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Sample records for single linkage group

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

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

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

  2. First-generation linkage map for the common frog Rana temporaria reveals sex-linkage group

    Science.gov (United States)

    Cano, J M; Li, M-H; Laurila, A; Vilkki, J; Merilä, J

    2011-01-01

    The common frog (Rana temporaria) has become a model species in the fields of ecology and evolutionary biology. However, lack of genomic resources has been limiting utility of this species for detailed evolutionary genetic studies. Using a set of 107 informative microsatellite markers genotyped in a large full-sib family (800 F1 offspring), we created the first linkage map for this species. This partial map—distributed over 15 linkage groups—has a total length of 1698.8 cM. In line with the fact that males are the heterogametic sex in this species and a reduction of recombination is expected, we observed a lower recombination rate in the males (map length: 1371.5 cM) as compared with females (2089.8 cM). Furthermore, three loci previously documented to be sex-linked (that is, carrying male-specific alleles) in adults from the wild mapped to the same linkage group. The linkage map described in this study is one of the densest ones available for amphibians. The discovery of a sex linkage group in Rana temporaria, as well as other regions with strongly reduced male recombination rates, should help to uncover the genetic underpinnings of the sex-determination system in this species. As the number of linkage groups found (n=15) is quite close to the actual number of chromosomes (n=13), the map should provide a useful resource for further evolutionary, ecological and conservation genetic work in this and other closely related species. PMID:21587305

  3. Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses.

    OpenAIRE

    Ulgen, Ayse; Li, Wentian

    2005-01-01

    Abstract We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage res...

  4. Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.

    Directory of Open Access Journals (Sweden)

    PJ. Maughan

    2011-03-01

    Full Text Available The grain amaranths ( sp. are important pseudo-cereals native to the New World. During the last decade they have garnered increased international attention for their nutritional quality, tolerance to abiotic stress, and importance as a symbol of indigenous cultures. We describe the development of the first single nucleotide polymorphism (SNP assays for amaranth. In addition, we report the characterization of the first complete genetic linkage map in the genus. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 41 accessions of the cultivated amaranth species and their putative ancestor species ( L. showed that the minor allele frequency (MAF of these markers ranged from 0.05 to 0.5 with an average MAF of 0.27 per SNP locus. One hundred and forty-one of the SNP loci were considered highly polymorphic (MAF ≥ 0.3. Linkage mapping placed all 411 markers into 16 linkage groups, presumably corresponding to each of the 16 amaranth haploid chromosomes. The map spans 1288 cM with an average marker density of 3.1 cM per marker. The work reported here represents the initial first steps toward the genetic dissection of agronomically important characteristics in amaranth.

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

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond-Paul

    2000-07-01

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

  6. LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms

    Directory of Open Access Journals (Sweden)

    Ji-Hyung Shin

    2006-09-01

    Full Text Available We describe the R function LDheatmap( which produces a graphical display, as a heat map, of pairwise linkage disequilibrium measurements between single nucleotide polymorphisms within a genomic region. LDheatmap( uses the grid graphics system, an alternative to the traditional R graphics system. The features of the LDheatmap( function and the use of tools from the grid package to modify heat maps are illustrated by examples.

  7. ON THE FORMATION OF AMIDE POLYMERS VIA CARBONYL–AMINO GROUP LINKAGES IN ENERGETICALLY PROCESSED ICES OF ASTROPHYSICAL RELEVANCE

    Energy Technology Data Exchange (ETDEWEB)

    Förstel, Marko; Maksyutenko, Pavlo; Jones, Brant M.; Kaiser, Ralf I. [Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, 96822 HI (United States); Sun, Bing J.; Lee, Huan C.; Chang, Agnes H. H., E-mail: ralfk@hawaii.edu, E-mail: hhchang@mail.ndhu.edu.tw [Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974, Taiwan (China)

    2016-04-01

    We report on the formation of organic amide polymers via carbonyl–amino group linkages in carbon monoxide and ammonia bearing energetically processed ices of astrophysical relevance. The first group comprises molecules with one carboxyl group and an increasing number of amine moieties starting with formamide (45 u), urea (60 u), and hydrazine carboxamide (75 u). The second group consists of species with two carboxyl (58 u) and up to three amine groups (73 u, 88 u, and 103 u). The formation and polymerization of these linkages from simple inorganic molecules via formamide und urea toward amide polymers is discussed in an astrophysical and astrobiological context. Our results show that long chain molecules, which are closely related to polypeptides, easily form by energetically processing simple, inorganic ices at very low temperatures and can be released into the gas phase by sublimation of the ices in star-forming regions. Our experimental results were obtained by employing reflectron time-of-flight mass spectroscopy, coupled with soft, single photon vacuum ultraviolet photoionization; they are complemented by theoretical calculations.

  8. Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms.

    Science.gov (United States)

    Badner, J A; Koller, D; Foroud, T; Edenberg, H; Nurnberger, J I; Zandi, P P; Willour, V L; McMahon, F J; Potash, J B; Hamshere, M; Grozeva, D; Green, E; Kirov, G; Jones, I; Jones, L; Craddock, N; Morris, D; Segurado, R; Gill, M; Sadovnick, D; Remick, R; Keck, P; Kelsoe, J; Ayub, M; MacLean, A; Blackwood, D; Liu, C-Y; Gershon, E S; McMahon, W; Lyon, G J; Robinson, R; Ross, J; Byerley, W

    2012-07-01

    Because of the high costs associated with ascertainment of families, most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. Although microsatellite markers spaced every 10 cM typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carried out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 single-nucleotide polymorphisms. Of the ~1100 families, 972 were informative for further analyses, and mean information content was 0.86 after pruning for linkage disequilibrium. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with bipolar II disorder (BPII) and 702 subjects with recurrent major depression. Three affection status models (ASMs) were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus recurrent major depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (non-parametric pairs LOD 3.4 for rs1046943 at 119 cM) and 9q21 (non-parametric pairs logarithm of odds (LOD) 3.4 for rs722642 at 78 cM) using only BPI and schizoaffective (SA), BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis, we observed 59 parametric LODs of 2 or greater, many of which are likely to be close to maximum possible scores. Although some linkage

  9. 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.

  10. Microseismic Event Grouping Based on PageRank Linkage at the Newberry Volcano Geothermal Site

    Science.gov (United States)

    Aguiar, A. C.; Myers, S. C.

    2016-12-01

    The Newberry Volcano DOE FORGE site in Central Oregon has been stimulated two times using high-pressure fluid injection to study the Enhanced Geothermal Systems (EGS) technology. Several hundred microseismic events were generated during the first stimulation in the fall of 2012. Initial locations of this microseismicity do not show well defined subsurface structure in part because event location uncertainties are large (Foulger and Julian, 2013). We focus on this stimulation to explore the spatial and temporal development of microseismicity, which is key to understanding how subsurface stimulation modifies stress, fractures rock, and increases permeability. We use PageRank, Google's initial search algorithm, to determine connectivity within the events (Aguiar and Beroza, 2014) and assess signal-correlation topology for the micro-earthquakes. We then use this information to create signal families and compare these to the spatial and temporal proximity of associated earthquakes. We relocate events within families (identified by PageRank linkage) using the Bayesloc approach (Myers et al., 2007). Preliminary relocations show tight spatial clustering of event families as well as evidence of events relocating to a different cluster than originally reported. We also find that signal similarity (linkage) at several stations, not just one or two, is needed in order to determine that events are in close proximity to one another. We show that indirect linkage of signals using PageRank is a reliable way to increase the number of events that are confidently determined to be similar to one another, which may lead to efficient and effective grouping of earthquakes with similar physical characteristics, such as focal mechanisms and stress drop. Our ultimate goal is to determine whether changes in the state of stress and/or changes in the generation of subsurface fracture networks can be detected using PageRank topology as well as aid in the event relocation to obtain more accurate

  11. Influence of Linkage Stereochemistry and Protecting Groups on Glycosidic Bond Stability of Sodium Cationized Glycosyl Phosphates

    Science.gov (United States)

    Zhu, Y.; Yang, Zhihua; Rodgers, M. T.

    2017-12-01

    Energy-resolved collision-induced dissociation (ER-CID) experiments of sodium cationized glycosyl phosphate complexes, [GP x +Na]+, are performed to elucidate the effects of linkage stereochemistry (α versus β), the geometry of the leaving groups (1,2- cis versus 1,2- trans), and protecting groups (cyclic versus non-cyclic) on the stability of the glycosyl phosphate linkage via survival yield analyses. A four parameter logistic dynamic fitting model is used to determine CID50% values, which correspond to the level of rf excitation required to produce 50% dissociation of the precursor ion complexes. Present results suggest that dissociation of 1,2- trans [GP x +Na]+ occurs via a McLafferty-type rearrangement that is facilitated by a syn orientation of the leaving groups, whereas dissociation of 1,2- cis [GPx+Na]+ is more energetic as it involves the formation of an oxocarbenium ion intermediate. Thus, the C1-C2 configuration plays a major role in determining the stability/reactivity of glycosyl phosphate stereoisomers. For 1,2- cis anomers, the cyclic protecting groups at the C4 and C6 positions stabilize the glycosidic bond, whereas for 1,2- trans anomers, the cyclic protecting groups at the C4 and C6 positions tend to activate the glycosidic bond. The C3 O-benzyl (3 BnO) substituent is key to determining whether the sugar or phosphate moiety retains the sodium cation upon CID. For 1,2- cis anomers, the 3 BnO substituent weakens the glycosidic bond, whereas for 1,2- trans anomers, the 3 BnO substituent stabilizes the glycosidic bond. The C2 O-benzyl substituent does not significantly impact the glycosidic bond stability regardless of its orientation. [Figure not available: see fulltext.

  12. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution.

    Science.gov (United States)

    Paesold, Susanne; Borchardt, Dietrich; Schmidt, Thomas; Dechyeva, Daryna

    2012-11-01

    We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  13. Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers

    OpenAIRE

    Antolin, M. F.; Bosio, C. F.; Cotton, J.; Sweeney, W.; Strand, M. R.; Black-IV, W. C.

    1996-01-01

    The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a d...

  14. Effect of Linkage Groups on Motional Cooperativity in Secondary Relaxations of Some Glassy Polymers

    Science.gov (United States)

    Li, Lei; Yee, Albert F.

    2000-03-01

    In our previous research we found that the secondary relaxation of bisphenol-A (BPA) polycarbonate is due to a cooperative motion which includes several repeat units. Clearly the linkage between neighboring BPA segments must play an important role. It is expected that a more flexible linkage would require less motional cooperativity. To demonstrate this idea, polyformals based on the comonomers BPA, tetramethyl-BPA and methylenechloride with controlled sequence structure were synthesized and DMA studies were conducted. The results show that the secondary relaxation behavior of copolyformals is not dependent on the block length of BPA segments, which suggest that the molecular motion does not require in-chain cooperation. The lower in-chain motional cooperativity of BPA-polyformal is attributed to the lower rotational energy barrier of the formal linkage.

  15. Genome Wide Linkage Analysis of 972 Bipolar Pedigrees Using Single Nucleotide Polymorphisms

    Science.gov (United States)

    Badner, Judith A; Koller, Daniel; Foroud, Tatiana; Edenberg, Howard; Nurnberger, John I; Zandi, Peter P; Willour, Virginia L.; McMahon, Francis J; Potash, James B; Hamshere, Marian; Grozeva, Detelina; Green, Elaine; Kirov, George; Jones, Ian; Jones, Lisa; Craddock, Nicholas; Morris, Derek; Segurado, Ricardo; Gill, Mike; Sadovnick, Dessa; Remick, Ronald; Keck, Paul; Kelsoe, John; Ayub, Muhammad; MacLean, Alan; Blackwood, Douglas; Liu, Chun-Yu; Gershon, Elliot S; McMahon, William; Lyon, Gholson; Robinson, Reid; Ross, Jessica; Byerley, William

    2011-01-01

    Because of the high costs associated with ascertainment of families most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. While microsatellite markers spaced every 10 centimorgans typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carry out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 SNPs. Of the ~1100 families, 972 were informative for further analyses and mean information content was 0.86 after pruning for LD. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with Bipolar II disorder (BPII) and 702 subjects with Recurrent Major Depression. Three affection status models were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus Recurrent Major Depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (Nonparametric Pairs Lod 3.4 for rs1046943 at 119 cM) and 9q21 (Nonparametric Pairs Lod 3.4 for rs722642 at 78 cM) using only BPI and SA, BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis we observed 59 parametric lods of 2 or greater, many of which are likely to be close to maximum possible scores. While some linkage findings may be false positives the results could help prioritize the search for rare variants

  16. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs.

    Science.gov (United States)

    Troggio, Michela; Malacarne, Giulia; Coppola, Giuseppina; Segala, Cinzia; Cartwright, Dustin A; Pindo, Massimo; Stefanini, Marco; Mank, Rolf; Moroldo, Marco; Morgante, Michele; Grando, M Stella; Velasco, Riccardo

    2007-08-01

    The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (SSRs), and 379 AFLP markers in a mapping population of 94 F(1) individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, are useful for evolutionary studies, and significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement.

  17. Absence of linkage of apparently single gene mediated ADHD with the human syntenic region of the mouse mutant coloboma

    Energy Technology Data Exchange (ETDEWEB)

    Hess, E.J.; Rogan, P.K.; Domoto, M. [Pennsylvania State Univ. College of Medicine, Hershey, PA (United States)] [and others

    1995-12-18

    Attention deficit disorder (ADHD) is a complex biobehavioral phenotype which affects up to 8% of the general population and often impairs social, academic, and job performance. Its origins are heterogeneous, but a significant genetic component is suggested by family and twin studies. The murine strain, coloboma, displays a spontaneously hyperactive phenotype that is responsive to dextroamphetamine and has been proposed as a genetic model for ADHD. Coloboma is a semi-dominant mutation that is caused by a hemizygous deletion of the SNAP-25 and other genes on mouse chromosome 2q. To test the possibility that the human homolog of the mouse coloboma gene(s) could be responsible for ADHD, we have carried out linkage studies with polymorphic markers in the region syntenic to coloboma (20p11-p12). Five families in which the pattern of inheritance of ADHD appears to be autosomal dominant were studied. Segregation analysis of the traits studied suggested that the best fitting model was a sex-influenced, single gene, Mendelian pattern. Several genetic models were evaluated based on estimates of penetrance, phenocopy rate, and allele frequency derived from our patient population and those of other investigators. No significant linkage was detected between the disease locus and markers spanning this chromosome 20 interval. 39 refs., 2 figs., 1 tab.

  18. ABO Blood Group and Dementia Risk ? A Scandinavian Record-Linkage Study

    OpenAIRE

    Vasan, Senthil K; Rostgaard, Klaus; Ullum, Henrik; Melbye, Mads; Hjalgrim, Henrik; Edgren, Gustaf

    2015-01-01

    Background Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined the relationship between ABO blood group and dementia-related disorders in detail. Methods We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden...

  19. ABO Blood Group and Dementia Risk--A Scandinavian Record-Linkage Study.

    Science.gov (United States)

    Vasan, Senthil K; Rostgaard, Klaus; Ullum, Henrik; Melbye, Mads; Hjalgrim, Henrik; Edgren, Gustaf

    2015-01-01

    Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined the relationship between ABO blood group and dementia-related disorders in detail. We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient and cause of death registers to investigate the relationship between blood groups and risk of different types of dementia. The incident rate ratios were estimated using log-linear Poisson regression models. Among 1,598,294 donors followed over 24 million person-years of observation we ascertained 3,615 cases of Alzheimer's disease, 1,842 cases of vascular dementia, and 9,091 cases of unspecified dementia. Overall, our study showed no association between ABO blood group and risk of Alzheimer's disease, vascular dementia or unspecified dementia. This was also true when analyses were restricted to donors aged 70 years or older except for a slight, but significantly decreased risk of all dementia combined in subjects with blood group A (IRR, 0.93; 95% confidence interval [CI], 0.88-0.98), compared to those with blood group O. Our results provide no evidence that ABO blood group influences the risk of dementia.

  20. ABO Blood Group and Dementia Risk--A Scandinavian Record-Linkage Study

    DEFF Research Database (Denmark)

    Vasan, Senthil K; Rostgaard, Klaus; Ullum, Henrik

    2015-01-01

    BACKGROUND: Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined...... the relationship between ABO blood group and dementia-related disorders in detail. METHODS: We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient...... and cause of death registers to investigate the relationship between blood groups and risk of different types of dementia. The incident rate ratios were estimated using log-linear Poisson regression models. RESULTS: Among 1,598,294 donors followed over 24 million person-years of observation we ascertained 3...

  1. Empowering rural women's groups for strengthening economic linkages: some Indian experiments.

    Science.gov (United States)

    Rajagopal

    1999-05-01

    Through organizing informal self-help groups (SHGs), rural women in India are provided credit and extension support for various production-oriented income-generating activities. These activities usually include garment-making, embroidery, food processing, bee-keeping, basketry, gem cutting, weaving, and knitting. SHGs are self-governed, with decisions about production and marketing taken collectively, although the group leader is responsible for identifying potential marketing centers and consumers. These groups represent a new culture in rural development, breaking with traditional bureaucracy and top-down management. Informal groups empower rural women to manage rural industries and make decisions collectively for their common economic interests. Experience with SHGs in Orissa, lessons from nongovernmental organization intervention, and a model for empowering poor people in a small town in Kerala are discussed.

  2. ABO Blood Group and Dementia Risk--A Scandinavian Record-Linkage Study.

    Directory of Open Access Journals (Sweden)

    Senthil K Vasan

    Full Text Available Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined the relationship between ABO blood group and dementia-related disorders in detail.We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient and cause of death registers to investigate the relationship between blood groups and risk of different types of dementia. The incident rate ratios were estimated using log-linear Poisson regression models.Among 1,598,294 donors followed over 24 million person-years of observation we ascertained 3,615 cases of Alzheimer's disease, 1,842 cases of vascular dementia, and 9,091 cases of unspecified dementia. Overall, our study showed no association between ABO blood group and risk of Alzheimer's disease, vascular dementia or unspecified dementia. This was also true when analyses were restricted to donors aged 70 years or older except for a slight, but significantly decreased risk of all dementia combined in subjects with blood group A (IRR, 0.93; 95% confidence interval [CI], 0.88-0.98, compared to those with blood group O.Our results provide no evidence that ABO blood group influences the risk of dementia.

  3. ABO Blood Group and Dementia Risk – A Scandinavian Record-Linkage Study

    Science.gov (United States)

    Vasan, Senthil K; Rostgaard, Klaus; Ullum, Henrik; Melbye, Mads; Hjalgrim, Henrik; Edgren, Gustaf

    2015-01-01

    Background Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined the relationship between ABO blood group and dementia-related disorders in detail. Methods We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient and cause of death registers to investigate the relationship between blood groups and risk of different types of dementia. The incident rate ratios were estimated using log-linear Poisson regression models. Results Among 1,598,294 donors followed over 24 million person-years of observation we ascertained 3,615 cases of Alzheimer’s disease, 1,842 cases of vascular dementia, and 9,091 cases of unspecified dementia. Overall, our study showed no association between ABO blood group and risk of Alzheimer’s disease, vascular dementia or unspecified dementia. This was also true when analyses were restricted to donors aged 70 years or older except for a slight, but significantly decreased risk of all dementia combined in subjects with blood group A (IRR, 0.93; 95% confidence interval [CI], 0.88-0.98), compared to those with blood group O. Conclusions Our results provide no evidence that ABO blood group influences the risk of dementia. PMID:26042891

  4. Automatic spike sorting for extracellular electrophysiological recording using unsupervised single linkage clustering based on grey relational analysis

    Science.gov (United States)

    Lai, Hsin-Yi; Chen, You-Yin; Lin, Sheng-Huang; Lo, Yu-Chun; Tsang, Siny; Chen, Shin-Yuan; Zhao, Wan-Ting; Chao, Wen-Hung; Chang, Yao-Chuan; Wu, Robby; Shih, Yen-Yu I.; Tsai, Sheng-Tsung; Jaw, Fu-Shan

    2011-06-01

    Automatic spike sorting is a prerequisite for neuroscience research on multichannel extracellular recordings of neuronal activity. A novel spike sorting framework, combining efficient feature extraction and an unsupervised clustering method, is described here. Wavelet transform (WT) is adopted to extract features from each detected spike, and the Kolmogorov-Smirnov test (KS test) is utilized to select discriminative wavelet coefficients from the extracted features. Next, an unsupervised single linkage clustering method based on grey relational analysis (GSLC) is applied for spike clustering. The GSLC uses the grey relational grade as the similarity measure, instead of the Euclidean distance for distance calculation; the number of clusters is automatically determined by the elbow criterion in the threshold-cumulative distribution. Four simulated data sets with four noise levels and electrophysiological data recorded from the subthalamic nucleus of eight patients with Parkinson's disease during deep brain stimulation surgery are used to evaluate the performance of GSLC. Feature extraction results from the use of WT with the KS test indicate a reduced number of feature coefficients, as well as good noise rejection, despite similar spike waveforms. Accordingly, the use of GSLC for spike sorting achieves high classification accuracy in all simulated data sets. Moreover, J-measure results in the electrophysiological data indicating that the quality of spike sorting is adequate with the use of GSLC.

  5. Peringkasan Tweet Berdasarkan Trending Topic Twitter Dengan Pembobotan TF-IDF dan Single Linkage AngglomerativeHierarchical Clustering

    Directory of Open Access Journals (Sweden)

    Annisa Annisa

    2016-10-01

    Full Text Available Trending topic is a feature provided by twitter that informs something widely discussed by users in a particular time. The form of a trending topic is a hashtag and can be selected by clicking. However, the number of tweets for each trending topics can be very large, so it will be difficult if we want to know all the contents. So, in order to make easy when reading the topic, a small number of tweets can be selected as the main idea of the topic. In this study, we applied the Agglomerative Single Linkage Hierarchical Clustering by calculating the TF-IDF value for each word in advance. We used 100 trending topics, where each topic consists of 50 tweets in Indonesian. For testing, we provided 30 trending topics which consist of 2 until 9 sub-topics. The result is that each trending topics can be summarized into shorter text contains 2 until 9 tweets. We were able to summarize 1 trending topics exactly same as the topic summarized by human expert. However, the rest of topics corresponded partially with human expert.

  6. Comparing Indirect Effects in Different Groups in Single-Group and Multi-Group Structural Equation Models

    Directory of Open Access Journals (Sweden)

    Ehri Ryu

    2017-05-01

    Full Text Available In this article, we evaluated the performance of statistical methods in single-group and multi-group analysis approaches for testing group difference in indirect effects and for testing simple indirect effects in each group. We also investigated whether the performance of the methods in the single-group approach was affected when the assumption of equal variance was not satisfied. The assumption was critical for the performance of the two methods in the single-group analysis: the method using a product term for testing the group difference in a single path coefficient, and the Wald test for testing the group difference in the indirect effect. Bootstrap confidence intervals in the single-group approach and all methods in the multi-group approach were not affected by the violation of the assumption. We compared the performance of the methods and provided recommendations.

  7. A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'.

    Science.gov (United States)

    Falginella, Luigi; Cipriani, Guido; Monte, Corinne; Gregori, Roberto; Testolin, Raffaele; Velasco, Riccardo; Troggio, Michela; Tartarini, Stefano

    2015-06-19

    Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru). In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'. A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple.

  8. A Community Support Group for Single Custodial Fathers.

    Science.gov (United States)

    Tedder, Sandra L.; And Others

    1981-01-01

    Discusses a five-session group experience within the context of establishing a support group for single custodial fathers. Includes topics of dating, remarriage, homemaking and house maintenance, and the effects of divorce on children. A follow-up showed fathers appreciated the sense of community and specific information and coping strategies.…

  9. 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

  10. Assignment of Atlantic salmon (Salmo salar linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Koop Ben F

    2009-08-01

    Full Text Available Abstract Background Most teleost species, especially freshwater groups such as the Esocidae which are the closest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48–52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication, its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96–104 seen in extant salmonids (e.g., rainbow trout. The Atlantic salmon is an exception among the salmonids as it has 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, which appear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon's linkage map and karyotype and to compare the chromosome map with that of rainbow trout. Results The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in the European subspecies using fluorescence in situ hybridization with BAC probes containing genetic markers mapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomes compared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosome map with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in these species, corresponding to entire chromosome arms in the rainbow trout. Conclusion It had been suggested that some of the large acrocentric chromosomes in Atlantic salmon are the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the arms represent the sites of chromosome fusions. The finding that the chromosomal regions on either side of the blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbow trout chromosome arms provides support for this hypothesis.

  11. Multi-group dynamic quantum secret sharing with single photons

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hongwei [School of Science and State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Ma, Haiqiang, E-mail: hqma@bupt.edu.cn [School of Science and State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Wei, Kejin [School of Science and State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Yang, Xiuqing [School of Science, Beijing Jiaotong University, Beijing 100044 (China); Qu, Wenxiu; Dou, Tianqi; Chen, Yitian; Li, Ruixue; Zhu, Wu [School of Science and State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing 100876 (China)

    2016-07-15

    In this letter, we propose a novel scheme for the realization of single-photon dynamic quantum secret sharing between a boss and three dynamic agent groups. In our system, the boss can not only choose one of these three groups to share the secret with, but also can share two sets of independent keys with two groups without redistribution. Furthermore, the security of communication is enhanced by using a control mode. Compared with previous schemes, our scheme is more flexible and will contribute to a practical application. - Highlights: • A multi-group dynamic quantum secret sharing with single photons scheme is proposed. • Any one of the groups can be chosen to share secret through controlling the polarization of photons. • Two sets of keys can be shared simultaneously without redistribution.

  12. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  13. Photoinduced nuclear spin conversion of methyl groups of single molecules

    International Nuclear Information System (INIS)

    Sigl, A.

    2007-01-01

    A methyl group is an outstanding quantum system due to its special symmetry properties. The threefold rotation around one of its bond is isomorphic to the group of even permutations of the remaining protons, a property which imposes severe quantum restrictions on the system, for instance a strict correlation of rotational states with nuclear spin states. The resulting long lifetimes of the rotational tunneling states of the methyl group can be exploited for applying certain high resolution optical techniques, like hole burning or single molecule spectroscopy to optically switch the methyl group from one tunneling state to another therebye changing the nuclear spin of the protons. One goal of the thesis was to perform this switching in single methyl groups. To this end the methyl group was attached to a chromophoric system, in the present case terrylene, which is well suited for single molecule spectroscopy as well as for hole burning. Experiments were performed with the bare terrylene molecule in a hexadecane lattice which served as a reference system, with alphamethyl terrylene and betamethyl terrylene, both embedded in hexadecane, too. A single molecular probe is a highly sensitive detector for dynamic lattice instabilities. Already the bare terrylene probe showed a wealth of interesting local dynamic effects of the hexadecane lattice which could be well acounted for by the assumption of two nearly degenerate sites with rather different optical and thermal properties, all of which could be determined in a quantitative fashion. As to the methylated terrylene systems, the experiments verified that for betamethyl terrylene it is indeed possible to measure rotational tunneling events in single methyl groups. However, the spectral patterns obtained was much more complicated than expected pointing to the presence of three spectroscopically different methyl groups. In order to achieve a definite assignement, molecular mechanics simulations of the terrylene probes in the

  14. An SSR-based linkage map of yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) and QTL analysis of pod length.

    Science.gov (United States)

    Kongjaimun, Alisa; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Shimizu, Takehiko; Shu, Yujian; Isemura, Takehisa; Vaughan, Duncan A; Srinives, Peerasak

    2012-02-01

    Yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) (2n = 2x = 22) is one of the most important vegetable legumes of Asia. The objectives of this study were to develop a genetic linkage map of yardlong bean using SSR makers from related Vigna species and to identify QTLs for pod length. The map was constructed from 226 simple sequence repeat (SSR) markers from cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata Unguiculata Group), azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), and mungbean (Vigna radiata (L.) Wilczek) in a BC(1)F(1) ((JP81610 × TVnu457) × JP81610) population derived from the cross between yardlong bean accession JP81610 and wild cowpea (Vigna unguiculata subsp. unguiculata var. spontanea) accession TVnu457. The markers were clustered into 11 linkage groups (LGs) spanning 852.4 cM in total length with a mean distance between adjacent markers of 3.96 cM. All markers on LG11 showed segregation distortion towards the homozygous yardlong bean JP81610 genotype. The markers on LG11 were also distorted in the rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) map, suggesting the presence of common segregation distortion factors in Vigna species on this LG. One major and six minor QTLs were identified for pod length variation between yardlong bean and wild cowpea. Using flanking markers, six of the seven QTLs were confirmed in an F(2) population of JP81610 × TVnu457. The molecular linkage map developed and markers linked to pod length QTLs would be potentially useful for yardlong bean and cowpea breeding.

  15. Assignment of Chinook Salmon (Oncorhynchus tshawytscha) Linkage Groups to Specific Chromosomes Reveals a Karyotype with Multiple Rearrangements of the Chromosome Arms of Rainbow Trout (Oncorhynchus mykiss)

    Science.gov (United States)

    Phillips, Ruth B.; Park, Linda K.; Naish, Kerry A.

    2013-01-01

    The Chinook salmon genetic linkage groups have been assigned to specific chromosomes using fluorescence in situ hybridization with bacterial artificial chromosome probes containing genetic markers mapped to each linkage group in Chinook salmon and rainbow trout. Comparison of the Chinook salmon chromosome map with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in these species, corresponding to entire chromosome arms in the rainbow trout as expected. In almost every case, the markers were found at approximately the same location on the chromosome arm in each species, suggesting conservation of marker order on the chromosome arms of the two species in most cases. Although theoretically a few centric fissions could convert the karyotype of rainbow trout (2N = 58–64) into that of Chinook salmon (2N = 68) or vice versa, our data suggest that chromosome arms underwent multiple centric fissions and subsequent new centric fusions to form the current karyotypes. The morphology of only approximately one-third of the chromosome pairs have been conserved between the two species. PMID:24170739

  16. Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms

    OpenAIRE

    Drago, Francesca; Karpasitou, Katerina; Poli, Francesca

    2009-01-01

    We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jka/Jkb, Fya/Fyb, S/s, K/k, Kpa/Kpb, Jsa/Jsb, Coa/Cob and Lua/Lub alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplif...

  17. Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms

    Science.gov (United States)

    Drago, Francesca; Karpasitou, Katerina; Poli, Francesca

    2009-01-01

    Summary We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jka/Jkb, Fya/Fyb, S/s, K/k, Kpa/Kpb, Jsa/Jsb, Coa/Cob and Lua/Lub alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplifies the alleles tested routinely, namely Jka/Jkb, Fya/Fyb, S/s, and K/k. PCR II amplifies those alleles that are typed less frequently. Biotinylated PCR products are hybridized in a single multiplex assay with the corresponding probe mixture. After incubation with R-phycoerythrin-conjugated streptavidin, the emitted fluorescence is analyzed with Luminex 100. So far, we have typed more than 2,000 subjects, 493 of whom with multiplex assay, and there have been no discrepancies with the serology results other than null and/or weak phenotypes. The cost of consumables and reagents for typing a single biallelic pair per sample is less than EUR 3.–, not including DNA extraction costs. The capability to perform multiplexed reactions makes the method markedly suitable for mass screening of red blood cell alleles. This genotyping approach represents an important tool in transfusion medicine. PMID:21113257

  18. Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms.

    Science.gov (United States)

    Drago, Francesca; Karpasitou, Katerina; Poli, Francesca

    2009-01-01

    We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jk(a)/Jk(b), Fy(a)/Fy(b), S/s, K/k, Kp(a)/Kp(b), Js(a)/Js(b), Co(a)/Co(b) and Lu(a)/Lu(b) alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplifies the alleles tested routinely, namely Jk(a)/Jk(b), Fy(a)/Fy(b), S/s, and K/k. PCR II amplifies those alleles that are typed less frequently. Biotinylated PCR products are hybridized in a single multiplex assay with the corresponding probe mixture. After incubation with R-phycoerythrin-conjugated streptavidin, the emitted fluorescence is analyzed with Luminex 100. So far, we have typed more than 2,000 subjects, 493 of whom with multiplex assay, and there have been no discrepancies with the serology results other than null and/or weak phenotypes. The cost of consumables and reagents for typing a single biallelic pair per sample is less than EUR 3.-, not including DNA extraction costs. The capability to perform multiplexed reactions makes the method markedly suitable for mass screening of red blood cell alleles. This genotyping approach represents an important tool in transfusion medicine.

  19. Renormalisation group analysis of single right-handed neutrino dominance

    International Nuclear Information System (INIS)

    King, S.F.; Nimai Singh, N.

    2000-01-01

    We perform a renormalisation group (RG) analysis of neutrino masses and mixing angles in the see-saw mechanism in the minimal supersymmetric standard model with three right-handed neutrinos, including the effects of the heavy neutrino thresholds. We focus on the case that one of the right-handed neutrinos provides the dominant contribution to the 23 block of the light Majorana matrix, causing its determinant to approximately vanish and giving an automatic neutrino mass hierarchy, so-called single right-handed neutrino dominance which may arise from a U(1) family symmetry. In these models radiative corrections can increase atmospheric and solar neutrino mixing by up to about 10% and 5%, respectively, and may help to achieve bi-maximal mixing. Significantly we find that the radiative corrections over the heavy neutrino threshold region are at least as important as those usually considered from the lightest right-handed neutrino down to low energies

  20. Neuropeptide Y receptor genes on human chromosome 4q31-q32 map to conserved linkage groups on mouse chromosomes 3 and 8

    Energy Technology Data Exchange (ETDEWEB)

    Lutz, C.M.; Frankel, W.N. [Jackson Lab., Bar Harbor, ME (United States); Richards, J.E. [Univ. of Michigan Medical School, Ann Arbor, MI (United States)] [and others

    1997-05-01

    Npy1r and Npy2r, the genes encoding mouse type 1 and type 2 neuropeptide Y receptors, have been mapped by interspecific backcross analysis. Previous studies have localized the human genes encoding these receptors to chromosome 4q31-q32. We have now assigned Npy1r and Npy2r to conserved linkage groups on mouse Chr 8 and Chr 3, respectively, which correspond to the distal region of human chromosome 4q. Using yeast artificial chromosomes, we have estimated the distance between the human genes to be approximately 6 cM. Although ancient tandem duplication events may account for some closely spaced G-protein-coupled receptor genes, the large genetic distance between the human type 1 and type 2 neuropeptide Y receptor genes raises questions about whether this mechanism accounts for their proximity. 20 refs., 1 fig.

  1. Single electron detachment of carbon group and oxygen group elements incident on helium

    International Nuclear Information System (INIS)

    Huang Yongyi; Li Guangwu; Gao Yinghui; Yang Enbo; Gao Mei; Lu Fuquan; Zhang Xuemei

    2006-01-01

    The absolute single electron detachment (SED) cross sections of carbon group elements C - , Si - , Ge - in the energy range of 0.05-0.29 a.u. (5 keV-30 keV) and oxygen group elements O - and S - 0.08-0.27 a.u. (5 keV-30 keV), incident on helium are measured with growth rate method. In our energy region, the SED cross sections of C - , Si - , S - and Ge - increase with the projectiles velocity, at the same time, O - cross sections reach a conspicuous maximum at 0.18 a.u. Some abnormal behavior occurs in measurement of SED cross sections for the oxygen group collision with helium. Our results have been compared with a previous work

  2. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Alfenas Acelino C

    2011-04-01

    Full Text Available Abstract Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized

  3. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus.

    Science.gov (United States)

    Neves, Leandro G; Mc Mamani, Eva; Alfenas, Acelino C; Kirst, Matias; Grattapaglia, Dario

    2011-04-14

    Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of

  4. A reference linkage map for Eucalyptus.

    Science.gov (United States)

    Hudson, Corey J; Freeman, Jules S; Kullan, Anand R K; Petroli, César D; Sansaloni, Carolina P; Kilian, Andrzej; Detering, Frank; Grattapaglia, Dario; Potts, Brad M; Myburg, Alexander A; Vaillancourt, René E

    2012-06-15

    Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.

  5. Isolated and Single Pedestrians and Pedestrian Groups on Sidewalks

    Directory of Open Access Journals (Sweden)

    Francesco Pinna

    2017-11-01

    Full Text Available Walking freedom can define the quality of an urban area, but this freedom is conditioned by various factors. The research objective is to study pedestrian behavior on sidewalks. Data are collected during on site surveys by means of concealed camcorders. For each pedestrian many factors are observed, such as gender, age, direction, distractions, transport of objects, etc., which could influence pedestrian behavior. Data processing allows the identification of mathematical models describing the average pedestrian’s behavior, subdivided for user type (isolated, single, group. In general, the mean walking pedestrian speed decreases depending on user type (in a linear manner if age class grows for isolated pedestrians, while with the square of age for other user types, of gender, and of facing type. Models obtained for the different pedestrian types were compared to understand the differences in speeds, underlining that pedestrian interferences play a significant role in defining behavior and, therefore, speed. The results support the idea that, to define a smooth pedestrian speed as an indicator of the “walkability” of a path, in addition to considering the path and user’s characteristics, it is also necessary to define the type of user for which the infrastructure is designed.

  6. Resistance to the tetracyclines and macrolide-lincosamide-streptogramin group of antibiotics and its genetic linkage - a review.

    Science.gov (United States)

    Marosevic, Durdica; Kaevska, Marija; Jaglic, Zoran

    2017-06-12

    An excessive use of antimicrobial agents poses a risk for the selection of resistant bacteria. Of particular interest are antibiotics that have large consumption rates in both veterinary and human medicine, such as the tetracyclines and macrolide-lincosamide-streptogramin (MLS) group of antibiotics. A high load of these agents increases the risk of transmission of resistant bacteria and/or resistance determinants to humans, leading to a subsequent therapeutic failure. An increasing incidence of bacteria resistant to both tetracyclines and MLS antibiotics has been recently observed. This review summarizes the current knowledge on different tetracycline and MLS resistance genes that can be linked together on transposable elements.

  7. Haplotype diversity and linkage disequilibrium at DRD2 locus--a study on four population groups of Andhra Pradesh, India.

    Science.gov (United States)

    Saraswathy, Kallur Nava; Mukhopadhyay, Rupak; Shukla, Deepti; Kaur, Harpreet; Sachdeva, Mohinder Pal; Rao, A P; Saksena, Deepti; Kalla, Aloke Kumar

    2009-02-01

    Dopamine receptor D2 (DRD2) is expressed in the central nervous system and has a high affinity for many antipsychotic drugs. Besides several epidemiological investigations on association of DRD2 locus polymorphism(s) with neuropsychiatric problems and addictive behavior, a few polymorphisms in this locus have also been used to understand genomic diversity and population migratory histories globally. The present study attempts to understand the genomic diversity/affinity among four endogamous groups of Andhra Pradesh (India) against the backdrop of diversity studies from other parts of India and the rest of the world, with special reference to DRD2 locus. The four population groups from Adilabad District of Andhra Pradesh, namely, Brahmin (n=50), Nayakpod (n=49), Thoti (n=52), and Kolam (n=53), were included in the study. The DRD2 markers typed for the present study are three biallelic restriction fragments, that is, TaqI A (rs1800497), TaqI B (rs1079597), and TaqI D (rs1800498). Scoring of DRD2 haplotypes with respect to the three TaqI sites shows that five out of eight possible haplotypes are shared by the four populations. Ancestral haplotype B2D2A1 is most frequent among Thotis (0.359). The results of the present study indicate a differential gene flow into South India followed by certain important demographic events resulting in diversified peopling of India.

  8. An X-chromosome pentaplex in two linkage groups: haplotype data in Alagoas and Rio de Janeiro populations from Brazil.

    Science.gov (United States)

    Ferreira da Silva, Iede H; Barbosa, Adriana G; Azevedo, Dalmo A; Sánchez-Diz, Paula; Gusmão, Leonor; Tavares, Celso C; Carvalho, Elizeu F; Ferreira da Silva, Luiz Antonio

    2010-07-01

    Genotype data were obtained for five X-Chr STRs (DXS10079, DXS10074, DXS10075, DXS7424 and DXS101) in two different populations from Brazil, namely Alagoas and Rio de Janeiro. Observed genotype distributions in female samples for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. Gametic association was tested for all pairs of loci in male samples. Significant association values were found between all pairs including DXS10079, DXS10074 and DXS10075, as well as between DXS7424 and DXS101, proving that these two groups of markers must be treated as haplotypes. No significant association could be found between markers from the two groups (DXS10079, DXS10074 or DXS10075 vs. DXS7424 or DXS101), although distances between them varied from 24 to 25cM. When comparing haplotype frequencies in Alagoas, Rio de Janeiro, Germany and Ghana, significant differences were found between the Brazilian and the Germany sample and that from Ghana. Nevertheless, no significant differences were found between Alagoas and Rio de Janeiro, as well as between these two populations and Germany. The combined power of discrimination in males and females were high in both Brazilian populations (>or=0.9996 and >or=0.9999998, respectively), showing the utility of these markers for human identification and paternity testing.

  9. An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

    Directory of Open Access Journals (Sweden)

    María Muñoz-Amatriaín

    2011-11-01

    Full Text Available Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP-based genotyping platform was developed and used to genotype 373 individuals in four barley ( L. mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

  10. Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype

    Directory of Open Access Journals (Sweden)

    Kim Tae-Ho

    2007-11-01

    Full Text Available Abstract Background Osteoporosis is defined as the loss of bone mineral density that leads to bone fragility with aging. Population-based case-control studies have identified polymorphisms in many candidate genes that have been associated with bone mass maintenance or osteoporotic fracture. To investigate single nucleotide polymorphisms (SNPs that are associated with osteoporosis, we examined the genetic variation among Koreans by analyzing 81 genes according to their function in bone formation and resorption during bone remodeling. Methods We resequenced all the exons, splice junctions and promoter regions of candidate osteoporosis genes using 24 unrelated Korean individuals. Using the common SNPs from our study and the HapMap database, a statistical analysis of deviation in heterozygosity depicted. Results We identified 942 variants, including 888 SNPs, 43 insertion/deletion polymorphisms, and 11 microsatellite markers. Of the SNPs, 557 (63% had been previously identified and 331 (37% were newly discovered in the Korean population. When compared SNPs in the Korean population with those in HapMap database, 1% (or less of SNPs in the Japanese and Chinese subpopulations and 20% of those in Caucasian and African subpopulations were significantly differentiated from the Hardy-Weinberg expectations. In addition, an analysis of the genetic diversity showed that there were no significant differences among Korean, Han Chinese and Japanese populations, but African and Caucasian populations were significantly differentiated in selected genes. Nevertheless, in the detailed analysis of genetic properties, the LD and Haplotype block patterns among the five sub-populations were substantially different from one another. Conclusion Through the resequencing of 81 osteoporosis candidate genes, 118 unknown SNPs with a minor allele frequency (MAF > 0.05 were discovered in the Korean population. In addition, using the common SNPs between our study and HapMap, an

  11. Ants farm subterranean aphids mostly in single clone groups

    DEFF Research Database (Denmark)

    Ivens, Aniek B.F.; Kronauer, Daniel Jan Christoph; Pen, Ido

    2012-01-01

    a single aphid species, a significantly higher percentage than expected from a random distribution. Over 60% of these single-species mounds had a single aphid clone, and clones tended to persist across subsequent years. Whenever multiple species/clones co-occurred in the same mound, they were spatially...... separated with more than 95% of the aphid chambers containing individuals of a single clone. Conclusions L. flavus “husbandry” is characterized by low aphid “livestock” diversity per colony, especially at the nest-chamber level, but it lacks the exclusive monocultures known from other cultivation mutualisms...... benefitting the domesticated aphids as long as their clone-mates reproduce successfully. The cost-benefit logic of this type of polyculture husbandry has striking analogies with human farming practices based on slaughtering young animals for meat to maximize milk-production by a carefully regulated adult...

  12. Online Scheduling on a Single Machine with Grouped Processing Times

    Directory of Open Access Journals (Sweden)

    Qijia Liu

    2015-01-01

    Full Text Available We consider the online scheduling problem on a single machine with the assumption that all jobs have their processing times in [p,(1+αp], where p>0 and α=(5-1/2. All jobs arrive over time, and each job and its processing time become known at its arrival time. The jobs should be first processed on a single machine and then delivered by a vehicle to some customer. When the capacity of the vehicle is infinite, we provide an online algorithm with the best competitive ratio of (5+1/2. When the capacity of the vehicle is finite, that is, the vehicle can deliver at most c jobs at a time, we provide another best possible online algorithm with the competitive ratio of (5+1/2.

  13. Integration of BpMADS4 on various linkage groups improves the utilization of the rapid cycle breeding system in apple.

    Science.gov (United States)

    Weigl, Kathleen; Wenzel, Stephanie; Flachowsky, Henryk; Peil, Andreas; Hanke, Magda-Viola

    2015-02-01

    Rapid cycle breeding in apple is a new approach for the rapid introgression of agronomically relevant traits (e.g. disease resistances) from wild apple species into domestic apple cultivars (Malus × domestica Borkh.). This technique drastically shortens the long-lasting juvenile phase of apple. The utilization of early-flowering apple lines overexpressing the BpMADS4 gene of the European silver birch (Betula pendula Roth.) in hybridization resulted in one breeding cycle per year. Aiming for the selection of non-transgenic null segregants at the end of the breeding process, the flower-inducing transgene and the gene of interest (e.g. resistance gene) that will be introgressed by hybridization need to be located on different chromosomes. To improve the flexibility of the existing approach in apple, this study was focused on the development and characterization of eleven additional BpMADS4 overexpressing lines of four different apple cultivars. In nine lines, the flowering gene was mapped to different linkage groups. The differences in introgressed T-DNA sequences and plant genome deletions post-transformation highlighted the unique molecular character of each line. However, transgenic lines demonstrated no significant differences in flower organ development and pollen functionality compared with non-transgenic plants. Hybridization studies using pollen from the fire blight-resistant wild species accession Malus fusca MAL0045 and the apple scab-resistant cultivar 'Regia' indicated that BpMADS4 introgression had no significant effect on the breeding value of each transgenic line. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  14. Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) by primed in situ labeling.

    Science.gov (United States)

    Wang, Y; Wang, J F; Yin, H; Gao, H Q; Zhuang, N S; Liu, J P

    2015-07-28

    Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) were achieved using primed in situ labeling. Amplified signals for both the EST507-1 and SSRY13-5 markers were consistently observed in different stages of cell division. A comparison of the length, arm ratio, and other morphological characteristics of somatic metaphase chromosomes in karyotype analysis indicated that the EST507-1 and SSRY13-5 markers were localized on the short and long arm of cassava chromosome 11 with the relative map positions of 41.67 and 23.07, respectively. The physical localization of the 2 markers on chromosome 11 of the karyotype corresponds to their positions on the 15th linkage group in cassava.

  15. VT Wildlife Linkage Habitat

    Data.gov (United States)

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

  16. Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group

    Science.gov (United States)

    1988-01-01

    A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease. PMID:2894402

  17. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

    Directory of Open Access Journals (Sweden)

    Kelly J. Vining

    2017-08-01

    Full Text Available Genotyping-by-sequencing (GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs in three biparental strawberry (Fragaria × ananassa populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.

  18. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

    Science.gov (United States)

    Shi, Yuan Yuan; Sun, Liang Xian; Huang, Zachary Y; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

    2013-01-01

    The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  19. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  20. JamesWattandhisLinkages

    Indian Academy of Sciences (India)

    Admin

    sometimes called) for a straight line. e gene ate a circle with ... See Figu e. A(1). Such an assembly is a linkage. In particular, it is a fou -ba linkage. A linkage can consist of any number of bodies and connections as well as a ... written to his friend and business partner Matthew Boulton: “I have got a glimpse of a method.

  1. Probabilistic record linkage.

    Science.gov (United States)

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

    2016-06-01

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

  2. Subsidiary Linkage Patterns

    DEFF Research Database (Denmark)

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

    2012-01-01

    This paper investigates the pattern of subsidiaries' local vertical linkages under varying levels of competition and subsidiary capabilities. Contrary to most previous literature, we explicitly account for the double role of such linkages as conduits of learning prospects as well as potential cha...

  3. [Single nucleotide polymorphisms of HIV coreceptor CCR5 gene in Chinese Yi ethnic group and its association with HIV infection].

    Science.gov (United States)

    Ma, Li-ying; Hong, Kun-xue; Lu, Xiao-zhi; Qin, Guang-ming; Chen, Jian-ping; Chen, Kang-lin; Ruan, Yu-hua; Xing, Hui; Zhu, Jia-hong; Shao, Yi-ming

    2005-11-30

    To investigate the single nucleotide polymorphism (SNP) of HIV-1 coreceptor CCR5 gene in Chinese Yi ethnic group and the association between these SNPs and HIV/AIDS. Peripheral blood samples of 102 HIV negative persons of Chinese Yi nationality, 87 males amd 15 females, aged 23 (12-37), and 68 HIV carriers, 61 males and 7 females, aged 27 (17-51). The regulatory and structural regions of the HIV coreceptor CCR5 gene were amplified from the genomic DNA by nested PCR, each of the two regions was divided into three gene fragments which were overlapped. High throughput DHPLC was used for screening of unknown mutations in each gene fragment. The PCR products showing different peak traces from wild types in DHPLC were sequenced by forward and reverse primers respectively. The sequences were analyzed with the help of Sequence Navigator software to search for SNP loci. Statistical analysis by SPSS and PPAP softwares were made to study the association between these SNPs and HIV infection. Five SNPs (A77G, G316A, T532C, C921T, and G668A) and a AGA deletion of the 686-688 nucleotides were discovered in the coding region of this gene in Chinese Yi ethnic group. C921T mutation was a nonsense mutation, and the other SNPs (A77G, G316A, T532C, and G668A) are sense mutation, with the amino acid changes of K26R, G106R, C178R, and R223Q. Only the frequency of R223Q allelic gene was high (0.08) but those of the others were low (less than 0.01). There was no significant difference in the allele frequency between the HIV negative and HIV positive groups (all P > 0.05). Five SNP loci (T58934G, G59029A, T59353C, G59402A, and C59653T) were found in the regulatory region of CCR5 gene with high allelic frequencies of 0.1912-0.2941. Between the HIV negative and HIV positive groups, there were no differences in the SNP loc (all P > 0.05). Statistical analysis of the association between the linkage of mutation loci with HIV infection suggested a significant difference in the haplotype frequency

  4. Identification of the linkage group of the Z sex chromosomes of the sand lizard (Lacerta agilis, Lacertidae) and elucidation of karyotype evolution in lacertid lizards.

