Scheffer, Ingrid E.; Sherr, Elliott; Wang, Quanli; Balling, Rudi; Barisic, Nina; Baulac, Stéphanie; Caglayan, Hande; Craiu, Dana; De Jonghe, Peter; Depienne, Christel; Guerrini, Renzo; Helbig, Ingo; Hjalgrim, Helle; Hoffman-Zacharska, Dorota; Jähn, Johanna A.; Klein, Karl Martin; Koeleman, Bobby; Komarek, Vladimir; Krause, Roland; Leguern, Eric; Lehesjoki, Anna-Elina; Lemke, Johannes R.; Lerche, Holger; Linnankivi, Tarja; Marini, Carla; May, Patrick; Møller, Rikke S.; Muhle, Hiltrud; Pal, Deb; Palotie, Aarno; Rosenow, Felix; Selmer, Kaja; Serratosa, Jose M.; Sisodiya, Sanjay M.; Stephani, Ulrich; Sterbova, Katalin; Striano, Pasquale; Suls, Arvid; Talvik, Tiina; von Spiczak, Sarah; Weber, Yvonne G.; Weckhuysen, Sarah; Zara, Federico; Abou-Khalil, Bassel; Alldredge, Brian K.; Amrom, Dina; Andermann, Eva; Andermann, Frederick; Bautista, Jocelyn F.; Bluvstein, Judith; Cascino, Gregory D.; Consalvo, Damian; Crumrine, Patricia; Devinsky, Orrin; Fiol, Miguel E.; Fountain, Nathan B.; French, Jacqueline; Friedman, Daniel; Haas, Kevin; Haut, Sheryl R.; Hayward, Jean; Joshi, Sucheta; Kanner, Andres; Kirsch, Heidi E.; Kossoff, Eric H.; Kuperman, Rachel; McGuire, Shannon M.; Motika, Paul V.; Novotny, Edward J.; Paolicchi, Juliann M.; Parent, Jack; Park, Kristen; Shellhaas, Renée A; Sirven, Joseph; Smith, Michael C.; Sullivan, Joseph; Thio, Liu Lin; Venkat, Anu; Vining, Eileen P. G.; Von Allmen, Gretchen K.; Weisenberg, Judith L.; Widdess-Walsh, Peter; Winawer, Melodie R.

    2017-01-01

    The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients

  3. Phylogeography of haplotypes of five microsatellites located in a low-recombination region of the X chromosome: studies worldwide and in Brazilian populations.

    Science.gov (United States)

    Pereira, Rinaldo Wellerson; Pena, Sérgio D J

    2006-01-01

    We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3-Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might

  4. Test of a new heat-flow equation for dense-fluid shock waves.

    Science.gov (United States)

    Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon

    2010-09-21

    Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes.

  5. Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA.

    Directory of Open Access Journals (Sweden)

    Simon Gemble

    2015-07-01

    Full Text Available Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at "difficult-to-replicate" sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS, a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3'-5' DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.

  6. Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

    Science.gov (United States)

    Kawakami, Takeshi; Mugal, Carina F; Suh, Alexander; Nater, Alexander; Burri, Reto; Smeds, Linnéa; Ellegren, Hans

    2017-08-01

    Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  7. Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies.

    Science.gov (United States)

    Xu, P; Wu, X; Wang, B; Luo, J; Liu, Y; Ehlers, J D; Close, T J; Roberts, P A; Lu, Z; Wang, S; Li, G

    2012-07-01

    Association mapping of important traits of crop plants relies on first understanding the extent and patterns of linkage disequilibrium (LD) in the particular germplasm being investigated. We characterize here the genetic diversity, population structure and genome wide LD patterns in a set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm from China. A diverse collection of 99 asparagus bean and normal cowpea accessions were genotyped with 1127 expressed sequence tag-derived single nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs across the collection was relatively low (39%), with an average number of SNPs per locus of 1.33. Bayesian population structure analysis indicated two subdivisions within the collection sampled that generally represented the 'standard vegetable' type (subgroup SV) and the 'non-standard vegetable' type (subgroup NSV), respectively. Level of LD (r(2)) was higher and extent of LD persisted longer in subgroup SV than in subgroup NSV, whereas LD decayed rapidly (0-2 cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈ 5 cM) five times longer than the shortest (≈ 1 cM). Partitioning of LD variance into within- and between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 10 may have undergone the most intensive epistatic selection toward traits favorable for vegetable use. This work provides a first population genetic insight into domestication history of asparagus bean and demonstrates the feasibility of mapping complex traits by genome wide association study in asparagus bean using a currently available cowpea SNPs marker platform.

  8. Isotopic disequilibrium among commingled hybrid magmas: Evidence for a two-stage magma mixing-commingling process in the Mt. Perkins Pluton, Arizona

    International Nuclear Information System (INIS)

    Metcalf, R.V.; Smith, E.I.; Reed, R.C.

    1995-01-01

    The syn-extensional Miocene Mt. Perkins pluton, northwestern Arizona, cooled rapidly due to its small size (6 km 2 ) and shallow emplacement (7.5 km) and allows examination of commingled rocks that experienced little isotopic exchange. Within the pluton, quartz dioritic to granodioritic host rocks (58-68 wt% SiO 2 ) enclose dioritic enclaves (50-55 wt% SiO 2 ) and a portion contains enclave-free granodiorite (70-74 wt% SiO 2 ). Fine-grained, crenulate enclave margins and a lack of advanced mixing structures (e.g., schlieren, flow fabrics, etc.) indicate an incipient stage of commingling. Isotopic variation between enclaves and enclosing host rocks is large (6.8 to 10.6 ε Nd units; 0.0036 to 0.0046 87 Sr/ 86 Sr units), suggesting isotopic disequilibrium. Comparison of an enclave core and rim suggests that isotopic exchange with the host magma was limited to the enclave rim. Enclaves and hosts collectively form a calc-alkaline suite exhibiting a large range of ε Nd (+1.2 to -12.5) and initial 87 Sr/ 86 Sr (0.705 to 0.71267) with a correlation among ε Nd , initial 87 Sr/ 86 Sr, and major and trace element compositions. Modeling suggests that the suite formed by magma hybridization involving magma mixing accompanied by fractional crystallization. The magma mixing must have predated commingling at the present exposure level and indicates a larger mixing chamber at depth. Isotopic and trace element data suggests mixing end-members were asthenospheric mantle-derived mafic and crustal-derived felsic magmas. Fractional crystallization facilitated mixing by reducing the rheological contrasts between the mafic and felsic mixing end-members. 58 refs., 11 figs., 3 tabs

  9. Radiographically determined growth kinetics of primary lung tumors in the dog

    International Nuclear Information System (INIS)

    Perry, R.E.; Weller, R.E.; Buschbom, R.L.; Dagle, G.E.; Park, J.F.

    1989-10-01

    Tumor growth rate patterns especially tumor doubling time (TDT), have been extensively evaluated in man. Studies involving the determination of TDT in humans are limited, however, by the number of cases, time consistent radiographic tumor measurements, and inability to perform experimental procedures. In animals similar constraints do not exist. Lifespan animal models lend themselves well to tumor growth pattern analysis. Experimental studies have been designed to evaluate both the biological effects and growth patterns of induced and spontaneous tumors. The purpose of this study was to calculate the tumor volume doubling times (TCDT) for radiation-induced and spontaneous primary pulmonary neoplasms in dogs to see if differences existed due to etiology, sex or histologic cell type, and to determine if the time of tumor onset could be extrapolated from the TVDT. 3 refs

  10. MERRA 3D IAU Tendency, Temperature, Diurnal (1.25x1.25L42) V5.2.0

    Data.gov (United States)

    National Aeronautics and Space Administration — The MATUCPTDT or tavgU_3d_tdt_Cp data product is the MERRA Data Assimilation System 3-Dimensional temperature tendencies that is time averaged on pressure levels at...

  11. MERRA 3D IAU Tendency, Temperature, Monthly Mean (1.25x1.25L42) V5.2.0

    Data.gov (United States)

    National Aeronautics and Space Administration — The MATMCPTDT or tavgM_3d_tdt_Cp data product is the MERRA Data Assimilation System 3-Dimensional temperature tendencies that is time averaged on pressure levels at...

  12. Exploring linkage disequilibrium

    Czech Academy of Sciences Publication Activity Database

    Baird, Stuart J. E.

    2015-01-01

    Roč. 15, č. 5 (2015), s. 1017-1019 ISSN 1755-098X Institutional support: RVO:68081766 Keywords : bioinfomatics/phyloinfomatics * genomics /proteomics * population genetics—theoretical * population genetics—empirical Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

  13. Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sereina Riniker

    2017-07-01

    Full Text Available The first challenge in the 2014 competition launched by the Teach-Discover-Treat (TDT initiative asked for the development of a tutorial for ligand-based virtual screening, based on data from a primary phenotypic high-throughput screen (HTS against malaria. The resulting Workflows were applied to select compounds from a commercial database, and a subset of those were purchased and tested experimentally for anti-malaria activity. Here, we present the two most successful Workflows, both using machine-learning approaches, and report the results for the 114 compounds tested in the follow-up screen. Excluding the two known anti-malarials quinidine and amodiaquine and 31 compounds already present in the primary HTS, a high hit rate of 57% was found.

  14. The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase

    Directory of Open Access Journals (Sweden)

    Yusuke Takezawa

    2016-06-01

    Full Text Available A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT, a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H–CuII–H. In this study, we investigated the effects of a metal cofactor, MgII ion, on the TdT-catalyzed polymerization of H nucleotides. At a high MgII concentration (10 mM, the reaction was halted after several H nucleotides were appended. In contrast, at lower MgII concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the MgII concentration. In the presence of excess MgII ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with MgII ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands.

  15. Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1 in five populations: implications for pharmacogenetic research

    Directory of Open Access Journals (Sweden)

    Sughondhabirom Atapol

    2007-10-01

    Full Text Available Abstract Background GABA transporter-1 (GAT-1; genetic locus SLC6A1 is emerging as a novel target for treatment of neuropsychiatric disorders. To understand how population differences might influence strategies for pharmacogenetic studies, we identified patterns of genetic variation and linkage disequilibrium (LD in SLC6A1 in five populations representing three continental groups. Results We resequenced 12.4 kb of SLC6A1, including the promoters, exons and flanking intronic regions in African-American, Thai, Hmong, Finnish, and European-American subjects (total n = 40. LD in SLC6A1 was examined by genotyping 16 SNPs in larger samples. Sixty-three variants were identified through resequencing. Common population-specific variants were found in African-Americans, including a novel 21-bp promoter region variable number tandem repeat (VNTR, but no such variants were found in any of the other populations studied. Low levels of LD and the absence of major LD blocks were characteristic of all five populations. African-Americans had the highest genetic diversity. European-Americans and Finns did not differ in genetic diversity or LD patterns. Although the Hmong had the highest level of LD, our results suggest that a strategy based on the use of tag SNPs would not translate to a major improvement in genotyping efficiency. Conclusion Owing to the low level of LD and presence of recombination hotspots, SLC6A1 may be an example of a problematic gene for association and haplotype tagging-based genetic studies. The 21-bp promoter region VNTR polymorphism is a putatively functional candidate allele for studies focusing on variation in GAT-1 function in the African-American population.

  16. TDT y servicio público. Retos del audiovisual iberoamericano

    Directory of Open Access Journals (Sweden)

    Francisco Sierra Caballero

    2011-03-01

    Full Text Available ¿Qué viabilidad tienen los medios públicos en Latinoamérica? ¿La radiotelevisión pública está acometiendo con garantías de éxito los retos de la Sociedad de la Información? ¿Qué sentido tiene hoy plantear la defensa del servicio público audiovisual ante la convergencia tecnológica que lideran las industrias culturales y los operadores privados? Son las preguntas que se intentan responder a partir de un análisis de situación de los medios públicos en la región. Se establecen tres retos importantes para que la radio televisión pública pueda ser una vía plausible: políticas culturales, apertura del espacio público y la democracia nacional, y acceso de las minorías y el pluralismo cultural.

  17. A Summary of the Rendezvous, Proximity Operations, Docking, and Undocking (RPODU) Lessons Learned from the Defense Advanced Research Project Agency (DARPA) Orbital Express (OE) Demonstration System Mission

    Science.gov (United States)

    Dennehy, Cornelius J.; Carpenter, James R.

    2011-01-01

    The Guidance, Navigation, and Control (GN&C) Technical Discipline Team (TDT) sponsored Dr. J. Russell Carpenter, a Navigation and Rendezvous Subject Matter Expert (SME) from NASA's Goddard Space Flight Center (GSFC), to provide support to the Defense Advanced Research Project Agency (DARPA) Orbital Express (OE) rendezvous and docking flight test that was conducted in 2007. When that DARPA OE mission was completed, Mr. Neil Dennehy, NASA Technical Fellow for GN&C, requested Dr. Carpenter document his findings (lessons learned) and recommendations for future rendezvous missions resulting from his OE support experience. This report captures lessons specifically from anomalies that occurred during one of OE's unmated operations.

  18. An Efficient Test for Gene-Environment Interaction in Generalized Linear Mixed Models with Family Data.

    Science.gov (United States)

    Mazo Lopera, Mauricio A; Coombes, Brandon J; de Andrade, Mariza

    2017-09-27

    Gene-environment (GE) interaction has important implications in the etiology of complex diseases that are caused by a combination of genetic factors and environment variables. Several authors have developed GE analysis in the context of independent subjects or longitudinal data using a gene-set. In this paper, we propose to analyze GE interaction for discrete and continuous phenotypes in family studies by incorporating the relatedness among the relatives for each family into a generalized linear mixed model (GLMM) and by using a gene-based variance component test. In addition, we deal with collinearity problems arising from linkage disequilibrium among single nucleotide polymorphisms (SNPs) by considering their coefficients as random effects under the null model estimation. We show that the best linear unbiased predictor (BLUP) of such random effects in the GLMM is equivalent to the ridge regression estimator. This equivalence provides a simple method to estimate the ridge penalty parameter in comparison to other computationally-demanding estimation approaches based on cross-validation schemes. We evaluated the proposed test using simulation studies and applied it to real data from the Baependi Heart Study consisting of 76 families. Using our approach, we identified an interaction between BMI and the Peroxisome Proliferator Activated Receptor Gamma ( PPARG ) gene associated with diabetes.

  19. Parus humilis

    Indian Academy of Sciences (India)

    The 29 primer pairs were further tested in 30 individuals, of which, seven were ... turing polyacrylamide gels, bands with a size of 50–350 bp were analysed using ... wise linkage disequilibrium (LD) and Hardy–Weinberg equi- librium (HWE) ...

  20. Fulltext PDF

    Indian Academy of Sciences (India)

    All SSR primers were tested using 33 individuals from one wild ... approximate 50 ng of template DNA, 0.5 μM of forward and reverse ... C for 50 s, locus-specific annealing ... age disequilibrium (LD), were performed using Genepop ver.

  1. Difference in cellular damage and cell death in thermal death time disks and high hydrostatic pressure treated Salmonella Enteritidis (ATCC13076) in liquid whole egg

    Science.gov (United States)

    Differences in membrane damage including leakage of intracellular UV-materials and loss of viability of Salmonella Enteritidis (ATCC13076) in liquid whole egg (LWE) following thermal-death-time (TDT) disk and high hydrostatic pressure treatments were examined. Salmonella enteritidis was inoculated ...

  2. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146, Malawi (n =30 and Zimbabwe (n =136 were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK and 0.24 (VD at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population

  3. A Family-Based Association Study of CYP11A1 and CYP11B1 Gene Polymorphisms With Autism in Chinese Trios.

    Science.gov (United States)

    Deng, Hong-Zhu; You, Cong; Xing, Yu; Chen, Kai-Yun; Zou, Xiao-Bing

    2016-05-01

    Autism spectrum disorder is a group of neurodevelopmental disorders with the higher prevalence in males. Our previous studies have indicated lower progesterone levels in the children with autism spectrum disorder, suggesting involvement of the cytochrome P-450scc gene (CYP11A1) and cytochrome P-45011beta gene (CYP11B1) as candidate genes in autism spectrum disorder. The aim of this study was to investigate the family-based genetic association between single-nucleotide polymorphisms, rs2279357 in the CYP11A1 gene and rs4534 and rs4541 in the CYP11B1 gene and autism spectrum disorder in Chinese children, which were selected according to the location in the coding region and 5' and 3' regions and minor allele frequencies of greater than 0.05 in the Chinese populations. The transmission disequilibrium test and case-control association analyses were performed in 100 Chinese Han autism spectrum disorder family trios. The genotype and allele frequency of the 3 single-nucleotide polymorphisms had no statistical difference between the children with autism spectrum disorder and their parents (P> .05). Transmission disequilibrium test analysis showed transmission disequilibrium of CYP11A1 gene rs2279357 single-nucleotide polymorphisms (χ(2)= 5.038,Pautism spectrum disorder exists within or near the CYP11A1 gene in the Han Chinese population. © The Author(s) 2015.

  4. Investigation of the various factors affecting the response of passive configuration track etch dosimeters to working level hour exposure in radon and radon daughter atmospheres. Final report

    International Nuclear Information System (INIS)

    Lovett, D.B.

    1976-01-01

    The work described in this report was directed toward identifying and devising methods to minimize the previously observed variability between working level hour exposures and the alpha particle track densities resulting on Track Etch films exposed to mine atmospheres containing radon and radon daughters. The disequilibrium between radon and its daughters was shown to directly affect the Track Etch film calibration factor. The wide range of disequilibrium states possible in mine situations amply explains the variability in the previous tests. A file of published mine atmosphere composition data was compiled and was used, along with atmospheric compositions derived from several theoretical models of the atmospheric behavior, to evaluate the variability of several dosimeter configurations and concepts

  5. A Modified Generalized Fisher Method for Combining Probabilities from Dependent Tests

    Directory of Open Access Journals (Sweden)

    Hongying (Daisy eDai

    2014-02-01

    Full Text Available Rapid developments in molecular technology have yielded a large amount of high throughput genetic data to understand the mechanism for complex traits. The increase of genetic variants requires hundreds and thousands of statistical tests to be performed simultaneously in analysis, which poses a challenge to control the overall Type I error rate. Combining p-values from multiple hypothesis testing has shown promise for aggregating effects in high-dimensional genetic data analysis. Several p-value combining methods have been developed and applied to genetic data; see [Dai, et al. 2012b] for a comprehensive review. However, there is a lack of investigations conducted for dependent genetic data, especially for weighted p-value combining methods. Single nucleotide polymorphisms (SNPs are often correlated due to linkage disequilibrium. Other genetic data, including variants from next generation sequencing, gene expression levels measured by microarray, protein and DNA methylation data, etc. also contain complex correlation structures. Ignoring correlation structures among genetic variants may lead to severe inflation of Type I error rates for omnibus testing of p-values. In this work, we propose modifications to the Lancaster procedure by taking the correlation structure among p-values into account. The weight function in the Lancaster procedure allows meaningful biological information to be incorporated into the statistical analysis, which can increase the power of the statistical testing and/or remove the bias in the process. Extensive empirical assessments demonstrate that the modified Lancaster procedure largely reduces the Type I error rates due to correlation among p-values, and retains considerable power to detect signals among p-values. We applied our method to reassess published renal transplant data, and identified a novel association between B cell pathways and allograft tolerance.

  6. Standardization of Thermal Processes for Local Foods with Emphasis on Low-Acid Foods

    Directory of Open Access Journals (Sweden)

    Estrella Alabastro

    1980-01-01

    Full Text Available The minimum process for selected low acid foods was established based on the thermal death time (TDT of P.A. 3679 in the food and the heat penetration characteristics of the food products. The products studied were: (a vegetable products - green papaya, langka, sitao, mushroom, waterchestnut and baby corn; (b meat products - lechon, paksiw, dinuguan, longaniza and caldereta; and (c seafood products - squid adobo. The integrated lethality approach was adopted for process calculations recommended by Stumbo (1973.The minimum thermal process was tested by a pilot scale production followed by microbiological, physico-chemical and sensory evaluation tests to check the soundness of the product.Preliminary research on the effect of the minimum process established on the retention of nutrients, particularly thiamine, was also carried out for lechon paksiw and sitao.

  7. T-lineage blast crisis of chronic myelogenous leukemia: simple record of 4 cases

    Directory of Open Access Journals (Sweden)

    Kartika W. Taroeno-Hariadi

    2005-09-01

    Full Text Available Blast crisis (BC transformation in chronic myelogenous leukemia (CML can involve each differentiation lineage of the hematopoietic system, i.e. granulocyte, monocyte, erythrocyte, megakaryocyte, and lymphocyte lineage. The lymphoid blast crisis (BC leukemia cells usually belong to B-lineage, commonly having the phenotype of Pre-B stage of the B-lineage, in which cell-surface immunoglobulin (sIg is not yet expressed. In contrast, T-lineage BC of CML is extremely rare. The objective of this study is to describe the fenotype, fusion transcript of bcr-abl, TdT, and cytoplasmic CD3 in T-lineage BC CML cases. Case report study. This report shows a simple summary of 4 cases of T-lineage BC of CML which have been collected in the phenotypic and genotypic analysis study for 17 years (1987-2004. In all cases, the chromosomal analysis revealed the presence of t(9;22(q34;q11 at presentation. Cell surface analysis were done at diagnosis. Cases’ mononuclear cells stored as 10% DMSO were retrieved to be performed reverse transcription (RT PCR BCR-ABL multiplex to demonstrate the presence of the fusion transcript of bcr-abl. RT-PCR was also performed for detecting the expression of cytoplasmic CD3ε and terminal deoxynucleotydil transferase (TdT. The results of cell surface antigen (CSA at presentation showed that 1 case was CD7+, CD5-, and CD2-; 1 case CD7+, CD5+, and CD2-; and 2 cases CD7+, CD5+ and CD2+ indicating that all these T-lineage BC of CML cells show the phenotype of pre-(pro- thymic stage phenotype. In the present study, two cases showed b2a2, one e1a2, and one negative bcr-abl transcript. The RT-PCR revealed the presence of CD3ε mRNA in all cases, and TdT mRNA in only one case. These results can constitute a basis for the future analysis of T-lineage BC of CML from now on. (Med J Indones 2005; 14: 184-9Keywords: chronic myelogenous leukemia (CML, blastic crisis (BC, T-lineage, bcr-abl fusion gene, CDε, TdT

  8. New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

    Science.gov (United States)

    De La Vega, Francisco M; Dailey, David; Ziegle, Janet; Williams, Julie; Madden, Dawn; Gilbert, Dennis A

    2002-06-01

    Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

  9. [Benefit of rotational exercises for patients with Meniere's syndrome, method used by the ENT department of St-Luc university clinic].

    Science.gov (United States)

    Nyabenda, A; Briart, C; Deggouj, N; Gersdorff, M

    2003-12-01

    To date, the effectiveness of balanced rehabilitation for patients with Meniere's syndrome has not been unanimously acknowledged by all physicians and physiotherapists. The purpose of this study is to assess the therapeutic efficacy of rotational exercises in the treatment of disequilibrium for patients with unilateral Meniere's syndrome. Rotational stimuli were used to symmetrize and reduce postrotatory nystagmic response. Three reference sources were used to assess the efficacy of this management: vestibulospinal function tests: pre- and post-treatment results at the Romberg test, the Unterberger-Fukuda stepping test, the Babinski-Weil test, and gait testing with eyes closed; rotational tests: pre- and post-treatment results; and the self-perceived impact of vertigo: assessed by the Dizziness Handicap Inventory (DHI) and a scale based on the guidelines of the Japanese Society of Equilibrium Research (JSER, 1993). The JSER scale provides quantitative vertigo evaluation; the DHI reflects the patient's perceptual evaluation of handicap. Patients required 11 sessions (mean value) to attain subjective improvement. Of the 23 patients, only seven required optokinetic stimulation (mean requirement: three sessions). Rotational tests and dynamic tests of the vestibulospinal function improved. The DHI and JSER results show that patients' post-rehabilitation perceptual evaluation significantly improved. The objective and subjective measures of disequilibrium in patients with unilateral Meniere's syndrome were significantly improved.

  10. Association mapping for kernel phytosterol content in almond

    Directory of Open Access Journals (Sweden)

    Carolina eFont i Forcada

    2015-07-01

    Full Text Available Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping, also known as linkage disequilibrium, was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance, resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM approach using co-ancestry values from population structure and kinship estimates (K model as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

  11. Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

    Science.gov (United States)

    Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

    2015-01-01

    Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

  12. Surface mu heavy chain signals down-regulation of the V(D)J-recombinase machinery in the absence of surrogate light chain components.

