WorldWideScience

Sample records for rank snp rs3018362

  1. RANK/RANKL/OPG pathway: genetic associations with stress fracture period prevalence in elite athletes.

    Science.gov (United States)

    Varley, Ian; Hughes, David C; Greeves, Julie P; Stellingwerff, Trent; Ranson, Craig; Fraser, William D; Sale, Craig

    2015-02-01

    The RANK/RANKL/OPG signalling pathway is important in the regulation of bone turnover, with single nucleotide polymorphisms (SNPs) in genes within this pathway associated with bone phenotypic adaptations. To determine whether four SNPs associated with genes in the RANK/RANKL/OPG signalling pathway were associated with stress fracture injury in elite athletes. Radiologically confirmed stress fracture history was reported in 518 elite athletes, forming the Stress Fracture Elite Athlete (SFEA) cohort. Data were analysed for the whole group and were sub-stratified into male and cases of multiple stress fracture groups. Genotypes were determined using proprietary fluorescence-based competitive allele-specific PCR assays. SNPs rs3018362 (RANK) and rs1021188 (RANKL) were associated with stress fracture injury (Pstress fracture group and 2.8% of the non-stress fracture group were homozygote for the rare allele of rs1021188. Allele frequency, heterozygotes and homozygotes for the rare allele of rs3018362 were associated with stress fracture period prevalence (Pstress fracture whilst 2.5% of the non-stress fracture group were homozygous. In cases of multiple stress fractures, homozygotes for the rare allele of rs1021188 and individuals possessing at least one copy of the rare allele of rs4355801 (OPG) were shown to be associated with stress fracture injury (Pstress fracture injury. The association of rs3018362 (RANK) and rs1021188 (RANKL) with stress fracture injury susceptibility supports their role in the maintenance of bone health and offers potential targets for therapeutic interventions. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. (SNP) markers

    African Journals Online (AJOL)

    SAM

    2014-05-21

    May 21, 2014 ... These accessions had been originally introduced from international germplasm collections. The multilocus SNP profiles ... the SNP profiles of reference trees maintained in the international cacao collections. The comparison ...... CAB International, CABI Publishing, Wallingford, Oxfordshire. Buckler ES ...

  3. SNP by SNP by environment interaction network of alcoholism.

    Science.gov (United States)

    Zollanvari, Amin; Alterovitz, Gil

    2017-03-14

    Alcoholism has a strong genetic component. Twin studies have demonstrated the heritability of a large proportion of phenotypic variance of alcoholism ranging from 50-80%. The search for genetic variants associated with this complex behavior has epitomized sequence-based studies for nearly a decade. The limited success of genome-wide association studies (GWAS), possibly precipitated by the polygenic nature of complex traits and behaviors, however, has demonstrated the need for novel, multivariate models capable of quantitatively capturing interactions between a host of genetic variants and their association with non-genetic factors. In this regard, capturing the network of SNP by SNP or SNP by environment interactions has recently gained much interest. Here, we assessed 3,776 individuals to construct a network capable of detecting and quantifying the interactions within and between plausible genetic and environmental factors of alcoholism. In this regard, we propose the use of first-order dependence tree of maximum weight as a potential statistical learning technique to delineate the pattern of dependencies underpinning such a complex trait. Using a predictive based analysis, we further rank the genes, demographic factors, biological pathways, and the interactions represented by our SNP [Formula: see text]SNP[Formula: see text]E network. The proposed framework is quite general and can be potentially applied to the study of other complex traits.

  4. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons for this is the availabil......In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...... for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  5. Tensor Rank

    OpenAIRE

    Erdtman, Elias; Jönsson, Carl

    2012-01-01

    This master's thesis addresses numerical methods of computing the typical ranks of tensors over the real numbers and explores some properties of tensors over finite fields. We present three numerical methods to compute typical tensor rank. Two of these have already been published and can be used to calculate the lowest typical ranks of tensors and an approximate percentage of how many tensors have the lowest typical ranks (for some tensor formats), respectively. The third method was developed...

  6. Rank Dynamics

    Science.gov (United States)

    Gershenson, Carlos

    Studies of rank distributions have been popular for decades, especially since the work of Zipf. For example, if we rank words of a given language by use frequency (most used word in English is 'the', rank 1; second most common word is 'of', rank 2), the distribution can be approximated roughly with a power law. The same applies for cities (most populated city in a country ranks first), earthquakes, metabolism, the Internet, and dozens of other phenomena. We recently proposed ``rank diversity'' to measure how ranks change in time, using the Google Books Ngram dataset. Studying six languages between 1800 and 2009, we found that the rank diversity curves of languages are universal, adjusted with a sigmoid on log-normal scale. We are studying several other datasets (sports, economies, social systems, urban systems, earthquakes, artificial life). Rank diversity seems to be universal, independently of the shape of the rank distribution. I will present our work in progress towards a general description of the features of rank change in time, along with simple models which reproduce it

  7. SNP ID-info: SNP ID searching and visualization platform.

    Science.gov (United States)

    Yang, Cheng-Hong; Chuang, Li-Yeh; Cheng, Yu-Huei; Wen, Cheng-Hao; Chang, Phei-Lang; Chang, Hsueh-Wei

    2008-09-01

    Many association studies provide the relationship between single nucleotide polymorphisms (SNPs), diseases and cancers, without giving a SNP ID, however. Here, we developed the SNP ID-info freeware to provide the SNP IDs within inputting genetic and physical information of genomes. The program provides an "SNP-ePCR" function to generate the full-sequence using primers and template inputs. In "SNPosition," sequence from SNP-ePCR or direct input is fed to match the SNP IDs from SNP fasta-sequence. In "SNP search" and "SNP fasta" function, information of SNPs within the cytogenetic band, contig position, and keyword input are acceptable. Finally, the SNP ID neighboring environment for inputs is completely visualized in the order of contig position and marked with SNP and flanking hits. The SNP identification problems inherent in NCBI SNP BLAST are also avoided. In conclusion, the SNP ID-info provides a visualized SNP ID environment for multiple inputs and assists systematic SNP association studies. The server and user manual are available at http://bio.kuas.edu.tw/snpid-info.

  8. dbSNP

    Data.gov (United States)

    U.S. Department of Health & Human Services — dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and...

  9. Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers

    Directory of Open Access Journals (Sweden)

    Khatkar Mehar S

    2010-10-01

    Full Text Available Abstract Background At the current price, the use of high-density single nucleotide polymorphisms (SNP genotyping assays in genomic selection of dairy cattle is limited to applications involving elite sires and dams. The objective of this study was to evaluate the use of low-density assays to predict direct genomic value (DGV on five milk production traits, an overall conformation trait, a survival index, and two profit index traits (APR, ASI. Methods Dense SNP genotypes were available for 42,576 SNP for 2,114 Holstein bulls and 510 cows. A subset of 1,847 bulls born between 1955 and 2004 was used as a training set to fit models with various sets of pre-selected SNP. A group of 297 bulls born between 2001 and 2004 and all cows born between 1992 and 2004 were used to evaluate the accuracy of DGV prediction. Ridge regression (RR and partial least squares regression (PLSR were used to derive prediction equations and to rank SNP based on the absolute value of the regression coefficients. Four alternative strategies were applied to select subset of SNP, namely: subsets of the highest ranked SNP for each individual trait, or a single subset of evenly spaced SNP, where SNP were selected based on their rank for ASI, APR or minor allele frequency within intervals of approximately equal length. Results RR and PLSR performed very similarly to predict DGV, with PLSR performing better for low-density assays and RR for higher-density SNP sets. When using all SNP, DGV predictions for production traits, which have a higher heritability, were more accurate (0.52-0.64 than for survival (0.19-0.20, which has a low heritability. The gain in accuracy using subsets that included the highest ranked SNP for each trait was marginal (5-6% over a common set of evenly spaced SNP when at least 3,000 SNP were used. Subsets containing 3,000 SNP provided more than 90% of the accuracy that could be achieved with a high-density assay for cows, and 80% of the high-density assay

  10. SNP-PHAGE – High throughput SNP discovery pipeline

    Directory of Open Access Journals (Sweden)

    Cregan Perry B

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs, amplified fragment length polymorphisms (AFLPs and simple sequence repeats (SSRs or microsatellite markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable. Results We developed SNP-PHAGE (SNP discovery Pipeline with additional features for identification of common haplotypes within a sequence tagged site (Haplotype Analysis and GenBank (-dbSNP submissions. This tool was applied for analyzing sequence traces from diverse soybean genotypes to discover over 10,000 SNPs. This package was developed on UNIX/Linux platform, written in Perl and uses a MySQL database. Scripts to generate a user-friendly web interface are also provided with common queries for preliminary data analysis. A machine learning tool developed by this group for increasing the efficiency of SNP discovery is integrated as a part of this package as an optional feature. The SNP-PHAGE package is being made available open source at http://bfgl.anri.barc.usda.gov/ML/snp-phage/. Conclusion SNP-PHAGE provides a bioinformatics

  11. SNP interaction pattern identifier (SIPI)

    DEFF Research Database (Denmark)

    Lin, Hui-Yi; Chen, Dung-Tsa; Huang, Po-Yu

    2016-01-01

    with the exact or similar pattern in the discovery and validation sets. A similar match for external validation of SNP-SNP interaction studies is suggested. We demonstrated that SIPI not only searches for more meaningful interaction patterns but can also overcome the unstable nature of interaction patterns...

  12. SAQC: SNP Array Quality Control

    Directory of Open Access Journals (Sweden)

    Li Ling-Hui

    2011-04-01

    Full Text Available Abstract Background Genome-wide single-nucleotide polymorphism (SNP arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC. SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm.

  13. Ranking library materials

    OpenAIRE

    Lewandowski, Dirk

    2015-01-01

    Purpose: This paper discusses ranking factors suitable for library materials and shows that ranking in general is a complex process and that ranking for library materials requires a variety of techniques. Design/methodology/approach: The relevant literature is reviewed to provide a systematic overview of suitable ranking factors. The discussion is based on an overview of ranking factors used in Web search engines. Findings: While there are a wide variety of ranking factors appl...

  14. Reduced Rank Regression

    DEFF Research Database (Denmark)

    Johansen, Søren

    2008-01-01

    The reduced rank regression model is a multivariate regression model with a coefficient matrix with reduced rank. The reduced rank regression algorithm is an estimation procedure, which estimates the reduced rank regression model. It is related to canonical correlations and involves calculating e...... eigenvalues and eigenvectors. We give a number of different applications to regression and time series analysis, and show how the reduced rank regression estimator can be derived as a Gaussian maximum likelihood estimator. We briefly mention asymptotic results......The reduced rank regression model is a multivariate regression model with a coefficient matrix with reduced rank. The reduced rank regression algorithm is an estimation procedure, which estimates the reduced rank regression model. It is related to canonical correlations and involves calculating...

  15. Report on ISFG SNP Panel Discussion

    DEFF Research Database (Denmark)

    Butler, John M.; Budowle, B.; Gill, P.

    2008-01-01

    Six scientists presented their views and experience with single nucleotide polymorphism (SNP) markers, multiplexes, and methods regarding their potential application in forensic identity and relationship testing. Benefits and limitations of SNPs were reviewed, as were different SNP marker...

  16. VaRank: a simple and powerful tool for ranking genetic variants

    Directory of Open Access Journals (Sweden)

    Véronique Geoffroy

    2015-03-01

    Full Text Available Background. Most genetic disorders are caused by single nucleotide variations (SNVs or small insertion/deletions (indels. High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians.Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients.Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.

  17. Ranking Operations Management conferences

    NARCIS (Netherlands)

    Steenhuis, H.J.; de Bruijn, E.J.; Gupta, Sushil; Laptaned, U

    2007-01-01

    Several publications have appeared in the field of Operations Management which rank Operations Management related journals. Several ranking systems exist for journals based on , for example, perceived relevance and quality, citation, and author affiliation. Many academics also publish at conferences

  18. (SNP) mining of Sorghum bicolor genome

    African Journals Online (AJOL)

    user

    2011-01-24

    Jan 24, 2011 ... SNPs are important tools in studying complex genetic traits and genome evolution. SNP mining ... In the present study, online SNP and allele detection tool HaploSNPer. (based on QualitySNP pipeline) ... some was provided to the computer program as input for cutting the large sequence into small parts.

  19. Sparse structure regularized ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-04-17

    Learning ranking scores is critical for the multimedia database retrieval problem. In this paper, we propose a novel ranking score learning algorithm by exploring the sparse structure and using it to regularize ranking scores. To explore the sparse structure, we assume that each multimedia object could be represented as a sparse linear combination of all other objects, and combination coefficients are regarded as a similarity measure between objects and used to regularize their ranking scores. Moreover, we propose to learn the sparse combination coefficients and the ranking scores simultaneously. A unified objective function is constructed with regard to both the combination coefficients and the ranking scores, and is optimized by an iterative algorithm. Experiments on two multimedia database retrieval data sets demonstrate the significant improvements of the propose algorithm over state-of-the-art ranking score learning algorithms.