    Science.gov (United States)

    Srikulnath, Kornsorn; Matsubara, Kazumi; Uno, Yoshinobu; Nishida, Chizuko; Olsson, Mats; Matsuda, Yoichi

    2014-12-01

    The sand lizard (Lacerta agilis, Lacertidae) has a chromosome number of 2n = 38, with 17 pairs of acrocentric chromosomes, one pair of microchromosomes, a large acrocentric Z chromosome, and a micro-W chromosome. To investigate the process of karyotype evolution in L. agilis, we performed chromosome banding and fluorescent in situ hybridization for gene mapping and constructed a cytogenetic map with 86 functional genes. Chromosome banding revealed that the Z chromosome is the fifth largest chromosome. The cytogenetic map revealed homology of the L. agilis Z chromosome with chicken chromosomes 6 and 9. Comparison of the L. agilis cytogenetic map with those of four Toxicofera species with many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis) showed highly conserved linkage homology of L. agilis chromosomes (LAG) 1, 2, 3, 4, 5(Z), 7, 8, 9, and 10 with macrochromosomes and/or macrochromosome segments of the four Toxicofera species. Most of the genes located on the microchromosomes of Toxicofera were localized to LAG6, small acrocentric chromosomes (LAG11-18), and a microchromosome (LAG19) in L. agilis. These results suggest that the L. agilis karyotype resulted from frequent fusions of microchromosomes, which occurred in the ancestral karyotype of Toxicofera and led to the disappearance of microchromosomes and the appearance of many small macrochromosomes.

  5. A pantograph linkage

    International Nuclear Information System (INIS)

    Cole, G.V.

    1982-01-01

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

  6. Discrimination of communication vocalizations by single neurons and groups of neurons in the auditory midbrain.

    Science.gov (United States)

    Schneider, David M; Woolley, Sarah M N

    2010-06-01

    Many social animals including songbirds use communication vocalizations for individual recognition. The perception of vocalizations depends on the encoding of complex sounds by neurons in the ascending auditory system, each of which is tuned to a particular subset of acoustic features. Here, we examined how well the responses of single auditory neurons could be used to discriminate among bird songs and we compared discriminability to spectrotemporal tuning. We then used biologically realistic models of pooled neural responses to test whether the responses of groups of neurons discriminated among songs better than the responses of single neurons and whether discrimination by groups of neurons was related to spectrotemporal tuning and trial-to-trial response variability. The responses of single auditory midbrain neurons could be used to discriminate among vocalizations with a wide range of abilities, ranging from chance to 100%. The ability to discriminate among songs using single neuron responses was not correlated with spectrotemporal tuning. Pooling the responses of pairs of neurons generally led to better discrimination than the average of the two inputs and the most discriminating input. Pooling the responses of three to five single neurons continued to improve neural discrimination. The increase in discriminability was largest for groups of neurons with similar spectrotemporal tuning. Further, we found that groups of neurons with correlated spike trains achieved the largest gains in discriminability. We simulated neurons with varying levels of temporal precision and measured the discriminability of responses from single simulated neurons and groups of simulated neurons. Simulated neurons with biologically observed levels of temporal precision benefited more from pooling correlated inputs than did neurons with highly precise or imprecise spike trains. These findings suggest that pooling correlated neural responses with the levels of precision observed in the

  7. Subsidiary Linkage Patterns

    DEFF Research Database (Denmark)

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

    This paper investigates local vertical linkages of foreign subsidiaries and the dual role of such linkages as conduits for learning as well as potential channels for spillovers to competitors. On the basis of data from 97 subsidiaries, we analyze the quality of such linkages under varying levels...... of competition and subsidiary capabilities. Our theoretical development and the results from the analysis document a far more complex and dynamic relationship between levels of competition and MNCs’ local participation in knowledge intensive activities, i.e. learning and spillovers, than previous studies do. We...... find a curvilinear relationship between the extent of competitive pressure and the quality of local linkages confirming our argument of a trade-off between learning prospects and spillover risks. Furthermore, the level of subsidiary capabilities moderates this relationship....

  8. [Analysis of linkage disequilibrium and linkage for 12 short tandem repeat loci on chromosome X].

    Science.gov (United States)

    Ye, Qiansu; Tang, Jianpin; Chen, Zucong; Li, Fagui; Yu, Xin; Wang, Ping; Lin, Hanguang; Shi, Meisen

    2014-12-01

    To analyze linkage disequilibrium of 12 short tandem repeat loci on chromosome X (X-STR) among an ethnic Han population from Guilin, Guangxi, and to study the genetic linkage and haplotype distributions of such loci in 2 linkage groups. 12 X-STR loci including DXS8378, DXS10159, DXS10162, DXS10164, DXS981, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12, GATA31E08 and DXS7423 were genotyped using an AGCU X12 STR PCR Amplification kit. A total of 119 pedigrees were analyzed for linkage and linkage disequilibrium. Two mutations were found at DXS7424, and 1 mutation was found at DXS10164. A total of 93 haplotypes of DXS10159-DXS10162-DXS10164 were constructed for 261 unrelated males and females, in addition with 167 haplotypes of DXS6789-DXS7424-DXS101-DXS7133. The values of recombination fraction between DXS10159 and DXS10162, DXS10162 and DXS10164, DXS6789 and DXS7424, and DXS7424 and DXS101 were 0.0269, 0.0236, 0.0505 and 0.0438, respectively. Linkage disequilibrium of X-STR does not only depend on physical and genetic distances. There was incomplete linkage relationship between loci on DXS10159-DXS1016-DXS10164 and DXS6789-DXS7424-DXS101 linkage groups.

  9. Containing psychotic patients with fragile boundaries: a single-session group case study.

    Science.gov (United States)

    Lavarenne, Anaïs; Segal, Emily; Sigman, Maxine

    2013-01-01

    This case study describes a single group psychotherapy session of six individuals suffering from schizophrenia or schizoaffective illness, which was characterized by numerous manifestations of fragile Ego boundaries. Based on these illustrations of fragile Ego boundaries, we explore some of the group's core therapeutic actions against psychosis. We discuss how the group (1) provides access to a structuring auxiliary Ego, (2) acts as a containing object by establishing firm boundaries and by mentalizing patients' psychotic productions, and (3) may become a solid object representation introjected by individuals wrestling with porous Ego boundaries and a poor sense of self. We conclude that, in addition to the known role of group therapy in increasing mature defenses, developing insight and providing social support, the group promotes healthier Ego boundaries, and eventually improves self-differentiation, and also tolerance to interpersonal proximity. This case study clarifies group therapy dynamics with individuals suffering from psychosis.

  10. Linkage of an ABCC transporter to a single QTL that controls Ostrinia nubilalis larval resistance to the Bacillus thuringiensis Cry1Fa toxin

    Science.gov (United States)

    Field evolved resistance of insect populations to Bacillus thuringiensis (Bt) crystalline (Cry) toxins expressed by crop plants has resulted in reduced control of insect feeding damage to field crops, and threatens the sustainability of Bt transgenic technologies. A single quantitative trait locus ...

  11. Intragroup Emotions: Physiological Linkage and Social Presence

    Science.gov (United States)

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

    2016-01-01

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

  12. 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

  13. Comparative DFT study of structure, reactivity and IR spectra of phosphorus-containing dendrons with Pdbnd Nsbnd Pdbnd S linkages, vinyl and azide functional groups

    Science.gov (United States)

    Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Gottis, S.; Laurent, R.; Kovalenko, V. I.

    2015-07-01

    Fourier transform IR spectra of the first generation dendrons built from thiophosphoryl core with terminal Psbnd Cl groups, vinyl (G1) and azide (G2) functional group at the level of the core have been recorded. The optimized geometries of low energy isomers of G1 and G2 have been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. DFT is used for analyzing the properties of each structural part (core, branches, surface). It was found that the repeated branching units of G1 and G2 contain planar sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd Prbond2 fragments. DFT results for the structure of G1 and G2 are in good agreement with X-ray diffraction measurements. A complete vibrational assignment is proposed for different parts of G1 and G2. The global and local reactivity descriptors have been used to characterize the reactivity pattern of the core functional and terminal groups. Natural bond orbital (NBO) analysis has been applied to comparative study of charge delocalization. Our study reveals why azide group linked to phosphorus has a different reactivity when compared to organic azides.

  14. Dimensional threshold for fracture linkage and hooking

    Science.gov (United States)

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

    2018-03-01

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

  15. Thermally actuated linkage arrangement

    International Nuclear Information System (INIS)

    Anderson, P.M.

    1981-01-01

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

  16. Using machine learning to identify structural breaks in single-group interrupted time series designs.

    Science.gov (United States)

    Linden, Ariel; Yarnold, Paul R

    2016-12-01

    Single-group interrupted time series analysis (ITSA) is a popular evaluation methodology in which a single unit of observation is being studied, the outcome variable is serially ordered as a time series and the intervention is expected to 'interrupt' the level and/or trend of the time series, subsequent to its introduction. Given that the internal validity of the design rests on the premise that the interruption in the time series is associated with the introduction of the treatment, treatment effects may seem less plausible if a parallel trend already exists in the time series prior to the actual intervention. Thus, sensitivity analyses should focus on detecting structural breaks in the time series before the intervention. In this paper, we introduce a machine-learning algorithm called optimal discriminant analysis (ODA) as an approach to determine if structural breaks can be identified in years prior to the initiation of the intervention, using data from California's 1988 voter-initiated Proposition 99 to reduce smoking rates. The ODA analysis indicates that numerous structural breaks occurred prior to the actual initiation of Proposition 99 in 1989, including perfect structural breaks in 1983 and 1985, thereby casting doubt on the validity of treatment effects estimated for the actual intervention when using a single-group ITSA design. Given the widespread use of ITSA for evaluating observational data and the increasing use of machine-learning techniques in traditional research, we recommend that structural break sensitivity analysis is routinely incorporated in all research using the single-group ITSA design. © 2016 John Wiley & Sons, Ltd.

  17. Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

    Directory of Open Access Journals (Sweden)

    Riccardo Frisenda

    2015-07-01

    Full Text Available We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene (OPE3, while having different aurophilic anchoring groups: thiol (SAc, methyl sulfide (SMe, pyridyl (Py and amine (NH2. The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current–voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings.

  18. Impact of Anchoring Groups on Ballistic Transport: Single Molecule vs Monolayer Junctions

    Science.gov (United States)

    2015-01-01

    Tuning the transport properties of molecular junctions by chemically modifying the molecular structure is one of the key challenges for advancing the field of molecular electronics. In the present contribution, we investigate current–voltage characteristics of differently linked metal–molecule–metal systems that comprise either a single molecule or a molecular assembly. This is achieved by employing density functional theory in conjunction with a Green’s function approach. We show that the conductance of a molecular system with a specific anchoring group is fundamentally different depending on whether a single molecule or a continuous monolayer forms the junction. This is a consequence of collective electrostatic effects that arise from dipolar elements contained in the monolayer and from interfacial charge rearrangements. As a consequence of these collective effects, the “ideal” choice for an anchoring group is clearly different for monolayer and single molecule devices. A particularly striking effect is observed for pyridine-docked systems. These are subject to Fermi-level pinning at high molecular packing densities, causing an abrupt increase of the junction current already at small voltages. PMID:26401191

  19. Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions

    DEFF Research Database (Denmark)

    He, Li; Steinocher, Helena; Shelar, Ashish

    2017-01-01

    of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated......Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively...... productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single...

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  1. Trajectories of Change in University Students' General Views of Group Work Following One Single Group Assignment: Significance of Instructional Context and Multidimensional Aspects of Experience

    Science.gov (United States)

    Wosnitza, Marold; Volet, Simone

    2014-01-01

    This paper examines how distinct trajectories of change in students' general views of group work over the duration of one single group assignment could be explained by multidimensional aspects of their experience and the overall instructional context. Science (336) and Education (377) students involved in a semester-long group assignment…

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

    Science.gov (United States)

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

    2013-05-01

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

  3. Comprehensive Wavelengths, Energy Levels, and Hyperfine Structure Parameters of Singly-Ionized Iron-Group Elements

    Science.gov (United States)

    Nave, Gillian

    We propose to measure wavelengths, energy levels, and hyperfine structure parameters of Ni II, Mn II, Sc II and other singly-ionized iron-group elements, covering the wavelength range 80 nm to 5500 nm. We shall use archival data from spectrometers at NIST and Kitt Peak National Observatory for spectra above 140 nm. Additional experimental observations will be taken if needed using Fourier transform spectrometers at NIST. Spectra will be taken using our normal incidence grating spectrograph to provide better sensitivity than the FT spectra and to extend the wavelength range down to 80 nm. We aim to produce a comprehensive description of the spectra of all singly-ionized iron- group elements. The wavelength uncertainty of the strong lines will be better than 1 part in 10^7. For most singly-ionized iron-group elements available laboratory data have uncertainties an order of magnitude larger than astronomical observations over wide spectra ranges. Some of these laboratory measurements date back to the 1960's. Since then, Fourier transform spectroscopy has made significant progress in improving the accuracy and quantity of data in the UV-vis-IR region, but high quality Fourier transform spectra are still needed for Mn II, Ni II and Sc II. Fourier transform spectroscopy has low sensitivity in the VUV region and is limited to wavelengths above 140 nm. Spectra measured with high-resolution grating spectrographs are needed in this region in order to obtain laboratory data of comparable quality to the STIS and COS spectrographs on the Hubble Space Telescope. Currently, such data exist only for Fe II and Cr II. Lines of Sc II, V II, and Mn II show hyperfine structure, but hyperfine structure parameters have been measured for relatively few lines of these elements. Significant errors can occur if hyperfine structure is neglected when abundances are determined from stellar spectra. Measurements of hyperfine structure parameters will be made using Fourier transform spectroscopy

  4. SINGLE-CASE INVESTIGATION OF AN EMOTION-FOCUSED THERAPY GROUP FOR ANXIETY AND DEPRESSION

    Directory of Open Access Journals (Sweden)

    Adèle Lafrance Robinson

    2012-11-01

    Full Text Available Emotion-focused therapy (EFT is an evidence-based treatment for depression and trauma and has shown promise for other presentations including anxiety. Minimal research exists investigating the outcomes of emotion-focused therapy in a group setting. The current research presents a mixed-method single-case study of one client’s experiences and outcomes following a nine-week EFT group for depression and anxiety. Weekly measures of session-feelings evaluations were collected. Follow-up measures, including a qualitative interview, were administered one year post-treatment. Pre-, post-, and follow-up measures assessed depression, anxiety, and emotional regulation. Results showed clinically significant improvements in anxiety, depression, and emotional regulation over time. Indirect and direct evidence of client change were detected. Five super-ordinate themes with sub-themes emerged from the qualitative analysis.

  5. Exploring the Relevance of Single-Gender Group Formation: What We Learn from a Massive Open Online Course (MOOC)

    Science.gov (United States)

    Bayeck, Rebecca Yvonne; Hristova, Adelina; Jablokow, Kathryn W.; Bonafini, Fernanda

    2018-01-01

    This paper reports the results of an exploratory study on participants' perception of the importance of single-gender grouping in a massive open online course (MOOC) delivered through the Coursera platform. Findings reveal that female and male learners' perception of single-gender grouping differs. Female students more than males indicated less…

  6. Evaluation of single-nucleotide polymorphisms as internal controls in prenatal diagnosis of fetal blood groups.

    Science.gov (United States)

    Doescher, Andrea; Petershofen, Eduard K; Wagner, Franz F; Schunter, Markus; Müller, Thomas H

    2013-02-01

    Determination of fetal blood groups in maternal plasma samples critically depends on adequate amplification of fetal DNA. We evaluated the routine inclusion of 52 single-nucleotide polymorphisms (SNPs) as internal reference in our polymerase chain reaction (PCR) settings to obtain a positive internal control for fetal DNA. DNA from 223 plasma samples of pregnant women was screened for RHD Exons 3, 4, 5, and 7 in a multiplex PCR including 52 SNPs divided into four primer pools. Amplicons were analyzed by single-base extension and the GeneScan method in a genetic analyzer. Results of D screening were compared to standard RHD genotyping of amniotic fluid or real-time PCR of fetal DNA from maternal plasma. The vast majority of all samples (97.8%) demonstrated differences in maternal and fetal SNP patterns when tested with four primer pools. These differences were not observed in less than 2.2% of the samples most probably due to an extraction failure for adequate amounts of fetal DNA. Comparison of the fetal genotypes with independent results did not reveal a single false-negative case among samples (n = 42) with positive internal control and negative fetal RHD typing. Coamplification of 52 SNPs with RHD-specific sequences for fetal blood group determination introduces a valid positive control for the amplification of fetal DNA to avoid false-negative results. This new approach does not require a paternal blood sample. It may also be applicable to other assays for fetal genotyping in maternal blood samples. © 2012 American Association of Blood Banks.

  7. Are medical treatments for individuals and groups like single-play and multiple-play gambles?

    Directory of Open Access Journals (Sweden)

    Michael L. DeKay

    2006-11-01

    Full Text Available People are often more likely to accept risky monetary gambles with positive expected values when the gambles will be played more than once. We investigated whether this distinction between single-play and multiple-play gambles extends to medical treatments for individual patients and groups of patients. Resident physicians and medical students (extit{n} = 69 and undergraduates (extit{n} = 99 ranked 9 different flu shots and a no-flu-shot option in 1 of 4 combinations of perspective (individual patient vs. group of 1000 patients and uncertainty frame (probability vs. frequency. The rank of the no-flu-shot option (a measure of preference for treatment vs. no treatment was not significantly related to perspective or participant population. The main effect of uncertainty frame and the interaction between perspective and uncertainty frame approached significance (0.1 {extgreater} extit{p} {extgreater} 0.05, with the no-flu-shot option faring particularly poorly (treatment faring particularly well when decisions about many patients were based on frequency information. Undergraduate participants believed that the no-flu-shot option would be less attractive (treatment would be more attractive in decisions about many patients, but these intuitions were inconsistent with the actual ranks. These results and those of other studies suggest that medical treatments for individuals and groups are not analogous to single-play and multiple-play monetary gambles, perhaps because many people are unwilling to aggregate treatment outcomes over patients in the same way that they would compute net gains or losses over monetary gambles.

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

    Science.gov (United States)

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

    2011-01-01

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

  9. Construction of genetic linkage map of the medicinal and ...

    Indian Academy of Sciences (India)

    got placed on 2 linkage groups, LLS and LPS on LG1 and. LLP, STP, POL and CPC on LG8. Discussion. Detailed genetic linkage maps of crop plant, on which molec- ular DNA markers are tightly placed and in which loci for morphological features, quantitative traits and specific genes have been located with reference to ...

  10. Construction of genetic linkage map of the medicinal and ...

    Indian Academy of Sciences (India)

    An integrated genetic linkage map of the medicinal and ornamental plant Catharanthus roseus, based on different types of molecular and morphological markers was constructed, using a F2 population of 144 plants. The map defines 14 linkage groups (LGs) and consists of 131 marker loci, including 125 molecular DNA ...

  11. Dialogic Linkage and Resonance in Autism

    Science.gov (United States)

    Hobson, R. Peter; Hobson, Jessica A.; Garcia-Perez, Rosa; Du Bois, John

    2012-01-01

    We evaluated how children with autism make linguistic adjustments when talking with someone else. We devised two novel measures to assess (a) overall conversational linkage and (b) utterance-by-utterance resonance within dialogue between an adult and matched participants with and without autism (n = 12 per group). Participants with autism were…

  12. The Barley Chromosome 5 Linkage Map

    DEFF Research Database (Denmark)

    Jensen, J.; Jørgensen, Jørgen Helms

    1975-01-01

    The distances between nine loci on barley chromosome 5 have been studied in five two-point tests, three three-point tests, and one four-point test. Our previous chromosome 5 linkage map, which contained eleven loci mapped from literature data (Jensen and Jørgensen 1975), is extended with four loci......: wst5 (white streaks), necl (necrotic leaf spots), Ml-nn (powdery mildew resistance), and Pa4 (leaf rust resistance). Further, the two sections of the map are united, and the precision of the map is improved. A system for designating the positions of the loci on the linkage map is proposed. A 0......-position is fixed on the map by a locus (necl), which has a good marker gene located centrally in the linkage group. The positions of the other loci are their distances in centimorgans from the 0-position; loci in the direction of the short chromosome arm are assigned positive values and those...

  13. A microsatellite linkage map of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Schully Sheri

    2004-05-01

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

  14. Influence of group cohesion on maternal well-being among participants in a support/education group program for single mothers.

    Science.gov (United States)

    Lipman, Ellen L; Waymouth, Marjorie; Gammon, Tara; Carter, Patricia; Secord, Margaret; Leung, Olivia; Mills, Brenda; Hicks, Frances

    2007-10-01

    Single mothers are at increased risk of psychosocial disadvantage, social isolation and physical and mental health difficulties. The authors present (1) the results of group cohesion assessments completed by mothers participating in a trial of community-based support/education groups, and (2) assessments of the association between group cohesion ratings and intervention outcomes of maternal self-evaluations of well-being (mood, self-esteem, and social support) and parenting. Mothers participating in groups completed the Group Atmosphere Scale, a measure of group cohesion, post-group. Overall, most participants provided strong ratings of group cohesion. Significant associations were found between group cohesion and specific positive outcomes. This suggests a positive association between group cohesion and mood, self-esteem, social support, and parenting, in this trial.

  15. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    Science.gov (United States)

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  16. Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

    Directory of Open Access Journals (Sweden)

    Chen Li-Jing

    2015-01-01

    Full Text Available A genetic linkage map of lily was constructed using RILs (recombinant inbred lines population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo and Gelria (Longiflomm cultivars through single-seed descent (SSD. SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

  17. Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin.

    Directory of Open Access Journals (Sweden)

    Ryo Iizuka

    Full Text Available Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.

  18. The stepping behavior analysis of pedestrians from different age groups via a single-file experiment

    Science.gov (United States)

    Cao, Shuchao; Zhang, Jun; Song, Weiguo; Shi, Chang'an; Zhang, Ruifang

    2018-03-01

    The stepping behavior of pedestrians with different age compositions in single-file experiment is investigated in this paper. The relation between step length, step width and stepping time are analyzed by using the step measurement method based on the calculation of curvature of the trajectory. The relations of velocity-step width, velocity-step length and velocity-stepping time for different age groups are discussed and compared with previous studies. Finally effects of pedestrian gender and height on stepping laws and fundamental diagrams are analyzed. The study is helpful for understanding pedestrian dynamics of movement. Meanwhile, it offers experimental data to develop a microscopic model of pedestrian movement by considering stepping behavior.

  19. Single-crystal growth of Group IVB and VB carbides by the floating-zone method

    International Nuclear Information System (INIS)

    Finch, C.B.; Chang, Y.K.; Abraham, M.M.

    1989-02-01

    The floating-zone method for the growth of Group IVB and VB carbides is described and reviewed. We have systematically investigated the technique and confirmed the growth of large single crystals of TiC/sub 0.95/, ZrC/sub 0.93/, ZrC/sub 0.98/, VC/sub 0.80/, NbC/sub 0.95/, TaC/sub 0.89/. Optimal growth conditions were in the 0.5-2.0 cm/h range under 8-12 atm helium. Good crystal growth results were achieved with hot-pressed starting rods of 90-95% density, using a ''double pancake'' induction coil and a 200-kHz/100- kW rf power supply. 36 refs., 5 figs., 3 tabs

  20. Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing.

    Science.gov (United States)

    Gonen, Serap; Lowe, Natalie R; Cezard, Timothé; Gharbi, Karim; Bishop, Stephen C; Houston, Ross D

    2014-02-27

    Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families. Approximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays. This Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of

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

    Science.gov (United States)

    Olsen, Aaron M; Westneat, Mark W

    2016-12-01

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

  2. The Effect of Single-Leg Stance on Dancer and Control Group Static Balance.

    Science.gov (United States)

    Kilroy, Elisabeth A; Crabtree, Olivia M; Crosby, Brittany; Parker, Amanda; Barfield, William R

    The purpose of this study was to compare kinetic differences of static balance between female dancers (D) with at least seven years of dance experience and female non-dancers (ND) who were typical college students. Participants were tested in single-leg stance. Both the dominant leg (DL) and non-dominant leg (NDL) were tested with the participants shod (S) and barefoot (BF). Kinetic variables (vertical, medio-lateral [ML], antero-posterior [AP] maximum ground reaction forces (GRF), and center of pressure (COP) ML and AP) were measured by a Bertec force platform at 1000 Hz with participants S and BF. Each subject's stance was measured over 3 × 30-second intervals. No significant differences (p≥0.05) existed between groups for height, body mass, or age. Significant differences existed between groups for balance time, AP GRF in both BF and S conditions for both DL and NDL, and ML GRF in BF NDL and S DL and NDL conditions. D and ND in BF and S conditions with DL and NDL static stance demonstrate different AP and ML GRF when balancing over a 30-second time interval. Data may suggest that ND are more prone to lose their balance. Further investigation is warranted to understand whether individuals in the rehabilitative field and athletic populations can use dance therapy for injury prevention and rehabilitation.

  3. Effect of Environmental Enrichment on Singly- and Group-Housed Squirrel Monkeys

    Science.gov (United States)

    Spring, Sarah E.; Clifford, James O.; Tomko, David L.; Hargens, Alan R. (Technical Monitor)

    1996-01-01

    Nonhuman primates display an interest in novel places, habituate to new situations, and spend most of their daily activity in the wild in large groups engaging in feeding behaviors. Captivity changes these behaviors, and disrupts normal social hierarchies. In captivity, animals may exhibit stereotypical behaviors which are thought to indicate decreased psychological well-being (PWB). If an animal's behaviors can be made to approach those seen in the wild, and stereotypical behaviors are minimal it is assumed that PWB is adequate. Environmental enrichment (EE) devices have been used to address the Animal Welfare Act's requirement that the PWB of captive nonhuman primates be considered. The purpose of the present study was to examine whether various EE devices improve the PWB of captive squirrel monkeys. The present study used behavioral observation to quantify the effectiveness of several EE devices in reducing stereotypical behaviors in squirrel monkeys housed singly or in groups. Results showed that the EE devices used did not affect the expression of normal or stereotypical behaviors, but that the type of housing did.

  4. A study of planar anchor groups for graphene-based single-molecule electronics.

    Science.gov (United States)

    Bailey, Steven; Visontai, David; Lambert, Colin J; Bryce, Martin R; Frampton, Harry; Chappell, David

    2014-02-07

    To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

  5. Effects of single sex lab groups on physics self-efficacy, behavior, and academic performance

    Science.gov (United States)

    Hunt, Gary L.

    The purpose of this study was to investigate the relationships between the gender composition of a laboratory group and student behaviors, self-efficacy, and quiz performance, within the college physics laboratory. A student population was chosen and subdivided into two groups, which were assigned either same-sex or coed laboratory teams while executing identical laboratory activities and instruction. Assessments were carried out prior to instruction, during the course, and at the end of one semester worth of instruction and laboratory activities. Students were assessed in three areas: behaviors exhibited during laboratory activities, self-efficacy, and scores on laboratory quizzes. Analyses considered the differences in outcomes after a single semester of physics laboratories that differed only in team gender organization. The results indicated that there were no statistically significant differences in behavior variable, self-efficacy or laboratory quiz scores between same sex teams and coed teams. There were also no statistically significant differences between genders, and no interaction effect present. In a post-hoc analysis of the individual behaviors data, it was noted that there is present a practical difference in the individual behaviors exhibited by males and females. This difference implies a difference in how males and females successfully engage in the laboratory activities.

  6. Comparing single-tree selection, group selection, and clearcutting for regenerating oaks and pines in the Missouri Ozarks

    Science.gov (United States)

    Randy G. Jensen; John M. Kabrick

    2008-01-01

    In the Missouri Ozarks, there is considerable concern about the effectiveness of the uneven-aged methods of single-tree selection and group selection for oak (Quercus L.) and shortleaf pine (Pinus echinata Mill.) regeneration. We compared the changes in reproduction density of oaks and pine following harvesting by single-tree...

  7. A microsatellite genetic linkage map of black rockfish ( Sebastes schlegeli)

    Science.gov (United States)

    Chu, Guannan; Jiang, Liming; He, Yan; Yu, Haiyang; Wang, Zhigang; Jiang, Haibin; Zhang, Quanqi

    2014-12-01

    Ovoviviparous black rockfish ( Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 cM and average inter-marker space of 13.3 cM. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 cM and average inter-marker distance of 12.4 cM. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

  8. Design of special planar linkages

    CERN Document Server

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

    2013-01-01

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

  9. A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids.

    Science.gov (United States)

    Kudo, Yu; Nikaido, Masato; Kondo, Azusa; Suzuki, Hikoyu; Yoshida, Kohta; Kikuchi, Kiyoshi; Okada, Norihiro

    2015-04-15

    Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Cognitive behavioral therapy for depression among adults in Japanese clinical settings: a single-group study

    Directory of Open Access Journals (Sweden)

    Kikuchi Toshiaki

    2010-06-01

    Full Text Available Abstract Background Empirical support for cognitive behavioral therapy (CBT for treating Japanese patients with major depression is lacking, therefore, a feasibility study of CBT for depression in Japanese clinical settings is urgently required. Findings A culturally adapted, 16-week manualized individual CBT program for Japanese patients with major depressive disorder was developed. A total of 27 patients with major depression were enrolled in a single-group study with the purpose of testing the feasibility of the program. Twenty six patients (96% completed the study. The mean total score on the Beck Depression Inventory-II (BDI-II for all patients (Intention-to-treat sample improved from 32.6 to 11.7, with a mean change of 20.8 (95% confidence interval: 17.0 to 24.8. Within-group effect size at the endpoint assessment was 2.64 (Cohen's d. Twenty-one patients (77.7% showed treatment response and 17 patients (63.0% achieved remission at the end of the program. Significant improvement was observed in measurement of subjective and objective depression severity (assessed by BDI-II, Quick Inventory of Depressive Symptomatology-Self Rated, and Hamilton Depression Rating Scale, dysfunctional attitude (assessed by Dysfunctional Attitude Scale, global functioning (assessed by Global Assessment of Functioning of DSM-IV and subjective well-being (assessed by WHO Subjective Well-being Inventory (all p values Conclusions Our manualized treatment comprised of a 16-week individual CBT program for major depression appears feasible and may achieve favorable treatment outcomes among Japanese patients with major depression. Further research involving a larger sample in a randomized, controlled trial design is warranted. Trial registration UMIN-CTR UMIN000002542.

  11. Cognitive behavioral therapy for depression among adults in Japanese clinical settings: a single-group study

    Science.gov (United States)

    2010-01-01

    Background Empirical support for cognitive behavioral therapy (CBT) for treating Japanese patients with major depression is lacking, therefore, a feasibility study of CBT for depression in Japanese clinical settings is urgently required. Findings A culturally adapted, 16-week manualized individual CBT program for Japanese patients with major depressive disorder was developed. A total of 27 patients with major depression were enrolled in a single-group study with the purpose of testing the feasibility of the program. Twenty six patients (96%) completed the study. The mean total score on the Beck Depression Inventory-II (BDI-II) for all patients (Intention-to-treat sample) improved from 32.6 to 11.7, with a mean change of 20.8 (95% confidence interval: 17.0 to 24.8). Within-group effect size at the endpoint assessment was 2.64 (Cohen's d). Twenty-one patients (77.7%) showed treatment response and 17 patients (63.0%) achieved remission at the end of the program. Significant improvement was observed in measurement of subjective and objective depression severity (assessed by BDI-II, Quick Inventory of Depressive Symptomatology-Self Rated, and Hamilton Depression Rating Scale), dysfunctional attitude (assessed by Dysfunctional Attitude Scale), global functioning (assessed by Global Assessment of Functioning of DSM-IV) and subjective well-being (assessed by WHO Subjective Well-being Inventory) (all p values < 0.001). Conclusions Our manualized treatment comprised of a 16-week individual CBT program for major depression appears feasible and may achieve favorable treatment outcomes among Japanese patients with major depression. Further research involving a larger sample in a randomized, controlled trial design is warranted. Trial registration UMIN-CTR UMIN000002542. PMID:20529252

  12. Biological process linkage networks.

    Directory of Open Access Journals (Sweden)

    Dikla Dotan-Cohen

    Full Text Available The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN.We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods.Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.

  13. North-South Business Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Kuada, John

    2006-01-01

    TNC-driven markets in developing countries); (3) The upgrading impact of FDI; (4) Non-equity linkages as a platform for business development, and (5) The learning perspective on international business linakges. The chapter offers at the end a three-dimanional model for impacts of business linkages....

  14. A Formalization of Linkage Analysis

    DEFF Research Database (Denmark)

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

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

  15. The first-generation Daphnia magna linkage map

    Directory of Open Access Journals (Sweden)

    De Meester Luc

    2010-09-01

    Full Text Available Abstract Background Daphnia magna is a well-established model species in ecotoxicology, ecology and evolution. Several new genomics tools are presently under development for this species; among them, a linkage map is a first requirement for estimating the genetic background of phenotypic traits in quantitative trait loci (QTL studies and is also very useful in assembling the genome. It also enables comparative studies between D. magna and D. pulex, for which a linkage map already exists. Results Here we describe the first genetic linkage map of D. magna. We generated 214 F2 (intercross clonal lines as the foundation of the linkage analysis. The linkage map itself is based on 109 microsatellite markers, which produced ten major linkage groups ranging in size from 31.1 cM to 288.5 cM. The total size of this linkage map extends to 1211.6 Kosambi cM, and the average interval for the markers within linkage groups is 15.1 cM. The F2 clones can be used to map QTLs for traits that differ between the parental clones. We successfully mapped the location of two loci with infertility alleles, one inherited from the paternal clone (Iinb1 and the other from the maternal clone (Xinb3. Conclusions The D. magna linkage map presented here provides extensive coverage of the genome and a given density of markers that enable us to detect QTLs of moderate to strong effects. It is similar in size to the linkage map of D. pulex.

  16. Growth and study of some gel grown group II single crystals of iodate

    Indian Academy of Sciences (India)

    Unknown

    Page 1 ... Abstract. Single crystals of calcium iodate and barium iodate were grown by simple gel technique by single diffusion method. The optimum conditions were established by varying various parameters such as pH of gel solution, gel concentration, gel setting time, concentration of the reactants etc. Crystals having ...

  17. A linkage map of the Atlantic salmon (Salmo salar based on EST-derived SNP markers

    Directory of Open Access Journals (Sweden)

    Kjøglum Sissel

    2008-05-01

    Full Text Available Abstract Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r2 dropped to half its maximum value (above baseline within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD' at inter-marker distances less than 5 cM. Conclusion The linkage map

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-06-30

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    , approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half......Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres – an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference....... mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  1. From Enclave to Linkage Economies?

    DEFF Research Database (Denmark)

    Hansen, Michael W.

    If African developing countries are to benefit fully from the current boom in foreign direct investment (FDI) in extractives (i.e. mining and oil/gas), it is essential that the foreign investors foster linkages to the local economy. Traditionally, extractive FDI in Africa has been seen as the enc......If African developing countries are to benefit fully from the current boom in foreign direct investment (FDI) in extractives (i.e. mining and oil/gas), it is essential that the foreign investors foster linkages to the local economy. Traditionally, extractive FDI in Africa has been seen...... as the enclave economy par excellence, moving in with fully integrated value chains, extracting resources and exporting them as commodities having virtually no linkages to the local economy. However, new opportunities for promoting linkages are offered by changing business strategies of local African enterprises...

  2. Persistent threats to validity in single-group interrupted time series analysis with a cross over design.

    Science.gov (United States)

    Linden, Ariel

    2017-04-01

    The basic single-group interrupted time series analysis (ITSA) design has been shown to be susceptible to the most common threat to validity-history-the possibility that some other event caused the observed effect in the time series. A single-group ITSA with a crossover design (in which the intervention is introduced and withdrawn 1 or more times) should be more robust. In this paper, we describe and empirically assess the susceptibility of this design to bias from history. Time series data from 2 natural experiments (the effect of multiple repeals and reinstatements of Louisiana's motorcycle helmet law on motorcycle fatalities and the association between the implementation and withdrawal of Gorbachev's antialcohol campaign with Russia's mortality crisis) are used to illustrate that history remains a threat to ITSA validity, even in a crossover design. Both empirical examples reveal that the single-group ITSA with a crossover design may be biased because of history. In the case of motorcycle fatalities, helmet laws appeared effective in reducing mortality (while repealing the law increased mortality), but when a control group was added, it was shown that this trend was similar in both groups. In the case of Gorbachev's antialcohol campaign, only when contrasting the results against those of a control group was the withdrawal of the campaign found to be the more likely culprit in explaining the Russian mortality crisis than the collapse of the Soviet Union. Even with a robust crossover design, single-group ITSA models remain susceptible to bias from history. Therefore, a comparable control group design should be included, whenever possible. © 2016 John Wiley & Sons, Ltd.

  3. When the Single Matters more than the Group (II): Addressing the Problem of High False Positive Rates in Single Case Voxel Based Morphometry Using Non-parametric Statistics.

    Science.gov (United States)

    Scarpazza, Cristina; Nichols, Thomas E; Seramondi, Donato; Maumet, Camille; Sartori, Giuseppe; Mechelli, Andrea

    2016-01-01

    In recent years, an increasing number of studies have used Voxel Based Morphometry (VBM) to compare a single patient with a psychiatric or neurological condition of interest against a group of healthy controls. However, the validity of this approach critically relies on the assumption that the single patient is drawn from a hypothetical population with a normal distribution and variance equal to that of the control group. In a previous investigation, we demonstrated that family-wise false positive error rate (i.e., the proportion of statistical comparisons yielding at least one false positive) in single case VBM are much higher than expected (Scarpazza et al., 2013). Here, we examine whether the use of non-parametric statistics, which does not rely on the assumptions of normal distribution and equal variance, would enable the investigation of single subjects with good control of false positive risk. We empirically estimated false positive rates (FPRs) in single case non-parametric VBM, by performing 400 statistical comparisons between a single disease-free individual and a group of 100 disease-free controls. The impact of smoothing (4, 8, and 12 mm) and type of pre-processing (Modulated, Unmodulated) was also examined, as these factors have been found to influence FPRs in previous investigations using parametric statistics. The 400 statistical comparisons were repeated using two independent, freely available data sets in order to maximize the generalizability of the results. We found that the family-wise error rate was 5% for increases and 3.6% for decreases in one data set; and 5.6% for increases and 6.3% for decreases in the other data set (5% nominal). Further, these results were not dependent on the level of smoothing and modulation. Therefore, the present study provides empirical evidence that single case VBM studies with non-parametric statistics are not susceptible to high false positive rates. The critical implication of this finding is that VBM can be used

  4. Internet-Based Intervention for Tinnitus: Outcome of a Single-Group Open Trial.

    Science.gov (United States)

    Beukes, Eldré W; Allen, Peter M; Manchaiah, Vinaya; Baguley, David M; Andersson, Gerhard

    2017-04-01

    Managing chronic tinnitus is challenging, and innovative ways to address the resulting health-care burden are required. Internet-based cognitive behavioral therapy (iCBT) for tinnitus shows promise as a cost-effective treatment option. The feasibility and effectiveness of iCBT in the United Kingdom are yet to be explored. Furthermore, it is not known if iCBT can be supported by an audiologist rather than a psychologist. This study aimed to determine the feasibility of guided iCBT using audiological support on tinnitus distress and tinnitus-related comorbidities. Furthermore, it aimed to establish the feasibility of iCBT for tinnitus distress in the United Kingdom, by determining recruitment, attrition, and compliance rates. Finally, it aimed to identify which aspects of the protocol require refinement for subsequent clinical trials. A single-group open trial design was implemented. This study would serve as a prerequisite study, to identify barriers, before undertaking effectiveness trials. Participants consisted of 37 adults (18 males, 19 females), with an age range of between 50 and 59 yr. The mean preintervention tinnitus severity rating was 56.15 (standard deviation = 18.35), which is categorized as "severe tinnitus" as measured by the Tinnitus Functional Index (TFI). Five participants withdrew during the study, and 29 of the remaining participants completed the postintervention questionnaire. The guided iCBT intervention ran over an eight-week period and consisted of 16 obligatory modules and five optional modules. The intervention was designed to be interactive, interesting, and stimulating. A key element was the provision of support from an audiologist throughout the program. Online questionnaires were used throughout the study. These were administered at baseline and postintervention to determine attrition and compliance rates and to facilitate sample size estimates for further clinical trials. Outcome measures for tinnitus severity, hearing handicap

  5. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.

    Science.gov (United States)

    Grattapaglia, D; Sederoff, R

    1994-08-01

    We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support > or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the

  6. A genetic linkage map of sole (Solea solea: a tool for evolutionary and comparative analyses of exploited (flatfishes.

    Directory of Open Access Journals (Sweden)

    Eveline Diopere

    Full Text Available Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L. is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes, Nile tilapia (Oreochromis niloticus, three-spined stickleback (Gasterosteus aculeatus and green spotted pufferfish (Tetraodon nigroviridis. This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus, another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

  7. A single blind randomized control trial on support groups for Chinese persons with mild dementia

    Directory of Open Access Journals (Sweden)

    Young DKW

    2014-12-01

    Full Text Available Daniel KW Young,1 Timothy CY Kwok,2 Petrus YN Ng1 1Department of Social Work, Hong Kong Baptist University, Kowloon Tong, Hong Kong; 2Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong Purpose: Persons with mild dementia experience multiple losses and manifest depressive symptoms. This research study aimed to evaluate the effectiveness of a support group led by a social worker for Chinese persons with mild dementia. Research methods: Participants were randomly assigned to either a ten-session support group or a control group. Standardized assessment tools were used for data collection at pretreatment and post-treatment periods by a research assistant who was kept blind to the group assignment of the participants. Upon completion of the study, 20 treatment group participants and 16 control group participants completed all assessments. Results: At baseline, the treatment and control groups did not show any significant difference on all demographic variables, as well as on all baseline measures; over one-half (59% of all the participants reported having depression, as assessed by a Chinese Geriatric Depression Scale score ≥8. After completing the support group, the depressive mood of the treatment group participants reduced from 8.83 (standard deviation =2.48 to 7.35 (standard deviation =2.18, which was significant (Wilcoxon signed-rank test; P=0.017, P<0.05, while the control group’s participants did not show any significant change. Conclusion: This present study supports the efficacy and effectiveness of the support group for persons with mild dementia in Chinese society. In particular, this present study shows that a support group can reduce depressive symptoms for participants. Keywords: support group, mild dementia, Chinese, depression

  8. LD-Spline: Mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Bush William S

    2009-12-01

    Full Text Available Abstract Background Gene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs prior to analysis. These approaches require knowledge about the relationships between SNPs on a genotyping platform and genes in the human genome. SNPs in the genome can represent broader genomic regions via linkage disequilibrium (LD, and population-specific patterns of LD can be exploited to generate a data-driven map of SNPs to genes. Methods In this study, we implemented LD-Spline, a database routine that defines the genomic boundaries a particular SNP represents using linkage disequilibrium statistics from the International HapMap Project. We compared the LD-Spline haplotype block partitioning approach to that of the four gamete rule and the Gabriel et al. approach using simulated data; in addition, we processed two commonly used genome-wide association study platforms. Results We illustrate that LD-Spline performs comparably to the four-gamete rule and the Gabriel et al. approach; however as a SNP-centric approach LD-Spline has the added benefit of systematically identifying a genomic boundary for each SNP, where the global block partitioning approaches may falter due to sampling variation in LD statistics. Conclusion LD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm.

  9. Summary report of the group on single-particle nonlinear dynamics

    International Nuclear Information System (INIS)

    Axinescu, S.; Bartolini, R.; Bazzani, A.

    1996-10-01

    This report summarizes the research on single-particle nonlinear beam dynamics. It discusses the following topics: analytical and semi-analytical tools; early prediction of the dynamic aperture; how the results are commonly presented; Is the mechanism of the dynamic aperture understand; ripple effects; and beam-beam effects

  10. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    NARCIS (Netherlands)

    Quevedo, Beatrice; Giertsen, Elin; Zijnge, Vincent; Luethi-Schaller, Helga; Guggenheim, Bernhard; Thurnheer, Thomas; Gmuer, Rudolf

    2011-01-01

    Background: The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to

  11. Single crystal X-ray structural features of aromatic compounds having a pentafluorosulfuranyl (SF5) functional group

    Czech Academy of Sciences Publication Activity Database

    Du, J.; Hua, G.; Beier, Petr; Slawin, A. M. Z.; Woollins, J. D.

    2017-01-01

    Roč. 28, č. 3 (2017), s. 723-733 ISSN 1040-0400 Institutional support: RVO:61388963 Keywords : pentafluorosulfuranyl (SF5) group * aromatic compounds * single crystal X-ray structure * intramolecular interactions * intermolecular interactions Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 1.582, year: 2016

  12. 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.

  13. Summary of Group Development and Testing for Single Shell Tank Closure at Hanford

    Energy Technology Data Exchange (ETDEWEB)

    Harbour, John, R.

    2005-04-28

    This report is a summary of the bench-scale and large scale experimental studies performed by Savannah River National Laboratory for CH2M HILL to develop grout design mixes for possible use in producing fill materials as a part of Tank Closure of the Single-Shell Tanks at Hanford. The grout development data provided in this report demonstrates that these design mixes will produce fill materials that are ready for use in Hanford single shell tank closure. The purpose of this report is to assess the ability of the proposed grout specifications to meet the current requirements for successful single shell tank closure which will include the contracting of services for construction and operation of a grout batch plant. The research and field experience gained by SRNL in the closure of Tanks 17F and 20F at the Savannah River Site was leveraged into the grout development efforts for Hanford. It is concluded that the three Hanford grout design mixes provide fill materials that meet the current requirements for successful placement. This conclusion is based on the completion of recommended testing using Hanford area materials by the operators of the grout batch plant. This report summarizes the regulatory drivers and the requirements for grout mixes as tank fill material. It is these requirements for both fresh and cured grout properties that drove the development of the grout formulations for the stabilization, structural and capping layers.

  14. A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

    Science.gov (United States)

    Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E Charles

    2014-08-21

    A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa. Copyright © 2014 Li et al.

  15. Wargaming Strategic Linkage

    Science.gov (United States)

    2009-01-01

    meetings and briefings fulfill many of these functions during single- venue and synchronous games . Some form of electronic communica- tions (telephone...directions, and current and future generations of leaders, analysts, and experts are more and more familiar with the conventions of the electronic game ...core motivation for any player. The competitive nature and desire to win is what McCarty-Little identified as a core driver behind war gaming

  16. The first linkage map of the American mink (Mustela vison)

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Menzorov, A.; Serov, O.

    2007-01-01

    Described herein, the first microsatellite linkage map for the American mink consists of 85 microsatellite markers resolved into 17 linkage groups. The map was constructed using 92 F1 progeny from five sire families created by crossing mink with different colour types. The linkage groups ranged...... from 0 to 137 cM. Thee linkage groups were assigned to 12 of the 14 mink autosomes using a somatic cell hybrid panel. The total map covered 690 sex-averaged Kosambi units with an average marker spacing of 8 cM. This map will facilitate further genetic mapping of monogenic characters and QTL....

  17. 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.

  18. Earliest Deadline Control of a Group of Heat Pumps with a Single Energy Source

    NARCIS (Netherlands)

    Fink, J.; van Leeuwen, Richard Pieter

    2016-01-01

    In this paper, we develop and investigate the optimal control of a group of 104 heat pumps and a central Combined Heat and Power unit (CHP). The heat pumps supply space heating and domestic hot water to households. Each house has a buffer for domestic hot water and a floor heating system for space

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

    Directory of Open Access Journals (Sweden)

    Abdullah-Al Mamun

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

  20. π-π interaction of aromatic groups in amphiphilic molecules directing for single-crystalline mesostructured zeolite nanosheets

    Science.gov (United States)

    Xu, Dongdong; Ma, Yanhang; Jing, Zhifeng; Han, Lu; Singh, Bhupendra; Feng, Ji; Shen, Xuefeng; Cao, Fenglei; Oleynikov, Peter; Sun, Huai; Terasaki, Osamu; Che, Shunai

    2014-06-01

    One of the challenges in material science has been to prepare macro- or mesoporous zeolite. Although examples of their synthesis exist, there is a need for a facile yet versatile approach to such hierarchical structures. Here we report a concept for designing a single quaternary ammonium head amphiphilic template with strong ordered self-assembling ability through π-π stacking in hydrophobic side, which stabilizes the mesostructure to form single-crystalline mesostructured zeolite nanosheets. The concept is demonstrated for the formation of a new type of MFI (zeolite framework code by International Zeolite Association) nanosheets joined with a 90° rotational boundary, which results in a mesoporous zeolite with highly specific surface area even after calcination. Low binding energies for this self-assembling system are supported by a theoretical analysis. A geometrical matching between the arrangement of aromatic groups and the zeolitic framework is speculated for the formation of single-crystalline MFI nanosheets.