    Science.gov (United States)

    Galler, Gunther R; Mundt, Cornelia; Parker, Mathew; Pelanda, Roberta; Mårtensson, Inga-Lill; Winkler, Thomas H

    2004-06-07

    Early B cell development is characterized by stepwise, ordered rearrangement of the immunoglobulin (Ig) heavy (HC) and light (LC) chain genes. Only one of the two alleles of these genes is used to produce a receptor, a phenomenon referred to as allelic exclusion. It has been suggested that pre-B cell receptor (pre-BCR) signals are responsible for down-regulation of the VDJH-recombinase machinery (Rag1, Rag2, and terminal deoxynucleotidyl transferase [TdT]), thereby preventing further rearrangement on the second HC allele. Using a mouse model, we show that expression of an inducible muHC transgene in Rag2-/- pro-B cells induces down-regulation of the following: (a) TdT protein, (b) a transgenic green fluorescent protein reporter reflecting endogenous Rag2 expression, and (c) Rag1 primary transcripts. Similar effects were also observed in the absence of surrogate LC (SLC) components, but not in the absence of the signaling subunit Ig-alpha. Furthermore, in wild-type mice and in mice lacking either lambda5, VpreB1/2, or the entire SLC, the TdT protein is down-regulated in muHC+LC- pre-B cells. Surprisingly, muHC without LC is expressed on the surface of pro-/pre-B cells from lambda5-/-, VpreB1-/-VpreB2-/-, and SLC-/- mice. Thus, SLC or LC is not required for muHC cell surface expression and signaling in these cells. Therefore, these findings offer an explanation for the occurrence of HC allelic exclusion in mice lacking SLC components.

  13. Scaling of volume to surface ratio and doubling time in growing unicellular organisms: Do cells appear quantum-mechanical systems?

    Science.gov (United States)

    Atanasov, Atanas Todorov

    2014-10-01

    The scaling of physical and biological characteristics of the living organisms is a basic method for searching of new biophysical laws. In series of previous studies the author showed that in Poikilotherms, Mammals and Aves, the volume to surface ratio V×S-1 (m) of organisms is proportional to their generation time Tgt(s) via growth rate v (m s-1): V×S-1 = vgr×Tr. The power and the correlation coefficients are near to 1.0. Aim of this study is: i) to prove with experimental data the validity of the above equation for Unicellular organisms and ii) to show that perhaps, the cells are quantum-mechanical systems. The data for body mass M (kg), density ρ (kg/m3), minimum and maximum doubling time Tdt (s) for 50 unicellular organisms are assembled from scientific sources, and the computer program `Statistics' is used for calculations. In result i) the analytical relationship from type: V×S-1 = 4.46ṡ10-11×Tdt was found, where vgr = 4.46×10-11 m/s and ii) it is shown that the products between cell mass M, cell length expressed by V/S ratio and growth rate vgr satisfied the Heisenberg uncertainty principle i.e. the inequalities V/S×M×vgr>h/2π and Tdt×M×vgr2>h/2π are valid, where h= 6.626×10-34 Jṡs is the Planck constant. This rise the question: do cells appear quantum-mechanical systems?

  14. Structural and population-based evaluations of TBC1D1 p.Arg125Trp.

    Directory of Open Access Journals (Sweden)

    Tom G Richardson

    Full Text Available Obesity is now a leading cause of preventable death in the industrialised world. Understanding its genetic influences can enhance insight into molecular pathogenesis and potential therapeutic targets. A non-synonymous polymorphism (rs35859249, p.Arg125Trp in the N-terminal TBC1D1 phosphotyrosine-binding (PTB domain has shown a replicated association with familial obesity in women. We investigated these findings in the Avon Longitudinal Study of Parents and Children (ALSPAC, a large European birth cohort of mothers and offspring, and by generating a predicted model of the structure of this domain. Structural prediction involved the use of three separate algorithms; Robetta, HHpred/MODELLER and I-TASSER. We used the transmission disequilibrium test (TDT to investigate familial association in the ALSPAC study cohort (N = 2,292 mother-offspring pairs. Linear regression models were used to examine the association of genotype with mean measurements of adiposity (Body Mass Index (BMI, waist circumference and Dual-energy X-ray absorptiometry (DXA assessed fat mass, and logistic regression was used to examine the association with odds of obesity. Modelling showed that the R125W mutation occurs in a location of the TBC1D1 PTB domain that is predicted to have a function in a putative protein:protein interaction. We did not detect an association between R125W and BMI (mean per allele difference 0.27 kg/m(2 (95% Confidence Interval: 0.00, 0.53 P = 0.05 or obesity (odds ratio 1.01 (95% Confidence Interval: 0.77, 1.31, P = 0.96 in offspring after adjusting for multiple comparisons. Furthermore, there was no evidence to suggest that there was familial association between R125W and obesity (χ(2 = 0.06, P = 0.80. Our analysis suggests that R125W in TBC1D1 plays a role in the binding of an effector protein, but we find no evidence that the R125W variant is related to mean BMI or odds of obesity in a general population sample.

  15. Baseline and Multimodal UAV GCS Interface Design

    Science.gov (United States)

    2013-07-01

    complete a computerized version of the NASA - TLX assessment of perceived mental workload. 2.3 Results The baseline condition ran smoothly and with...System MALE Medium-altitude, Long-endurance NASA - TLX NASA Task Load Index SA Situation Awareness TDT Tucker Davis Technologies UAV Uninhabited Aerial

  16. A Headset Method for Measuring the Visual Temporal Discrimination Threshold in Cervical Dystonia

    Directory of Open Access Journals (Sweden)

    Anna Molloy

    2014-07-01

    Full Text Available Background: The visual temporal discrimination threshold (TDT is the shortest time interval at which one can determine two stimuli to be asynchronous and meets criteria for a valid endophenotype in adult‐onset idiopathic focal dystonia, a poorly penetrant disorder. Temporal discrimination is assessed in the hospital laboratory; in unaffected relatives of multiplex adult‐onset dystonia patients distance from the hospital is a barrier to data acquisition. We devised a portable headset method for visual temporal discrimination determination and our aim was to validate this portable tool against the traditional laboratory‐based method in a group of patients and in a large cohort of healthy controls. Methods: Visual TDTs were examined in two groups 1 in 96 healthy control participants divided by age and gender, and 2 in 33 cervical dystonia patients, using two methods of data acquisition, the traditional table‐top laboratory‐based system, and the novel portable headset method. The order of assessment was randomized in the control group. The results obtained by each technique were compared. Results: Visual temporal discrimination in healthy control participants demonstrated similar age and gender effects by the headset method as found by the table‐top examination. There were no significant differences between visual TDTs obtained using the two methods, both for the control participants and for the cervical dystonia patients. Bland–Altman testing showed good concordance between the two methods in both patients and in controls.Discussion: The portable headset device is a reliable and accurate method for visual temporal discrimination testing for use outside the laboratory, and will facilitate increased TDT data collection outside of the hospital setting. This is of particular importance in multiplex families where data collection in all available members of the pedigree is important for exome sequencing studies.

  17. How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet?

    Science.gov (United States)

    Kleidon, Axel

    2012-01-01

    The Earth's chemical composition far from chemical equilibrium is unique in our Solar System, and this uniqueness has been attributed to the presence of widespread life on the planet. Here, I show how this notion can be quantified using non-equilibrium thermodynamics. Generating and maintaining disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. With this approach and associated limits, I show that the ability of abiotic processes to generate geochemical free energy that can be used to transform the surface–atmosphere environment is strongly limited to less than 1 TW. Photosynthetic life generates more than 200 TW by performing photochemistry, thereby substantiating the notion that a geochemical composition far from equilibrium can be a sign for strong biotic activity. Present-day free energy consumption by human activity in the form of industrial activity and human appropriated net primary productivity is of the order of 50 TW and therefore constitutes a considerable term in the free energy budget of the planet. When aiming to predict the future of the planet, we first note that since global changes are closely related to this consumption of free energy, and the demands for free energy by human activity are anticipated to increase substantially in the future, the central question in the context of predicting future global change is then how human free energy demands can increase sustainably without negatively impacting the ability of the Earth system to generate free energy. This question could be evaluated with climate models, and the potential deficiencies in these models to adequately represent the thermodynamics of the Earth system are discussed. Then, I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would

  18. How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet?

    Science.gov (United States)

    Kleidon, Axel

    2012-03-13

    The Earth's chemical composition far from chemical equilibrium is unique in our Solar System, and this uniqueness has been attributed to the presence of widespread life on the planet. Here, I show how this notion can be quantified using non-equilibrium thermodynamics. Generating and maintaining disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. With this approach and associated limits, I show that the ability of abiotic processes to generate geochemical free energy that can be used to transform the surface-atmosphere environment is strongly limited to less than 1 TW. Photosynthetic life generates more than 200 TW by performing photochemistry, thereby substantiating the notion that a geochemical composition far from equilibrium can be a sign for strong biotic activity. Present-day free energy consumption by human activity in the form of industrial activity and human appropriated net primary productivity is of the order of 50 TW and therefore constitutes a considerable term in the free energy budget of the planet. When aiming to predict the future of the planet, we first note that since global changes are closely related to this consumption of free energy, and the demands for free energy by human activity are anticipated to increase substantially in the future, the central question in the context of predicting future global change is then how human free energy demands can increase sustainably without negatively impacting the ability of the Earth system to generate free energy. This question could be evaluated with climate models, and the potential deficiencies in these models to adequately represent the thermodynamics of the Earth system are discussed. Then, I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would

  19. Membrane damage and viability loss of thermally treated and high hydrostatic pressurized E. coli 0157:H7 and Salmonella spp. in apple juice

    Science.gov (United States)

    Differences in membrane damage including leakage of intracellular UV-materials and loss of viability of Salmonella spp. and Escherichia coli O157:H7 bacteria in apple juice following thermal death time disk (TDT) and high hydrostatic pressure treatments were investigated. Salmonella and E. coli O157...

  20. A neurotological study of patients with pontine hyperintense lesions on T2 weighted MRI

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Toru; Tominaga, Satoru; Yukimasa, Akiko; Oku, Masaya; Sakagami, Masafumi [Hyogo Coll. of Medicine, Nishinomiya (Japan)

    2002-03-01

    Pontine hyperintense lesions seen on T2-weighted MRI were thought to be related to disequilibrium. Some of these lesions have a low signal on T1-weighted imaging, while others have an iso-signal. The purpose of this study was to clarify the relationship between neurological findings and pontine lesions detected by MRI. The subjects were 11 patients (6 males, 5 females; age range: 30 to 83 years [mean: 64.1 years]) with pontine hyperintense lesions identified on T2-weighted MRI. We compared the clinical signs and the MRI findings. Six of the patients had low-intensity areas on T1-weighted images, and the other 5 had iso-intensity areas. Six patients complained of vertigo, and 5 complained of dizziness. Eight complained of positionaly evoked disequilibrium. Positional nystagmus was seen in 4 patients. In 9 patients, abnormalities were found on the ENG test, including the saccadic eye movement test, ETT, and OKP. Numbness on the lips occurred in 2 patients, and cerebellar signs were present in 4. None of the patients had facial paralysis. Disequilibrium originating in the central nervous system was suggested in 10 patients. Clinical examinations revealed similar findings in patients with a low signal on T1-weighted MRI and those with an iso-signal. Our results indicate that pontine lesions identified by T2-weighted MRI cause vertigo or dizziness, and, in most cases, these lesions cause abnormal neurological or neurological abnormalities. (author)

  1. A neurotological study of patients with pontine hyperintense lesions on T2 weighted MRI

    International Nuclear Information System (INIS)

    Seo, Toru; Tominaga, Satoru; Yukimasa, Akiko; Oku, Masaya; Sakagami, Masafumi

    2002-01-01

    Pontine hyperintense lesions seen on T2-weighted MRI were thought to be related to disequilibrium. Some of these lesions have a low signal on T1-weighted imaging, while others have an iso-signal. The purpose of this study was to clarify the relationship between neurological findings and pontine lesions detected by MRI. The subjects were 11 patients (6 males, 5 females; age range: 30 to 83 years [mean: 64.1 years]) with pontine hyperintense lesions identified on T2-weighted MRI. We compared the clinical signs and the MRI findings. Six of the patients had low-intensity areas on T1-weighted images, and the other 5 had iso-intensity areas. Six patients complained of vertigo, and 5 complained of dizziness. Eight complained of positionaly evoked disequilibrium. Positional nystagmus was seen in 4 patients. In 9 patients, abnormalities were found on the ENG test, including the saccadic eye movement test, ETT, and OKP. Numbness on the lips occurred in 2 patients, and cerebellar signs were present in 4. None of the patients had facial paralysis. Disequilibrium originating in the central nervous system was suggested in 10 patients. Clinical examinations revealed similar findings in patients with a low signal on T1-weighted MRI and those with an iso-signal. Our results indicate that pontine lesions identified by T2-weighted MRI cause vertigo or dizziness, and, in most cases, these lesions cause abnormal neurological or neurological abnormalities. (author)

  2. The reliability of cytoplasmic CD3 and CD22 antigen expression in the immunodiagnosis of acute leukemia: a study of 500 cases.

    Science.gov (United States)

    Janossy, G; Coustan-Smith, E; Campana, D

    1989-03-01

    Current views about the origin of acute lymphoid leukemia (ALL) emphasize the importance of maturation arrest at a precursor cell level. Recently, the CD22 antigen has been identified in the cytoplasm of normal bone marrow-borne immature B lineage cells, while the CD3 antigen (epsilon chain) has been detected within normal immature thymic blasts. In the first part our study performed on 100 cases of known acute leukemias, the expression of such cytoplasmic molecules, referred to as cCD22 and cCD3, was analyzed together with their appearance in the leukemic cells' membrane (mCD22 and mCD3). The presence of cCD22 in B-lineage ALL and that of cCD3 in T-ALL has indeed fully confirmed the diagnosis reached by other markers, and mCD22 and mCD3 were expressed on only a few cases of B- and T-lineage ALL, also revealing a degree of developmental asynchrony within leukemic blasts. In the subsequent analysis both cCD22 and cCD3 have been included in a standard panel of diagnostic reagents applied on 500 consecutive cases of acute leukemia. Here the aim was to analyze both the diagnostic precision of individual markers and the heterogeneity of various leukemic types in terms of the expression of membrane and intracellular antigens and their cytochemical features (Sudan Black B and esterases). It has been found that cCD22 and cCD3 are exquisitely specific for B-precursor ALL (TdT+, CD19+) and T-ALL (TdT+, CD7+), respectively, while both markers are absent in acute myeloblastic leukemia (AML) and acute myelomonocytic and monocytic leukemia (AMML/AMoL). These observations contrast the findings which demonstrate that 31% of cases among nonlymphoid acute leukemia (including AML and AMML) express CD7 and/or TdT. The study of myeloid antigens detected by CD13, CD33, and CD14 is also informative and complementary, both in diagnosing and subdividing the AML and AMML/AMoL groups. The peculiar main observation of this study is that only with the combined use of these markers in a

  3. Exploiting Topic Pragmatics for New Event Detection in TDT-2003

    National Research Council Canada - National Science Library

    Braun, Ronald K; Kaneshiro, Ryan

    2003-01-01

    .... We combined a number of "pragmatics-based" classifiers in an ensemble-learning framework to identify the first story of a new topic to link subsequent stories together as they unfold across multiple news streams...

  4. Cellular damage of Escherichia coli 0157:H7 and Salmonella spp. in apple juice treated with high hydrostatic pressure and thermal death time disks

    Science.gov (United States)

    Differences in membrane damage including leakage of intracellular UV-materials and loss of viability of Salmonella spp. and Escherichia coli O157:H7 bacteria in apple juice, pH 3.1 following thermal-death-time (TDT) disk and high hydrostatic pressure (HHP) treatments were investigated. Salmonella an...

  5. Neutronics calculation of an heterogeneous compact and thermal core by means of deterministic and stochastic transport theory. Application to the experimental reactor of the University of Strasbourg; Modelisation neutronique d`un coeur thermique compact et heterogene en theorie du transport deterministe et probabiliste. Application au reacteur experimental de l`Universite de Strasbourg

    Energy Technology Data Exchange (ETDEWEB)

    Jammes, Ch

    1997-11-28

    The aim of this work is to create, validate theoretically and experimentally a calculation route for a thermal irradiation reactor. This is the research reactor of the University of Strasbourg, which presents all of characteristics of this reactor-type: compact and heterogeneous core, slab-type fuel with a high 235-uranium enrichment. This calculation route is based on the first use of the following two modern transport methods: the TDT method and the Monte Carlo method. The former, programmed within the APOLLO2 code, is a two dimensional collision probabilities method. The later, used by the TRIPOLI4 code, is a stochastic method. Both can be applied to complex geometries. After a few theoretical reminders about transport codes, a set of integral experiments is described which have been realized within the research reactor of the University of Strasbourg. One of them has been performed for this study. At the beginning of the theoretical part, significant errors are apparent due to the use of calculation route based on homogenization, condensation and the diffusion approximation. An extensive comparison between the discrete ordinates method and the TDT method carries out that the use of the TDT method is relevant for the studied reactor. The treatment of axial leakage with this method is the only disadvantage. Therefore, the use of the code TRIPOLI4 is recommended for a more accurate study of leakage within a reflector. By means of the experimental data, the ability of our calculation route is confirmed for essential neutronics questions such as the critical mass determination, the power distribution and the fuel management. (author)

  6. PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size

    Directory of Open Access Journals (Sweden)

    Camp Nicola J

    2006-04-01

    Full Text Available Abstract Background We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families. Results The results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10–2.35, p = 0.019. Conclusion PedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate NBS1 may play a role in the genetic etiology of heritable breast cancer.

  7. Purification and characterization of fetal hematopoietic cells that express the common acute lymphoblastic leukemia antigen (CALLA)

    DEFF Research Database (Denmark)

    Hokland, P; Rosenthal, P; Griffin, J D

    1983-01-01

    lymphoblastic leukemia cell with respect to surface marker phenotype. A population of CALLA- cells devoid of mature erythroid and myeloid surface markers was found to contain higher numbers of TdT+ cells but lower numbers of cyto-mu, B1, and Ia+ cells than the CALLA+ subset. In vitro analysis of normal...

  8. Adapting Structuration Theory as a Comprehensive Theory for Distance Education: The ASTIDE Model

    Science.gov (United States)

    Aktaruzzaman, Md; Plunkett, Margaret

    2016-01-01

    Distance Education (DE) theorists have argued about the requirement for a theory to be comprehensive in a way that can explicate many of the activities associated with DE. Currently, Transactional Distance Theory (TDT) (Moore, 1993) and the Theory of Instructional Dialogue (IDT) (Caspi & Gorsky, 2006) are the most prominent theories, yet they…

  9. Palaeoclimate significance of speleothems in crystalline rocks: a test case from the Late Glacial and early Holocene (Vinschgau, northern Italy)

    Science.gov (United States)

    Koltai, Gabriella; Cheng, Hai; Spötl, Christoph

    2018-03-01

    Partly coeval flowstones formed in fractured gneiss and schist were studied to test the palaeoclimate significance of this new type of speleothem archive on a decadal-to-millennial timescale. The samples encompass a few hundred to a few thousand years of the Late Glacial and the early Holocene. The speleothem fabric is primarily comprised of columnar fascicular optic calcite and acicular aragonite, both indicative of elevated Mg / Ca ratios in the groundwater. Stable isotopes suggest that aragonite is more prone to disequilibrium isotope fractionation driven by evaporation and prior calcite/aragonite precipitation than calcite. Changes in mineralogy are therefore attributed to these two internal fracture processes rather than to palaeoclimate. Flowstones formed in the same fracture show similar δ18O changes on centennial scales, which broadly correspond to regional lacustrine δ18O records, suggesting that such speleothems may provide an opportunity to investigate past climate conditions in non-karstic areas. The shortness of overlapping periods in flowstone growth and the complexity of in-aquifer processes, however, render the establishment of a robust stacked δ18O record challenging.

  10. An efficient study design to test parent-of-origin effects in family trios.

    Science.gov (United States)

    Yu, Xiaobo; Chen, Gao; Feng, Rui

    2017-11-01

    Increasing evidence has shown that genes may cause prenatal, neonatal, and pediatric diseases depending on their parental origins. Statistical models that incorporate parent-of-origin effects (POEs) can improve the power of detecting disease-associated genes and help explain the missing heritability of diseases. In many studies, children have been sequenced for genome-wide association testing. But it may become unaffordable to sequence their parents and evaluate POEs. Motivated by the reality, we proposed a budget-friendly study design of sequencing children and only genotyping their parents through single nucleotide polymorphism array. We developed a powerful likelihood-based method, which takes into account both sequence reads and linkage disequilibrium to infer the parental origins of children's alleles and estimate their POEs on the outcome. We evaluated the performance of our proposed method and compared it with an existing method using only genotypes, through extensive simulations. Our method showed higher power than the genotype-based method. When either the mean read depth or the pair-end length was reasonably large, our method achieved ideal power. When single parents' genotypes were unavailable or parental genotypes at the testing locus were not typed, both methods lost power compared with when complete data were available; but the power loss from our method was smaller than the genotype-based method. We also extended our method to accommodate mixed genotype, low-, and high-coverage sequence data from children and their parents. At presence of sequence errors, low-coverage parental sequence data may lead to lower power than parental genotype data. © 2017 WILEY PERIODICALS, INC.

  11. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus populations

    Directory of Open Access Journals (Sweden)

    Li Meng-Hua

    2010-08-01

    Full Text Available Abstract Background Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1 and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively were significantly (P FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.

  12. The extinction of Equidae and Proboscidea in South America. A test using Carbon isotope data

    Directory of Open Access Journals (Sweden)

    Prado, J. L.

    2011-12-01

    Full Text Available Carbon isotopes, preserved in 166 samples of fossil teeth and bone, provide key data for understanding the ecology of extinct horses and gomphotheres during the Plio-Pleistocene in South America. To analyze the patterns of dietary partitioning throughout this time we divided the samples into 19 groups, taking into account the genus and the age of the corresponding localities. In this study, the diets of both groups are assessed to test extinction hypotheses. The strong resource partitioning among herbivores assumed under Co-evolutionary disequilibrium hypothesis is supported by isotopic data of horses from latest Pleistocene. Hippidon and Equus had very different diets. In contrast, species of gomphotheres from late Pleistocene in South America seem to have had less specialized diets containing a broad mix of both C3 and C4 plants, which is in line with the dietary assumptions of the mosaic-nutrient hypothesis, but does not support the assumptions of Co-evolutionary disequilibrium hypothesis.

    Los isótopos del carbono preservados en 166 muestras de dientes y huesos fósiles son un dato clave para entender la ecología de los de caballos y gonfoterios durante el Plio-Pleistoceno en América del Sur. Para analizar los cambios en las reconstrucciones de la dieta durante este lapso temporal hemos dividido las muestras en 19 grupos, teniendo en cuenta la sistemática y la cronología de cada localidad. En este estudio, las dietas de ambos grupos son evaluadas para probar las hipótesis sobre su extinción. El alto fraccionamiento en el uso de los recursos entre los herbívoros que asume la hipótesis del desequilibrio co-evolutivo es sustentada por los datos isotópicos de los caballos del Pleistoceno tardío. Hippidion y Equus tenían una dieta muy diferente. En contraste, las especies de gonfoterios de finales del Pleistoceno parecen tener una dieta menos especializada con una combinación de

  13. Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2008-01-01

    Full Text Available Abstract Background Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs and short insertion and/or deletions (indels to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (θ = 0.0056, as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88. Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2, with a large proportion of the inbred lines being assigned to one of them (G1. Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance. Conclusion Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop

  14. Synergistic effect of alkaline pretreatment and Fe dosing on batch anaerobic digestion of maize straw

    International Nuclear Information System (INIS)

    Khatri, Shailendra; Wu, Shubiao; Kizito, Simon; Zhang, Wanqin; Li, Jiaxi; Dong, Renjie

    2015-01-01

    Highlights: • Synergistic effect of NaOH treatment and Fe dosage to maize straw was investigated. • Combining NaOH treatment and Fe dosing resulted in 57% and 56% higher biogas and methane yield respectively. • Combined treatment shortened the technical digestion time from 48 days to 7 days. • Methane content did not differ significantly among the straw treatments. - Abstract: The synergistic effect of alkaline pretreatment and Fe dosing on anaerobic digestion of maize straw was investigated using mesophilic batch reactors. Three straw treatments were investigated as follows: NaOH (4% and 6%) pretreatment, Fe dosage (50, 200, 1000 and 2000 mg/L), and combined NaOH pretreatment and Fe dosage. Compared to the control, NaOH pretreatment alone increased methane yield by 3.5% (313.3 mL CH_4/gVS) and 22.5% (370.9 mL CH_4/gVS) and shortened the technical digestion time (TDT) from 48 days to 19 days and 10 days in 4% NaOH and 6% NaOH pretreatment respectively. Moreover, Fe dosing (200–1000 mg/L) alone gave a methane yield higher (9.4%) than that obtained from 4% NaOH and 7.5% less than the methane yield from 6% NaOH pretreatment; however, the TDT was 10 days longer. Combining NaOH pretreatment and Fe dosage (200–1000 mg/L) significantly increased the methane yield even further to 21.8% (368.8 mL CH_4/gVS) and 56.2% (472.9 mL CH_4/gVS), and shortened TDT from 48 days to 13 days and 7 days in 4% NaOH and 6% NaOH pretreatment respectively. This synergistic effect may be attributed to the fact that the alkaline treatment improved accessibility of the biodegradable fraction of the straw while Fe contributed to increased microbial enzyme activity.