  20. SNP-SNP interactions in breast cancer susceptibility

    Directory of Open Access Journals (Sweden)

    Wang Yuanyuan

    2006-05-01

    Full Text Available Abstract Background Breast cancer predisposition genes identified to date (e.g., BRCA1 and BRCA2 are responsible for less than 5% of all breast cancer cases. Many studies have shown that the cancer risks associated with individual commonly occurring single nucleotide polymorphisms (SNPs are incremental. However, polygenic models suggest that multiple commonly occurring low to modestly penetrant SNPs of cancer related genes might have a greater effect on a disease when considered in combination. Methods In an attempt to identify the breast cancer risk conferred by SNP interactions, we have studied 19 SNPs from genes involved in major cancer related pathways. All SNPs were genotyped by TaqMan 5'nuclease assay. The association between the case-control status and each individual SNP, measured by the odds ratio and its corresponding 95% confidence interval, was estimated using unconditional logistic regression models. At the second stage, two-way interactions were investigated using multivariate logistic models. The robustness of the interactions, which were observed among SNPs with stronger functional evidence, was assessed using a bootstrap approach, and correction for multiple testing based on the false discovery rate (FDR principle. Results None of these SNPs contributed to breast cancer risk individually. However, we have demonstrated evidence for gene-gene (SNP-SNP interaction among these SNPs, which were associated with increased breast cancer risk. Our study suggests cross talk between the SNPs of the DNA repair and immune system (XPD-[Lys751Gln] and IL10-[G(-1082A], cell cycle and estrogen metabolism (CCND1-[Pro241Pro] and COMT-[Met108/158Val], cell cycle and DNA repair (BARD1-[Pro24Ser] and XPD-[Lys751Gln], and within carcinogen metabolism (GSTP1-[Ile105Val] and COMT-[Met108/158Val] pathways. Conclusion The importance of these pathways and their communication in breast cancer predisposition has been emphasized previously, but their

  1. Maximum Waring ranks of monomials

    OpenAIRE

    Holmes, Erik; Plummer, Paul; Siegert, Jeremy; Teitler, Zach

    2013-01-01

    We show that monomials and sums of pairwise coprime monomials in four or more variables have Waring rank less than the generic rank, with a short list of exceptions. We asymptotically compare their ranks with the generic rank.

  2. How to Rank Journals.

    Science.gov (United States)

    Bradshaw, Corey J A; Brook, Barry W

    2016-01-01

    There are now many methods available to assess the relative citation performance of peer-reviewed journals. Regardless of their individual faults and advantages, citation-based metrics are used by researchers to maximize the citation potential of their articles, and by employers to rank academic track records. The absolute value of any particular index is arguably meaningless unless compared to other journals, and different metrics result in divergent rankings. To provide a simple yet more objective way to rank journals within and among disciplines, we developed a κ-resampled composite journal rank incorporating five popular citation indices: Impact Factor, Immediacy Index, Source-Normalized Impact Per Paper, SCImago Journal Rank and Google 5-year h-index; this approach provides an index of relative rank uncertainty. We applied the approach to six sample sets of scientific journals from Ecology (n = 100 journals), Medicine (n = 100), Multidisciplinary (n = 50); Ecology + Multidisciplinary (n = 25), Obstetrics & Gynaecology (n = 25) and Marine Biology & Fisheries (n = 25). We then cross-compared the κ-resampled ranking for the Ecology + Multidisciplinary journal set to the results of a survey of 188 publishing ecologists who were asked to rank the same journals, and found a 0.68-0.84 Spearman's ρ correlation between the two rankings datasets. Our composite index approach therefore approximates relative journal reputation, at least for that discipline. Agglomerative and divisive clustering and multi-dimensional scaling techniques applied to the Ecology + Multidisciplinary journal set identified specific clusters of similarly ranked journals, with only Nature & Science separating out from the others. When comparing a selection of journals within or among disciplines, we recommend collecting multiple citation-based metrics for a sample of relevant and realistic journals to calculate the composite rankings and their relative uncertainty windows.

  3. Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism

    Science.gov (United States)

    Storer, Caroline G.; Pascal, Carita E.; Roberts, Steven B.; Templin, William D.; Seeb, Lisa W.; Seeb, James E.

    2012-01-01

    Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: FST, informativeness (In), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from FST, In, and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available. PMID:23185290

  4. Academic rankings: an approach to a Portuguese ranking

    OpenAIRE

    Bernardino, Pedro; Marques,Rui

    2009-01-01

    The academic rankings are a controversial subject in higher education. However, despite all the criticism, academic rankings are here to stay and more and more different stakeholders use rankings to obtain information about the institutions’ performance. The two most well-known rankings, The Times and the Shanghai Jiao Tong University rankings have different methodologies. The Times ranking is based on peer review, whereas the Shanghai ranking has only quantitative indicators and is mainly ba...

  5. Assessing SNP-SNP interactions among DNA repair, modification and metabolism related pathway genes in breast cancer susceptibility.

    Directory of Open Access Journals (Sweden)

    Yadav Sapkota

    Full Text Available Genome-wide association studies (GWASs have identified low-penetrance common variants (i.e., single nucleotide polymorphisms, SNPs associated with breast cancer susceptibility. Although GWASs are primarily focused on single-locus effects, gene-gene interactions (i.e., epistasis are also assumed to contribute to the genetic risks for complex diseases including breast cancer. While it has been hypothesized that moderately ranked (P value based weak single-locus effects in GWASs could potentially harbor valuable information for evaluating epistasis, we lack systematic efforts to investigate SNPs showing consistent associations with weak statistical significance across independent discovery and replication stages. The objectives of this study were i to select SNPs showing single-locus effects with weak statistical significance for breast cancer in a GWAS and/or candidate-gene studies; ii to replicate these SNPs in an independent set of breast cancer cases and controls; and iii to explore their potential SNP-SNP interactions contributing to breast cancer susceptibility. A total of 17 SNPs related to DNA repair, modification and metabolism pathway genes were selected since these pathways offer a priori knowledge for potential epistatic interactions and an overall role in breast carcinogenesis. The study design included predominantly Caucasian women (2,795 cases and 4,505 controls from Alberta, Canada. We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 and MDM2-rs769412 in logistic regression that conferred elevated risks for breast cancer (P(interaction<7.3 × 10(-3. Logic regression identified an interaction involving four SNPs (MBD2-rs4041245, MLH1-rs1799977, MDM2-rs769412, BRCA2-rs1799943 (P(permutation = 2.4 × 10(-3. SNPs involved in SNP-SNP interactions also showed single-locus effects with weak statistical significance, while BRCA2-rs1799943 showed stronger statistical significance (P

  6. Ranking Economic History Journals

    DEFF Research Database (Denmark)

    Di Vaio, Gianfranco; Weisdorf, Jacob Louis

    This study ranks - for the first time - 12 international academic journals that have economic history as their main topic. The ranking is based on data collected for the year 2007. Journals are ranked using standard citation analysis where we adjust for age, size and self-citation of journals. We...... also compare the leading economic history journals with the leading journals in economics in order to measure the influence on economics of economic history, and vice versa. With a few exceptions, our results confirm the general idea about what economic history journals are the most influential...

  7. Ranking economic history journals

    DEFF Research Database (Denmark)

    Di Vaio, Gianfranco; Weisdorf, Jacob Louis

    2010-01-01

    This study ranks-for the first time-12 international academic journals that have economic history as their main topic. The ranking is based on data collected for the year 2007. Journals are ranked using standard citation analysis where we adjust for age, size and self-citation of journals. We also...... compare the leading economic history journals with the leading journals in economics in order to measure the influence on economics of economic history, and vice versa. With a few exceptions, our results confirm the general idea about what economic history journals are the most influential for economic...

  8. Recurrent fuzzy ranking methods

    Science.gov (United States)

    Hajjari, Tayebeh

    2012-11-01

    With the increasing development of fuzzy set theory in various scientific fields and the need to compare fuzzy numbers in different areas. Therefore, Ranking of fuzzy numbers plays a very important role in linguistic decision-making, engineering, business and some other fuzzy application systems. Several strategies have been proposed for ranking of fuzzy numbers. Each of these techniques has been shown to produce non-intuitive results in certain case. In this paper, we reviewed some recent ranking methods, which will be useful for the researchers who are interested in this area.

  9. Asset ranking manager (ranking index of components)

    Energy Technology Data Exchange (ETDEWEB)

    Maloney, S.M.; Engle, A.M.; Morgan, T.A. [Applied Reliability, Maracor Software and Engineering (United States)

    2004-07-01

    The Ranking Index of Components (RIC) is an Asset Reliability Manager (ARM), which itself is a Web Enabled front end where plant database information fields from several disparate databases are combined. That information is used to create a specific weighted number (Ranking Index) relating to that components health and risk to the site. The higher the number, the higher priority that any work associated with that component receives. ARM provides site Engineering, Maintenance and Work Control personnel with a composite real time - (current condition) look at the components 'risk of not working' to the plant. Information is extracted from the existing Computerized Maintenance management System (CMMS) and specific site applications and processed nightly. ARM helps to ensure that the most important work is placed into the workweeks and the non value added work is either deferred, frequency changed or deleted. This information is on the web, updated each night, and available for all employees to use. This effort assists the work management specialist when allocating limited resources to the most important work. The use of this tool has maximized resource usage, performing the most critical work with available resources. The ARM numbers are valued inputs into work scoping for the workweek managers. System and Component Engineers are using ARM to identify the components that are at 'risk of failure' and therefore should be placed into the appropriate work week schedule.

  10. Multiplex PageRank.

    Directory of Open Access Journals (Sweden)

    Arda Halu

    Full Text Available Many complex systems can be described as multiplex networks in which the same nodes can interact with one another in different layers, thus forming a set of interacting and co-evolving networks. Examples of such multiplex systems are social networks where people are involved in different types of relationships and interact through various forms of communication media. The ranking of nodes in multiplex networks is one of the most pressing and challenging tasks that research on complex networks is currently facing. When pairs of nodes can be connected through multiple links and in multiple layers, the ranking of nodes should necessarily reflect the importance of nodes in one layer as well as their importance in other interdependent layers. In this paper, we draw on the idea of biased random walks to define the Multiplex PageRank centrality measure in which the effects of the interplay between networks on the centrality of nodes are directly taken into account. In particular, depending on the intensity of the interaction between layers, we define the Additive, Multiplicative, Combined, and Neutral versions of Multiplex PageRank, and show how each version reflects the extent to which the importance of a node in one layer affects the importance the node can gain in another layer. We discuss these measures and apply them to an online multiplex social network. Findings indicate that taking the multiplex nature of the network into account helps uncover the emergence of rankings of nodes that differ from the rankings obtained from one single layer. Results provide support in favor of the salience of multiplex centrality measures, like Multiplex PageRank, for assessing the prominence of nodes embedded in multiple interacting networks, and for shedding a new light on structural properties that would otherwise remain undetected if each of the interacting networks were analyzed in isolation.

  11. Multiplex PageRank.

    Science.gov (United States)

    Halu, Arda; Mondragón, Raúl J; Panzarasa, Pietro; Bianconi, Ginestra

    2013-01-01

    Many complex systems can be described as multiplex networks in which the same nodes can interact with one another in different layers, thus forming a set of interacting and co-evolving networks. Examples of such multiplex systems are social networks where people are involved in different types of relationships and interact through various forms of communication media. The ranking of nodes in multiplex networks is one of the most pressing and challenging tasks that research on complex networks is currently facing. When pairs of nodes can be connected through multiple links and in multiple layers, the ranking of nodes should necessarily reflect the importance of nodes in one layer as well as their importance in other interdependent layers. In this paper, we draw on the idea of biased random walks to define the Multiplex PageRank centrality measure in which the effects of the interplay between networks on the centrality of nodes are directly taken into account. In particular, depending on the intensity of the interaction between layers, we define the Additive, Multiplicative, Combined, and Neutral versions of Multiplex PageRank, and show how each version reflects the extent to which the importance of a node in one layer affects the importance the node can gain in another layer. We discuss these measures and apply them to an online multiplex social network. Findings indicate that taking the multiplex nature of the network into account helps uncover the emergence of rankings of nodes that differ from the rankings obtained from one single layer. Results provide support in favor of the salience of multiplex centrality measures, like Multiplex PageRank, for assessing the prominence of nodes embedded in multiple interacting networks, and for shedding a new light on structural properties that would otherwise remain undetected if each of the interacting networks were analyzed in isolation.

  12. Ranking of Rankings: Benchmarking Twenty-Five Higher Education Ranking Systems in Europe

    Science.gov (United States)

    Stolz, Ingo; Hendel, Darwin D.; Horn, Aaron S.

    2010-01-01

    The purpose of this study is to evaluate the ranking practices of 25 European higher education ranking systems (HERSs). Ranking practices were assessed with 14 quantitative measures derived from the Berlin Principles on Ranking of Higher Education Institutions (BPs). HERSs were then ranked according to their degree of congruence with the BPs.…

  13. From rankings to mission.

    Science.gov (United States)

    Kirch, Darrell G; Prescott, John E

    2013-08-01

    Since the 1980s, school ranking systems have been a topic of discussion among leaders of higher education. Various ranking systems are based on inadequate data that fail to illustrate the complex nature and special contributions of the institutions they purport to rank, including U.S. medical schools, each of which contributes uniquely to meeting national health care needs. A study by Tancredi and colleagues in this issue of Academic Medicine illustrates the limitations of rankings specific to primary care training programs. This commentary discusses, first, how each school's mission and strengths, as well as the impact it has on the community it serves, are distinct, and, second, how these schools, which are each unique, are poorly represented by overly subjective ranking methodologies. Because academic leaders need data that are more objective to guide institutional development, the Association of American Medical Colleges (AAMC) has been developing tools to provide valid data that are applicable to each medical school. Specifically, the AAMC's Medical School Admissions Requirements and its Missions Management Tool each provide a comprehensive assessment of medical schools that leaders are using to drive institutional capacity building. This commentary affirms the importance of mission while challenging the leaders of medical schools, teaching hospitals, and universities to use reliable data to continually improve the quality of their training programs to improve the health of all.