  1. Analysis of single oil-bearing fluid inclusions in mid-Proterozoic sandstones (Roper Group, Australia)

    Science.gov (United States)

    Siljeström, Sandra; Volk, Herbert; George, Simon C.; Lausmaa, Jukka; Sjövall, Peter; Dutkiewicz, Adriana; Hode, Tomas

    2013-12-01

    Hydrocarbons and organic biomarkers extracted from black shales and other carbonaceous sedimentary rocks are valuable sources of information on the biodiversity and environment of early Earth. However, many Precambrian hydrocarbons including biomarkers are suspected of being younger contamination. An alternative approach is to study biomarkers trapped in oil-bearing fluid inclusions by bulk crushing samples and subsequently analysing the extracted hydrocarbons with gas chromatography-mass spectrometry. However, this method does not constrain the hydrocarbons to one particular oil inclusion, which means that if several different generations of oil inclusions are present in the sample, a mix of the content from these oil inclusions will be analysed. In addition, samples with few and/or small inclusions are often below the detection limit. Recently, we showed that it is possible to detect organic biomarkers in single oil-bearing fluid inclusions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). In the present study, single fluid inclusion analysis has been performed on Proterozoic samples for the first time. Four individual oil-bearing fluid inclusions, found in 1430 Ma sandstone from the Roper Superbasin in Northern Australia, were analysed with ToF-SIMS. The ToF-SIMS spectra of the oil in the different inclusions are very similar to each other and are consistent with the presence of n-alkanes/branched alkanes, monocyclic alkanes, bicyclic alkanes, aromatic hydrocarbons, and tetracyclic and pentacyclic hydrocarbons. These results are in agreement with those obtained from bulk crushing of inclusions trapped in the same samples. The capability to analyse the hydrocarbon and biomarker composition of single oil-bearing fluid inclusions is a major breakthrough, as it opens up a way of obtaining molecular compositional data on ancient oils without the ambiguity of the origin of these hydrocarbons. Additionally, this finding suggests that it will be possible

  2. Comparative investigation of methods to determine the group velocity dispersion of an endlessly single-mode photonic crystal fiber

    Science.gov (United States)

    Baselt, Tobias; Popp, Tobias; Nelsen, Bryan; Lasagni, Andrés. Fabián.; Hartmann, Peter

    2017-05-01

    Endlessly single-mode fibers, which enable single mode guidance over a wide spectral range, are indispensable in the field of fiber technology. A two-dimensional photonic crystal with a silica central core and a micrometer-spaced hexagonal array of air holes is an established method to achieve endless single-mode guidance. There are two possible ways to determine the dispersion: measurement and calculation. We calculate the group velocity dispersion GVD based on the measurement of the fiber structure parameters, the hole diameter and the pitch of a presumed homogeneous hexagonal array and compare the calculation with two methods to measure the wavelength-dependent time delay. We measure the time delay on a three hundred meter test fiber with a homemade supercontinuum light source, a set of bandpass filters and a fast detector and compare the results with a white light interferometric setup. To measure the dispersion of optical fibers with high accuracy, a time-frequency-domain setup based on a Mach-Zehnder interferometer is used. The experimental setup allows the determination of the wavelength dependent differential group delay of light travelling through a thirty centimeter piece of test fiber in the wavelength range from VIS to NIR. The determination of the GVD using different methods enables the evaluation of the individual methods for characterizing the endlessly single-mode fiber.

  3. 'Single-checked' Patient Group Directions during initial nurse assessment within paediatric emergency departments of the UK and Ireland.

    Science.gov (United States)

    Bird, Chris K; Sinclair, Anthony G; Hartshorn, Stuart

    2017-01-10

    Double checking medications at initial assessment within paediatric emergency departments (EDs) has the potential to delay patient flow, and doubt has been cast on the efficacy of double checking in all but high-risk medications. We aimed to benchmark current practice for the use of Patient Group Direction (PGD) medications at initial assessment in EDs within the Paediatric Emergency Research UK and Ireland (PERUKI) network, with a focus on the use of 'single-checker' PGDs. Online survey was distributed to the research representative at each PERUKI site. The survey was open for 5 weeks (from March 2015 to April 2015) and was completed by any appropriate clinician within the site. The response rate was 84% (36/43 EDs). From these, 22 out of 36 (61%) EDs were using single-checker PGDs. The commonest single-checked medications in use were paracetamol and ibuprofen for pain. Among PERUKI sites, 21.9% of EDs reported drug errors related to standard (double-checked) PGDs, whereas 13.6% of those with single-checked PGDs reported drug errors (Fisher's exact test with significance level of 0.05, P=0.501). The commonest errors reported were duplicated dose, incorrect weight, incorrect volume drawn up, contraindication missed. Single-checker PGDs are currently in use in nearly two-thirds of PERUKI sites. No evidence of increased medication errors was reported with this practice; however, more detailed studies are required to support this finding and to inform best practice.

  4. Improved location features for linkage of regions across ipsilateral mammograms

    NARCIS (Netherlands)

    Tanner, C.; Schie, G. van; Lesniak, J.M.; Karssemeijer, N.; Szekely, G.

    2013-01-01

    Improved performance has been reported for computer aided detection (CADe) methods using information from multiple mammographic views over single-view CADe approaches. Linkage across the views is based on assuming that location and image features from the same lesion depicted in both views will be

  5. Modelling and visualizing fine-scale linkage disequilibrium structure

    DEFF Research Database (Denmark)

    Edwards, David

    2013-01-01

    Background Detailed study of genetic variation at the population level in humans and other species is now possible due to the availability of large sets of single nucleotide polymorphism data. Alleles at two or more loci are said to be in linkage disequilibrium (LD) when they are correlated...

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

    Indian Academy of Sciences (India)

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

  7. From DNA to protein: Transformations and their possible role in linkage learning

    Energy Technology Data Exchange (ETDEWEB)

    Kargupta, H.; Stafford, B.

    1997-04-01

    This paper first extends the traditional perspective of linkage using the basic concepts developed in the SEARCH framework and identifies the fundamental objectives of linkage learning. It then explores the computational role of gene-expression (DNA{r_arrow}RNA{r_arrow}Protein transformations) in evolutionary linkage learning, using group representation theory. It offers strong evidence to support the hypothesis that the transformations in gene-expression define a group of symmetry transformations that leaves the fitness invariant; however, they change the eigen functions leading to identifying independent subspaces of the search space (a major objective of linkage learning) using irreducible representations of such transformations.

  8. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

    Science.gov (United States)

    Wang, Jing; Zhang, Kaichun; Zhang, Xiaoming; Yan, Guohua; Zhou, Yu; Feng, Laibao; Ni, Yang; Duan, Xuwei

    2015-01-01

    A cross between the sweet cherry (Prunus avium) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding. PMID:26516760

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

    Science.gov (United States)

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

    2007-01-01

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

  10. STAKEHOLDER LINKAGES FOR SUSTAINABLE LAND ...

    African Journals Online (AJOL)

    Osondu

    This paper presents stakeholder types involved in sustainable land management (SLM), their interests and ... (DAs), and Rural Kebele Administration (RKA) offices were major stakeholders involved in SLM activities in the ... Key words: Stakeholders; farmer-expert linkages; resource management; Ethiopia. Introduction.

  11. Examination of genetic linkage of chromosome 15 to schizophrenia in a large Veterans Affairs Cooperative Study sample.

    Science.gov (United States)

    Tsuang, D W; Skol, A D; Faraone, S V; Bingham, S; Young, K A; Prabhudesai, S; Haverstock, S L; Mena, F; Menon, A S; Bisset, D; Pepple, J; Sauter, F; Baldwin, C; Weiss, D; Collins, J; Boehnke, M; Schellenberg, G D; Tsuang, M T

    2001-12-08

    Previous studies have reported genetic linkage evidence for a schizophrenia gene on chromosome 15q. Here, chromosome 15 was examined by genetic linkage analysis using 166 schizophrenia families, each with two or more affected subjects. The families, assembled from multiple centers by the Department of Veterans Affairs Cooperative Study Program, consisted of 392 sampled affected subjects and 216 affected sibling pairs. By DSM-III-R criteria, 360 subjects (91.8%) had a diagnosis of schizophrenia and 32 (8.2%) were classified as schizo-affective disorder, depressed. Participating families had diverse ethnic backgrounds. The largest single group were northern European American families (n = 62, 37%), but a substantial proportion was African American kindreds (n = 60, 36%). The chromosome 15 markers tested were spaced at intervals of approximately 10 cM over the entire chromosome and 2-5 cM for the region surrounding the alpha-7 nicotinic cholinergic receptor subunit gene (CHRNA7). These markers were genotyped and the data analyzed using semiparametric affecteds-only linkage analysis. In the European American families, there was a maximum Z-score of 1.65 between markers D15S165 and D15S1010. These markers are within 1 cM from CHRNA-7, the site previously implicated in schizophrenia. However, there was no evidence for linkage to this region in the African America kindreds. Copyright 2001 Wiley-Liss, Inc.

  12. Earliest Deadline Control of a Group of Heat Pumps with a Single Energy Source

    Directory of Open Access Journals (Sweden)

    Jiří Fink

    2016-07-01

    Full Text Available In this paper, we develop and investigate the optimal control of a group of 104 heat pumps and a central Combined Heat and Power unit (CHP. The heat pumps supply space heating and domestic hot water to households. Each house has a buffer for domestic hot water and a floor heating system for space heating. Electricity for the heat pumps is generated by a central CHP unit, which also provides thermal energy to a district heating system. The paper reviews recent smart grid control approaches for central and distributed levels. An online algorithm is described based on the earliest deadline first theory that can be used on the aggregator level to control the CHP and to give signals to the heat pump controllers if they should start or should wait. The central controller requires only a limited amount of privacy-insensitive information from the heat pump controllers about their deadlines, which the heat pump controllers calculate for themselves by model predictions. In this way, a robust heat pump and CHP control is obtained, which is able to minimize energy demand and results in the desired thermal comfort for the households. The simulations demonstrate fast computation times due to minor computational and communication overheads.

  13. Isotherm, thermodynamic, kinetics, and adsorption mechanism studies of Ethidium bromide by single-walled carbon nanotube and carboxylate group functionalized single-walled carbon nanotube.

    Science.gov (United States)

    Moradi, Omid; Fakhri, Ali; Adami, Saeideh; Adami, Sepideh

    2013-04-01

    The studies of kinetics and thermodynamics of adsorption of Ethidium bromide in aqueous solutions on single-walled carbon nanotube (SWCNT) and carboxylate group functionalized single-walled carbon nanotube (SWCNT-COOH) surfaces were by UV-Vis spectroscopy. The adsorption kinetics for SWCNT-COOH and SWCNTs were well described by a intra-particle diffusion model, while Langmuir, Freundlich, Harkins-Jura, and Halsey isotherms described the adsorption isotherms, and the adsorption thermodynamic parameters of equilibrium constant (K0), standard free energy (ΔG0), standard enthalpy (ΔH0), and standard entropy changes (ΔS0) were measured. The maximum surface coverage for SWCNTs is 36.10% and for SWCNT-COOH is 38.42%. The values of ΔH0 and ΔG0 suggested that the adsorption of EtBr on SWCNT-COOH and SWCNTs was endothermic and spontaneous. The adsorption of EtBr on SWCNT-COOH is more than SWCNTs surfaces. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. The use of Lorentz group formalism in solving polarization effects of a birefringent single mode optical fiber

    International Nuclear Information System (INIS)

    Ishiekwene, G.C.; Brown, C.S.; Mensah, S.Y.; Bak, A.E.

    2000-07-01

    A theoretical analysis on the polarization effects of a light beam propagating in a birefringent single-mode fiber is presented. We derive a system of differential equations representing the evolution of Stokes parameters and illustrate their application to polarization effects in a straight birefringent single mode optical fiber. The solutions to the set of equations are obtained using specifically the methods of the unified formalism for polarization optics which adopt the use of the Stokes-Mueller equation and the Lorentz group to model polarization phenomena in media such as optical fibers. The analytical results presented using this approach are identical to results obtained from other conventional methods. We observe the characteristic exponential decrease in the total intensity of the input light due to attenuation by the fiber. (author)

  15. Correlated spectroscopic imaging of calf muscle in three spatial dimensions using group sparse reconstruction of undersampled single and multichannel data.

    Science.gov (United States)

    Wilson, Neil E; Burns, Brian L; Iqbal, Zohaib; Thomas, M Albert

    2015-11-01

    To implement a 5D (three spatial + two spectral) correlated spectroscopic imaging sequence for application to human calf. Nonuniform sampling was applied across the two phase encoded dimensions and the indirect spectral dimension of an echo planar-correlated spectroscopic imaging sequence. Reconstruction was applied that minimized the group sparse mixed ℓ2,1-norm of the data. Multichannel data were compressed using a sensitivity map-based approach with a spatially dependent transform matrix and utilized the self-sparsity of the individual coil images to simplify the reconstruction. Single channel data with 8× and 16× undersampling are shown in the calf of a diabetic patient. A 15-channel scan with 12× undersampling of a healthy volunteer was reconstructed using 5 virtual channels and compared to a fully sampled single slice scan. Group sparse reconstruction faithfully reconstructs the lipid cross peaks much better than ℓ1 minimization. COSY spectra can be acquired over a 3D spatial volume with scan time under 15 min using echo planar readout with highly undersampled data and group sparse reconstruction. © 2015 Wiley Periodicals, Inc.

  16. Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar Genome

    Directory of Open Access Journals (Sweden)

    Hsin Y. Tsai

    2016-07-01

    Full Text Available High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species’ genome. Genomic resources for Atlantic salmon (Salmo salar include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the ‘ssalar01’ high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95. While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research.

  17. Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.

    Science.gov (United States)

    Tsai, Hsin Y; Robledo, Diego; Lowe, Natalie R; Bekaert, Michael; Taggart, John B; Bron, James E; Houston, Ross D

    2016-07-07

    High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. Copyright © 2016 Tsai et al.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-01-15

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

  19. Efficient Record Linkage Algorithms Using Complete Linkage Clustering

    Science.gov (United States)

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

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times. PMID:27124604

  20. Efficient Record Linkage Algorithms Using Complete Linkage Clustering.

    Science.gov (United States)

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

    2016-01-01

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

  1. Hybrid scaffold bearing polymer-siloxane Schiff base linkage for bone tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Nair, Bindu P., E-mail: bindumelekkuttu@gmail.com; Gangadharan, Dhanya; Mohan, Neethu; Sumathi, Babitha; Nair, Prabha D., E-mail: pdnair49@gmail.com

    2015-07-01

    Scaffolds that can provide the requisite biological cues for the fast regeneration of bone are highly relevant to the advances in tissue engineering and regenerative medicine. In the present article, we report the fabrication of a chitosan–gelatin–siloxane scaffold bearing interpolymer-siloxane Schiff base linkage, through a single-step dialdehyde cross-linking and freeze-drying method using 3-aminopropyltriethoxysilane as the siloxane precursor. Swelling of the scaffolds in phosphate buffered saline indicates enhancement with increase in siloxane concentration, whereas compressive moduli of the wet scaffolds reveal inverse dependence, owing to the presence of siloxane, rich in silanol groups. It is suggested that through the strategy of dialdehyde cross-linking, a limiting siloxane loading of 20 wt.% into a chitosan-gelatin matrix should be considered ideal for bone tissue engineering, because the scaffold made with 30 wt.% siloxane loading degrades by 48 wt.%, in 21 days. The hybrid scaffolds bearing Schiff base linkage between the polymer and siloxane, unlike the stable linkages in earlier reports, are expected to give a faster release of siloxanes and enhancement in osteogenesis. This is verified by the in vitro evaluation of the hybrid scaffolds using rabbit adipose mesenchymal stem cells, which revealed osteogenic cell-clusters on a polymer-siloxane scaffold, enhanced alkaline phosphatase activity and the expression of bone-specific genes, whereas the control scaffold without siloxane supported more of cell-proliferation than differentiation. A siloxane concentration dependent enhancement in osteogenic differentiation is also observed. - Highlights: • A hybrid scaffold bearing interpolymer-siloxane Schiff base linkage • A limiting siloxane loading of 20 wt.% into chitosan–gelatin matrix • A siloxane concentration dependent enhancement in osteogenic differentiation.

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

    Science.gov (United States)

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

    2010-05-01

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

  3. An examination of variations in the cepstral spectral index of dysphonia across a single breath group in connected speech.

    Science.gov (United States)

    Watts, Christopher R; Awan, Shaheen N

    2015-01-01

    The purpose of this study was to use spectral and cepstral analyses of speech to investigate whether underlying physiological changes in voice result in changes in acoustic estimates of dysphonia severity in continuous speech contexts within a single breath group. The effect of dysphonia on acoustic estimates of dysphonia severity, frequency, relative intensity, and vocalization time across initial and terminal segments of a single breath group using a common clinical stimulus was investigated. Prospective quasi-experimental controlled design. Digitized recordings of the Consensus Auditory-Perceptual Evaluation of Voice sentence "We were away a year ago" were obtained from 20 treatment-seeking dysphonic individuals (females, mean age = 39 years) and 20 normal controls (females, mean age = 39 years). Each recorded sample was separated into the first four syllables ("We were away … ") and second four syllables ("…a year ago.") of the breath group. Cepstral and spectral measures, intensity measures, and temporal analyses were obtained and used in calculations of the Cepstral Spectral Index of Dysphonia (CSID, an acoustic estimate of dysphonia severity), fundamental frequency (F0), vocalization time, and relative vocal intensity (dB SLP). Statistical analyses were applied to calculations of change (delta [Δ]) in these measures from one breath group segment to the next. Results revealed a significant effect of group on measures of CSID and F0, but not relative intensity or vocalization time. Dysphonic speakers exhibited a significant increase in the CSID from the first to second breath group segment and limited variation in F0 compared with controls. These results may support the hypothesis that voice impairment increases in severity toward the termination of a breath group even within a short temporal frame (i.e., 2 seconds or less of connected speech), and that this portion of the breath group may be an important determinant of perceptual impressions. Further

  4. Landscape linkages and biodiversity in European landscapes

    NARCIS (Netherlands)

    Jongman, R.H.G.

    2004-01-01

    Linear features are structuring landscape elements. We change our landscapes and rebuild them into new linkages, and landscapes are even constructed around these linkages. Landscape linkages are important for species migration and dispersal on a large scale and a small scale: storks, bats and

  5. Comparing a single case to a control group - Applying linear mixed effects models to repeated measures data.

    Science.gov (United States)

    Huber, Stefan; Klein, Elise; Moeller, Korbinian; Willmes, Klaus

    2015-10-01

    In neuropsychological research, single-cases are often compared with a small control sample. Crawford and colleagues developed inferential methods (i.e., the modified t-test) for such a research design. In the present article, we suggest an extension of the methods of Crawford and colleagues employing linear mixed models (LMM). We first show that a t-test for the significance of a dummy coded predictor variable in a linear regression is equivalent to the modified t-test of Crawford and colleagues. As an extension to this idea, we then generalized the modified t-test to repeated measures data by using LMMs to compare the performance difference in two conditions observed in a single participant to that of a small control group. The performance of LMMs regarding Type I error rates and statistical power were tested based on Monte-Carlo simulations. We found that starting with about 15-20 participants in the control sample Type I error rates were close to the nominal Type I error rate using the Satterthwaite approximation for the degrees of freedom. Moreover, statistical power was acceptable. Therefore, we conclude that LMMs can be applied successfully to statistically evaluate performance differences between a single-case and a control sample. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. From Enclave to Linkage Economies?

    DEFF Research Database (Denmark)

    Hansen, Michael W.

    If African developing countries are to benefit fully from the current boom in foreign direct investment (FDI) in extractives (i.e. mining and oil/gas), it is essential that the foreign investors foster linkages to the local economy. Traditionally, extractive FDI in Africa has been seen....... At the same time, local African enterprises are eager to, and increasingly capable of, linking up to the foreign investors in order to expand their activities and acquire technology, skills and market access. The changing strategies of MNCs and the improving capabilities of African enterprises offer new...... opportunities for governments and donors to mobilize extractive FDI for development goals. This paper seeks to take stock of what we know about the state of and driving forces of linkage formation in South Sahel Africa extractives based on a review of the extant literature. The paper argues that while MNCs...

  7. A single amino acid substitution in the group 1 Trypanosoma brucei gambiense haptoglobin-hemoglobin receptor abolishes TLF-1 binding.

    Directory of Open Access Journals (Sweden)

    E DeJesus

    Full Text Available Critical to human innate immunity against African trypanosomes is a minor subclass of human high-density lipoproteins, termed Trypanosome Lytic Factor-1 (TLF-1. This primate-specific molecule binds to a haptoglobin-hemoglobin receptor (HpHbR on the surface of susceptible trypanosomes, initiating a lytic pathway. Group 1 Trypanosoma brucei gambiense causes human African Trypanosomiasis (HAT, escaping TLF-1 killing due to reduced uptake. Previously, we found that group 1 T. b. gambiense HpHbR (TbgHpHbR mRNA levels were greatly reduced and the gene contained substitutions within the open reading frame. Here we show that a single, highly conserved amino acid in the TbgHpHbR ablates high affinity TLF-1 binding and subsequent endocytosis, thus evading TLF-1 killing. In addition, we show that over-expression of TbgHpHbR failed to rescue TLF-1 susceptibility. These findings suggest that the single substitution present in the TbgHpHbR directly contributes to the reduced uptake and resistance to TLF-1 seen in these important human pathogens.

  8. Improving linkage with substance abuse treatment using brief case management and motivational interviewing.

    Science.gov (United States)

    Rapp, Richard C; Otto, Amy L; Lane, D Timothy; Redko, Cristina; McGatha, Sue; Carlson, Robert G

    2008-04-01

    Poor linkage with substance abuse treatment remains a problem, negating the benefits that can accrue to both substance abusers and the larger society. Numerous behavioral interventions have been tested to determine their potential role in improving linkage. A randomized clinical trial of 678 substance abusers compared the linkage effect of two brief interventions with the referral standard of care (SOC) at a centralized intake unit (CIU). Interventions included five sessions of strengths-based case management (SBCM) or one session of motivational interviewing (MI). A priori hypotheses predicted that both interventions would be better than the standard of care in predicting linkage and that SBCM would be more effective than MI. We analyzed the effect of the two interventions on overall treatment linkage rates and by treatment modality. Logistic regression analysis examined predictors of treatment linkage for the sample and each group. Two hypotheses were confirmed in that SBCM (n=222) was effective in improving linkage compared to the SOC (n=230), 55.0% vs. 38.7% (pMotivational interviewing (n=226) was not significantly more effective in improving linkage than the standard of care (44.7% vs. 38.7%; p>.05). The three trial groups differed only slightly on the client characteristics that predicted linkage with treatment. The results of this study confirm a body of literature that supports the effectiveness of case management in improving linkage with treatment. The role of motivational interviewing in improving linkage was not supported. Results are discussed in the context of other case management and motivational interviewing linkage studies.

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

    NARCIS (Netherlands)

    Font-Gonzalez, A.

    2016-01-01

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

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

    African Journals Online (AJOL)

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

  11. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1population of octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

    2017-05-12

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

  12. Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS).

    Science.gov (United States)

    Guajardo, Verónica; Solís, Simón; Sagredo, Boris; Gainza, Felipe; Muñoz, Carlos; Gasic, Ksenija; Hinrichsen, Patricio

    2015-01-01

    Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a 'Rainier' x 'Rivedel' (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in 'Rainier', 'Rivedel' and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for 'Rainier', 'Rivedel' and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both 'Rainier' and 'Rivedel' maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

  13. The first genetic linkage map of Eucommia ulmoides

    Indian Academy of Sciences (India)

    markers each, and 18 markers without a group. The 14 link- age groups ranged in length from 41.8 to 108.6 cM. The num- ber of markers per linkage group ranged from four (LFLG3 and LFLG13) to 20 (LFLG6). The linked markers covered. 1116.1 cM and the distance between two adjacent markers ranged from 0.6 to 35.2 ...

  14. Privacy preserving interactive record linkage (PPIRL).

    Science.gov (United States)

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

    2014-01-01

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

  15. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    Science.gov (United States)

    2011-01-01

    Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of

  16. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    Directory of Open Access Journals (Sweden)

    Thurnheer Thomas

    2011-01-01

    Full Text Available Abstract Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of

  17. Oxygenated organic functional groups and their sources in single and submicron organic particles in MILAGRO 2006 campaign

    Directory of Open Access Journals (Sweden)

    S. Liu

    2009-09-01

    Full Text Available Fourier Transform Infrared (FTIR and X-ray Fluorescence (XRF were used to measure organic functional groups and elements of submicron particles collected during MILAGRO in March 2006 on three platforms: the Mexico City urban area (SIMAT, the high altitude site at 4010 m (Altzomoni, and the NCAR C130 aircraft. Scanning Transmission X-ray Microscopy (STXM and Near-Edge X-ray Absorption Fine Structure (NEXAFS were applied to single particle organic functional group abundance analysis of particles simultaneously collected at SIMAT and C130. Correlations of elemental concentrations showed different groups of source-related elements at SIMAT, Altzomoni, and C130, suggesting different processes affecting the air masses sampled at the three platforms. Cluster analysis resulted in seven distinct clusters of FTIR spectra, with the last three clusters consisting of spectra collected almost exclusively on the C130 platform, reflecting the variety of sources contributing to C130 samples. Positive Matrix Factorization (PMF of STXM-NEXAFS spectra identified three main factors representing soot, secondary, and biomass burning type spectra. PMF of FTIR spectra resulted in two fossil fuel combustion factors and one biomass burning factor, the former representative of source regions to the northeast and southwest of SIMAT. Alkane, carboxylic acid, amine, and alcohol functional groups were mainly associated with combustion related sources, while non-acid carbonyl groups were likely from biomass burning events. The majority of OM and O/C was attributed to combustion sources, although no distinction between direct emissions and atmospherically processed OM could be identified.

  18. Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

    Directory of Open Access Journals (Sweden)

    Goddard Mike E

    2004-05-01

    Full Text Available Abstract A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.

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

    Science.gov (United States)

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

    2015-08-01

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

  20. Effect of ABO blood group incompatibility on the outcome of single-unit cord blood transplantation after myeloablative conditioning.

    Science.gov (United States)

    Konuma, Takaaki; Kato, Seiko; Ooi, Jun; Oiwa-Monna, Maki; Ebihara, Yasuhiro; Mochizuki, Shinji; Yuji, Koichiro; Ohno, Nobuhiro; Kawamata, Toyotaka; Jo, Norihide; Yokoyama, Kazuaki; Uchimaru, Kaoru; Tojo, Arinobu; Takahashi, Satoshi

    2014-04-01

    ABO blood group incompatibility between donor and recipient has been associated with poor transplant outcomes in allogeneic hematopoietic stem cell transplantation. However, its effect on the outcome of cord blood transplantation (CBT) has yet to be clarified. We retrospectively analyzed 191 adult patients who received single-unit CBT after myeloablative conditioning for malignant disease in our institute. Major mismatch showed a significantly lower incidence of platelet engraftment compared with ABO match as a reference (hazard ratio, .57; P = .01). Nevertheless, there was no increase in graft-versus-host disease, transplant-related mortality, and overall mortality after ABO-incompatible CBT. These data suggested that donor-recipient ABO incompatibility does not have a significant impact on outcome after myeloablative CBT for hematological malignancies. Copyright © 2014 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

  1. Phylogenetic Diversity and Single-Cell Genome Analysis of "Melainabacteria", a Non-Photosynthetic Cyanobacterial Group, in the Termite Gut.

    Science.gov (United States)

    Utami, Yuniar Devi; Kuwahara, Hirokazu; Murakami, Takumi; Morikawa, Takahiro; Sugaya, Kaito; Kihara, Kumiko; Yuki, Masahiro; Lo, Nathan; Deevong, Pinsurang; Hasin, Sasitorn; Boonriam, Warin; Inoue, Tetsushi; Yamada, Akinori; Ohkuma, Moriya; Hongoh, Yuichi

    2018-03-29

    Termite guts harbor diverse yet-uncultured bacteria, including a non-photosynthetic cyanobacterial group, the class "Melainabacteria". We herein reported the phylogenetic diversity of "Melainabacteria" in the guts of diverse termites and conducted a single-cell genome analysis of a melainabacterium obtained from the gut of the termite Termes propinquus. We performed amplicon sequencing of 16S rRNA genes from the guts of 60 termite and eight cockroach species, and detected melainabacterial sequences in 48 out of the 68 insect species, albeit with low abundances (0.02-1.90%). Most of the melainabacterial sequences obtained were assigned to the order "Gastranaerophilales" and appeared to form clusters unique to termites and cockroaches. A single-cell genome of a melainabacterium, designated phylotype Tpq-Mel-01, was obtained using a fluorescence-activated cell sorter and whole genome amplification. The genome shared basic features with other melainabacterial genomes previously reconstructed from the metagenomes of human and koala feces. The bacterium had a small genome (~1.6 Mb) and possessed fermentative pathways possibly using sugars and chitobiose as carbon and energy sources, while the pathways for photosynthesis and carbon fixation were not found. The genome contained genes for flagellar components and chemotaxis; therefore, the bacterium is likely motile. A fluorescence in situ hybridization analysis showed that the cells of Tpq-Mel-01 and/or its close relatives are short rods with the dimensions of 1.1±0.2 μm by 0.5±0.1 μm; for these bacteria, we propose the novel species, "Candidatus Gastranaerophilus termiticola". Our results provide fundamental information on "Melainabacteria" in the termite gut and expand our knowledge on this underrepresented, non-photosynthetic cyanobacterial group.

  2. Development and evaluation of a modified brief assertiveness training for nurses in the workplace: a single-group feasibility study.

    Science.gov (United States)

    Nakamura, Yohei; Yoshinaga, Naoki; Tanoue, Hiroki; Kato, Sayaka; Nakamura, Sayoko; Aoishi, Keiko; Shiraishi, Yuko

    2017-01-01

    Effective communication has a great impact on nurses' job satisfaction, team relationships, as well as patient care/safety. Previous studies have highlighted the various beneficial effects of enhancing communication through assertiveness training programs for nurses. However, most programs take a long time to implement; thus, briefer programs are urgently required for universal on-the-job-training in the workplace. The purpose of this feasibility study was to develop and evaluate a modified brief assertiveness training program (with cognitive techniques) for nurses in the workplace. This study was carried out as a single-group, open trial (pre-post comparison without a control group). Registered nurses and assistant nurses, working at two private psychiatric hospitals in Miyazaki Prefecture in Japan, were recruited. After enrolling in the study, participants received a program of two 90-min sessions with a 1-month interval between sessions. The primary outcome was the Rathus Assertiveness Schedule (RAS), with secondary measurements using the Brief Version of the Fear of Negative Evaluation Scale (BFNE) and the Brief Job Stress Questionnaire (BJSQ). Assessments were conducted at baseline and after a 1-month interval (pre- and post-intervention). A total of 22 participants enrolled in the study and completed the program. The mean total score on the primary outcome (RAS) significantly improved from -12.9 (SD = 17.2) to -8.6 (SD = 18.6) ( p  = 0.01). The within-group effect size at the post-intervention was Cohen's d = 0.24; this corresponds to the small effect of the program. Regarding secondary outcomes, there were no statistically significant effects on the BFNE or any of the BJSQ subscales (job-stressors, psychological distress, physical distress, worksite support, and satisfaction). This single-group feasibility study demonstrated that our modified brief assertiveness training for nurses seems feasible and may achieve a favorable outcome in improving their

  3. Pharmacokinetics of serelaxin in patients with hepatic impairment: a single-dose, open-label, parallel group study.

    Science.gov (United States)

    Kobalava, Zhanna; Villevalde, Svetlana; Kotovskaya, Yulia; Hinrichsen, Holger; Petersen-Sylla, Marc; Zaehringer, Andreas; Pang, Yinuo; Rajman, Iris; Canadi, Jasna; Dahlke, Marion; Lloyd, Peter; Halabi, Atef

    2015-06-01

    Serelaxin is a recombinant form of human relaxin-2 in development for treatment of acute heart failure. This study aimed to evaluate the pharmacokinetics (PK) of serelaxin in patients with hepatic impairment. Secondary objectives included evaluation of immunogenicity, safety and tolerability of serelaxin. This was an open-label, parallel group study (NCT01433458) comparing the PK of serelaxin following a single 24 h intravenous (i.v.) infusion (30 μg kg(-1)  day(-1) ) between patients with mild, moderate or severe hepatic impairment (Child-Pugh class A, B, C) and healthy matched controls. Blood sampling and standard safety assessments were conducted. Primary non-compartmental PK parameters [including area under the serum concentration-time curve AUC(0-48 h) and AUC(0-∞) and serum concentration at 24 h post-dose (C24h )] were compared between each hepatic impairment group and healthy controls. A total of 49 subjects (including 25 patients with hepatic impairment) were enrolled, of which 48 subjects completed the study. In all groups, the serum concentration of serelaxin increased over the first few hours of infusion, reached steady-state at 12-24 h and then declined following completion of infusion, with a mean terminal half-life of 7-8 h. All PK parameter estimates were comparable between each group of patients with hepatic impairment and healthy controls. No serious adverse events, discontinuations due to adverse events or deaths were reported. No serelaxin treatment-related antibodies developed during this study. The PK and safety profile of serelaxin were not affected by hepatic impairment. No dose adjustment is needed for serelaxin treatment of 48 h i.v. infusion in patients with hepatic impairment. © 2014 The British Pharmacological Society.

  4. Improved blastocyst development of single cow OPU-derived presumptive zygotes by group culture with agarose-embedded helper embryos

    Directory of Open Access Journals (Sweden)

    Dey Shukla

    2011-08-01

    Full Text Available Abstract Background The in vitro culture of presumed zygotes derived from single cow ovum pick-up (OPU is important for the production of quality blastocysts maintaining pedigree. The aim of the present study was to evaluate the agar chip-embedded helper embryo coculture system for single cow OPU-derived zygotes by assessing embryo quality. Methods Cumulus oocyte complexes (COCs were collected from Hanwoo cows with high genetic merit twice a week using the ultra-sound guided OPU technique and from slaughterhouse ovaries. The Hanwoo cow COCs and slaughterhouse ovaries were matured in vitro, fertilized in vitro with thawed Hanwoo sperm and cultured for 24 h. The presumed zygotes were subsequently placed in three different culture systems: (1 control OPU (controlOPU with single cow OPU-derived presumed zygotes (2~8; (2 agar chip-embedded slaughterhouse helper embryo coculture (agarOPU with ten presumed zygotes including all presumed zygotes from a cow (2~8 and the rest from agar chip-embedded slaughterhouse presumed zygotes (8~2; and (3 slaughterhouse in vitro embryo production (sIVP with ten slaughterhouse ovary-derived presumed zygotes, each in 50 μL droplets. Day 8 blastocysts were assayed for apoptosis and gene expression using real time PCR. Results The coculture system promoted higher blastocyst development in OPU zygotes compared to control OPU zygotes cultured alone (35.2 vs. 13.9%; P CD9, 0.4-fold; AKRAB1, 0.3-fold and in cocultured zygotes (CD9, 0.3-fold; AKRAB1, 0.3-fold compared to sIVP blastocysts (1.0-fold. Moreover, genes involved in implantation and/or normal calf delivery were up-regulated (P PGSH2, 5.0-fold; TXN, 4.3-fold; PLAU, 1.7-fold and cocultured zygotes (PGSH2, 14.5-fold; TXN, 3.2-fold; PLAU, 6.8-fold compared to sIVP (1.0-fold blastocysts. However, the expression of PLAC8, TGF-β1, ODC1, ATP5A1 and CASP3 did not differ between the three culture groups. Conclusions Results show that the agar chip-embedded helper embryo

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

    Directory of Open Access Journals (Sweden)

    Jingqun Ao

    2015-11-01

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

  6. Linkage of PRA models. Phase 1, Results

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-12-01

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

  7. Confirmatory linkage study of hypochondroplasia

    Energy Technology Data Exchange (ETDEWEB)

    Hecht, J.T.; Herrera, C.; Greenhaw, G.A. [Univ. of Texas Medical School, Houston, TX (United States)] [and others

    1994-09-01

    Hypochondroplasia is an autosomal dominant form of disproportionate short stature disorder that has clinical and radiographic findings similar to but milder than achondroplasia. Based on these findings it has been suggested that achondroplasia and hypochondroplasia are allelic conditions. We and others have mapped the achondroplasia locus to telomeric region of chromosome 4. Tested linkage to 4p markers in 6 hypochondroplasia families and a maximum LOD score of 1.7 at {theta} = 0 was found for IUDA. Here we report the results of a linkage study in 4 multigenerational families with hypochondroplasia using 7 short tandem repeat markers (D4S127, D4S412, D4S43, D4S115, IUDA, D4S227, D4S169) from the short arm of chromosome 4. These families have been well characterized and show the typical clinical and radiographic features of hypochondroplasia. One family was Afro-American, one Hispanic and two were Caucasian. We found a maximum multipoint LOD score of 2.9 at D4S115. The results of this study provide confirmatory evidence that achondroplasia and hypochondroplasia map to the same chromosomal location and suggests that they are indeed allelic conditions.

  8. Genome-wide linkage and association scans for pulse pressure in Chinese twins.

    Science.gov (United States)

    Zhang, Dongfeng; Pang, Zengchang; Li, Shuxia; Jiang, Wenjie; Wang, Shaojie; Thomassen, Mads; Hjelmborg, Jacob V B; Kruse, Torben A; Ohm Kyvik, Kirsten; Christensen, Kaare; Zhu, Gu; Tan, Qihua

    2012-11-01

    Elevated pulse pressure (PP) is associated with cardiovascular disorders and mortality in various populations. The genetic influence on PP has been confirmed by heritability estimates using related individuals. Recently, efforts have been made by mapping genes that are linked to the phenotype. We report the results of our gene mapping studies conducted in the Chinese population in mainland China. The genome-wide linkage and association scans were carried out on 63 middle-aged dizygotic twin pairs using high-density markers. The linkage analysis identified three significant linkage peaks (all with a single point Ppeaks closely overlapping with linkage peaks reported by two American studies. Multiple regions with suggestive linkages were identified, with many of the peaks overlapping with published linkage regions. The genome-wide association analysis detected a suggestive association on chromosome 4 (rs17031508, P<8.34e(-08)) located within a wide region of suggestive linkage. Our results provide some evidence for genetic linkages and associations with PP in the Chinese population. Further investigation is warranted to replicate the findings and to explore the susceptibility loci or genes for PP.

  9. A Genome Wide Linkage Search for Breast Cancer Susceptibility Genes

    Science.gov (United States)

    Smith, Paula; McGuffog, Lesley; Easton, Douglas F.; Mann, Graham J.; Pupo, Gulietta M.; Newman, Beth; Chenevix-Trench, Georgia; Szabo, Csilla; Southey, Melissa; Renard, Hélène; Odefrey, Fabrice; Lynch, Henry; Stoppa-Lyonnet, Dominique; Couch, Fergus; Hopper, John L.; Giles, Graham G.; McCredie, Margaret R. E.; Buys, Saundra; Andrulis, Irene; Senie, Ruby; Goldgar, David E.; Oldenburg, Rogier; Kroeze-Jansema, Karin; Kraan, Jaennelle; Meijers-Heijboer, Hanne; Klijn, Jan G. M.; van Asperen, Christi; van Leeuwen, Inge; Vasen, Hans F. A.; Cornelisse, Cees J.; Devilee, Peter; Baskcomb, Linda; Seal, Sheila; Barfoot, Rita; Mangion, Jon; Hall, Anita; Edkins, Sarah; Rapley, Elizabeth; Wooster, Richard; Chang-Claude, Jenny; Eccles, Diana; Evans, D. Gareth; Futreal, P. Andrew; Nathanson, Katherine L.; Weber, Barbara L.; Rahman, Nazneen; Stratton, Michael R.

    2009-01-01

    Mutations in known breast cancer susceptibility genes account for a minority of the familial aggregation of the disease. To search for further breast cancer susceptibility genes, we performed a combined analysis of four genome-wide linkage screens, which included a total of 149 multiple case breast cancer families. All families included at least three cases of breast cancer diagnosed below age 60 years, at least one of whom had been tested and found not to carry a BRCA1 or BRCA2 mutation. Evidence for linkage was assessed using parametric linkage analysis, assuming both a dominant and a recessive mode of inheritance, and using nonparametric methods. The highest LOD score obtained in any analysis of the combined data was 1.80 under the dominant model, in a region on chromosome 4 close to marker D4S392. Three further LOD scores over 1 were identified in the parametric analyses and two in the nonparametric analyses. A maximum LOD score of 2.40 was found on chromosome arm 2p in families with four or more cases of breast cancer diagnosed below age 50 years. The number of linkage peaks did not differ from the number expected by chance. These results suggest regions that may harbor novel breast cancer susceptibility genes. They also indicate that no single gene is likely to account for a large fraction of the familial aggregation of breast cancer that is not due to mutations in BRCA1 or BRCA2. PMID:16575876

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

    Directory of Open Access Journals (Sweden)

    Matthew C. Hale

    2017-11-01

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

  11. The Type and Impact of Evidence Review Group Exploratory Analyses in the NICE Single Technology Appraisal Process.

    Science.gov (United States)

    Carroll, Christopher; Kaltenthaler, Eva; Hill-McManus, Daniel; Scope, Alison; Holmes, Michael; Rice, Stephen; Rose, Micah; Tappenden, Paul; Woolacott, Nerys

    2017-06-01

    As part of the UK National Institute for Health and Care Excellence (NICE) single technology appraisal process, independent evidence review groups (ERGs) critically appraise a company's submission relating to a specific technology and indication. To explore the type of additional exploratory analyses conducted by ERGs and their impact on the recommendations made by NICE. The 100 most recently completed single technology appraisals with published guidance were selected for inclusion. A content analysis of relevant documents was undertaken to identify and extract relevant data, and narrative synthesis was used to rationalize and present these data. The types of exploratory analysis conducted in relation to companies' models were fixing errors, addressing violations, addressing matters of judgment, and the provision of a new, ERG-preferred base case. Ninety-three of the 100 ERG reports contained at least one of these analyses. The most frequently reported type of analysis in these 93 ERG reports related to the category "Matters of judgment," which was reported in 83 reports (89%). At least one of the exploratory analyses conducted and reported by an ERG is mentioned in 97% of NICE appraisal consultation documents and 94% of NICE final appraisal determinations, and had a clear influence on recommendations in 72% of appraisal consultation documents and 47% of final appraisal determinations. These results suggest that the additional analyses undertaken by ERGs in the appraisal of company submissions are highly influential in the policy-making and decision-making process. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  12. An introduction to recombination and linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mcpeek, M.S. [Univ. of Chicago, IL (United States)

    1996-12-31

    With a garden as his laboratory, Mendel was able to discern basic probabilistic laws of heredity. Although it first appeared as a baffling exception to one of Mendel`s principles, the phenomenon of variable linkage between characters was soon recognized to be a powerful tool in the process of chromosome mapping and location of genes of interest. In this introduction, we first describe Mendel`s work and the subsequent discovery of linkage. Next we describe the apparent cause of variable linkage, namely recombination, and we introduce linkage analysis. 33 refs., 1 fig., 2 tabs.

  13. Synthesis of deoxycytidine oligomers containing phosphorodithioate linkages

    DEFF Research Database (Denmark)

    Grandas, Ana; Marshall, William S.; Nielsen, John

    1989-01-01

    Deoxydicytidine phosphoramidite, 4-chlorobenzylmercaptan and tetrazole reacted to form dinucleoside thiophosphite. Oxidation with sulfur yields phosphorodithioates which were used to synthesize pentadecadeoxyoligonucleotides containing nuclease resistant phosphorodithioate internucleotide linkages....

  14. Challenges in administrative data linkage for research

    Directory of Open Access Journals (Sweden)

    Katie Harron

    2017-12-01

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

  15. Power of a Labrador Retriever-Greyhound pedigree for linkage analysis of hip dysplasia and osteoarthritis.

    Science.gov (United States)

    Todhunter, Rory J; Casella, George; Bliss, Stuart P; Lust, George; Williams, Alma Jo; Hamilton, Samuel; Dykes, Nathan L; Yeager, Amy E; Gilbert, Robert O; Burton-Wurster, Nancy I; Mellersh, Cathryn C; Acland, Gregory M

    2003-04-01

    To estimate the number of dogs required to find linkage to heritable traits of hip dysplasia in dogs from an experimental pedigree. 147 Labrador Retrievers, Greyhounds, and their crossbreed offspring. Labrador Retrievers with hip dysplasia were crossed with unaffected Greyhounds. Age at detection of femoral capital ossification, distraction index (DI), hip joint dorsolateral subluxation (DLS) score, and hip joint osteoarthritis (OA) were recorded. Power to find linkage of a single marker to a quantitative trait locus (QTL) controlling 100% of the variation in a dysplastic trait in the backcross dogs was determined. For the DI at the observed effect size, recombination fraction of 0.05, and heterozygosity of 0.75, 35 dogs in the backcross of the F1 to the Greyhound generation would yield linkage at a power of 0.8. For the DLS score, 35 dogs in the backcross to the Labrador Retriever generation would be required for linkage at the same power. For OSS, 45 dogs in the backcross to the founding Labrador Retrievers would yield linkage at the same power. Fewer dogs were projected to be necessary to find linkage to hip OA. Testing for linkage to the DLS at 4 loci simultaneously, each controlling 25% of the phenotypic variation, yielded an overall power of 0.7 CONCLUSIONS AND CLINICAL SIGNIFICANCE: Based on this conservative single-marker estimate, this pedigree has the requisite power to find microsatellites linked to susceptibility loci for hip dysplasia and hip OA by breeding a reasonable number of backcross dogs.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  17. Single case design studies in music therapy: resurrecting experimental evidence in small group and individual music therapy clinical settings.

    Science.gov (United States)

    Geist, Kamile; Hitchcock, John H

    2014-01-01

    The profession would benefit from greater and routine generation of causal evidence pertaining to the impact of music therapy interventions on client outcomes. One way to meet this goal is to revisit the use of Single Case Designs (SCDs) in clinical practice and research endeavors in music therapy. Given the appropriate setting and goals, this design can be accomplished with small sample sizes and it is often appropriate for studying music therapy interventions. In this article, we promote and discuss implementation of SCD studies in music therapy settings, review the meaning of internal study validity and by extension the notion of causality, and describe two of the most commonly used SCDs to demonstrate how they can help generate causal evidence to inform the field. In closing, we describe the need for replication and future meta-analysis of SCD studies completed in music therapy settings. SCD studies are both feasible and appropriate for use in music therapy clinical practice settings, particularly for testing effectiveness of interventions for individuals or small groups. © the American Music Therapy Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Is modified brief assertiveness training for nurses effective? A single-group study with long-term follow-up.

    Science.gov (United States)

    Yoshinaga, Naoki; Nakamura, Yohei; Tanoue, Hiroki; MacLiam, Fionnula; Aoishi, Keiko; Shiraishi, Yuko

    2018-01-01

    To evaluate the long-term effectiveness of modified brief assertiveness training (with cognitive techniques) for nurses. Most assertiveness training takes a long time to conduct; thus, briefer training is required for universal on-the-job training in the workplace. In this single-group study, nurses received two 90-min training sessions with a 1-month interval between sessions. The degree of assertiveness was assessed by using the Rathus Assertiveness Schedule as the primary outcome, at four time points: pre- and post-training, 3-month follow-up and 6-month follow-up. A total of 33 nurses received the training, and the mean Rathus Assertiveness Schedule score improved from -14.2 (SD = 16.5) pre-training to -10.5 (SD = 18.0) post-training (p training. Modified brief assertiveness training seems feasible and may achieve long-term favourable outcomes in improving assertiveness among nurses. The ease of implementation of assertiveness training is important because creating an open environment for communication leads to improved job satisfaction, improved nursing care and increased patient safety. © 2017 The Authors. Journal of Nursing Management Published by John Wiley & Sons Ltd.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  20. Ponatinib for Treating Chronic Myeloid Leukaemia: An Evidence Review Group Perspective of a NICE Single Technology Appraisal.

    Science.gov (United States)

    Pandor, Abdullah; Stevenson, Matt; Stevens, John; James, Marrissa Martyn-St; Hamilton, Jean; Byrne, Jenny; Rudin, Claudius; Rawdin, Andrew; Wong, Ruth

    2018-02-26

    As part of its single technology appraisal process, the National Institute for Health and Care Excellence (NICE) invited the company that manufactures ponatinib (Inclusig ® ; Incyte Corporation) to submit evidence for the clinical and cost effectiveness for previously treated chronic myeloid leukaemia (CML) and Philadelphia-chromosome-positive acute lymphoblastic leukaemia (Ph+ ALL). This paper focusses on the three phases of CML: the chronic phase (CP), the accelerated phase (AP) and the blast crisis phase (BP). The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG). This article presents the critical review of the company's submission by the ERG and the outcome of the NICE guidance. Clinical evidence for ponatinib was derived from a phase II, industry-sponsored, single-arm, open-label, multicentre, non-comparative study. Despite the limited evidence and potential for biases, this study demonstrated that ponatinib was likely to be an effective treatment (in terms of major cytogenetic response and major haematological response) with an acceptable safety profile for patients with CML. Given the absence of any head-to-head studies comparing ponatinib with other relevant comparators, the company undertook a matching-adjusted indirect comparison (MAIC) of ponatinib with bosutinib. The approach was only used for patients with CP-CML because comprehensive data were not available for the AP- or BP-CML groups to allow the matching technique to be used. Despite the uncertainty about the MAIC approach, ponatinib was considered likely to offer advantages over bosutinib in the third-line setting, particularly for complete cytogenetic response. The company developed two health economic models to assess the cost effectiveness of ponatinib for the treatment of patients in CP-CML or in advanced CML (AP- or BP-CML, which were modelled separately). The company did

  1. A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.).

    Science.gov (United States)

    Zhong, Yu-Juan; Zhou, Yang-Yang; Li, Jun-Xing; Yu, Ting; Wu, Ting-Quan; Luo, Jian-Ning; Luo, Shao-Bo; Huang, He-Xun

    2017-10-06

    Pumpkin (Cucurbita moschata) is an economically worldwide crop. Few quantitative trait loci (QTLs) were reported previously due to the lack of genomic and genetic resources. In this study, a high-density linkage map of C. moschata was structured by double-digest restriction site-associated DNA sequencing, using 200 F2 individuals of CMO-1 × CMO-97. By filtering 74,899 SNPs, a total of 3,470 high quality SNP markers were assigned to the map spanning a total genetic distance of 3087.03 cM on 20 linkage groups (LGs) with an average genetic distance of 0.89 cM. Based on this map, both pericarp color and strip were fined mapped to a novel single locus on LG8 in the same region of 0.31 cM with phenotypic variance explained (PVE) of 93.6% and 90.2%, respectively. QTL analysis was also performed on carotenoids, sugars, tuberculate fruit, fruit diameter, thickness and chamber width with a total of 12 traits. 29 QTLs distributed in 9 LGs were detected with PVE from 9.6% to 28.6%. It was the first high-density linkage SNP map for C. moschata which was proved to be a valuable tool for gene or QTL mapping. This information will serve as significant basis for map-based gene cloning, draft genome assembling and molecular breeding.