  15. Effect of storage temperature on survival and recovery of thermal and extrusion injured Escherichia coli K-12 in whey protein concentrate and corn meal.

    Science.gov (United States)

    Ukuku, Dike O; Mukhopadhyay, Sudarsan; Onwulata, Charles

    2013-01-01

    Previously, we reported inactivation of Escherichia coli populations in corn product (CP) and whey protein product (WPP) extruded at different temperatures. However, information on the effect of storage temperatures on injured bacterial populations was not addressed. In this study, the effect of storage temperatures on the survival and recovery of thermal death time (TDT) disks and extrusion injured E. coli populations in CP and WPP was investigated. CP and WPP inoculated with E. coli bacteria at 7.8 log(10) CFU/g were conveyed separately into the extruder with a series 6300 digital type T-35 twin screw volumetric feeder set at a speed of 600 rpm and extruded at 35°C, 55°C, 75°C, and 95°C, or thermally treated with TDT disks submerged into water bath set at 35°C, 55°C, 75°C, and 95°C for 120 s. Populations of surviving bacteria including injured cells in all treated samples were determined immediately and every day for 5 days, and up to 10 days for untreated samples during storage at 5°C, 10°C, and 23°C. TDT disks treatment at 35°C and 55°C did not cause significant changes in the population of the surviving bacteria including injured populations. Extrusion treatment at 35°C and 55°C led to significant (pagar plates. The results of this study showed that further inactivation of the injured populations occurred during storage at 5°C for 5 days suggesting the need for immediate storage of 75°C extruded CP and WPP at 5°C for at least 24 h to enhance their microbial safety.

  16. Evolutionary relationships and functional diversity of plant sulfate transporters.

    Science.gov (United States)

    Takahashi, Hideki; Buchner, Peter; Yoshimoto, Naoko; Hawkesford, Malcolm J; Shiu, Shin-Han

    2011-01-01

    Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR, and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal SUL and animal anion exchangers (SLC26). The lineage of plant SULTR family is expanded into four subfamilies (SULTR1-SULTR4) in land plant species. By contrast, the putative SULTR homologs from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4), and the other diverged before the appearance of lineages for SUL, SULTR, and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13) and plant tonoplast-localized dicarboxylate transporters (TDT). The putative sulfur-sensing protein (SAC1) and SAC1-like transporters (SLT) of Chlorophyte green algae, bryophyte, and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  17. Evolutionary relationships and functional diversity of plant sulfate transporters

    Directory of Open Access Journals (Sweden)

    Hideki eTakahashi

    2012-01-01

    Full Text Available Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal sulfate transporters (SUL and animal anion exchangers (SLC26. The lineage of plant SULTR family is expanded into four subfamilies (SULTR1 to SULTR4 in land plant species. By contrast, the putative SULTR homologues from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4, and the other diverged before the appearance of lineages for SUL, SULTR and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13 and plant tonoplast-localized dicarboxylate transporters (TDT. The putative sulfur-sensing protein (SAC1 and SAC1-like transporters (SLT of Chlorophyte green algae, bryophyte and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is completely absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  18. Evaluation of the Atmospheric Chemical Entropy Production of Mars

    Directory of Open Access Journals (Sweden)

    Alfonso Delgado-Bonal

    2015-07-01

    Full Text Available Thermodynamic disequilibrium is a necessary situation in a system in which complex emergent structures are created and maintained. It is known that most of the chemical disequilibrium, a particular type of thermodynamic disequilibrium, in Earth’s atmosphere is a consequence of life. We have developed a thermochemical model for the Martian atmosphere to analyze the disequilibrium by chemical reactions calculating the entropy production. It follows from the comparison with the Earth atmosphere that the magnitude of the entropy produced by the recombination reaction forming O3 (O + O2 + CO2 ⥦ O3 + CO2 in the atmosphere of the Earth is larger than the entropy produced by the dominant set of chemical reactions considered for Mars, as a consequence of the low density and the poor variety of species of the Martian atmosphere. If disequilibrium is needed to create and maintain self-organizing structures in a system, we conclude that the current Martian atmosphere is unable to support large physico-chemical structures, such as those created on Earth.

  19. Antibody repertoire development in fetal and neonatal piglets. XXII. Lambda rearrangement precedes kappa rearrangement during B-cell lymphogenesis in swine

    Science.gov (United States)

    PCR was used to detect VDJ and VJ rearrangement, expression of RAG-1, TdT and VpreB and the presence of signal joint circles (SJC) in an effort to identify sites of B cell lymphogenesis in tissue lysates and sorted leukocytes of fetal and newborn piglets. VDJ, VlambdaJlambda but not VkappaJkappa re...

  20. Structure and function of DNA polymerase μ

    International Nuclear Information System (INIS)

    Matsumoto, Takuro; Maezawa, So

    2013-01-01

    DNA polymerases are enzymes playing the central role in DNA metabolism, including DNA replication, DNA repair and recombination. DNA polymerase μ (pol μ DNA polymerase λ (pol λ) and terminal deoxynucleotidyltransferase (TdT) in X family DNA polymerases function in non-homologous end-joining (NHEJ), which is the predonmiant repair pathway for DNA double-strand breaks (DSBs). NHEJ involves enzymes that capture both ends of the broken DNA strand, bring them together in a synaptic DNA-protein complex, and repair the DSB. Pol μ and pol λ fill in the gaps at the junction to maintain the genomic integrity. TdT synthesizes N region at the junction during V(D)J recombination and promotes diversity of immunoglobulin or T-cell receptor gene. Among these three polymerases, the regulatory mechanisms of pol μ remain rather unclear. We have approached the mechanism of pol μ from both sides of structure and cellular dynamics. Here, we propose some new insights into pol μ and the probable NHEJ model including our findings. (author)

  1. Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.

    Directory of Open Access Journals (Sweden)

    Carolina Font i Forcada

    Full Text Available To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain, and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM approach using co-ancestry values from population structure and kinship estimates (K model as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

  2. Bubble fusion: Preliminary estimates

    International Nuclear Information System (INIS)

    Krakowski, R.A.

    1995-01-01

    The collapse of a gas-filled bubble in disequilibrium (i.e., internal pressure much-lt external pressure) can occur with a significant focusing of energy onto the entrapped gas in the form of pressure-volume work and/or acoustical shocks; the resulting heating can be sufficient to cause ionization and the emission of atomic radiations. The suggestion that extreme conditions necessary for thermonuclear fusion to occur may be possible has been examined parametrically in terms of the ratio of initial bubble pressure relative to that required for equilibrium. In this sense, the disequilibrium bubble is viewed as a three-dimensional ''sling shot'' that is ''loaded'' to an extent allowed by the maximum level of disequilibrium that can stably be achieved. Values of this disequilibrium ratio in the range 10 -5 --10 -6 are predicted by an idealized bubble-dynamics model as necessary to achieve conditions where nuclear fusion of deuterium-tritium might be observed. Harmonic and aharmonic pressurizations/decompressions are examined as means to achieve the required levels of disequilibrium required to create fusion conditions. A number of phenomena not included in the analysis reported herein could enhance or reduce the small levels of nuclear fusions predicted

  3. A family-based association study identified CYP17 as a candidate gene for obesity susceptibility in Caucasians.

    Science.gov (United States)

    Yan, H; Guo, Y; Yang, T-L; Zhao, L-J; Deng, H-W

    2012-08-06

    The cytochrome P450c17α gene (CYP17) encodes a key biosynthesis enzyme of estrogen, which is critical in regulating adipogenesis and adipocyte development in humans. We therefore hypothesized that CYP17 is a candidate gene for predicting obesity. In order to test this hypothesis, we performed a family-based association test to investigate the relationship between the CYP17 gene and obesity phenotypes in a large sample comprising 1873 subjects from 405 Caucasian nuclear families of European origin recruited by the Osteoporosis Research Center of Creighton University, USA. Both single SNPs and haplotypes were tested for associations with obesity-related phenotypes, including body mass index (BMI) and fat mass. We identified three SNPs to be significantly associated with BMI, including rs3740397, rs6163, and rs619824. We further characterized the linkage disequilibrium structure for CYP17 and found that the whole CYP17 gene was located in a single-linkage disequilibrium block. This block was observed to be significantly associated with BMI. A major haplotype in this block was significantly associated with both BMI and fat mass. In conclusion, we suggest that the CYP17 gene has an effect on obesity in the Caucasian population. Further independent studies will be needed to confirm our findings.

  4. Multivariate Analysis, Mass Balance Techniques, and Statistical Tests as Tools in Igneous Petrology: Application to the Sierra de las Cruces Volcanic Range (Mexican Volcanic Belt)

    Science.gov (United States)

    Velasco-Tapia, Fernando

    2014-01-01

    Magmatic processes have usually been identified and evaluated using qualitative or semiquantitative geochemical or isotopic tools based on a restricted number of variables. However, a more complete and quantitative view could be reached applying multivariate analysis, mass balance techniques, and statistical tests. As an example, in this work a statistical and quantitative scheme is applied to analyze the geochemical features for the Sierra de las Cruces (SC) volcanic range (Mexican Volcanic Belt). In this locality, the volcanic activity (3.7 to 0.5 Ma) was dominantly dacitic, but the presence of spheroidal andesitic enclaves and/or diverse disequilibrium features in majority of lavas confirms the operation of magma mixing/mingling. New discriminant-function-based multidimensional diagrams were used to discriminate tectonic setting. Statistical tests of discordancy and significance were applied to evaluate the influence of the subducting Cocos plate, which seems to be rather negligible for the SC magmas in relation to several major and trace elements. A cluster analysis following Ward's linkage rule was carried out to classify the SC volcanic rocks geochemical groups. Finally, two mass-balance schemes were applied for the quantitative evaluation of the proportion of the end-member components (dacitic and andesitic magmas) in the comingled lavas (binary mixtures). PMID:24737994

  5. Multivariate Analysis, Mass Balance Techniques, and Statistical Tests as Tools in Igneous Petrology: Application to the Sierra de las Cruces Volcanic Range (Mexican Volcanic Belt

    Directory of Open Access Journals (Sweden)

    Fernando Velasco-Tapia

    2014-01-01

    Full Text Available Magmatic processes have usually been identified and evaluated using qualitative or semiquantitative geochemical or isotopic tools based on a restricted number of variables. However, a more complete and quantitative view could be reached applying multivariate analysis, mass balance techniques, and statistical tests. As an example, in this work a statistical and quantitative scheme is applied to analyze the geochemical features for the Sierra de las Cruces (SC volcanic range (Mexican Volcanic Belt. In this locality, the volcanic activity (3.7 to 0.5 Ma was dominantly dacitic, but the presence of spheroidal andesitic enclaves and/or diverse disequilibrium features in majority of lavas confirms the operation of magma mixing/mingling. New discriminant-function-based multidimensional diagrams were used to discriminate tectonic setting. Statistical tests of discordancy and significance were applied to evaluate the influence of the subducting Cocos plate, which seems to be rather negligible for the SC magmas in relation to several major and trace elements. A cluster analysis following Ward’s linkage rule was carried out to classify the SC volcanic rocks geochemical groups. Finally, two mass-balance schemes were applied for the quantitative evaluation of the proportion of the end-member components (dacitic and andesitic magmas in the comingled lavas (binary mixtures.

  6. Climate change as (dis)equilibrium

    DEFF Research Database (Denmark)

    Tejsner, Pelle; Veldhuis, Djuke

    2018-01-01

    Despite the evident challenges posed by arctic environments past and present, and despite the widespread acknowledgement that human population histories in the Arctic have historically been quite dynamic, it is often assumed that traditional pre-colonial populations were in perfect equilibrium wi...

  7. Anastomosing Rivers are Disequilibrium Patterns

    NARCIS (Netherlands)

    Lavooi, E.; Haas, de T.; Kleinhans, M.G.; Makaske, B.; Smith, D.G.

    2010-01-01

    Anastomosing rivers have multiple interconnected channels that enclose floodbasins. Various theories have been proposed to explain this pattern, including an increased discharge conveyance and sediment transport capacity of multiple channels, or, alternatively, a tendency to avulse due to upstream

  8. Following the Social Media: Aspect Evolution of Online Discussion

    Science.gov (United States)

    Tang, Xuning; Yang, Christopher C.

    Due to the advance of Internet and Web 2.0 technologies, it is easy to extract thousands of threads about a topic of interest from an online forum but it is nontrivial to capture the blueprint of different aspects (i.e., subtopic, or facet) associated with the topic. To better understand and analyze a forum discussion given topic, it is important to uncover the evolution relationships (temporal dependencies) between different topic aspects (i.e. how the discussion topic is evolving). Traditional Topic Detection and Tracking (TDT) techniques usually organize topics as a flat structure but it does not present the evolution relationships between topic aspects. In addition, the properties of short and sparse messages make the content-based TDT techniques difficult to perform well in identifying evolution relationships. The contributions in this paper are two-folded. We formally define a topic aspect evolution graph modeling framework and propose to utilize social network information, content similarity and temporal proximity to model evolution relationships between topic aspects. The experimental results showed that, by incorporating social network information, our technique significantly outperformed content-based technique in the task of extracting evolution relationships between topic aspects.

  9. GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of th...

  10. Benign paroxysmal positional vertigo and comorbid conditions.

    Science.gov (United States)

    Cohen, Helen S; Kimball, Kay T; Stewart, Michael G

    2004-01-01

    To determine the prevalence of comorbid disease in patients with benign paroxysmal positional vertigo (BPPV) and the relationship of comorbid disease to symptoms of vertigo, disequilibrium, and anxiety. Patients who had posterior semicircular canal BPPV and who had been referred for vestibular rehabilitation at a tertiary care center completed a health status questionnaire and the Vertigo Symptom Scale, answered questions about level of vertigo, and were tested on computerized dynamic posturography. Subjects had high rates of diabetes, mild head trauma, and probable sinus disease. Balance was generally impaired, worse in diabetics and subjects with significant vestibular weakness. Subjects who smoked or had had mild head trauma had higher levels of anxiety. Comorbid conditions, particularly diabetes, mild head trauma, and sinus disease, are unusually prevalent in BPPV patients. Message: Patients with comorbid disease are at risk for having increased vertigo, anxiety, and disequilibrium compared to other patients. Copyright 2004 S. Karger AG, Basel

  11. 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)).

  12. Uranium/thorium dating of Late Pleistocene peat deposits in NW Europe, uranium/thorium isotope systematics and open-system behaviour of peat layers

    NARCIS (Netherlands)

    Heijnis, H.; Plicht, J. van der

    1992-01-01

    The possibility of dating peat by the uranium-series disequilibrium method is discussed. In principle, this method can be used to date peat to approximately 350 ka. The application of the U/Th disequilibrium method (UTD) on peat provides us with the probability of constructing a new chronology for

  13. Synthesis, spectroscopic properties, and photoconductivity of black absorbers consisting of pt(bipyridine)(dithiolate) charge transfer complexes in the presence and absence of nitrofluorenone acceptors.

    Science.gov (United States)

    Browning, Charles; Hudson, Joshua M; Reinheimer, Eric W; Kuo, Fang-Ling; McDougald, Roy N; Rabaâ, Hassan; Pan, Hongjun; Bacsa, John; Wang, Xiaoping; Dunbar, Kim R; Shepherd, Nigel D; Omary, Mohammad A

    2014-11-19

    The diimine-dithiolato ambipolar complexes Pt(dbbpy)(tdt) and Pt(dmecb)(bdt) (dbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine; tdt(2-) = 3,4-toluenedithiolate; dmecb = 4,4'-dimethoxyester-2,2'-bipyridine; bdt(2-) = benzene-1,2-dithiolate) are prepared herein. Pt(dmecb)(bdt) exhibits photoconductivity that remains constant (photocurrent density of 1.6 mA/cm(2) from a 20 nm thin film) across the entire visible region of the solar spectrum in a Schottky diode device structure. Pt(dbbpy)(tdt) acts as donor when combined with the strong nitrofluorenone acceptors 2,7-dinitro-9-fluorenone (DNF), 2,4,7-trinitro-9-fluorenone (TRNF), or 2,4,5,7-tetranitro-9-fluorenone (TENF). Supramolecular charge transfer stacks form and exhibit various donor-acceptor stacking patterns. The crystalline solids are "black absorbers" that exhibit continuous absorptions spanning the entire visible region and significant ultraviolet and near-infrared wavelengths, the latter including long wavelengths that the donor or acceptor molecules alone do not absorb. Absorption spectra reveal the persistence of donor-acceptor interactions in solution, as characterized by low-energy donor/acceptor charge transfer (DACT) bands. Crystal structures show closely packed stacks with distances that underscore intermolecular DACT. (1)H NMR provides further evidence of DACT, as manifested by upfield shifts of aromatic protons in the binary adducts versus their free components, whereas 2D nuclear Overhauser effect spectroscopy (NOESY) spectra suggest coupling between dithiolate donor protons with nitrofluorenone acceptor protons, in correlation with the solid-state stacking. The NMR spectra also show significant peak broadening, indicating some paramagnetism verified by magnetic susceptibility data. Solid-state absorption spectra reveal further red shifts and increased relative intensities of DACT bands for the solid adducts vs solution, suggesting cooperativity of the DACT phenomenon in the solid state, as further

  14. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations.

    Science.gov (United States)

    Duan, Qing; Xu, Zheng; Raffield, Laura M; Chang, Suhua; Wu, Di; Lange, Ethan M; Reiner, Alex P; Li, Yun

    2018-04-01

    Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA. © 2017 WILEY PERIODICALS, INC.

  15. A New Role for LOC101928437 in Non-Syndromic Intellectual Disability: Findings from a Family-Based Association Test.

    Science.gov (United States)

    Zhou, Shaohe; Shi, Zhangyan; Cui, Meng; Li, Junlin; Ma, Zhe; Shi, Yuanyu; Zheng, Zijian; Zhang, Fuchang; Jin, Tianbo; Geng, Tingting; Chen, Chao; Guo, Yale; Zhou, Jianping; Huang, Shaoping; Guo, Xingli; Gao, Lin; Gong, Pingyuan; Gao, Xiaocai; Zhang, Kejin

    2015-01-01

    Non-syndromic intellectual disability (NSID) is mental retardation in persons of normal physical appearance who have no recognisable features apart from obvious deficits in intellectual functioning and adaptive ability; however, its genetic etiology of most patients has remained unknown. The main purpose of this study was to fine map and identify specific causal gene(s) by genotyping a NSID family cohort using a panel of markers encompassing a target region reported in a previous work. A total of 139 families including probands, parents and relatives were included in the household survey, clinical examinations and intelligence tests, recruited from the Qinba mountain region of Shannxi province, western China. A collection of 34 tagged single nucleotide polymorphisms (tSNPs) spanning five microsatellite marker (STR) loci were genotyped using an iPLEX Gold assay. The association between tSNPs and patients was analyzed by family-based association testing (FBAT) and haplotype analysis (HBAT). Four markers (rs5974392, rs12164331, rs5929554 and rs3116911) in a block that showed strong linkage disequilibrium within the first three introns of the LOC101928437 locus were found to be significantly associated with NSID (all P<0.01) by the FBAT method for a single marker in additive, dominant and recessive models. The results of haplotype tests of this block also revealed a significant association with NSID (all P<0.05) using 2-window and larger HBAT analyses. These results suggest that LOC101928437 is a novel candidate gene for NSID in Han Chinese individuals of the Qinba region of China. Although the biological function of the gene has not been well studied, knowledge about this gene will provide insights that will increase our understanding of NSID development.

  16. A New Role for LOC101928437 in Non-Syndromic Intellectual Disability: Findings from a Family-Based Association Test.

    Directory of Open Access Journals (Sweden)

    Shaohe Zhou

    Full Text Available Non-syndromic intellectual disability (NSID is mental retardation in persons of normal physical appearance who have no recognisable features apart from obvious deficits in intellectual functioning and adaptive ability; however, its genetic etiology of most patients has remained unknown. The main purpose of this study was to fine map and identify specific causal gene(s by genotyping a NSID family cohort using a panel of markers encompassing a target region reported in a previous work. A total of 139 families including probands, parents and relatives were included in the household survey, clinical examinations and intelligence tests, recruited from the Qinba mountain region of Shannxi province, western China. A collection of 34 tagged single nucleotide polymorphisms (tSNPs spanning five microsatellite marker (STR loci were genotyped using an iPLEX Gold assay. The association between tSNPs and patients was analyzed by family-based association testing (FBAT and haplotype analysis (HBAT. Four markers (rs5974392, rs12164331, rs5929554 and rs3116911 in a block that showed strong linkage disequilibrium within the first three introns of the LOC101928437 locus were found to be significantly associated with NSID (all P<0.01 by the FBAT method for a single marker in additive, dominant and recessive models. The results of haplotype tests of this block also revealed a significant association with NSID (all P<0.05 using 2-window and larger HBAT analyses. These results suggest that LOC101928437 is a novel candidate gene for NSID in Han Chinese individuals of the Qinba region of China. Although the biological function of the gene has not been well studied, knowledge about this gene will provide insights that will increase our understanding of NSID development.

  17. TDT-2002 Topic Tracking at Maryland: First Experiments with the Lemur Toolkit

    National Research Council Canada - National Science Library

    He, Daqing; Park, Hyuk R; Murray, G. C; Subotin, Michael; Oard, Douglas W

    2003-01-01

    .... Two of the Perl runs used native Arabic orthography with two-best translation based on a statistical lexicon, obtaining similar results to those obtained with the Arabic-to-English translations...

  18. The importance of a sub-region on chromosome 19q13.3 for prognosis of multiple myeloma patients after high-dose treatment and stem cell support: a linkage disequilibrium mapping in RAI and CD3EAP

    DEFF Research Database (Denmark)

    Vangsted, Annette Juul; Klausen, Tobias Wirenfeldt; Gimsing, Peter

    2011-01-01

    The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor ¿B (NF-¿B). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated with inte......The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor ¿B (NF-¿B). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated...... with interferon-a (INF-a) as maintenance treatment, 177 patients treated with thalidomide, and 74 patients treated with bortezomib at relapse and address if the effects of polymorphisms in CD3EAP and RAI are modified by a functional polymorphism in NF¿B1. By linkage disequilibrium mapping, we found that variant...... alleles of several polymorphisms in a sub-region of 19q13.3 spanning the regions RAI-intron1-1 to RAI intron1-3 and the region exon1 to exon3-6 in CD3EAP were associated with prolonged time-to-treatment failure (TTF; p¿=¿0.003) and overall survival (OS; p¿=¿0.02). Haplotype analyses revealed that none...

  19. The importance of a sub-region on chromosome 19q13.3 for prognosis of multiple myeloma patients after high-dose treatment and stem cell support: a linkage disequilibrium mapping in RAI and CD3EAP

    DEFF Research Database (Denmark)

    Vangsted, Annette J.; Klausen, Tobias Wirenfeldt; Gimsing, Peter

    2011-01-01

    The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor κB (NF–κB). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated with inte......The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor κB (NF–κB). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated...... with interferon-α (INF-α) as maintenance treatment, 177 patients treated with thalidomide, and 74 patients treated with bortezomib at relapse and address if the effects of polymorphisms in CD3EAP and RAI are modified by a functional polymorphism in NFКB1. By linkage disequilibrium mapping, we found that variant...... alleles of several polymorphisms in a sub-region of 19q13.3 spanning the regions RAI-intron1-1 to RAI intron1-3 and the region exon1 to exon3–6 in CD3EAP were associated with prolonged time-to-treatment failure (TTF; p = 0.003) and overall survival (OS; p = 0.02). Haplotype analyses revealed that none...

  20. Some inconvenient truths about biosignatures involving two chemical species on Earth-like exoplanets.

    Science.gov (United States)

    Rein, Hanno; Fujii, Yuka; Spiegel, David S

    2014-05-13

    The detection of strong thermochemical disequilibrium in the atmosphere of an extrasolar planet is thought to be a potential biosignature. In this article we present a previously unidentified kind of false positive that can mimic a disequilibrium or any other biosignature that involves two chemical species. We consider a scenario where the exoplanet hosts a moon that has its own atmosphere and neither of the atmospheres is in chemical disequilibrium. Our results show that the integrated spectrum of the planet and the moon closely resembles that of a single object in strong chemical disequilibrium. We derive a firm limit on the maximum spectral resolution that can be obtained for both directly imaged and transiting planets. The spectral resolution of even idealized space-based spectrographs that might be achievable in the next several decades is in general insufficient to break the degeneracy. Both chemical species can only be definitively confirmed in the same object if absorption features of both chemicals can be unambiguously identified and their combined depth exceeds 100%.

  1. Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression.

    Science.gov (United States)

    Hüls, Anke; Ickstadt, Katja; Schikowski, Tamara; Krämer, Ursula

    2017-06-12

    SNPs estimated by a multivariate elastic net regression were shown to be a powerful tool to detect gene-environment interactions in scenarios of high Linkage disequilibrium and noise.

  2. Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster.

    Science.gov (United States)

    Tatarenkov, Andrey; Ayala, Francisco J

    2007-08-01

    We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.