  14. Dynamic Matrix Rank

    DEFF Research Database (Denmark)

    Frandsen, Gudmund Skovbjerg; Frandsen, Peter Frands

    2009-01-01

    We consider maintaining information about the rank of a matrix under changes of the entries. For n×n matrices, we show an upper bound of O(n1.575) arithmetic operations and a lower bound of Ω(n) arithmetic operations per element change. The upper bound is valid when changing up to O(n0.575) entries...... in a single column of the matrix. We also give an algorithm that maintains the rank using O(n2) arithmetic operations per rank one update. These bounds appear to be the first nontrivial bounds for the problem. The upper bounds are valid for arbitrary fields, whereas the lower bound is valid for algebraically...... closed fields. The upper bound for element updates uses fast rectangular matrix multiplication, and the lower bound involves further development of an earlier technique for proving lower bounds for dynamic computation of rational functions....

  15. A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Zuber Verena

    2012-10-01

    Full Text Available Abstract Background Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be taken into account. Hence, increasingly modern computationally expensive regression methods are employed for SNP selection that consider all markers simultaneously and thus incorporate dependencies among SNPs. Results We develop a novel multivariate algorithm for large scale SNP selection using CAR score regression, a promising new approach for prioritizing biomarkers. Specifically, we propose a computationally efficient procedure for shrinkage estimation of CAR scores from high-dimensional data. Subsequently, we conduct a comprehensive comparison study including five advanced regression approaches (boosting, lasso, NEG, MCP, and CAR score and a univariate approach (marginal correlation to determine the effectiveness in finding true causal SNPs. Conclusions Simultaneous SNP selection is a challenging task. We demonstrate that our CAR score-based algorithm consistently outperforms all competing approaches, both uni- and multivariate, in terms of correctly recovered causal SNPs and SNP ranking. An R package implementing the approach as well as R code to reproduce the complete study presented here is available from http://strimmerlab.org/software/care/.

  16. Does replication groups scoring reduce false positive rate in SNP interaction discovery?

    Directory of Open Access Journals (Sweden)

    Demsar Janez

    2010-01-01

    Full Text Available Abstract Background Computational methods that infer single nucleotide polymorphism (SNP interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008 proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups, rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions. Results A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups reported fewer false positives. Conclusions With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse.

  17. Diversifying customer review rankings.

    Science.gov (United States)

    Krestel, Ralf; Dokoohaki, Nima

    2015-06-01

    E-commerce Web sites owe much of their popularity to consumer reviews accompanying product descriptions. On-line customers spend hours and hours going through heaps of textual reviews to decide which products to buy. At the same time, each popular product has thousands of user-generated reviews, making it impossible for a buyer to read everything. Current approaches to display reviews to users or recommend an individual review for a product are based on the recency or helpfulness of each review. In this paper, we present a framework to rank product reviews by optimizing the coverage of the ranking with respect to sentiment or aspects, or by summarizing all reviews with the top-K reviews in the ranking. To accomplish this, we make use of the assigned star rating for a product as an indicator for a review's sentiment polarity and compare bag-of-words (language model) with topic models (latent Dirichlet allocation) as a mean to represent aspects. Our evaluation on manually annotated review data from a commercial review Web site demonstrates the effectiveness of our approach, outperforming plain recency ranking by 30% and obtaining best results by combining language and topic model representations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. OutRank

    DEFF Research Database (Denmark)

    Müller, Emmanuel; Assent, Ira; Steinhausen, Uwe

    2008-01-01

    Outlier detection is an important data mining task for consistency checks, fraud detection, etc. Binary decision making on whether or not an object is an outlier is not appropriate in many applications and moreover hard to parametrize. Thus, recently, methods for outlier ranking have been proposed...

  19. Improving Ranking Using Quantum Probability

    OpenAIRE

    Melucci, Massimo

    2011-01-01

    The paper shows that ranking information units by quantum probability differs from ranking them by classical probability provided the same data used for parameter estimation. As probability of detection (also known as recall or power) and probability of false alarm (also known as fallout or size) measure the quality of ranking, we point out and show that ranking by quantum probability yields higher probability of detection than ranking by classical probability provided a given probability of ...

  20. Fractional cointegration rank estimation

    DEFF Research Database (Denmark)

    Lasak, Katarzyna; Velasco, Carlos

    We consider cointegration rank estimation for a p-dimensional Fractional Vector Error Correction Model. We propose a new two-step procedure which allows testing for further long-run equilibrium relations with possibly different persistence levels. The fi…rst step consists in estimating the parame......We consider cointegration rank estimation for a p-dimensional Fractional Vector Error Correction Model. We propose a new two-step procedure which allows testing for further long-run equilibrium relations with possibly different persistence levels. The fi…rst step consists in estimating...... to control for stochastic trend estimation effects from the first step. The critical values of the tests proposed depend only on the number of common trends under the null, p - r, and on the interval of the cointegration degrees b allowed, but not on the true cointegration degree b0. Hence, no additional...

  1. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

    Directory of Open Access Journals (Sweden)

    Esteras Cristina

    2012-02-01

    Full Text Available Abstract Background Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP, was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL. Results We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo × Scallop (subsp. ovifera. The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research

  2. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

    Science.gov (United States)

    Esteras, Cristina; Gómez, Pedro; Monforte, Antonio J; Blanca, José; Vicente-Dólera, Nelly; Roig, Cristina; Nuez, Fernando; Picó, Belén

    2012-02-22

    Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in

  3. SNP-SNP interaction analysis of NF-κB signaling pathway on breast cancer survival

    DEFF Research Database (Denmark)

    Jamshidi, Maral; Fagerholm, Rainer; Khan, Sofia

    2015-01-01

    , in an extensive dataset (n = 30,431) from the Breast Cancer Association Consortium, we investigated the association of 917 SNPs in 75 genes in the NF-κB pathway with breast cancer prognosis. We explored SNP-SNP interactions on survival using the likelihood-ratio test comparing multivariate Cox' regression models...

  4. SNPMeta: SNP annotation and SNP metadata collection without a reference genome

    Science.gov (United States)

    The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNPs. Currently, these data are only available through curation, or comparison to a ...

  5. Can College Rankings Be Believed?

    Directory of Open Access Journals (Sweden)

    Meredith Davis

    Full Text Available The article summarizes literature on college and university rankings worldwide and the strategies used by various ranking organizations, including those of government and popular media. It traces the history of national and global rankings, indicators used by ranking systems, and the effect of rankings on academic programs and their institutions. Although ranking systems employ diverse criteria and most weight certain indicators over others, there is considerable skepticism that most actually measure educational quality. At the same time, students and their families increasingly consult these evaluations when making college decisions, and sponsors of faculty research consider reputation when forming academic partnerships. While there are serious concerns regarding the validity of ranking institutions when so little data can support differences between one institution and another, college rankings appear to be here to stay.

  6. Ranking Baltic States Researchers

    Directory of Open Access Journals (Sweden)

    Gyula Mester

    2017-10-01

    Full Text Available In this article, using the h-index and the total number of citations, the best 10 Lithuanian, Latvian and Estonian researchers from several disciplines are ranked. The list may be formed based on the h-index and the total number of citations, given in Web of Science, Scopus, Publish or Perish Program and Google Scholar database. Data for the first 10 researchers are presented. Google Scholar is the most complete. Therefore, to define a single indicator, h-index calculated by Google Scholar may be a good and simple one. The author chooses the Google Scholar database as it is the broadest one.

  7. Sync-rank: Robust Ranking, Constrained Ranking and Rank Aggregation via Eigenvector and SDP Synchronization

    Science.gov (United States)

    2015-04-28

    eigenvector of the associated Laplacian matrix (i.e., the Fiedler vector) matches that of the variables. In other words, this approach (reminiscent of...S1), i.e., Dii = ∑n j=1Gi,j is the degree of node i in the measurement graph G. 3: Compute the Fiedler vector of S (eigenvector corresponding to the...smallest nonzero eigenvalue of LS). 4: Output the ranking induced by sorting the Fiedler vector of S, with the global ordering (increasing or decreasing

  8. Rankings from Fuzzy Pairwise Comparisons

    NARCIS (Netherlands)

    van den Broek, P.M.; Noppen, J.A.R.; Mohammadian, M.

    2006-01-01

    We propose a new method for deriving rankings from fuzzy pairwise comparisons. It is based on the observation that quantification of the uncertainty of the pairwise comparisons should be used to obtain a better crisp ranking, instead of a fuzzified version of the ranking obtained from crisp pairwise

  9. PageRank (II): Mathematics

    African Journals Online (AJOL)

    maths/stats

    INTRODUCTION. PageRank is Google's system for ranking web pages. A page with a higher PageRank is deemed more important and is more likely to be listed above a ... Felix U. Ogban, Department of Mathematics/Statistics and Computer Science, Faculty of Science, University of ..... probability, 2004, 41, (3): 721-734.

  10. University Rankings and Social Science

    Science.gov (United States)

    Marginson, Simon

    2014-01-01

    University rankings widely affect the behaviours of prospective students and their families, university executive leaders, academic faculty, governments and investors in higher education. Yet the social science foundations of global rankings receive little scrutiny. Rankings that simply recycle reputation without any necessary connection to real…

  11. Sequential rank agreement methods for comparison of ranked lists

    DEFF Research Database (Denmark)

    Ekstrøm, Claus Thorn; Gerds, Thomas Alexander; Jensen, Andreas Kryger

    2015-01-01

    The comparison of alternative rankings of a set of items is a general and prominent task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according to the personalized risk of an event, and genetic studies...... are illustrated using gene rankings, and using data from two Danish ovarian cancer studies where we assess the within and between agreement of different statistical classification methods.......The comparison of alternative rankings of a set of items is a general and prominent task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according to the personalized risk of an event, and genetic studies...

  12. SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus.

    Science.gov (United States)

    Durstewitz, G; Polley, A; Plieske, J; Luerssen, H; Graner, E M; Wieseke, R; Ganal, M W

    2010-11-01

    Oilseed rape (Brassica napus) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

  13. SNP-SNP interaction network in angiogenesis genes associated with prostate cancer aggressiveness.

    Science.gov (United States)

    Lin, Hui-Yi; Amankwah, Ernest K; Tseng, Tung-Sung; Qu, Xiaotao; Chen, Dung-Tsa; Park, Jong Y

    2013-01-01

    Angiogenesis has been shown to be associated with prostate cancer development. The majority of prostate cancer studies focused on individual single nucleotide polymorphisms (SNPs) while SNP-SNP interactions are suggested having a great impact on unveiling the underlying mechanism of complex disease. Using 1,151 prostate cancer patients in the Cancer Genetic Markers of Susceptibility (CGEMS) dataset, 2,651 SNPs in the angiogenesis genes associated with prostate cancer aggressiveness were evaluated. SNP-SNP interactions were primarily assessed using the two-stage Random Forests plus Multivariate Adaptive Regression Splines (TRM) approach in the CGEMS group, and were then re-evaluated in the Moffitt group with 1,040 patients. For the identified gene pairs, cross-evaluation was applied to evaluate SNP interactions in both study groups. Five SNP-SNP interactions in three gene pairs (MMP16+ ROBO1, MMP16+ CSF1, and MMP16+ EGFR) were identified to be associated with aggressive prostate cancer in both groups. Three pairs of SNPs (rs1477908+ rs1387665, rs1467251+ rs7625555, and rs1824717+ rs7625555) were in MMP16 and ROBO1, one pair (rs2176771+ rs333970) in MMP16 and CSF1, and one pair (rs1401862+ rs6964705) in MMP16 and EGFR. The results suggest that MMP16 may play an important role in prostate cancer aggressiveness. By integrating our novel findings and available biomedical literature, a hypothetical gene interaction network was proposed. This network demonstrates that our identified SNP-SNP interactions are biologically relevant and shows that EGFR may be the hub for the interactions. The findings provide valuable information to identify genotype combinations at risk of developing aggressive prostate cancer and improve understanding on the genetic etiology of angiogenesis associated with prostate cancer aggressiveness.

  14. SNP-SNP interaction network in angiogenesis genes associated with prostate cancer aggressiveness.

    Directory of Open Access Journals (Sweden)

    Hui-Yi Lin

    Full Text Available Angiogenesis has been shown to be associated with prostate cancer development. The majority of prostate cancer studies focused on individual single nucleotide polymorphisms (SNPs while SNP-SNP interactions are suggested having a great impact on unveiling the underlying mechanism of complex disease. Using 1,151 prostate cancer patients in the Cancer Genetic Markers of Susceptibility (CGEMS dataset, 2,651 SNPs in the angiogenesis genes associated with prostate cancer aggressiveness were evaluated. SNP-SNP interactions were primarily assessed using the two-stage Random Forests plus Multivariate Adaptive Regression Splines (TRM approach in the CGEMS group, and were then re-evaluated in the Moffitt group with 1,040 patients. For the identified gene pairs, cross-evaluation was applied to evaluate SNP interactions in both study groups. Five SNP-SNP interactions in three gene pairs (MMP16+ ROBO1, MMP16+ CSF1, and MMP16+ EGFR were identified to be associated with aggressive prostate cancer in both groups. Three pairs of SNPs (rs1477908+ rs1387665, rs1467251+ rs7625555, and rs1824717+ rs7625555 were in MMP16 and ROBO1, one pair (rs2176771+ rs333970 in MMP16 and CSF1, and one pair (rs1401862+ rs6964705 in MMP16 and EGFR. The results suggest that MMP16 may play an important role in prostate cancer aggressiveness. By integrating our novel findings and available biomedical literature, a hypothetical gene interaction network was proposed. This network demonstrates that our identified SNP-SNP interactions are biologically relevant and shows that EGFR may be the hub for the interactions. The findings provide valuable information to identify genotype combinations at risk of developing aggressive prostate cancer and improve understanding on the genetic etiology of angiogenesis associated with prostate cancer aggressiveness.