  2. Building linkages and bargaining power between smallholder ...

    African Journals Online (AJOL)

    Mo

    This paper emphasizes the importance of facilitating the process of linkages between smallholder farmers and service providers as ... have used the same principles to form linkages with fertiliser suppliers to access other inputs such as manures, ... however, be used for other innovation systems in community development.

  3. Linkage activities amongst researchers, extension agents, farmers ...

    African Journals Online (AJOL)

    This paper examined the research- extension- farmer- input dealer and marketer linkage activities in the North West Province of South Africa. A simple random sampling technique was used to select researchers, extension agents, farmers, agricultural input dealers and marketers. Their responses in linkage activities were ...

  4. Correlation between disruptive behaviors and school grouping (single-sex vs. coeducational) in students from Callao, Peru

    OpenAIRE

    Gordillo, Enrique G.

    2013-01-01

    Debate on single-sex vs. coeducational schooling has increased over the last years. The purpose of the following study is to produce empirical evidence on this debate by comparing the frequency of disruptive behaviors in students thatattend single-sex and coeducational schools, in order to find statistical correlation.The frequency of disruptive behaviors in students coming from 5 single-sex schools was compared to that coming from 5 coeducational ones. Data came from 844 students aged 14, at...

  5. Hybrid scaffold bearing polymer-siloxane Schiff base linkage for bone tissue engineering.

    Science.gov (United States)

    Nair, Bindu P; Gangadharan, Dhanya; Mohan, Neethu; Sumathi, Babitha; Nair, Prabha D

    2015-01-01

    Scaffolds that can provide the requisite biological cues for the fast regeneration of bone are highly relevant to the advances in tissue engineering and regenerative medicine. In the present article, we report the fabrication of a chitosan-gelatin-siloxane scaffold bearing interpolymer-siloxane Schiff base linkage, through a single-step dialdehyde cross-linking and freeze-drying method using 3-aminopropyltriethoxysilane as the siloxane precursor. Swelling of the scaffolds in phosphate buffered saline indicates enhancement with increase in siloxane concentration, whereas compressive moduli of the wet scaffolds reveal inverse dependence, owing to the presence of siloxane, rich in silanol groups. It is suggested that through the strategy of dialdehyde cross-linking, a limiting siloxane loading of 20 wt.% into a chitosan -gelatin matrix should be considered ideal for bone tissue engineering, because the scaffold made with 30 wt.% siloxane loading degrades by 48 wt.%, in 21 days. The hybrid scaffolds bearing Schiff base linkage between the polymer and siloxane, unlike the stable linkages in earlier reports, are expected to give a faster release of siloxanes and enhancement in osteogenesis. This is verified by the in vitro evaluation of the hybrid scaffolds using rabbit adipose mesenchymal stem cells, which revealed osteogenic cell-clusters on a polymer-siloxane scaffold, enhanced alkaline phosphatase activity and the expression of bone-specific genes, whereas the control scaffold without siloxane supported more of cell-proliferation than differentiation. A siloxane concentration dependent enhancement in osteogenic differentiation is also observed. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Degarelix for Treating Advanced Hormone-Dependent Prostate Cancer: An Evidence Review Group Perspective of a NICE Single Technology Appraisal.

    Science.gov (United States)

    Uttley, Lesley; Whyte, Sophie; Gomersall, Timothy; Ren, Shijie; Wong, Ruth; Chambers, Duncan; Tappenden, Paul

    2017-07-01

    As part of its Single Technology Appraisal Process, the National Institute for Health and Care Excellence (NICE) invited the manufacturer of degarelix (Ferring Pharmaceuticals) to submit evidence for the clinical and cost effectiveness of degarelix for the treatment of advanced hormone-dependent prostate cancer. The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG). The ERG produced a critical review of the evidence contained within the company's submission to NICE. The evidence, which included a randomised controlled trial (RCT) of degarelix versus leuprorelin, found that degarelix was non-inferior to leuprorelin for reduction of testosterone levels and that degarelix achieved a more rapid suppression of prostate-specific antigen levels and subsequently decreased incidences of testosterone flare associated with luteinising hormone releasing-hormone (LHRH) agonists. However, protection against testosterone flare for the comparators in the clinical trials was not employed in line with UK clinical practice. Further claims surrounding overall survival, cardiovascular adverse events and clinical equivalence of the comparator drugs from six RCTs of degarelix should be regarded with caution because of flaws and inconsistencies in the pooling of trial data to draw conclusions. The cost-effectiveness evidence included a de novo economic model. Based on the ERG's preferred base case, the deterministic incremental cost-effectiveness analysis (ICER) for degarelix versus 3-monthly triptorelin was £14,798 per quality-adjusted life-year (QALY) gained. Additional scenario analyses undertaken by the ERG resulted in ICERs for degarelix versus 3-monthly triptorelin ranging from £17,067 to £35,589 per QALY gained. Subgroup analyses undertaken using the Appraisal Committee's preferred assumptions suggested that degarelix was not cost effective for the subgroup with

  7. 41 CFR 301-71.102 - May we issue a single authorization for a group of employees?

    Science.gov (United States)

    2010-07-01

    ... Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES AGENCY RESPONSIBILITIES 71-AGENCY TRAVEL ACCOUNTABILITY REQUIREMENTS Travel Authorization § 301-71.102 May we issue a single authorization... are traveling together on a single trip. However, you must attach a list of all travelers to the...

  8. Construction of a Genetic Linkage Map and QTL Analysis of Fruit-related Traits in an F1 Red Fuji x Hongrou Apple Hybrid

    Directory of Open Access Journals (Sweden)

    Liu Zunchun

    2016-01-01

    Full Text Available A genetic linkage map of the apple, composed of 175 SSR and 105 SRAP markers, has been constructed using 110 F1 individuals obtained from a cross between the ‘Red Fuji’ Malus domestica and ‘Hongrou’ Malus sieversii cultivars, which have relatively high levels of DNA marker polymorphism and differ remarkably in fruit-related traits. The linkage map comprised 17 linkage groups, covering 1299.67 cM with an average marker distance of 4.6 cM between adjacent markers, or approximately 91% of Malus genome. Linkage groups were well populated and, although marker density ranged from 2.1 to 9.5 cM, just 10 gaps of more than 15 cM were observed. Moreover, just 12.5% of markers displayed segregation distortion. The present genetic linkage map was used to identify quantitative trait loci (QTLs affecting fruit-related traits. 23 QTLs for ten fruit traits were detected by multiple interval mapping: 3 QTLs for Vc content, One QTL for single fruit weight, 2 QTLs for peel-phenols content, 2 QTLs for flesh-hardness, 2 QTLs for diameter, 6 QTLs for acid content, 1 QTL for sugar content, 2 QTLs for soluble solids content, 2 QTLs for flesh-phenols and 2 QTLs for brittleness. These QTLs were located on linkage groups C1, C2, C3, C5, C6, C7, C9, C10, C14 and C17, respectively. The phenotypic variations exhibited by each QTL ranged from 2% to 72%, and their LOD values varied from 2.03 to 8.93, of which five QTLs were major effect genes (R2 ≥ 10%. The tight linkage markers (*me2em7-460f, *MS01a03-180m, *me1em6-307m, *CH05c06-102f, *me1em8-423f would be helpful to elucidate the molecular mechanisms of apple domestication and breeding in the future.

  9. Construction of a genetic linkage map and QTL analysis in bambara groundnut.

    Science.gov (United States)

    Ahmad, Nariman Salih; Redjeki, Endah Sri; Ho, Wai Kuan; Aliyu, Siise; Mayes, Katie; Massawe, Festo; Kilian, Andrzej; Mayes, Sean

    2016-07-01

    Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a "narrow" cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes.

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

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

    Linkage for Education and Research in Nursing (LEARN), une initiative de TIC-D dans les Caraïbes. Les infirmières représentent le plus important groupe de professionnels de la santé pouvant influer sur la qualité des soins dans les services de santé. Les efforts pour ... Barbados Community College. Pays d' institution.

  11. INDONESIAN COUNTRY PAPER MECHANISMS USED TO STRENGTHEN INFORMATION LINKAGES

    Directory of Open Access Journals (Sweden)

    Achmad Djuhamsa

    2011-12-01

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

  12. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Sraphet, Supajit; Boonchanawiwat, Athipong; Thanyasiriwat, Thanwanit; Boonseng, Opas; Tabata, Satoshi; Sasamoto, Shigemi; Shirasawa, Kenta; Isobe, Sachiko; Lightfoot, David A; Tangphatsornruang, Sithichoke; Triwitayakorn, Kanokporn

    2011-04-01

    Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.

  13. Linkage experiment at Mt. Chacaltaya

    International Nuclear Information System (INIS)

    Honda, Ken

    1983-01-01

    At Mt. Chakaltaya, AS-EC linkage experiments have been made to study the hadrons and the high energy gamma-ray at the center of air showers. Thirty-five particle detectors for air showers were distributed in an area of radius 50 m. At the center, X-ray films were inserted at intervals of 2 c.u. in lead stack. Under this detector, there was a burst detector. The correspondence of the data of an emulsion chamber (EC) and those of an air shower was determined. The correspondence of high energy events was found easily, but it became hard in case of the events with energy less than 10 TeV. The age distribution of burst data was obtained. The air showers with large burst size had, on an average, young age. The lateral distribution of burst size was obtained. The results suggested that the age was an important parameter of the development of air showers. In the case of large burst size, the energy was large. (Kato, T.)

  14. Correlation between disruptive behaviors and school grouping (single-sex vs. coeducational in students from Callao, Peru

    Directory of Open Access Journals (Sweden)

    Enrique G. Gordillo

    2013-10-01

    Full Text Available Debate on single-sex vs. coeducational schooling has increased over the last years. The purpose of the following study is to produce empirical evidence on this debate by comparing the frequency of disruptive behaviors in students thatattend single-sex and coeducational schools, in order to find statistical correlation.The frequency of disruptive behaviors in students coming from 5 single-sex schools was compared to that coming from 5 coeducational ones. Data came from 844 students aged 14, attending public schools in Callao, Peru. Students from single-sex schools showed less frequent disruptive behavior in each of the three measured categories—disruptive behaviors, behaviors that show lack of responsibility and anti-social behavior. A weak correlation was found between each of the three categories and the main variable. The study controlled for extraneous variables.

  15. A single-group pilot feasibility study of cognitive behavioural therapy in people with multiple sclerosis with depressive symptoms.

    Science.gov (United States)

    Chruzander, Charlotte; Gottberg, Kristina; Ytterberg, Charlotte; Backenroth, Gunnel; Fredrikson, Sten; Widén Holmqvist, Lotta; Johansson, Sverker

    2016-12-01

    The aims were to evaluate (a) the feasibility of face-to-face cognitive behavioural therapy (CBT) in people with MS (PwMS) with depressive symptoms; (b) the feasibility of methods and measurements used; and (c) the outcome of the intervention before the conducting of an equivalence study of comparative methods of face-to-face CBT. A single-group pilot feasibility study. PwMS (n = 15) with sub-threshold to moderate depressive symptoms, recruited at the Karolinska University Hospital, Stockholm, Sweden. The intervention consisted of 15-20 sessions of face-to-face CBT. Feasibility outcomes included recruitment rate, recruitment procedure and adverse events. Primary clinical outcome was the Beck Depression Inventory-II (BDI-II). Follow-ups were conducted after 3 weeks and 3 months. An estimated sample size calculation was conducted. The face-to-face CBT intervention, methods and measurements used were feasible. The outcome on BDI-II indicated that face-to-face CBT is an effective method for alleviating sub-threshold to moderate depressive symptoms in PwMS. Face-to-face CBT is feasible for use in PwMS aiming at decrease depressive symptoms. For an equivalence study, a screening process for depressive symptoms and two comparative intervention arms including traditional face-to-face CBT and low-intensity face-to-face CBT is recommended. Primary outcomes should include the BDI-II and also assessment of anxiety symptoms. Implications for Rehabilitation Depression is common among people with MS (PwMS), however, depressed PwMS do not always receive adequate treatment for depression which may lead to increased disability and worse health-related quality of life (HRQL). Cognitive behavioural therapy (CBT) is a psychological treatment method that might be beneficial for PwMS with depressive symptoms, but the evidence is still weak and further research is needed. The results from our pilot feasibility study demonstrate that for an effectiveness study of face-to-face CBT for

  16. Cervical myelopathy due to single level prolapsed disc and spondylosis: a comparative study on outcome between two groups

    Science.gov (United States)

    Ryu, Jong-Seon; Chae, Jong-Woo; Cho, Woo-Jin; Chang, Han; Kim, Sung-Soo

    2010-01-01

    This article describes a retrospective study on myelopathy, induced by monosegmental prolapsed disc and spondylosis. To assess pre- and postoperative clinical and radiological findings related to myelopathy, and factors influencing the outcome, 20 disc herniation (group A) and 11 spondylosis patients (group B) were studied. Average duration of myelopathy in groups A and B were 3 and 8.7 months, respectively. Anterior decompression and fusion were performed. Pre- and postoperative clinical and radiological findings and outcomes were assessed. Average preoperative disc heights were 85.9% of normal in group A and 72.7% in group B. Average anteroposterior canal diameter and Pavlov ratio at diseased level were 13.9 mm and 0.81 in group A, respectively, and 12.1 mm and 0.78 in group B. Five group A (25.0%) and four group B cases (36.4%) had radiculopathy. Cord compressions among 20 group A patients were median in seven and paramedian in 13. In the 11 group B patients, nine were median and two were paramedian. High signal intensity was observed in 19 group A and ten group B patients. Postoperative regression of T2-weighted high signal intensity in 14 group A (73.7%) and two group B patients (20.0%) was observed. Preoperative JOA scores in groups A and B were 10.3 and 12.8, respectively, which became 66.2 and 22.5 postoperatively. Neurological recovery was poorer in group B than in group A. Outcome was influenced by chronicity of myelopathy. PMID:20108087

  17. Safety and pharmacokinetics of single and multiple intravenous bolus doses of diclofenac sodium compared with oral diclofenac potassium 50 mg: A randomized, parallel-group, single-center study in healthy subjects.

    Science.gov (United States)

    Munjal, Sagar; Gautam, Anirudh; Okumu, Franklin; McDowell, James; Allenby, Kent

    2016-01-01

    In a randomized, parallel-group, single-center study in 42 healthy adults, the safety and pharmacokinetic parameters of an intravenous formulation of 18.75 and 37.5 mg diclofenac sodium (DFP-08) following single- and multiple-dose bolus administration were compared with diclofenac potassium 50 mg oral tablets. Mean AUC0-inf values for a 50-mg oral tablet and an 18.75-mg intravenous formulation were similar (1308.9 [393.0]) vs 1232.4 [147.6]). As measured by the AUC, DFP-08 18.75 mg and 37.5 mg demonstrated dose proportionality for extent of exposure. One subject in each of the placebo and DFP-08 18.75-mg groups and 2 subjects in the DFP-08 37.5-mg group reported adverse events that were considered by the investigator to be related to the study drug. All were mild in intensity and did not require treatment. Two subjects in the placebo group and 1 subject in the DFP-08 18.75-mg group reported grade 1 thrombophlebitis; no subjects reported higher than grade 1 thrombophlebitis after receiving a single intravenous dose. The 18.75- and 37.5-mg doses of intravenous diclofenac (single and multiple) were well tolerated for 7 days. Additional efficacy and safety studies are required to fully characterize the product. © 2015, The American College of Clinical Pharmacology.

  18. The effect of genotyping error in sib-pair genomewide linkage scans depends crucially upon the method of analysis.

    Science.gov (United States)

    Walters, Kevin

    2005-01-01

    In genomewide linkage scans for complex diseases involving many loci with small genetic effects, it may be the case that no loci reach conventional statistical significance. A complementary method of evaluating linkage results, locus counting, may provide evidence for the existence of a number of genetic loci in these cases. Sib-pair study designs are often used in genomewide linkage scans, but because all genotype configurations are consistent with Mendelian inheritance, genotyping error will go largely undetected. Previous work on the effect of genotyping error has focused on a single disease locus. We considered the effect of two levels of genotyping error on genomewide evidence for linkage by using the simulated GAW 13 data. For affected sib-pair and non-parametric quantitative trait study designs, a 0.5% genotyping error rate reduced the number of independent linkage regions towards that expected under the null hypothesis of no linkage. A 2% genotyping error rate yielded less independent linkage regions than expected under the null hypothesis of no linkage. For a quantitative trait analysed using a parametric regression-based method, there was very little erosion of the linkage signal, even for error rates as high as 2%.

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

    Science.gov (United States)

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

    2017-12-01

    We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.

  20. Evolutionary Conservation of Equine Gc Alleles and of Mammalian Gc/Albumin Linkage

    Science.gov (United States)

    Weitkamp, Lowell R.; Allen, Peter Z.

    1979-01-01

    Ancient origin of the equine vitamin D binding protein (Gc) polymorphism is suggested by the finding of two alleles, GcF and GcS, in each of three equine subgenera, Equus, Asinus and Hippotigris. The equine Gc and albumin loci are closely linked (lod score = 6). Although no recombinants were observed, the data are not inconsistent with a map distance similar to the 2 centimorgans reported for the human albumin/Gc linkage relationship. Gametic association between the GcF and AlbF alleles appears probable in the American Standardbred horse, perhaps as a result of population structure. Since Gc and albumin are both polymorphic in rodents and possibly other orders, this linkage group will be useful for studies of the evolution of mammalian linkage groups, as well as for a comparison of meiotic recombination frequencies and linkage disequilibria in different species. PMID:17248956

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

    Directory of Open Access Journals (Sweden)

    Lance Stacey L

    2009-07-01

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

  2. Resource linkages and sustainable development

    Science.gov (United States)

    Anouti, Yahya

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

  3. Accommodating chromosome inversions in linkage analysis.

    Science.gov (United States)

    Chen, Gary K; Slaten, Erin; Ophoff, Roel A; Lange, Kenneth

    2006-08-01

    This work develops a population-genetics model for polymorphic chromosome inversions. The model precisely describes how an inversion changes the nature of and approach to linkage equilibrium. The work also describes algorithms and software for allele-frequency estimation and linkage analysis in the presence of an inversion. The linkage algorithms implemented in the software package Mendel estimate recombination parameters and calculate the posterior probability that each pedigree member carries the inversion. Application of Mendel to eight Centre d'Etude du Polymorphisme Humain pedigrees in a region containing a common inversion on 8p23 illustrates its potential for providing more-precise estimates of the location of an unmapped marker or trait gene. Our expanded cytogenetic analysis of these families further identifies inversion carriers and increases the evidence of linkage.

  4. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

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

  5. Multiobjective optimization of a steering linkage

    International Nuclear Information System (INIS)

    Sleesonsom, S.; Bureerat, S.

    2016-01-01

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

  6. Multiobjective optimization of a steering linkage

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-08-15

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

  7. Confirmatory linkage of hypochondroplasia to chromosome arm 4p

    Energy Technology Data Exchange (ETDEWEB)

    Hectht, J.T.; Herrera, C.A.; Greenhaw, G.A. [Univ. of Texas Medical School, Houston, TX (United States)] [and others

    1995-07-03

    Hypochondroplasia is an inherited chondrodystrophy that is characterized by disproportionate short stature. A recent linkage study by LeMerrer et al. suggested that hypochondroplasia and achondroplasia are allelic conditions. Three groups have now mapped the achondroplasia locus to the telomeric region of chromosome 4. Recently, two mutations in fibroblast growth factor receptor 3 (FGFR3) at nucleotide 1138, in the transmembrane domain, were identified in 169 of 170 unrelated individuals with achondroplasia. Here, we report the results of a linkage study in 4 multigenerational families with hypochondroplasia and mutational analysis of nucleotide 1138 in one individual from each of these families, two nonfamilial hypochondroplasia individuals and sequencing of the transmembrane domain of the FGFR3 in three affected unrelated individuals. 13 refs., 1 tab.

  8. A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica.

    Science.gov (United States)

    Bushakra, Jill M; Bryant, Douglas W; Dossett, Michael; Vining, Kelly J; VanBuren, Robert; Gilmore, Barbara S; Lee, Jungmin; Mockler, Todd C; Finn, Chad E; Bassil, Nahla V

    2015-08-01

    We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.

  9. The Sort on Radioactive Waste Type model: A method to sort single-shell tanks into characteristic groups. Revision 2

    Energy Technology Data Exchange (ETDEWEB)

    Hill, J.G.; Anderson, G.S. [Pacific Northwest Lab., Richland, WA (United States); Simpson, B.C. [Westinghouse Hanford Co., Richland, WA (United States)

    1995-03-01

    The SORWT model presents a methodology to group SSTs that is both simple to understand and logical in its assumptions and construction. The SORWT model has predicted the existence of 24 groups of SSTs ranging from 22 tanks per group to two tanks per group. These 24 groups encompass 133 tanks and 93% of the total waste contained in SSTs. The first 14 groups (i.e., those that contain four tanks per group or more) represent 109 tanks and 83% of the total waste volume. This demonstrates the potential for using the SORWT model to efficiently allocate resources and to maximize characterization information gained by a minimum number of sampling events. The verification study has shown that the SST groups predicted by the SORWT model are statistically significant and reduce the variability in the concentrations for all analytes examined. The SORWT model organizes a vast amount of information and presents clear options on which SSTs are more desirable to sample. The model is also simple and flexible in its ability to incorporate new parameters such as new SST analytical data, shifting programmatic needs, and/or risk assessment-oriented criteria. This report presents the nominal composition, inventory, and uncertainty for five of the 24 SORWT groups, representing 28 tanks, 10% of the total waste volume, and 29% of the total sludge volume in SSTs. Consequently, this document provides a logical beginning framework for tank waste characterization until further information becomes available or different programmatic needs are identified.

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

    Science.gov (United States)

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

    2013-11-01

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

  11. Evaluating EIV, OLS, and SEM Estimators of Group Slope Differences in the Presence of Measurement Error: The Single-Indicator Case

    Science.gov (United States)

    Culpepper, Steven Andrew

    2012-01-01

    Measurement error significantly biases interaction effects and distorts researchers' inferences regarding interactive hypotheses. This article focuses on the single-indicator case and shows how to accurately estimate group slope differences by disattenuating interaction effects with errors-in-variables (EIV) regression. New analytic findings were…

  12. Fault linkage and continental breakup

    Science.gov (United States)

    Cresswell, Derren; Lymer, Gaël; Reston, Tim; Stevenson, Carl; Bull, Jonathan; Sawyer, Dale; Morgan, Julia

    2017-04-01

    The magma-poor rifted margin off the west coast of Galicia (NW Spain) has provided some of the key observations in the development of models describing the final stages of rifting and continental breakup. In 2013, we collected a 68 x 20 km 3D seismic survey across the Galicia margin, NE Atlantic. Processing through to 3D Pre-stack Time Migration (12.5 m bin-size) and 3D depth conversion reveals the key structures, including an underlying detachment fault (the S detachment), and the intra-block and inter-block faults. These data reveal multiple phases of faulting, which overlap spatially and temporally, have thinned the crust to between zero and a few km thickness, producing 'basement windows' where crustal basement has been completely pulled apart and sediments lie directly on the mantle. Two approximately N-S trending fault systems are observed: 1) a margin proximal system of two linked faults that are the upward extension (breakaway faults) of the S; in the south they form one surface that splays northward to form two faults with an intervening fault block. These faults were thus demonstrably active at one time rather than sequentially. 2) An oceanward relay structure that shows clear along strike linkage. Faults within the relay trend NE-SW and heavily dissect the basement. The main block bounding faults can be traced from the S detachment through the basement into, and heavily deforming, the syn-rift sediments where they die out, suggesting that the faults propagated up from the S detachment surface. Analysis of the fault heaves and associated maps at different structural levels show complementary fault systems. The pattern of faulting suggests a variation in main tectonic transport direction moving oceanward. This might be interpreted as a temporal change during sequential faulting, however the transfer of extension between faults and the lateral variability of fault blocks suggests that many of the faults across the 3D volume were active at least in part

  13. Vulvar field resection based on ontogenetic cancer field theory for surgical treatment of vulvar carcinoma: a single-centre, single-group, prospective trial.

    Science.gov (United States)

    Höckel, Michael; Trott, Sophia; Dornhöfer, Nadja; Horn, Lars-Christian; Hentschel, Bettina; Wolf, Benjamin

    2018-03-09

    The incidence of vulvar cancer is increasing, but surgical treatment-the current standard of care-often leads to unsatisfactory outcomes, especially in patients with node-positive disease. Preliminary results at our centre showed that locoregional spread of vulvar carcinoma occurs within tissue domains defined by stepwise embryonic and fetal development (ontogenetic cancer fields and associated lymph node regions). We propose that clinical translation of these insights into practice could improve outcomes of surgical treatment of vulvar cancer. We did a single-centre prospective trial at the University of Leipzig's Cancer Center. Eligible patients were aged 18 years or older, had ontogenetic stage 1-3b histologically proven primary carcinoma of the vulva, and had not undergone previous surgical or radiotherapy treatment for vulvar cancer or any other major perineal or pelvic disease. In view of staged morphogenesis of the vulva from the cloacal membrane endoderm at Carnegie stage 11 to adulthood, we defined the tissue domains of tumour spread according to the theory of ontogenetic cancer fields. On the basis of ontogenetic staging, patients were treated locally with partial, total, or extended vulvar field resection; regionally with therapeutic inguinopelvic lymph node dissection; and anatomical reconstruction without adjuvant radiotherapy. The primary endpoints were recurrence-free survival, disease-specific survival, and early postoperative complications. Analysis of tumour spread and early postoperative surgical complications was done by intention to treat (ie, all patients were included), whereas outcome analyses were done per protocol. This ongoing trial is registered with the German Clinical Trials Register, number DRKS00013358. Between March 1, 2009, and June 8, 2017, 97 consecutive patients were included in the study, of whom 94 were treated per protocol with vulvar field resection, therapeutic inguinopelvic lymph node dissection, and anatomical

  14. A dense genetic linkage map for common carp and its integration with a BAC-based physical map.

    Directory of Open Access Journals (Sweden)

    Lan Zhao

    Full Text Available BACKGROUND: Common carp (Cyprinus carpio is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. RESULTS: The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. CONCLUSION: We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for

  15. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group

    OpenAIRE

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Mal...

  16. Comparing linkage designs based on land facets to linkage designs based on focal species.

    Science.gov (United States)

    Brost, Brian M; Beier, Paul

    2012-01-01

    Least-cost modeling for focal species is the most widely used method for designing conservation corridors and linkages. However, these designs depend on today's land covers, which will be altered by climate change. We recently proposed an alternative approach based on land facets (recurring landscape units of relatively uniform topography and soils). The rationale is that corridors with high continuity of individual land facets will facilitate movement of species associated with each facet today and in the future. Conservation practitioners might like to know whether a linkage design based on land facets is likely to provide continuity of modeled breeding habitat for species needing connectivity today, and whether a linkage for focal species provides continuity and interspersion of land facets. To address these questions, we compared linkages designed for focal species and land facets in three landscapes in Arizona, USA. We used two variables to measure linkage utility, namely distances between patches of modeled breeding habitat for 5-16 focal species in each linkage, and resistance profiles for focal species and land facets between patches connected by the linkage. Compared to focal species designs, linkage designs based on land facets provided as much or more modeled habitat connectivity for 25 of 28 species-landscape combinations, failing only for the three species with the most narrowly distributed habitat. Compared to land facets designs, focal species linkages provided lower connectivity for about half the land facets in two landscapes. In areas where a focal species approach to linkage design is not possible, our results suggest that conservation practitioners may be able to implement a land facets approach with some confidence that the linkage design would serve most potential focal species. In areas where focal species designs are possible, we recommend using the land facet approach to complement, rather than replace, focal species approaches.

  17. Ants farm subterranean aphids mostly in single clone groups : An example of prudent husbandry for carbohydrates and proteins?

    NARCIS (Netherlands)

    Ivens, Aniek B. F.; Kronauer, Daniel J. C.; Pen, Ido; Weissing, Franz J.; Boomsma, Jacobus J.

    2012-01-01

    Background: Mutualistic interactions are wide-spread but the mechanisms underlying their evolutionary stability and ecological dynamics remain poorly understood. Cultivation mutualisms in which hosts consume symbionts occur in phylogenetically diverse groups, but often have symbiont monocultures for

  18. Photoinduced nuclear spin conversion of methyl groups of single molecules; Photoinduzierte Kernspinkonversion von Methylgruppen an einzelnen Molekuelen. Lochbrenn- und Einzelmolekuelspektroskopie an Terrylen und Methylderivaten

    Energy Technology Data Exchange (ETDEWEB)

    Sigl, A.

    2007-12-28

    A methyl group is an outstanding quantum system due to its special symmetry properties. The threefold rotation around one of its bond is isomorphic to the group of even permutations of the remaining protons, a property which imposes severe quantum restrictions on the system, for instance a strict correlation of rotational states with nuclear spin states. The resulting long lifetimes of the rotational tunneling states of the methyl group can be exploited for applying certain high resolution optical techniques, like hole burning or single molecule spectroscopy to optically switch the methyl group from one tunneling state to another therebye changing the nuclear spin of the protons. One goal of the thesis was to perform this switching in single methyl groups. To this end the methyl group was attached to a chromophoric system, in the present case terrylene, which is well suited for single molecule spectroscopy as well as for hole burning. Experiments were performed with the bare terrylene molecule in a hexadecane lattice which served as a reference system, with alphamethyl terrylene and betamethyl terrylene, both embedded in hexadecane, too. A single molecular probe is a highly sensitive detector for dynamic lattice instabilities. Already the bare terrylene probe showed a wealth of interesting local dynamic effects of the hexadecane lattice which could be well acounted for by the assumption of two nearly degenerate sites with rather different optical and thermal properties, all of which could be determined in a quantitative fashion. As to the methylated terrylene systems, the experiments verified that for betamethyl terrylene it is indeed possible to measure rotational tunneling events in single methyl groups. However, the spectral patterns obtained was much more complicated than expected pointing to the presence of three spectroscopically different methyl groups. In order to achieve a definite assignement, molecular mechanics simulations of the terrylene probes in the

  19. Group vs. single mindfulness meditation: exploring avoidance, impulsivity, and weight management in two separate mindfulness meditation settings.

    Science.gov (United States)

    Mantzios, Michail; Giannou, Kyriaki

    2014-07-01

    Recent research has identified that mindfulness meditation in group settings supports people who are trying to lose weight. The present research investigated mindfulness meditation in group and individual settings, and explored the potential impact on weight loss and other factors (i.e. mindfulness, impulsivity, and avoidance) that may assist or hinder weight loss. Specifically, the hypotheses tested were that the group setting assisted dieters more than the individual setting by reducing weight, cognitive-behavioral avoidance, and impulsivity and by increasing mindfulness. Participants (n = 170) who were trying to lose weight were randomly assigned to practice meditation for 6 weeks within a group or independently. Measurements in mindfulness, cognitive-behavioral avoidance, impulsivity, and weight occurred twice (pre- and post-intervention). Results indicated that participants in the group setting lost weight and lowered their levels of cognitive-behavioral avoidance, while impulsivity and mindfulness remained stable. On the other hand, participants in the individual condition lost less weight, while there was an increase in cognitive-behavioral avoidance and mindfulness scores, but a decrease in impulsivity. Seeing that benefits and limitations observed in group settings are not replicated when people meditate alone, this study concluded that mindfulness meditation in individual settings needs to be used with caution, although there are some potential benefits that could aid future weight loss research. © 2014 The International Association of Applied Psychology.

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

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

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

  1. Spectroscopic Investigation of Lignin Linkages: UV and IR Signatures of Primary Dilignols

    Science.gov (United States)

    Dean, Jacob C.; Walsh, Patrick S.; Gord, Joseph R.; Biswas, Bidyut; Ramachandran, P. V.; Zwier, Timothy S.

    2012-06-01

    Lignin is an abundant, aromatic biopolymer ubiquitous to all plant matter; its properties are vital to the structural rigidity of plants as well as protection of the cell wall from degradation. As the major structural framework for plants, the breakdown of lignin for harvestable biomass is a formidable challenge. At a fundamental level, the characterization of lignin sequences and structures lag far behind those of proteins. One of the unique aspects of lignin is that it is composed of only three monolignols which are themselves structurally similar, all of which are aromatic derivatives. The structural complexity of lignin is in large measure due to the unique variety of chemical linkages between these three sub-units. As a result, there is a need for spectroscopic characterization of individual lignin linkages, and for elucidating potential fragmentation pathways and the relative energetics associated with those linkages in the polymer network. In this light, spectroscopic interrogation of these dilignol bichromophores yield signatures characteristic of their specific linkages which can also be found in high-order lignin oligomers. The β-O-4 and β-β linkages have been studied and their UV and IR signatures have been uncovered on a single-conformation basis in a supersonic expansion by use of IR/UV-UV HB and RIDIR spectroscopy. Fragmentation following resonant two-photon ionization of the neutral species was also explored and evidence for linkage-specific fragmentation has been revealed.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  3. A genome wide linkage scan for dizygotic twinning in 525 families of mothers of dizygotic twins.

    Science.gov (United States)

    Painter, Jodie N; Willemsen, Gonneke; Nyholt, Dale; Hoekstra, Chantal; Duffy, David L; Henders, Anjali K; Wallace, Leanne; Healey, Sue; Cannon-Albright, Lisa A; Skolnick, Mark; Martin, Nicholas G; Boomsma, Dorret I; Montgomery, Grant W

    2010-06-01

    The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning, we conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism marker panels. Non-parametric linkage analyses, including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL), produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential logarithm of odds [(exp)LOD] score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (P = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5' untranslated region of FSHR that segregated with the DZ twinning phenotype in the Utah family. Our data provide further evidence for complex inheritance of familial DZ twinning.

  4. The Ten-Group Robson Classification: A Single Centre Approach Identifying Strategies to Optimise Caesarean Section Rates

    Directory of Open Access Journals (Sweden)

    Keisuke Tanaka

    2017-01-01

    Full Text Available Caesarean section (CS rates have been increasing worldwide and have caused concerns. For meaningful comparisons to be made World Health Organization recommends the use of the Ten-Group Robson classification as the global standard for assessing CS rates. 2625 women who birthed over a 12-month period were analysed using this classification. Women with previous CS (group 5 comprised 10.9% of the overall 23.5% CS rate. Women with one previous CS who did not attempt VBAC contributed 5.3% of the overall 23.5% CS rate. Second largest contributor was singleton nulliparous women with cephalic presentation at term (5.1% of the total 23.5%. Induction of labour was associated with higher CS rate (groups 1 and 3 (24.5% versus 11.9% and 6.2% versus 2.6%, resp.. For postdates IOL we recommend a gatekeeper booking system to minimise these being performed <41 weeks. We suggest setting up dedicated VBAC clinic to support for women with one previous CS. Furthermore review of definition of failure to progress in labour not only may lower CS rates in groups 1 and 2a but also would reduce the size of group 5 in the future.

  5. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group.

    Science.gov (United States)

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Malaysia and were confirmed by In-house TTS1-PCR. Isolates were subjected for multi-locus sequence typing (MLST) to explore their genotypic diversity and to investigate for possible clonal clustering of a certain sequence type. Patient's clinical information was examined to investigate for clinical correlation among the different genotypes. In spite of small sample set, MLST results indicated predictive results; considerable genotypic diversity, predominance and novelty among B. pseudomallei collected over a single geographically-located population in Malaysia. Massive genotypic heterogeneity was observed; 8 different sequence types with predominance of sequence type 54 and discovery of two novel sequence types. However, no clear pathogenomic or organ tropism clonal relationships were predicted.

  6. Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22.

    Directory of Open Access Journals (Sweden)

    Mine S Cicek

    Full Text Available A substantial proportion of familial colorectal cancer (CRC is not a consequence of known susceptibility loci, such as mismatch repair (MMR genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI-high tumors, or no evidence of linkage to MMR genes. Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR, the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142 and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093. Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively. Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036. These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated.

  7. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Shokeen Bhumika

    2011-02-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. Results A microsatellite enriched library of chickpea (enriched for (GT/CAn and (GA/CTn repeats was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded × JG-62 (double podded] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3% were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map

  8. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Gaur, Rashmi; Sethy, Niroj K; Choudhary, Shalu; Shokeen, Bhumika; Gupta, Varsha; Bhatia, Sabhyata

    2011-02-17

    Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. A microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea

  9. Colorectal Cancer Linkage on Chromosomes 4q21, 8q13, 12q24, and 15q22

    Science.gov (United States)

    Cicek, Mine S.; Cunningham, Julie M.; Fridley, Brooke L.; Serie, Daniel J.; Bamlet, William R.; Diergaarde, Brenda; Haile, Robert W.; Le Marchand, Loic; Krontiris, Theodore G.; Younghusband, H. Banfield; Gallinger, Steven; Newcomb, Polly A.; Hopper, John L.; Jenkins, Mark A.; Casey, Graham; Schumacher, Fredrick; Chen, Zhu; DeRycke, Melissa S.; Templeton, Allyson S.; Winship, Ingrid; Green, Roger C.; Green, Jane S.; Macrae, Finlay A.; Parry, Susan; Young, Graeme P.; Young, Joanne P.; Buchanan, Daniel; Thomas, Duncan C.; Bishop, D. Timothy; Lindor, Noralane M.; Thibodeau, Stephen N.; Potter, John D.; Goode, Ellen L.

    2012-01-01

    A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. PMID:22675446

  10. Myofascial force transmisison between antagonistic rat lower limb muscles: effects of single muscle or muscle group lengthening

    NARCIS (Netherlands)

    Meijer, Hanneke J.M; Rijkelijkhuizen, Josina M.; Huijing, P.A.J.B.M.

    2007-01-01

    Effects of lengthening of the whole group of anterior crural muscles (tibialis anterior and extensor hallucis longus muscles (TA + EHL) and extensor digitorum longus (EDL)) on myofascial interaction between synergistic EDL and TA + EHL muscles, and on myofascial force transmission between anterior

  11. Myofascial force transmission between antagonistic rat lower limb muscles: Effects of single muscle or muscle group lengthening.

    NARCIS (Netherlands)

    Meijer, H.J.M.; Rijkelijkhuizen, J.M.; Huijing, P.A.J.B.M.

    2007-01-01

    Effects of lengthening of the whole group of anterior crural muscles (tibialis anterior and extensor hallucis longus muscles (TA + EHL) and extensor digitorum longus (EDL)) on myofascial interaction between synergistic EDL and TA + EHL muscles, and on myofascial force transmission between anterior

  12. Evidence of secondary traumatic stress, safety concerns, and burnout among a homogeneous group of judges in a single jurisdiction.

    Science.gov (United States)

    Chamberlain, Jared; Miller, Monica K

    2009-01-01

    Active judges are likely to face numerous work-related experiences (e.g., traumatic cases) that affect performance of their occupational duties. Three occupational experiences (secondary traumatic stress [STS], safety concerns, and burnout) are outlined and applied to the judiciary. Results from nine case study interviews conducted in a single jurisdiction among a homogeneous cohort suggest that judges are at risk of having these experiences. Although no judge demonstrated extreme symptoms, all had low levels of symptoms associated with STS, safety concerns, and/or burnout. Several recommendations are proposed to prevent or minimize these occupational experiences. Recognizing and addressing the problem are essential for the protection of our nation's judges and the integrity of our judicial system.

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

    Directory of Open Access Journals (Sweden)

    Shashi N. Goonetilleke

    2018-01-01

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

  14. Fibrous polymer grafted magnetic chitosan beads with strong poly(cation-exchange) groups for single step purification of lysozyme.

    Science.gov (United States)

    Bayramoglu, Gulay; Tekinay, Turgay; Ozalp, V Cengiz; Arica, M Yakup

    2015-05-15

    Lysozyme is an important polypetide used in medical and food applications. We report a novel magnetic strong cation exchange beads for efficient purification of lysozyme from chicken egg white. Magnetic chitosan (MCHT) beads were synthesized via phase inversion method, and then grafted with poly(glycidyl methacrylate) (p(GMA)) via the surface-initiated atom transfer radical polymerization (SI-ATRP). Epoxy groups of the grafted polymer, were modified into strong cation-exchange groups (i.e., sulfonate groups) in the presence of sodium sulfite. The MCTH and MCTH-g-p(GMA)-SO3H beads were characterized by ATR-FTIR, SEM, and VSM. The sulphonate groups content of the modified MCTH-g-p(GMA)-4 beads was found to be 0.53mmolg(-1) of beads by the potentiometric titration method. The MCTH-g-p(GMA)-SO3H beads were first used as an ion-exchange support for adsorption of lysozyme from aqueous solution. The influence of different experimental parameters such as pH, contact time, and temperature on the adsorption process was evaluated. The maximum adsorption capacity was found to be 208.7mgg(-1) beads. Adsorption of lysozyme on the MCTH-g-p(GMA)-SO3H beads fitted to Langmuir isotherm model and followed the pseudo second-order kinetic. More than 93% of the adsorbed lysozyme was desorbed using Na2CO3 solution (pH 11.0). The purity of the lysozyme was checked by HPLC and SDS gel electrophoresis. In addition, the MCTH-g-p(GMA)-SO3H beads prepared in this work showed promising potential for separation of various anionic molecules. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Some methods for blindfolded record linkage

    Directory of Open Access Journals (Sweden)

    Christen Peter

    2004-06-01

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

  16. Linkages between informal and formal caregivers in home-care networks of frail older adults

    NARCIS (Netherlands)

    Jacobs, M.T.; van Tilburg, T.G.; Groenewegen, P.; Broese Van Groenou, M.I.

    2016-01-01

    In ageing societies, policy makers aim for more contact between informal and formal care-givers as it may enhance the quality of care. So far, the linkage between formal and informal care-givers is generally studied from a one-sided or a single dyadic perspective, without taking into account that

  17. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

    Science.gov (United States)

    A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

  18. Bayesian framework for prediction of future number of failures from a single group of units in the field

    International Nuclear Information System (INIS)

    Ebrahimi, Nader

    2009-01-01

    This paper considers prediction of unknown number of failures in a future inspection of a group of in-service units based on number of failures observed from an earlier inspection. We develop a flexible Bayesian model and calculate Bayesian estimator for this unknown number and other quantities of interest. The paper also includes an illustration of our method in an example about heat exchanger. A main advantage of our approach is in its nonparametric nature. By nonparametric here we simply mean that no assumption is required about the failure time distribution of a unit

  19. Design of catalysts by different substituent groups to the ;cut g-C3N4; single layer

    Science.gov (United States)

    Xu, Weiwei; Tang, Chao; Chen, Chongyang; Li, Youyong; Xu, Lai

    2017-09-01

    Graphitic carbon nitride has been wildly studied as a kind of promising photocatalysts for hydrogen evolution. However, it has a low intrinsic activity. Herein, we designed new periodic structures "cut g-C3N4", and adding the new substituent groups. We employed density functional theory to calculate the charge distribution and catalytic properties of hydrogen evolution on the structures. We got a theoretical view that introducing conjugate substituents can enhance the catalytic performance for hydrogen evolution. Furthermore, it provided a theoretical guidance for the reasonable design of two dimensional non-metallic photocatalysts, with lower activation barrier of the catalytic reaction.

  20. Confirmation of protoplast fusion-derived linkages in Staphylococcus aureus by transformation with protoplast DNA.

    Science.gov (United States)

    Stahl, M L; Pattee, P A

    1983-01-01

    Transformation provided definitive evidence for linkage between tyrB282::Tn551 ermB321 and omega (Chr::Tn551)34, and thus between the separate large linkage groups containing these markers, in Staphylococcus aureus NCTC 8325. Transformation also defined the chromosomal loci for the purC193::Tn551 and omega (Chr::Tn551)42 markers and the linkage of a tetracycline resistance marker (tet-3490) with a fusidic acid resistance marker (fus-149). The use of DNA isolated from protoplasts under conditions that reduced hydrodynamic shear greatly facilitated the demonstration of most of these linkages. These results provide direct evidence confirming several of the linkages predicted by a microcomputer-assisted protoplast fusion analysis in a previous study (M. L. Stahl and P. A. Pattee, J. Bacteriol. 154:395-405, 1983); those markers whose predicted linkages were not confirmed by transformation are probably separated by chromosomal distances that exceed the limits of detection by transformation, even with protoplast DNA. PMID:6572625

  1. Effect of azo and ester linkages on rod shaped Schiff base liquid crystals and their photophysical investigations

    Science.gov (United States)

    Selvarasu, Chinnaiyan; Kannan, Palaninathan

    2016-12-01

    Two new series of rod shaped Schiff base containing liquid crystal compounds with azo and ester linkages have been synthesized and characterized respectively. The rod like molecules containing cinnamate linkages with four different alkyl spacers (n = 6, 8, 10 and 12) and influence of linking group have been elucidated. Considerable changes in mesomorphic properties were noticed starting from Nematic to Smectic-C on changing of azo and ester linkages along with different terminal alkyl chain lengths. The mesomorphic properties of both series are compared. Photosensitive azobenzene group undergoes photoisomerization under UV light and monitored by UV-Visible spectroscopy.

  2. Effectiveness of service linkages in primary mental health care: a narrative review part 1

    Directory of Open Access Journals (Sweden)

    Parker Sharon

    2011-04-01

    Full Text Available Abstract Background With the move to community care and increased involvement of generalist health care providers in mental health, the need for health service partnerships has been emphasised in mental health policy. Within existing health system structures the active strategies that facilitate effective partnership linkages are not clear. The objective of this study was to examine the evidence from peer reviewed literature regarding the effectiveness of service linkages in primary mental health care. Methods A narrative and thematic review of English language papers published between 1998 and 2009. Studies of analytic, descriptive and qualitative designs from Australia, New Zealand, UK, Europe, USA and Canada were included. Data were extracted to examine what service linkages have been used in studies of collaboration in primary mental health care. Findings from the randomised trials were tabulated to show the proportion that demonstrated clinical, service delivery and economic benefits. Results A review of 119 studies found ten linkage types. Most studies used a combination of linkage types and so the 42 RCTs were grouped into four broad linkage categories for meaningful descriptive analysis of outcomes. Studies that used multiple linkage strategies from the suite of "direct collaborative activities" plus "agreed guidelines" plus "communication systems" showed positive clinical (81%, service (78% and economic (75% outcomes. Most evidence of effectiveness came from studies of depression. Long term benefits were attributed to medication concordance and the use of case managers with a professional background who received expert supervision. There were fewer randomised trials related to collaborative care of people with psychosis and there were almost none related to collaboration with the wider human service sectors. Because of the variability of study types we did not exclude on quality or attempt to weight findings according to power or effect

  3. Reproductive Outcomes After Gestational Trophoblastic Neoplasia. A Comparison Between Single-Agent and Multiagent Chemotherapy: Retrospective Analysis From the MITO-9 Group.

    Science.gov (United States)

    Cioffi, Raffaella; Bergamini, Alice; Gadducci, Angiolo; Cormio, Gennaro; Giorgione, Veronica; Petrone, Micaela; Rabaiotti, Emanuela; Pella, Francesca; Candiani, Massimo; Mangili, Giorgia

    2018-02-01

    Gestational trophoblastic neoplasia affects women of reproductive age and is usually treated by chemotherapy. Major concerns related to chemotherapy in young women are the possible infertility, risk of early menopause, and teratogenic effects on subsequent pregnancies. The study's aim was to analyze menstrual and reproductive outcomes of women treated with single-agent versus multiagent chemotherapy for gestational trophoblastic neoplasia. One-hundred fifty-one patients were treated. Seventy-six patients older than 45 years, with a placental site or epithelioid trophoblastic tumor, undergoing hysterectomy for patient choice, or undergoing human chorionic gonadotropin follow-up at the time of the analysis were excluded. Seventy-five patients were divided into subgroups according to International Federation of Gynecology and Obstetrics score: patients scoring less than 7, receiving single-agent chemotherapy (group A, n = 42); patients scoring 7 or greater, receiving combination treatment (group B, n = 33). Patients' outcomes were compared by univariate and multivariate analyses. Temporary amenorrhea occurred in 33% of group A patients and 66.7% of group B (P = 0.01). Premature menopause occurred in 3 patients in group B (0% vs 9%, P = 0.02). Ten patients in group B underwent salvage hysterectomy. Pregnancy desire did not differ between the 2 groups (P = 0.555). In group A, 57.1% became pregnant; in group B, 36.4% did (P = 0.060). Instead, pregnancy rate was 52.2% among high-risk patients not undergoing hysterectomy (57.1% vs 52.2%, P = 0.449). There was no difference in miscarriage (P = 0.479) and premature birth (P = 0.615) rates. In a multivariate analysis that included age, International Federation of Gynecology and Obstetrics score, chemotherapy type, use of assisted reproductive technologies, previous pregnancies, and pregnancy desire, only age (P = 0.006) and pregnancy desire (P = 0.002) had a significant impact on the probability to have subsequent pregnancies

  4. Azide groups in higher oxidation state manganese cluster chemistry: from structural aesthetics to single-molecule magnets.