  3. An overview of selected NASP aeroelastic studies at the NASA Langley Research Center

    Science.gov (United States)

    Spain, Charles V.; Soistmann, David L.; Parker, Ellen C.; Gibbons, Michael D.; Gilbert, Michael G.

    1990-01-01

    Following an initial discussion of the NASP flight environment, the results of recent aeroelastic testing of NASP-type highly swept delta-wing models in Langley's Transonic Dynamics Tunnel (TDT) are summarized. Subsonic and transonic flutter characteristics of a variety of these models are described, and several analytical codes used to predict flutter of these models are evaluated. These codes generally provide good, but conservative predictions of subsonic and transonic flutter. Also, test results are presented on a nonlinear transonic phenomena known as aileron buzz which occurred in the wind tunnel on highly swept delta wings with full-span ailerons. An analytical procedure which assesses the effects of hypersonic heating on aeroelastic instabilities (aerothermoelasticity) is also described. This procedure accurately predicted flutter of a heated aluminum wing on which experimental data exists. Results are presented on the application of this method to calculate the flutter characteristics of a fine-element model of a generic NASP configuration. Finally, it is demonstrated analytically that active controls can be employed to improve the aeroelastic stability and ride quality of a generic NASP vehicle flying at hypersonic speeds.

  4. Hematological remission and long term hematological control of acute myeloblastic leukemia induced and maintained by granulocyte-colony stimulating factor (G-CSF) therapy.

    Science.gov (United States)

    Xavier, Luciana; Cunha, Manuel; Gonçalves, Cristina; Teixeira, Maria dos Anjos; Coutinho, Jorge; Ribeiro, António Carlos Pinto; Lima, Margarida

    2003-12-01

    We describe a case of a patient with CD34+, TdT+, CD13-, CD33-, MPO- undifferentiated acute leukemia who refused chemotherapy and who achieved complete hematological remission 14 months after the diagnosis, during a short course of granulocyte-colony stimulating factor (G-CSF) for neutropenia and life threatening infection. Relapse occurred approximately one year later and G-CSF was reintroduced, being maintained for 4 months, at a dose and frequency adapted to maintain normal blood counts, a complete hematological remission being achieved again. Five months after withdrawing the G-CSF therapy a second relapse was observed; G-CSF was tried again with success, resulting in a very good hematological response that was sustained by G-CSF maintenance therapy. One year latter there was the need of increasing the doses of G-CSF in order to obtain the same hematological effect, at same time blast cells acquired a more mature CD34+, TdT-, CD13+, CD33-, MPO+ myeloid phenotype. Finally, the patient developed progressive neutropenia, anemia, thrombocytopenia and acute leukemia in spite of G-CSF therapy, dying 64 months after initial diagnosis (50 months after starting G-CSF therapy) with overt G-CSF resistant acute myeloblastic leukemia (AML), after failure of conventional induction chemotherapy.

  5. Development of a simple gel permeation clean-up procedure coupled to a rapid disequilibrium enzyme-linked immunosorbent assay (ELISA) for the detection of Sudan I dye in spices and sauces.

    Science.gov (United States)

    Oplatowska, Michalina; Stevenson, Paul J; Schulz, Claudia; Hartig, Lutz; Elliott, Christopher T

    2011-09-01

    Sudan dyes have been found to be added to chilli and chilli products for illegal colour enhancement purposes. Due to the possible carcinogenic effect, they are not authorized to be used in food in the European Union or the USA. However, over the last few years, many products imported from Asian and African countries have been reported via the Rapid Alert System for Food and Feed in the European Union to be contaminated with these dyes. In order to provide fast screening method for the detection of Sudan I (SI), which is the most widely abused member of Sudan dyes family, a unique (20 min without sample preparation) direct disequilibrium enzyme-linked immunosorbent assay (ELISA) was developed. The assay was based on polyclonal antibodies highly specific to SI. A novel, simple gel permeation chromatography clean-up method was developed to purify extracts from matrices containing high amounts of fat and natural pigments, without the need for a large dilution of the sample. The assay was validated according to the Commission Decision 2002/657/EC criteria. The detection capability was determined to be 15 ng g(-1) in sauces and 50 ng g(-1) in spices. The recoveries found ranged from 81% to 116% and inter- and intra-assay coefficients of variation from 6% to 20%. The assay was used to screen a range of products (85 samples) collected from different retail sources within and outside the European Union. Three samples were found to contain high amounts (1,649, 722 and 1,461 ng g(-1)) of SI by ELISA. These results were confirmed by liquid chromatography-tandem mass spectrometry method. The innovative procedure allows for the fast, sensitive and high throughput screening of different foodstuffs for the presence of the illegal colorant SI.

  6. VULCAN: An Open-source, Validated Chemical Kinetics Python Code for Exoplanetary Atmospheres

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Shang-Min; Grosheintz, Luc; Kitzmann, Daniel; Heng, Kevin [University of Bern, Center for Space and Habitability, Sidlerstrasse 5, CH-3012, Bern (Switzerland); Lyons, James R. [Arizona State University, School of Earth and Space Exploration, Bateman Physical Sciences, Tempe, AZ 85287-1404 (United States); Rimmer, Paul B., E-mail: shang-min.tsai@space.unibe.ch, E-mail: kevin.heng@csh.unibe.ch, E-mail: jimlyons@asu.edu [University of St. Andrews, School of Physics and Astronomy, St. Andrews, KY16 9SS (United Kingdom)

    2017-02-01

    We present an open-source and validated chemical kinetics code for studying hot exoplanetary atmospheres, which we name VULCAN. It is constructed for gaseous chemistry from 500 to 2500 K, using a reduced C–H–O chemical network with about 300 reactions. It uses eddy diffusion to mimic atmospheric dynamics and excludes photochemistry. We have provided a full description of the rate coefficients and thermodynamic data used. We validate VULCAN by reproducing chemical equilibrium and by comparing its output versus the disequilibrium-chemistry calculations of Moses et al. and Rimmer and Helling. It reproduces the models of HD 189733b and HD 209458b by Moses et al., which employ a network with nearly 1600 reactions. We also use VULCAN to examine the theoretical trends produced when the temperature–pressure profile and carbon-to-oxygen ratio are varied. Assisted by a sensitivity test designed to identify the key reactions responsible for producing a specific molecule, we revisit the quenching approximation and find that it is accurate for methane but breaks down for acetylene, because the disequilibrium abundance of acetylene is not directly determined by transport-induced quenching, but is rather indirectly controlled by the disequilibrium abundance of methane. Therefore we suggest that the quenching approximation should be used with caution and must always be checked against a chemical kinetics calculation. A one-dimensional model atmosphere with 100 layers, computed using VULCAN, typically takes several minutes to complete. VULCAN is part of the Exoclimes Simulation Platform (ESP; exoclime.net) and publicly available at https://github.com/exoclime/VULCAN.

  7. Closed expressions for $\\int_{0}^{1} t^{-1} log^{n-1}t log^{p}(1 - t) dt$

    CERN Document Server

    Kölbig, Kurt Siegfried

    1982-01-01

    Closed expressions for the integral integral /sub 0//sup 1/ t/sup -1/ log/sup n-1/t log/sup p/(1-t)dt, whose general form is given elsewhere, are listed for n=1(1)9, p=1(1)9. A formula is derived which allows an easy evaluation of these expressions by formula manipulation on a computer. The majority of the above expressions are given in a microfiche supplement to the paper.

  8. Predicting Chronic Climate-Driven Disturbances and Their Mitigation

    Energy Technology Data Exchange (ETDEWEB)

    McDowell, Nate G.; Michaletz, Sean T.; Bennett, Katrina E.; Solander, Kurt C.; Xu, Chonggang; Maxwell, Reed M.; Middleton, Richard S.

    2018-01-01

    Society increasingly demands the stable provision of ecosystem resources to support our population. Resource risks from climate-driven disturbances--including drought, heat, insect outbreaks, and wildfire--are rising as a chronic state of disequilibrium results from increasing temperatures and a greater frequency of extreme events. This confluence of increased demand and risk may soon reach critical thresholds. We explain here why extreme chronic disequilibrium of ecosystem function is likely to increase dramatically across the globe, creating no-analog conditions that challenge adaptation. We also present novel mechanistic theory that combines models for disturbance mortality and metabolic scaling to link size-dependent plant mortality to changes in ecosystem stocks and fluxes. Efforts must anticipate and model chronic ecosystem disequilibrium to properly prepare for resilience planning.

  9. The measurement of airborne rodon daughter concentrations in the atmosphere

    International Nuclear Information System (INIS)

    Ha, C.W.; Lee, J.K.; Moon, P.S.

    1979-01-01

    A simple method for determining the airborne concentration of radon daughter products has been developed, which is based on gross alpha counting of the air filter collections at several time intervals after completion of air sampling. The concentration of each nuclide is then obtained from an equation involving the alpha disintegrations, the sampling time, and the known numerical coefficients. The state of radioactive disequilibrium is also inventigated. The atmosphere sampled in the TRIGA Mark-III reactor room was largely in disequilibrium. The extent of radioactive disequilibrium between radon daughter products seems likely depend on sampling times associated with turbulence conditions. The data obtained here will certainly provide useful information on the evaluation of internal exposure and calibration of effluent monitoring instruments. (author)

  10. Subsonic Ultra Green Aircraft Research. Phase II - Volume I; Truss Braced Wing Design Exploration

    Science.gov (United States)

    Bradley, Marty K.; Droney, Christopher K.; Allen, Timothy J.

    2015-01-01

    This report summarizes the Truss Braced Wing (TBW) work accomplished by the Boeing Subsonic Ultra Green Aircraft Research (SUGAR) team, consisting of Boeing Research and Technology, Boeing Commercial Airplanes, General Electric, Georgia Tech, Virginia Tech, NextGen Aeronautics, and Microcraft. A multi-disciplinary optimization (MDO) environment defined the geometry that was further refined for the updated SUGAR High TBW configuration. Airfoil shapes were tested in the NASA TCT facility, and an aeroelastic model was tested in the NASA TDT facility. Flutter suppression was successfully demonstrated using control laws derived from test system ID data and analysis models. Aeroelastic impacts for the TBW design are manageable and smaller than assumed in Phase I. Flutter analysis of TBW designs need to include pre-load and large displacement non-linear effects to obtain a reasonable match to test data. With the updated performance and sizing, fuel burn and energy use is reduced by 54% compared to the SUGAR Free current technology Baseline (Goal 60%). Use of the unducted fan version of the engine reduces fuel burn and energy by 56% compared to the Baseline. Technology development roadmaps were updated, and an airport compatibility analysis established feasibility of a folding wing aircraft at existing airports.

  11. The rs10757278 Polymorphism of the 9p21.3 Locus in Children with Arterial Ischemic Stroke: A Family-Based and Case-Control Study.

    Science.gov (United States)

    Niemiec, Pawel; Balcerzyk, Anna; Iwanicki, Tomasz; Emich-Widera, Ewa; Kopyta, Ilona; Nowak, Tomasz; Pilarska, Ewa; Pienczk-Ręcławowicz, Karolina; Kaciński, Marek; Wendorff, Janusz; Gorczynska-Kosiorz, Sylwia; Trautsolt, Wanda; Grzeszczak, Władysław; Zak, Iwona

    2017-12-01

    The association of 9p21.3 locus single nucleotide polymorphisms with arterial ischemic stroke in adults was demonstrated in many studies, but there are no studies in pediatric arterial ischemic stroke patients. We investigated whether the 9p21.3 locus polymorphism, namely rs10757278, is associated with the arterial ischemic stroke risk in children. The study group consisted of 335 individuals: 80 children with arterial ischemic stroke, their biological parents (n = 122), and 133 children (age and sex matched) without any symptoms of arterial ischemic stroke as a control group. The rs10757278 polymorphism was genotyped using the TaqMan® Pre-designed SNP Genotyping Assay (Applied Biosystems). Two different study design models were used: family-based association test (transmission-disequilibrium test) and case-control model. There were no statistically significant differences in the distribution of genotypes and alleles of the rs10757278 polymorphism between groups of children with arterial ischemic stroke and controls. The frequency of both transmitted alleles in transmission-disequilibrium test analysis was identical (50%). The A allele carrier state (AA+AG genotype) was more frequent in arterial ischemic stroke children with hemiparesis than in patients without this symptom (94.5% versus 68.0%, P = .004). There is no evidence to consider the 9p21.3 locus polymorphism as a risk factor for childhood arterial ischemic stroke. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  12. How Terrorism Works: Terrorism as a Disequalizing Input to the Social System

    Science.gov (United States)

    2007-12-01

    28 Johnson contends that when values and environments are not in balance, disequilibrium occurs. This imbalance or disequilibrium is necessary...would argue that the competition for resources, status, or power is our natural state. They contend that social change occurs as a result of these...offered as a framework for academic debate and policy rumination , not for those mounting-up for tomorrows patrol. D. FUTURE RESEARCH 1. Warfare

  13. Association of the TPO gene in Colombian families with type 1 diabetes Asociación del gen TPO en familias colombianas con la diabetes tipo 1

    Directory of Open Access Journals (Sweden)

    Federico Uribe Londoño

    2009-11-01

    transmission disequilibrium test (TDT.

    It was found that 86% of the patients presented at least one of the three auto-antibodies tested. Both parents and probands were found in HWE for both SNPs. In addition, the two markers were found in tight LD (p < 0.0001. A haplotype associated with susceptibility to the disease was identified (p = 0.0116.

    Autoimmunity was found in a proportion similar to that previously reported. It was found that a haplotype at TPO gene is associated with the disease. Such haplotype is characterized by alleles G and A at rs4927611 and rs732609 SNPs, respectively. Our results suggest a possible causative participation of the TPO gene in T1D. In order to verify them, a sample of equivalent size is currently being collected, from the same population in Colombia.

    Hemos encontrado ligamiento y asociación de la diabetes mellitus tipo 1 (T1D con 2p25. En esta región se halla el gen TPO. Nuestro objetivo fue estudiar la asociación de dicho gen con la susceptibilidad a la T1D en un grupo de familias colombianas, todas ellas originarias de Antioquia, una población especial en el noroccidente del país. Se analizaron cien tríos familiares con T1D. Estas familias ya habían sido estudiadas para anticuerpos contra la ácido-glutámico-descarboxilasa (GAD y el locus marcador D2S319

  14. Common variations in ALG9 are not associated with bipolar I disorder: a family-based study

    Directory of Open Access Journals (Sweden)

    Bacanu Silviu-Alin

    2006-07-01

    Full Text Available Abstract Background A mannosyltransferase gene (ALG9, DIBD1 at chromosome band 11q23 was previously identified to be disrupted by a balanced chromosomal translocation t(9;11(p24;q23 co-segregating with bipolar affective disorder in a small family. Inborn ALG9 deficiency (congenital disorders of glycosylation type IL is associated with progressive microcephaly, seizures, developmental delay, and hepatomegaly. It is unknown whether common variations of ALG9 predispose to bipolar affective disorder. Methods We tested five polymorphic markers spanning ALG9 (three intragenic and one upstream microsatellite repeats and one common missense variation, V289I (rs10502151 for their association with bipolar I disorder in two pedigree series. The NIMH (National Institute of Mental Health pedigrees had a total of 166 families showing transmissions to 250 affected offspring, whereas The PITT (The University of Pittsburgh pedigrees had a total of 129 families showing transmissions to 135 cases. We used transmission disequilibrium test for the association analyses. Results We identified three common and distinct haplotypes spanning the ALG9 gene. We found no statistically-significant evidence of transmission disequilibrium of marker alleles or multi-marker haplotypes to the affected offspring with bipolar I disorder. Conclusion These results suggest that common variations in ALG9 do not play a major role in predisposition to bipolar affective disorder.

  15. Effect of flomoxef on blood coagulation and alcohol metabolism.

    Science.gov (United States)

    Uchida, K; Matsubara, T

    1991-01-01

    The effect of flomoxef, a newly developed oxacephem antibiotic with an N-hydroxyethyltetrazolethiol (HTT) side chain, on blood coagulation and alcohol metabolism was compared with that of a series of cephalosporin antibiotics with N-methyltetrazolethiol (NMTT), thiadiazolethiol (TDT) or methylthiadiazolethiol (MTDT) side chains in position 3' of the cephalosporin nucleus known to cause hypoprothrombinemia and bleeding in patients who are malnourished, debilitated and/or of high age. A disulfiram-like effect caused by inhibition of aldehyde dehydrogenase was observed for NMTT-containing antibiotics. Studies were carried out on healthy volunteers and on rats. Eight-day treatment with 2 g flomoxef i.v. once or twice daily in five and six healthy male volunteers, respectively, did not cause any significant changes in prothrombin time (PT), coagulation factors II, VII, IX or X, in hepaplastin values or fibrinogen levels, activated partial thromboplastin time (APTT), platelet counts, bleeding time, or collagen- and ADP-induced platelet aggregation. Inhibition of vitamin K epoxide reductase was observed in rats treated with flomoxef, yet to a much lesser extent than observed for cephalosporins with NMTT, TDT or MTDT side chains. This defect was quickly normalized by vitamin K injection. There were no differences between oxacephem (1-O) and cephem (1-S) compounds with respect to effects on blood clotting and platelet aggregation. Flomoxef and its side chain HTT showed no influence on alcohol metbolism.

  16. Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis).

    Science.gov (United States)

    Kapheim, Karen M; Pollinger, John P; Wcislo, William T; Wayne, Robert K

    2009-11-01

    We developed a library of twelve polymorphic di- and tri-nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7-20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy-Weinberg equilibrium proportions or was found to be in gametic disequilibrium. © 2009 Blackwell Publishing Ltd.

  17. Nerovnováha na peněžním trhu v teorii endogenních peněz

    OpenAIRE

    Korda, Jan

    2007-01-01

    The thesis deals with monetary disequilibrium in the theory of endogenous money. In the new consensus economics, money is endogenous and passive. Money market is not considered and if yes, then only in an implicit equilibrium, whereas mechanisms ensuring this equilibrium are not discussed. In post-Keynesian economics, there is an explicit discussion, whether monetary disequilibrium may occur. Horizontalists argued for equality of money supply and money demand. On the other hand, arguments of ...

  18. Assessment of sedimentation rate based on disequilibrium in the {sup 232}Th decay series in an artificial pond downstream a former uranium mine

    Energy Technology Data Exchange (ETDEWEB)

    Reyss, J.L. [Laboratoire des Sciences du Climat et de l' Environnement - LSCE/IPSL, Unite Mixte de Recherche 8212 CEA, CNRS, UVSQ, F-91198 Gif-sur-Yvette Cedex (France); Mangeret, A.; Courbet, C.; Saadi, Z.; Guillevic, J. [Institut de Radioprotection et de Surete Nucleaire (IRSN), BP 17, 92262 Fontenay aux Roses (France); Thouvenot, A. [LMGE, UMR CNRS 6023, Lab Microorganismes Genome et Environnement, 63 177 Aubiere (France)

    2014-07-01

    In rivers and lakes, sediment dynamics are very difficult to quantify by field measurements as well as by modeling studies (Olley et al. 1997 WRR 33, 1319-1326). The well-known {sup 210}Pb excess method (Appleby 2000 Limnology 59-S.1, 1-14; Perga et al. 2010 Limnol. and Ocean. 55, 803-816) cannot be used for quantifying sedimentation rates over granitic catchments as large amounts of {sup 210}Pb produced by granite weathering tend to dilute the atmospheric {sup 210}Pb. The knowledge of sedimentation rates in lakes is however very important for understanding the geochemical mechanisms involved in contaminant scavenging and remobilization at the sediment-water interface (SWI). Moreover, these measurements are crucial for developing solute transport models, especially for radionuclides and metals in pore waters and through the SWI. In order to overcome these issues, this study focuses on an artificial pound located in a granitic catchment, down-gradient from a former uranium mining site that ceased operations at the beginning of the 80's (Guillevic and Reyss 2011 ICRER 2011). Sediment sampling was carried out in this artificial lake with an UWITEC{sup R} hand corer. All the samples were dried and the activities of artificial and natural radionuclides were measured by gamma spectrometry, at the Underground Laboratory of Modane and alpha spectrometry after radiochemical purification. The profile of {sup 210}Pb activities in the sediment increased with depth in the core and did not allow to distinguish the atmospheric {sup 210}Pb from the {sup 210}Pb produced by watering processes in this uranium enriched environment. Another method for quantifying sediment accumulation rates is therefore proposed here using the disequilibrium between {sup 228}Ra (half-life of 5.75 years) and {sup 232}Th, the parent isotope. The excess of {sup 228}Ra over its respective parent {sup 232}Th has already been demonstrated by (Olley et al. 1997 WRR 33, 1319-1326) in river and lake

  19. Apparent Disequilibrium of Inorganic and Organic Carbon Compounds in Serpentinizing Fluids

    Science.gov (United States)

    Robinson, K.; Shock, E.

    2014-12-01

    During serpentinization of ultramafic rocks, ferrous iron in silicates is oxidized to ferric minerals and H2O is reduced to H2. This process is accompanied by the reduction of inorganic carbon, as observed in experiments and natural systems. To test the extent to which stable and metastable equilibria are reached among aqueous organic compounds during serpentinization, we sampled water and dissolved gases from circumneutral surface pools and hyperalkaline seeps in the Samail ophiolite in the Sultanate of Oman and analyzed for various carbon constituents, including dissolved inorganic carbon, dissolved organic carbon, methane, carbon monoxide, formate, acetate, and other small organic acid anions. Measurements of temperature, pH, dissolved H2, O2, major cations, major anions, and major and trace elements were also made. The aqueous composition of the analyzed samples was speciated based on ionic equilibrium interactions in order to obtain activities for inorganic carbon species, reduced carbon species, H2, and O2. The redox disequilibria among carbon species was then assessed using data and parameters for the revised HKF equations of state. This analysis demonstrates that the carbon species in this system are out of equilibrium with respect to one another in ways that cannot be compensated by altering the abundance of the other constituents within analytical uncertainties. Specifically, there is too much formate and too little methane relative to stable and metastable equilibria. This result implies the following: 1) Methane and formate equilibrated in separate parts of the system, given that no reasonable temperature, pressure, or composition changes satisfy equilibrium with their measured abundances. 2) Methane production is kinetically inhibited, as seen in experiments. 3) Microbial methane oxidation altered the abundance of methane and formate; methane oxidation to formate or carbonate is calculated to be extremely thermodynamically favorable in these fluids.

  20. Shared genetic aetiology between cognitive functions and physical and mental health in UK Biobank (N=112 151) and 24 GWAS consortia

    Science.gov (United States)

    Hagenaars, S P; Harris, S E; Davies, G; Hill, W D; Liewald, D C M; Ritchie, S J; Marioni, R E; Fawns-Ritchie, C; Cullen, B; Malik, R; Worrall, B B; Sudlow, C L M; Wardlaw, J M; Gallacher, J; Pell, J; McIntosh, A M; Smith, D J; Gale, C R; Deary, I J

    2016-01-01

    Causes of the well-documented association between low levels of cognitive functioning and many adverse neuropsychiatric outcomes, poorer physical health and earlier death remain unknown. We used linkage disequilibrium regression and polygenic profile scoring to test for shared genetic aetiology between cognitive functions and neuropsychiatric disorders and physical health. Using information provided by many published genome-wide association study consortia, we created polygenic profile scores for 24 vascular–metabolic, neuropsychiatric, physiological–anthropometric and cognitive traits in the participants of UK Biobank, a very large population-based sample (N=112 151). Pleiotropy between cognitive and health traits was quantified by deriving genetic correlations using summary genome-wide association study statistics and to the method of linkage disequilibrium score regression. Substantial and significant genetic correlations were observed between cognitive test scores in the UK Biobank sample and many of the mental and physical health-related traits and disorders assessed here. In addition, highly significant associations were observed between the cognitive test scores in the UK Biobank sample and many polygenic profile scores, including coronary artery disease, stroke, Alzheimer's disease, schizophrenia, autism, major depressive disorder, body mass index, intracranial volume, infant head circumference and childhood cognitive ability. Where disease diagnosis was available for UK Biobank participants, we were able to show that these results were not confounded by those who had the relevant disease. These findings indicate that a substantial level of pleiotropy exists between cognitive abilities and many human mental and physical health disorders and traits and that it can be used to predict phenotypic variance across samples. PMID:26809841

  1. Large cell lymphoma in children and adolescents of the Instituto Nacional de Cancerologia E.S.E. (Bogota, Colombia): 1980-2001

    International Nuclear Information System (INIS)

    De los Reyes I; Martinez, T; Vizcaino M; Moreno C

    2005-01-01

    Objective: to characterize and establish the survival of pediatric patients with lymphoma treated at the National Cancer Institute of Colombia, the period 1980-2001. Methods: clinical records of nineteen patients were reviewed, diagnosis was confirmed by morphology, and immune-phenotype was established with CD20, CD30, CD43, CD45RB, CD45RO, CD68, CD3, ALK, tdt and S-100 antibodies. Associations were established by using Fisher's exact test, Kaplan-Meier's method for survival, and the log rank test to compare survival trends. Results: ten patients were girls; the age median was eleven years, with a range between three and sixteen years. Seven cases presented lymphoma at the neck, which was the most frequent localization, nine patients were at stage l; the most frequent immune-phenotype was that of T cells, with eleven cases. Thirteen patients presented complete remission. After two years, event-free survival was 47.3%, disease-free survival was 99.8%, and global survival 68%. After five years, event-free survival was 28,8%. Conclusion: a bigger number of patients must be studied in order to establish more precise estimations concerning clinical features and survival

  2. Why Is There a Disequilibrium Between Power and Trust in Educational Settings?

    Directory of Open Access Journals (Sweden)

    Faruk Levent

    2018-02-01

    Full Text Available The purpose of this paper is to explore the relationship between school administrators' power sources and teachers' organizational trust levels according to the teachers' perceptions. The sample of the study, which employed a survey research method, consisted of 401 school teachers, working in both the private and public sectors in Istanbul, Turkey. One data gathering instrument of the study incorporated the "School Administrators' Organizational Power Sources Scale" developed by Zafer (2008 and the other was the "Organizational Trust Scale" first developed by Daboval, Comish, Swindle and Gaster (1994 and adapted to Turkish by Yılmaz (2005. Descriptive statistics and parametric analysis tests were used to determine the relationship between the power and trust dimensions. According to the research findings a moderately positive relationship was found between power sources except coercive and all organizational trust subscales. There is a positively low level of relationship between coercive power and all organizational trust sub-dimensions. There is a positively moderate relationship between sensitivity to employees and communication environment sub-dimensions of organizational trust and legitimate power, as well as a low positive relationship with openness to innovation and trust to administration subscales. Thus, the results revealed that sub-dimensions of organizational power significantly predicted organizational trust scores.