  15. SNP marker detection and genotyping in tilapia

    NARCIS (Netherlands)

    Bers, van N.E.M.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Dibbits, B.W.; Komen, J.

    2012-01-01

    We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the

  16. SNP Array in Hematopoietic Neoplasms: A Review

    Directory of Open Access Journals (Sweden)

    Jinming Song

    2015-12-01

    Full Text Available Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH studies. Single nucleotide polymorphism (SNP arrays offer high-resolution identification of copy number variants (CNVs and acquired copy-neutral loss of heterozygosity (LOH/uniparental disomy (UPD that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.

  17. Snap: An Integrated SNP Annotation Platform

    DEFF Research Database (Denmark)

    Li, S.; Ma, L.; Li, H.

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

  18. Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP

    DEFF Research Database (Denmark)

    Johansen, Morten Bo; Gonzalez-Izarzugaza, Jose Maria; Brunak, Søren

    2013-01-01

    We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features...... assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates...... cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further...

  19. Ranking nodes in growing networks: When PageRank fails.

    Science.gov (United States)

    Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng

    2015-11-10

    PageRank is arguably the most popular ranking algorithm which is being applied in real systems ranging from information to biological and infrastructure networks. Despite its outstanding popularity and broad use in different areas of science, the relation between the algorithm's efficacy and properties of the network on which it acts has not yet been fully understood. We study here PageRank's performance on a network model supported by real data, and show that realistic temporal effects make PageRank fail in individuating the most valuable nodes for a broad range of model parameters. Results on real data are in qualitative agreement with our model-based findings. This failure of PageRank reveals that the static approach to information filtering is inappropriate for a broad class of growing systems, and suggest that time-dependent algorithms that are based on the temporal linking patterns of these systems are needed to better rank the nodes.

  20. Neophilia Ranking of Scientific Journals

    Science.gov (United States)

    Packalen, Mikko; Bhattacharya, Jay

    2017-01-01

    The ranking of scientific journals is important because of the signal it sends to scientists about what is considered most vital for scientific progress. Existing ranking systems focus on measuring the influence of a scientific paper (citations)—these rankings do not reward journals for publishing innovative work that builds on new ideas. We propose an alternative ranking based on the proclivity of journals to publish papers that build on new ideas, and we implement this ranking via a text-based analysis of all published biomedical papers dating back to 1946. In addition, we compare our neophilia ranking to citation-based (impact factor) rankings; this comparison shows that the two ranking approaches are distinct. Prior theoretical work suggests an active role for our neophilia index in science policy. Absent an explicit incentive to pursue novel science, scientists underinvest in innovative work because of a coordination problem: for work on a new idea to flourish, many scientists must decide to adopt it in their work. Rankings that are based purely on influence thus do not provide sufficient incentives for publishing innovative work. By contrast, adoption of the neophilia index as part of journal-ranking procedures by funding agencies and university administrators would provide an explicit incentive for journals to publish innovative work and thus help solve the coordination problem by increasing scientists' incentives to pursue innovative work. PMID:28713181

  1. An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions

    Directory of Open Access Journals (Sweden)

    Junliang Shang

    2015-01-01

    Full Text Available SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.

  2. An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.

    Science.gov (United States)

    Shang, Junliang; Sun, Yan; Li, Shengjun; Liu, Jin-Xing; Zheng, Chun-Hou; Zhang, Junying

    2015-01-01

    SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.

  3. [Research progress on the phenotype informative SNP in forensic science].

    Science.gov (United States)

    Liu, Yu-Xuan; Hu, Qing-Qing; Ma, Hong-Du; Huang, Dai-Xin

    2014-10-01

    Single nucleotide polymorphism (SNP) refers to the single base sequence variation in specific location of the human genome. Phenotype informative SNP has gradually become one of the research hot spots in forensic science. In this paper, the forensic research situation and application prospect of phenotype informative SNP in the characteristics of hair, eye and skin color, height, and facial feature are reviewed.

  4. A SNP panel for identification of DNA and RNA specimens

    NARCIS (Netherlands)

    Yousefi, Soheil; Abbassi-Daloii, Tooba; Kraaijenbrink, Thirsa; Vermaat, Martijn; Mei, Hailiang; van 't Hof, Peter; van Iterson, Maarten; Zhernakova, Daria V; Claringbould, Annique; Franke, Lude; 't Hart, Leen M; Slieker, Roderick C; van der Heijden, Amber; de Knijff, Peter; 't Hoen, Peter A C

    2018-01-01

    BACKGROUND: SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for

  5. Wikipedia ranking of world universities

    Science.gov (United States)

    Lages, José; Patt, Antoine; Shepelyansky, Dima L.

    2016-03-01

    We use the directed networks between articles of 24 Wikipedia language editions for producing the wikipedia ranking of world Universities (WRWU) using PageRank, 2DRank and CheiRank algorithms. This approach allows to incorporate various cultural views on world universities using the mathematical statistical analysis independent of cultural preferences. The Wikipedia ranking of top 100 universities provides about 60% overlap with the Shanghai university ranking demonstrating the reliable features of this approach. At the same time WRWU incorporates all knowledge accumulated at 24 Wikipedia editions giving stronger highlights for historically important universities leading to a different estimation of efficiency of world countries in university education. The historical development of university ranking is analyzed during ten centuries of their history.

  6. Low-rank coal research

    Energy Technology Data Exchange (ETDEWEB)

    Weber, G. F.; Laudal, D. L.

    1989-01-01

    This work is a compilation of reports on ongoing research at the University of North Dakota. Topics include: Control Technology and Coal Preparation Research (SO{sub x}/NO{sub x} control, waste management), Advanced Research and Technology Development (turbine combustion phenomena, combustion inorganic transformation, coal/char reactivity, liquefaction reactivity of low-rank coals, gasification ash and slag characterization, fine particulate emissions), Combustion Research (fluidized bed combustion, beneficiation of low-rank coals, combustion characterization of low-rank coal fuels, diesel utilization of low-rank coals), Liquefaction Research (low-rank coal direct liquefaction), and Gasification Research (hydrogen production from low-rank coals, advanced wastewater treatment, mild gasification, color and residual COD removal from Synfuel wastewaters, Great Plains Gasification Plant, gasifier optimization).

  7. Statistical methods for ranking data

    CERN Document Server

    Alvo, Mayer

    2014-01-01

    This book introduces advanced undergraduate, graduate students and practitioners to statistical methods for ranking data. An important aspect of nonparametric statistics is oriented towards the use of ranking data. Rank correlation is defined through the notion of distance functions and the notion of compatibility is introduced to deal with incomplete data. Ranking data are also modeled using a variety of modern tools such as CART, MCMC, EM algorithm and factor analysis. This book deals with statistical methods used for analyzing such data and provides a novel and unifying approach for hypotheses testing. The techniques described in the book are illustrated with examples and the statistical software is provided on the authors’ website.

  8. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  9. Ranking nodes in growing networks: When PageRank fails

    Science.gov (United States)

    Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng

    2015-11-01

    PageRank is arguably the most popular ranking algorithm which is being applied in real systems ranging from information to biological and infrastructure networks. Despite its outstanding popularity and broad use in different areas of science, the relation between the algorithm’s efficacy and properties of the network on which it acts has not yet been fully understood. We study here PageRank’s performance on a network model supported by real data, and show that realistic temporal effects make PageRank fail in individuating the most valuable nodes for a broad range of model parameters. Results on real data are in qualitative agreement with our model-based findings. This failure of PageRank reveals that the static approach to information filtering is inappropriate for a broad class of growing systems, and suggest that time-dependent algorithms that are based on the temporal linking patterns of these systems are needed to better rank the nodes.

  10. Exhaustive Genome-Wide Search for SNP-SNP Interactions Across 10 Human Diseases

    Directory of Open Access Journals (Sweden)

    William Murk

    2016-07-01

    Full Text Available The identification of statistical SNP-SNP interactions may help explain the genetic etiology of many human diseases, but exhaustive genome-wide searches for these interactions have been difficult, due to a lack of power in most datasets. We aimed to use data from the Resource for Genetic Epidemiology Research on Adult Health and Aging (GERA study to search for SNP-SNP interactions associated with 10 common diseases. FastEpistasis and BOOST were used to evaluate all pairwise interactions among approximately N = 300,000 single nucleotide polymorphisms (SNPs with minor allele frequency (MAF ≥ 0.15, for the dichotomous outcomes of allergic rhinitis, asthma, cardiac disease, depression, dermatophytosis, type 2 diabetes, dyslipidemia, hemorrhoids, hypertensive disease, and osteoarthritis. A total of N = 45,171 subjects were included after quality control steps were applied. These data were divided into discovery and replication subsets; the discovery subset had > 80% power, under selected models, to detect genome-wide significant interactions (P < 10−12. Interactions were also evaluated for enrichment in particular SNP features, including functionality, prior disease relevancy, and marginal effects. No interaction in any disease was significant in both the discovery and replication subsets. Enrichment analysis suggested that, for some outcomes, interactions involving SNPs with marginal effects were more likely to be nominally replicated, compared to interactions without marginal effects. If SNP-SNP interactions play a role in the etiology of the studied conditions, they likely have weak effect sizes, involve lower-frequency variants, and/or involve complex models of interaction that are not captured well by the methods that were utilized.

  11. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

    Directory of Open Access Journals (Sweden)

    Steve Davis

    2015-08-01

    Full Text Available The analysis of next-generation sequence (NGS data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide polymorphisms (i.e., a SNP matrix for a set of individuals. The management and chaining of these software pieces and their outputs can often be a cumbersome and difficult task. Here, we present CFSAN SNP Pipeline, which combines into a single package the mapping of NGS reads to a reference genome with Bowtie2, processing of those mapping (BAM files using SAMtools, identification of variant sites using VarScan, and production of a SNP matrix using custom Python scripts. We also introduce a Python package (CFSAN SNP Mutator that when given a reference genome will generate variants of known position against which we validate our pipeline. We created 1,000 simulated Salmonella enterica sp. enterica Serovar Agona genomes at 100× and 20× coverage, each containing 500 SNPs, 20 single-base insertions and 20 single-base deletions. For the 100× dataset, the CFSAN SNP Pipeline recovered 98.9% of the introduced SNPs and had a false positive rate of 1.04 × 10−6; for the 20× dataset 98.8% of SNPs were recovered and the false positive rate was 8.34 × 10−7. Based on these results, CFSAN SNP Pipeline is a robust and accurate tool that it is among the first to combine into a single executable the myriad steps required to produce a SNP matrix from NGS data. Such a tool is useful to those working in an applied setting (e.g., food safety traceback investigations as well as for those interested in evolutionary questions.

  12. Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

    Science.gov (United States)

    Chagné, David; Crowhurst, Ross N.; Troggio, Michela; Davey, Mark W.; Gilmore, Barbara; Lawley, Cindy; Vanderzande, Stijn; Hellens, Roger P.; Kumar, Satish; Cestaro, Alessandro; Velasco, Riccardo; Main, Dorrie; Rees, Jasper D.; Iezzoni, Amy; Mockler, Todd; Wilhelm, Larry; Van de Weg, Eric; Gardiner, Susan E.; Bassil, Nahla; Peace, Cameron

    2012-01-01

    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple. PMID:22363718

  13. A Bayesian Framework for SNP Identification

    Energy Technology Data Exchange (ETDEWEB)

    Webb-Robertson, Bobbie-Jo M.; Havre, Susan L.; Payne, Deborah A.

    2005-07-01

    Current proteomics techniques, such as mass spectrometry, focus on protein identification, usually ignoring most types of modifications beyond post-translational modifications, with the assumption that only a small number of peptides have to be matched to a protein for a positive identification. However, not all proteins are being identified with current techniques and improved methods to locate points of mutation are becoming a necessity. In the case when single-nucleotide polymorphisms (SNPs) are observed, brute force is the most common method to locate them, quickly becoming computationally unattractive as the size of the database associated with the model organism grows. We have developed a Bayesian model for SNPs, BSNP, incorporating evolutionary information at both the nucleotide and amino acid levels. Formulating SNPs as a Bayesian inference problem allows probabilities of interest to be easily obtained, for example the probability of a specific SNP or specific type of mutation over a gene or entire genome. Three SNP databases were observed in the evaluation of the BSNP model; the first SNP database is a disease specific gene in human, hemoglobin, the second is also a disease specific gene in human, p53, and the third is a more general SNP database for multiple genes in mouse. We validate that the BSNP model assigns higher posterior probabilities to the SNPs defined in all three separate databases than can be attributed to chance under specific evolutionary information, for example the amino acid model described by Majewski and Ott in conjunction with either the four-parameter nucleotide model by Bulmer or seven-parameter nucleotide model by Majewski and Ott.