    Science.gov (United States)

    Stamatatos, Theocharis C; Christou, George

    2009-04-20

    This Forum Article overviews the recent amalgamation of two long-established areas, manganese/oxo coordination cluster chemistry involving the higher Mn(II)/Mn(IV) oxidation states and transition-metal azide (N(3)(-)) chemistry. The combination of azide and alkoxide- or carboxylate-containing ligands in Mn chemistry has led to a variety of new polynuclear clusters, high-spin molecules, and single-molecule magnets, with metal nuclearities ranging from Mn(4) to Mn(32) and with ground-state spin values as large as S = 83/2. The organic bridging/chelating ligands are discussed separately as follows: (i) pyridyl alkoxides [the anions of 2-(hydroxymethyl)pyridine (hmpH), 2,6-pyridinedimethanol (pdmH(2)), and the gem-diol form of di-2-pyridyl ketone (dpkdH(2))]; (ii) non-pyridyl alkoxides [the anions of 1,1,1-tris(hydroxymethyl)ethane (thmeH(3)), triethanolamine (teaH(3)), and N-methyldiethanolamine (mdaH(2))]; (iii) other alcohols [the anions of 2,6-dihydroxymethyl-4-methylphenol (LH(3)) and Schiff bases]; (iv) pyridyl monoximes/dioximes [the anions of methyl-2-pyridyl ketone oxime (mpkoH), phenyl-2-pyridyl ketone oxime (ppkoH), and 2,6-diacetylpyridine dioxime (dapdoH(2))]; (v) non-pyridyl oximes [the anions of salicylaldoxime (saoH(2)) and its derivatives R-saoH(2)]. The large structural diversity of the resulting complexes stems from the combined ability of the azide and organic ligands to adopt a variety of ligation and bridging modes. The combined work demonstrates the synthetic novelty that arises when azide is used in conjunction with alcohol-based chelates, the aesthetic beauty of the resulting molecules, and the often fascinating magnetic properties that these compounds possess. This continues to emphasize the extensive and remarkable ability of Mn chemistry to satisfy a variety of different tastes.

  5. Whole body and local cryotherapy in restless legs syndrome: A randomized, single-blind, controlled parallel group pilot study.

    Science.gov (United States)

    Happe, Svenja; Evers, Stefan; Thiedemann, Christian; Bunten, Sabine; Siegert, Rudolf

    2016-11-15

    Treatment of restless legs syndrome (RLS) is primarily based on drugs. Since many patients report improvement of symptoms due to cooling their legs, we examined the efficacy of cryotherapy in RLS. 35 patients (28 women, 60.9±12.5years) with idiopathic RLS and symptoms starting not later than 6pm were randomized into three groups: cold air chamber at -60°C (n=12); cold air chamber at -10°C (n=12); local cryotherapy at -17°C (n=11). After a two week baseline, the different therapies were applied three minutes daily at 6pm over two weeks, followed by a four week observation period. The patients completed several questionnaires regarding RLS symptoms, sleep, and quality of life on a weekly basis (IRLS, ESS), VAS and sleep/morning protocol were completed daily, MOSS/RLS-QLI were completed once in each period. Additionally, the PLM index was measured by a mobile device at the end of baseline, intervention, and follow-up. The IRLS score was chosen as primary efficacy parameter. At the end of follow-up, significant improvement of RLS symptoms and quality of life could be observed only in the -60°C group as compared to baseline (IRLS: p=0.009; RLS-QLI: p=0.006; ESS: p=0.020). Local cryotherapy led to improvement in quality of life (VAS4: p=0.028; RLS-QLI: p=0.014) and sleep quality (MOSS: p=0.020; MOSS2: p=0.022) but not in IRLS and ESS. In the -10°C group, the only significant effect was shortening of number of wake phases per night. Serious side-effects were not reported. Whole body cryotherapy at -60°C and, to a less extent, local cryotherapy seem to be a treatment option for RLS in addition to conventional pharmacological treatment. However, the exact mode of cryotherapy needs to be established. Copyright © 2016. Published by Elsevier B.V.

  6. One-Year Follow-Up of the Effectiveness of Cognitive Behavioral Group Therapy for Patients’ Depression: A Randomized, Single-Blinded, Controlled Study

    Directory of Open Access Journals (Sweden)

    Kai-Jo Chiang

    2015-01-01

    Full Text Available The aim of the study was to investigate the long-term (one year effectiveness of a 12-session weekly cognitive behavior group therapy (CBGT on patients with depression. This was a single-blind randomized controlled study with a 2-arm parallel group design. Eighty-one subjects were randomly assigned to 12 sessions intervention group (CBGT or control group (usual outpatient psychiatric care group and 62 completed the study. The primary outcome was depression measured with Beck Depression Inventory (BDI-II and Hamilton Rating Scale for Depression (HRSD. The secondary outcomes were automatic thoughts measured by automatic thoughts questionnaire (ATQ. Both groups were evaluated at the pretest (before 2 weeks, posttest (after 12 therapy sessions, and short- (3 months, medium- (6 months, and long-term (12 months follow-up. After receiving CBGT, the experimental group had a statistically significant reduction in the BDI-II from 40.30 at baseline to 17.82 points at session eight and to 10.17 points at postintervention (P<0.001. Similar effects were seen on the HRSD. ATQ significantly decreased at the 12th session, 6 months after sessions, and 1 year after the sessions ended (P<0.001. We concluded that CBGT is effective for reducing depression and continued to be effective at 1 year of follow-up.

  7. Testing random forest classification for identifying lava flows and mapping age groups on a single Landsat 8 image

    Science.gov (United States)

    Li, Long; Solana, Carmen; Canters, Frank; Kervyn, Matthieu

    2017-10-01

    Mapping lava flows using satellite images is an important application of remote sensing in volcanology. Several volcanoes have been mapped through remote sensing using a wide range of data, from optical to thermal infrared and radar images, using techniques such as manual mapping, supervised/unsupervised classification, and elevation subtraction. So far, spectral-based mapping applications mainly focus on the use of traditional pixel-based classifiers, without much investigation into the added value of object-based approaches and into advantages of using machine learning algorithms. In this study, Nyamuragira, characterized by a series of > 20 overlapping lava flows erupted over the last century, was used as a case study. The random forest classifier was tested to map lava flows based on pixels and objects. Image classification was conducted for the 20 individual flows and for 8 groups of flows of similar age using a Landsat 8 image and a DEM of the volcano, both at 30-meter spatial resolution. Results show that object-based classification produces maps with continuous and homogeneous lava surfaces, in agreement with the physical characteristics of lava flows, while lava flows mapped through the pixel-based classification are heterogeneous and fragmented including much "salt and pepper noise". In terms of accuracy, both pixel-based and object-based classification performs well but the former results in higher accuracies than the latter except for mapping lava flow age groups without using topographic features. It is concluded that despite spectral similarity, lava flows of contrasting age can be well discriminated and mapped by means of image classification. The classification approach demonstrated in this study only requires easily accessible image data and can be applied to other volcanoes as well if there is sufficient information to calibrate the mapping.

  8. Probabilistic linkage in household survey on hospital care usage

    Directory of Open Access Journals (Sweden)

    Coeli Cláudia Medina

    2003-01-01

    Full Text Available OBJECTIVE: To evaluate the potential advantages and limitations of the use of the Brazilian hospital admission authorization forms database and the probabilistic record linkage methodology for the validation of reported utilization of hospital care services in household surveys. METHODS: A total of 2,288 households interviews were conducted in the county of Duque de Caxias, Brazil. Information on the occurrence of at least one hospital admission in the year preceding the interview was obtained from a total of 10,733 household members. The 130 records of household members who reported at least one hospital admission in a public hospital were linked to a hospital database with 801,587 records, using an automatic probabilistic approach combined with an extensive clerical review. RESULTS: Seventy-four (57% of the 130 household members were identified in the hospital database. Yet only 60 subjects (46% showed a record of hospitalization in the hospital database in the study period. Hospital admissions due to a surgery procedure were significantly more likely to have been identified in the hospital database. The low level of concordance seen in the study can be explained by the following factors: errors in the linkage process; a telescoping effect; and an incomplete record in the hospital database. CONCLUSIONS: The use of hospital administrative databases and probabilistic linkage methodology may represent a methodological alternative for the validation of reported utilization of health care services, but some strategies should be employed in order to minimize the problems related to the use of this methodology in non-ideal conditions. Ideally, a single identifier, such as a personal health insurance number, and the universal coverage of the database would be desirable.

  9. 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 ...

  10. Haldane and the analysis of linkage

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 5. HALDANE AND THE ANALYSIS OF LINKAGE. J .H. Edwards. HALDANE AT 125 Volume 96 Issue 5 November 2017 pp 783-794. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/05/0783-0794. Abstract ...

  11. Producer Services, Manufacturing Linkages, and Trade

    NARCIS (Netherlands)

    J.F. François (Joseph); J. Kepler; J. Woerz

    2007-01-01

    textabstractWorking with a mix of panel data on goods and services trade for the OECD for 1994-2004, combined with social accounts data (i.e. data on intermediate linkages) for 78 countries benchmarked to the panel midpoint, we examine the role of services as inputs in manufacturing, with a

  12. Linkage between psychological contract and employee retention ...

    African Journals Online (AJOL)

    The study examines the linkage between psychological contract and employees' retention, performance and productivity in organizations in Nigeria. It studies the interplay between psychological contract and the variables with a view to understanding their interactions and impacts in organizations. The methodology is ...

  13. Utilizing linkage disequilibrium information from Indian Genome ...

    Indian Academy of Sciences (India)

    Utilizing linkage disequilibrium information from Indian Genome. Variation Database for mapping mutations: SCA12 case study. SAMIRA BAHL1, IKHLAK AHMED2, THE INDIAN GENOME VARIATION CONSORTIUM3 and MITALI MUKERJI1. 1Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), ...

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

    African Journals Online (AJOL)

    p2333147

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

  15. agricultural research and extension linkage in ethiopia

    African Journals Online (AJOL)

    AUA

    aimed at strengthening research and extension linkages will differ from country to country depending on historical working relationships between research and extension organisations as well as their organizational structures, responsiveness to the ever- growing challenges and how divergent or convergent their goals are ...

  16. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    Directory of Open Access Journals (Sweden)

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  17. Progress and Prospect of the Growth of Wide-Band-Gap Group III Nitrides: Development of the Growth Method for Single-Crystal Bulk GaN

    Science.gov (United States)

    Amano, Hiroshi

    2013-05-01

    Thin films of III-V compound semiconductors such as GaAs and InP can be grown on native substrates, whereas such growth was difficult for group III nitride semiconductors. Despite this drawback, scientists have gradually become able to use the functions of group III nitride semiconductors by growing their thin films on non-native substrates such as sapphire and Si substrates. With the continuously increasing demand for the conservation and generation of energy, bulk substrates of group III nitride semiconductors are highly expected to maximize their potential. In this report, I review the current status of the growth methods for bulk GaN single crystals used for substrates as well as summarize the characteristics of blue light-emitting diodes (LEDs), heterojunction field-effect transistors (HFETs), and photovoltaic cells on GaN substrates.

  18. Construction and Comparative Analyses of Highly Dense Linkage Maps of Two Sweet Cherry Intra-Specific Progenies of Commercial Cultivars

    Science.gov (United States)

    Quero-García, José; Guzmán, Alejandra; Mansur, Levi; Gratacós, Eduardo; Silva, Herman; Rosyara, Umesh R.; Iezzoni, Amy; Meisel, Lee A.; Dirlewanger, Elisabeth

    2013-01-01

    Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1–LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family. PMID:23382953

  19. Early-onset group B streptococcal disease following culture-based screening in Japan: a single center study.

    Science.gov (United States)

    Miyata, Akane; Takahashi, Hironori; Kubo, Takahiko; Watanabe, Noriyoshi; Tsukamoto, Keiko; Ito, Yushi; Sago, Haruhiko

    2012-08-01

    We investigated trends in early-onset group B streptococcal disease (EOD) after the introduction of culture-based screening in Japan. A retrospective cohort study examined EOD trends in 9506 pregnancies and 10 715 neonates at our center from 2002 to 2009. EOD occurred in four neonates (4/7332: 0.55/1000 live births). The EOD incidence among infants born to women positive for GBS by screening was 0.90 cases per 1000 live births (1/1107). In contrast, the EOD incidence among infants negative by GBS screening was 0.48 cases per 1000 live births (3/6225). Thus, of the four affected neonates, three had mothers who tested negative on antepartum GBS screening. Two neonates had symptoms of infection during labor and intrapartum antibiotic agents were administered. The other two neonates received no antibiotics because deliveries were uneventful and they were negative on GBS screening. The incidence of EOD is 0.90 cases per 1000 live births among GBS-positive women and 0.48 cases per 1000 live births among GBS-negative women. The results of our study implied that EOD can develop regardless of GBS screening and intrapartum clinical course, although the method of sample collection, indications for antibiotic prophylaxis, and the antibiotics regimen should be considered. © 2012 The Authors. Journal of Obstetrics and Gynaecology Research © 2012 Japan Society of Obstetrics and Gynecology.

  20. Generation and Stability of the gem-Diol Forms in Imidazole Derivatives Containing Carbonyl Groups. Solid-State NMR and Single-Crystal X-ray Diffraction Studies.

    Science.gov (United States)

    Crespi, Ayelén Florencia; Byrne, Agustín Jesús; Vega, Daniel; Chattah, Ana Karina; Monti, Gustavo Alberto; Lázaro-Martínez, Juan Manuel

    2018-01-18

    The stability of gem-diol forms in imidazolecarboxaldehyde isomers was studied by solid-state nuclear magnetic resonance (ss-NMR) combined with single-crystal X-ray diffraction studies. These methodologies also allowed determining the factors governing the occurrence of such rare functionalization in carbonyl moieties. Results indicated that the position of the carbonyl group is the main factor that governs the generation of geminal diols, having a clear and direct effect on hydration, since, under the same experimental conditions, only 36% of 5-imidazolecarboxaldehydes and 5% of 4-imidazolecarboxaldehydes were hydrated, as compared to 2-imidazolecarboxaldehydes, with which a 100% hydration was achieved. Not only did trifluoroacetic acid favor the addition of water to the carbonyl group but also it allowed obtaining single crystals. Single crystals of the gem-diol and the hemiacetal forms 2-imidazolecarboxaldehyde and N-methyl-2-imidazolecarboxaldehyde, respectively, were isolated and studied through 1 H ss-NMR. Mass spectrometry and solution-state NMR experiments were also performed to study the hydration process.

  1. Hybrid Pareto artificial bee colony algorithm for multi-objective single machine group scheduling problem with sequence-dependent setup times and learning effects.

    Science.gov (United States)

    Yue, Lei; Guan, Zailin; Saif, Ullah; Zhang, Fei; Wang, Hao

    2016-01-01

    Group scheduling is significant for efficient and cost effective production system. However, there exist setup times between the groups, which require to decrease it by sequencing groups in an efficient way. Current research is focused on a sequence dependent group scheduling problem with an aim to minimize the makespan in addition to minimize the total weighted tardiness simultaneously. In most of the production scheduling problems, the processing time of jobs is assumed as fixed. However, the actual processing time of jobs may be reduced due to "learning effect". The integration of sequence dependent group scheduling problem with learning effects has been rarely considered in literature. Therefore, current research considers a single machine group scheduling problem with sequence dependent setup times and learning effects simultaneously. A novel hybrid Pareto artificial bee colony algorithm (HPABC) with some steps of genetic algorithm is proposed for current problem to get Pareto solutions. Furthermore, five different sizes of test problems (small, small medium, medium, large medium, large) are tested using proposed HPABC. Taguchi method is used to tune the effective parameters of the proposed HPABC for each problem category. The performance of HPABC is compared with three famous multi objective optimization algorithms, improved strength Pareto evolutionary algorithm (SPEA2), non-dominated sorting genetic algorithm II (NSGAII) and particle swarm optimization algorithm (PSO). Results indicate that HPABC outperforms SPEA2, NSGAII and PSO and gives better Pareto optimal solutions in terms of diversity and quality for almost all the instances of the different sizes of problems.

  2. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua

    Directory of Open Access Journals (Sweden)

    Higgins Brent

    2010-03-01

    Full Text Available Abstract Background Atlantic cod (Gadus morhua is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST program, focusing on fish originating from Canadian waters. Results A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%. 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26% SNPs were monomorphic for all populations tested. In total, 64 (4% of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620 were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141. Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141, we determined that 36% (51 are non-synonymous. Many loci (1033 SNPs; 64% are polymorphic in all populations tested. However a small number of SNPs (184 that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs. Conclusions These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to

  3. SNP-based linkage mapping for validation of QTLs for resistance to ascochyta blight in lentil

    Directory of Open Access Journals (Sweden)

    Shimna Sudheesh

    2016-11-01

    Full Text Available Lentil (Lens culinaris Medik. is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB, caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP and simple sequence repeat (SSR markers have been developed from three recombinant inbred line (RIL populations. The IH x NF map contained 460 loci across 1461.6 cM, while the IH x DIG map contained 329 loci across 1302.5 cM and the third map, NF x DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across 7 linkage groups (LGs, with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs explaining 52% and 69% of phenotypic variation for resistance to infection in the IH x DIG and IH x NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted

  4. Bifurcations of a Controlled Two-Bar Linkage Motion with Considering Viscous Frictions

    Directory of Open Access Journals (Sweden)

    Qingkai Han

    2011-01-01

    Full Text Available In this paper, we investigate the joint viscous friction effects on the motions of a two-bar linkage under controlling of OPCL. The dynamical model of the two-bar linkage with an OPCL controller is firstly set up with considering the two joints' viscous frictions. Thereafter, the motion bifurcations of the two-bar linkage along the values of joint viscous frictions are obtained using shooting method. Then, single-periodic, multiple-periodic, quasi-periodic and chaotic motions of link rotating angles are simulated with given different viscous friction values, and they are illustrated in time domain waveforms, phase space portraits, amplitude spectra and Poincare mapping graphs, respectively. Additionally, for the chaotic case, Lyapunov exponents and hypothesis possibilities of the two joint motions are also estimated.

  5. A d-statistic for single-case designs that is equivalent to the usual between-groups d-statistic.

    Science.gov (United States)

    Shadish, William R; Hedges, Larry V; Pustejovsky, James E; Boyajian, Jonathan G; Sullivan, Kristynn J; Andrade, Alma; Barrientos, Jeannette L

    2014-01-01

    We describe a standardised mean difference statistic (d) for single-case designs that is equivalent to the usual d in between-groups experiments. We show how it can be used to summarise treatment effects over cases within a study, to do power analyses in planning new studies and grant proposals, and to meta-analyse effects across studies of the same question. We discuss limitations of this d-statistic, and possible remedies to them. Even so, this d-statistic is better founded statistically than other effect size measures for single-case design, and unlike many general linear model approaches such as multilevel modelling or generalised additive models, it produces a standardised effect size that can be integrated over studies with different outcome measures. SPSS macros for both effect size computation and power analysis are available.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  7. Genomewide linkage scan for diabetic renal failure and albuminuria: the FIND study.

    Science.gov (United States)

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

    2011-01-01

    Diabetic nephropathy (DN) is a leading cause of mortality and morbidity in patients with type 1 and type 2 diabetes. The multicenter FIND consortium aims to identify genes for DN and its associated quantitative traits, e.g. the urine albumin:creatinine ratio (ACR). Herein, the results of whole-genome linkage analysis and a sparse association scan for ACR and a dichotomous DN phenotype are reported in diabetic individuals. A genomewide scan comprising more than 5,500 autosomal single nucleotide polymorphism markers (average spacing of 0.6 cM) was performed on 1,235 nuclear and extended pedigrees (3,972 diabetic participants) ascertained for DN from African-American (AA), American-Indian (AI), European-American (EA) and Mexican-American (MA) populations. Strong evidence for linkage to DN was detected on chromosome 6p (p = 8.0 × 10(-5), LOD = 3.09) in EA families as well as suggestive evidence for linkage to chromosome 7p in AI families. Regions on chromosomes 3p in AA, 7q in EA, 16q in AA and 22q in MA displayed suggestive evidence of linkage for urine ACR. The linkage peak on chromosome 22q overlaps the MYH9/APOL1 gene region, previously implicated in AA diabetic and nondiabetic nephropathies. These results strengthen the evidence for previously identified genomic regions and implicate several novel loci potentially involved in the pathogenesis of DN. Copyright © 2011 S. Karger AG, Basel.

  8. A dense SNP-based linkage map for Atlantic salmon (Salmo salar reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

    Directory of Open Access Journals (Sweden)

    Lien Sigbjørn

    2011-12-01

    Full Text Available Abstract Background The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs, multisite variants (MSVs and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species. Results A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus. The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1 which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres. Conclusion The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization, aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence.

  9. A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa.

    Science.gov (United States)

    Davik, Jahn; Sargent, Daniel James; Brurberg, May Bente; Lien, Sigbjørn; Kent, Matthew; Alsheikh, Muath

    2015-01-01

    The cultivated strawberry (Fragaria ×ananassa Duch.) is an allo-octoploid considered difficult to disentangle genetically due to its four relatively similar sub-genomic chromosome sets. This has been alleviated by the recent release of the strawberry IStraw90 whole genome genotyping array. However, array resolution relies on the genotypes used in the array construction and may be of limited general use. SNP detection based on reduced genomic sequencing approaches has the potential of providing better coverage in cases where the studied genotypes are only distantly related from the SNP array's construction foundation. Here we have used double digest restriction-associated DNA sequencing (ddRAD) to identify SNPs in a 145 seedling F1 hybrid population raised from the cross between the cultivars Sonata (♀) and Babette (♂). A linkage map containing 907 markers which spanned 1,581.5 cM across 31 linkage groups representing the 28 chromosomes of the species. Comparing the physical span of the SNP markers with the F. vesca genome sequence, the linkage groups resolved covered 79% of the estimated 830 Mb of the F. × ananassa genome. Here, we have developed the first linkage map for F. × ananassa using ddRAD and show that this technique and other related techniques are useful tools for linkage map development and downstream genetic studies in the octoploid strawberry.

  10. A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa.

    Directory of Open Access Journals (Sweden)

    Jahn Davik

    Full Text Available The cultivated strawberry (Fragaria ×ananassa Duch. is an allo-octoploid considered difficult to disentangle genetically due to its four relatively similar sub-genomic chromosome sets. This has been alleviated by the recent release of the strawberry IStraw90 whole genome genotyping array. However, array resolution relies on the genotypes used in the array construction and may be of limited general use. SNP detection based on reduced genomic sequencing approaches has the potential of providing better coverage in cases where the studied genotypes are only distantly related from the SNP array's construction foundation. Here we have used double digest restriction-associated DNA sequencing (ddRAD to identify SNPs in a 145 seedling F1 hybrid population raised from the cross between the cultivars Sonata (♀ and Babette (♂. A linkage map containing 907 markers which spanned 1,581.5 cM across 31 linkage groups representing the 28 chromosomes of the species. Comparing the physical span of the SNP markers with the F. vesca genome sequence, the linkage groups resolved covered 79% of the estimated 830 Mb of the F. × ananassa genome. Here, we have developed the first linkage map for F. × ananassa using ddRAD and show that this technique and other related techniques are useful tools for linkage map development and downstream genetic studies in the octoploid strawberry.

  11. Gamma-glutamyl and D- or L-peptide linkages in mycobacillin, a cyclic peptide antibiotic.

    Science.gov (United States)

    Sengupta, S; Banerjee, A B; Bose, S K

    1971-03-01

    Mycobacillin lacks amino groups but contains two free alpha-carboxyl groups, indicating the presence of two side-chain peptide linkages. The five aspartic acid residues of mycobacillin are all in alpha-peptide linkage whereas the two glutamic acid residues are in gamma-linkage. Mycobacillin does not react with hydroxylamine to give hydroxamate, indicating the absence of anhydride, lactone and ester linkages. This is also confirmed by i.r. spectroscopy and titration of the molecule. Of the 15 peptides obtained from partial hydrolysates of mycobacillin, 12 contain aspartic acid. Results obtained by treatment of hydrolysates of aspartic acid-containing peptides with d-amino acid oxidase and l-glutamate decarboxylase (containing l-aspartate decarboxylase activity) indicate that residue 5 is l-aspartic acid and residues 2, 8, 11 and 13 are d-aspartic acid. The d- or l-peptide sequence and nature of peptide linkages in mycobacillin are proposed on the basis of these findings and the amino acid sequence reported earlier.

  12. Actors affecting the effectiveness of extension linkages between ...

    African Journals Online (AJOL)

    Actors affecting the effectiveness of extension linkages between agricultural development programmes (ADPs) and universites in South-Eastern Nigeria. ... as facilitators of linkage effectiveness, indicated that for linkages to be effective, all the physical, psychological and social factors of human relationships must be made to ...

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

    Directory of Open Access Journals (Sweden)

    Mia Kanak

    2014-07-01

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

  14. Combination of electromembrane extraction and liquid-phase microextraction in a single step: Simultaneous group separation of acidic and basic drugs

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Seip, Knut Fredrik; Gjelstad, Astrid

    2015-01-01

    Electromembrane extraction (EME) and liquid-phase microextraction (LPME) were combined in a single step for the first time to realize simultaneous and clear group separation of basic and acidic drugs. Using 2-nitrophenyl octyl ether as the supported liquid membrane (SLM) for EME and dihexyl ether...... as the SLM for LPME, basic and acidic drugs were extracted and separated simultaneously from a low pH sample by EME and LPME, respectively. After 15 min of extraction, basic drugs (citalopram and sertraline) were exhaustively extracted, whereas the recoveries for acidic drugs (ketoprofen and ibuprofen) were...... in the range of 76%-86%. Longer extraction time provided higher recoveries for the acidic drugs, but this somewhat deteriorated the group separation. Matrices effects from the coexisting acidic drugs/basic drugs were tested, and we observed that simultaneous EME/LPME was not affected by coexisting drugs...

  15. Clinical evaluation of 1,132 zirconia-based single crowns: a retrospective cohort study from the AIOP clinical research group.

    Science.gov (United States)

    Monaco, Carlo; Caldari, Mauro; Scotti, Roberto

    2013-01-01

    The aim of this retrospective cohort study was to gather the outcomes of zirconia single crowns made by 16 members of the Italian Academy of Prosthetic Dentistry (AIOP) over a time period of up to 5 years. A total of 398 patients treated in private practices with 1,132 zirconia-based single-crown restorations made on natural teeth from January 2005 to July 2010 were included. Three hundred forty-three anterior restorations (30.3%) and 789 posterior crowns (69.7%) were made with 16 types of zirconia, using primarily chamfer or knife-edge tooth preparation, and examined according to the esthetic, functional, and biologic criteria. To evaluate the relationship of parafunction with mechanical failure, patients with clenching or bruxism were not excluded from the study group. The cumulative survival rate of all restorations was 98.1%, while the cumulative success rate was 94.3%. Functional criteria had the highest number of failures. The odds ratio (OR) for all restorations was calculated to clarify the relationship between patients who were subject/not subject to parafunctions and technical complications; the OR was 2.60. An association between parafunction and mechanical failure was found in patients with severe parafunction. Porcelain-veneered zirconia single crowns with chamfer and knife-edge preparations showed good clinical results over a period of up to 5 years. Technical complications were few and were limited primarily to patients with parafunction.

  16. Have North-South Growth Linkages Changed?

    OpenAIRE

    Willy W. Hoffmaister; Mahmood Pradhan; Hossein Samiei

    1996-01-01

    This paper provides preliminary econometric evidence suggesting that the traditional trade-based business cycle linkages between the North and the South have changed. Many countries in the South, in particular in Asia, appear to have become more resilient to cyclical movements in the North, and to have come to play a more significant role in sustaining global activity, in particular during the 1991-93 slowdown. A number of factors may have contributed to these changes: improved domestic polic...

  17. Commodities and Linkages: Meeting the Policy Challenge

    OpenAIRE

    Kaplinsky, Raphael; Morris, Adam; Kaplan, David

    2011-01-01

    The results of detailed empirical enquiry into the nature and determinants of the breadth and depth of linkages in and out of the commodities sector in eight SSA countries (Angola, Botswana, Gabon, Ghana, Nigeria, South Africa Tanzania, and Zambia) and six sectors (copper, diamonds, gold, oil and gas, mining services and timber) has shown extensive scope for industrial development (MMCP DP 13, 2011). A primary conclusion of this research was that policy in both the private and public realm wa...

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

    Directory of Open Access Journals (Sweden)

    Kakioka Ryo

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Renato Nunes Mariz

    2013-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  1. It IS worth the effort: Patient knowledge of reproductive aspects of inflammatory bowel disease improves dramatically after a single group education session.

    Science.gov (United States)

    Mountifield, Réme; Andrews, Jane M; Bampton, Peter

    2014-08-01

    Individuals with Inflammatory Bowel Disease (IBD) have poor knowledge regarding the implications of disease for fertility and pregnancy. Previous studies suggest that this poor knowledge adversely influences reproductive decision making. To examine the effect of a single group education session on IBD-specific reproductive knowledge in subjects with IBD. People with IBD attending an educational event were invited to complete the CCPKnow questionnaire, testing reproductive knowledge in IBD, before and after an evidenced based presentation on this topic delivered by a Gastroenterologist. Of 248 attendees, 155 participated; 69% female, mean age 40.3years. CCPKnow scores (maximum 17) were low at baseline and increased significantly post education (mean 5.4 pre vs. 14.5 post education; p<0.0001). A large majority (65.1%) of subjects had "poor" (score <8) knowledge at baseline, compared with only 1.9% after education (p<0.0001). Whilst all subareas of knowledge improved after education, the most important improvement was in attitudes toward medication use in pregnancy: 33.5% of subjects indicated at baseline that women should avoid all drugs in pregnancy compared with only 1.2% post education (p<0.0001). A single group-delivered education event focussed on reproductive issues in IBD can dramatically improve patient knowledge. This has the potential to change reproductive behaviour and may reduce voluntary childlessness resulting from misperceptions amongst individuals with IBD. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  2. JLIN: A java based linkage disequilibrium plotter

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    McCaskie Pamela A

    2006-02-01

    Full Text Available Abstract Background A great deal of effort and expense are being expended internationally in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Techniques such as Linkage Disequilibrium mapping are being increasingly used to examine and compare markers across increasingly large datasets. Visualisation techniques are becoming essential to analyse the ever-growing volume of data and results available with any given analysis. Results JLIN (Java LINkage disequilibrium plotter is a software package designed for customisable, intuitive visualisation of Linkage Disequilibrium (LD across all common computing platforms. Customisation allows the user to choose particular visualisations, statistical measures and measurement ranges. JLIN also allows the user to export images of the LD visualisation in several common document formats. Conclusion JLIN allows the user to visually compare and contrast the results of a range of statistical measures on the input dataset(s. These measures include the commonly used D' and r2 statistics and empirical p-values. JLIN has a number of unique and novel features that improve on existing LD visualisation tools.

  3. A Randomized Single Blind Parallel Group Study Comparing Monoherbal Formulation Containing Holarrhena antidysenterica Extract with Mesalamine in Chronic Ulcerative Colitis Patients

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    Sarika Johari

    2016-01-01

    Full Text Available Background: Incidences of side effects and relapses are very common in chronic ulcerative colitis patients after termination of the treatment. Aims and Objectives: This study aims to compare the treatment with monoherbal formulation of Holarrhena antidysenterica with Mesalamine in chronic ulcerative colitis patients with special emphasis to side effects and relapse. Settings and Design: Patients were enrolled from an Ayurveda Hospital and a private Hospital, Gujarat. The study was randomized, parallel group and single blind design. Materials and Methods: The protocol was approved by Institutional Human Research Ethics Committee of Anand Pharmacy College on 23rd Jan 2013. Three groups (n = 10 were treated with drug Mesalamine (Group I, monoherbal tablet (Group II and combination of both (Group III respectively. Baseline characteristics, factors affecting quality of life, chronicity of disease, signs and symptoms, body weight and laboratory investigations were recorded. Side effects and complications developed, if any were recorded during and after the study. Statistical Analysis Used: Results were expressed as mean ± SEM. Data was statistically evaluated using t-test, Wilcoxon test, Mann Whitney U test, Kruskal Wallis test and ANOVA, wherever applicable, using GraphPad Prism 6. Results: All the groups responded positively to the treatments. All the patients were positive for occult blood in stool which reversed significantly after treatment along with rise in hemoglobin. Patients treated with herbal tablets alone showed maximal reduction in abdominal pain, diarrhea, and bowel frequency and stool consistency scores than Mesalamine treated patients. Treatment with herbal tablet alone and in combination with Mesalamine significantly reduced the stool infection. Patients treated with herbal drug alone and in combination did not report any side effects, relapse or complications while 50% patients treated with Mesalamine exhibited the relapse with

  4. Genomic diversity and affinities in population groups of North West India: an analysis of Alu insertion and a single nucleotide polymorphism.

    Science.gov (United States)

    Saini, J S; Kumar, A; Matharoo, K; Sokhi, J; Badaruddoza; Bhanwer, A J S

    2012-12-15

    The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy-Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764......, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report...

  6. A First Generation Microsatellite- and SNP-Based Linkage Map of Jatropha

    Science.gov (United States)

    Wang, Chun Ming; Liu, Peng; Yi, Chengxin; Gu, Keyu; Sun, Fei; Li, Lei; Lo, Loong Chueng; Liu, Xiaokun; Feng, Felicia; Lin, Grace; Cao, Suying; Hong, Yan; Yin, Zhongchao; Yue, Gen Hua

    2011-01-01

    Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation. PMID:21901124

  7. A first generation microsatellite- and SNP-based linkage map of Jatropha.

    Directory of Open Access Journals (Sweden)

    Chun Ming Wang

    Full Text Available Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation.

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

    Science.gov (United States)

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

    2015-05-22

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

  9. SSR genetic linkage map construction of pea (Pisum sativum L. based on Chinese native varieties

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    Xuelian Sun

    2014-04-01

    Full Text Available Simple sequence repeat (SSR markers have previously been applied to linkage mapping of the pea (Pisum sativum L. genome. However, the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited. A novel set of pea SSR markers was accordingly developed. Together with existing SSR sequences, the genome of the G0003973 (winter hardy × G0005527 (cold sensitive cross was mapped using 190 F2 individuals. In total, 157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM. The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.

  10. Ampelomyces mycoparasites from apple powdery mildew identified as a distinct group based on single-stranded conformation polymorphism analysis of the rDNA ITS region.

    Science.gov (United States)

    Szentiványi, Orsolya; Kiss, Levente; Russell, John C; Kovács, Gábor M; Varga, Krisztina; Jankovics, Tünde; Lesemann, Silke; Xu, Xiang-Ming; Jeffries, Peter

    2005-04-01

    Pycnidial fungi belonging to the genus Ampelomyces are the most common natural antagonists of powdery mildews worldwide. During a study of the interactions between apple powdery mildew (Podosphaera leucotricha) and Ampelomyces mycoparasites, 52 new Ampelomyces isolates were obtained from P. leucotricha and, in addition, 13 new isolates from other species of the Erysiphaceae in four European countries. Their genetic diversity was screened using single-stranded conformation polymorphism (SSCP) analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA). For comparison, 24 isolates obtained from genetic resource collections or other sources were included in this study. Based on the ITS-SSCP patterns, the isolates were placed in eight groups. The isolates belonged to two types based on their growth in culture. The faster-growing and the slower-growing isolates were included in different SSCP groups. A phylogenetic analysis of the ITS sequences of representatives of these groups confirmed the results obtained with the SSCP method, and showed that the faster-growing isolates do not belong to Ampelomyces as suggested by earlier studies. All the isolates from P. leucotricha fell into a distinct SSCP group of genetically homogeneous isolates. This suggests that Ampelomyces mycoparasites which occur in apple powdery mildew are slightly different from the other Ampelomyces groups which contain mycoparasites from various powdery mildew species. This may be because the main growth period of Ampelomyces mycoparasites in apple powdery mildew is isolated in time from that of Ampelomyces isolates that occur in other species of the Erysiphaceae. P. leucotricha starts its life-cycle early in the season, usually in March-April, while most powdery mildews are active in the same environments only late in the year.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  12. Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae

    Directory of Open Access Journals (Sweden)

    Naumann Julia

    2011-12-01

    Full Text Available Abstract Background The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae, one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools. Results We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia. Conclusions Single (or very low copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of

  13. Behavioural interventions for sleep problems in people with an intellectual disability: a systematic review and meta-analysis of single case and group studies.

    Science.gov (United States)

    Priday, L J; Byrne, C; Totsika, V

    2017-01-01

    Behavioural interventions are frequently used to address sleep problems in people with intellectual disabilities (ID). The current study aimed to systematically review evidence on the efficacy of behavioural interventions for children and adults with ID and sleep problems. Electronic and hand searches identified seven studies for inclusion (N = 169). Standardised mean difference effect sizes (d) were calculated for group studies (N = 4). Non-overlap effect sizes (Tau-U) were calculated for single case experimental design studies (SCEDs; N = 3). A large effect size (weighted d = 0.923, confidence interval: 0.705 to 1.151) across group studies indicated large improvements in sleep problems following behavioural intervention. Effect size across SCEDs (weighted Tau-U: 0.528, confidence interval: 0.351 to 0.705) indicated a 53% improvement compared with baseline. Sleep initiation and sleep maintenance problems showed significant improvements post-intervention. Follow-up effects were less consistent across study designs and suggested that some sleep problems maintain gains better than others. Meta-analytic evidence from group and SCEDs can provide complementary information about efficacy. Findings propose that behavioural interventions are a promising evidence-based practice for improving sleep problems in people with ID. © 2016 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

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

    Directory of Open Access Journals (Sweden)

    Patel Hardip R

    2011-08-01

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

  15. A Complex Multiherbal Regimen Based on Ayurveda Medicine for the Management of Hepatic Cirrhosis Complicated by Ascites: Nonrandomized, Uncontrolled, Single Group, Open-Label Observational Clinical Study.

    Science.gov (United States)

    Patel, Manish V; Patel, Kalapi B; Gupta, Shivenarain; Michalsen, Andreas; Stapelfeldt, Elmar; Kessler, Christian S

    2015-01-01

    Hepatic cirrhosis is one of the leading causes of death worldwide, especially if complicated by ascites. This chronic condition can be related to the classical disease entity jalodara in Traditional Indian Medicine (Ayurveda). The present paper aims to evaluate the general potential of Ayurvedic therapy for overall clinical outcomes in hepatic cirrhosis complicated by ascites (HCcA). In form of a nonrandomized, uncontrolled, single group, open-label observational clinical study, 56 patients fulfilling standardized diagnostic criteria for HCcA were observed during their treatment at the P. D. Patel Ayurveda Hospital, Nadiad, India. Based on Ayurvedic tradition, a standardized treatment protocol was developed and implemented, consisting of oral administration of single and compound herbal preparations combined with purificatory measures as well as dietary and lifestyle regimens. The outcomes were assessed by measuring liver functions through specific clinical features and laboratory parameters and by evaluating the Child-Pugh prognostic grade score. After 6 weeks of treatment and a follow-up period of 18 weeks, the outcomes showed statistically significant and clinically relevant improvements. Further larger and randomized trials on effectiveness, safety, and quality of the Ayurvedic approach in the treatment of HCcA are warranted to support these preliminary findings.

  16. Constraining the Single-degenerate Channel of Type Ia Supernovae with Stable Iron-group Elements in SNR 3C 397

    Energy Technology Data Exchange (ETDEWEB)

    Dave, Pranav; Kashyap, Rahul; Fisher, Robert [Department of Physics, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02740 (United States); Timmes, Frank [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Townsley, Dean [Department of Physics and Astronomy, Box 870324, University of Alabama, Tuscaloosa, AL 35487 (United States); Byrohl, Chris [Institut für Astrophysik, Georg August Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen (Germany)

    2017-05-20

    Recent Suzaku X-ray spectra of supernova remnant (SNR) 3C 397 indicate enhanced stable iron group element abundances of Ni, Mn, Cr, and Fe. Seeking to address key questions about the progenitor and explosion mechanism of 3C 397, we compute nucleosynthetic yields from a suite of multidimensional hydrodynamics models in the near-Chandrasekhar-mass, single-degenerate paradigm for Type Ia supernovae (SNe Ia). Varying the progenitor white dwarf (WD) internal structure, composition, ignition, and explosion mechanism, we find that the best match to the observed iron peak elements of 3C 397 are dense (central density ≥6 × 10{sup 9} g cm{sup −3}), low-carbon WDs that undergo a weak, centrally ignited deflagration, followed by a subsequent detonation. The amount of {sup 56}Ni produced is consistent with a normal or bright normal SNe Ia. A pure deflagration of a centrally ignited, low central density (≃2 × 10{sup 9} g cm{sup −3}) progenitor WD, frequently considered in the literature, is also found to produce good agreement with 3C 397 nucleosynthetic yields, but leads to a subluminous SN Ia event, in conflict with X-ray line width data. Additionally, in contrast to prior work that suggested a large supersolar metallicity for the WD progenitor for SNR 3C 397, we find satisfactory agreement for solar- and subsolar-metallicity progenitors. We discuss a range of implications our results have for the single-degenerate channel.

  17. A comparison of rofecoxib versus celecoxib in treating pain after dental surgery: a single-center, randomized, double-blind, placebo- and active-comparator-controlled, parallel-group, single-dose study using the dental impaction pain model.

    Science.gov (United States)

    Malmstrom, Kerstin; Fricke, James R; Kotey, Paul; Kress, Barbara; Morrison, Briggs

    2002-10-01

    Rofecoxib and celecoxib, selective cyclooxygenase-2 inhibitors, have analgesic efficacy similar to that of nonselective nonsteroidal anti-inflammatory drugs. This study was designed to confirm earlier findings that the overall analgesic efficacy of rofecoxib 50 mg was superior to that of celecoxib 200 mg and to extend the comparison to include celecoxib 400 mg. In this single-center, randomized, double-blind, placebo- and active-comparator-controlled, parallel-group, single-dose study, patients who experienced moderate or severe pain after surgical extraction of at least 2 third molars received a single oral dose of either rofecoxib 50 mg, celecoxib 400 mg, celecoxib 200 mg, ibuprofen 400 mg, or placebo. Patients recorded scores of pain intensity, pain relief, and global assessment at prespecified time intervals throughout the 24-hour period after dosing. The end points were total pain relief (TOPAR) score over 8 hours (TOPAR8; primary end point), TOPAR score over 12 hours (TOPAR12), sum of pain intensity difference (SPID) over 8 and 12 hours (SPID8 and SPID12), patient's global assessment of study drug at 8 hours, time to confirmed perceptible pain relief (ie, time to onset of analgesic effect), peak pain intensity difference (PID), peak pain relief, time to first dose of rescue medication (ie, duration of analgesic effect), and percentage of patients using rescue medication. A total of 482 patients (358 females, 124 males; mean age, 22.1 years) were enrolled. Rofecoxib 50 mg (n = 151 patients) demonstrated significantly greater overall analgesic efficacy compared with celecoxib 400 mg (n = 151), as measured by TOPAR8 (least squares mean [SE] 17.2 [0.8] vs 15.0 [0.8]; P TOPAR12 (25.3 [1.2] vs 21.0 [1.2]; P TOPAR8 scores (17.2 [0.8] vs 11.5 [1.1]; P TOPAR8, TOPAR12, SPID8, SPID12, and patient's global assessment] for all study drugs). The adverse-events (AE) profile was generally similar in all treatment groups. The 3 most common AEs were nausea, postextraction

  18. Can a Single Session of a Community-Based Group Exercise Program Combining Step Aerobics and Bodyweight Resistance Exercise Acutely Reduce Blood Pressure?

    Directory of Open Access Journals (Sweden)

    Mendes Romeu

    2014-12-01

    Full Text Available This study aimed to analyze the acute effects of a single session of a community-based group exercise program combining step aerobics and bodyweight resistance exercise on blood pressure in healthy young adult women. Twentythree healthy young adult women (aged 31.57 ± 7.87 years participated in two experimental sessions (exercise and control in a crossover study design. Blood pressure was monitored before, immediately after and at 10, 20 and 30 min of recovery. The exercise session consisted of four phases: 1 a warm-up (5 min of dance aerobics; 2 aerobic exercise training (30 min of step aerobics; 3 resistance exercise training (six sets of 12 repetitions of three bodyweight exercises in a circuit mode, 10 min; and 4 a cool-down (5 min of breathing and flexibility exercises; totaling 50 min of duration. Systolic blood pressure after exercise was significantly lower compared to control at the 10th min (-10.83 ± 2.13 vs. -2.6 ± 2.13 mmHg; p = 0.009, 20th min (-11.26 ± 2.13 vs. -3.04 ± 2.13 mmHg; p = 0.009 and 30th min of recovery (-10.87 ± 2.39 vs. -0.48 ± 2.39 mmHg; p = 0.004. A single session of a community-based group exercise program combining step aerobics and bodyweight resistance exercise was effective in inducing significant post-exercise hypotension in healthy young adult women. This type of low-cost exercise interventions may have an important role in the prevention of cardiovascular diseases and in community health promotion.

  19. A single source precursor route to group 13 homo- and heterometallic oxides as highly active supports for gold-catalyzed aerobic epoxidation of trans-stilbene

    KAUST Repository

    Mishra, Shashank K.

    2012-12-14

    A new Mitsubishi-type of star-shaped homoleptic derivative of indium(III), In4(mdea)6 (2, mdeaH2 = N-methyldiethanolamine) , was synthesized by the chloro-aminoalkoxo exchange reaction of a heteroleptic complex In6Cl6(mdea)6 (1) and used as a facile single source molecular precursor for the sol-gel preparation of high surface area indium oxide. Successful deposition of gold nanoparticles (1 wt.-%) of average size 3.3 nm on the above metal oxide by using HAuCl4· 3H2O afforded a highly efficient Au/In2O3 catalyst for the aerobic epoxidation of trans-stilbene at low temperature. The above single source precursor approach was further extended to obtain other group 13 homo- and heterometallic oxides, namely, α-Ga2O 3, β-Ga2O3 and Al4Ga 2O9, as highly active supports for gold catalysts. The obtained Au/M2O3 (M = Ga, In) and Au/Al4Ga 2O9 catalysts were thoroughly characterized by using several physicochemical techniques such as XRD, high resolution transmission electron microscopy (HR-TEM), energy-dispersive X-ray (EDX) spectroscopy, and X-ray photoelectron spectroscopy (XPS). A comparative study of the above catalysts for the model aerobic oxidation of stilbene in methylcyclohexane was undertaken. Highly efficient catalysts for aerobic oxidation reactions were obtained by depositing gold nanoparticles on group 13 mono- or mixed metal oxides prepared from the hydrolysis of well-characterized homo- and heterometallic N-methyldiethanolaminate derivatives. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo.

    Science.gov (United States)

    Gong, L; Pachner, M; Kalai, K; Lelley, T

    2008-11-01

    The first SSR-based genetic linkage map of Cucurbita moschata was created by integrating the maps of two F2 populations with one common parent developed from the crosses Waltham Butternut (WB) x Nigerian Local (NL) and ZHOU (a hull-less type) x WB. The integrated C. moschata map comprises 205 SSR markers and two morphological traits (Gr and n). The map is composed of 27 linkage groups with a marker density of 7 cM. Comparing the C. moschata map with the published Cucurbita pepo map, we found a high level of macrosynteny. Seventy-two of 76 common SSR markers between C. moschata and C. pepo were located in homologous linkage groups. These markers in general have conserved orders and similar genetic distances; they represent orthologous loci. A reference map based on these SSRs was obtained. No major chromosomal rearrangement between the two species could be detected at present, although four SSR markers were mapped in nonhomologous linkage groups. The comparative alignment of SSR markers did not provide any indication of a possible ancient polyploid origin of the species. The comparative mapping of C. moschata and C. pepo reported here will be useful for further studies on Cucurbit evolution, gene isolation, and breeding work.

  1. Efficient sequential and parallel algorithms for record linkage.

    Science.gov (United States)

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

    2014-01-01

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

  2. Strike-slip tectonics during rift linkage

    Science.gov (United States)

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

    2017-12-01

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

  3. A Novel Flux Linkage Indirect Measurement for Switched Reluctance Motor

    Science.gov (United States)

    Li, Pang; Zhang, Lei; Yu, Yue

    2017-05-01

    This paper presents a indirect detection system of flux linkage characteristic of switched reluctance motor based on dsPACE, fixed rotor position by mechanical indexing for Static flux linkage detection, the phase windings is excited by the step voltage signal, the voltage and phase current are collected real -time, and calculate flux linkage. The advantages of the method is that the parameters are optimized by ControlDesk, the flux linkage detection model is built by Simulink, no writing program, simple, easy implementation. An 1.5kw three-phase 12/8 SRM experimental prototype was constructed, the detection results of the Static flux linkage and dynamic flux linkage verified its validity and feasibility.

  4. Asperger syndrome and anxiety disorders (PAsSA) treatment trial: a study protocol of a pilot, multicentre, single-blind, randomised crossover trial of group cognitive behavioural therapy

    Science.gov (United States)

    Langdon, Peter E; Murphy, Glynis H; Wilson, Edward; Shepstone, Lee; Fowler, David; Heavens, David; Malovic, Aida; Russell, Alexandra

    2013-01-01

    Introduction A number of studies have established that children, adolescents and adults with Asperger syndrome (AS) and high functioning autism (HFA) have significant problems with anxiety. Cognitive behavioural therapy (CBT) is an effective treatment for anxiety in a variety of clinical populations. There is a growing interest in exploring the effectiveness of CBT for people with AS who have mental health problems, but currently there are no known clinical trials involving adults with AS or HFA. Studies with children who have AS have reported some success. The current study aims to examine whether modified group CBT for clinically significant anxiety in an AS population is likely to be efficacious. Methods and analysis This study is a randomised, single-blind crossover trial. At least 36 individuals will be recruited and randomised into a treatment arm or a waiting-list control arm. During treatment, individuals will receive 3 sessions of individual CBT, followed by 21 sessions of group CBT. Primary outcome measures focus on anxiety. Secondary outcome measures focus on everyday social and psychiatric functioning, additional measures of anxiety and fear, depression, health-related quality of life and treatment cost. Assessments will be administered at pregroup and postgroup and at follow-up by researchers who are blinded to group allocation. The trial aims to find out whether or not psychological treatments for anxiety can be adapted and used to successfully treat the anxiety experienced by people with AS. Furthermore, we aim to determine whether this intervention represents good value for money. Ethics and dissemination The trial received a favourable ethical opinion from a National Health Service (NHS) Research Ethics Committee. All participants provided written informed consent. Findings will be shared with all trial participants, and the general public, as well as the scientific community. Trial Registration ISRCTN 30265294 (DOI: 10.1186/ISRCTN30265294), UKCRN

  5. Asperger syndrome and anxiety disorders (PAsSA) treatment trial: a study protocol of a pilot, multicentre, single-blind, randomised crossover trial of group cognitive behavioural therapy.