  3. Genome-wide association study identifies polymorphisms associated with the analgesic effect of fentanyl in the preoperative cold pressor-induced pain test

    Directory of Open Access Journals (Sweden)

    Kaori Takahashi

    2018-03-01

    Full Text Available Opioid analgesics are widely used for the treatment of moderate to severe pain. The analgesic effects of opioids are well known to vary among individuals. The present study focused on the genetic factors that are associated with interindividual differences in pain and opioid sensitivity. We conducted a multistage genome-wide association study in subjects who were scheduled to undergo mandibular sagittal split ramus osteotomy and were not medicated until they received fentanyl for the induction of anesthesia. We preoperatively conducted the cold pressor-induced pain test before and after fentanyl administration. The rs13093031 and rs12633508 single-nucleotide polymorphisms (SNPs near the LOC728432 gene region and rs6961071 SNP in the tcag7.1213 gene region were significantly associated with the analgesic effect of fentanyl, based on differences in pain perception latency before and after fentanyl administration. The associations of these three SNPs that were identified in our exploratory study have not been previously reported. The two polymorphic loci (rs13093031 and rs12633508 were shown to be in strong linkage disequilibrium. Subjects with the G/G genotype of the rs13093031 and rs6961071 SNPs presented lower fentanyl-induced analgesia. Our findings provide a basis for investigating genetics-based analgesic sensitivity and personalized pain control. Keywords: Opioid sensitivity, Analgesia, Fentanyl, Polymorphism, GWAS

  4. Efficient strategy for detecting gene × gene joint action and its application in schizophrenia.

    Science.gov (United States)

    Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G; Hofmann, A; Lange, Christoph

    2014-01-01

    We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the genome-wide level and has reasonable statistical power under most genetic models. We found that the presence of any gene × gene joint action may imply differences in three types of genetic components: the minor allele frequencies and the amounts of Hardy-Weinberg disequilibrium may differ between cases and controls, and between the two genetic loci the degree of linkage disequilibrium may differ between cases and controls. Using Fisher's method, it is possible to combine the different sources of genetic information in an overall test for detecting gene × gene joint action. The proposed statistical analysis is efficient and its simplicity makes it applicable to GWASs. In the current study, we applied the proposed approach to a GWAS on schizophrenia and found several potential gene × gene interactions. Our application illustrates the practical advantage of the proposed method. © 2013 WILEY PERIODICALS, INC.

  5. Orientation geochemical survey for uranium exploration using 230Th

    International Nuclear Information System (INIS)

    Xia Dingliang.

    1985-01-01

    The distribution of 230 Th in soils, rocks and ores and its relationship with respect to uranium ore formation are discussed for its possible use in geochemical exploration for U. 230 Th, U and Ra, being members of the same decay series, are different in their geochemical behavior upon which the study is orientated. Twenty uranium deposits and occurrences located in western and southern Hunan province are tested. Geochemical data obtained are comprehensively correlated. It is suggested that 230 Th is useful not only in U-Ra disequilibrium study but also in understanding the geochemical evolution of U ores. The data aid to interpret the genesis of uranium deposits and to assess the radioactive anomalies and uranium-bearing zones. Therefore, it can be adopted as a tool for searching in deep-buried uranium ores. The field procedure is rather simple and flexible to meet any geological environment. It is easy to read out and is less influnced by any kind of interference. In case of disequilibrium caused by oxidation and reduction during the period of ore formation it still gives good indication compared with that of radiometry, radonmetry and geochemical sampling for U

  6. Reconstruction of drip-water δ18O based on calcite oxygen and clumped isotopes of speleothems from Bunker Cave (Germany

    Directory of Open Access Journals (Sweden)

    T. Kluge

    2013-02-01

    Full Text Available The geochemical signature of many speleothems used for reconstruction of past continental climates is affected by kinetic isotope fractionation. This limits quantitative paleoclimate reconstruction and, in cases where the kinetic fractionation varies with time, also affects relative paleoclimate interpretations. In carbonate archive research, clumped isotope thermometry is typically used as proxy for absolute temperatures. In the case of speleothems, however, clumped isotopes provide a sensitive indicator for disequilibrium effects. The extent of kinetic fractionation co-varies in Δ47 and δ18O so that it can be used to account for disequilibrium in δ18O and to extract the past drip-water composition. Here we apply this approach to stalagmites from Bunker Cave (Germany and calculate drip-water δ18Ow values for the Eemian, MIS3, and the Holocene, relying on independent temperature estimates and accounting for disequilibrium. Applying the co-variation method to modern calcite precipitates yields drip-water δ18Ow values in agreement with modern cave drip-water δ18Ow of −7.9 ± 0.3‰, despite large and variable disequilibrium effects in both calcite δ18Oc and Δ47. Reconstructed paleo-drip-water δ18Ow values are lower during colder periods (e.g., MIS3: −8.6 ± 0.4‰ and the early Holocene at 11 ka: −9.7 ± 0.2‰ and show higher values during warmer climatic periods (e.g., the Eemian: −7.6 ± 0.2‰ and the Holocene Climatic Optimum: −7.2 ± 0.3‰. This new approach offers a unique possibility for quantitative climate reconstruction including the assessment of past hydrological conditions while accounting for disequilibrium effects.

  7. Modeling Programs Increase Aircraft Design Safety

    Science.gov (United States)

    2012-01-01

    Flutter may sound like a benign word when associated with a flag in a breeze, a butterfly, or seaweed in an ocean current. When used in the context of aerodynamics, however, it describes a highly dangerous, potentially deadly condition. Consider the case of the Lockheed L-188 Electra Turboprop, an airliner that first took to the skies in 1957. Two years later, an Electra plummeted to the ground en route from Houston to Dallas. Within another year, a second Electra crashed. In both cases, all crew and passengers died. Lockheed engineers were at a loss as to why the planes wings were tearing off in midair. For an answer, the company turned to NASA s Transonic Dynamics Tunnel (TDT) at Langley Research Center. At the time, the newly renovated wind tunnel offered engineers the capability of testing aeroelastic qualities in aircraft flying at transonic speeds near or just below the speed of sound. (Aeroelasticity is the interaction between aerodynamic forces and the structural dynamics of an aircraft or other structure.) Through round-the-clock testing in the TDT, NASA and industry researchers discovered the cause: flutter. Flutter occurs when aerodynamic forces acting on a wing cause it to vibrate. As the aircraft moves faster, certain conditions can cause that vibration to multiply and feed off itself, building to greater amplitudes until the flutter causes severe damage or even the destruction of the aircraft. Flutter can impact other structures as well. Famous film footage of the Tacoma Narrows Bridge in Washington in 1940 shows the main span of the bridge collapsing after strong winds generated powerful flutter forces. In the Electra s case, faulty engine mounts allowed a type of flutter known as whirl flutter, generated by the spinning propellers, to transfer to the wings, causing them to vibrate violently enough to tear off. Thanks to the NASA testing, Lockheed was able to correct the Electra s design flaws that led to the flutter conditions and return the

  8. Development and characterization of polymorphic microsatellitemarkers for the crested caracara, Caracara cheriway

    Science.gov (United States)

    Vaughn, Erin E.; Dwyer, James F.; Morrison, Joan L.; Culver, Melanie

    2015-01-01

    We isolated novel microsatellites from the crested caracara (Caracara cheriway) with a shotgun pyrosequencing approach. We tested 80 loci for polymorphism among 20 individuals from the threatened Florida population. Fourteen loci were polymorphic. The mean number of alleles was 2.21 (range 2–3) and the mean observed heterozygosity was 0.41 (range 0.15–0.65). None of the 14 polymorphic loci exhibited significant linkage disequilibrium nor did they deviate significantly from Hardy–Weinberg expectations. We also report 16 monomorphic loci.

  9. On the mathematical analysis and the numerical simulation of boiling flow models in nuclear power plants thermal hydraulics

    International Nuclear Information System (INIS)

    Nguyen, Thi-Phuong-Kieu

    2016-01-01

    We investigated some finite volume methods for the numerical simulation of a flow involving two incompressible phases or general two compressible phases in mechanical disequilibrium. The main difficulties of the regime where there is either a phase appearance or a phase disappearance is the singularity of the velocity. We show that using the entropy fix will much improve these problems. Finally, we perform some important numerical tests to verify the numerical methods, such as a phase separation by gravity or a boiling channel. (author) [fr

  10. On the mathematical analysis and the numerical simulation of boiling flow models in nuclear power plants thermal hydraulics

    International Nuclear Information System (INIS)

    Nguyen, Thi Phuong Kieu

    2016-01-01

    We investigated some finite volume methods for the numerical simulation of a flow involving two incompressible phases or general two compressible phases in mechanical disequilibrium. The main difficulties of the regime where there is either a phase appearance or a phase disappearance is the singularity of the velocity. We show that using the entropy fix will much improve these problems. Finally, we perform some important numerical tests to verify the numerical methods, such as a phase separation by gravity or a boiling channel. (author)

  11. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  12. Genomic selection in maritime pine.

    Science.gov (United States)

    Isik, Fikret; Bartholomé, Jérôme; Farjat, Alfredo; Chancerel, Emilie; Raffin, Annie; Sanchez, Leopoldo; Plomion, Christophe; Bouffier, Laurent

    2016-01-01

    A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Kinetics of heat-induced color change of a tuna-vegetable mixture

    OpenAIRE

    Scherer, Erika; Sandoval, Aleida J; Barreiro, José A

    2009-01-01

    Heat induced color change kinetics in a tuna-vegetable mixture was evaluated by measuring color parameter "L" (Hunter-Lab) and 5-hydroxi-methyl-furfural (5-HMF) accumulation. For this purpose small reusable stainless steel TDT cans were used and the kinetic studies performed in a temperature range characteristic of thermal processing of low acid canned foods (110-125°C). The color parameter L was better described by a pseudo zero order while a pseudo first order reaction was found for 5-HMF a...

  14. Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon

    DEFF Research Database (Denmark)

    Mailund, T; Schauser, Leif

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

  15. Interdependence, Disequilibrium and Growth: Reflections on the ...

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

    ... on North-South relations. Interdépendance, déséquilibre et croissance will appeal to academics, students, and researchers in development studies, international relations, economics, political sciences, and sustainable development studies. It will also appeal to development professionals and informed "internationalists" ...

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

    African Journals Online (AJOL)

    sunny t

    2016-11-16

    Nov 16, 2016 ... related to drought tolerance (YongSheng et al., 2009). Among the variety of ... (Li et al., 2013), yield (LiFang et al., 2010) and fibre traits. (Islam et al., 2014). ..... such molecular markers as SSRs (Bertini et al., 2006;. Zhang et al.

  17. Economic Cycles in a Behavioral Disequilibrium Perspective

    DEFF Research Database (Denmark)

    Mosekilde, Erik; Sterman, J.D.

    1997-01-01

    The paper reviews the characteristic features of the main economic cycles and discusses the behavioral foundation for each mode at the microlevel. The analysis continues to illustrate some of the nonlinear dynamic phenomena that can arise through interaction between the various modes and through...

  18. Interdependence, Disequilibrium and Growth: Reflections on the ...

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

    Globalization has had a profound effect on North-South relations buthas affected different regions and countries to different degrees. The extent of ... Professor Loxley is the author of Debt and Disorder: External Financing for Development and the coordinator of the Alternative Federal Budget exercise in Canada.

  19. Utilizing linkage disequilibrium information from Indian Genome ...

    Indian Academy of Sciences (India)

    Using LD information derived from Indian Genome Variation database (IGVdb) on populations .... Line diagram represents the SNPs selected in Indian (upper panel) and CEPH .... out procedure for extracting DNA from human nucleated cells.

  20. U-series disequilibrium dating of Quaternary carbonates

    International Nuclear Information System (INIS)

    Stirling, C.

    2006-01-01

    One of the key dating methods used in paleoclimate research utilizes the natural radioactive decay of uranium to thorium in archives containing U-bearing minerals, such as the calcium carbonate forming the skeletons of fossil corals and speleothems. More specifically, this chronometer, commonly referred to as the U-series dating method, is based on the decay of 238 U to its longest-lived intermediate daughters, 234 U and 230 Th, and subsequent decay through to stable isotopes of Pb. It is the respective 250,000 and 75,000 year half-lives of these daughter isotopes, which make the U-series system particularly useful for dating Quaternary climate events spanning the last 600,000 years of Earth's history. The U-series thus bridges the gap between the ∼45,000 year upper limit of conventional radiocarbon dating and the ∼200,000 year lower limit of K-Ar and 40 Ar- 39 Ar dating. 2 refs., 5 figs

  1. Temporal discrimination threshold: VBM evidence for an endophenotype in adult onset primary torsion dystonia.

    LENUS (Irish Health Repository)

    Bradley, D

    2012-02-01

    Familial adult-onset primary torsion dystonia is an autosomal dominant disorder with markedly reduced penetrance. Most adult-onset primary torsion dystonia patients are sporadic cases. Disordered sensory processing is found in adult-onset primary torsion dystonia patients; if also present in their unaffected relatives this abnormality may indicate non-manifesting gene carriage. Temporal discrimination thresholds (TDTs) are abnormal in adult-onset primary torsion dystonia, but their utility as a possible endophenotype has not been examined. We examined 35 adult-onset primary torsion dystonia patients (17 familial, 18 sporadic), 42 unaffected first-degree relatives of both familial and sporadic adult-onset primary torsion dystonia patients, 32 unaffected second-degree relatives of familial adult-onset primary torsion dystonia (AOPTD) patients and 43 control subjects. TDT was measured using visual and tactile stimuli. In 33 unaffected relatives, voxel-based morphometry was used to compare putaminal volumes between relatives with abnormal and normal TDTs. The mean TDT in 26 control subjects under 50 years of age was 22.85 ms (SD 8.00; 95% CI: 19.62-26.09 ms). The mean TDT in 17 control subjects over 50 years was 30.87 ms (SD 5.48; 95% CI: 28.05-33.69 ms). The upper limit of normal, defined as control mean + 2.5 SD, was 42.86 ms in the under 50 years group and 44.58 ms in the over 50 years group. Thirty out of thirty-five (86%) AOPTD patients had abnormal TDTs with similar frequencies of abnormalities in sporadic and familial patients. Twenty-two out of forty-two (52%) unaffected first-degree relatives had abnormal TDTs with similar frequencies in relatives of sporadic and familial AOPTD patients. Abnormal TDTs were found in 16\\/32 (50%) of second-degree relatives. Voxel-based morphometry analysis comparing 13 unaffected relatives with abnormal TDTs and 20 with normal TDTs demonstrated a bilateral increase in putaminal grey matter in unaffected relatives with abnormal

  2. Visualizing the Acute Effects of Vascular-Targeted Therapy In Vivo Using Intravital Microscopy and Magnetic Resonance Imaging: Correlation with Endothelial Apoptosis, Cytokine Induction, and Treatment Outcome

    Directory of Open Access Journals (Sweden)

    Mukund Seshadri

    2007-02-01

    Full Text Available The acute effects of the vascular-disrupting agent 5,6-dimethylxanthenone-4-acetic acid (DMXAA were investigated in vivo using intravital microscopy (IVM and magnetic resonance imaging (MRI. Changes in vascular permeability and blood flow of syngeneic CT-26 murine colon adenocarcinomas were assessed at 4 and 24 hours after DMXAA treatment (30 mg/kg, i.p. and correlated with induction of tumor necrosis factor-α (TNF-α, endothelial damage [CD31/terminal deoxynucleotidyl transferase (TdT], and treatment outcome. Intravital imaging revealed a marked increase in vascular permeability 4 hours after treatment, consistent with increases in intratumoral mRNA and protein levels of TNF-α. Parallel contrast-enhanced MRI studies showed a ~ 4-fold increase in longitudinal relaxation rates (ΔR1, indicative of increased contrast agent accumulation within the tumor. Dualimmunostained tumor sections (CD31/TdT revealed evidence of endothelial apoptosis at this time point. Twenty-four hours after treatment, extensive hemorrhage and complete disruption of vascular architecture were observed with IVM, along with a significant reduction in ΔR1 and virtual absence of CD31 immunostaining. DMXAA-induced tumor vascular damage resulted in significant long-term (60-day cures compared to untreated controls. Multimodality imaging approaches are useful in visualizing the effects of antivascular therapy in vivo. Such approaches allow cross validation and correlation of findings with underlying molecular changes contributing to treatment outcome.

  3. Separation of 210 Pb, 210 Bi and 210 Po by ion exchange and their liquid scintillation standardization

    International Nuclear Information System (INIS)

    Rodriguez, L.; Jimenez, A.; Grau, A.

    1996-01-01

    We applied the CIEMAT/NIST method and alpha/beta discrimination to ''210 Pb samples in equilibrium with its daughters, by preparing homogeneous and gel samples. The stability of samples was tested in different available cocktails, HiSafe''tm II, HiSafe''tmIII, Ultima-Gold''tm, Ultima-Gold''tmXR, Ultima-Gold''tmAB, Insta-Gel and e Insta-Gel II. Also we analyzed the disequilibrium of the radioactive chain ''210Pb+''210Bi+''210Po, achieving and excellent agreement between the results of the spectrum unfolding method and the experimental values. (Author) 13 refs

  4. On high interest rates in Brazil

    Directory of Open Access Journals (Sweden)

    Francisco Lafaiete Lopes

    2014-03-01

    Full Text Available This article examines the question of why interest rates are so high in Brazil as compared to the international average. It looks at theoretical arguments based on excessive government deficits, structural lack of private savings, inflation bias, excessive investment demand and fear of floating. An informal look at the evidence does not strongly corroborate any of these arguments. Hence a wise central bank should consider "testing" the market to make sure it is not dealing with an extreme equilibrium configuration or a long standing disequilibrium.

  5. Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

    Science.gov (United States)

    2010-01-01

    Background Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P body condition score, reduced milk yield and shorter gestation (P fertility in the Holstein-Friesian dairy cow. PMID:20670403

  6. El reto de la televisión. El "apagón analógico" y la consolidación de lo digital

    Directory of Open Access Journals (Sweden)

    Marta Roel

    2014-12-01

    Full Text Available La migración a la tecnología digital no es una opción, es un imperativo inevitable. Estamos ante un nuevo paradigma de comunicación que apuesta por el consumo individualizado y selectivo, similar al que usamos cuando navegamos en Internet. En este contexto, la audiencia deja de ser masa y el emisor pasa a comunicarse unilateralmente con sus públicos. En América Latina, la televisión digital terrestre TDT, por hoy, apenas es un proyecto más que una realidad.

  7. Testing Testing Testing.

    Science.gov (United States)

    Deville, Craig; O'Neill, Thomas; Wright, Benjamin D.; Woodcock, Richard W.; Munoz-Sandoval, Ana; Gershon, Richard C.; Bergstrom, Betty

    1998-01-01

    Articles in this special section consider (1) flow in test taking (Craig Deville); (2) testwiseness (Thomas O'Neill); (3) test length (Benjamin Wright); (4) cross-language test equating (Richard W. Woodcock and Ana Munoz-Sandoval); (5) computer-assisted testing and testwiseness (Richard Gershon and Betty Bergstrom); and (6) Web-enhanced testing…

  8. Association testing to detect gene-gene interactions on sex chromosomes in trio data

    Directory of Open Access Journals (Sweden)

    Yeonok eLee

    2013-11-01

    Full Text Available Autism Spectrum Disorder (ASD occurs more often among males than females in a 4:1 ratio. Among theories used to explain the causes of ASD, the X chromosome and the Y chromosome theories attribute ASD to X-linked mutation and the male-limited gene expressions on the Y chromosome, respectively. Despite the rationale of the theory, studies have failed to attribute the sex-biased ratio to the significant linkage or association on the regions of interest on X chromosome. We further study the gender biased ratio by examining the possible interaction effects between two genes in the sex chromosomes. We propose a logistic regression model with mixed effects to detect gene-gene interactions on sex chromosomes. We investigated the power and type I error rates of the approach for a range of minor allele frequencies and varying linkage disequilibrium between markers and QTLs. We also evaluated the robustness of the model to population stratification. We applied the model to a trio-family data set with an ASD affected male child to study gene-gene interactions on sex chromosomes.

  9. The functional role of the triceps surae muscle during human locomotion.

    Directory of Open Access Journals (Sweden)

    Jean-Louis Honeine

    Full Text Available AIM: Despite numerous studies addressing the issue, it remains unclear whether the triceps surae muscle group generates forward propulsive force during gait, commonly identified as 'push-off'. In order to challenge the push-off postulate, one must probe the effect of varying the propulsive force while annulling the effect of the progression velocity. This can be obtained by adding a load to the subject while maintaining the same progression velocity. METHODS: Ten healthy subjects initiated gait in both unloaded and loaded conditions (about 30% of body weight attached at abdominal level, for two walking velocities, spontaneous and fast. Ground reaction force and EMG activity of soleus and gastrocnemius medialis and lateralis muscles of the stance leg were recorded. Centre of mass velocity and position, centre of pressure position, and disequilibrium torque were calculated. RESULTS: At spontaneous velocity, adding the load increased disequilibrium torque and propulsive force. However, load had no effect on the vertical braking force or amplitude of triceps activity. At fast progression velocity, disequilibrium torque, vertical braking force and triceps EMG increased with respect to spontaneous velocity. Still, adding the load did not further increase braking force or EMG. CONCLUSIONS: Triceps surae is not responsible for the generation of propulsive force but is merely supporting the body during walking and restraining it from falling. By controlling the disequilibrium torque, however, triceps can affect the propulsive force through the exchange of potential into kinetic energy.

  10. The Functional Role of the Triceps Surae Muscle during Human Locomotion

    Science.gov (United States)

    Honeine, Jean-Louis; Schieppati, Marco; Gagey, Olivier; Do, Manh-Cuong

    2013-01-01

    Aim Despite numerous studies addressing the issue, it remains unclear whether the triceps surae muscle group generates forward propulsive force during gait, commonly identified as ‘push-off’. In order to challenge the push-off postulate, one must probe the effect of varying the propulsive force while annulling the effect of the progression velocity. This can be obtained by adding a load to the subject while maintaining the same progression velocity. Methods Ten healthy subjects initiated gait in both unloaded and loaded conditions (about 30% of body weight attached at abdominal level), for two walking velocities, spontaneous and fast. Ground reaction force and EMG activity of soleus and gastrocnemius medialis and lateralis muscles of the stance leg were recorded. Centre of mass velocity and position, centre of pressure position, and disequilibrium torque were calculated. Results At spontaneous velocity, adding the load increased disequilibrium torque and propulsive force. However, load had no effect on the vertical braking force or amplitude of triceps activity. At fast progression velocity, disequilibrium torque, vertical braking force and triceps EMG increased with respect to spontaneous velocity. Still, adding the load did not further increase braking force or EMG. Conclusions Triceps surae is not responsible for the generation of propulsive force but is merely supporting the body during walking and restraining it from falling. By controlling the disequilibrium torque, however, triceps can affect the propulsive force through the exchange of potential into kinetic energy. PMID:23341916

  11. Forcing lateral electron disequilibrium to spare lung tissue: a novel technique for stereotactic body radiation therapy of lung cancer

    International Nuclear Information System (INIS)

    Disher, Brandon; Hajdok, George; Gaede, Stewart; Mulligan, Matthew; Battista, Jerry J

    2013-01-01

    Stereotactic body radiation therapy (SBRT) has quickly become a preferred treatment option for early-stage lung cancer patients who are ineligible for surgery. This technique uses tightly conformed megavoltage (MV) x-ray beams to irradiate a tumour with ablative doses in only a few treatment fractions. Small high energy x-ray fields can cause lateral electron disequilibrium (LED) to occur within low density media, which can reduce tumour dose. These dose effects may be challenging to predict using analytic dose calculation algorithms, especially at higher beam energies. As a result, previous authors have suggested using low energy photons ( 5 × 5 cm 2 ) for lung cancer patients to avoid the negative dosimetric effects of LED. In this work, we propose a new form of SBRT, described as LED-optimized SBRT (LED-SBRT), which utilizes radiotherapy (RT) parameters designed to cause LED to advantage. It will be shown that LED-SBRT creates enhanced dose gradients at the tumour/lung interface, which can be used to manipulate tumour dose, and/or normal lung dose. To demonstrate the potential benefits of LED-SBRT, the DOSXYZnrc (National Research Council of Canada, Ottawa, ON) Monte Carlo (MC) software was used to calculate dose within a cylindrical phantom and a typical lung patient. 6 MV or 18 MV x-ray fields were focused onto a small tumour volume (diameter ∼1 cm). For the phantom, square fields of 1 × 1 cm 2 , 3 × 3 cm 2 , or 5 × 5 cm 2 were applied. However, in the patient, 3 × 1 cm 2 , 3 × 2 cm 2 , 3 × 2.5 cm 2 , or 3 × 3 cm 2 field sizes were used in simulations to assure target coverage in the superior–inferior direction. To mimic a 180° SBRT arc in the (symmetric) phantom, a single beam profile was calculated, rotated, and beams were summed at 1° segments to accumulate an arc dose distribution. For the patient, a 360° arc was modelled with 36 equally weighted (and spaced) fields focused on the tumour centre. A planning target volume (PTV) was generated

  12. European rational approach for the genetics of diabetic complications--EURAGEDIC: patient populations and strategy

    DEFF Research Database (Denmark)

    Tarnow, L.; Groop, P.H.; Hadjadj, S.