  14. University Rankings in Critical Perspective

    Science.gov (United States)

    Pusser, Brian; Marginson, Simon

    2013-01-01

    This article addresses global postsecondary ranking systems by using critical-theoretical perspectives on power. This research suggests rankings are at once a useful lens for studying power in higher education and an important instrument for the exercise of power in service of dominant norms in global higher education. (Contains 1 table and 1…

  15. University Ranking as Social Exclusion

    Science.gov (United States)

    Amsler, Sarah S.; Bolsmann, Chris

    2012-01-01

    In this article we explore the dual role of global university rankings in the creation of a new, knowledge-identified, transnational capitalist class and in facilitating new forms of social exclusion. We examine how and why the practice of ranking universities has become widely defined by national and international organisations as an important…

  16. PageRank tracker: from ranking to tracking.

    Science.gov (United States)

    Gong, Chen; Fu, Keren; Loza, Artur; Wu, Qiang; Liu, Jia; Yang, Jie

    2014-06-01

    Video object tracking is widely used in many real-world applications, and it has been extensively studied for over two decades. However, tracking robustness is still an issue in most existing methods, due to the difficulties with adaptation to environmental or target changes. In order to improve adaptability, this paper formulates the tracking process as a ranking problem, and the PageRank algorithm, which is a well-known webpage ranking algorithm used by Google, is applied. Labeled and unlabeled samples in tracking application are analogous to query webpages and the webpages to be ranked, respectively. Therefore, determining the target is equivalent to finding the unlabeled sample that is the most associated with existing labeled set. We modify the conventional PageRank algorithm in three aspects for tracking application, including graph construction, PageRank vector acquisition and target filtering. Our simulations with the use of various challenging public-domain video sequences reveal that the proposed PageRank tracker outperforms mean-shift tracker, co-tracker, semiboosting and beyond semiboosting trackers in terms of accuracy, robustness and stability.

  17. SNP sets and reading ability: testing confirmation of a 10-SNP set in a population sample.

    Science.gov (United States)

    Luciano, Michelle; Montgomery, Grant W; Martin, Nicholas G; Wright, Margaret J; Bates, Timothy C

    2011-06-01

    A set of 10 SNPs associated with reading ability in 7-year-olds was reported based on initial pooled analyses of 100K SNP chip data, with follow-up testing stages using pooling and individual testing. Here we examine this association in an adolescent population sample of Australian twins and siblings (N = 1177) aged 12 to 25 years. One (rs1842129) of the 10 SNPs approached significance (P = .05) but no support was found for the remaining 9 SNPs or the SNP set itself. Results indicate that these SNPs are not associated with reading ability in an Australian population. The results are interpreted as supporting use of much larger SNP sets in common disorders where effects are small.

  18. saSNP Approach for Scalable SNP Analyses of Multiple Bacterial or Viral Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Slezak, Tom [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2010-07-27

    With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs. The method is fast to compute, finding SNPs and building a SNP phylogeny in seconds to hours. We use it to identify thousands of putative SNPs from all publicly available Filoviridae, Poxviridae, foot-and-mouth disease virus, Bacillus, and Escherichia coli genomes and plasmids. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle as input hundreds of gigabases of sequence in a single run. The algorithm is based on k-mer analysis using a suffix array, so we call it saSNP.

  19. Universal scaling in sports ranking

    Science.gov (United States)

    Deng, Weibing; Li, Wei; Cai, Xu; Bulou, Alain; Wang, Qiuping A.

    2012-09-01

    Ranking is a ubiquitous phenomenon in human society. On the web pages of Forbes, one may find all kinds of rankings, such as the world's most powerful people, the world's richest people, the highest-earning tennis players, and so on and so forth. Herewith, we study a specific kind—sports ranking systems in which players' scores and/or prize money are accrued based on their performances in different matches. By investigating 40 data samples which span 12 different sports, we find that the distributions of scores and/or prize money follow universal power laws, with exponents nearly identical for most sports. In order to understand the origin of this universal scaling we focus on the tennis ranking systems. By checking the data we find that, for any pair of players, the probability that the higher-ranked player tops the lower-ranked opponent is proportional to the rank difference between the pair. Such a dependence can be well fitted to a sigmoidal function. By using this feature, we propose a simple toy model which can simulate the competition of players in different matches. The simulations yield results consistent with the empirical findings. Extensive simulation studies indicate that the model is quite robust with respect to the modifications of some parameters.

  20. Universal scaling in sports ranking

    CERN Document Server

    Deng, Weibing; Cai, Xu; Bulou, Alain; Wang, Qiuping A

    2011-01-01

    Ranking is a ubiquitous phenomenon in the human society. By clicking the web pages of Forbes, you may find all kinds of rankings, such as world's most powerful people, world's richest people, top-paid tennis stars, and so on and so forth. Herewith, we study a specific kind, sports ranking systems in which players' scores and prize money are calculated based on their performances in attending various tournaments. A typical example is tennis. It is found that the distributions of both scores and prize money follow universal power laws, with exponents nearly identical for most sports fields. In order to understand the origin of this universal scaling we focus on the tennis ranking systems. By checking the data we find that, for any pair of players, the probability that the higher-ranked player will top the lower-ranked opponent is proportional to the rank difference between the pair. Such a dependence can be well fitted to a sigmoidal function. By using this feature, we propose a simple toy model which can simul...

  1. SNP-RFLPing: restriction enzyme mining for SNPs in genomes

    Directory of Open Access Journals (Sweden)

    Cheng Yu-Huei

    2006-02-01

    Full Text Available Abstract Background The restriction fragment length polymorphism (RFLP is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs. Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. Results Three user-friendly inputs are included: 1 NCBI dbSNP "rs" or "ss" IDs; 2 NCBI Entrez gene ID and HUGO gene name; 3 any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. Conclusion This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at http://bio.kuas.edu.tw/snp-rflp/.

  2. PageRank of integers

    Science.gov (United States)

    Frahm, K. M.; Chepelianskii, A. D.; Shepelyansky, D. L.

    2012-10-01

    We up a directed network tracing links from a given integer to its divisors and analyze the properties of the Google matrix of this network. The PageRank vector of this matrix is computed numerically and it is shown that its probability is approximately inversely proportional to the PageRank index thus being similar to the Zipf law and the dependence established for the World Wide Web. The spectrum of the Google matrix of integers is characterized by a large gap and a relatively small number of nonzero eigenvalues. A simple semi-analytical expression for the PageRank of integers is derived that allows us to find this vector for matrices of billion size. This network provides a new PageRank order of integers.

  3. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik

    2007-01-01

    manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

  4. Ranking in evolving complex networks

    Science.gov (United States)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang

    2017-05-01

    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  5. Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

    OpenAIRE

    Ling-Yun Wu; Rui-Sheng Wang; Xiang-Sun Zhang; Wei Zhang

    2006-01-01

    The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expecte...

  6. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  7. RANK and RANK ligand expression in primary human osteosarcoma

    Directory of Open Access Journals (Sweden)

    Daniel Branstetter

    2015-09-01

    Our results demonstrate RANKL expression was observed in the tumor element in 68% of human OS using IHC. However, the staining intensity was relatively low and only 37% (29/79 of samples exhibited≥10% RANKL positive tumor cells. RANK expression was not observed in OS tumor cells. In contrast, RANK expression was clearly observed in other cells within OS samples, including the myeloid osteoclast precursor compartment, osteoclasts and in giant osteoclast cells. The intensity and frequency of RANKL and RANK staining in OS samples were substantially less than that observed in GCTB samples. The observation that RANKL is expressed in OS cells themselves suggests that these tumors may mediate an osteoclastic response, and anti-RANKL therapy may potentially be protective against bone pathologies in OS. However, the absence of RANK expression in primary human OS cells suggests that any autocrine RANKL/RANK signaling in human OS tumor cells is not operative, and anti-RANKL therapy would not directly affect the tumor.

  8. Ranking structures and Rank-Rank Correlations of Countries. The FIFA and UEFA cases

    CERN Document Server

    Ausloos, Marcel; Gadomski, Adam; Vitanov, Nikolay K

    2014-01-01

    Ranking of agents competing with each other in complex systems may lead to paradoxes according to the pre-chosen different measures. A discussion is presented on such rank-rank, similar or not, correlations based on the case of European countries ranked by UEFA and FIFA from different soccer competitions. The first question to be answered is whether an empirical and simple law is obtained for such (self-) organizations of complex sociological systems with such different measuring schemes. It is found that the power law form is not the best description contrary to many modern expectations. The stretched exponential is much more adequate. Moreover, it is found that the measuring rules lead to some inner structures, in both cases.

  9. Ranking structures and rank-rank correlations of countries: The FIFA and UEFA cases

    Science.gov (United States)

    Ausloos, Marcel; Cloots, Rudi; Gadomski, Adam; Vitanov, Nikolay K.

    2014-04-01

    Ranking of agents competing with each other in complex systems may lead to paradoxes according to the pre-chosen different measures. A discussion is presented on such rank-rank, similar or not, correlations based on the case of European countries ranked by UEFA and FIFA from different soccer competitions. The first question to be answered is whether an empirical and simple law is obtained for such (self-) organizations of complex sociological systems with such different measuring schemes. It is found that the power law form is not the best description contrary to many modern expectations. The stretched exponential is much more adequate. Moreover, it is found that the measuring rules lead to some inner structures in both cases.

  10. A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

    Science.gov (United States)

    Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

    2017-01-01

    A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be

  11. University Ranking Systems; Criteria and Critiques

    OpenAIRE

    Saka, Yavuz; YAMAN, Süleyman

    2011-01-01

    The purpose of this paper is to explore international university ranking systems. As a compilation study this paper provides specific criteria that each ranking system uses and main critiques regarding these ranking systems. Since there are many ranking systems in this area of research, this study focused on only most cited and referred ranking systems. As there is no consensus in terms of the criteria that these systems use, this paper has no intention of identifying the best ranking system ...

  12. SNP List (Phase III) - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available he best tagSNP or not. 1: Best tagSNP 0: non-best tagSNP -: SNP not included in LD bin calculation (MAF (MAF Best tagSNP The flag that indicates whether the SNP is t...ter QCs by sample call rate and SNP call rate, the final data for 87 CHMs (876K SNPs) was obtained. See “LD bin List” for the calcula...tion of LD bins. Number of data entries 876,399 entries Data item Description RefSN...ck Search) tagSNP The flag that indicates whether the SNP is a tagSNP or not. 1: tagSNP 0: non-tagSNP -: SNP

  13. SNIT: SNP identification for strain typing

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2011-09-01

    Full Text Available Abstract With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs and small insertions/deletions (indels. Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html

  14. Atomic Force Microscopy for DNA SNP Identification

    Science.gov (United States)

    Valbusa, Ugo; Ierardi, Vincenzo

    The knowledge of the effects of single-nucleotide polymorphisms (SNPs) in the human genome greatly contributes to better comprehension of the relation between genetic factors and diseases. Sequence analysis of genomic DNA in different individuals reveals positions where variations that involve individual base substitutions can occur. Single-nucleotide polymorphisms are highly abundant and can have different consequences at phenotypic level. Several attempts were made to apply atomic force microscopy (AFM) to detect and map SNP sites in DNA strands. The most promising approach is the study of DNA mutations producing heteroduplex DNA strands and identifying the mismatches by means of a protein that labels the mismatches. MutS is a protein that is part of a well-known complex of mismatch repair, which initiates the process of repairing when the MutS binds to the mismatched DNA filament. The position of MutS on the DNA filament can be easily recorded by means of AFM imaging.

  15. Ranking species in mutualistic networks.

    Science.gov (United States)

    Domínguez-García, Virginia; Muñoz, Miguel A

    2015-02-02

    Understanding the architectural subtleties of ecological networks, believed to confer them enhanced stability and robustness, is a subject of outmost relevance. Mutualistic interactions have been profusely studied and their corresponding bipartite networks, such as plant-pollinator networks, have been reported to exhibit a characteristic "nested" structure. Assessing the importance of any given species in mutualistic networks is a key task when evaluating extinction risks and possible cascade effects. Inspired in a recently introduced algorithm--similar in spirit to Google's PageRank but with a built-in non-linearity--here we propose a method which--by exploiting their nested architecture--allows us to derive a sound ranking of species importance in mutualistic networks. This method clearly outperforms other existing ranking schemes and can become very useful for ecosystem management and biodiversity preservation, where decisions on what aspects of ecosystems to explicitly protect need to be made.

  16. University rankings in computer science

    DEFF Research Database (Denmark)

    Ehret, Philip; Zuccala, Alesia Ann; Gipp, Bela

    2017-01-01

    This is a research-in-progress paper concerning two types of institutional rankings, the Leiden and QS World ranking, and their relationship to a list of universities’ ‘geo-based’ impact scores, and Computing Research and Education Conference (CORE) participation scores in the field of computer...... science. A ‘geo-based’ impact measure examines the geographical distribution of incoming citations to a particular university’s journal articles for a specific period of time. It takes into account both the number of citations and the geographical variability in these citations. The CORE participation...... score is calculated on the basis of the number of weighted proceedings papers that a university has contributed to either an A*, A, B, or C conference as ranked by the Computing Research and Education Association of Australasia. In addition to calculating the correlations between the distinct university...

  17. Evaluation of the Ion Torrent™ HID SNP 169-plex

    DEFF Research Database (Denmark)

    Børsting, Claus; Fordyce, Sarah L; Olofsson, Jill Katharina

    2014-01-01

    in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent™ HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent™ HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals...