    Science.gov (United States)

    Langdon, Peter E; Murphy, Glynis H; Wilson, Edward; Shepstone, Lee; Fowler, David; Heavens, David; Malovic, Aida; Russell, Alexandra

    2013-07-30

    A number of studies have established that children, adolescents and adults with Asperger syndrome (AS) and high functioning autism (HFA) have significant problems with anxiety. Cognitive behavioural therapy (CBT) is an effective treatment for anxiety in a variety of clinical populations. There is a growing interest in exploring the effectiveness of CBT for people with AS who have mental health problems, but currently there are no known clinical trials involving adults with AS or HFA. Studies with children who have AS have reported some success. The current study aims to examine whether modified group CBT for clinically significant anxiety in an AS population is likely to be efficacious. This study is a randomised, single-blind crossover trial. At least 36 individuals will be recruited and randomised into a treatment arm or a waiting-list control arm. During treatment, individuals will receive 3 sessions of individual CBT, followed by 21 sessions of group CBT. Primary outcome measures focus on anxiety. Secondary outcome measures focus on everyday social and psychiatric functioning, additional measures of anxiety and fear, depression, health-related quality of life and treatment cost. Assessments will be administered at pregroup and postgroup and at follow-up by researchers who are blinded to group allocation. The trial aims to find out whether or not psychological treatments for anxiety can be adapted and used to successfully treat the anxiety experienced by people with AS. Furthermore, we aim to determine whether this intervention represents good value for money. The trial received a favourable ethical opinion from a National Health Service (NHS) Research Ethics Committee. All participants provided written informed consent. Findings will be shared with all trial participants, and the general public, as well as the scientific community. ISRCTN 30265294 (DOI: 10.1186/ISRCTN30265294), UKCRN 8370.

  6. Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.).

    Science.gov (United States)

    Ogundiwin, Ebenezer A; Berke, Terry F; Massoudi, Mark; Black, Lowell L; Huestis, Gordon; Choi, Doil; Lee, Sanghyeob; Prince, James P

    2005-08-01

    Two linkage maps of pepper were constructed and used to identify quantitative trait loci (QTLs) conferring resistance to Phytophthora capsici. Inoculations were done with 7 isolates: 3 from Taiwan, 3 from California, and 1 from New Mexico. The first map was constructed from a set of recombinant inbred lines (RILs) of the PSP-11 (susceptible) x PI201234 (resistant) cross; and the second map was from a set of F(2) lines of the Joe E. Parker' (susceptible) x 'Criollo de Morelos 334' (resistant) cross. The RIL map covered 1466.1 cM of the pepper genome, and it consisted of 144 markers -- 91 amplified fragment length polymorphisms (AFLPs), 34 random amplified polymorphic DNA (RAPDs), 15 simple sequence repeats (SSRs), 1 sequence characterized amplified region (SCAR), and 3 morphological markers -- distributed over 17 linkage groups. The morphological markers mapped on this population were erect fruit habit (up), elongated fruit shape (fs(e)), and fasciculate fruit clusters (fa). The F(2) map consisted of 113 markers (51 AFLPs, 45 RAPDs, 14 SSRs, and 3 SCARs) distributed in 16 linkage groups, covering a total of 1089.2 cM of the pepper genome. Resistance to both root rot and foliar blight were evaluated in the RIL population using the 3 Taiwan isolates; the remaining isolates were used for the root-rot test only. Sixteen chromosomal regions of the RIL map contained single QTLs or clusters of resistance QTLs that had an effect on root rot and (or) foliar blight, revealing a complex set of genetics involved in resistance to P. capsici. Five QTLs were detected in the F(2) map that had an effect on resistance to root rot.

  7. 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...

  8. Hydrogen peroxide elimination from C4a-hydroperoxyflavin in a flavoprotein oxidase occurs through a single proton transfer from flavin N5 to a peroxide leaving group.

    Science.gov (United States)

    Sucharitakul, Jeerus; Wongnate, Thanyaporn; Chaiyen, Pimchai

    2011-05-13

    C4a-hydroperoxyflavin is found commonly in the reactions of flavin-dependent monooxygenases, in which it plays a key role as an intermediate that incorporates an oxygen atom into substrates. Only recently has evidence for its involvement in the reactions of flavoprotein oxidases been reported. Previous studies of pyranose 2-oxidase (P2O), an enzyme catalyzing the oxidation of pyranoses using oxygen as an electron acceptor to generate oxidized sugars and hydrogen peroxide (H(2)O(2)), have shown that C4a-hydroperoxyflavin forms in P2O reactions before it eliminates H(2)O(2) as a product (Sucharitakul, J., Prongjit, M., Haltrich, D., and Chaiyen, P. (2008) Biochemistry 47, 8485-8490). In this report, the solvent kinetic isotope effects (SKIE) on the reaction of reduced P2O with oxygen were investigated using transient kinetics. Our results showed that D(2)O has a negligible effect on the formation of C4a-hydroperoxyflavin. The ensuing step of H(2)O(2) elimination from C4a-hydroperoxyflavin was shown to be modulated by an SKIE of 2.8 ± 0.2, and a proton inventory analysis of this step indicates a linear plot. These data suggest that a single-proton transfer process causes SKIE at the H(2)O(2) elimination step. Double and single mixing stopped-flow experiments performed in H(2)O buffer revealed that reduced flavin specifically labeled with deuterium at the flavin N5 position generated kinetic isotope effects similar to those found with experiments performed with the enzyme pre-equilibrated in D(2)O buffer. This suggests that the proton at the flavin N5 position is responsible for the SKIE and is the proton-in-flight that is transferred during the transition state. The mechanism of H(2)O(2) elimination from C4a-hydroperoxyflavin is consistent with a single proton transfer from the flavin N5 to the peroxide leaving group, possibly via the formation of an intramolecular hydrogen bridge.

  9. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

    Directory of Open Access Journals (Sweden)

    Matsumoto Takashi

    2010-04-01

    Full Text Available Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin. Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7% deviated (p Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker

  10. Single-stage osseointegrated reconstruction and rehabilitation of lower limb amputees: the Osseointegration Group of Australia Accelerated Protocol-2 (OGAAP-2) for a prospective cohort study.

    Science.gov (United States)

    Al Muderis, Munjed; Lu, William; Tetsworth, Kevin; Bosley, Belinda; Li, Jiao Jiao

    2017-03-22

    Lower limb amputations have detrimental influences on the quality of life, function and body image of the affected patients. Following amputation, prolonged rehabilitation is required for patients to be fitted with traditional socket prostheses, and many patients experience symptomatic socket-residuum interface problems which lead to reduced prosthetic use and quality of life. Osseointegration has recently emerged as a novel approach for the reconstruction of amputated limbs, which overcomes many of the socket-related problems by directly attaching the prosthesis to the skeletal residuum. To date, the vast majority of osseointegration procedures worldwide have been performed in 2 stages, which require at least 4 months and up to 18 months for the completion of reconstruction and rehabilitation from the time of the initial surgery. The current prospective cohort study evaluates the safety and efficacy of a single-stage osseointegration procedure performed under the Osseointegration Group of Australia Accelerated Protocol-2 (OGAAP-2), which dramatically reduces the time of recovery to ∼3-6 weeks. The inclusion criteria for osseointegrated reconstruction under the OGAAP-2 procedure are age over 18 years, unilateral transfemoral amputation and experiencing problems or difficulties in using socket prostheses. All patients receive osseointegrated implants which are press-fitted into the residual bone. Functional and quality-of-life outcome measures are recorded preoperatively and at defined postoperative follow-up intervals up to 2 years. Postoperative adverse events are also recorded. The preoperative and postoperative values are compared for each outcome measure, and the benefits and harms of the single-stage OGAAP-2 procedure will be compared with the results obtained using a previously employed 2-stage procedure. This study has received ethics approval from the University of Notre Dame, Sydney, Australia (014153S). The study outcomes will be disseminated

  11. Genome scan of schizophrenia families in a large Veterans Affairs Cooperative Study sample: evidence for linkage to 18p11.32 and for racial heterogeneity on chromosomes 6 and 14.

    Science.gov (United States)

    Faraone, S V; Skol, A D; Tsuang, D W; Young, K A; Haverstock, S L; Prabhudesai, S; Mena, F; Menon, A S; Leong, L; Sautter, F; Baldwin, C; Bingham, S; Weiss, D; Collins, J; Keith, T; Vanden Eng, J L; Boehnke, M; Tsuang, M T; Schellenberg, G D

    2005-11-05

    Genome-wide linkage analyses of schizophrenia have identified several regions that may harbor schizophrenia susceptibility genes but, given the complex etiology of the disorder, it is unlikely that all susceptibility regions have been detected. We report results from a genome scan of 166 schizophrenia families collected through the Department of Veterans Affairs Cooperative Studies Program. Our definition of affection status included schizophrenia and schizoaffective disorder, depressed type and we defined families as European American (EA) and African American (AA) based on the probands' and parents' races based on data collected by interviewing the probands. We also assessed evidence for racial heterogeneity in the regions most suggestive of linkage. The maximum LOD score across the genome was 2.96 for chromosome 18, at 0.5 cM in the combined race sample. Both racial groups showed LOD scores greater than 1.0 for chromosome 18. The empirical P-value associated with that LOD score is 0.04 assuming a single genome scan for the combined sample with race narrowly defined, and 0.06 for the combined sample allowing for broad and narrow definitions of race. The empirical P-value of observing a LOD score as large as 2.96 in the combined sample, and of at least 1.0 in each racial group, allowing for narrow and broad racial definitions, is 0.04. Evidence for the second and third largest linkage signals come solely from the AA sample on chromosomes 6 (LOD = 2.11 at 33.2 cM) and 14 (LOD = 2.13 at 51.0). The linkage evidence differed between the AA and EA samples (chromosome 6 P-value = 0.007 and chromosome 14 P-value = 0.004). (c) 2005 Wiley-Liss, Inc.

  12. A case study of single hygroscopicity parameter and its link to the functional groups and phase transition for urban aerosols in Taipei City

    Science.gov (United States)

    Hung, Hui-Ming; Hsu, Chia-Hung; Lin, Wei-Ting; Chen, Yu-Quan

    2016-05-01

    The hygroscopicity, functional groups and phase transitions of urban aerosol particles in Taipei City were studied using a cloud condensation nuclei counter (CCNc) with a scanning mobility particle sizer (SMPS) and an attenuated total reflectance with infrared (ATR-IR) detection technique. With the assumption of larger particles being activated first, the derived single hygroscopicity parameter (κ) exhibited an increasing trend with particle size, i.e., from 0.022 ± 0.01 at 87 ± 10 nm to 0.13 ± 0.03 at 240 ± 20 nm. The collected size-selected particles were characterized using ATR-IR for the functional groups of alkyl, carbonyl, ammonium, sulfate and nitrate, which showed various size dependence patterns, linked to different formation mechanisms. The hygroscopic response based on the ratio (xW_solute) for sample film of absorption by the enhanced water-stretching peak to that by the selected solute showed a better consistency with pure ammonium sulfate for sub-micron size particles. Based on the derived ammonium sulfate volume fraction from IR analysis, the κ received from CCNc measurements was concluded mainly contributed by ammonium sulfate for sub-micrometer particles. The increasing trend of sodium nitrate absorbance at aerosol diameter ≥1 μm was due to a reaction of nitric acid with sea salt particles. The micrometer sized particles were apparent not only in a significantly higher xW_solute than pure sodium nitrate but also had a deliquescence RH of 69 ± 1%, similar to that of sodium nitrate-sodium chloride mixtures. Overall, the organic species in this study exhibited a low hygroscopicity with less than 0.036 of contribution for the overall κ, and the major hygroscopic material of urban aerosols consisted primarily of ammonium sulfate in the sub-micrometer particles and sodium nitrate with sea salt in the coarse particles.

  13. HEAD - TO - HEAD COMPARISON OF TOLERABILITY AND ACCEPTABILITY OF SINGLE DOSE OF FOUR TOPICAL NSAIDS IN PATIENTS UNDERGOING CATARACT SURGERY : A RANDOMIZED OPEN LABEL PARALLEL GROUP STUDY

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar

    2015-07-01

    Full Text Available INTRODUCTION : Ophthalmic NSAIDs are used to control pain , discomfort and inflammation associated with ocular conditions and also , following ophthalmic cataract surgeries. These drugs can cause ocular discomfort following administration which lasts for a short duration. However , there exist differences in the intensity and duration of burning sensation among the c ommonly used ophthalmic NSAIDs. Hence , we evaluated the tolerability and acceptability of four topical NSAIDS i.e. , 0.3% nepafenac (N , 0.5% ketorolac (K , 0.4% ketorolac (K LS and 0.09% bromfenac (B after instilling a single drop. METHODS: This randomized , open label , parallel group study was conducted in the department of Ophthalmology in Narayana Medical College , Nellore. A total number of 80 patients participated in the study. Randomization list was computer generated in a ratio of 1:1:1:1 of N , K , K L Sand B. Each patient received one drop of the study drug either in right or left eye which was also decidedat random.Patients of either gender above21 years of age , having no ocular surface pathology and eligible for cataract surgery were include d in the study. Outcome variables included ocular burning intensity on VAS (0 - 100 mm at 0 min (immediately , 2 min and 6 min after administration of medications , time to complete pain relief and global medication performance rated by patient as 0 (bad , 1 (fair , 2(good or 3 (severe . RESULTS: The mean age of patients was 52.85±17.46 years. All groups were age matched , however there were more females than males (pN>K LS >K on global medication performance. CONCLUSION: Bromfenac had better tolerability and acceptability as compared to other tested topical NSAIDs , which was in the order of B>N> K LS >K.

  14. Evaluation of a multiple-encounter in situ simulation for orientation of staff to a new paediatric emergency service: a single-group pretest/post-test study.

    Science.gov (United States)

    Davison, Michelle; Kinnear, Frances B; Fulbrook, Paul

    2017-10-01

    To assess the utility of a multiple-encounter in-situ (MEIS) simulation as an orientation tool for multidisciplinary staff prior to opening a new paediatric emergency service. A single-group pretest/post-test study was conducted. During the MEIS simulation, multidisciplinary staff with participant or observer roles managed eight children (mannequins) who attended triage with their parent/guardians (clinical facilitators) for a range of emergency presentations (structured scenarios designed to represent the expected range of presentations plus test various clinical pathways/systems). Participants were debriefed to explore clinical, systems and crisis-resource management issues. Participants also completed a pre-intervention and post-intervention questionnaire comprising statements about role confidence and orientation adequacy. Pre-test and post-test results were analysed using t-test and Wilcoxon signed rank test. Eighty-nine staff participated in the MEIS simulation, with the majority completing the pre-simulation and post-simulation questionnaire. There was a significant improvement in post-intervention versus pre-intervention Likert scores for role confidence and orientation adequacy (p=0.001 and simulation was of utility in orientation of staff, at least with respect to self-reported role confidence and orientation adequacy. Its effectiveness in practice or compared with other orientation techniques was not assessed, but it did identify several flaws in planned systems allowing remediation prior to opening.

  15. Linkage to HIV, TB and non-communicable disease care from a mobile testing unit in Cape Town, South Africa.

    Directory of Open Access Journals (Sweden)

    Darshini Govindasamy

    Full Text Available HIV counseling and testing may serve as an entry point for non-communicable disease screening.To determine the yield of newly-diagnosed HIV, tuberculosis (TB symptoms, diabetes and hypertension, and to assess CD4 count testing, linkage to care as well as correlates of linkage and barriers to care from a mobile testing unit.A mobile unit provided screening for HIV, TB symptoms, diabetes and hypertension in Cape Town, South Africa between March 2010 and September 2011. The yield of newly-diagnosed cases of these conditions was measured and clients were followed-up between January and November 2011 to assess linkage. Linkage to care was defined as accessing care within one, three or six months post-HIV diagnosis (dependent on CD4 count and one month post-diagnosis for other conditions. Clinical and socio-demographic correlates of linkage to care were evaluated using Poisson regression and barriers to care were determined.Of 9,806 clients screened, the yield of new diagnoses was: HIV (5.5%, TB suspects (10.1%, diabetes (0.8% and hypertension (58.1%. Linkage to care for HIV-infected clients, TB suspects, diabetics and hypertensives was: 51.3%, 56.7%, 74.1% and 50.0%. Only disclosure of HIV-positive status to family members or partners (RR=2.6, 95% CI: 1.04-6.3, p=0.04 was independently associated with linkage to HIV care. The main barrier to care reported by all groups was lack of time to access a clinic.Screening for HIV, TB symptoms and hypertension at mobile units in South Africa has a high yield but inadequate linkage. After-hours and weekend clinics may overcome a major barrier to accessing care.

  16. Linkage to care and treatment for TB and HIV among people newly diagnosed with TB or HIV-associated TB at a large, inner city South African hospital.

    Directory of Open Access Journals (Sweden)

    Yara Voss De Lima

    Full Text Available To assess the outcomes of linkage to TB and HIV care and identify risk factors for poor referral outcomes.Cohort study of TB patients diagnosed at an urban hospital.Linkage to care was determined by review of clinic files, national death register, and telephone contact, and classified as linked to care, delayed linkage to care (>7 days for TB treatment, >30 days for HIV care, or failed linkage to care. We performed log-binomial regression to identify patient and referral characteristics associated with poor referral outcomes.Among 593 TB patients, 23% failed linkage to TB treatment and 30.3% of the 77.0% who linked to care arrived late. Among 486 (86.9% HIV-infected TB patients, 38.3% failed linkage to HIV care, and 32% of the 61.7% who linked to care presented late. One in six HIV-infected patients failed linkage to both TB and HIV care. Only 20.2% of HIV-infected patients were referred to a single clinic for integrated care. A referral letter was present in 90.3%, but only 23.7% included HIV status and 18.8% CD4 cell count. Lack of education (RR 1.85 and low CD4 count (CD4≤50 vs. >250cells/mm(3; RR 1.66 were associated with failed linkage to TB care. Risk factors for failed linkage to HIV care were antiretroviral-naïve status (RR 1.29, and absence of referral letter with HIV or CD4 cell count (RR1.23.Linkage to TB/HIV care should be strengthened by communication of HIV and CD4 results, ART initiation during hospitalization and TB/HIV integration at primary care.

  17. 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

    In fine mapping of a large-scale experimental population where collection of phenotypes are very expensive, difficult to record or time-demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage...... 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...... 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...

  18. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.

    Science.gov (United States)

    Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R; Wang, Xiaolu

    2016-03-01

    Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.

  19. Preliminary genetic linkage maps of Chinese herb Dendrobium ...

    Indian Academy of Sciences (India)

    2013-08-05

    Aug 5, 2013 ... [Feng S., Zhao H., Lu J., Liu J., Shen B. and Wang H. 2013 Preliminary genetic linkage maps of Chinese herb Dendrobium nobile and. D. moniliforme. J. Genet. 92, 205–212]. Introduction ..... ity, and inbreeding depression make F2 or backcross popu- lations rarely available for genetic linkage mapping ...

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

    Science.gov (United States)

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

    2014-08-01

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

  1. Linkages and Networks in the Structure of Personal Power.

    Science.gov (United States)

    MacConkey, Dorothy I.

    1980-01-01

    People in academic social systems who are interested in promotions learn about decision-making processes in academe, and about communication linkages. They learn to grasp the impact of these linkages and the support networks. An irrefutable ingredient is a sterling professional performance. Applying personal power requires individual tailoring.…

  2. Urban-rural linkages enhancing European territorial competitiveness: background paper

    OpenAIRE

    Davidson, Gill

    2008-01-01

    This background paper provides the context for the seminar on urban-rural linkages enhancing European territorial competitiveness, to be held by DG REGIO on 17th September 2008. This seminar forms part of an ongoing debate at European level on the importance of urban-rural linkages for territorial competitiveness, and on appropriate support mechanisms to assist these developments in Member States.

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

    African Journals Online (AJOL)

    This article examines the linkages between the tourism and agriculture sectors in Botswana using evidence gathered from the country's growing safari lodge accommodation sector. The findings reveal limited local linkages between agriculture and tourism, and instead the existence of high levels of food imports from ...

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

    African Journals Online (AJOL)

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

  5. Genome-wide linkage analysis for human longevity

    DEFF Research Database (Denmark)

    Beekman, Marian; Blanché, Hélène; Perola, Markus

    2013-01-01

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

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

    African Journals Online (AJOL)

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

  7. A preliminary linkage map using spotted melanic laboratory strains ...

    Indian Academy of Sciences (India)

    Kondo S. et al. 2000 A detailed linkage map of Medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics. 154, 1773–1784. Nichols K. M., Young W. P., Danzmann R. G., Robison B. D.,. Rexroad C., Noakes M. et al. 2003 A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim.

  8. Hypothesis testing in genetic linkage analysis via Gibbs sampling ( )

    African Journals Online (AJOL)

    hope&shola

    2010-12-06

    Dec 6, 2010 ... Genetic linkage analysis involves estimating parameters in a genetic model in which a genetic trait is regressed on some factors such as ... Key words: Gibbs sampling, pedigree, linkage analysis, likelihood. INTRODUCTION ..... Pattern Analysis and Machine Intelligence, 6: 721-741. Guo SW, Thompson EA ...

  9. Linkage localization of X-linked Charcot-Marie-Tooth disease

    Energy Technology Data Exchange (ETDEWEB)

    Bergoffen, J. (Children' s Hospital, Philadelphia, PA (United States) Univ. of Pennsylvania, Philadelphia (United States)); Trofatter, J.; Haines, J.L. (Massachusetts General Hospital, Boston (United States)); Pericak-Vance, M.A. (Duke Univ., Durham, NC (United States)); Chance, P.F. (Univ. of Utah, Salt Lake City (United States)); Fischbeck, K.H. (Univ. of Pennsylvania, Philadelphia (United States))

    1993-02-01

    Charcot-Marie-Tooth disease (CMT), also known as hereditary motor and sensory neuropathy, is a heterogeneous group of slowly progressive, degenerative disorders of peripheral nerve. X-linked CMT (CMTX) (McKusick 302800), a subdivision of type I, or demyelinating, CMT is an X-linked dominant condition with variable penetrance. Previous linkage analysis using RFLPs demonstrated linkage to markers on the proximal long and short arms of the X chromosome, with the more likely localization on the proximal long arm of the X chromosome. Available variable simple-sequence repeats (VSSRs) broaden the possibilities for linkage analysis. This paper presents new linkage data and recombination analysis derived from work with four VSSR markers - AR, PGKP1, DXS453, and DXYS1X - in addition to analysis using RFLP markers described elsewhere. These studies localize the CMTX gene to the proximal Xq segment between PGKP1 (Xq11.2-12) and DXS72 (Xq21.1), with a combined maximum multipoint lod score of 15.3 at DXS453 ([theta] = 0). 32 refs., 3 figs., 2 tabs.

  10. Thermally activated, single component epoxy systems

    KAUST Repository

    Unruh, David A.

    2011-08-23

    A single component epoxy system in which the resin and hardener components found in many two-component epoxies are combined onto the same molecule is described. The single molecule precursor to the epoxy resin contains both multiple epoxide moieties and a diamine held latent by thermally degradable carbamate linkages. These bis-carbamate "single molecule epoxies" have an essentially infinite shelf life and access a significant range in curing temperatures related to the structure of the carbamate linkages used. © 2011 American Chemical Society.

  11. Dimensional synthesis of six-bar Stephenson II linkage for fifteen precision points path generation

    Directory of Open Access Journals (Sweden)

    Khalid Nafees

    2016-09-01

    Full Text Available This paper presents the dimensional synthesis of a planar six-bar Stephenson II linkage having single degree of freedom with rotational constraints. The objective of the synthesis is to determine all the link lengths with their orientations of the linkage that is capable to follow the path specified by fifteen precision points. The analytical loop closure equations are formed using dyad and triad technique by means of complex number mathematics for path generation. These equations are solved simultaneously for fifteen displacement positions of coupler tracing point to determine various link lengths with their corresponding orientations. The displacement vector and coupler link motion are the prescribed parameters. The effectiveness of mechanism synthesis has been demonstrated on a numerical example. The solution of loop closure equations has been obtained using a MATLAB code. Finally, the determined link lengths with their orientations have been verified using SAM software.

  12. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  14. The Efficacy and Tolerability of the Clonidine Transdermal Patch in the Treatment for Children with Tic Disorders: A Prospective, Open, Single-Group, Self-Controlled Study.

    Science.gov (United States)

    Song, Pan-Pan; Jiang, Li; Li, Xiu-Juan; Hong, Si-Qi; Li, Shuang-Zi; Hu, Yue

    2017-01-01

    To evaluate the efficacy and tolerability of a clonidine transdermal patch in the treatment of children with tic disorders (TD) and to establish a predictive model for patients. Forty-one patients who met the inclusion criteria entered into 12 weeks of prospective, open, single-group, self-controlled treatment with a clonidine transdermal patch. The Yale Global Tic Severity Scale (YGTSS) was employed before therapy (baseline) and at 4, 8, and 12 weeks after therapy. (1) The total effect rates of treatment with a clonidine transdermal patch were 29.27, 53.66, and 63.41% at 4, 8, and 12 weeks, respectively. Compared with the baseline, the differences were significant at three different observation periods. (2) Compared to the level of 25% reduction, there were significant decreases in the score-reducing rate of motor tic and total tic severities at 12 weeks. (3) If the disease course was ≤24 months and the motor tic score was tic score was >16, there was an effective rate of 57.1%. If the disease course was >24 months and the clinical classification was chronic TD, there was an effective rate of 62.5%. If the disease course was >24 months and the clinical classification was Tourette's syndrome, 90% of the patients were invalid. (4) The main adverse events were rash, slight dizziness, and headache. (1) When patients were pretreated with a D2-dopamine receptor antagonist that was ineffective or not tolerated well, switching to a clonidine transdermal patch treatment was effective and safe. (2) A clonidine transdermal patch could be a first-line medication for mild and moderate TD cases that are characterized by motor tics.

  15. Induction with Infliximab and a Plant-Based Diet as First-Line (IPF) Therapy for Crohn Disease: A Single-Group Trial.

    Science.gov (United States)

    Chiba, Mitsuro; Tsuji, Tsuyotoshi; Nakane, Kunio; Tsuda, Satoko; Ishii, Hajime; Ohno, Hideo; Watanabe, Kenta; Ito, Mai; Komatsu, Masafumi; Sugawara, Takeshi

    2017-01-01

    Approximately 30% of patients with Crohn disease (CD) are unresponsive to biologics. No previous study has focused on a plant-based diet in an induction phase of CD treatment. To investigate the remission rate of infliximab combined with a plant-based diet as first-line (IPF) therapy for CD. This was a prospective single-group trial conducted at tertiary hospitals. Subjects included consecutive adults with a new diagnosis (n = 26), children with a new diagnosis (n = 11), and relapsing adults (n = 9) with CD who were naïve to treatment with biologics. Patients were admitted and administered a standard induction therapy with infliximab (5 mg/kg; 3 infusions at 0, 2, and 6 weeks). Additionally, they received a lacto-ovo-semivegetarian diet. The primary end point was remission, defined as the disappearance of active CD symptoms at week 6. Secondary end points were Crohn Disease Activity Index (CDAI) score, C-reactive protein (CRP) concentration, and mucosal healing. Two adults with a new diagnosis were withdrawn from the treatment protocol because of intestinal obstruction. The remission rates by the intention-to-treat and per-protocol analyses were 96% (44/46) and 100% (44/44), respectively. Mean CDAI score (314) on admission decreased to 63 at week 6 (p < 0.0001). Mean CRP level on admission (5.3 mg/dL) decreased to 0.2 (p < 0.0001). Mucosal healing was achieved in 46% (19/41) of cases. IPF therapy can induce remission in most patients with CD who are naïve to biologics regardless of age or whether they have a new diagnosis or relapse.

  16. Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group.

    Science.gov (United States)

    Hakovirta, Janetta R; Prezioso, Samantha; Hodge, David; Pillai, Segaran P; Weigel, Linda M

    2016-11-01

    Analysis of 16S rRNA genes is important for phylogenetic classification of known and novel bacterial genera and species and for detection of uncultivable bacteria. PCR amplification of 16S rRNA genes with universal primers produces a mixture of amplicons from all rRNA operons in the genome, and the sequence data generally yield a consensus sequence. Here we describe valuable data that are missing from consensus sequences, variable effects on sequence data generated from nonidentical 16S rRNA amplicons, and the appearance of data displayed by different software programs. These effects are illustrated by analysis of 16S rRNA genes from 50 strains of the Bacillus cereus group, i.e., Bacillus anthracis, Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis These species have 11 to 14 rRNA operons, and sequence variability occurs among the multiple 16S rRNA genes. A single nucleotide polymorphism (SNP) previously reported to be specific to B. anthracis was detected in some B. cereus strains. However, a different SNP, at position 1139, was identified as being specific to B. anthracis, which is a biothreat agent with high mortality rates. Compared with visual analysis of the electropherograms, basecaller software frequently missed gene sequence variations or could not identify variant bases due to overlapping basecalls. Accurate detection of 16S rRNA gene sequences that include intragenomic variations can improve discrimination among closely related species, improve the utility of 16S rRNA databases, and facilitate rapid bacterial identification by targeted DNA sequence analysis or by whole-genome sequencing performed by clinical or reference laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  17. The effect of a career activity on the students' perception of the nursing profession and their career plan: A single-group experimental study.

    Science.gov (United States)

    Yilmaz, Arzu Akman; Ilce, Arzu; Can Cicek, Saadet; Yuzden, Ganime Esra; Yigit, Ummuhan

    2016-04-01

    Students' conceptualizations of nursing and their reasons for choosing the profession motivate them and affect their education, work performance and career plans. Nursing educators should support them to plan their careers consciously during their education. The study aimed to investigate the effect of career-planning event for nursing students on their conceptualizations of the nursing profession and their career plans. The study was as single-group experimental study using a pre-test and post-test. The career-planning event was held in the conference hall of the university involved in the current study, and was open to the all students of the nursing school. The sample of the study consisted of 105 students who participated in the "Nursing Career Symposium" held on 27 March 2015. Methods At the event, the importance of career planning and the opportunities of the nursing profession was presented. The data were collected using a questionnaire consisted of two sections including descriptive characteristics and the opinions of the students regarding their career plans and Perception of Nursing Profession Scale. The students completed the first section of the questionnaire before the career event began and the second section of the questionnaire and scale both before and after the event. The participants had positive conceptualizations of the profession. Following a career event, the participants' opinions of professional qualities and professional status as measured through the Perception of Nursing Profession Scale showed a significant increase, and that the event had made an important contribution to their career plans. In the light of these results, it is possible to suggest that such events have an important place during education in that they introduce the nursing profession, and they develop the students' positive thoughts regarding the profession in terms of both course content and teaching methodology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Feasibility and Safety of a Powered Exoskeleton for Assisted Walking for Persons With Multiple Sclerosis: A Single-Group Preliminary Study.

    Science.gov (United States)

    Kozlowski, Allan J; Fabian, Michelle; Lad, Dipan; Delgado, Andrew D

    2017-07-01

    To examine the feasibility, safety, and secondary benefit potential of exoskeleton-assisted walking with one device for persons with multiple sclerosis (MS). Single-group longitudinal preliminary study with 8-week baseline, 8-week intervention, and 4-week follow-up. Outpatient MS clinic, tertiary care hospital. Participants (N=13; age range, 38-62y) were mostly women with Expanded Disability Status Scale scores ranging from 5.5 to 7.0. Exoskeleton-assisted walk training. Primary outcomes were accessibility (enrollment/screen pass), tolerability (completion/dropout), learnability (time to event for standing, walking, and sitting with little or no assistance), acceptability (satisfaction on the device subscale of the Quebec User Evaluation of Satisfaction with Assistive Technology version 2), and safety (event rates standardized to person-time exposure in the powered exoskeleton). Secondary outcomes were walking without the device (timed 25-foot walk test and 6-minute walk test distance), spasticity (Modified Ashworth Scale), and health-related quality of life (Patient-Reported Outcomes Measurement and Information System pain interference and Quality of Life in Neurological Conditions fatigue, sleep disturbance, depression, and positive affect and well-being). The device was accessible to 11 and tolerated by 5 participants. Learnability was moderate, with 5 to 15 sessions required to walk with minimal assistance. Safety was good; the highest adverse event rate was for skin issues at 151 per 1000 hours' exposure. Acceptability ranged from not very satisfied to very satisfied. Participants who walked routinely improved qualitatively on sitting, standing, or walking posture. Two participants improved and 2 worsened on ≥1 quality of life domain. The pattern of spasticity scores may indicate potential benefit. The device appeared feasible and safe for about a third of our sample, for whom routine exoskeleton-assisted walking may offer secondary benefits. Copyright

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

    NARCIS (Netherlands)

    Kraakman, A.T.W.

    2005-01-01

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

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

    OpenAIRE

    Kraakman, A.T.W.

    2005-01-01

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

  1. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rabbi, Ismail Yusuf; Kulembeka, Heneriko Philbert; Masumba, Esther; Marri, Pradeep Reddy; Ferguson, Morag

    2012-07-01

    Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.

  2. Accuracy of Probabilistic Linkage Using the Enhanced Matching System for Public Health and Epidemiological Studies.

    Science.gov (United States)

    Aldridge, Robert W; Shaji, Kunju; Hayward, Andrew C; Abubakar, Ibrahim

    2015-01-01

    The Enhanced Matching System (EMS) is a probabilistic record linkage program developed by the tuberculosis section at Public Health England to match data for individuals across two datasets. This paper outlines how EMS works and investigates its accuracy for linkage across public health datasets. EMS is a configurable Microsoft SQL Server database program. To examine the accuracy of EMS, two public health databases were matched using National Health Service (NHS) numbers as a gold standard unique identifier. Probabilistic linkage was then performed on the same two datasets without inclusion of NHS number. Sensitivity analyses were carried out to examine the effect of varying matching process parameters. Exact matching using NHS number between two datasets (containing 5931 and 1759 records) identified 1071 matched pairs. EMS probabilistic linkage identified 1068 record pairs. The sensitivity of probabilistic linkage was calculated as 99.5% (95%CI: 98.9, 99.8), specificity 100.0% (95%CI: 99.9, 100.0), positive predictive value 99.8% (95%CI: 99.3, 100.0), and negative predictive value 99.9% (95%CI: 99.8, 100.0). Probabilistic matching was most accurate when including address variables and using the automatically generated threshold for determining links with manual review. With the establishment of national electronic datasets across health and social care, EMS enables previously unanswerable research questions to be tackled with confidence in the accuracy of the linkage process. In scenarios where a small sample is being matched into a very large database (such as national records of hospital attendance) then, compared to results presented in this analysis, the positive predictive value or sensitivity may drop according to the prevalence of matches between databases. Despite this possible limitation, probabilistic linkage has great potential to be used where exact matching using a common identifier is not possible, including in low-income settings, and for vulnerable

  3. Accuracy of Probabilistic Linkage Using the Enhanced Matching System for Public Health and Epidemiological Studies.

    Directory of Open Access Journals (Sweden)

    Robert W Aldridge

    Full Text Available The Enhanced Matching System (EMS is a probabilistic record linkage program developed by the tuberculosis section at Public Health England to match data for individuals across two datasets. This paper outlines how EMS works and investigates its accuracy for linkage across public health datasets.EMS is a configurable Microsoft SQL Server database program. To examine the accuracy of EMS, two public health databases were matched using National Health Service (NHS numbers as a gold standard unique identifier. Probabilistic linkage was then performed on the same two datasets without inclusion of NHS number. Sensitivity analyses were carried out to examine the effect of varying matching process parameters.Exact matching using NHS number between two datasets (containing 5931 and 1759 records identified 1071 matched pairs. EMS probabilistic linkage identified 1068 record pairs. The sensitivity of probabilistic linkage was calculated as 99.5% (95%CI: 98.9, 99.8, specificity 100.0% (95%CI: 99.9, 100.0, positive predictive value 99.8% (95%CI: 99.3, 100.0, and negative predictive value 99.9% (95%CI: 99.8, 100.0. Probabilistic matching was most accurate when including address variables and using the automatically generated threshold for determining links with manual review.With the establishment of national electronic datasets across health and social care, EMS enables previously unanswerable research questions to be tackled with confidence in the accuracy of the linkage process. In scenarios where a small sample is being matched into a very large database (such as national records of hospital attendance then, compared to results presented in this analysis, the positive predictive value or sensitivity may drop according to the prevalence of matches between databases. Despite this possible limitation, probabilistic linkage has great potential to be used where exact matching using a common identifier is not possible, including in low-income settings, and for

  4. Impact analysis of coal-electricity pricing linkage scheme in China based on stochastic frontier cost function

    International Nuclear Information System (INIS)

    Li, Hong-Zhou; Tian, Xian-Liang; Zou, Tao

    2015-01-01

    Highlights: • This study evaluates the coal-electricity pricing linkage policy in China. • Six stochastic frontier cost models are used to estimate efficiency measures. • The coal-electricity pricing linkage scheme is a double-edged sword. • We suggest the threshold value of 5% or group specific. - Abstract: This study evaluates the feasibility and fairness of 2012 amendment to coal-electricity pricing linkage policy in China. Our empirical design is based on several stochastic frontier cost functions and the results show that the amended pricing linkage scheme is a double-edged sword as follows. On the one hand, it provides incentives for less-efficient (with efficiency less than 90%) power plants to increase their efficiency. One the other hand, it imposes a penalty to highly-efficient power plants (with efficiency more than 90%). And even worse, the higher the efficiency is, the bigger the penalty will be. To make the current coal-electricity pricing linkage scheme more feasible, we suggest the threshold value of 5 instead of 10%, and a group specific threshold value instead of the current one-size-for-all practice

  5. Linkage analysis in familial Angelman syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Wagstaff, J. (Harvard Medical School, Boston, MA (United States)); Shugart, Y.Y. (Columbia Univ., New York (United States)); Lalande, M. (Harvard Medical School, Boston, MA (United States) Howard Hughes Medical Institute, Boston, MA (United States))

    1993-07-01

    Familial Angelman syndrome (AS) can result from mutations in chromosome 15q11q13 that, when transmitted from father to child, result in no phenotypic abnormality but, when transmitted from mother to child, cause AS. These mutations therefore behave neither as dominant nor as recessive mutations but, rather, show an imprinted mode of inheritance. The authors have analyzed two sibling pairs with AS and a larger family with four AS offspring of three sisters with several recently described microsatellite polymorphisms in the AS region. AS siblings inherited the same maternal alleles at the GABRB3 and GABRA5 loci, and the unaffected siblings of AS individuals inherited the other maternal alleles at these loci. In one of the AS sibling pairs, analysis of a recombination event indicates that the mutation responsible for AS is distal to locus D15S63. This result is consistent with a previously described imprinted submicroscopic deletion causing AS, a deletion that includes loci D15S10, D15S113, and GABRB3, all distal to D15S63. The analysis of the larger AS family provides the first clear demonstration of a new mutation in nondeletion AS. Analysis of linkage of AS to GABRB3 in these three families, on the assumption of imprinted inheritance (i.e., penetrance of an AS mutation is 1 if transmitted maternally and is 0 if transmitted paternally), indicates a maximum lod score of 3.52 at 6 = 0. 34 refs., 4 figs., 1 tab.

  6. Linkages at Tourism Destinations: Challenges in Zanzibar

    Directory of Open Access Journals (Sweden)

    Wineaster Anderson

    2011-06-01

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

  7. Rates, intrinsic linkages, and multistate population dynamics.

    Science.gov (United States)

    Schoen, Robert

    2017-01-01

    Demographic analyses of multistate populations are commonplace, as are situations where population stocks are known but population flows are not. Still, demographic models for multistate populations with changing rates remain at an early stage of development, limiting dynamic analyses and analytical projections. Here, a new approach, the Intrinsic Linkage-Rate Ratio (IL-RR) model, is presented and explored. The key IL parameter, w , is a simple weight for projecting populations. Using the ultimate state composition implied by the prevailing rates, the IL-RR model provides new relationships that connect multistate populations over time and allow analytical population projections. Parameter w reflects population metabolism and scales the level of the transfer rates. Compositional change is driven by the sequence of implicit stable population compositions. The IL-RR approach also provides a new method for estimating transfer rates within an interval from population numbers at the beginning and end of the interval. The new relationships developed advance the ability of demographers to model multistate populations with changing rates and to relate population stocks and flows.

  8. ANALYSIS OF INTER SECTORAL LINKAGES IN SEMARANG REGENCY

    Directory of Open Access Journals (Sweden)

    Fafurida

    2014-03-01

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

  9. A transparent and transportable methodology for evaluating Data Linkage software.

    Science.gov (United States)

    Ferrante, Anna; Boyd, James

    2012-02-01

    There has been substantial growth in Data Linkage (DL) activities in recent years. This reflects growth in both the demand for, and the supply of, linked or linkable data. Increased utilisation of DL "services" has brought with it increased need for impartial information about the suitability and performance capabilities of DL software programs and packages. Although evaluations of DL software exist; most have been restricted to the comparison of two or three packages. Evaluations of a large number of packages are rare because of the time and resource burden placed on the evaluators and the need for a suitable "gold standard" evaluation dataset. In this paper we present an evaluation methodology that overcomes a number of these difficulties. Our approach involves the generation and use of representative synthetic data; the execution of a series of linkages using a pre-defined linkage strategy; and the use of standard linkage quality metrics to assess performance. The methodology is both transparent and transportable, producing genuinely comparable results. The methodology was used by the Centre for Data Linkage (CDL) at Curtin University in an evaluation of ten DL software packages. It is also being used to evaluate larger linkage systems (not just packages). The methodology provides a unique opportunity to benchmark the quality of linkages in different operational environments. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Two single group, prospective, baseline-controlled feeding studies in infants and children with chronic diarrhea fed a hypoallergenic free amino acid-based formula.

    Science.gov (United States)

    Borschel, Marlene W; Antonson, Dean L; Murray, Nancy D; Oliva-Hemker, Maria; Mattis, Lynn E; Kerzner, Benny; Tolia, Vasundhara; Baggs, Geraldine

    2014-05-29

    Infants and children with chronic diarrhea (CD) often require specialized foods or parenteral nutrition (PN) to achieve adequate nutrient intakes to support growth and development. We assessed the efficacy of an amino acid-based formula (AAF) in supporting growth and improving symptoms in infants and children with CD from multiple etiologies. Two studies were conducted: CD study in children (CD-C) and CD study in infants (CD-I). Each was a single group, baseline-controlled study in which each subject served as his/her own control. At enrollment, all subjects had CD lasting > 2 weeks and had ≥ 4 stools/day. Subjects were fed an AAF for 80 days starting at SD5, and were assessed at SD 28 and 84. 18 of 19 subjects completed the study. At enrollment, the mean age was 5.6 ± 0.7 years, the most common diagnosis was short bowel syndrome (SBS) (n = 13), and 5 subjects with SBS were on PN. Subjects achieved significant increases in weight-for-age z-scores (p = 0.026). Over 50% of subjects achieved improvements in clinical outcomes targeted most frequently by their physicians. Of the five subjects on PN at enrollment, four had substantial weight gain and four had their PN requirements decreased. CD-I: 22 of 27 subjects completed the study. At enrollment, the mean age was 3.3 ± 0.3 months, the most common diagnosis was food allergy (n = 20), and no subjects were on PN. Subjects achieved significant increases in weight-for-age z-scores (p = 0.0023), significant decreases in the number of stools/day (p = 0.0012), and improvements in stool consistency (p = 0.0024). Over 80% of subjects achieved improvements in the clinical outcomes targeted most frequently by their physicians. Infants and children with CD fed an AAF for three months displayed significant improvements in weight-for-age z-scores and clinical symptoms. Children dependent on PN also grew well and four of five decreased their dependence on PN. Both trials were registered on ClinTrials.gov (CD-C, NCT01812629; CD

  11. Linkage and whole genome sequencing identify a locus on 6q25-26 for formal thought disorder and implicate MEF2A regulation

    DEFF Research Database (Denmark)

    Thygesen, Johan Hilge; Zambach, Sine Katharina; Ingason, Andrés

    2015-01-01

    Formal thought disorder is a major feature of schizophrenia and other psychotic disorders. It is heritable, found in healthy relatives of patients with schizophrenia and other mental disorders but knowledge of specific genetic factors is lacking. The aim of this study was to search for biologically...... relevant high-risk variants. Formal thought disorder was assessed in participants in the Copenhagen Schizophrenia Linkage Study (N=236), a unique high-risk family study comprised of six large pedigrees. Microsatellite linkage analysis of formal thought disorder was performed and subsequent haplotype...... analysis of the implicated region using phased microsatellite and SNP genotypes. Whole genome sequencing (N=3) was used in the attempt to identify causative variants in the linkage region. Linkage analysis of formal thought disorder resulted in a single peak at chromosome 6(q26-q27) centred on marker D6S...

  12. Rivaroxaban for Preventing Atherothrombotic Events in People with Acute Coronary Syndrome and Elevated Cardiac Biomarkers: An Evidence Review Group Perspective of a NICE Single Technology Appraisal.

    Science.gov (United States)

    Pandor, Abdullah; Pollard, Daniel; Chico, Tim; Henderson, Robert; Stevenson, Matt

    2016-05-01

    As part of its Single Technology Appraisal process, the National Institute for Health and Care Excellence (NICE) invited the company that manufactures rivaroxaban (Xarelto, Bayer) to submit evidence of the clinical and cost effectiveness of rivaroxaban for the prevention of adverse outcomes in patients after the acute management of acute coronary syndrome (ACS). The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG). The ERG produced a critical review of the evidence for the clinical and cost effectiveness of the technology, based upon the company's submission to NICE. The evidence was derived mainly from a randomised, double-blind, phase III, placebo-controlled trial of rivaroxaban (either 2.5 or 5 mg twice daily) in patients with recent ACS [unstable angina, non-ST segment elevation myocardial infarction (NSTEMI) or ST segment elevation myocardial infarction (STEMI)]. In addition, all patients received antiplatelet therapy [aspirin alone or aspirin and a thienopyridine either as clopidogrel (approximately 99 %) or ticlopidine (approximately 1 %) according to national or local guidelines]. The higher dose of rivaroxaban (5 mg twice daily) did not form part of the marketing authorisation. A post hoc subgroup analysis of the licensed patients who had ACS with elevated cardiac biomarkers (that is, patients with STEMI and NSTEMI) without prior stroke or transient ischaemic stroke showed that compared with standard care, the addition of rivaroxaban (2.5 mg twice daily) to existing antiplatelet therapy reduced the composite endpoint of cardiovascular mortality, myocardial infarction or stroke, but increased the risk of major bleeding and intracranial haemorrhage. However, there were a number of limitations in the evidence base that warrant caution in its interpretation. In particular, the evidence may be confounded because of the post hoc subgroup

  13. Nalmefene for Reducing Alcohol Consumption in People with Alcohol Dependence: An Evidence Review Group Perspective of a NICE Single Technology Appraisal.

    Science.gov (United States)

    Stevenson, Matt; Pandor, Abdullah; Stevens, John W; Rawdin, Andrew; Rice, Peter; Thompson, Jez; Morgan, Marsha Y

    2015-08-01

    As part of its single technology appraisal process, the National Institute for Health and Care Excellence (NICE) invited the company (Lundbeck) marketing nalmefene (Selincro) to submit evidence of its clinical and cost effectiveness for reducing alcohol consumption in people with alcohol dependence. The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG) and to produce a critical review of the company's submission to NICE. The clinical evidence was derived from three phase III, company-sponsored, randomised, double-blind, placebo-controlled trials in adults with a diagnosis of alcohol dependence comparing nalmefene, taken on an as-needed basis, in conjunction with psychosocial support with placebo in conjunction with psychosocial support. Psychosocial support was provided in the form of BRENDA, an intervention of lower intensity than that recommended in NICE Clinical Guideline 115 (NICE CG115). Post-hoc subgroup analyses were conducted in people who were drinking at high or very high risk levels at baseline and maintained this level of drinking during the screening phase prior to randomisation. This subgroup forms the licensed population. There were a number of limitations and uncertainties in the clinical evidence base which warrant caution in its interpretation. In particular, the post-hoc subgroup analyses and high dropout rates in the three nalmefene studies meant that the inference of treatment effects might be confounded. The company's economic evaluation showed that use of nalmefene in conjunction with psychosocial support in the form of BRENDA dominated the use of BRENDA in conjunction with placebo, providing more quality-adjusted life-years (QALYs) at a reduced cost. However, this evaluation did not meet the final scope issued by NICE, which specified that the comparator should be psychological intervention as defined in NICE CG115. The ERG

  14. Integrating linkage and radiation hybrid mapping data for bovine chromosome 15

    Directory of Open Access Journals (Sweden)

    Takasuga Akiko

    2004-10-01

    Full Text Available Abstract Background Bovine chromosome (BTA 15 contains a quantitative trait loci (QTL for meat tenderness, as well as several breaks in synteny with human chromosome (HSA 11. Both linkage and radiation hybrid (RH maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs. Results The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments. Conclusions Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about

  15. Construction of a microsatellite-based genetic linkage map for half-smooth tongue sole Cynoglossus semilaevis

    Directory of Open Access Journals (Sweden)

    Wentao SONG, Guidong MIAO, Yongwei ZHAO, Yuze NIU, Renyi PANG, Xiaolin LIAO, Changwei SHAO, Songlin CHEN

    2013-02-01

    Full Text Available The half-smooth tongue sole Cynoglossus semilaevis is an important cultured marine fish and a promising model fish for the study of sex determination. Sex-specific genetic linkage maps of half-smooth tongue sole were developed with 567 markers (565 microsatellite markers and two SCAR markers. The parents and F1 progeny (92 individuals were used as segregating populations. The female map was composed of 480 markers in 21 linkage groups, covering a total of 1388.1 cM, with an average interval 3.06 cM between markers. The male map consisted of 417 markers in 21 linkage groups, spanning 1480.9 cM, with an average interval of 3.75 cM. The female and male maps had 474 and 416 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1522.9 cM for females and 1649.1cM for males. Based on estimations of map length, the female and male maps covered 91.1% and 89.8% of the genome, respectively. Furthermore, two female-specific SCAR markers, f-382 and f-783, were mapped on LG15f (linkage group 15 in female maps. The present study presents a mid-density genetic linkage map for half-smooth tongue sole. These improved genetic linkage maps may facilitate systematic genome searches to identify quantitative trait loci (QTL, such as disease resistance, growth and sex-related traits, and are very useful for marker-assisted selection breeding programs for economically important traits in half-smooth tongue sole [Current Zoology 59 (1: 99–108, 2013].