    2008-01-01

    in 541 independent parent-offspring trios with or without diabetic nephropathy was applied for validation of consistency. Candidate genes were selected based on previous linkage studies, knowledge of metabolic pathways, and animal models. A comprehensive SNP discovery in more than 100 candidate genes......BACKGROUND: Diabetic nephropathy is likely to be a complex genetic trait. To date, most diabetic nephropathy candidate gene studies have tested a limited number of genes and variants in small sized populations, or in populations that were poorly matched or phenotyped. The main objective...... of the EURAGEDIC study was to address these problems. METHODS: Single nucleotide polymorphisms (SNPs) in candidate genes were tested for association with overt diabetic nephropathy (persistent albuminuria >300 mg/24 h) in a large (n=2499) Type 1 diabetes case/control study. Testing for transmission disequilibrium...

  13. U-Th and 10Be constraints on sediment recycling in proglacial settings, Lago Buenos Aires, Patagonia

    Science.gov (United States)

    Cogez, Antoine; Herman, Frédéric; Pelt, Éric; Reuschlé, Thierry; Morvan, Gilles; Darvill, Christopher M.; Norton, Kevin P.; Christl, Marcus; Märki, Lena; Chabaux, François

    2018-03-01

    The estimation of sediment transfer times remains a challenge to our understanding of sediment budgets and the relationships between erosion and climate. Uranium (U) and thorium (Th) isotope disequilibria offer a means of more robustly constraining sediment transfer times. Here, we present new uranium and thorium disequilibrium data for a series of nested moraines around Lago Buenos Aires in Argentine Patagonia. The glacial chronology for the area is constrained using in situ cosmogenic 10Be analysis of glacial outwash. Sediment transfer times within the periglacial domain were estimated by comparing the deposition ages of moraines to the theoretical age of sediment production, i.e., the comminution age inferred from U disequilibrium data and recoil loss factor estimates. Our data show first that the classical comminution age approach must include weathering processes accounted for by measuring Th disequilibrium. Second, our combined data suggest that the pre-deposition history of the moraine sediments is not negligible, as evidenced by the large disequilibrium of the youngest moraines despite the equilibrium of the corresponding glacial flour. Monte Carlo simulations suggest that weathering was more intense before the deposition of the moraines and that the transfer time of the fine sediments to the moraines was on the order of 100-200 kyr. Long transfer times could result from a combination of long sediment residence times in the proglacial lake (recurrence time of a glacial cycle) and the remobilization of sediments from moraines deposited during previous glacial cycles. 10Be data suggest that some glacial cycles are absent from the preserved moraine record (seemingly every second cycle), supporting a model of reworking moraines and/or fluctuations in the extent of glacial advances. The chronological pattern is consistent with the U-Th disequilibrium data and the 100-200 kyr transfer time. This long transfer time raises the question of the proportion of freshly

  14. U–Th and 10Be constraints on sediment recycling in proglacial settings, Lago Buenos Aires, Patagonia

    Directory of Open Access Journals (Sweden)

    A. Cogez

    2018-03-01

    Full Text Available The estimation of sediment transfer times remains a challenge to our understanding of sediment budgets and the relationships between erosion and climate. Uranium (U and thorium (Th isotope disequilibria offer a means of more robustly constraining sediment transfer times. Here, we present new uranium and thorium disequilibrium data for a series of nested moraines around Lago Buenos Aires in Argentine Patagonia. The glacial chronology for the area is constrained using in situ cosmogenic 10Be analysis of glacial outwash. Sediment transfer times within the periglacial domain were estimated by comparing the deposition ages of moraines to the theoretical age of sediment production, i.e., the comminution age inferred from U disequilibrium data and recoil loss factor estimates. Our data show first that the classical comminution age approach must include weathering processes accounted for by measuring Th disequilibrium. Second, our combined data suggest that the pre-deposition history of the moraine sediments is not negligible, as evidenced by the large disequilibrium of the youngest moraines despite the equilibrium of the corresponding glacial flour. Monte Carlo simulations suggest that weathering was more intense before the deposition of the moraines and that the transfer time of the fine sediments to the moraines was on the order of 100–200 kyr. Long transfer times could result from a combination of long sediment residence times in the proglacial lake (recurrence time of a glacial cycle and the remobilization of sediments from moraines deposited during previous glacial cycles. 10Be data suggest that some glacial cycles are absent from the preserved moraine record (seemingly every second cycle, supporting a model of reworking moraines and/or fluctuations in the extent of glacial advances. The chronological pattern is consistent with the U–Th disequilibrium data and the 100–200 kyr transfer time. This long transfer time raises the

  15. Development of new multigrid schemes for the method of characteristics in neutron transport theory

    International Nuclear Information System (INIS)

    Grassi, G.

    2006-01-01

    This dissertation is based upon our doctoral research that dealt with the conception and development of new non-linear multigrid techniques for the Method of the Characteristics (MOC) within the TDT code. Here we focus upon a two-level scheme consisting of a fine level on which the neutron transport equation is iteratively solved using the MOC algorithm, and a coarse level defined by a more coarsely discretized phase space on which a low-order problem is considered. The solution of this problem is then used in order to correct the angular flux moments resulting from the previous transport iteration. A flux-volume homogenization procedure is employed to evaluate the coarse-level material properties after each transport iteration. This entails the non-linearity of the methods. According to the Generalised Equivalence Theory (GET), additional degrees of freedom are introduced for the low-order problem so that the convergence of the acceleration scheme can be ensured. We present two classes of non-linear methods: transport-like methods and discussion-like methods. Transport-like methods consider a homogenized low-order transport problem on the coarse level. This problem is iteratively solved using the same MOC algorithm as for the transport problem on the fine level. Discontinuity factors are then employed, per region or per surface, in order to reconstruct the currents evaluated by the low-order operator, which ensure the convergence of the acceleration scheme. On the other hand, discussion-like methods consider a low-order problem inspired by diffusion. We studied the non-linear Coarse Mesh Finite Difference (CMFD) method, already present in literature, in the perspective of integrating it into TDT code. Then, we developed a new non-linear method on the model of CMFD. From the latter, we borrowed the idea to establish a simple relation between currents and fluxes in order to obtain a problem involving only coarse fluxes. Finally, those non-linear methods have been

  16. Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models.

    Science.gov (United States)

    He, Zhangyi; Beaumont, Mark; Yu, Feng

    2017-07-05

    We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. Copyright © 2017 He et al.

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

    Science.gov (United States)

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

    2013-07-08

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

  18. Do Hf isotopes in magmatic zircons represent those of their host rocks?

    Science.gov (United States)

    Wang, Di; Wang, Xiao-Lei; Cai, Yue; Goldstein, Steven L.; Yang, Tao

    2018-04-01

    Lu-Hf isotopic system in zircon is a powerful and widely used geochemical tracer in studying petrogenesis of magmatic rocks and crustal evolution, assuming that zircon Hf isotopes can represent initial Hf isotopes of their parental whole rock. However, this assumption may not always be valid. Disequilibrium partial melting of continental crust would preferentially melt out non-zircon minerals with high time-integrated Lu/Hf ratios and generate partial melts with Hf isotope compositions that are more radiogenic than those of its magma source. Dissolution experiments (with hotplate, bomb and sintering procedures) of zircon-bearing samples demonstrate this disequilibrium effect where partial dissolution yielded variable and more radiogenic Hf isotope compositions than fully dissolved samples. A case study from the Neoproterozoic Jiuling batholith in southern China shows that about half of the investigated samples show decoupled Hf isotopes between zircons and the bulk rocks. This decoupling could reflect complex and prolonged magmatic processes, such as crustal assimilation, magma mixing, and disequilibrium melting, which are consistent with the wide temperature spectrum from ∼630 °C to ∼900 °C by Ti-in-zircon thermometer. We suggest that magmatic zircons may only record the Hf isotopic composition of their surrounding melt during crystallization and it is uncertain whether their Hf isotopic compositions can represent the primary Hf isotopic compositions of the bulk magmas. In this regard, using zircon Hf isotopic compositions to trace crustal evolution may be biased since most of these could be originally from disequilibrium partial melts.

  19. Keeping Earth at work: Using thermodynamics to develop a holistic theory of the Earth system

    Science.gov (United States)

    Kleidon, Axel

    2010-05-01

    The Earth system is unique among terrestrial planets in that it is maintained in a state far from thermodynamic equilibrium. Practically all processes are irreversible in their nature, thereby producing entropy, and these would act to destroy this state of disequilibrium. In order to maintain disequilibrium in steady state, driving forces are required that perform the work to maintain the Earth system in a state far from equilibrium. To characterize the functioning of the Earth system and the interactions among its subsystems we need to consider all terms of the first and second law of thermodynamics. While the global energy balance is well established in climatology, the global entropy and work balances receive little, if any, attention. Here I will present first steps in developing a holistic theory of the Earth system including quantifications of the relevant terms that is based on the first and second laws of thermodynamics. This theory allows us to compare the significance of different processes in driving and maintaining disequilibrium, allows us to explore interactions by investigating the role of power transfer among processes, and specifically illustrate the significance of life in driving planetary disequilibrium. Furthermore, the global work balance demonstrates the significant impact of human activity and it provides an estimate for the availability of renewable sources of free energy within the Earth system. Hence, I conclude that a holistic thermodynamic theory of the Earth system is not just some academic exercise of marginal use, but essential for a profound understanding of the Earth system and its response to change.

  20. Young Women do it Better: Sexual Dimorphism in Temporal Discrimination.

    Science.gov (United States)

    Williams, Laura Jane; Butler, John S; Molloy, Anna; McGovern, Eavan; Beiser, Ines; Kimmich, Okka; Quinlivan, Brendan; O'Riordan, Sean; Hutchinson, Michael; Reilly, Richard B

    2015-01-01

    The temporal discrimination threshold (TDT) is the shortest time interval at which two sensory stimuli presented sequentially are detected as asynchronous by the observer. TDTs are known to increase with age. Having previously observed shorter thresholds in young women than in men, in this work we sought to systematically examine the effect of sex and age on temporal discrimination. The aims of this study were to examine, in a large group of men and women aged 20-65 years, the distribution of TDTs with an analysis of the individual participant's responses, assessing the "point of subjective equality" and the "just noticeable difference" (JND). These respectively assess sensitivity and accuracy of an individual's response. In 175 participants (88 women) aged 20-65 years, temporal discrimination was faster in women than in men under the age of 40 years by a mean of approximately 13 ms. However, age-related decline in temporal discrimination was three times faster in women so that, in the age group of 40-65 years, the female superiority was reversed. The point of subjective equality showed a similar advantage in younger women and more marked age-related decline in women than men, as the TDT. JND values declined equally in both sexes, showing no sexual dimorphism. This observed sexual dimorphism in temporal discrimination is important for both (a) future clinical research assessing disordered mid-brain covert attention in basal-ganglia disorders, and (b) understanding the biology of this sexual dimorphism which may be genetic or hormonal.

  1. A Pilot Study to Assess the Vestibular Apparatus Function with Videonystagmography During Chronic Otitis Media with Effusion.

    Science.gov (United States)

    Saliba, Issam; Dagher, Chady; El-Zir, Elie; Yammine, Fady G

    2015-01-01

    To assess the effect of chronic middle ear effusion (CMEE) on balance and equilibrium. Prospective study controlling two groups of children. The active arm consisted of children having a unilateral or bilateral CMEE that persisted for at least 3 months. The control group consisted of children presenting with normal middle ear. Children and parents in both groups were questioned about any symptom of vertigo, dizziness, disequilibrium or child's tendency to fall. ENT exam included an assessment with pneumatic and microscopic otoscopy, evaluation of the vestibular system with the Romberg test, the Fukuda test, the head-shaking test and the Starwalk test. The study group consisted of 15 children (mean = 6.5 years, SD = 2; 10 females and 5 males). The control group consisted also of 15 children (mean = 7.2 years, SD = 1.8; 8 females and 7 males). The duration of MEE was between 3 and 12 months (mean = 8 months). Three children (20%) in the study group had a history of vertigo, imbalance, disequilibrium and/or tendency to fall. None of the children in the control group had such a history (p = 0.22); Five children in the study group had abnormal head-shaking test, Fukuda and/or Starwalk tests (33.33%). Two children in the control group had such a finding (13.33%) (p = 0.39). Romberg test was normal in all children in both groups. In the study group, one child showed positional and spontaneous nystagmus on VNG testing. Another one showed positional nystagmus. Hence, 2 children had abnormal findings on VNG (13.33%). In the control group, VNG was normal in all children (p = 0.46). Tympanometry showed a type B curve in 26 ears, a type C curve in 3 ears and type A in one ear. In the control group all patients presented a type A curve. This paper describes the first study using VNG in a population of children with CMEE. The presence of balance disturbances associated or not with hearing loss is of paramount importance to the clinician as to the indications of myringotomy with a

  2. Stable isotope compositions (O-C) of reef fish otoliths from the Taiaro lagoon (Tuamotu, French Polynesia): isotopic and biologic implications

    International Nuclear Information System (INIS)

    Blamart, D.; Juillet-Leclerc, A.; Ouahdi, R.; Escoubeyrou, K.; Lecomte-Finiger, R.

    2002-01-01

    Nuclei (larval stage) and outer parts (adult stage) of fish otoliths from the Taiaro closed lagoon (French Polynesia) and adjacent ocean have been analysed for the C-O isotopic compositions. δ 18 O values of the nuclei of both populations indicate that isotopic equilibrium is reached. This implies that the lagoonal fish population has done its complete biological cycle in the lagoon and represents an adaptation in a closed system. δ 18 O values of the outer parts show a slight isotopic disequilibrium ( 13 C values exhibit a strong isotopic disequilibrium related to metabolic activity. (authors)

  3. Separation of 210Pb, 210Bi and 210Po by ion exchange and their Iiquid scintillation standardization

    International Nuclear Information System (INIS)

    Rodriguez, L.; Jimenez, A.; Grau, A.

    1996-01-01

    We applied the CIEMAT/NIST method and alpha/beta discrimination to ''210Pb samples in equilibrium with its daughters, by preparing homogeneous and gel samples. The stability of samples was tested in different available cocktails, HiSafe''TM II, HiSafe''TM III, Ultima-Gold''TM, Ultima-Gold''TM XR, Ultima-Gold''TM AB, Insta-Gel''R and e Insta-Gel''R lI. Also we analyzed the disequilibrium of the radioactive chain 210Pb+210Bi+210Po, achieving an excellent agreement between the results of the spectrum unfolding method and the experimental values. (Author) 13 refs

  4. GWA Analysis for Milk Production Traits in Dairy Sheep and Genetic Support for a QTN Influencing Milk Protein Percentage in the LALBA Gene

    DEFF Research Database (Denmark)

    García-Gámez, Elsa; Gutiérrez-Gil, Beatriz; Sahana, Goutam

    2012-01-01

    In this study, we used the Illumina OvineSNP50 BeadChip to conduct a genome-wide association (GWA) analysis for milk production traits in dairy sheep by analyzing a commercial population of Spanish Churra sheep. The studied population consisted of a total of 1,681 Churra ewes belonging to 16 half...... identified was located within the coding gene sequence (LALBA_g.242T.C) and was predicted to cause an amino acid change in the protein (Val27Ala). Different approaches, including GWA analysis, a combined linkage and linkage disequilibrium study and a concordance test with the QTL segregating status...

  5. Distribution of Ra-226 in the Ross Sea, Antarctica

    International Nuclear Information System (INIS)

    Bettoli, M.G.; Cantelli, L.; Queirazza, G.; Roveri, M.; Tositti, L.; Tubertini, O.; Valcher, S.

    1996-01-01

    An improved procedure for the determination of Rn-222 and Ra-226 in seawater developed for easier on-board operations is presented. Data on the radioactive disequilibrium between the mentioned radionuclides as directly determined in the field can be greatly helpful in the study of the gas-exchange processes at the air-sea interface, especially as far as the Antarctic Ocean is concerned. The method employed has been preliminary tested in laboratory on a set of seawater samples collected in the Ross Sea and Ra-226 data collected are discussed and compared to literature data. (UK)

  6. Construcció d'un HTPC basat en programari lliure

    OpenAIRE

    Ribugent Navarro, Gerard

    2010-01-01

    Els avenços tecnològics en els camps de la informàtica i l'entreteniment ha evolucionat molt ràpidament els darrers anys. Els ordinadors han augmentat la seva potència, han anat adquirint capacitats multimèdia i han arribat al punt de poder reproduir tranquil·lament els nous formats d'alta definició. El televisors i reproductors han passat un procés de sofisticació, el qual els ha dotat de noves característiques, com el teletext, el suport per les funcionalitats de la tdt i capacitat...

  7. El paper de la dona comunicadora a les televisions del Maresme

    OpenAIRE

    Izquierdo Romagosa, Ester

    2015-01-01

    La recerca té com a objectiu conèixer la situació de les dones que treballen en el procés comunicatiu de les televisions del Maresme, tant si són per TDT com per Internet. Hem analitzat cinc televisions, de les quals hem observat la presència femenina als llocs de treball, als càrrecs de responsabilitat i als continguts emesos i també hem realitzat una enquesta a les dones que hi treballen. La investigación tiene como objetivo conocer la situación de las mujeres que trabajan en el proceso ...

  8. Los mecanismos de control de los informativos en las televisiones públicas: el caso de Canal 9

    OpenAIRE

    Sánchez Castillo, Sebastián

    2016-01-01

    Las instituciones y normas de control de los informativos se perciben como la última oportunidad de las televisiones públicas para lograr y mantener el pluralismo, que se revela casi como utópico. La situación en España, y también en otros países del entorno, es de emergencia en muchos casos. La crisis general, unida a la que sufre el sector audiovisual como consecuencia de la implantación de la TDT, ha puesto a las televisiones públicas españolas, carentes desde su fundación de un modelo de ...

  9. Hematogônias: distinção com blastos da leucemia linfóide aguda de células B por citometria de fluxo Hematogones: differentiation from B-lineage acute lymphoblastic leukemia by flow cytometry

    Directory of Open Access Journals (Sweden)

    Fátima M. G. Jorge

    2006-12-01

    Full Text Available Hematogônias são precursores normais de linhagem B que apresentam características morfológicas e, algumas vezes, imunológicas similares aos linfoblastos das leucemias linfóides agudas (LLA. O objetivo desse trabalho é realizar análise comparativa por citometria de fluxo, utilizando três cores, entre sub-populações de hematogônias e blastos da LLA-B, em crianças. O Grupo 1 constou de amostras de medulas ósseas, não neoplásicas, que apresentaram hematogônias identificadas pela microscopia óptica e o Grupo 2 de casos novos de LLA-B. O painel de anticorpos monoclonais utilizado era direcionado para: CD19, CD10, CD45, CD34, IgM, TdT e CD22. A análise das hematogônias, utilizando como parâmetro a intensidade de fluorescência de CD10 X CD45, mostrou três sub-populações representando células imaturas, intermediárias e maduras. A expressão dos marcadores CD34, IgM, TdT e CD22 reforçou esses achados. Os blastos leucêmicos se apresentaram formando uma única população, com expressão de positividade apenas para antígenos de imaturidade. Considerando não só a presença ou ausência de um determinado antígeno, mas sim a sua intensidade de expressão, verificamos que hematogônias e blastos apresentam perfis imunofenotípicos diferentes.Hematogones are normal B-lineage cell precursors with morphologic and sometimes immunophenotypic, similarities to neoplastic lymphoblasts. The aim of this work is to compare using flow cytometry sub-populations of B-lineage cells: normal bone marrow precursors (hematogones and lymphoblasts. Normal bone marrow from patients with hematogones observed by optical microscopy and new cases of acute lymphoblastic leukemia of B-cell precursors were included in the study. Antibodies directed against CD19, CD10, CD45, CD34, IgM and CD22 were used. Analysis of hematogones, using CD10 x CD45 fluorescence intensity as a parameter, showed three sub-populations: immature, intermediary and mature marker

  10. A Test of the Fundamental Physics Underlying Exoplanet Climate Models

    Science.gov (United States)

    Beatty, Thomas; Keating, Dylan; Cowan, Nick; Gaudi, Scott; Kataria, Tiffany; Fortney, Jonathan; Stassun, Keivan; Collins, Karen; Deming, Drake; Bell, Taylor; Dang, Lisa; Rogers, Tamara; Colon, Knicole

    2018-05-01

    A fundamental issue in how we understand exoplanet atmospheres is the assumed physical behavior underlying 3D global circulation models (GCMs). Modeling an entire 3D atmosphere is a Herculean task, and so in exoplanet GCMs we generally assume that there are no clouds, no magnetic effects, and chemical equilibrium (e.g., Kataria et al 2016). These simplifying assumptions are computationally necessary, but at the same time their exclusion allows for a large theoretical lee-way when comparing to data. Thus, though significant discrepancies exist between almost all a priori GCM predictions and their corresponding observations, these are assumed to be due to the lack of clouds, or atmospheric drag, or chemical disequilibrium, in the models (e.g., Wong et al. 2016, Stevenson et al. 2017, Lewis et al. 2017, Zhang et al. 2018). Since these effects compete with one another and have large uncertainties, this makes tests of the fundamental physics in GCMs extremely difficult. To rectify this, we propose to use 88.4 hours of Spitzer time to observe 3.6um and 4.5um phase curves of the transiting giant planet KELT-9b. KELT-9b has an observed dayside temperature of 4600K (Gaudi et al. 2017), which means that there will very likely be no clouds on the day- or nightside, and is hot enough that the atmosphere should be close to local chemical equilibrium. Additionally, we plan to leverage KELT-9b's high temperature to make the first measurement of global wind speed on an exoplanet (Bell & Cowan 2018), giving a constraint on atmospheric drag and magnetic effects. Combined, this means KELT-9b is close to a real-world GCM, without most of the effects present on lower temperature planets. Additionally, since KELT-9b orbits an extremely bright host star these will be the highest signal-to-noise ratio phase curves taken with Spitzer by more than a factor of two. This gives us a unique opportunity to make the first precise and direct investigation into the fundamental physics that are the

  11. Weinberg disequilibrium and association study of insertion/deletion ...

    African Journals Online (AJOL)

    Omayma M. Hassanin

    2014-09-10

    Sep 10, 2014 ... In the case of a reduced number of observed heterozygous patients, as may occur ... examined for a variety of genotyping errors and pseudo-SNP models. For the majority of genotyping models ... selected rather than a random sample, invalidating direct com- parisons with other populations. Therefore, we ...

  12. Evidence of topographic disequilibrium in the Subarnarekha River ...

    Indian Academy of Sciences (India)

    37

    knickpoints using a digital elevation model and correlating it with the bedrock geology and structural ..... application, allows the generation of a vector layer containing the normalized steepness index. (ksn), for each ..... Abdullah S N, Abdoh Ghaleeb A 2013 Landsat ETM-7 for lineament mapping using automatic extraction ...

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

    African Journals Online (AJOL)

    A large proportion of these false associations (or lack of it) result from population stratification, while the rest may be caused by other demographic and evolutionary processes that create a statistical association between a marker allele and the trait, such as bottlenecks, natural selection, hybridization and genetic drift.