  18. Rank distributions: Frequency vs. magnitude.

    Science.gov (United States)

    Velarde, Carlos; Robledo, Alberto

    2017-01-01

    We examine the relationship between two different types of ranked data, frequencies and magnitudes. We consider data that can be sorted out either way, through numbers of occurrences or size of the measures, as it is the case, say, of moon craters, earthquakes, billionaires, etc. We indicate that these two types of distributions are functional inverses of each other, and specify this link, first in terms of the assumed parent probability distribution that generates the data samples, and then in terms of an analog (deterministic) nonlinear iterated map that reproduces them. For the particular case of hyperbolic decay with rank the distributions are identical, that is, the classical Zipf plot, a pure power law. But their difference is largest when one displays logarithmic decay and its counterpart shows the inverse exponential decay, as it is the case of Benford law, or viceversa. For all intermediate decay rates generic differences appear not only between the power-law exponents for the midway rank decline but also for small and large rank. We extend the theoretical framework to include thermodynamic and statistical-mechanical concepts, such as entropies and configuration.

  19. Rankings Methodology Hurts Public Institutions

    Science.gov (United States)

    Van Der Werf, Martin

    2007-01-01

    In the 1980s, when the "U.S. News & World Report" rankings of colleges were based solely on reputation, the nation's public universities were well represented at the top. However, as soon as the magazine began including its "measures of excellence," statistics intended to define quality, public universities nearly disappeared from the top. As the…

  20. Let Us Rank Journalism Programs

    Science.gov (United States)

    Weber, Joseph

    2014-01-01

    Unlike law, business, and medical schools, as well as universities in general, journalism schools and journalism programs have rarely been ranked. Publishers such as "U.S. News & World Report," "Forbes," "Bloomberg Businessweek," and "Washington Monthly" do not pay them much mind. What is the best…

  1. Multiple graph regularized protein domain ranking

    Directory of Open Access Journals (Sweden)

    Wang Jim

    2012-11-01

    Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  2. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-11-19

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  3. The Globalization of College and University Rankings

    Science.gov (United States)

    Altbach, Philip G.

    2012-01-01

    In the era of globalization, accountability, and benchmarking, university rankings have achieved a kind of iconic status. The major ones--the Academic Ranking of World Universities (ARWU, or the "Shanghai rankings"), the QS (Quacquarelli Symonds Limited) World University Rankings, and the "Times Higher Education" World…

  4. GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.

    Science.gov (United States)

    Giannoulatou, Eleni; Yau, Christopher; Colella, Stefano; Ragoussis, Jiannis; Holmes, Christopher C

    2008-10-01

    Current genotyping algorithms typically call genotypes by clustering allele-specific intensity data on a single nucleotide polymorphism (SNP) by SNP basis. This approach assumes the availability of a large number of control samples that have been sampled on the same array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. Our algorithm exhibits high concordance with current methods and >99% call accuracy on HapMap samples. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving small sample sizes and provides a valuable independent quality control metric for other population-based approaches. http://www.stats.ox.ac.uk/~giannoul/GenoSNP/.

  5. Time evolution of Wikipedia network ranking

    Science.gov (United States)

    Eom, Young-Ho; Frahm, Klaus M.; Benczúr, András; Shepelyansky, Dima L.

    2013-12-01

    We study the time evolution of ranking and spectral properties of the Google matrix of English Wikipedia hyperlink network during years 2003-2011. The statistical properties of ranking of Wikipedia articles via PageRank and CheiRank probabilities, as well as the matrix spectrum, are shown to be stabilized for 2007-2011. A special emphasis is done on ranking of Wikipedia personalities and universities. We show that PageRank selection is dominated by politicians while 2DRank, which combines PageRank and CheiRank, gives more accent on personalities of arts. The Wikipedia PageRank of universities recovers 80% of top universities of Shanghai ranking during the considered time period.

  6. Validating rankings in soccer championships

    Directory of Open Access Journals (Sweden)

    Annibal Parracho Sant'Anna

    2012-08-01

    Full Text Available The final ranking of a championship is determined by quality attributes combined with other factors which should be filtered out of any decision on relegation or draft for upper level tournaments. Factors like referees' mistakes and difficulty of certain matches due to its accidental importance to the opponents should have their influence reduced. This work tests approaches to combine classification rules considering the imprecision of the number of points as a measure of quality and of the variables that provide reliable explanation for it. Two home-advantage variables are tested and shown to be apt to enter as explanatory variables. Independence between the criteria is checked against the hypothesis of maximal correlation. The importance of factors and of composition rules is evaluated on the basis of correlation between rank vectors, number of classes and number of clubs in tail classes. Data from five years of the Brazilian Soccer Championship are analyzed.

  7. Minkowski metrics in creating universal ranking algorithms

    Directory of Open Access Journals (Sweden)

    Andrzej Ameljańczyk

    2014-06-01

    Full Text Available The paper presents a general procedure for creating the rankings of a set of objects, while the relation of preference based on any ranking function. The analysis was possible to use the ranking functions began by showing the fundamental drawbacks of commonly used functions in the form of a weighted sum. As a special case of the ranking procedure in the space of a relation, the procedure based on the notion of an ideal element and generalized Minkowski distance from the element was proposed. This procedure, presented as universal ranking algorithm, eliminates most of the disadvantages of ranking functions in the form of a weighted sum.[b]Keywords[/b]: ranking functions, preference relation, ranking clusters, categories, ideal point, universal ranking algorithm

  8. Combined Reduced-Rank Transform

    Directory of Open Access Journals (Sweden)

    Anatoli Torokhti

    2006-04-01

    Full Text Available We propose and justify a new approach to constructing optimal nonlinear transforms of random vectors. We show that the proposed transform improves such characteristics of {rank-reduced} transforms as compression ratio, accuracy of decompression and reduces required computational work. The proposed transform ${mathcal T}_p$ is presented in the form of a sum with $p$ terms where each term is interpreted as a particular rank-reduced transform. Moreover, terms in ${mathcal T}_p$ are represented as a combination of three operations ${mathcal F}_k$, ${mathcal Q}_k$ and ${oldsymbol{varphi}}_k$ with $k=1,ldots,p$. The prime idea is to determine ${mathcal F}_k$ separately, for each $k=1,ldots,p$, from an associated rank-constrained minimization problem similar to that used in the Karhunen--Lo`{e}ve transform. The operations ${mathcal Q}_k$ and ${oldsymbol{varphi}}_k$ are auxiliary for f/inding ${mathcal F}_k$. The contribution of each term in ${mathcal T}_p$ improves the entire transform performance. A corresponding unconstrained nonlinear optimal transform is also considered. Such a transform is important in its own right because it is treated as an optimal filter without signal compression. A rigorous analysis of errors associated with the proposed transforms is given.

  9. Functional Multiplex PageRank

    Science.gov (United States)

    Iacovacci, Jacopo; Rahmede, Christoph; Arenas, Alex; Bianconi, Ginestra

    2016-10-01

    Recently it has been recognized that many complex social, technological and biological networks have a multilayer nature and can be described by multiplex networks. Multiplex networks are formed by a set of nodes connected by links having different connotations forming the different layers of the multiplex. Characterizing the centrality of the nodes in a multiplex network is a challenging task since the centrality of the node naturally depends on the importance associated to links of a certain type. Here we propose to assign to each node of a multiplex network a centrality called Functional Multiplex PageRank that is a function of the weights given to every different pattern of connections (multilinks) existent in the multiplex network between any two nodes. Since multilinks distinguish all the possible ways in which the links in different layers can overlap, the Functional Multiplex PageRank can describe important non-linear effects when large relevance or small relevance is assigned to multilinks with overlap. Here we apply the Functional Page Rank to the multiplex airport networks, to the neuronal network of the nematode C. elegans, and to social collaboration and citation networks between scientists. This analysis reveals important differences existing between the most central nodes of these networks, and the correlations between their so-called pattern to success.

  10. Ranking Support Vector Machine with Kernel Approximation.

    Science.gov (United States)

    Chen, Kai; Li, Rongchun; Dou, Yong; Liang, Zhengfa; Lv, Qi

    2017-01-01

    Learning to rank algorithm has become important in recent years due to its successful application in information retrieval, recommender system, and computational biology, and so forth. Ranking support vector machine (RankSVM) is one of the state-of-art ranking models and has been favorably used. Nonlinear RankSVM (RankSVM with nonlinear kernels) can give higher accuracy than linear RankSVM (RankSVM with a linear kernel) for complex nonlinear ranking problem. However, the learning methods for nonlinear RankSVM are still time-consuming because of the calculation of kernel matrix. In this paper, we propose a fast ranking algorithm based on kernel approximation to avoid computing the kernel matrix. We explore two types of kernel approximation methods, namely, the Nyström method and random Fourier features. Primal truncated Newton method is used to optimize the pairwise L2-loss (squared Hinge-loss) objective function of the ranking model after the nonlinear kernel approximation. Experimental results demonstrate that our proposed method gets a much faster training speed than kernel RankSVM and achieves comparable or better performance over state-of-the-art ranking algorithms.

  11. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    resolution SNP arrays to investigate 33 patients with syndromic and nonsyndromic oral clefts in whom standard karyotyping analyses showed normal karyotypes. We aim to identify the genomic aetiology and candidate genes in patients with ...

  12. In silico characterization of functional SNP within the oestrogen ...

    Indian Academy of Sciences (India)

    Keywords. ESR1 gene; polymorphism; prediction; bioinformatic tools; association studies. Abstract. Single-nucleotide polymorphism (SNP) association studies have become crucial in uncovering the genetic correlations of genomic variants with complex diseases, quantitative traits and physiological responses to drugs.

  13. Characterization of fifteen SNP markers by mining EST in sea ...

    Indian Academy of Sciences (India)

    pdf]. Introduction. Fifteen single nucleotide polymorphism (SNP) markers were validated and characterized in the sea cucumber ... ers are powerful tools for conservation and management of natural resources, and for marker-assisted selection in.

  14. SNP List (Phase II) - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ries Data item Description RefSNP ID RefSNP ID (rs number) given by dbSNP. (Linked to dbSNP in Quick Search)...les MAF Minor allele frequency Genotypes Genotypes for the 74 CHM samples LD bin Name of LD bin (Linked to LD bin list in Quick

  15. The Privilege of Ranking: Google Plays Ball.

    Science.gov (United States)

    Wiggins, Richard

    2003-01-01

    Discussion of ranking systems used in various settings, including college football and academic admissions, focuses on the Google search engine. Explains the PageRank mathematical formula that scores Web pages by connecting the number of links; limitations, including authenticity and accuracy of ranked Web pages; relevancy; adjusting algorithms;…

  16. Methodology, Meaning and Usefulness of Rankings

    Science.gov (United States)

    Williams, Ross

    2008-01-01

    University rankings are having a profound effect on both higher education systems and individual universities. In this paper we outline these effects, discuss the desirable characteristics of a good ranking methodology and document existing practice, with an emphasis on the two main international rankings (Shanghai Jiao Tong and THES-QS). We take…

  17. TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP-SNP interactions.

    Science.gov (United States)

    Fang, Yao-Hwei; Wang, Jie-Huei; Hsiung, Chao A

    2017-11-15

    Identification of single nucleotide polymorphism (SNP) interactions is an important and challenging topic in genome-wide association studies (GWAS). Many approaches have been applied to detecting whole-genome interactions. However, these approaches to interaction analysis tend to miss causal interaction effects when the individual marginal effects are uncorrelated to trait, while their interaction effects are highly associated with the trait. A grouped variable selection technique, called two-stage grouped sure independence screening (TS-GSIS), is developed to study interactions that may not have marginal effects. The proposed TS-GSIS is shown to be very helpful in identifying not only causal SNP effects that are uncorrelated to trait but also their corresponding SNP-SNP interaction effects. The benefit of TS-GSIS are gaining detection of interaction effects by taking the joint information among the SNPs and determining the size of candidate sets in the model. Simulation studies under various scenarios are performed to compare performance of TS-GSIS and current approaches. We also apply our approach to a real rheumatoid arthritis (RA) dataset. Both the simulation and real data studies show that the TS-GSIS performs very well in detecting SNP-SNP interactions. R-package is delivered through CRAN and is available at: https://cran.r-project.org/web/packages/TSGSIS/index.html. hsiung@nhri.org.tw. Supplementary data are available at Bioinformatics online.

  18. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System.

    Science.gov (United States)

    De la Vega, Francisco M; Lazaruk, Katherine D; Rhodes, Michael D; Wenz, Michael H

    2005-06-03

    In this review we describe the principles, protocols, and applications of two commercially available SNP genotyping platforms, the TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Combined, these two technologies meet the requirements of multiple SNP applications in genetics research and pharmacogenetics. We also describe a set of SNP selection tools and validated assay resources which we developed to accelerate the cycle of experimentation on these platforms. Criteria for selecting the more appropriate of these two genotyping technologies are presented: the genetic architecture of the trait of interest, the throughput required, and the number of SNPs and samples needed for a successful study. Overall, the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable. The SNPlex Genotyping System, on the other hand, is well suited for SNP applications in which throughput and cost-efficiency are essential, e.g., applications requiring either the testing of large numbers of SNPs and samples, or the flexibility to select various SNP subsets.