  16. Inheritance and Linkage Map Positions of Genes Conferring Agromorphological Traits in Lens culinaris Medik.

    Directory of Open Access Journals (Sweden)

    Gopesh C. Saha

    2013-01-01

    Full Text Available Agromorphological traits have immense importance in breeding lentils for higher yield and stability. We studied the genetics and identified map positions of some important agro-morphological traits including days to 50% flowering, plant height, seed diameter, 100 seed weight, cotyledon color, and growth habit in Lens culinaris. Earlier developed RILs for stemphylium blight resistance (ILL-5888 × ILL-6002, contrasted for those agro-morphological traits, were used in our study. Three QTLs for days to 50% flowering were detected with additive and epistatic effects. One QTL for days to 50% flowering, QLG483 (QTL at linkage group 4 at 83 cM position, accounted for an estimated 20.2% of the variation, while QLG124 × QLG1352 and QLG484 × QLG138 accounted for 15.6% and 24.2% of the variation, respectively. Epistatic effects accounted for most of the variation in plant height, but the main effect of one QTL, QLG84, accounted for 15.3%. For seed diameter, three QTLs were detected, and one QTL, QLG482, accounted for 32.6% of the variation. For 100 seed weight, five QTLs were identified with significant additive effects and four with significant interaction effects. The main effect of one QTL, QLG482, also accounted for 17.5% of the variation in seed diameter. QLG482-83 which appears to affect days to 50% flowering, seed diameter, and 100 seed weight is flanked by RAPD markers, UBC 34 and UBC1. Growth habit and cotyledon color are controlled by single genes with prostrate dominant to erect and red cotyledon dominant to yellow. The QTL information presented here will assist in the selection of breeding lines for early maturity, upright growth habit, and improved seed quality.

  17. Genome-wide linkage analysis of malaria infection intensity and mild disease.

    Directory of Open Access Journals (Sweden)

    Christian Timmann

    2007-03-01

    Full Text Available Although balancing selection with the sickle-cell trait and other red blood cell disorders has emphasized the interaction between malaria and human genetics, no systematic approach has so far been undertaken towards a comprehensive search for human genome variants influencing malaria. By screening 2,551 families in rural Ghana, West Africa, 108 nuclear families were identified who were exposed to hyperendemic malaria transmission and were homozygous wild-type for the established malaria resistance factors of hemoglobin (HbS, HbC, alpha(+ thalassemia, and glucose-6-phosphate-dehydrogenase deficiency. Of these families, 392 siblings aged 0.5-11 y were characterized for malaria susceptibility by closely monitoring parasite counts, malaria fever episodes, and anemia over 8 mo. An autosome-wide linkage analysis based on 10,000 single-nucleotide polymorphisms was conducted in 68 selected families including 241 siblings forming 330 sib pairs. Several regions were identified which showed evidence for linkage to the parasitological and clinical phenotypes studied, among them a prominent signal on Chromosome 10p15 obtained with malaria fever episodes (asymptotic z score = 4.37, empirical p-value = 4.0 x 10(-5, locus-specific heritability of 37.7%; 95% confidence interval, 15.7%-59.7%. The identification of genetic variants underlying the linkage signals may reveal as yet unrecognized pathways influencing human resistance to malaria.

  18. 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)).

  19. The color of a Dalmatian's spots: Linkage evidence to support the TYRP1 gene

    Directory of Open Access Journals (Sweden)

    Strain George M

    2005-07-01

    Full Text Available Abstract Background The distinctive coat pattern of a Dalmatian is the result of the interaction of several loci. While the encoded function of these genes is not fully understood, it is known the Piebald, Ticking, and Flecking loci interact to produce the Dalmatian's classic pigmented spots on a white background. The color of the pigmented spots in purebred Dalmatians can either be black or liver, but the locus responsible for color determination is unknown. Studies have been conducted to determine the underlying genes involved in coat color determination in the dog, e.g., in the Labrador Retriever, but none to date have addressed black versus liver in the Dalmatian. Results A genome scan was conducted in a multi-generational kindred of Dalmatians segregating black and liver spot color. Linkage analysis was performed using a total of 113 polymorphic microsatellite markers from the kindred. Linkage was found between spot color and a single microsatellite marker, FH2319 (LOD = 12.5 on chromosome 11. Conclusion The TYRP1 (Brown locus is located at position 50.1 Mb on chromosome 11, which is approximately 0.4 Mb from marker FH2319. Given the recent characterization of TYRP1 genetic variations in the dog and the linkage evidence reported here, TYRP1 is likely responsible for the spot color variation of black versus liver seen in the Dalmatian.

  20. LINKAGES: An Individual-based Forest Ecosystem Biogeochemistry Model

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This model product contains the source codes for version 1 of the individual-based forest ecosystem biogeochemistry model LINKAGES and two subsequent...

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

    NARCIS (Netherlands)

    Temel, T.

    2004-01-01

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

  2. LINKAGES: An Individual-based Forest Ecosystem Biogeochemistry Model

    Data.gov (United States)

    National Aeronautics and Space Administration — This model product contains the source codes for version 1 of the individual-based forest ecosystem biogeochemistry model LINKAGES and two subsequent versions as...

  3. FHWA planning and environmental linkages annual report fiscal year 2011.

    Science.gov (United States)

    2012-01-20

    This report highlights the Federal Highway Administration's (FHWA) Planning and Environment Linkages (PEL) program activities for Fiscal Year 2011 (FY11). The PEL program's purpose is to provide transportation agencies with tools and resources to int...

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

    Directory of Open Access Journals (Sweden)

    Tung-Pi Wu

    2015-12-01

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

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

    Science.gov (United States)

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

    2017-07-10

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

  6. On the Consequences of Purging and Linkage on Fitness and Genetic Diversity

    Directory of Open Access Journals (Sweden)

    Diego Bersabé

    2016-01-01

    Full Text Available Using computer simulation we explore the consequences of linkage on the inbreeding load of an equilibrium population, and on the efficiency of purging and the loss of genetic diversity after a reduction in population size. We find that linkage tends to cause increased inbreeding load due to the build up of coupling groups of (partially recessive deleterious alleles. It also induces associative overdominance at neutral sites but rarely causes increased neutral genetic diversity in equilibrium populations. After a reduction in population size, linkage can cause some delay both for the expression of the inbreeding load and the corresponding purging. However, reasonable predictions can be obtained for the evolution of fitness under inbreeding and purging by using empirical estimates of the inbreeding depression rate. Purging selection against homozygotes for deleterious alleles affects the population’s pedigree. Furthermore, it can slow the loss of genetic diversity compared to that expected from the variance of gametic contributions to the breeding group and even from pedigree inbreeding. Under some conditions, this can lead to a smaller loss of genetic diversity, even below that expected from population size in the absence of selection.

  7. Commodities and Linkages: Industrialisation in Sub-Saharan Africa

    OpenAIRE

    Kaplinsky, Raphael; Morris, Adam; Kaplan, David

    2011-01-01

    In a complementary Discussion Paper (MMCP DP 12 2011) we set out the reasons why we believe that there is extensive scope for linkage development into and out of SSA’s commodities sectors. In this Discussion Paper, we present the findings of our detailed empirical enquiry into the determinants of the breadth and depth of linkages in eight SSA countries (Angola, Botswana, Gabon, Ghana, Nigeria, South Africa Tanzania, and Zambia) and six sectors (copper, diamonds, gold, oil and gas, mining serv...

  8. Shoulder complex linkage mechanism for humanlike musculoskeletal robot arms.

    Science.gov (United States)

    Ikemoto, Shuhei; Kimoto, Yuya; Hosoda, Koh

    2015-11-05

    The shoulder complex in the human body consists of the scapula, clavicle, humerus, and thorax and bears the load imposed by arm movements while at the same time realizing a wide range of motions. To mimic and exploit its role, several musculoskeletal robot arms with shoulder complex mechanisms have been developed. However, although many research groups have tried to design the structures using links and joints that faithfully correspond to the bones and joints in the human shoulder complex, its function has not been successfully reproduced because biologically plausible designs seriously compromise engineering plausibility. In this paper, we propose a linkage mechanism that can reproduce complex three-dimensional scapulo movements and considers the trade-off between biological and engineering plausibilities. Subsequently, the design was validated by driving the mechanism using pneumatic artificial muscles (PAMs) placed similarly to muscles in humans. Further, we present experiments in which the robot was controlled by surface electromyographic signals from a human. We show that the proposed design, due to its kinematic similarity with human musculoskeletal systems, eases the conversion between the surface electromyogram signals and the PAMs control inputs.

  9. Path analytic, sib-pair linkage and co-twin control studies of asthma and atopy

    Energy Technology Data Exchange (ETDEWEB)

    Duffy, D.L.; Healey, S.C.; Martin, N.G. [Queensland Institute of Medical Research, Brisband (Austria)

    1994-09-01

    Asthma and atopy are complex traits with multifactorial determinants, and require appropriate choice of phenotypes and analyses, including a linkage analysis of the putative 11q atopy locus. Participants in a large registry-based twin study of asthma were invited to take part in clinical testing. A total of 863 individuals including 419 complete twin pairs (where one or both members reported a history of wheeze) underwent histamine inhalation challenge, allergen skin prick testing, and venesection. Total serum immunoglobulin E (IgE) and bronchial responsiveness (BR) to histamine were highest in those who had wheezed most recently, and whose skin tests demonstrated allergy to house dust mite, cockroach, and rye grass. In ascertainment-corrected path analyses (FISHER), the heritability of IgE and BR were both 60%. Monozygotic (MZ) co-twin control analyses suggested house dust mite sensitization was the single strongest environmentally controlled risk factor for wheeze, while path analyses suggested genetic determination. In dizygotic (DZ) co-twin control analyses, sensitization to grasses was also an important predictor, suggesting pollinosis to be genetically correlated with wheezing, rather than causative. Multivariate path analyses suggested separate (correlated) genetic factors for BR, IgE, and allergy to house dust mite. A sib-pair (Haseman-Elston) linkage analysis of 220 DZ twin pairs did not support linkage to the high-affinity IgE receptor beta-subunit gene on 11q13 of atopy or BR. More recent linkage analyses that include parental genotyping will also be discussed. We conclude that the atopic phenotype consists of a number of traits with specific genetic allergens. Exposure to particular allergens can then cause specific outcomes, such as asthma.

  10. Genome-wide Linkage and Association Analyses to Identify Genes Influencing Adiponectin Levels: The GEMS Study

    Science.gov (United States)

    Ling, Hua; Waterworth, Dawn M.; Stirnadel, Heide A.; Pollin, Toni I.; Barter, Philip J.; Kesäniemi, Y. Antero; Mahley, Robert W.; McPherson, Ruth; Waeber, Gérard; Bersot, Thomas P.; Cohen, Jonathan C.; Grundy, Scott M.; Mooser, Vincent E.; Mitchell, Braxton D.

    2014-01-01

    Adiponectin has a variety of metabolic effects on obesity, insulin sensitivity, and atherosclerosis. To identify genes influencing variation in plasma adiponectin levels, we performed genome-wide linkage and association scans of adiponectin in two cohorts of subjects recruited in the Genetic Epidemiology of Metabolic Syndrome Study. The genome-wide linkage scan was conducted in families of Turkish and southern European (TSE, n = 789) and Northern and Western European (NWE, N = 2,280) origin. A whole genome association (WGA) analysis (500K Affymetrix platform) was carried out in a set of unrelated NWE subjects consisting of approximately 1,000 subjects with dyslipidemia and 1,000 overweight subjects with normal lipids. Peak evidence for linkage occurred at chromosome 8p23 in NWE subjects (lod = 3.10) and at chromosome 3q28 near ADIPOQ, the adiponectin structural gene, in TSE subjects (lod = 1.70). In the WGA analysis, the single-nucleotide polymorphisms (SNPs) most strongly associated with adiponectin were rs3774261 and rs6773957 (P < 10−7). These two SNPs were in high linkage disequilibrium (r2 = 0.98) and located within ADIPOQ. Interestingly, our fourth strongest region of association (P < 2 × 10−5) was to an SNP within CDH13, whose protein product is a newly identified receptor for high-molecular-weight species of adiponectin. Through WGA analysis, we confirmed previous studies showing SNPs within ADIPOQ to be strongly associated with variation in adiponectin levels and further observed these to have the strongest effects on adiponectin levels throughout the genome. We additionally identified a second gene (CDH13) possibly influencing variation in adiponectin levels. The impact of these SNPs on health and disease has yet to be determined. PMID:19165155

  11. A Molecular Genetic Linkage Map of Eucommia ulmoides and Quantitative Trait Loci (QTL Analysis for Growth Traits

    Directory of Open Access Journals (Sweden)

    Yu Li

    2014-01-01

    Full Text Available Eucommia ulmoides is an economically important tree species for both herbal medicine and organic chemical industry. Effort to breed varieties with improved yield and quality is limited by the lack of knowledge on the genetic basis of the traits. A genetic linkage map of E. ulmoides was constructed from a full-sib family using sequence-related amplified polymorphism, amplified fragment length polymorphism, inter-simple sequence repeat and simple sequence repeat markers. In total, 706 markers were mapped in 25 linkage groups covering 2133 cM. The genetic linkage map covered approximately 89% of the estimated E. ulmoides genome with an average of 3.1 cM between adjacent markers. The present genetic linkage map was used to identify quantitative trait loci (QTL affecting growth-related traits. Eighteen QTLs were found to explain 12.4%–33.3% of the phenotypic variance. This genetic linkage map provides a tool for marker-assisted selection and for studies of genome in E. ulmoides.

  12. Emergency transfusion of patients with unknown blood type with blood group O Rhesus D positive red blood cell concentrates: a prospective, single-centre, observational study.

    Science.gov (United States)

    Selleng, Kathleen; Jenichen, Gregor; Denker, Kathrin; Selleng, Sixten; Müllejans, Bernd; Greinacher, Andreas

    2017-05-01

    Emergency patients with unknown blood type usually receive O Rhesus D negative (RhD-) red blood cell concentrates until their blood group is determined to prevent RhD+ related adverse transfusion reactions. As 85% of individuals are RhD+, this consumption of O RhD- red blood cell concentrates contributes to shortages of O RhD- red blood cell concentrates, sometimes forcing transfusion of known RhD- patients with RhD+ red blood cell concentrates. Here we report the outcome of this transfusion policy transfusing all emergency patients with unknown blood type with O RhD+ red blood cell concentrates. In this prospective single-centre observational study done between Jan 1, 2001, and Dec 31, 2015, we assessed all consecutive RhD- patients at the University Medicine Greifswald who received RhD+ red blood cell concentrates (emergency patients with unknown blood type; and RhD- patients receiving RhD+ red blood cell concentrates during RhD- red blood cell concentrate shortages). No patients were excluded. The primary endpoint was anti-D allo-immunisation at 2 months follow-up or later. Patients were followed up and tested for immunisation against red blood cell antigens using the direct antiglobulin test and an antibody screen every 3-5 days for 4 weeks or until death, or hospital discharge. Surviving patients were screened for development of anti-D antibodies for up to 12 months (at the predefined timepoints 2, 3, 6, and 12 months) after RhD+ red blood cell transfusion. 437 emergency patients, of whom 85 (20%) were RhD-, received 2836 RhD+ red blood cell concentrates. The overall risk of inducing anti-D antibodies (in all 437 recipients) was 17 (4%, 95% CI 2·44-6·14) of 437 (assuming all patients lost to follow-up developed anti-D allo-immunisation). During this period, 110 known RhD- patients received RhD+ red blood cell concentrates during RhD- red blood cell concentrate shortages. Of these, 29 (26%; 95% CI 19·0-35·3) developed anti-D allo-immunisation (assuming all

  13. Linkage analysis of alcohol dependence symptoms in the community.

    Science.gov (United States)

    Hansell, Narelle K; Agrawal, Arpana; Whitfield, John B; Morley, Katherine I; Gordon, Scott D; Lind, Penelope A; Pergadia, Michele L; Montgomery, Grant W; Madden, Pamela A F; Todd, Richard D; Heath, Andrew C; Martin, Nicholas G

    2010-01-01

    We have previously identified suggestive linkage for alcohol consumption in a community-based sample of Australian adults. In this companion paper, we explore the strength of genetic linkage signals for alcohol dependence symptoms. An alcohol dependence symptom score, based on DSM-IIIR and DSM-IV criteria, was examined. Twins and their nontwin siblings (1,654 males, 2,518 females), aged 21 to 81 years, were interviewed, with 803 individuals interviewed on 2 occasions, approximately 10 years apart. Linkage analyses were conducted on datasets compiled to maximize data collected at either the younger or the older age. In addition, linkage was compared between full samples and truncated samples that excluded the lightest drinkers (approximately 10% of the sample). Suggestive peaks on chromosome 5p (LODs >2.2) were found in a region previously identified in alcohol linkage studies using clinical populations. Linkage signal strength was found to vary between full and truncated samples and when samples differed only on the collection age for a sample subset. The results support the finding that large community samples can be informative in the study of alcohol-related traits.

  14. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas.

    Science.gov (United States)

    Hippolyte, Isabelle; Bakry, Frederic; Seguin, Marc; Gardes, Laetitia; Rivallan, Ronan; Risterucci, Ange-Marie; Jenny, Christophe; Perrier, Xavier; Carreel, Françoise; Argout, Xavier; Piffanelli, Pietro; Khan, Imtiaz A; Miller, Robert N G; Pappas, Georgios J; Mbéguié-A-Mbéguié, Didier; Matsumoto, Takashi; De Bernardinis, Veronique; Huttner, Eric; Kilian, Andrzej; Baurens, Franc-Christophe; D'Hont, Angélique; Cote, François; Courtois, Brigitte; Glaszmann, Jean-Christophe

    2010-04-13

    The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.

  15. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

    Science.gov (United States)

    2010-01-01

    Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation. PMID:20388207

  16. Conformational Populations of β-(1→4) O-Glycosidic Linkages Using Redundant NMR J-Couplings and Circular Statistics.

    Science.gov (United States)

    Zhang, Wenhui; Turney, Toby; Meredith, Reagan; Pan, Qingfeng; Sernau, Luke; Wang, Xiaocong; Hu, Xiaosong; Woods, Robert J; Carmichael, Ian; Serianni, Anthony S

    2017-04-13

    Twelve disaccharides containing β-(1→4) linkages and displaying systematic structural variations in the vicinity of these linkages were selectively labeled with 13 C to facilitate measurements of multiple NMR spin-spin (scalar; J) coupling constants (J CH and J CC values) across their O-glycosidic linkages. Ensembles of spin-couplings ( 2 J COC , 3 J COCH , 3 J COCC ) sensitive to the two linkage torsion angles, phi (ϕ) and psi (ψ), were analyzed by using parametrized equations obtained from density functional theory (DFT) calculations, Fredholm theory, and circular statistics to calculate experiment-based rotamer populations for ϕ and ψ in each disaccharide. With the statistical program MA'AT, torsion angles ϕ and ψ were modeled as a single von Mises distribution, which yielded two parameters, the mean position and the circular standard deviation (CSD) for each angle. The NMR-derived rotamer populations were compared to those obtained from 1 μs aqueous molecular dynamics (MD) simulations and crystallographic database statistical analyses. Conformer populations obtained exclusively from the MA'AT treatment of redundant J-couplings were in very good agreement with those obtained from the MD simulations, providing evidence that conformational populations can be determined by NMR for mobile molecular elements such as O-glycosidic linkages with minimal input from theory. The approach also provides an experimental means to validate the conformational preferences predicted from MD simulations. The conformational behaviors of ϕ in the 12 disaccharides were very similar, but those of ψ varied significantly, allowing a classification of the 12 disaccharides based on preferred linkage conformation in solution.

  17. Linkage and association analysis of CACNG3 in childhood absence epilepsy

    DEFF Research Database (Denmark)

    Everett, Kate V; Chioza, Barry; Aicardi, Jean

    2007-01-01

    Childhood absence epilepsy (CAE) is an idiopathic generalised epilepsy characterised by absence seizures manifested by transitory loss of awareness with 2.5-4 Hz spike-wave complexes on ictal EEG. A genetic component to aetiology is established but the mechanism of inheritance and the genes...... did not identify any putative causal variants. A linkage disequilibrium (LD) map of CACNG3 was constructed using 23 single nucleotide polymorphisms (SNPs). Transmission disequilibrium was sought using individual SNPs and SNP-based haplotypes with the pedigree disequilibrium test in 217 CAE trios...

  18. Polyphenon E, non-futile at neuroprotection in multiple sclerosis but unpredictably hepatotoxic: Phase I single group and phase II randomized placebo-controlled studies.

    Science.gov (United States)

    Lovera, Jesus; Ramos, Alexander; Devier, Deidre; Garrison, Virginia; Kovner, Blake; Reza, Tara; Koop, Dennis; Rooney, William; Foundas, Anne; Bourdette, Dennis

    2015-11-15

    Phase I (PhI): assess the safety of Polyphenon E in people with multiple sclerosis (MS) and determine the futility of Polyphenon E as a neuroprotective agent. Correlate plasma levels of EGCG with neuroprotective effects. Phase II (PhII): Further assess safety and confirm the neuroprotective effects of Polyphenon E. PhI: single group futility study. PhII: parallel group randomized double-blind placebo-controlled study. Recruitment area (both studies): LSU MS Center, New Orleans, LA and general public from surrounding areas. Inclusion criteria (both studies): 1) MS per 2005 McDonald criteria; 2) relapsing remitting or secondary progressive MS; 3) stable for six months prior to enrollment on either no therapy or glatiramer acetate (GA) for the PhI study and on either on GA or Interferon β for the PhII study. Exclusion criteria (both studies): 1) complete bone marrow ablation or alentuzumab use at any time; 2) mitoxantrone, cyclophosphamide, natalizumab or fingolimod use in the prior nine months; 3) liver problems or significant medical problems. PhI: Polyphenon E, a green tea extract containing 50% of the antioxidant Epigallocatechin-gallate (EGCG), two capsules twice daily (200mg of EGCG per capsule; total daily dose 800mg) for six months. PhII: Polyphenon E or matching placebo capsules, same dose for one year. Only the research pharmacist knew treatment assignment and she randomized participants (one-to-one, stratified by GA or Interferon β, blocks of 4 or 6). Outcome evaluators did not discuss side effects with participants. PhI: 1) adverse events (AE); 2) futility: decrease in N-acetyl aspartate (NAA) from baseline to six months of 10% or more; 3) association between EGCG plasma levels and change in NAA. PhII: 1) AEs; 2) difference in the rate of change of NAA-levels over twelve months.We measured NAA using a point resolved magnetic resonance spectroscopic imaging sequence (TE30/TR2000) on a 10cm×10cm×1cm volume of interest (VOI) located just superior to the

  19. The investigation into CYP2E1 in relation to the level of response to alcohol through a combination of linkage and association analysis.

    Science.gov (United States)

    Webb, Amy; Lind, Penelope A; Kalmijn, Jelger; Feiler, Heidi S; Smith, Tom L; Schuckit, Marc A; Wilhelmsen, Kirk

    2011-01-01

    A low level of response to alcohol during an individual's early experience with alcohol is associated with an increase risk of alcoholism. A family-based genome-wide linkage analysis using sibling pairs that underwent an alcohol challenge where the level of response to alcohol was measured with the Subjective High Assessment Scale (SHAS) implicated the 10q terminal (10qter) region. CYP2E1, a gene known for its involvement with ethanol metabolism, maps to this region. Variance component multipoint linkage analysis was performed on a combined map of single-nucleotide polymorphism (SNP) and microsatellite data. To account for the heterogeneity evident in the dataset, a calculation assuming locus heterogeneity was made using the Heterogeneity Log of Odds (HLOD) score. Association between SNP marker allele counts and copy number and SHAS scores were evaluated using a logistic regression model. Linkage analysis detected significant linkage to CYP2E1, which was diminished because of apparent locus heterogeneity traced to a single family with extreme phenotypes. In retrospect, circumstances recorded during testing for this family suggest that their phenotype data are likely to be unreliable. Significant allelic associations were detected for several CYP2E1 polymorphisms and the SHAS score. DNA sequencing from families that contributed the greatest evidence for linkage did not detect any changes directly affecting the primary amino acid sequence. With the removal of a single family, combined evidence from microsatellites and SNPs offers significant linkage between the level of response to alcohol and the region on the end of chromosome 10. Combined linkage and association indicate that sequence changes in or near CYP2E1 affect the level of response to alcohol providing a predictor of risk of alcoholism. The absence of coding sequence changes indicates that regulatory sequences are responsible. Implicating CYP2E1 in the level of response to alcohol allows inferences to be

  20. The investigation of CYP2E1 in relation to the level of response to alcohol through a combination of linkage and association analysis

    Science.gov (United States)

    Webb, Amy; Lind, Penelope A.; Kalmijn, Jelger; Feiler, Heidi S.; Smith, Tom L.; Schuckit, Marc A.; Wilhelmsen, Kirk

    2010-01-01

    Background A low level of response to alcohol during an individual’s early experience with alcohol is associated with an increase risk for alcoholism. A family-based genome-wide linkage analysis using sibling pairs that underwent an alcohol challenge where the level of response to alcohol was measured with the Subjective High Assessment Scale (SHAS) implicated the 10q terminal region. CYP2E1, a gene known for its involvement with ethanol metabolism, maps to this region. Methods Variance component multipoint linkage analysis was performed on a combined map of single nucleotide polymorphism (SNP) and microsatellite data. To account for the heterogeneity evident in the dataset, a calculation assuming locus heterogeneity was made using the HLOD (heterogeneity LOD) score. Association between SNP marker allele counts and copy number and SHAS scores were evaluated using a logistic regression model. Results Linkage analysis detected significant linkage to CYP2E1 which was diminished due to apparent locus heterogeneity traced to a single family with extreme phenotypes. In retrospect, circumstances recorded during testing for this family suggest that their phenotype data are likely to be unreliable. Significant allelic associations were detected for several CYP2E1 polymorphisms and the SHAS score. DNA sequencing from families that contributed the greatest evidence for linkage did not detect any changes directly affecting the primary amino acid sequence. With the removal of a single family, combined evidence from microsatellites and SNPs offer significant linkage between the level of response to alcohol and the region on the end of chromosome 10. Conclusion Combined linkage and association indicate that sequence changes in or near CYP2E1 affect the level of response to alcohol providing a predictor of risk for alcoholism. The absence of coding sequence changes indicates that regulatory sequences are responsible. Implicating CYP2E1 in the level of response to alcohol allows

  1. Linkages between terrestrial ecosystems and the atmosphere

    Science.gov (United States)

    Bretherton, Francis; Dickinson, Robert E.; Fung, Inez; Moore, Berrien, III; Prather, Michael; Running, Steven W.; Tiessen, Holm

    1992-01-01

    The primary research issue in understanding the role of terrestrial ecosystems in global change is analyzing the coupling between processes with vastly differing rates of change, from photosynthesis to community change. Representing this coupling in models is the central challenge to modeling the terrestrial biosphere as part of the earth system. Terrestrial ecosystems participate in climate and in the biogeochemical cycles on several temporal scales. Some of the carbon fixed by photosynthesis is incorporated into plant tissue and is delayed from returning to the atmosphere until it is oxidized by decomposition or fire. This slower (i.e., days to months) carbon loop through the terrestrial component of the carbon cycle, which is matched by cycles of nutrients required by plants and decomposers, affects the increasing trend in atmospheric CO2 concentration and imposes a seasonal cycle on that trend. Moreover, this cycle includes key controls over biogenic trace gas production. The structure of terrestrial ecosystems, which responds on even longer time scales (annual to century), is the integrated response to the biogeochemical and environmental constraints that develop over the intermediate time scale. The loop is closed back to the climate system since it is the structure of ecosystems, including species composition, that sets the terrestrial boundary condition in the climate system through modification of surface roughness, albedo, and, to a great extent, latent heat exchange. These separate temporal scales contain explicit feedback loops which may modify ecosystem dynamics and linkages between ecosystems and the atmosphere. The long-term change in climate, resulting from increased atmospheric concentrations of greenhouse gases (e.g., CO2, CH4, and nitrous oxide (N2O)) will further modify the global environment and potentially induce further ecosystem change. Modeling these interactions requires coupling successional models to biogeochemical models to

  2. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

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

    Science.gov (United States)

    Firestone, William A.; Wilson, Bruce L.

    1985-01-01

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

  4. Dietary A- and B-type procyanidins : characterization and biofunctional potential of an abundant and diverse group of phenolics

    NARCIS (Netherlands)

    Appeldoorn, M.M.

    2009-01-01

    Procyanidins (PCs) are phenolic compounds that belong to the class of flavonoids and are oligomers of monomeric (epi)catechin units. These monomeric units can be linked to each other by a single C4-C8 or C4-C6 linkage, which is referred to as B-type. Besides these single linkages an additional ether

  5. Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers.

    Science.gov (United States)

    Brondani, Rosana P V; Brondani, C; Grattapaglia, D

    2002-05-01

    A novel set of 50 highly polymorphic microsatellite markers were developed and mapped on existing RAPD framework maps of Eucalyptus grandis and E. urophylla. Together with the twenty previously developed microsatellite markers, these were used to align the existing maps for the two most commercially important Eucalyptus species in the tropics. Sixty-three microsatellite markers were placed on the E. grandis map in 11 linkage groups, and 53 on the E. urophylla map distributed in 10 linkage groups. Approximately 66% of the microsatellite markers segregated in a fully informative fashion, allowing the establishment of colinear syntenic linkage groups between the two maps. The 50 new microsatellite markers were highly informative, with an average of 14 alleles per locus, and average expected heterozygosity between 0.82 and 0.87. Furthermore, within the subgenus Symphyomyrtus, to which the vast majority of commercially important Eucalyptus species belong, these markers display on average 90% transportability. This set of 70 mapped microsatellite markers represents a significant step toward the development of a genus-wide reference linkage map for Eucalyptus. These highly multiallelic and transportable markers constitute a powerful tool for QTL discovery and validation, and can be used in directed searches for QTL allele variation across Eucalyptus pedigrees.

  6. First Indian initiative for preparation of low-titer group “O” single-donor platelets with platelet additive solution

    Directory of Open Access Journals (Sweden)

    Puneet Jain

    2018-01-01

    Conclusion: O group SDPs can be prepared with PAS and the beneficial effects were significant with respect to antibody titers. Quality parameters were well maintained. Availability of PAS units has benefitted patients.

  7. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes).

    Science.gov (United States)

    Zhang, Xiang; Mizukoshi, Misaki; Zhang, Hong; Tan, Engkong; Igarashi, Yoji; Suzuki, Yutaka; Mitsuyama, Susumu; Kinoshita, Shigeharu; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

    2018-02-26

    Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu ( Takifugu rubripes ) as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH) population without above requirements. Low-coverage (≈1×) whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs) calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5). This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated.

  8. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    2018-02-01

    Full Text Available Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu (Takifugu rubripes as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH population without above requirements. Low-coverage (≈1× whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5. This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated.

  9. Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis.

    Science.gov (United States)

    Li, Shuxian; Chen, Ying; Gao, Handong; Yin, Tongming

    2010-02-25

    Exploring the genetic mechanisms underlying speciation is a hot topic in modern genetics and evolutionary studies. Distortion of marker transmission ratio is frequently ascribed to selection against alleles that cause hybrid incompatibility. The natural introgression between P. massoniana and P. hwangshanensis and their distribution ranges lead to the emergence of the two species as desirable organisms to study the genetic mechanisms for speciation. Using seeds sampled from trees at different elevations, we consistently detected sharp decreases in seed germination rates of trees in the hybrid zone, which might be due largely to the hybrid incompatibility. A genetic map was established using 192 megagametophytes from a single tree in the hybrid zone of the two species. Segregation distortion analysis revealed that the percentage of significant-segregation-distortion (SSD) markers was extremely high, accounting for more than 25% of the segregating markers. The extension range, the distortion direction, and the distortion intensity of SSD markers also varied dramatically on different linkage groups. In this study, we display the potential chromosomal introgression barriers between P. massoniana and P. hwangshanensis. Our study provides a valuable platform for conducting genome-wide association of hybrid incompatible QTLs and/or candidate genes with marker transmission ratio distortion in the hybrid.

  10. Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis

    Directory of Open Access Journals (Sweden)

    Yin Tongming

    2010-02-01

    Full Text Available Abstract Background Exploring the genetic mechanisms underlying speciation is a hot topic in modern genetics and evolutionary studies. Distortion of marker transmission ratio is frequently ascribed to selection against alleles that cause hybrid incompatibility. The natural introgression between P. massoniana and P. hwangshanensis and their distribution ranges lead to the emergence of the two species as desirable organisms to study the genetic mechanisms for speciation. Results Using seeds sampled from trees at different elevations, we consistently detected sharp decreases in seed germination rates of trees in the hybrid zone, which might be due largely to the hybrid incompatibility. A genetic map was established using 192 megagametophytes from a single tree in the hybrid zone of the two species. Segregation distortion analysis revealed that the percentage of significant-segregation-distortion (SSD markers was extremely high, accounting for more than 25% of the segregating markers. The extension range, the distortion direction, and the distortion intensity of SSD markers also varied dramatically on different linkage groups. Conclusions In this study, we display the potential chromosomal introgression barriers between P. massoniana and P. hwangshanensis. Our study provides a valuable platform for conducting genome-wide association of hybrid incompatible QTLs and/or candidate genes with marker transmission ratio distortion in the hybrid.

  11. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland; Muylle, Hilde

    2010-01-01

    Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps...... 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set...... of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well...

  12. A linkage between DNA markers on the X chromosome and male sexual orientation

    Energy Technology Data Exchange (ETDEWEB)

    Hamer, D.H.; Hu, S.; Magnuson, V.L.; Hu, N.; Pattatucci, A.M.L.

    1993-07-16

    The role of genetics in male sexual orientation was investigated by pedigree and linkage analyses on 114 families of homosexual men. Increased rates of same-sex orientation were found in the maternal uncles and male cousins of these subjects, but not in their fathers or paternal relatives, suggesting the possibility of sex-linked transmission in a portion of the population. DNA linkage analysis of a selected group of 40 families in which there were two gay brothers and no indication of nonmaternal transmission revealed a correlation between homosexual orientation and the inheritance of polymorphic markers on the X chromosome in approximately 64 percent of the sib-pairs tested. The linkage to markers on Xq28, the subtelomeric region of the long arm of the sex chromosome, had a multipoint lod score of 4.0(P = 10[sup [minus]5]), indicating a statistical confidence level of more than 99 percent that at least one subtype of male sexual orientation is genetically influenced.

  13. Genetic mapping of the gene for Usher syndrome: Linkage analysis in a large Samaritan kindred

    Energy Technology Data Exchange (ETDEWEB)

    Bonne-Tamir, B.; Korostishevsky, M.; Kalinsky, H.; Seroussi, E.; Beker, R.; Weiss, S. (Sackler Faculty of Medicine, Ramat-Aviv (Israel)); Godel, V. (Ichilov Hospital, Tel-Aviv (Israel))

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed. 35 refs., 2 figs., 6 tabs.

  14. Nature–society linkages in the Aral Sea region

    Directory of Open Access Journals (Sweden)

    Kristopher D. White

    2013-01-01

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

  15. Autosomal dominant distal myopathy: Linkage to chromosome 14

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-02-01

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

  16. Organizing population data into complex family pedigrees: application of a second-order data linkage to state birth defects registries.

    Science.gov (United States)

    Tu, Shihfen; Mason, Craig A

    2004-09-01

    Researchers and health officials are increasingly using electronic linkage of large-scale health data systems as a tool for assembling a comprehensive picture of birth defects at a population level. Current linkage and database techniques are limited to first-order linkage--linking information on a single individual in one database with information on that same individual in another database. For example, while current strategies may indicate whether a child with a certain birth defect also has a specific metabolic disorder or risk factor, they are unable to readily determine whether he or she also has any siblings or other relatives with the same pattern. In contrast, the current manuscript proposes a second-order linkage--one that organizes data so that individual-level data can readily be organized into families or extended family pedigrees across an entire population. The ability to link and organize population data into family pedigrees can have significant, broad impact upon health research and service delivery. This can lead to large-scale analysis of genetic factors and, with the linking of environmental data, the potential for large-scale studies of gene-environment interactions. In addition, it expands the potential for epidemiological research by readily allowing the examination of familial effects upon population rates of birth defects, and provides valuable information that can assist in applied public health. An example of a second order database incorporating an electronic birth defects registry is presented. Copyright 2004 Wiley-Liss, Inc.

  17. Factors associated with linkage to HIV care and TB treatment at community-based HIV testing services in Cape Town, South Africa.

    Science.gov (United States)

    Meehan, Sue-Ann; Sloot, Rosa; Draper, Heather R; Naidoo, Pren; Burger, Ronelle; Beyers, Nulda

    2018-01-01

    Diagnosing HIV and/or TB is not sufficient; linkage to care and treatment is conditional to reduce the burden of disease. This study aimed to determine factors associated with linkage to HIV care and TB treatment at community-based services in Cape Town, South Africa. This retrospective cohort study utilized routinely collected data from clients who utilized stand-alone (fixed site not attached to a health facility) and mobile HIV testing services in eight communities in the City of Cape Town Metropolitan district, between January 2008 and June 2012. Clients were included in the analysis if they were ≥12 years and had a known HIV status. Generalized estimating equations (GEE) logistic regression models were used to assess the association between determinants (sex, age, HIV testing service and co-infection status) and self-reported linkage to HIV care and/or TB treatment. Linkage to HIV care was 3 738/5 929 (63.1%). Linkage to HIV care was associated with the type of HIV testing service. Clients diagnosed with HIV at mobile services had a significantly reduced odds of linking to HIV care (aOR 0.7 (CI 95%: 0.6-0.8), p<0.001. Linkage to TB treatment was 210/275 (76.4%). Linkage to TB treatment was not associated with sex and service type, but was associated with age. Clients in older age groups were less likely to link to TB treatment compared to clients in the age group 12-24 years (all, p-value<0.05). A large proportion of clients diagnosed with HIV at mobile services did not link to care. Almost a quarter of clients diagnosed with TB did not link to treatment. Integrated community-based HIV and TB testing services are efficient in diagnosing HIV and TB, but strategies to improve linkage to care are required to control these epidemics.

  18. Daily electronic self-monitoring in bipolar disorder using smartphones - the MONARCA I trial: a randomized, placebo-controlled, single-blind, parallel group trial.

    Science.gov (United States)

    Faurholt-Jepsen, M; Frost, M; Ritz, C; Christensen, E M; Jacoby, A S; Mikkelsen, R L; Knorr, U; Bardram, J E; Vinberg, M; Kessing, L V

    2015-10-01

    The number of studies on electronic self-monitoring in affective disorder and other psychiatric disorders is increasing and indicates high patient acceptance and adherence. Nevertheless, the effect of electronic self-monitoring in patients with bipolar disorder has never been investigated in a randomized controlled trial (RCT). The objective of this trial was to investigate in a RCT whether the use of daily electronic self-monitoring using smartphones reduces depressive and manic symptoms in patients with bipolar disorder. A total of 78 patients with bipolar disorder according to ICD-10 criteria, aged 18-60 years, and with 17-item Hamilton Depression Rating Scale (HAMD-17) and Young Mania Rating Scale (YMRS) scores ≤17 were randomized to the use of a smartphone for daily self-monitoring including a clinical feedback loop (the intervention group) or to the use of a smartphone for normal communicative purposes (the control group) for 6 months. The primary outcomes were differences in depressive and manic symptoms measured using HAMD-17 and YMRS, respectively, between the intervention and control groups. Intention-to-treat analyses using linear mixed models showed no significant effects of daily self-monitoring using smartphones on depressive as well as manic symptoms. There was a tendency towards more sustained depressive symptoms in the intervention group (B = 2.02, 95% confidence interval -0.13 to 4.17, p = 0.066). Sub-group analysis among patients without mixed symptoms and patients with presence of depressive and manic symptoms showed significantly more depressive symptoms and fewer manic symptoms during the trial period in the intervention group. These results highlight that electronic self-monitoring, although intuitive and appealing, needs critical consideration and further clarification before it is implemented as a clinical tool.

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

    Science.gov (United States)

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

    2017-10-01

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

  20. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

    DEFF Research Database (Denmark)

    Wasmund, Kenneth; Cooper, Myriel; Schreiber, Lars

    2016-01-01

    The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affilia......The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene...... that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding...... dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many...

  1. Privacy preserving probabilistic record linkage (P3RL): a novel method for linking existing health-related data and maintaining participant confidentiality.

    Science.gov (United States)

    Schmidlin, Kurt; Clough-Gorr, Kerri M; Spoerri, Adrian

    2015-05-30

    Record linkage of existing individual health care data is an efficient way to answer important epidemiological research questions. Reuse of individual health-related data faces several problems: Either a unique personal identifier, like social security number, is not available or non-unique person identifiable information, like names, are privacy protected and cannot be accessed. A solution to protect privacy in probabilistic record linkages is to encrypt these sensitive information. Unfortunately, encrypted hash codes of two names differ completely if the plain names differ only by a single character. Therefore, standard encryption methods cannot be applied. To overcome these challenges, we developed the Privacy Preserving Probabilistic Record Linkage (P3RL) method. In this Privacy Preserving Probabilistic Record Linkage method we apply a three-party protocol, with two sites collecting individual data and an independent trusted linkage center as the third partner. Our method consists of three main steps: pre-processing, encryption and probabilistic record linkage. Data pre-processing and encryption are done at the sites by local personnel. To guarantee similar quality and format of variables and identical encryption procedure at each site, the linkage center generates semi-automated pre-processing and encryption templates. To retrieve information (i.e. data structure) for the creation of templates without ever accessing plain person identifiable information, we introduced a novel method of data masking. Sensitive string variables are encrypted using Bloom filters, which enables calculation of similarity coefficients. For date variables, we developed special encryption procedures to handle the most common date errors. The linkage center performs probabilistic record linkage with encrypted person identifiable information and plain non-sensitive variables. In this paper we describe step by step how to link existing health-related data using encryption methods to

  2. An Integrated Resource for Barley Linkage Map and Malting Quality QTL Alignment

    Directory of Open Access Journals (Sweden)

    Péter Szűcs

    2009-07-01

    Full Text Available Barley ( L. is an economically important model plant for genetics research. Barley is currently served by an increasingly comprehensive set of tools for genetic analysis that have recently been augmented by high-density genetic linkage maps built with gene-based single nucleotide polymorphisms (SNPs. These SNP-based maps need to be aligned with earlier generation maps, which were used for quantitative trait locus (QTL detection, by integrating multiple types of markers into a single map. A 2383 locus linkage map was developed using the Oregon Wolfe Barley (OWB Mapping Population to allow such alignments. The map is based on 1472 SNP, 722 DArT, and 189 prior markers which include morphological, simple sequence repeat (SSR, Restriction Fragment Length Polymorphism (RFLP, and sequence tagged site (STS loci. This new OWB map forms, therefore, a useful bridge between high-density SNP-only maps and prior QTL reports. The application of this bridge concept is shown using malting-quality QTLs from multiple mapping populations, as reported in the literature. This is the first step toward developing a Barley QTL Community Curation workbook for all types of QTLs and maps, on the GrainGenes website. The OWB-related resources are available at OWB Data and GrainGenes Tools (OWB-DGGT (.

  3. 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.

  4. MNC Strategies and Linkage Effects in Developing Countries

    DEFF Research Database (Denmark)

    Hansen, Michael Wendelboe; Pedersen, Torben; Petersen, Bent

    2007-01-01

    . It is hypothesized that compared to investments undertaken by MNCs following strategies of global integration, investments of MNCs pursuing local responsiveness create more jobs but imply less job upgrading in developing countries. The hypotheses are tested on a sample of Danish MNCs with extensive investments......The paper addresses the question of which implications MNC strategies have to FDI linkage effects in developing countries. Two contrasting MNC strategies reflecting an integration-responsiveness dichotomy are scrutinized as to their job effects on local linkage partners in developing countries...... in developing countries....

  5. MNC Strategies and Linkage Effects in Developing Countries

    DEFF Research Database (Denmark)

    Hansen, Michael Wendelboe; Pedersen, Torben; Petersen, Bent

    2007-01-01

    The paper addresses the question of which implications MNC strategies have to FDI linkage effects in developing countries. Two contrasting MNC strategies reflecting an integration-responsiveness dichotomy are scrutinized as to their job effects on local linkage partners in developing countries....... It is hypothesized that compared to investments undertaken by MNCs following strategies of global integration, investments of MNCs pursuing local responsiveness create more jobs but imply less job upgrading in developing countries. The hypotheses are tested on a sample of Danish MNCs with extensive investments...

  6. Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes

    OpenAIRE

    Landthaler, Markus; Shub, David A.

    1999-01-01

    Analysis of RNA that can be labeled with GTP indicates the existence of group I introns in genes of at least three transcriptional classes in the genome of Staphylococcus aureus bacteriophage Twort. A single ORF of 142 amino acids (Orf142) is interrupted by three self-splicing group I introns, providing the first example of a phage gene with multiple intron insertions. Twort Orf142 is encoded in a message that is abundant 15–20 min after infection and is highly similar to a late gene product ...

  7. snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package.

    Science.gov (United States)

    Luna, Augustin; Nicodemus, Kristin K

    2007-03-15

    snp.plotter is a newly developed R package which produces high-quality plots of results from genetic association studies. The main features of the package include options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D' LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme. snp.plotter can plot single SNP and/or haplotype data and simultaneously plot multiple sets of results. R is a free software environment for statistical computing and graphics available for most platforms. The proposed package provides a simple way to convey both association and LD information in a single appealing graphic for genetic association studies. Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html and http://www.r-project.org.

  8. Frequency of LCT -13910C>T single nucleotide polymorphism associated with adult-type hypolactasia/lactase persistence among Brazilians of different ethnic groups

    Directory of Open Access Journals (Sweden)

    Silva Joyce MK

    2009-10-01

    Full Text Available Abstract Background Adult-type hypolactasia, the physiological decline of lactase some time after weaning, was previously associated with the LCT -13910C>T polymorphism worldwide except in Africa. Lactase non-persistence is the most common phenotype in humans, except in northwestern Europe with its long history of pastoralism and milking. We had previously shown association of LCT -13910C>T polymorphism with adult-type hypolactasia in Brazilians; thus, we assessed its frequency among different Brazilian ethnic groups. Methods We investigated the ethnicity-related frequency of this polymorphism in 567 Brazilians [mean age, 42.1 ± 16.8 years; 157 (27.7% men]; 399 (70.4% White, 50 (8.8% Black, 65 (11.5% Brown, and 53 (9.3% Japanese-Brazilian. DNA was extracted from leukocytes; LCT -13910C>T polymorphism was analyzed by PCR-restriction fragment length polymorphism. Results Prevalence of the CC genotype associated with hypolactasia was similar (57% among White and Brown groups; however, prevalence was higher among Blacks (80% and those of Japanese descent (100%. Only 2 (4% Blacks had TT genotype, and 8 (16% had the CT genotype. Assuming an association between CC genotype and hypolactasia, and CT and TT genotypes with lactase persistence, 356 (62.8% individuals had hypolactasia and 211 (37.2% had lactase persistence. The White and Brown groups had the same hypolactasia prevalence (~57%; nevertheless, was 80% among Black individuals and 100% among Japanese-Brazilians (P Conclusion The lactase persistence allele, LCT -13910T, was found in about 43% of both White and Brown and 20% of the Black Brazilians, but was absent among all Japanese Brazilians studied.

  9. First principles study of electronic and structural properties of single walled zigzag boron nitride nanotubes doped with the elements of group IV

    Science.gov (United States)

    Bahari, Ali; jalalinejad, Amir; Bagheri, Mosahhar; Amiri, Masoud

    2017-11-01

    In this paper, structural and electronic properties and stability of (10, 0) born nitride nanotube (BNNT) are considered within density functional theory by doping group IV elements of the periodic table. The HOMO-LUMO gap has been strongly modified and treated a dual manner by choosing B or N sites for dopant atoms. Formation energy calculation shows that B site doping is more stable than N site doping. Results also show that all dopants turn the pristine BNNT into a p-type semiconductor except for carbon-doped BNNT at B site.