  14. Evidence of topographic disequilibrium in the Subarnarekha River ...

    Indian Academy of Sciences (India)

    Shantamoy Guha

    2017-10-16

    Oct 16, 2017 ... Earth Sciences Discipline, Indian Institute of Technology, Gandhinagar 382 355, India. 2. Department of ... framework has thus been used in this study, incor- porating qualitative methods to decipher the exis- tent geologic and ...

  15. Deliberate Disequilibrium: Preparing for a Community College Presidency

    Science.gov (United States)

    McNair, Delores E.

    2015-01-01

    Anticipated retirements and relatively short tenure in office create a shortage of community college presidents in the United States. To fill the unprecedented number of vacancies requires a cadre of candidates well prepared for the demands of the position. Using Satir's change model as a theoretical framework, this year-long reflective study…

  16. Transmission disequilibrium of small CNVs in simplex autism.

    Science.gov (United States)

    Krumm, Niklas; O'Roak, Brian J; Karakoc, Emre; Mohajeri, Kiana; Nelson, Ben; Vives, Laura; Jacquemont, Sebastien; Munson, Jeff; Bernier, Raphe; Eichler, Evan E

    2013-10-03

    We searched for disruptive, genic rare copy-number variants (CNVs) among 411 families affected by sporadic autism spectrum disorder (ASD) from the Simons Simplex Collection by using available exome sequence data and CoNIFER (Copy Number Inference from Exome Reads). Compared to high-density SNP microarrays, our approach yielded ∼2× more smaller genic rare CNVs. We found that affected probands inherited more CNVs than did their siblings (453 versus 394, p = 0.004; odds ratio [OR] = 1.19) and that the probands' CNVs affected more genes (921 versus 726, p = 0.02; OR = 1.30). These smaller CNVs (median size 18 kb) were transmitted preferentially from the mother (136 maternal versus 100 paternal, p = 0.02), although this bias occurred irrespective of affected status. The excess burden of inherited CNVs among probands was driven primarily by sibling pairs with discordant social-behavior phenotypes (p 0.5). Finally, we found enrichment of brain-expressed genes unique to probands, especially in the SRS-discordant group (p = 0.0035). In a combined model, our inherited CNVs, de novo CNVs, and de novo single-nucleotide variants all independently contributed to the risk of autism (p role in the etiology of simplex autism. Importantly, the small size of these variants aids in the identification of specific genes as additional risk factors associated with ASD. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  17. Distribution and linkage disequilibrium analysis of polymorphisms of ...

    Indian Academy of Sciences (India)

    2Five-Star Animal Health Pharmaceutical Factory of Jilian Province, 5333 Xi'an Road, Changchun, Jilin 130062,. People's .... showed that GH peptide sequence of mature protein in. Rongjiang pig ..... 1, white. (PIC value <0.25, low polymorphism; 0.25

  18. Automating Test Activities: Test Cases Creation, Test Execution, and Test Reporting with Multiple Test Automation Tools

    OpenAIRE

    Loke Mun Sei

    2015-01-01

    Software testing has become a mandatory process in assuring the software product quality. Hence, test management is needed in order to manage the test activities conducted in the software test life cycle. This paper discusses on the challenges faced in the software test life cycle, and how the test processes and test activities, mainly on test cases creation, test execution, and test reporting is being managed and automated using several test automation tools, i.e. Jira, ...

  19. Are genes associated with energy metabolism important in asthma and BMI?

    Science.gov (United States)

    Szczepankiewicz, Aleksandra; Breborowicz, Anna; Sobkowiak, Paulina; Popiel, Anna

    2009-02-01

    Increased serum leptin levels have been observed in asthmatic patients. Leptin, via proliferation and activation of Th2 cells, may induce inflammation in asthma. It has also been demonstrated that leptin mRNA expression and protein levels increase in response to inflammatory stimuli. We hypothesized that polymorphisms in the leptin receptor, leptin and ghrelin genes, may affect their expression and, therefore, be responsible for altered response to increased leptin levels observed in asthma. To our knowledge, there were no studies on a potential role of LEPR, LEP, and GHRL polymorphisms in asthma. We analyzed 129 pediatric patients with asthma and 114 healthy children from the control group ranging from 6 to 18 years of age. The diagnosis of allergic asthma was based on clinical symptoms, the lung function test, and the positive skin prick test and/or increased immunoglobulin E (IgE) levels. Polymorphisms were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Statistical analyses were performed with Statistica v.7.1 software (Statistica, StatSoft, Poland; available free at http://www.broad.mit.edu/mpg/haploview/index.php). Linkage disequilibrium analysis was performed with Haploview v.4.0. We observed a statistically significant association of the 3'UTR A/G and the -2549A/G polymorphisms of the leptin gene with asthma. No association with asthma was observed for the K109R and the Q223R polymorphisms of the LEPR gene and the Met72Leu polymorphism of the ghrelin gene. In the analysis of body mass index (BMI) stratified by genotype, we found an association of the -2549A/G LEP, but not of LEPR and GHRL polymorphisms, with higher BMI values in asthmatic patients. We found suggestive evidence for linkage between the two polymorphisms of the LEPR gene (D' = 0.84 CI: 0.71-0.92; r(2) = 0.29) in linkage disequilibrium analysis: The GG haplotype was more frequent in the control healthy group (p = 0.057). No linkage

  20. The Effect of Inconsistency Appeals on the Influence of Direct-to-Consumer Prescription Drug Advertisements: An Application of Goal Disruption Theory.

    Science.gov (United States)

    Rosenberg, Benjamin D; Siegel, Jason T

    2016-01-01

    Scholars across multiple domains have identified the presence of inconsistency-arousing information in direct-to-consumer prescription drug advertisements and have suggested that these appeals, which highlight differences between people's actual and desired lives, may create psychological disequilibrium. However, experimental assessment of the distinct influence of inconsistency-arousing information in this domain is rare. Guided by goal disruption theory-a framework that outlines people's reactions to goal expectation violations-we created direct-to-consumer advertisements designed to make people's life inconsistencies salient. The influence of these ads on people's perceptions of, and intentions to use, prescription drugs was then assessed. Results from a structural equation modeling analysis supported the proposed model, indicating that compared to a control ad, an ad containing a goal expectation violation manipulation resulted in higher levels of psychological disequilibrium; in turn, psychological disequilibrium led to positive evaluations of the ad and the drug, positive outcome expectations of the drug, increased purposive harm endurance, and increased usage intentions. The current results suggest a psychological pathway that begins with a negative goal expectation violation and ends with increased usage intentions and a greater willingness to endure harm to make use possible.

  1. The use of radiometric-logging techniques to determine uranium grade in certain mineralised Karoo boreholes

    International Nuclear Information System (INIS)

    Corner, B.; De Beer, G.P.

    1976-05-01

    During the period September-October 1975, 22 mineralised boreholes in nine different Karoo uranium occurrences were logged radiometrically with the aim of determining to what accuracy the actual uranium grade could be predicted from the gamma logs. The true uranium grades of the mineralised zones logged were known from existing chemical analyses. The results showed that the uranium grades could be predicted to an accuracy of better than 10% through the use of gamma-logging equipment calibrated at Pelindaba, provided that the ore was in equilibrium and that little or no thorium was present. Disequilibrium is, however, prevalent in the Karoo, and in the holes logged it occurred by depletion of uranium relative to its gamma-emitting daughter products. Such effects were mostly confined to the zone above the water table, and it is concluded that for Karoo-type occurrences, the high radiometric background levels observed over extended distances in some boreholes were indicative of radon-gas buildup, and hence of disequilibrium. It is further concluded that radiometric borehole logging can largely replace chemical analyses in the determination of uranium grade for ore-reserve calculations, although chemical checks for disequilibrium would always be necessary [af

  2. An inbreeding model of associative overdominance during a population bottleneck.

    Science.gov (United States)

    Bierne, N; Tsitrone, A; David, P

    2000-08-01

    Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.

  3. Contribution to the study of sedimentation rates in some french Polynesian lakes and lagoon

    International Nuclear Information System (INIS)

    Serra, C.; Poletiko, C.; Badie, C.

    1991-03-01

    210 Pb measurements using 210 Po deposition technique were performed in several marine and lacustrine sediments of French Polynesia to determine sedimentation rates in lakes and lagoons. Some results in terrigeneous sediments were acceptable and permit rate measurements; on the contrary other sediments, especially coral sands provided a 210 Pb/ 226 Ra disequilibrium (0.33 to 0.69). The occurring phenomena seem to be related to 222 Rn scavenging and geothermal endoupwelling which induces 226 Ra enhancement; this leads to the same 210 Pb/ 226 Ra disequilibrium as in deep ocean waters as described, for instance by Thomson and Turekian (1976) in an upwelling zone on Peru coasts [fr

  4. Fuzzy operation and real time surveillance of a nuclear reactor

    International Nuclear Information System (INIS)

    Si-Fodil, M.; Guely, F.; Siarry, P.; Tyran, J.L.

    1997-01-01

    The operating power of nuclear power plants needs to be modulated according to the thin evolutions of electric power demand. Two parameters are concerned by load following operations: the power axial disequilibrium and the position of control rods. This paper deals with the automation of the control of power axial disequilibrium using boration-dilution. An automatic system based on fuzzy logic is proposed which can be substituted to the expert operator who is in charge of this fastidious manual task. The management of water and boron flow rates are studied in details. A Graphic interface was designed for the real-time surveillance of the reactor. (J.S.)

  5. The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum.

    Science.gov (United States)

    Stenøien, H K; Shaw, A J; Stengrundet, K; Flatberg, K I

    2011-02-01

    It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80,000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years.

  6. A comparison of isozyme and quantitative genetic variation in Pinus contorta ssp. latifolia by F{sub ST}

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Rong-Cai; Yeh, F.C. [Univ. of Alberta, Edmonton (Canada); Yanchuk, A.D. [British Columbia Ministry of Forests (Canada)

    1996-03-01

    We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (F{sub ST}) for six quantitative traits were compared with the overall estimate of the differentiation (F*{sub ST}) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the F{sub ST} estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the F*{sub ST} estimate, as judged from the 95% confidence intervals by bootstrapping, the F{sub ST} estimates for branch angle and branch diameter were indistinguishable from the F*{sub ST} estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of F{sub ST} due to Hardy-Weinberg disequilibrium (F{sub IS} {ne} 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia. 48 refs., 1 fig., 3 tabs.

  7. The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum

    Science.gov (United States)

    Stenøien, H K; Shaw, A J; Stengrundet, K; Flatberg, K I

    2011-01-01

    It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80 000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years. PMID:20717162

  8. Population genetic structure of the major malaria vector Anopheles darlingi (Diptera: Culicidae from the Brazilian Amazon, using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Vera Margarete Scarpassa

    2007-06-01

    Full Text Available The population genetic structure of Anopheles darlingi, the major human malaria vector in the Neotropics, was examined using seven microsatellite loci from nine localities in central and western Amazonian Brazil. High levels of genetic variability were detected (5-25 alleles per locus; H E = 0.519-0.949. There was deviation from Hardy-Weinberg Equilibrium for 59.79% of the tests due to heterozygote deficits, while the analysis of linkage disequilibrium was significant for only two of 189 (1.05% tests, most likely caused by null alleles. Genetic differentiation (F ST = 0.001-0.095; Nm = 4.7-363.8 indicates that gene flow is extensive among locations < 152 km apart (with two exceptions and reduced, but not absent, at a larger geographic scale. Genetic and geographic distances were significantly correlated (R² = 0.893, P < 0.0002, supporting the isolation by distance (IBD model. The overall estimate of Ne was 202.4 individuals under the linkage disequilibrium model, and 8 under the heterozygote excess model. Analysis of molecular variance showed that nearly all variation (~ 94% was within sample locations. The UPGMA phenogram clustered the samples geographically, with one branch including 5/6 of the state of Amazonas localities and the other branch the Acre, Rondônia, and remaining Amazonas localities. Taken together, these data suggest little genetic structure for An. darlingi from central and western Amazonian Brazil. These findings also imply that the IBD model explains nearly all of the differentiation detected. In practical terms, populations of An. darlingi at distances < 152 km should respond similarly to vector control measures, because of high gene flow.

  9. Nature of radioactive contamination of components of ecosystems of streamflows from tunnels of Degelen massif

    International Nuclear Information System (INIS)

    Panitskiy, A.V.; Lukashenko, S.N.

    2015-01-01

    The paper provides data on environmental contamination due to radionuclides' migration with water. As a result of investigations there was obtained data on character of contamination of soil cover, surface water and underflow from tunnels of Degelen massif. Character of radionuclides' spatial distribution in environment was also shown. Mobility ranges of radionuclides' vertical and horizontal movements have been established in soils both across and along the stream flow. There was also shown a possibility to forecast radionuclides' concentration in soil by specific activity of these radionuclides in water. Different concentrations of radionuclides in associated components of the ecosystem (surface waters – ground waters – soils) have shown disequilibrium of their condition in this system. Generalization of investigation results for tunnel water streams' with water inflows, chosen as investigation objects in this work, allows to forecast radionuclides' behavior in meadow soils and other ecosystems of water streams from tunnels of Degelen test site. Based on analysis of curves, describing radionuclides' behavior in horizontal direction, we can forecast, that at this stage 137 Cs and 239+240 Pu would not be distributed more than 1.5 km from the access to the daylight surface, 90 Sr – not more than 2 km. - Highlights: • Contamination of soil cover, surface water and groundwater from tunnels of Degelen nuclear test area. • Radionuclides in associated components of the ecosystem showed disequilibrium. • Forecast that 137 Cs and 239+240 Pu will not be distributed more than 1.5 km from tunnel exits. • Forecast that 90 Sr will not be distributed more than 2 km

  10. Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758, using Illumina MiSeq next generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Violeta López-Márquez

    2016-03-01

    Full Text Available In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

  11. Comparison Of Vented And Absolute Pressure Transducers For Water-Level Monitoring In Hanford Site Central Plateau Wells

    International Nuclear Information System (INIS)

    Mcdonald, J.P.

    2011-01-01

    Automated water-level data collected using vented pressure transducers deployed in Hanford Site Central Plateau wells commonly display more variability than manual tape measurements in response to barometric pressure fluctuations. To explain this difference, it was hypothesized that vented pressure transducers installed in some wells are subject to barometric pressure effects that reduce water-level measurement accuracy. Vented pressure transducers use a vent tube, which is open to the atmosphere at land surface, to supply air pressure to the transducer housing for barometric compensation so the transducer measurements will represent only the water pressure. When using vented transducers, the assumption is made that the air pressure between land surface and the well bore is in equilibrium. By comparison, absolute pressure transducers directly measure the air pressure within the wellbore. Barometric compensation is achieved by subtracting the well bore air pressure measurement from the total pressure measured by a second transducer submerged in the water. Thus, no assumption of air pressure equilibrium is needed. In this study, water-level measurements were collected from the same Central Plateau wells using both vented and absolute pressure transducers to evaluate the different methods of barometric compensation. Manual tape measurements were also collected to evaluate the transducers. Measurements collected during this study demonstrated that the vented pressure transducers over-responded to barometric pressure fluctuations due to a pressure disequilibrium between the air within the wellbores and the atmosphere at land surface. The disequilibrium is thought to be caused by the relatively long time required for barometric pressure changes to equilibrate between land surface and the deep vadose zone and may be exacerbated by the restriction of air flow between the well bore and the atmosphere due to the presence of sample pump landing plates and well caps. The

  12. Complex expression patterns of lymphocyte-specific genes during the development of cartilaginous fish implicate unique lymphoid tissues in generating an immune repertoire

    Science.gov (United States)

    Miracle, A. L.; Anderson, M. K.; Litman, R. T.; Walsh, C. J.; Luer, C. A.; Rothenberg, E. V.; Litman, G. W.

    2001-01-01

    Cartilaginous fish express canonical B and T cell recognition genes, but their lymphoid organs and lymphocyte development have been poorly defined. Here, the expression of Ig, TCR, recombination-activating gene (Rag)-1 and terminal deoxynucleosidase (TdT) genes has been used to identify roles of various lymphoid tissues throughout development in the cartilaginous fish, Raja eglanteria (clearnose skate). In embryogenesis, Ig and TCR genes are sharply up-regulated at 8 weeks of development. At this stage TCR and TdT expression is limited to the thymus; later, TCR gene expression appears in peripheral sites in hatchlings and adults, suggesting that the thymus is a source of T cells as in mammals. B cell gene expression indicates more complex roles for the spleen and two special organs of cartilaginous fish-the Leydig and epigonal (gonad-associated) organs. In the adult, the Leydig organ is the site of the highest IgM and IgX expression. However, the spleen is the first site of IgM expression, while IgX is expressed first in gonad, liver, Leydig and even thymus. Distinctive spatiotemporal patterns of Ig light chain gene expression also are seen. A subset of Ig genes is pre-rearranged in the germline of the cartilaginous fish, making expression possible without rearrangement. To assess whether this allows differential developmental regulation, IgM and IgX heavy chain cDNA sequences from specific tissues and developmental stages have been compared with known germline-joined genomic sequences. Both non-productively rearranged genes and germline-joined genes are transcribed in the embryo and hatchling, but not in the adult.

  13. Non-transfusion dependent thalassemia: translating evidence to guidelines

    Directory of Open Access Journals (Sweden)

    Afif R. Harb

    2014-12-01

    Full Text Available The thalassemias are a group of inherited disorders of hemoglobin synthesis characterized by various degrees of defective production of the α- or β-globin chains of adult hemoglobin A. Non-transfusion- dependent thalassemia (NTDT includes a group of thalassemia patients who do not require regular RBC transfusions for survival, but may require occasional transfusions due to infection or pregnancy or may require more regular transfusions later in life due to splenomegaly or other complications. Due to the rising phenomenon of global migration, this previously well-localized entity is currently spreading more and more worldwide reaching Northern America and Northern Europe. The clinical picture of NTDT is governed by the severity of the ineffective erythropoiesis and the chronic hemolytic anemia, which, in turn, lead to iron overload, hypercoagulability, and an array of clinical complications involving almost every organ system. Patients with NTDT suffer from complications that are distinct from those encountered in patients with transfusion- dependent thalassemia (TDT in addition to the complications shared by both TDT and NTDT. As a consequence, patients with NTDT deserve a care specifically tailored to their needs. In the care of patients with NTDT, aiming at a standardized yet personalized care is not an easy task especially that NTDT patients lie on a heterogeneous spectrum with a wide variability in their clinical presentation and response to therapy. Therefore, guidelines emerge as a necessity to answer the specific needs of NTDT patients and the clinicians caring for them. In this article, we summarize the complications most commonly associated with NTDT and the recommendations of the guidelines for the management of patients with NTDT, based on the best available evidence.

  14. Temporal discrimination, a cervical dystonia endophenotype: penetrance and functional correlates.

    Science.gov (United States)

    Kimmich, Okka; Molloy, Anna; Whelan, Robert; Williams, Laura; Bradley, David; Balsters, Joshua; Molloy, Fiona; Lynch, Tim; Healy, Daniel G; Walsh, Cathal; O'Riordan, Seán; Reilly, Richard B; Hutchinson, Michael

    2014-05-01

    The pathogenesis of adult-onset primary dystonia remains poorly understood. There is variable age-related and gender-related expression of the phenotype, the commonest of which is cervical dystonia. Endophenotypes may provide insight into underlying genetic and pathophysiological mechanisms of dystonia. The temporal discrimination threshold (TDT)-the shortest time interval at which two separate stimuli can be detected as being asynchronous-is abnormal both in patients with cervical dystonia and in their unaffected first-degree relatives. Functional magnetic resonance imaging (fMRI) studies have shown that putaminal activation positively correlates with the ease of temporal discrimination between two stimuli in healthy individuals. We hypothesized that abnormal temporal discrimination would exhibit similar age-related and gender-related penetrance as cervical dystonia and that unaffected relatives with an abnormal TDT would have reduced putaminal activation during a temporal discrimination task. TDTs were examined in a group of 192 healthy controls and in 158 unaffected first-degree relatives of 84 patients with cervical dystonia. In 24 unaffected first-degree relatives, fMRI scanning was performed during a temporal discrimination task. The prevalence of abnormal TDTs in unaffected female relatives reached 50% after age 48 years; whereas, in male relatives, penetrance of the endophenotype was reduced. By fMRI, relatives who had abnormal TDTs, compared with relatives who had normal TDTs, had significantly less activation in the putamina and in the middle frontal and precentral gyri. Only the degree of reduction of putaminal activity correlated significantly with worsening of temporal discrimination. These findings further support abnormal temporal discrimination as an endophenotype of cervical dystonia involving disordered basal ganglia circuits. © 2014 International Parkinson and Movement Disorder Society.

  15. Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions

    DEFF Research Database (Denmark)

    Schoeps, Anja; Rudolph, Anja; Seibold, Petra

    2014-01-01

    recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714......,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three...... in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8...

  16. Thermal analysis and microstructural characterization of Mg-Al-Zn system alloys

    Science.gov (United States)

    Król, M.; Tański, T.; Sitek, W.

    2015-11-01

    The influence of Zn amount and solidification rate on the characteristic temperature of the evaluation of magnesium dendrites during solidification at different cooling rates (0.6-2.5°C) were examined by thermal derivative analysis (TDA). The dendrite coherency point (DCP) is presented with a novel approach based on second derivative cooling curve. Solidification behavior was examined via one thermocouple thermal analysis method. Microstructural assessments were described by optical light microscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy. These studies showed that utilization of d2T/dt2 vs. the time curve methodology provides for analysis of the dendrite coherency point

  17. Annealing Effects on the Normal-State Resistive Properties of Underdoped Cuprates

    Science.gov (United States)

    Vovk, R. V.; Khadzhai, G. Ya.; Nazyrov, Z. F.; Kamchatnaya, S. N.; Feher, A.; Dobrovolskiy, O. V.

    2018-05-01

    The influence of room-temperature annealing on the parameters of the basal-plane electrical resistance of underdoped YBa_2Cu_3O_{7-δ } and HoBa_2Cu_3O_{7-δ } single crystals in the normal and superconducting states is investigated. The form of the derivatives dρ (T)/dT makes it possible to determine the onset temperature of the fluctuation conductivity and indicates a nonuniform distribution of the labile oxygen. Annealing has been revealed to lead to a monotonic decrease in the oxygen deficiency, that primarily manifests itself as a decrease in the residual resistance, an increase of T_c, and a decrease in the Debye temperature.

  18. Fokker-Planck equation resolution for N variables-Application examples

    International Nuclear Information System (INIS)

    Munoz Roldan, A.; Garcia-Olivares, A.

    1994-01-01

    A set of problems which are reducible to Fokker-Planck equations are presented. Those problems have been solved by using the CHAPKOL library. This library of programs solves stochastic ''Fokker-Planck'' equations in one or several dimensions by using the Chapman-Kolmogorov integral. This method calculates the probability distribution at a time t+dt from a distribution given at time t through a convolution integral in which the integrant is the product of the distribution function at time t and the Green function of the Fokker-Planck equation. The method have some numerical advantages when compared with finite differences algorithms. The accuracy of the method is analysed in several specific cases

  19. Comparing the benefits of caffeine, naps and placebo on verbal, motor and perceptual memory.

    Science.gov (United States)

    Mednick, Sara C; Cai, Denise J; Kanady, Jennifer; Drummond, Sean P A

    2008-11-03

    Caffeine, the world's most common psychoactive substance, is used by approximately 90% of North Americans everyday. Little is known, however, about its benefits for memory. Napping has been shown to increase alertness and promote learning on some memory tasks. We directly compared caffeine (200mg) with napping (60-90min) and placebo on three distinct memory processes: declarative verbal memory, procedural motor skills, and perceptual learning. In the verbal task, recall and recognition for unassociated words were tested after a 7h retention period (with a between-session nap or drug intervention). A second, different, word list was administered post-intervention and memory was tested after a 20min retention period. The non-declarative tasks (finger tapping task (FTT) and texture discrimination task (TDT)) were trained before the intervention and then retested afterwards. Naps enhanced recall of words after a 7h and 20min retention interval relative to both caffeine and placebo. Caffeine significantly impaired motor learning compared to placebo and naps. Napping produced robust perceptual learning compared with placebo; however, naps and caffeine were not significantly different. These findings provide evidence of the limited benefits of caffeine for memory improvement compared with napping. We hypothesize that impairment from caffeine may be restricted to tasks that contain explicit information; whereas strictly implicit learning is less compromised.