  19. Tool for Ranking Research Options

    Science.gov (United States)

    Ortiz, James N.; Scott, Kelly; Smith, Harold

    2005-01-01

    Tool for Research Enhancement Decision Support (TREDS) is a computer program developed to assist managers in ranking options for research aboard the International Space Station (ISS). It could likely also be adapted to perform similar decision-support functions in industrial and academic settings. TREDS provides a ranking of the options, based on a quantifiable assessment of all the relevant programmatic decision factors of benefit, cost, and risk. The computation of the benefit for each option is based on a figure of merit (FOM) for ISS research capacity that incorporates both quantitative and qualitative inputs. Qualitative inputs are gathered and partly quantified by use of the time-tested analytical hierarchical process and used to set weighting factors in the FOM corresponding to priorities determined by the cognizant decision maker(s). Then by use of algorithms developed specifically for this application, TREDS adjusts the projected benefit for each option on the basis of levels of technical implementation, cost, and schedule risk. Based partly on Excel spreadsheets, TREDS provides screens for entering cost, benefit, and risk information. Drop-down boxes are provided for entry of qualitative information. TREDS produces graphical output in multiple formats that can be tailored by users.

  20. Issue Management Risk Ranking Systems

    Energy Technology Data Exchange (ETDEWEB)

    Novack, Steven David; Marshall, Frances Mc Clellan; Stromberg, Howard Merion; Grant, Gary Michael

    1999-06-01

    Thousands of safety issues have been collected on-line at the Idaho National Engineering and Environmental Laboratory (INEEL) as part of the Issue Management Plan. However, there has been no established approach to prioritize collected and future issues. The authors developed a methodology, based on hazards assessment, to identify and risk rank over 5000 safety issues collected at INEEL. This approach required that it was easily applied and understandable for site adaptation and commensurate with the Integrated Safety Plan. High-risk issues were investigated and mitigative/preventive measures were suggested and ranked based on a cost-benefit scheme to provide risk-informed safety measures. This methodology was consistent with other integrated safety management goals and tasks providing a site-wide risk informed decision tool to reduce hazardous conditions and focus resources on high-risk safety issues. As part of the issue management plan, this methodology was incorporated at the issue collection level and training was provided to management to better familiarize decision-makers with concepts of safety and risk. This prioritization methodology and issue dissemination procedure will be discussed. Results of issue prioritization and training efforts will be summarized. Difficulties and advantages of the process will be reported. Development and incorporation of this process into INEELs lessons learned reporting and the site-wide integrated safety management program will be shown with an emphasis on establishing self reliance and ownership of safety issues.

  1. Partitioned learning of deep Boltzmann machines for SNP data.

    Science.gov (United States)

    Hess, Moritz; Lenz, Stefan; Blätte, Tamara J; Bullinger, Lars; Binder, Harald

    2017-10-15

    Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen the joint distribution of SNPs, followed by training several DBMs on SNP partitions that were identified by the screening. Aggregate features representing SNP patterns and the corresponding SNPs are extracted from the DBMs by a combination of statistical tests and sparse regression. In simulated case-control data, we show how this can uncover complex SNP patterns and augment results from univariate approaches, while maintaining type 1 error control. Time-to-event endpoints are considered in an application with acute myeloid leukemia patients, where SNP patterns are modeled after a pre-screening based on gene expression data. The proposed approach identified three SNPs that seem to jointly influence survival in a validation dataset. This indicates the added value of jointly investigating SNPs compared to standard univariate analyses and makes partitioned learning of DBMs an interesting complementary approach when analyzing SNP data. A Julia package is provided at 'http://github.com/binderh/BoltzmannMachines.jl'. binderh@imbi.uni-freiburg.de. Supplementary data are available at Bioinformatics online.

  2. Heterogeneous computing architecture for fast detection of SNP-SNP interactions.

    Science.gov (United States)

    Sluga, Davor; Curk, Tomaz; Zupan, Blaz; Lotric, Uros

    2014-06-25

    The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems.

  3. Two-dimensional ranking of Wikipedia articles

    Science.gov (United States)

    Zhirov, A. O.; Zhirov, O. V.; Shepelyansky, D. L.

    2010-10-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists ab aeterno. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

  4. Genetic algorithm-generated SNP barcodes of the mitochondrial D-loop for chronic dialysis susceptibility.

    Science.gov (United States)

    Chen, Jin-Bor; Chuang, Li-Yeh; Lin, Yu-Da; Liou, Chia-Wei; Lin, Tsu-Kung; Lee, Wen-Chin; Cheng, Ben-Chung; Chang, Hsueh-Wei; Yang, Cheng-Hong

    2014-06-01

    Single nucleotide polymorphism (SNP) interaction analysis can simultaneously evaluate the complex SNP interactions present in complex diseases. However, it is less commonly applied to evaluate the predisposition of chronic dialysis and its computational analysis remains challenging. In this study, we aimed to improve the analysis of SNP-SNP interactions within the mitochondrial D-loop in chronic dialysis. The SNP-SNP interactions between 77 reported SNPs within the mitochondrial D-loop in chronic dialysis study were evaluated in terms of SNP barcodes (different SNP combinations with their corresponding genotypes). We propose a genetic algorithm (GA) to generate SNP barcodes. The χ(2) values were then calculated by the occurrences of the specific SNP barcodes and their non-specific combinations between cases and controls. Each SNP barcode (2- to 7-SNP) with the highest value in the χ(2) test was regarded as the best SNP barcode (11.304 to 23.310; p algorithm to address the SNP-SNP interactions and demonstrated that many non-significant SNPs within the mitochondrial D-loop may play a role in jointed effects to chronic dialysis susceptibility.

  5. DoGSD: the dog and wolf genome SNP database.

    Science.gov (United States)

    Bai, Bing; Zhao, Wen-Ming; Tang, Bi-Xia; Wang, Yan-Qing; Wang, Lu; Zhang, Zhang; Yang, He-Chuan; Liu, Yan-Hu; Zhu, Jun-Wei; Irwin, David M; Wang, Guo-Dong; Zhang, Ya-Ping

    2015-01-01

    The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼ 19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. An SNP caused loss of seed shattering during rice domestication.

    Science.gov (United States)

    Konishi, Saeko; Izawa, Takeshi; Lin, Shao Yang; Ebana, Kaworu; Fukuta, Yoshimichi; Sasaki, Takuji; Yano, Masahiro

    2006-06-02

    Loss of seed shattering was a key event in the domestication of major cereals. We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication.

  7. Rank Modulation for Translocation Error Correction

    CERN Document Server

    Farnoud, Farzad; Milenkovic, Olgica

    2012-01-01

    We consider rank modulation codes for flash memories that allow for handling arbitrary charge drop errors. Unlike classical rank modulation codes used for correcting errors that manifest themselves as swaps of two adjacently ranked elements, the proposed \\emph{translocation rank codes} account for more general forms of errors that arise in storage systems. Translocations represent a natural extension of the notion of adjacent transpositions and as such may be analyzed using related concepts in combinatorics and rank modulation coding. Our results include tight bounds on the capacity of translocation rank codes, construction techniques for asymptotically good codes, as well as simple decoding methods for one class of structured codes. As part of our exposition, we also highlight the close connections between the new code family and permutations with short common subsequences, deletion and insertion error-correcting codes for permutations and permutation arrays.

  8. Dynamics of Ranking Processes in Complex Systems

    Science.gov (United States)

    Blumm, Nicholas; Ghoshal, Gourab; Forró, Zalán; Schich, Maximilian; Bianconi, Ginestra; Bouchaud, Jean-Philippe; Barabási, Albert-László

    2012-09-01

    The world is addicted to ranking: everything, from the reputation of scientists, journals, and universities to purchasing decisions is driven by measured or perceived differences between them. Here, we analyze empirical data capturing real time ranking in a number of systems, helping to identify the universal characteristics of ranking dynamics. We develop a continuum theory that not only predicts the stability of the ranking process, but shows that a noise-induced phase transition is at the heart of the observed differences in ranking regimes. The key parameters of the continuum theory can be explicitly measured from data, allowing us to predict and experimentally document the existence of three phases that govern ranking stability.

  9. Error analysis of stochastic gradient descent ranking.

    Science.gov (United States)

    Chen, Hong; Tang, Yi; Li, Luoqing; Yuan, Yuan; Li, Xuelong; Tang, Yuanyan

    2013-06-01

    Ranking is always an important task in machine learning and information retrieval, e.g., collaborative filtering, recommender systems, drug discovery, etc. A kernel-based stochastic gradient descent algorithm with the least squares loss is proposed for ranking in this paper. The implementation of this algorithm is simple, and an expression of the solution is derived via a sampling operator and an integral operator. An explicit convergence rate for leaning a ranking function is given in terms of the suitable choices of the step size and the regularization parameter. The analysis technique used here is capacity independent and is novel in error analysis of ranking learning. Experimental results on real-world data have shown the effectiveness of the proposed algorithm in ranking tasks, which verifies the theoretical analysis in ranking error.

  10. Ranking in Swiss system chess team tournaments

    OpenAIRE

    Csató, László

    2015-01-01

    The paper uses paired comparison-based scoring procedures for ranking the participants of a Swiss system chess team tournament. We present the main challenges of ranking in Swiss system, the features of individual and team competitions as well as the failures of official lexicographical orders. The tournament is represented as a ranking problem, our model is discussed with respect to the properties of the score, generalized row sum and least squares methods. The proposed procedure is illustra...

  11. A universal rank-size law

    CERN Document Server

    Ausloos, Marcel

    2016-01-01

    A mere hyperbolic law, like the Zipf's law power function, is often inadequate to describe rank-size relationships. An alternative theoretical distribution is proposed based on theoretical physics arguments starting from the Yule-Simon distribution. A modeling is proposed leading to a universal form. A theoretical suggestion for the "best (or optimal) distribution", is provided through an entropy argument. The ranking of areas through the number of cities in various countries and some sport competition ranking serves for the present illustrations.

  12. Methodology for ranking restoration options

    Energy Technology Data Exchange (ETDEWEB)

    Hedemann Jensen, Per

    1999-04-01

    The work described in this report has been performed as a part of the RESTRAT Project FI4P-CT95-0021a (PL 950128) co-funded by the Nuclear Fission Safety Programme of the European Commission. The RESTRAT project has the overall objective of developing generic methodologies for ranking restoration techniques as a function of contamination and site characteristics. The project includes analyses of existing remediation methodologies and contaminated sites, and is structured in the following steps: characterisation of relevant contaminated sites; identification and characterisation of relevant restoration techniques; assessment of the radiological impact; development and application of a selection methodology for restoration options; formulation of generic conclusions and development of a manual. The project is intended to apply to situations in which sites with nuclear installations have been contaminated with radioactive materials as a result of the operation of these installations. The areas considered for remedial measures include contaminated land areas, rivers and sediments in rivers, lakes, and sea areas. Five contaminated European sites have been studied. Various remedial measures have been envisaged with respect to the optimisation of the protection of the populations being exposed to the radionuclides at the sites. Cost-benefit analysis and multi-attribute utility analysis have been applied for optimisation. Health, economic and social attributes have been included and weighting factors for the different attributes have been determined by the use of scaling constants. (au)

  13. Ranking documents with a thesaurus.

    Science.gov (United States)

    Rada, R; Bicknell, E

    1989-09-01

    This article reports on exploratory experiments in evaluating and improving a thesaurus through studying its effect on retrieval. A formula called DISTANCE was developed to measure the conceptual distance between queries and documents encoded as sets of thesaurus terms. DISTANCE references MeSH (Medical Subject Headings) and assesses the degree of match between a MeSH-encoded query and document. The performance of DISTANCE on MeSH is compared to the performance of people in the assessment of conceptual distance between queries and documents, and is found to simulate with surprising accuracy the human performance. The power of the computer simulation stems both from the tendency of people to rely heavily on broader-than (BT) relations in making decisions about conceptual distance and from the thousands of accurate BT relations in MeSH. One source for discrepancy between the algorithms' measurement of closeness between query and document and people's measurement of closeness between query and document is occasional inconsistency in the BT relations. Our experiments with adding non-BT relations to MeSH showed how these non-BT non-BT relations to MeSH showed how these non-BT relations could improve document ranking, if DISTANCE were also appropriately revised to treat these relations differently from BT relations.

  14. SNP-based pathway enrichment analysis for genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Potkin Steven G

    2011-04-01

    Full Text Available Abstract Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs, have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1 for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2 ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one

  15. Communities in Large Networks: Identification and Ranking

    DEFF Research Database (Denmark)

    Olsen, Martin

    2008-01-01

    We study the problem of identifying and ranking the members of a community in a very large network with link analysis only, given a set of representatives of the community. We define the concept of a community justified by a formal analysis of a simple model of the evolution of a directed graph. ...... and its immediate surroundings. The members are ranked with a “local” variant of the PageRank algorithm. Results are reported from successful experiments on identifying and ranking Danish Computer Science sites and Danish Chess pages using only a few representatives....

  16. Citation graph based ranking in Invenio

    CERN Document Server

    Marian, Ludmila; Rajman, Martin; Vesely, Martin

    2010-01-01

    Invenio is the web-based integrated digital library system developed at CERN. Within this framework, we present four types of ranking models based on the citation graph that complement the simple approach based on citation counts: time-dependent citation counts, a relevancy ranking which extends the PageRank model, a time-dependent ranking which combines the freshness of citations with PageRank and a ranking that takes into consideration the external citations. We present our analysis and results obtained on two main data sets: Inspire and CERN Document Server. Our main contributions are: (i) a study of the currently available ranking methods based on the citation graph; (ii) the development of new ranking methods that correct some of the identified limitations of the current methods such as treating all citations of equal importance, not taking time into account or considering the citation graph complete; (iii) a detailed study of the key parameters for these ranking methods. (The original publication is ava...