  10. Outcomes of Total Parathyroidectomy with Autotransplantation versus Subtotal Parathyroidectomy with Routine Addition of Thymectomy to both Groups: Single Center Experience of Secondary Hyperparathyroidism

    Directory of Open Access Journals (Sweden)

    Cem Kaan Parsak

    2014-03-01

    Full Text Available Background: Secondary hyperparathyroidism is a common acquired disorder seen in chronic renal failure. It may result in potentially serious complications including metabolic bone diseases, severe atherosclerosis and undesirable cardiovascular events. Parathyroidectomy is required in about 20% of patients after 3-10 years of dialysis and in up to 40% after 20 years. Aims: The aim of the current study was to evaluate the short-term and long-term outcomes of patients with secondary hyperparathyroidism who had undergone total parathyroidectomy with autotransplantation and thymectomy or subtotal parathyroidectomy with thymectomy by the same surgical team during the study period. Study Design: Retrospective comparative study. Methods: Clinical data of 50 patients who underwent parathyroid surgery for secondary hyperparathyroidism between 2003 and 2011 were reviewed retrospectively. Patients were divided into two subgroups of total parathyroidectomy with autotransplantation or subtotal parathyroidectomy. Thymectomy was routinely performed for both groups. Short term outcome parameters included intact parathyroid hormone, ionized calcium and alkaline phosphatase levels. Bone pain, bone fractures, persistent or recurrent disease were included in long term outcome parameters. Results: The mean duration of dialysis was eight years. The mean ionized calcium levels dropped significantly in the total parathyroidectomy with autotransplantation group (p=0.016. No serious postoperative complications were observed. Postoperative intravenous calcium supplementation was required in four patients in the total parathyroidectomy with autotransplantation group (total PTX+AT and in three patients in the subtotal parathyroidectomy group (subtotal PTX. Postoperatively, all patients received oral calcium carbonate and calcitriol. The length of average hospital stay was 5 (3-10 days. Including nine patients who underwent successful renal transplantation pre-operative bone

  11. Exclusion of linkage between cleft lip with or without cleft palate and markers on chromosomes 4 and 6

    Energy Technology Data Exchange (ETDEWEB)

    Blanton, S.H. [Univ. of Virginia, Charlottesville, VA (United States); Malcolm, S.; Winter, R. [Institute of Child Health, London (United Kingdom)] [and others

    1996-01-01

    Nonsyndromic cleft lip with or without associate cleft palate (CLP) is a common craniofacial defect, occurring in {approximately}1/1,000 live births. While the defect generally occurs sporadically, multiplex families have been reported. Segregation analyses have demonstrated that, in some families, CLP is inherited as an autosomal dominant/codominant disorder with low penetrance. Several clefting loci have been proposed on multiple chromosomes, including 6p24, 4q, and 19q13.1. Association studies and linkage studies suggested a locus that mapped to 6p24. We were unable to confirm this in a linkage study of 12 multigenerational families. A subsequent linkage study by Carinci et al., however, found evidence for linkage to this region in 14 of 21 clefting families. Additionally, Davies et al. studied the chromosomes of three individuals with cleft lip and palate, all of whom had a rearrangement involving 6p24. Their investigation supported a locus at 6p24. Carinci et al. reported that the most likely position for a clefting locus was at D6S89, which is centromeric to EDN1. This is in contrast to the findings of Davies et al., who suggested a placement telomeric to EDN1. F13A, which had been implicated in the initial association studies, is telomeric to EDN1. Thus, the region between F13A and D6S89 encompasses the regions proposed by both Davies et al. and Carinci et al. A second clefting locus, at 4q, was proposed by Beiraghi et al., who studied a single multigenerational family by linkage analysis. Their data suggested a locus near D4S175 and D4S192. 10 refs., 1 tab.

  12. On moving targets and magic bullets: Can the UK lead the way with responsible data linkage for health research?

    Science.gov (United States)

    Laurie, G; Ainsworth, J; Cunningham, J; Dobbs, C; Jones, K H; Kalra, D; Lea, N C; Sethi, N

    2015-11-01

    To provide an overview of essential elements of good governance of data linkage for health-related research, to consider lessons learned so far and to examine key factors currently impeding the delivery of good governance in this area. Given the considerable hurdles which must be overcome and the changing landscape of health research and data linkage, a principled, proportionate, risk-based approach to governance is advocated. In light of the considerable value of data linkage to health and well-being, the United Kingdom aspires to design and deliver good governance in health-related research. A string of projects have been asking: what does good governance look like in data linkage for health research? It is argued here that considerable progress can and must be made in order to develop the UK's contribution to future health and wealth economies, particularly in light of mis-start initiatives such as care.data in NHS England. Discussion centres around lessons learned from previous successful health research initiatives, identifying those governance mechanisms which are essential to achieving good governance. This article suggests that a crucial element in any step-increase of research capability will be the adoption of adaptive governance models. These must recognise a range of approaches to delivering safe and effective data linkage, while remaining responsive to public and research user expectations and needs as these shift and change with time and experience. The targets are multiple and constantly moving. There is not--nor should we seek--a single magic bullet in delivering good governance in health research. Copyright © 2015. Published by Elsevier Ireland Ltd.

  13. Synthesis of aminobenzyltriethylenetetraaminohexaacetic acid: conjugation of the chelator to protein by an alkylamine linkage.

    Science.gov (United States)

    Bhargava, K K; Zhang, Z Y; Palestro, C J; Acharya, S A

    1999-10-01

    The conjugation of a chelating agent to an antibody as an anchoring site for a radionuclide is the first step in the successful preparation of a radiolabeled antibody for a diagnostic and therapeutic application. The high affinity of the protein bound chelator towards radionuclide ensures a higher selectivity in the delivery of the radionuclide to the targeted tissue. 4-Aminobenzylderivativetriethlenetetraaminohexaacetic acid (TTHA), a hexadentate chelating agent has been now prepared for conjugation with proteins in view of the higher affinity of TTHA metal ions as compared to DTPA. The latent crosslinking potential of alpha-hydroxy aldehydes has been used to conjugate the new chelating agent to proteins through an alkylamine linkage. On incubation of amino benzyl TTHA with glycoladehyde at neutral pH and room temperature, the reagent is converted to oxo ethyl amino benzyl TTHA. On addition of albumin to this reaction mixture, the oxo ethylamino benzyl TTHA generates reversible schiff base adducts with the amino groups of albumin. The reduction of the Schiff base adducts of the chelator with the protein by sodium cyanoborohydride stabilizes the schiff base adducts as stable alkylamine linkages. 4-Thiocyanatobenzyl TTHA has also been prepared and conjugated to albumin through a thiocarbamoyl linkage. Both preparations of TTHA conjugated albumin complexed with 99mTc and 111In, with high affinity and no decomposition of the complex was noticed for at least up to 6 hrs after the preparation. The radiolabels complexed with these TTHA -albumin conjugates could not be 'chased' out by free DTPA. A comparison of the biodistribution of 111In, bound to the TTHA conjugated through an alkylamine and a thiocarbamoyl linkage showed that 111In complexed with alkylamine linked TTHA was retained in blood to a level nearly 17% higher compared to that seen with thicarbamoyl linked TTHA, one hr after the injection into mice. Thus, the alkylamine linkage appears to be more stable under

  14. Linkage disequilibrium organization of the human KIR superlocus: implications for KIR data analyses

    OpenAIRE

    Gourraud, Pierre-Antoine; Meenagh, Ashley; Cambon-Thomsen, Anne; Middleton, Derek

    2010-01-01

    An extensive family-based study of linkage disequilibrium (LD) in the killer cell immunoglobulin-like receptors (KIR) cluster was performed. We aimed to describe the LD structure in the KIR gene cluster using a sample of 418 founder haplotypes identified by segregation in a group of 106 families from Northern Ireland. The LD was studied at two levels of polymorphism: the structural level (presence or absence of KIR genes) and the allelic level (between alleles of KIR genes). LD was further as...

  15. A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection.

    Science.gov (United States)

    Sargent, D J; Passey, T; Surbanovski, N; Lopez Girona, E; Kuchta, P; Davik, J; Harrison, R; Passey, A; Whitehouse, A B; Simpson, D W

    2012-05-01

    The linkage maps of the cultivated strawberry, Fragaria × ananassa (2n = 8x = 56) that have been reported to date have been developed predominantly from AFLPs, along with supplementation with transferrable microsatellite (SSR) markers. For the investigation of the inheritance of morphological characters in the cultivated strawberry and for the development of tools for marker-assisted breeding and selection, it is desirable to populate maps of the genome with an abundance of transferrable molecular markers such as microsatellites (SSRs) and gene-specific markers. Exploiting the recent release of the genome sequence of the diploid F. vesca, and the publication of an extensive number of polymorphic SSR markers for the genus Fragaria, we have extended the linkage map of the 'Redgauntlet' × 'Hapil' (RG × H) mapping population to include a further 330 loci, generated from 160 primer pairs, to create a linkage map for F. × ananassa containing 549 loci, 490 of which are transferrable SSR or gene-specific markers. The map covers 2140.3 cM in the expected 28 linkage groups for an integrated map (where one group is composed of two separate male and female maps), which represents an estimated 91% of the cultivated strawberry genome. Despite the relative saturation of the linkage map on the majority of linkage groups, regions of apparent extensive homozygosity were identified in the genomes of 'Redgauntlet' and 'Hapil' which may be indicative of allele fixation during the breeding and selection of modern F. × ananassa cultivars. The genomes of the octoploid and diploid Fragaria are largely collinear, but through comparison of mapped markers on the RG × H linkage map to their positions on the genome sequence of F. vesca, a number of inversions were identified that may have occurred before the polyploidisation event that led to the evolution of the modern octoploid strawberry species.

  16. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  17. SNPs, linkage disequilibrium, and chronic mountain sickness in Tibetan Chinese

    Directory of Open Access Journals (Sweden)

    Buroker NE

    2017-07-01

    Full Text Available Norman E Buroker,1 Xue-Han Ning,1,2,† Zhao-Nian Zhou,3 Kui Li,4 Wei-Jun Cen,4 Xiu-Feng Wu,3 Wei-Zhong Zhu,5 C Ronald Scott,1 Shi-Han Chen1 1Department of Pediatrics, University of Washington, 2Division of Cardiology, Seattle Children’s Hospital Research Foundation, Seattle, WA, USA; 3Laboratory of Hypoxia Physiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; 4Lhasa People Hospital, Lhasa, Tibet; 5Center for Cardiovascular Biology and Regenerative Medicine, University of Washington, Seattle, WA, USA †Xue-Han Ning passed away on April 20, 2015 Abstract: Chronic mountain sickness (CMS is estimated at 1.2% in Tibetans living at the Qinghai–Tibetan Plateau. Eighteen single-nucleotide polymorphisms (SNPs from nine nuclear genes that have an association with CMS in Tibetans have been analyzed by using pairwise linkage disequilibrium (LD. The SNPs included are the angiotensin-converting enzyme (rs4340, the angiotensinogen (rs699, and the angiotensin II type 1 receptor (AGTR1 (rs5186 from the renin–angiotensin system. A low-density lipoprotein apolipoprotein B (rs693 SNP was also included. From the hypoxia-inducible factor oxygen signaling pathway, the endothetal Per-Arnt-Sim domain protein 1 (EPAS1 and the egl nine homolog 1 (ENGL1 (rs480902 SNPs were included in the study. SNPs from the vascular endothelial growth factor (VEGF signaling pathway included are the v-akt murine thymoma viral oncogene homolog 3 (rs4590656 and rs2291409, the endothelial cell nitric oxide synthase 3 (rs1007311 and rs1799983, and the (VEGFA (rs699947, rs34357231, rs79469752, rs13207351, rs28357093, rs1570360, rs2010963, and rs3025039. An increase in LD occurred in 40 pairwise comparisons, whereas a decrease in LD was found in 55 pairwise comparisons between the controls and CMS patients. These changes were found to occur within and between signaling pathways, which suggests that there is an interaction between SNP

  18. Autosomal linkage analysis for the level of response to alcohol.

    Science.gov (United States)

    Schuckit, Marc A; Wilhelmsen, Kirk; Smith, Tom L; Feiler, Heidi S; Lind, Penelope; Lange, Leslie A; Kalmijn, Jelger

    2005-11-01

    The level of response (LR) to alcohol is a genetically-influenced phenotype related to the alcoholism risk. Usually measured by evaluating psychological and physiological changes that follow the administration of alcohol, the heritability of LR is estimated to be between 0.4 and 0.6, and efforts are being made to find genes related to this phenotype. This paper presents data from a family-based genome with linkage analysis focusing on alcohol challenge determinants of LR. The subjects were 18-to-29-year-old sibling pairs with at least one parent who was alcohol-dependent and who had experience with alcohol but were not yet alcohol-dependent themselves. Both members of the sibling pairs were given oral alcohol challenges (0.75-0.90 ml/kg of ethanol for females and males, respectively), with LR established using the Subjective High Assessment Scale (SHAS) and changes in body sway (BS) repeatedly over a 3.5-hr. period. Blood samples from siblings and at least one parent were genotyped using 811 microsatellite markers, with results evaluated using several related variance component approaches as implemented in SOLAR for continuous traits. In addition, association was tested using single nucleotide polymorphisms (SNPs) within the KCNMA1, HTR7 and SLC18A2 genes that may relate to a finding on chromosome 10. Data were generated from 238 sib-pairs representing 365 individuals (41.6% were males) from 165 families. The most consistent results across methods and samples were observed for SHAS on chromosome 10 between 120 and 140 cM (with a maximum LOD score of 2.6 at 122 cM), and a second region of possible interest at 173 cM (LOD = 1.2). Statistical analysis with the KCNMA1, HTR7 and SLC18A2 genes, which lie in the support region of interest revealed no evidence for association after correction for multiple comparisons. These evaluations from the largest known alcohol challenge-based genetic study to date highlight the potential importance of genes on chromosome 10 as

  19. Describing the linkages of the immigration, refugees and citizenship Canada permanent resident data and vital statistics death registry to Ontario's administrative health database.

    Science.gov (United States)

    Chiu, Maria; Lebenbaum, Michael; Lam, Kelvin; Chong, Nelson; Azimaee, Mahmoud; Iron, Karey; Manuel, Doug; Guttmann, Astrid

    2016-10-21

    be conducted. Analytic techniques to account for sub-optimal linkage rates may be required in studies of certain ethnic groups or certain causes of death among children and infants.

  20. All Wales Injury Surveillance System revised: development of a population-based system to evaluate single-level and multilevel interventions.

    Science.gov (United States)

    Lyons, Ronan A; Turner, Samantha; Lyons, Jane; Walters, Angharad; Snooks, Helen A; Greenacre, Judith; Humphreys, Ciaran; Jones, Sarah J

    2016-04-01

    Injury surveillance has been established since the 1990s, but is still largely based upon single-source data from sentinel sites. The growth of electronic health records and developments in privacy protecting linkage technologies provide an opportunity for more sophisticated surveillance systems. To describe the evolution of an injury surveillance system to support the evaluation of interventions, both simple and complex in terms of organisation. The paper describes the evolution of the system from one that relied upon data only from emergency departments to one that include multisource data and are now embedded in a total population privacy protecting data linkage system. Injury incidence estimates are compared by source and data linkage used to aid understanding of data quality issues. Examples of applications, challenges and solutions are described. The age profile and estimated incidence of injuries recorded in general practice, emergency departments and hospital admissions differ considerably. Data linkage has enabled the evaluation of complex interventions and measurement of longer-term impact of a wide range of exposures. Embedding injury surveillance within privacy protecting data linkage environment can transform the utility of a traditional single-source surveillance system to a multisource system. It also facilitates greater involvement in the evaluation of simple and complex healthcare and non-healthcare interventions and contributes to the growing evidence basis underlying the science of injury prevention and control. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  1. Magnetic Topology of Coronal Hole Linkages

    Science.gov (United States)

    Titov, V. S.; Mikic, Z.; Linker, J. A.; Lionello, R.; Antiochos, S. K.

    2010-01-01

    In recent work, Antiochos and coworkers argued that the boundary between the open and closed field regions on the Sun can be extremely complex with narrow corridors of open ux connecting seemingly disconnected coronal holes from the main polar holes, and that these corridors may be the sources of the slow solar wind. We examine, in detail, the topology of such magnetic configurations using an analytical source surface model that allows for analysis of the eld with arbitrary resolution. Our analysis reveals three important new results: First, a coronal hole boundary can join stably to the separatrix boundary of a parasitic polarity region. Second, a single parasitic polarity region can produce multiple null points in the corona and, more important, separator lines connecting these points. Such topologies are extremely favorable for magnetic reconnection, because it can now occur over the entire length of the separators rather than being con ned to a small region around the nulls. Finally, the coronal holes are not connected by an open- eld corridor of finite width, but instead are linked by a singular line that coincides with the separatrix footprint of the parasitic polarity. We investigate how the topological features described above evolve in response to motion of the parasitic polarity region. The implications of our results for the sources of the slow solar wind and for coronal and heliospheric observations are discussed.

  2. Modeling Resource Hotspots: Critical Linkages and Processes

    Science.gov (United States)

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

    2017-12-01

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

  3. Genomewide linkage of Obstructive Sleep Apnea and High Density Lipoprotein Cholesterol in a Filipino Family

    Science.gov (United States)

    Relf, Bronwyn L; Larkin, Emma K; de Torres, Carina; Baur, Louise A; Christodoulou, John; Waters, Karen A

    2015-01-01

    Summary Increasing evidence supports an association between obstructive sleep apnoea and metabolic syndrome in both children and adults suggesting a genetic component. However, the genetic relationship between the diseases remains unclear. We performed a bivariate linkage scan on a single Filipino family with a high prevalence of obstructive sleep apnoea and metabolic syndrome to explore the genetic pathways underlying these diseases. A large rural family (N=50, 50% adults) underwent a 10cM genome-wide scan. Fasting blood was used to measure insulin, triglycerides, total cholesterol and HDL cholesterol. Attended overnight polysomnography was used to quantify the respiratory disturbance index (RDI), a measure of sleep apnea. BMI z-scores and insulin resistance scores were calculated. Bivariate multipoint linkage analyses were performed on RDI and metabolic syndrome components. Obstructive sleep apnea prevalence was 46% (n=23; 9 adults, 14 children) in our participants. Metabolic syndrome phenotype was present in 40% of adults (n=10) and 48% of children (n=12). Linkage peaks with a LOD score > 3 were demonstrated on chromosome 19q13·4 (LOD=3·04) for the trait pair RDI and high density lipoprotein (HDL) cholesterol. Candidate genes identified in this region include the killer-like immunoglobulin receptor (KIR) genes. These genes are associated with modulating inflammatory responses in reaction to cellular stress and initiation of atherosclerotic plaque formation. We have identified a novel locus for genetic links between RDI and lipid factors associated with metabolic syndrome in a chromosomal region containing genes associated with inflammatory responses. PMID:20149069

  4. The Fibromyalgia Family Study: A Genome-Scan Linkage Study

    Science.gov (United States)

    Arnold, Lesley M.; Fan, Jinbo; Russell, I. Jon; Yunus, Muhammad B.; Khan, Muhammad Asim; Kushner, Irving; Olson, Jane M.; Iyengar, Sudha K.

    2013-01-01

    Objective Familial aggregation of fibromyalgia has been increasingly recognized. The goal of the current study was to conduct a genome wide linkage scan to identify susceptibility loci for fibromyalgia. Methods We genotyped members of 116 families from the Fibromyalgia Family Study and performed a model-free genome-wide linkage analysis of fibromyalgia with 341 microsatellite markers, using the Haseman-Elston regression approach. Results The estimated sibling recurrence risk ratio (λs) for fibromyalgia was 13.6 (95% CI: 10.0–18.5), based on a reported population prevalence of 2%. Genome-wide suggestive evidence of linkage was found at marker D17S2196 (Empirical P =0.00030) and D17S1294 (Empirical P =0.00035) on chromosome 17p11.2-q11.2. Conclusion The estimated sibling recurrence risk ratio suggests a strong genetic component of fibromyalgia. This is the first study to report genome-wide suggestive linkage of fibromyalgia to the chromosome 17p11.2-q11.2 region. Further investigation of these multi-case families from the Fibromyalgia Family Study is warranted to identify potential causal risk variants for fibromyalgia. PMID:23280346

  5. Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig

    NARCIS (Netherlands)

    Amaral, A.J.; Megens, H.J.W.C.; Crooijmans, R.P.M.A.; Heuven, H.C.M.; Groenen, M.A.M.

    2008-01-01

    Linkage disequilibrium (LD) may reveal much about domestication and breed history. Ail investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total,

  6. Roots of Acetate-Vanadium Linkage Isomerism: A QTAIM Study.

    Science.gov (United States)

    Teixeira, Filipe; Mosquera, Ricardo; Melo, André; Freire, Cristina; Cordeiro, M Natália D S

    2016-04-04

    The possibility of linkage isomerism in a number of vanadium(IV) and vanadium(V) complexes with acetate was surveyed using Density Functional Theory (DFT) and Bader's Quantum Theory of Atoms in Molecules (QTAIM). The results show that vanadium-acetate linkages may be classified as bidentate symmetrical, bidentate asymmetrical, or monodentate, the latter being observed in about 40% of the cases. These latter ones correspond to situations where the two oxygen atoms of the acetate moiety are not equivalent. They are associated with an energy penalty of about 263 kJ·mol(-1), as determined by the distribution of the scaled kinetic energy of the atomic basins forming the acetate ligand. In the presence of bidentate symmetrical vanadium-acetate linkages, the inner valence-shell charge concentrations on the vanadium atom deviate from the traditional VSEPR-derived arrangement, with an energy penalty of about 780 kJ·mol(-1). A compromise situation is partially accomplished in the case of bidentate asymmetrical linkages, which allow a Gillespiean-like arrangement of the inner valence-shell charge concentrations. In this case, one of these local charge concentrations lies close to a V-OAcO bond, which slightly disrupts the equivalence between the two oxygen atoms in the acetate ligand.

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

    Indian Academy of Sciences (India)

    Guillén, Adolfo Cordero-Rivera, Erik I. Svensson and Bengt Hansson. J. Genet. 92, 115–119. Table 1. Descriptive data for microsatellite loci that were used in the present linkage mapping study. GenBank. Expected. Actual. Number of accession.

  8. A genetic linkage map of Japanese scallop Mizuhopecten ...

    African Journals Online (AJOL)

    A genetic linkage map of the Japanese scallop Mizuhopecten yessoensis was constructed based on 302 markers, including 263 amplified fragment length polymorphism (AFLP) markers and 39 microsatellite (SSR) markers. The two parental maps were constructed according to the double pseudo-test cross strategy with an ...

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

    Science.gov (United States)

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

    2008-01-01

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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock with superior yields, growth rates, and evolutionary potential. Such genes can be located using the candidate gene approach, genome wide scans, or by within family mapping. Linkage disequilibrium.

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

    African Journals Online (AJOL)

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

  13. (Lathyrus sativus L.): origin, morphology, inheritance and linkage ...

    Indian Academy of Sciences (India)

    Dibyendu Talukdar

    2018-04-06

    Apr 6, 2018 ... Indian Academy of Sciences https://doi.org/10.1007/s12041-018-0924-x. RETRACTION NOTE. Retraction Note to: Dwarf mutations in grass pea (Lathyrus sativusL.): origin, morphology, inheritance and linkage studies. DIBYENDU TALUKDAR. Department of Botany, University of Kalyani, Kalyani 741 235, ...

  14. Comparative mapping reveals similar linkage of functional genes to ...

    Indian Academy of Sciences (India)

    logous genes and QTL of yield-related traits by silico map- ping and population mapping in O. sativa. Our results revealed that B. napus and O. sativa shared homologous se- quences of genes with similar functions, as well as consistent linkage relationships between genes and agronomic traits. Materials and methods.

  15. A consensus linkage map of the chicken genome

    NARCIS (Netherlands)

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

    2000-01-01

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

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

    NARCIS (Netherlands)

    Nooteboom, B

    1999-01-01

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

  17. LINKAGE MAPPING OF THE SPINAL MUSCULAR-ATROPHY GENE

    NARCIS (Netherlands)

    BURGHES, AHM; INGRAHAM, SE; KOTEJARAI, Z; ROSENFELD, S; HERTA, N; NADKARNI, N; DIDONATO, CJ; CARPTEN, J; HURKO, O; FLORENCE, J; MOXLEY, RT; COBBEN, JM; MENDELL, [No Value

    Spinal muscular atrophy (SMA) is a common autosomal recessive disorder resulting in loss of motor neurons. We have performed linkage analysis on a panel of families using nine markers that are closely linked to the SMA gene. The highest lod score was obtained with the marker D5S351 (Z(max) = 10.04

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

    NARCIS (Netherlands)

    Kroeze-Gil, J.

    2003-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Haishu Qiao

    2015-01-01

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

  20. THE MEASUREMENT OF INTERINDUSTRY LINKAGES - KEY SECTORS IN THE NETHERLANDS

    NARCIS (Netherlands)

    DIETZENBACHER, E

    1992-01-01

    The present paper proposes a new method for the measurement of sectoral interdependencies. It is shown that the elements of the eigenvector corresponding to the dominant eigenvalue of a matrix may be used for measuring interindustry linkages. In an empirical study, the eigenvector method is compared

  1. Can University-Industry Linkages Stimulate Student Employability?

    Science.gov (United States)

    Ishengoma, Esther; Vaaland, Terje I.

    2016-01-01

    Purpose: The purpose of this paper is to identify important university-industry linkage (UIL) activities that can stimulate the likelihood of employability among students. Design/methodology/approach: A total of 404 respondents located in Tanzania, comprising students, faculty members and employees from 20 companies operating within the oil and…

  2. The first genetic linkage map of Primulina eburnea (Gesneriaceae ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE. The first genetic linkage map of Primulina eburnea ... 1Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden,. Chinese Academy of Sciences, ... We observed a high level diversity of flower traits among populations in the common-garden test ...

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

    African Journals Online (AJOL)

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

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

    Science.gov (United States)

    Rukumnuaykit, Pungpond; Pholphirul, Piriya

    2016-01-01

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

  5. Distribution and linkage disequilibrium analysis of polymorphisms of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 95; Issue 1. Distribution and linkage disequilibrium analysis of polymorphisms of GH1 gene in different populations of pigs associated with body size. Yunyun Cheng Songcai Liu Dan Su Chao Lu Xin Zhang Qingyan Wu Siming Li Haoyu Fu Hao Yu Linlin Hao. Research Article ...

  6. The first genetic linkage map of Primulina eburnea (Gesneriaceae ...

    Indian Academy of Sciences (India)

    Ofthe 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. Thelinkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage mapprovides a framework for identification of important genes in breeding ...

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

  9. Computerized crime linkage systems: a critical review and research agenda

    NARCIS (Netherlands)

    Bennell, C.; Snook, B.; MacDonald, S.; House, J. C.; Taylor, Paul J

    2012-01-01

    Computerized crime linkage systems are meant to assist the police in determining whether crimes have been committed by the same offender. In this article, the authors assess these systems critically and identify four assumptions that affect the effectiveness of these systems. These assumptions are

  10. the linkage between geological setting and human health in ethiopia

    African Journals Online (AJOL)

    preferred customer

    geo-sciences in Ethiopia to investigate the linkage between geo-environments and associated health risks. Fluoride and related diseases are the most widely studied from geological ... Key words: Geochemical diseases, geo-environmental setting, Ethiopia, health belts .... Highly leached iron, aluminum and silica-rich.

  11. Learning and Competence Building through Cross-cultural Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull

    2006-01-01

    The aim of the chapter is to study upgrading of companies in developing countries in a learning perspective. Both formal and experiential and tacit knowledge is discussed. Learning effects of different management modes, expatriates, linkages to customers and suppliers are discussed as are learnin...

  12. Distribution and linkage disequilibrium analysis of polymorphisms of ...

    Indian Academy of Sciences (India)

    gene are associated with the body size of pigs providing genetic basis for pig breeding with the improved economic benefits. [Cheng Y., Liu S., Su D., Lu C., Zhang X., Wu Q., Li S., Fu H., Yu H. and Hao L. 2016 Distribution and linkage disequilibrium analysis of polymorphisms of GH1 gene in different populations of pigs ...

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  14. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

    NARCIS (Netherlands)

    Vilhjálmsson, Bjarni J.; Yang, Jian; Finucane, Hilary K.; Gusev, Alexander; Lindström, Sara; Ripke, Stephan; Genovese, Giulio; Loh, Po-Ru; Bhatia, Gaurav; Do, Ron; Hayeck, Tristan; Won, Hong-Hee; Kathiresan, Sekar; Pato, Michele; Pato, Carlos; Tamimi, Rulla; Stahl, Eli; Zaitlen, Noah; Pasaniuc, Bogdan; Belbin, Gillian; Kenny, Eimear E.; Schierup, Mikkel H.; de Jager, Philip; Patsopoulos, Nikolaos A.; McCarroll, Steve; Daly, Mark; Purcell, Shaun; Chasman, Daniel; Neale, Benjamin; Goddard, Michael; Visscher, Peter M.; Kraft, Peter; Patterson, Nick; Price, Alkes L.; Neale, Benjamin M.; Corvin, Aiden; Walters, James T. R.; Farh, Kai-How; Holmans, Peter A.; Lee, Phil; Bulik-Sullivan, Brendan; Collier, David A.; Huang, Hailiang; Pers, Tune H.; Agartz, Ingrid; Agerbo, Esben; Albus, Margot; Alexander, Madeline; Amin, Farooq; Bacanu, Silviu A.; Begemann, Martin; Belliveau, Richard A.; Bene, Judit; Bergen, Sarah E.; Bevilacqua, Elizabeth; Bigdeli, Tim B.; Black, Donald W.; Bruggeman, Richard; Buccola, Nancy G.; Buckner, Randy L.; Byerley, William; Cahn, Wiepke; Cai, Guiqing; Campion, Dominique; Cantor, Rita M.; Carr, Vaughan J.; Carrera, Noa; Catts, Stanley V.; Chambert, Kimberly D.; Chan, Raymond C. K.; Chen, Ronald Y. L.; Chen, Eric Y. H.; Cheng, Wei; Cheung, Eric F. C.; Chong, Siow Ann; Cloninger, C. Robert; Cohen, David; Cohen, Nadine; Cormican, Paul; Craddock, Nick; Crowley, James J.; Curtis, David; Davidson, Michael; Davis, Kenneth L.; Degenhardt, Franziska; del Favero, Jurgen; DeLisi, Lynn E.; Demontis, Ditte; Dikeos, Dimitris; Dinan, Timothy; Djurovic, Srdjan; Donohoe, Gary; Drapeau, Elodie; Duan, Jubao; Dudbridge, Frank; Durmishi, Naser; Eichhammer, Peter; Eriksson, Johan; Escott-Price, Valentina; Essioux, Laurent; Fanous, Ayman H.; Farrell, Martilias S.; Frank, Josef; Franke, Lude; Freedman, Robert; Freimer, Nelson B.; Friedl, Marion; Friedman, Joseph I.; Fromer, Menachem; Georgieva, Lyudmila; Gershon, Elliot S.; Giegling, Ina; Giusti-Rodrguez, Paola; Godard, Stephanie; Goldstein, Jacqueline I.; Golimbet, Vera; Gopal, Srihari; Gratten, Jacob; Grove, Jakob; de Haan, Lieuwe; Hammer, Christian; Hamshere, Marian L.; Hansen, Mark; Hansen, Thomas; Haroutunian, Vahram; Hartmann, Annette M.; Henskens, Frans A.; Herms, Stefan; Hirschhorn, Joel N.; Hoffmann, Per; Hofman, Andrea; Hollegaard, Mads V.; Hougaard, David M.; Ikeda, Masashi; Joa, Inge; Julia, Antonio; Kahn, Rene S.; Kalaydjieva, Luba; Karachanak-Yankova, Sena; Karjalainen, Juha; Kavanagh, David; Keller, Matthew C.; Kelly, Brian J.; Kennedy, James L.; Khrunin, Andrey; Kim, Yunjung; Klovins, Janis; Knowles, James A.; Konte, Bettina; Kucinskas, Vaidutis; Kucinskiene, Zita Ausrele; Kuzelova-Ptackova, Hana; Kahler, Anna K.; Laurent, Claudine; Keong, Jimmy Lee Chee; Lee, S. Hong; Legge, Sophie E.; Lerer, Bernard; Li, Miaoxin; Li, Tao; Liang, Kung-Yee; Lieberman, Jeffrey; Limborska, Svetlana; Loughland, Carmel M.; Lubinski, Jan; Lnnqvist, Jouko; Macek, Milan; Magnusson, Patrik K. E.; Maher, Brion S.; Maier, Wolfgang; Mallet, Jacques; Marsal, Sara; Mattheisen, Manuel; Mattingsdal, Morten; McCarley, Robert W.; McDonald, Colm; McIntosh, Andrew M.; Meier, Sandra; Meijer, Carin J.; Melegh, Bela; Melle, Ingrid; Mesholam-Gately, Raquelle I.; Metspalu, Andres; Michie, Patricia T.; Milani, Lili; Milanova, Vihra; Mokrab, Younes; Morris, Derek W.; Mors, Ole; Mortensen, Preben B.; Murphy, Kieran C.; Murray, Robin M.; Myin-Germeys, Inez; Mller-Myhsok, Bertram; Nelis, Mari; Nenadic, Igor; Nertney, Deborah A.; Nestadt, Gerald; Nicodemus, Kristin K.; Nikitina-Zake, Liene; Nisenbaum, Laura; Nordin, Annelie; O'Callaghan, Eadbhard; O'Dushlaine, Colm; O'Neill, F. Anthony; Oh, Sang-Yun; Olincy, Ann; Olsen, Line; van Os, Jim; Pantelis, Christos; Papadimitriou, George N.; Papiol, Sergi; Parkhomenko, Elena; Pato, Michele T.; Paunio, Tiina; Pejovic-Milovancevic, Milica; Perkins, Diana O.; Pietilinen, Olli; Pimm, Jonathan; Pocklington, Andrew J.; Powell, John; Price, Alkes; Pulver, Ann E.; Purcell, Shaun M.; Quested, Digby; Rasmussen, Henrik B.; Reichenberg, Abraham; Reimers, Mark A.; Richards, Alexander L.; Roffman, Joshua L.; Roussos, Panos; Ruderfer, Douglas M.; Salomaa, Veikko; Sanders, Alan R.; Schall, Ulrich; Schubert, Christian R.; Schulze, Thomas G.; Schwab, Sibylle G.; Scolnick, Edward M.; Scott, Rodney J.; Seidman, Larry J.; Shi, Jianxin; Sigurdsson, Engilbert; Silagadze, Teimuraz; Silverman, Jeremy M.; Sim, Kang; Slominsky, Petr; Smoller, Jordan W.; So, Hon-Cheong; Spencer, Chris C. A.; Stahl, Eli A.; Stefansson, Hreinn; Steinberg, Stacy; Stogmann, Elisabeth; Straub, Richard E.; Strengman, Eric; Strohmaier, Jana; Stroup, T. Scott; Subramaniam, Mythily; Suvisaari, Jaana; Svrakic, Dragan M.; Szatkiewicz, Jin P.; Sderman, Erik; Thirumalai, Srinivas; Toncheva, Draga; Tooney, Paul A.; Tosato, Sarah; Veijola, Juha; Waddington, John; Walsh, Dermot; Wang, Dai; Wang, Qiang; Webb, Bradley T.; Weiser, Mark; Wildenauer, Dieter B.; Williams, Nigel M.; Williams, Stephanie; Witt, Stephanie H.; Wolen, Aaron R.; Wong, Emily H. M.; Wormley, Brandon K.; Wu, Jing Qin; Xi, Hualin Simon; Zai, Clement C.; Zheng, Xuebin; Zimprich, Fritz; Wray, Naomi R.; Stefansson, Kari; Adolfsson, Rolf; Andreassen, Ole A.; Blackwood, Douglas H. R.; Bramon, Elvira; Buxbaum, Joseph D.; Børglum, Anders D.; Cichon, Sven; Darvasi, Ariel; Domenici, Enrico; Ehrenreich, Hannelore; Esko, Tonu; Gejman, Pablo V.; Gill, Michael; Gurling, Hugh; Hultman, Christina M.; Iwata, Nakao; Jablensky, Assen V.; Jonsson, Erik G.; Kendler, Kenneth S.; Kirov, George; Knight, Jo; Lencz, Todd; Levinson, Douglas F.; Li, Qingqin S.; Liu, Jianjun; Malhotra, Anil K.; McCarroll, Steven A.; McQuillin, Andrew; Moran, Jennifer L.; Mowry, Bryan J.; Nthen, Markus M.; Ophoff, Roel A.; Owen, Michael J.; Palotie, Aarno; Pato, Carlos N.; Petryshen, Tracey L.; Posthuma, Danielle; Rietschel, Marcella; Riley, Brien P.; Rujescu, Dan; Sham, Pak C.; Sklar, Pamela; St Clair, David; Weinberger, Daniel R.; Wendland, Jens R.; Werge, Thomas; Daly, Mark J.; Sullivan, Patrick F.; O'Donovan, Michael C.; Hunter, David J.; Adank, Muriel; Ahsan, Habibul; Aittomäki, Kristiina; Baglietto, Laura; Berndt, Sonja; Blomquist, Carl; Canzian, Federico; Chang-Claude, Jenny; Chanock, Stephen J.; Crisponi, Laura; Czene, Kamila; Dahmen, Norbert; Silva, Isabel Dos Santos; Easton, Douglas; Eliassen, A. Heather; Figueroa, Jonine; Fletcher, Olivia; Garcia-Closas, Montserrat; Gaudet, Mia M.; Gibson, Lorna; Haiman, Christopher A.; Hall, Per; Hazra, Aditi; Hein, Rebecca; Henderson, Brian E.; Hofman, Albert; Hopper, John L.; Irwanto, Astrid; Johansson, Mattias; Kaaks, Rudolf; Kibriya, Muhammad G.; Lichtner, Peter; Lund, Eiliv; Makalic, Enes; Meindl, Alfons; Meijers-Heijboer, Hanne; Müller-Myhsok, Bertram; Muranen, Taru A.; Nevanlinna, Heli; Peeters, Petra H.; Peto, Julian; Prentice, Ross L.; Rahman, Nazneen; Sánchez, María José; Schmidt, Daniel F.; Schmutzler, Rita K.; Southey, Melissa C.; Travis, Ruth; Turnbull, Clare; Uitterlinden, Andre G.; van der Luijt, Rob B.; Waisfisz, Quinten; Wang, Zhaoming; Whittemore, Alice S.; Yang, Rose; Zheng, Wei

    2015-01-01

    Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to

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

    African Journals Online (AJOL)

    The study used the innovation system approach to ascertain the intensity and trends of linkages among key actors in the climate change and food security innovation system in Nigeria, Sierra Leone and Liberia. Data were collected through the use of semi structured interview schedule, key informant interviews and focus ...

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

    African Journals Online (AJOL)

    The study examined the linkage behaviour and practices of agencies in the agricultural innovation transfer sub system in Southeastern Nigeria. A total sample size of 210 respondents purposively selected from ADPs(60), LGs(60), profit NGOs(60), non- profit NGOs(30) were used. Data were collected by the use of ...

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

    African Journals Online (AJOL)

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

  18. Autosomal linkage analysis for cannabis use behaviors in Australian adults.

    Science.gov (United States)

    Agrawal, Arpana; Morley, Katherine I; Hansell, Narelle K; Pergadia, Michele L; Montgomery, Grant W; Statham, Dixie J; Todd, Richard D; Madden, Pamela A F; Heath, Andrew C; Whitfield, John; Martin, Nicholas G; Lynskey, Michael T

    2008-12-01

    Cannabis is the most commonly used illicit drug in developed and in developing nations. Twin studies have highlighted the role of genetic influences on early stages of cannabis use, such as a lifetime history of use, early-onset use and frequent use, however, we are not aware of any genomic studies that have examined these phenotypes. Using data on 2314 families consisting of 5600 adult Australian offspring and their parents, all of whom were scanned using 1399 unique autosomal markers, we conducted autosomal linkage analyses for lifetime history of cannabis initiation, early-onset cannabis use and frequency of use, using a variance components approach in the linkage package MERLIN. Suggestive evidence for linkage was found on chromosome 18 (LOD 2.14 for frequency of use, LOD 1.97 for initiation, at 90-97 cM) and also on chromosome 19 (LOD 1.92 for early-onset at 17 cM). These LOD scores did not meet genome-wide significance. Further replication of these linkage regions in other samples will be required, although these initial results suggest further targeted efforts on chromosome 18 may yield interesting candidate genes for early stages of cannabis-related behaviors.

  19. Re-inventing the Future: Linkages between Human Rights, Foreign ...

    African Journals Online (AJOL)

    This paper raises questions concerning the emerging trends of regional and international relations. In this endeavour, it examines new insights from traditional perspectives. The paper explores the outer contours of the conceptual linkages between human rights, foreign policy and regional integration in the East African ...

  20. Construction of microsatellite-based linkage map and mapping of ...

    Indian Academy of Sciences (India)

    Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum. MEIYING HOU, CAIPING CAI, SHUWEN ZHANG, WANGZHEN GUO, TIANZHEN ZHANG and BAOLIANG ZHOU. ∗. State Key Laboratory of Crop Genetics and Germplasm Enhancement, ...

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

    Directory of Open Access Journals (Sweden)

    Dr Serah K Mbetwa

    2015-08-01

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

  2. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  3. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.

    Science.gov (United States)

    Isobe, Sachiko N; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

    2013-02-01

    The cultivated strawberry (Fragaria × ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

  4. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  5. Linkage disequilibrium and population structure in Fragaria chiloensis revealed by SSR markers transferred from commercial strawberry

    Directory of Open Access Journals (Sweden)

    Felipe Alberto Oñate

    2017-11-01

    Full Text Available The Chilean strawberry [Fragaria chiloensis (L. Mill.] is the maternal progenitor of the commercial strawberry (Fragaria ´ ananassa Duch., which is characterized by fruits with high organoleptic quality and is well-suited to areas where drought and salinity represent a constraint on crop growth and productivity. We examined the patterns of linkage disequilibrium, genetic diversity and population structure among 54 accessions of F. chiloensis to understand the genetic basis of this species. We used a core microsatellite marker set (n = 95 from a consensus linkage map of strawberry. A transferability rate of 82.1% (78/95 was found, and 38 markers were selected for this study. The SSR primers produced a total of 259 alleles, which varied between 112 and 342 bp. Lower genetic diversity at the species level (HE = 0.17, Shannon’s index = 0.28 was found compared to previous studies of this species. No climatic region pattern for SSR diversity was observed. Structure analysis suggests that the accessions are grouped into three significantly differentiated clusters. Pairwise estimates of φST indicated a low degree of differentiation between the three genetic groups (φST = 0.023 to 0.06. These groups are in concordance with potential glacial refugia in the region, with many accessions being an admixture of them.

  6. Dynamical Groups

    Science.gov (United States)

    Paldus, Josef

    The well known symmetry (invariance, degeneracy) dynamical groups or algebras of quantum mechanical Hamiltonians provide quantum numbers (conservation laws, integrals of motion) for state labeling and the associated selection rules. In addition, it is often advantageous to employ much larger groups, referred to as the dynamical groups (noninvariance groups, dynamical algebras, spectrum generating algebras), which may or may not be the invariance groups of the studied system [4.1,2,3,4,5,6,7]. In all known cases, they are Lie groups (LGs), or rather corresponding Lie algebras (LAs), and one usually requires that all states of interest of a system be contained in a single irreducible representation (irrep). Likewise, one may require that the Hamiltonian be expressible in terms of the Casimir operators of the corresponding universal enveloping algebra [4.8,9]. In a weaker sense, one regards any group (or corresponding algebra) as a dynamical group if the Hamiltonian can be expressed in terms of its generators [4.10,11,12]. In nuclear physics, one sometimes distinguishes exact (baryon number preserving), almost exact (e.g., total isospin), approximate (e.g., SU(3) of the "eightfold way") and model (e.g., nuclear shell model) dynamical symmetries [4.13]. The dynamical groups of interest in atomic and molecular physics can be conveniently classified by their topological characteristic of compactness. Noncompact LGs (LAs) generally arise in simple problems involving an infinite number of bound states, while those involving a finite number of bound states (e.g., molecular vibrations or ab initio models of electronic structure) exploit compact LG's.

  7. Abiraterone Acetate for the Treatment of Chemotherapy-Naïve Metastatic Castration-Resistant Prostate Cancer: An Evidence Review Group Perspective of an NICE Single Technology Appraisal.

    Science.gov (United States)

    Ramaekers, Bram L T; Riemsma, Rob; Tomini, Florian; van Asselt, Thea; Deshpande, Sohan; Duffy, Steven; Armstrong, Nigel; Severens, Johan L; Kleijnen, Jos; Joore, Manuela A

    2017-02-01

    The National Institute for Health and Care Excellence (NICE) invited Janssen, the company manufacturing abiraterone acetate (AA; tradename Zytiga ® ), to submit evidence for the clinical and cost effectiveness of AA in combination with prednisone/prednisolone (AAP) compared with watchful waiting (i.e. best supportive care [BSC]) for chemotherapy-naïve patients with metastatic castration-resistant prostate cancer (mCRPC). Kleijnen Systematic Reviews Ltd (KSR), in collaboration with Maastricht University Medical Center, was commissioned as the Evidence Review Group (ERG). This paper presents a summary of the company submission (CS), the ERG report, subsequent addenda, and the development of the NICE guidance for the use of this drug in England and Wales by the Appraisal Committee (AC). The ERG produced a critical review of the clinical and cost effectiveness of AAP based on the CS. An important question in this appraisal was, according to the ERG, whether AAP followed by docetaxel is more effective than BSC followed by docetaxel. In the COU-AA-302 trial, 239 of 546 (43.8 %) AAP patients and 304 of 542 (56.1 %) BSC patients received docetaxel as subsequent therapy, following AA or placebo. The results for this specific group of patients were not presented in the CS; therefore, the ERG asked the company to provide these data in the clarification letter; however, these data were presented as commercial-in-confidence and cannot therefore be reported here. The ERG's critical assessment of the company's economic evaluation highlighted a number of concerns, including (a) not using the intention-to-treat (ITT) population; (b) inconsistencies in estimating prediction equations; (c) not fully incorporating the impact of adverse events; (d) incorrectly incorporating the new patient access scheme (PAS); and (e) the assumption that AA non-compliance leads to recoverable drug costs. Although some of these issues were adjusted in the ERG base case, the ERG could not estimate

  8. Autosomal dominant familial spastic paraplegia: Tight linkage to chromosome 15q

    Energy Technology Data Exchange (ETDEWEB)

    Fink, J.K.; Wu, C.T.B.; Jones, S.M.

    1994-09-01

    Familial spastic paraplegia (FSP) (MIM No.18260) constitutes a clinically and genetically diverse group of disorders that share the primary feature of progressive, severe, lower extremity spasticity. FSP is classified according to the mode of inheritance and whether progressive spasticity occurs in isolation ({open_quotes}uncomplicated FSP{close_quotes}) or with other neurologic abnormalities ({open_quotes}complicated FSP{close_quotes}), including optic neuropathy, retinopathy, extrapyramidal disturbance, dementia, ataxia, ichthyosis, mental retardation, or deafness. Recently, autosomal dominant, uncomplicated FSP was shown to be genetically heterogeneous and tightly linked to a group of microsatellite markers on chromosome 14q in one large kindred. We examined 126 members of a non-consanguineous North American kindred of Irish descent. FSP was diagnosed in 31 living subjects who developed insidiously progressive gait disturbance between ages 12 and 35 years. Using genetic linkage analysis to microsatellite DNA polymorphisms, we showed that the FSP locus on chromosome 14q was exluded from linkage with the disorder in our family. Subsequently, we searched for genetic linkage between the disorder and microsatellite DNA polymorphisms spanning approximately 50% of the genome. We observed significantly positive, two-point maximum lod scores (Z) for markers on chromosome 15q: D15S128 (Z=9.70, {theta}=0.05), D15S165 (Z=3.30, {theta}=0.10), and UT511 (Z=3.86, {theta}=0.10). Our data clearly establishes that one locus for autosomal dominant, uncomplicated FSP is mapped to the pericentric region of chromosome 15q. Identifying genes responsible for chromosome 15q-linked and chromosome 14q-linked FSP will greatly advance our understanding of this condition and hopefully other inherited and degenerative brain and spinal cord disorders that are also characterized by axonal degeneration.

  9. ICOADS: Lessons Learned and Oceanographic Data Linkages

    Science.gov (United States)

    Worley, S. J.; Freeman, E.; Angel, W.; Brohan, P.; Dumenil-Gates, L.; Kent, E. C.; Smith, S. R.; Woodruff, S. D.

    2016-02-01

    The International Comprehensive Ocean-Atmosphere Data Set (ICOADS) is the largest collection of surface marine in situ observations, spanning 1662 to present, and provides access to a wealth of surface atmospheric elements over the ocean. This presentation will review a number of past innovations in ICOADS data management and quality control. More recently for example, in developing ICOADS Release 3.0 (planned for availability by mid 2016), the benefits of including a more extensive range of near-surface oceanographic parameters alongside surface meteorological parameters are being realized. A new Near-Surface Oceanographic (Nocn) "attachment" to the extensible International Maritime Meteorological Archive (IMMA) format has been developed to include oceanographic elements, such as near-surface salinity and temperature, their associated measurement depths and other selected observational metadata. The inclusion of the oceanographic parameters allows users to locate surface oceanographic and lower atmospheric observations over the ocean within a single dataset and in a common format, for potential uses such as studies of air-sea interactions and coupled ocean-atmosphere model validations. Release 3.0 includes near-surface ocean profile measurements from sources such as the World Ocean Database (WOD 2013). In addition, the Nocn attachment will be used to provide underway surface ocean observations from ships participating in the Shipboard Automated Meteorological and Oceanographic System (SAMOS) and Global Ocean Surface Underway Data (GOSUD) initiatives, and to expand the range of parameters available from moored buoys. An in-depth description of the Nocn attachment, lessons learned during its development, and anticipated uses and advantages for the marine community will be further discussed.

  10. Selection and validation of potato candidate genes for maturity corrected resistance to Phytophthora infestans based on differential expression combined with SNP association and linkage mapping

    Directory of Open Access Journal