  20. TU-CD-304-06: Using FFF Beams Improves Tumor Control in Radiotherapy of Lung Cancers

    Energy Technology Data Exchange (ETDEWEB)

    Vassiliev, O [Mary Bird Perkins Cancer Center, Baton Rouge, LA (United States); Wang, H [UT MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose: Electron disequilibrium at the lung-tumor interface results in an under-dosage of tumor regions close to its surface. This under-dosage is known to be significant and can compromise tumor control. Previous studies have shown that in FFF beams, disequilibrium effects are less pronounced, which is manifested in an increased skin dose. In this study we investigate the improvement in tumor dose coverage that can be achieved with FFF beams. The significance of this improvement is evaluated by comparing tumor control probabilities of FFF beams and conventional flattened beams. Methods: The dosimetric coverage was investigated in a virtual phantom representing the chest wall, lung tissue and the tumor. A range of tumor sizes was investigated, and two tumor locations – central and adjacent to the chest wall. Calculations were performed with BEAMnrc Monte Carlo code. Parallel-opposed and multiple coplanar 6-MV beams were simulated. The tumor control probabilities were calculated using the logistic model with parameters derived from clinical data for non-small lung cancer patients. Results: FFF beams were not entirely immune to disequilibrium effects. They nevertheless consistently delivered more uniform dose distribution throughout the volume of the tumor, and eliminated up to ∼15% of under-dosage in the most affected by disequilibrium 1-mm thick surface region of the tumor. A voxel-by-voxel comparison of tumor control probabilities between FFF and conventional flattened beams showed an advantage of FFF beams that, depending on the set up, was from a few to ∼9 percent. Conclusion: A modest improvement in tumor control probability on the order of a few percent can be achieved by replacing conventional flattened beams with FFF beams. However, given the large number of lung cancer patients undergoing radiotherapy, these few percent can potentially prevent local tumor recurrence for a significant number of patients.

  1. Family-Based Association Study Between SLC2A1, HK1, and LEPR Polymorphisms With Myelomeningocele in Chile

    Science.gov (United States)

    Suazo, José; Castillo, Silvia; Martin, Luz Maria; Rojas, Francisca; Santos, José Luis; Rotter, Karin; Solar, Margarita; Tapia, Eva

    2013-01-01

    Obese/diabetic mothers present a higher risk to develop offspring with myelomeningocele (MM), evidence supporting the role of energy homeostasis-related genes in neural tube defects. Using polymerase chain reaction–restriction fragment length polymorphism, we have genotyped SLC2A1, HK1, and LEPR single-nucleotide polymorphisms in 105 Chilean patients with MM and their parents in order to evaluate allele–phenotype associations by means of allele/haplotype transmission test (TDT) and parent-of-origin effects. We detected an undertransmission for the SLC2A1 haplotype T-A (rs710218-rs2229682; P = .040), which was not significant when only lower MM (90% of the cases) was analyzed. In addition, the leptin receptor rs1137100 G allele showed a significant increase in the risk of MM for maternal-derived alleles in the whole sample (2.43-fold; P = .038) and in lower MM (3.20-fold; P = .014). Our results support the role of genes involved in energy homeostasis in the risk of developing MM, thus sustaining the hypothesis of diverse pathways and genetic mechanisms acting in the expression of such birth defect. PMID:23427181

  2. 230Th-238U disequilibria in historical lavas from Iceland

    International Nuclear Information System (INIS)

    Condomines, M.; Morand, P.; Alleegre, C.J.; Sigvaldason, G.

    1981-01-01

    The 230 Th- 238 U disequilibrium studies on historical lavas from Iceland show a relative homogeneity for Th/U ratios and also a variation for ( 230 Th/ 232 Th) activity ratios at the scale of the island. The ( 230 Th/ 238 U) disequilibrium ratio is always greater than 1 which indicates that partial melting produces magmas with Th/U ratios greater than those of the mantle source. Furthermore, there seems to be a correlation between the variations of ( 230 Th/ 232 Th) (and delta 18 O) ratios and the geographical location of the samples along the active zones of Iceland. We develop and discuss several models in order to explain these variations. (orig.)

  3. Modelling the dispersion of non-conservative radionuclides in tidal waters. Pt. 1: Conceptual and mathematical model

    International Nuclear Information System (INIS)

    Perianez, R.; Abril, J.M.; Garcia-Leon, M.

    1996-01-01

    A 2D four-phase model to study the dispersion of non-conservative radionuclides in tidal waters, in conditions of disequilibrium for ionic exchanges, has been developed. At disequilibrium conditions, ionic exchanges cannot be formulated using distribution coefficients k d . Thus, kinetic transfer coefficients have been used. The model includes ionic exchanges among water and the solid phases (suspended matter and two grain size fractions of sediments), the deposition and resuspension of suspended matter and advective plus diffusive transport. In the second part of this work, which is presented in a separate paper, the model is applied to simulate 226 Ra dispersion, discharged from a fertilizer processing plant, in an estuarine system in the south-west of Spain. (Author)

  4. The impact of accelerating faster than exponential population growth on genetic variation.

    Science.gov (United States)

    Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

    2014-03-01

    Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models' effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.

  5. Thematic network on the analysis of thorium and its isotopes in workplace materials

    International Nuclear Information System (INIS)

    Bernot, C.; Butler, O.; Howe, A.

    2002-05-01

    An EC-funded thematic network was established to bring together experts in the field of thorium analysis in order to co-ordinate research activity and identify best analytical practice, requirements for reference materials, etc. The work programme of the network included (i) a survey of past, current and proposed research to determine future research needs; (ii) a series of intercomparison exercises to test the performance of methods for measuring thorium in workplace materials; and (iii) a workshop to promote best practice and transfer information to regulatory authorities and industry. Three interlaboratory comparisons were carried out, as planned, to test the performance of techniques and methodologies available for measurement of thorium. Test solutions containing 232 Th and 228 Th in equilibrium, test solutions containing 232 Th and 228 Th in disequilibrium and solid test samples containing 232 Th and 228 Th in equilibrium were supplied to participants. These were analysed by a variety of techniques. Full details of the three laboratory intercomparisons are given in a series of HSL reports and in other publications

  6. Test for positional candidate genes for body composition on pig chromosome 6

    Directory of Open Access Journals (Sweden)

    Pérez-Enciso Miguel

    2002-07-01

    Full Text Available Abstract One QTL affecting backfat thickness (BF, intramuscular fat content (IMF and eye muscle area (MA was previously localized on porcine chromosome 6 in an F2 cross between Iberian and Landrace pigs. This work was done to study the effect of two positional candidate genes on these traits: H-FABP and LEPR genes. The QTL mapping analysis was repeated with a regression method using genotypes for seven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP and LEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis. The effects of the candidate gene polymorphisms were analyzed in two ways. When an animal model was fitted, both genes showed significant effects on fatness traits, the H-FABP polymorphism showed significant effects on IMF and MA, and the LEPR polymorphism on BF and IMF. But when the candidate gene effect was included in a QTL regression analysis these associations were not observed, suggesting that they must not be the causal mutations responsible for the effects found. Differences in the results of both analyses showed the inadequacy of the animal model approach for the evaluation of positional candidate genes in populations with linkage disequilibrium, when the probabilities of the parental origin of the QTL alleles are not included in the model.

  7. Isolation and characterization of 29 microsatellite markers for the bumphead parrotfish, Bolbometopon muricatum, and cross amplification in 12 related species

    KAUST Repository

    Priest, Mark

    2014-10-14

    We isolated and characterized 29 microsatellite loci for the bumphead parrotfish, Bolbometopon muricatum, a wide-ranging parrotfish listed as vulnerable by the International Union for Conservation of Nature (IUCN). The 29 loci were tested on 95 individuals sampled from the Solomon Islands. The number of alleles ranged from two to ten. Evidence of linkage disequilibrium was found for only one pair of loci (Bm54 and Bm112). Two loci (Bm20 and Bm119) showed significant departure from Hardy-Weinberg equilibrium. We also tested each locus for amplification and polymorphism on 11 other scarine labrid species and one labrid species. Amplification success ranged from zero to ten loci per species. These microsatellite loci are the first specific set for B. muricatum and will be a useful tool for assessing genetic population structure, genetic diversity, and parentage in future studies.

  8. Association of TMEM106B gene polymorphism with age at onset in granulin mutation carriers and plasma granulin protein levels.

    Science.gov (United States)

    Cruchaga, Carlos; Graff, Caroline; Chiang, Huei-Hsin; Wang, Jun; Hinrichs, Anthony L; Spiegel, Noah; Bertelsen, Sarah; Mayo, Kevin; Norton, Joanne B; Morris, John C; Goate, Alison

    2011-05-01

    To test whether rs1990622 (TMEM106B) is associated with age at onset (AAO) in granulin (GRN) mutation carriers and with plasma GRN levels in mutation carriers and healthy, elderly individuals. Rs1990622 (TMEM106B) was identified as a risk factor for frontotemporal lobar degeneration with TAR DNA-binding protein inclusions (FTLD-TDP) in a recent genome-wide association. Rs1990622 was genotyped in GRN mutation carriers and tested for association with AAO using the Kaplan-Meier method and a Cox proportional hazards model. Alzheimer's Disease Research Center. Subjects  We analyzed 50 affected and unaffected GRN mutation carriers from 4 previously reported FTLD-TDP families (HDDD1, FD1, HDDD2, and the Karolinska family). The GRN plasma levels were also measured in 73 healthy, elderly individuals. Age at onset and GRN plasma levels. The risk allele of rs1990622 was associated with a mean decrease of the AAO of 13 years (P = 9.9 × 10(-7)) and with lower plasma GRN levels in both healthy older adults (P = 4 × 10(-4)) and GRN mutation carriers (P = .0027). Analysis of the HapMap database identified a nonsynonymous single-nucleotide polymorphism rs3173615 (T185S) in perfect linkage disequilibrium with rs1990622. The association of rs1990622 with AAO explains, in part, the wide range in the AAO of disease among GRN mutation carriers. We hypothesize that rs1990622 or another variant in linkage disequilibrium could act in a manner similar to APOE in Alzheimer disease, increasing risk for disease in the general population and modifying AAO in mutation carriers. Our results also suggest that genetic variation in TMEM106B may influence risk for FTLD-TDP by modulating secreted levels of GRN.

  9. TMEM106B gene polymorphism is associated with age at onset in granulin mutation carriers and plasma granulin protein levels

    Science.gov (United States)

    Cruchaga, Carlos; Graff, Caroline; Chiang, Huei-Hsin; Wang, Jun; Hinrichs, Anthony L.; Spiegel, Noah; Bertelsen, Sarah; Mayo, Kevin; Norton, Joanne B.; Morris, John C.; Goate, Alison

    2011-01-01

    Objective A recent genome-wide association study for frontotemporal lobar degeneration with TAR DNA-binding protein inclusions (FTLD-TDP), identified rs1990622 (TMEM106B) as a risk factor for FTLD-TDP. In this study we tested whether rs1990622 is associated with age at onset (AAO) in granulin (GRN) mutation carriers and with plasma GRN levels in mutation carriers and healthy elderly individuals. Design Rs1990622 was genotyped in GRN mutation carriers and tested for association with AAO using the Kaplan-Meier and a Cox proportional hazards model. Subjects We analyzed 50 affected and unaffected GRN mutation carriers from four previously reported FTLD-TDP families (HDDD1, FD1, HDDD2 and the Karolinska family). GRN plasma levels were also measured in 73 healthy, elderly individuals. Results The risk allele of rs1990622 is associated with a mean decrease of the age at onset of thirteen years (p=9.9×10−7), with lower plasma granulin levels in both healthy older adults (p = 4×10−4) and GRN mutation carriers (p=0.0027). Analysis of the HAPMAP database identified a non-synonymous single nucleotide polymorphism, rs3173615 (T185S) in perfect linkage disequilibrium with rs1990622. Conclusions The association of rs1990622 with AAO explains, in part, the wide range in the age at onset of disease among GRN mutation carriers. We hypothesize that rs1990622 or another variant in linkage disequilibrium could act in a manner similar to APOE in Alzheimer’s disease, increasing risk for disease in the general population and modifying AAO in mutation carriers. Our results also suggest that genetic variation in TMEM106B may influence risk for FTLD-TDP by modulating secreted levels of GRN. PMID:21220649

  10. Uranium series disequilibrium studies at the Broubster analogue site

    International Nuclear Information System (INIS)

    Longworth, G.; Ivanovich, M.; Wilkins, M.A.

    1990-11-01

    Uranium series measurements at a natural analogue site at Broubster, Caithness have been used to investigate radionuclide migration over periods ranging from several hundred to 10 6 years. The measured values for the uranium concentration and activity values 234 U/ 238 U and 230 Th/ 234 U indicate that the geochemical system is more complicated than that originally proposed of uranium dispersion and water transport into a peat bog. There appears to be little thorium mobility although there is evidence for an appreciable fraction of thorium on the colloidal phase. (author)

  11. Uranium series disequilibrium studies at the Broubster analogue site

    International Nuclear Information System (INIS)

    Longworth, G.; Ivanovich, M.; Wilkins, M.A.

    1989-09-01

    Uranium series measurements at a natural analogue site at Broubster, Caithness have been used to investigate radionuclide migration over a period of several hundred to 10 6 years. The measured values for the uranium concentration and activity ratios 234 U/ 238 U and 230 Th/ 234 U indicate that the geochemical system is more complicated than that originally proposed of uranium dispersion and water transport into a peat bog. There appears to be little thorium mobility although there is evidence for an appreciable fraction of thorium on the colloidal phases. (author)

  12. Nutrient disequilibrium in agro-ecosystems: Concepts and case studies

    International Nuclear Information System (INIS)

    Smaling, Eric

    2002-01-01

    Full text: Amongst the problems that African agriculture faces, soil fertility decline is mentioned as a major pressure. The declining state (lower soil fertility) has led to different responses by researchers, landusers and policy makers. All responses directly or indirectly boil down to some form of 'Integrated Nutrient Management' (INM), which is defined as the 'judicious' manipulation of nutrient stocks and flows. As INM is complex and multi-faceted, it is difficult to derive simple indicators for policy makers from it. The concept of stocks (state) and flows (pressure), however, links well with economic sciences. A continental study revealed that Africa is losing nutrients at a rather alarming rate, i.e., 22 kg N, 2.5 kg P and 15 kg K per ha per year (Stoorvogel and Smaling, 1990). These values represent the sum of the outputs minus the sum of the inputs mentioned below. IN 1 mineral fertilizer OUT 1 nutrients in harvested parts, milk, meat, etc. IN 2 organic fertilizer OUT 2 nutrients in removed crop residues IN 3 atmospheric deposition OUT 3 leaching IN 4 biological N fixation OUT 4 gaseous losses IN 5 sedimentation OUT 5 runoff and erosion This study however, commissioned by FAO, had to deal with a lot of higher-scale problems, i.e., using FAO's production yearbooks, using the 1:5,000,000 FAO Soil Map of the World, generalisation, simplification, and the use of proxies (transfer functions). It triggered many studies at lower spatial scales (field, farm, village, watershed), in which inputs and outputs are accompanied by internal flows within the system. In other words, INM can be geared towards: adding nutrients to the system; saving nutrient from being lost from the system; recycling so as to maximize nutrient use efficiency. Measurement of nutrient flows is complex: a simple fertilizer trial implies adding nutrients, and harvesting part of the extra nutrients, but what happens to the nutrients that were not taken up by the crop? More spatially complex is the ring management system in West Africa where animals spend the night and early morning around the village, fertilizing this area, while they eat and deplete the bushlands during daytime. IFPRI has, for its Vision 2020 study, grouped the tropical world into five 'agricultural landscapes', i.e.: Irrigated lands; High quality rainfed lands; Densely populated marginal lands; Extensive agriculture in marginal lands; (Peri)urban agriculture. The complexity of measuring the nutrient balance for these 'landscapes' will be highlighted. Measurement problems seem to be scientific issues, but they do come back at the policy level. In The Netherlands, a mineral book keeping system is in place (MINAS), which works with farmgate balances. However, a surface balance approach would give other figures and would encompass different incentives for the land user. More accurate compartment approaches are liked by the researcher but generally regarded as too cumbersome to build policies on. It is very difficult to scale up point research to higher spatial and temporal scales. Examples are given of agricultural landscapes in Madagascar and Nigeria that may help in deciding where to focus research efforts. It is crucial that scientific development on INM is closely related to policy and landuse, as all these fields are changing simultaneously. Policies are increasingly developed at decentral levels, opening up avenues for INM approaches that were not applied before. Also, landusers become more vocal, and want to be involved in research for development (e.g., participatory technology development). INM therefore should be a joint effort between researchers, policy makers and land users. Research has a key role to play in development of sound methodologies for measurement, modelling and monitoring. (author)

  13. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

    DEFF Research Database (Denmark)

    Vilhjálmsson, Bjarni J; Yang, Jian; Finucane, Hilary K

    2015-01-01

    to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred...

  14. Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans.

    Science.gov (United States)

    Reitz, Christiane; Jun, Gyungah; Naj, Adam; Rajbhandary, Ruchita; Vardarajan, Badri Narayan; Wang, Li-San; Valladares, Otto; Lin, Chiao-Feng; Larson, Eric B; Graff-Radford, Neill R; Evans, Denis; De Jager, Philip L; Crane, Paul K; Buxbaum, Joseph D; Murrell, Jill R; Raj, Towfique; Ertekin-Taner, Nilufer; Logue, Mark; Baldwin, Clinton T; Green, Robert C; Barnes, Lisa L; Cantwell, Laura B; Fallin, M Daniele; Go, Rodney C P; Griffith, Patrick; Obisesan, Thomas O; Manly, Jennifer J; Lunetta, Kathryn L; Kamboh, M Ilyas; Lopez, Oscar L; Bennett, David A; Hendrie, Hugh; Hall, Kathleen S; Goate, Alison M; Byrd, Goldie S; Kukull, Walter A; Foroud, Tatiana M; Haines, Jonathan L; Farrer, Lindsay A; Pericak-Vance, Margaret A; Schellenberg, Gerard D; Mayeux, Richard

    2013-04-10

    Genetic variants associated with susceptibility to late-onset Alzheimer disease are known for individuals of European ancestry, but whether the same or different variants account for the genetic risk of Alzheimer disease in African American individuals is unknown. Identification of disease-associated variants helps identify targets for genetic testing, prevention, and treatment. To identify genetic loci associated with late-onset Alzheimer disease in African Americans. The Alzheimer Disease Genetics Consortium (ADGC) assembled multiple data sets representing a total of 5896 African Americans (1968 case participants, 3928 control participants) 60 years or older that were collected between 1989 and 2011 at multiple sites. The association of Alzheimer disease with genotyped and imputed single-nucleotide polymorphisms (SNPs) was assessed in case-control and in family-based data sets. Results from individual data sets were combined to perform an inverse variance-weighted meta-analysis, first with genome-wide analyses and subsequently with gene-based tests for previously reported loci. Presence of Alzheimer disease according to standardized criteria. Genome-wide significance in fully adjusted models (sex, age, APOE genotype, population stratification) was observed for a SNP in ABCA7 (rs115550680, allele = G; frequency, 0.09 cases and 0.06 controls; odds ratio [OR], 1.79 [95% CI, 1.47-2.12]; P = 2.2 × 10(-9)), which is in linkage disequilibrium with SNPs previously associated with Alzheimer disease in Europeans (0.8 Alzheimer disease but not reaching significance in genome-wide analyses were replicated in gene-based analyses accounting for linkage disequilibrium between markers and correcting for number of tests performed per gene (CR1, BIN1, EPHA1, CD33; 0.0005 Alzheimer disease was significantly associated with variants in ABCA7 and with other genes that have been associated with Alzheimer disease in individuals of European ancestry. Replication and functional

  15. The role of metals and dithiolate ligands on structural, electronic and optical properties of [M(bipyridine)(dithiolate)] complexes: A theoretical study

    Science.gov (United States)

    Samiee, Sepideh; Taghvaeian, Samira

    2018-06-01

    A series of [M(diimine)(dithiolate)] complexes of general formula [M(bpy)(dithiolate)] {bpy = 2,2‧-bipyridine;dithiolate = 1,2-benzenedithiolate (bdt2-), 3,4-toluenedithiolate (tdt2-) and 4-cyanobenzene-1,2-dithiolate (cbdt2-); M = Ni(II), Pd(II) and Pt(II)} have been studied by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations. The geometries, stabilities, electronic structures, optical absorption spectra in different phases as well as thermodynamic parameters are explored. The changes of metal ion center and dithiolate ligands on some molecular properties are also discussed. These calculated results are in good agreement with the experimental data. The bonding analyses show that the Msbnd S bond is covalent so that always polarized towards sulfur atom, whereas the Msbnd N bond exhibits a considerable amount of electrostatic interaction. Detailed NBO analysis indicates that these complexes can be easily oxidized than reduced, and acts as the reducing agent. The HOMO-LUMO energy gaps of all complexes under study are founded about 2 eV and the strong absorption from 400 to 700 nm which match with the solar spectra very well. Besides, the simulated absorption spectra are in accordance with the trends of energy gaps. Comparison of the absorption spectra in dichloromethane solution with those in gas phase show that the solvatochromic effect. The order of magnitude for light harvesting efficiencies (LHE) of all complexes is Pt > Pd > Ni and cbdt2- > bdt2- > tdt2-. Our results confirm the effect and role of metals and dithiolate ligands on enhancing the optical properties of these complexes. Thus, the result of this work can serve as a rational tool for the design and synthesis of diimine-dithiolate complexes and broadens the scope for further investigations into potential dyes for use in the field of dye-sensitized solar cells (DSSC).

  16. MULTI PERIOD SHOCKS ROLES ON GOVERNMENT SPENDING IN INDONESIA

    Directory of Open Access Journals (Sweden)

    Jaka Sriyana

    2011-09-01

    Full Text Available This paper proposes an alternative dynamic model of government spending in Indonesia. The model is based on short term disequilibrium assumption, in which multi period of shocks variables may play an important role. This research applies a loss function approach and uses optimum shock variables as the determinant for government spending during 1970-2010. The result shows that real GDP, population, and multi period shock of government spending are statistically significant. It provides evidence of the impact of multi period shocks to the realization of government spending. It implies that government faces a serious disequilibrium in determining their spending both in short and long terms.Keywords: Fiscal, government spending, deficit budget, shockJEL classification numbers: H53, H62, C22

  17. Test Review: TestDaF

    Science.gov (United States)

    Norris, John; Drackert, Anastasia

    2018-01-01

    The Test of German as a Foreign Language (TestDaF) plays a critical role as a standardized test of German language proficiency. Developed and administered by the Society for Academic Study Preparation and Test Development (g.a.s.t.), TestDaF was launched in 2001 and has experienced persistent annual growth, with more than 44,000 test takers in…

  18. Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni.

    Directory of Open Access Journals (Sweden)

    Jacob A Tennessen

    Full Text Available New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite. However, few molecular markers linked to resistance have been identified and characterized in snails.Here we test six independent genetic loci for their influence on resistance to Schistosoma mansoni strain PR1 in the 13-16-R1 strain of the snail Biomphalaria glabrata. We first identify a genomic region, RADres, showing the highest differentiation between susceptible and resistant inbred lines among 1611 informative restriction-site associated DNA (RAD markers, and show that it significantly influences resistance in an independent set of 439 outbred snails. The additive effect of each RADres resistance allele is 2-fold, similar to that of the previously identified resistance gene sod1. The data fit a model in which both loci contribute independently and additively to resistance, such that the odds of infection in homozygotes for the resistance alleles at both loci (13% infected is 16-fold lower than the odds of infection in snails without any resistance alleles (70% infected. Genome-wide linkage disequilibrium is high, with both sod1 and RADres residing on haplotype blocks >2 Mb, and with other markers in each block also showing significant effects on resistance; thus the causal genes within these blocks remain to be demonstrated. Other candidate loci had no effect on resistance, including the Guadeloupe Resistance Complex and three genes (aif, infPhox, and prx1 with immunological roles and expression patterns tied to resistance, which must therefore be trans-regulated.The loci RADres and sod1 both have strong effects on resistance to S. mansoni. Future approaches to control schistosomiasis may benefit from further efforts to characterize and harness this natural genetic variation.

  19. Radiometric dating by alpha spectrometry on uranium series nuclides

    International Nuclear Information System (INIS)

    Wijk, A. van der.

    1987-01-01

    This thesis describes the analytical and technical procedures that are required for routine application of both the 230 Th/ 234 U disequilibrium dating method for peat and the 210 Pb dating method for lake sediments. Its principal aim is to test, refine and discuss the reliability and validity of these methods. On the other hand, the analytical procedures that were introduced open a wide range of other interesting fields of research that are not necessarily restricted to geological problems only. Chapter 5 reports an obviously not foreseen application: detection of alpha emitting nuclides released in the first weeks of May, 1986 during the accident with the nuclear power plant in Chernobyl, USSR. 128 refs.; 43 figs.; 15 tabs

  20. Separation of 210Pb, 210Bi and 210Po by ion exchange and their Iiquid scintillation standardization; Separacion del 210Pb, 210Bi y 2I0Po mediante columna de cambio ionico y su calibracion por centelleo liquido

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, L.; Jimenez, A.; Grau, A.

    1996-07-01

    We applied the CIEMAT/NIST method and alpha/beta discrimination to ''210Pb samples in equilibrium with its daughters, by preparing homogeneous and gel samples. The stability of samples was tested in different available cocktails, HiSafe''TM II, HiSafe''TM III, Ultima-Gold''TM, Ultima-Gold''TM XR, Ultima-Gold''TM AB, Insta-Gel''R and e Insta-Gel''R lI. Also we analyzed the disequilibrium of the radioactive chain 210Pb+210Bi+210Po, achieving an excellent agreement between the results of the spectrum unfolding method and the experimental values. (Author) 13 refs.