  17. snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

    Science.gov (United States)

    Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

    2012-01-01

    The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

  18. HiSeeker: Detecting High-Order SNP Interactions Based on Pairwise SNP Combinations

    Directory of Open Access Journals (Sweden)

    Jie Liu

    2017-05-01

    Full Text Available Detecting single nucleotide polymorphisms’ (SNPs interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space. In this paper, we proposed a flexible two-stage approach (called HiSeeker to detect high-order interactions. In the screening stage, HiSeeker employs the chi-squared test and logistic regression model to efficiently obtain candidate pairwise combinations, which have intermediate or significant associations with the phenotype for interaction detection. In the search stage, two different strategies (exhaustive search and ant colony optimization-based search are utilized to detect high-order interactions from candidate combinations. The experimental results on simulated datasets demonstrate that HiSeeker can more efficiently and effectively detect high-order interactions than related representative algorithms. On two real case-control datasets, HiSeeker also detects several significant high-order interactions, whose individual SNPs and pairwise interactions have no strong main effects or pairwise interaction effects, and these high-order interactions can hardly be identified by related algorithms.

  19. Single nucleotide polymorphism (SNP) detection on a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Dufva, Martin

    2013-01-01

    We present a magnetoresistive sensor platform for hybridization assays and demonstrate its applicability on single nucleotide polymorphism (SNP) genotyping. The sensor relies on anisotropic magnetoresistance in a new geometry with a local negative reference and uses the magnetic field from the se...... for external electromagnets and thus allows for miniaturization of the sensor platform....

  20. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and ...

  1. Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

    Directory of Open Access Journals (Sweden)

    Ling-Yun Wu

    2006-01-01

    Full Text Available The Minimum Error Correction (MEC is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expected. We first prove the MCIH problem to be NP-hard. To evaluate the practicality of the new model we design an exact algorithm (a dynamic programming procedure to implement MCIH on a special data structure. The numerical experience indicates that it is fairly effective to use MCIH at the cost of related genotype information, especially in the case of SNP fragments with a high error rate. Moreover, we present a feed-forward neural network algorithm to solve MCIH for general data structure and large size instances. Numerical results on real biological data and simulation data show that the algorithm works well and MCIH is a potential alternative in individual haplotyping.

  2. Genomic scans for selective sweeps using SNP data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob

    2005-01-01

    of the selection coefficient. To illustrate the method, we apply our approach to data from the Seattle SNP project and to Chromosome 2 data from the HapMap project. In Chromosome 2, the most extreme signal is found in the lactase gene, which previously has been shown to be undergoing positive selection. Evidence...

  3. SNP Discovery and Linkage Map Construction in Cultivated Tomato

    Science.gov (United States)

    Shirasawa, Kenta; Isobe, Sachiko; Hirakawa, Hideki; Asamizu, Erika; Fukuoka, Hiroyuki; Just, Daniel; Rothan, Christophe; Sasamoto, Shigemi; Fujishiro, Tsunakazu; Kishida, Yoshie; Kohara, Mitsuyo; Tsuruoka, Hisano; Wada, Tsuyuko; Nakamura, Yasukazu; Sato, Shusei; Tabata, Satoshi

    2010-01-01

    Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/. PMID:21044984

  4. Identification of novel SNP in caprine β-lactoglobulin gene

    Indian Academy of Sciences (India)

    [Gharedaghi L., Moradi Shahrbabak H. and Sadeghi M. 2016 Identification of novel SNP in caprine β-lactoglobulin gene. J. Genet. 95, 485–490]. Introduction. Goat species are an important component of animal genetic resources that provide products and services required for humans worldwide. In developed countries ...

  5. Sodium nitroprusside (SNP) alleviates the oxidative stress induced ...

    African Journals Online (AJOL)

    Oxidative damage is often induced by abiotic stress, nitric oxide (NO) is considered as a functional molecule in modulating antioxidant metabolism of plants. In the present study, effects of sodium nitroprusside (SNP), a NO donor, on the phenotype, antioxidant capacity and chloroplast ultrastructure of cucumber leaves were ...

  6. Minimum conflict individual haplotyping from SNP fragments and related genotype.

    Science.gov (United States)

    Zhang, Xiang-Sun; Wang, Rui-Sheng; Wu, Ling-Yun; Zhang, Wei

    2007-02-16

    The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expected. We first prove the MCIH problem to be NP-hard. To evaluate the practicality of the new model we design an exact algorithm (a dynamic programming procedure) to implement MCIH on a special data structure. The numerical experience indicates that it is fairly effective to use MCIH at the cost of related genotype information, especially in the case of SNP fragments with a high error rate. Moreover, we present a feed-forward neural network algorithm to solve MCIH for general data structure and large size instances. Numerical results on real biological data and simulation data show that the algorithm works well and MCIH is a potential alternative in individual haplotyping.

  7. (SNP) assay for population stratification test between eastern Asians ...

    African Journals Online (AJOL)

    Yomi

    2012-01-03

    Jan 3, 2012 ... al., 2008), pharmacogenetics (Falzoi et al., 2010; Dorey,. 2001), and human papilloma viruses examination. (Soderlund-Strand et al., 2008). The Sequenom Mass-. ARRAY platform has several attractive features for users desiring an accurate custom SNP genotyping assay with modest multiplexing and ...

  8. Ranked Conservation Opportunity Areas for Region 7 (ECO_RES.RANKED_OAS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The RANKED_OAS are all the Conservation Opportunity Areas identified by MoRAP that have subsequently been ranked by patch size, landform representation, and the...

  9. Ranking scientific publications: the effect of nonlinearity.

    Science.gov (United States)

    Yao, Liyang; Wei, Tian; Zeng, An; Fan, Ying; Di, Zengru

    2014-10-17

    Ranking the significance of scientific publications is a long-standing challenge. The network-based analysis is a natural and common approach for evaluating the scientific credit of papers. Although the number of citations has been widely used as a metric to rank papers, recently some iterative processes such as the well-known PageRank algorithm have been applied to the citation networks to address this problem. In this paper, we introduce nonlinearity to the PageRank algorithm when aggregating resources from different nodes to further enhance the effect of important papers. The validation of our method is performed on the data of American Physical Society (APS) journals. The results indicate that the nonlinearity improves the performance of the PageRank algorithm in terms of ranking effectiveness, as well as robustness against malicious manipulations. Although the nonlinearity analysis is based on the PageRank algorithm, it can be easily extended to other iterative ranking algorithms and similar improvements are expected.

  10. Ranking scientific publications: the effect of nonlinearity

    Science.gov (United States)

    Yao, Liyang; Wei, Tian; Zeng, An; Fan, Ying; di, Zengru

    2014-10-01

    Ranking the significance of scientific publications is a long-standing challenge. The network-based analysis is a natural and common approach for evaluating the scientific credit of papers. Although the number of citations has been widely used as a metric to rank papers, recently some iterative processes such as the well-known PageRank algorithm have been applied to the citation networks to address this problem. In this paper, we introduce nonlinearity to the PageRank algorithm when aggregating resources from different nodes to further enhance the effect of important papers. The validation of our method is performed on the data of American Physical Society (APS) journals. The results indicate that the nonlinearity improves the performance of the PageRank algorithm in terms of ranking effectiveness, as well as robustness against malicious manipulations. Although the nonlinearity analysis is based on the PageRank algorithm, it can be easily extended to other iterative ranking algorithms and similar improvements are expected.

  11. Entity Ranking using Wikipedia as a Pivot

    NARCIS (Netherlands)

    R. Kaptein; P. Serdyukov; A.P. de Vries (Arjen); J. Kamps

    2010-01-01

    htmlabstractIn this paper we investigate the task of Entity Ranking on the Web. Searchers looking for entities are arguably better served by presenting a ranked list of entities directly, rather than a list of web pages with relevant but also potentially redundant information about

  12. Entity ranking using Wikipedia as a pivot

    NARCIS (Netherlands)

    Kaptein, R.; Serdyukov, P.; de Vries, A.; Kamps, J.; Huang, X.J.; Jones, G.; Koudas, N.; Wu, X.; Collins-Thompson, K.

    2010-01-01

    In this paper we investigate the task of Entity Ranking on the Web. Searchers looking for entities are arguably better served by presenting a ranked list of entities directly, rather than a list of web pages with relevant but also potentially redundant information about these entities. Since

  13. Biplots in Reduced-Rank Regression

    NARCIS (Netherlands)

    Braak, ter C.J.F.; Looman, C.W.N.

    1994-01-01

    Regression problems with a number of related response variables are typically analyzed by separate multiple regressions. This paper shows how these regressions can be visualized jointly in a biplot based on reduced-rank regression. Reduced-rank regression combines multiple regression and principal

  14. Mining Feedback in Ranking and Recommendation Systems

    Science.gov (United States)

    Zhuang, Ziming

    2009-01-01

    The amount of online information has grown exponentially over the past few decades, and users become more and more dependent on ranking and recommendation systems to address their information seeking needs. The advance in information technologies has enabled users to provide feedback on the utilities of the underlying ranking and recommendation…

  15. Using centrality to rank web snippets

    NARCIS (Netherlands)

    Jijkoun, V.; de Rijke, M.; Peters, C.; Jijkoun, V.; Mandl, T.; Müller, H.; Oard, D.W.; Peñas, A.; Petras, V.; Santos, D.

    2008-01-01

    We describe our participation in the WebCLEF 2007 task, targeted at snippet retrieval from web data. Our system ranks snippets based on a simple similarity-based centrality, inspired by the web page ranking algorithms. We experimented with retrieval units (sentences and paragraphs) and with the

  16. Generating and ranking of Dyck words

    CERN Document Server

    Kasa, Zoltan

    2010-01-01

    A new algorithm to generate all Dyck words is presented, which is used in ranking and unranking Dyck words. We emphasize the importance of using Dyck words in encoding objects related to Catalan numbers. As a consequence of formulas used in the ranking algorithm we can obtain a recursive formula for the nth Catalan number.

  17. University ranking methodologies. An interview with Ben Sowter about the Quacquarelli Symonds World University Ranking

    OpenAIRE

    Alberto Baccini; Antono Banfi; Giuseppe De Nicolao; Paola Galimberti

    2015-01-01

    University rankings represent a controversial issue in the debate about higher education policy. One of the best known university ranking is the Quacquarelli Symonds World University Rankings (QS), published annually since 2004 by Quacquarelli Symonds ltd, a company founded in 1990 and headquartered in London. QS provides a ranking based on a score calculated by weighting six different indicators. The 2015 edition, published in October 2015, introduced major methodological innovations and, as...

  18. SNP selection and classification of genome-wide SNP data using stratified sampling random forests.

    Science.gov (United States)

    Wu, Qingyao; Ye, Yunming; Liu, Yang; Ng, Michael K

    2012-09-01

    For high dimensional genome-wide association (GWA) case-control data of complex disease, there are usually a large portion of single-nucleotide polymorphisms (SNPs) that are irrelevant with the disease. A simple random sampling method in random forest using default mtry parameter to choose feature subspace, will select too many subspaces without informative SNPs. Exhaustive searching an optimal mtry is often required in order to include useful and relevant SNPs and get rid of vast of non-informative SNPs. However, it is too time-consuming and not favorable in GWA for high-dimensional data. The main aim of this paper is to propose a stratified sampling method for feature subspace selection to generate decision trees in a random forest for GWA high-dimensional data. Our idea is to design an equal-width discretization scheme for informativeness to divide SNPs into multiple groups. In feature subspace selection, we randomly select the same number of SNPs from each group and combine them to form a subspace to generate a decision tree. The advantage of this stratified sampling procedure can make sure each subspace contains enough useful SNPs, but can avoid a very high computational cost of exhaustive search of an optimal mtry, and maintain the randomness of a random forest. We employ two genome-wide SNP data sets (Parkinson case-control data comprised of 408 803 SNPs and Alzheimer case-control data comprised of 380 157 SNPs) to demonstrate that the proposed stratified sampling method is effective, and it can generate better random forest with higher accuracy and lower error bound than those by Breiman's random forest generation method. For Parkinson data, we also show some interesting genes identified by the method, which may be associated with neurological disorders for further biological investigations.

  19. Universal emergence of PageRank

    Energy Technology Data Exchange (ETDEWEB)

    Frahm, K M; Georgeot, B; Shepelyansky, D L, E-mail: frahm@irsamc.ups-tlse.fr, E-mail: georgeot@irsamc.ups-tlse.fr, E-mail: dima@irsamc.ups-tlse.fr [Laboratoire de Physique Theorique du CNRS, IRSAMC, Universite de Toulouse, UPS, 31062 Toulouse (France)

    2011-11-18

    The PageRank algorithm enables us to rank the nodes of a network through a specific eigenvector of the Google matrix, using a damping parameter {alpha} Element-Of ]0, 1[. Using extensive numerical simulations of large web networks, with a special accent on British University networks, we determine numerically and analytically the universal features of the PageRank vector at its emergence when {alpha} {yields} 1. The whole network can be divided into a core part and a group of invariant subspaces. For {alpha} {yields} 1, PageRank converges to a universal power-law distribution on the invariant subspaces whose size distribution also follows a universal power law. The convergence of PageRank at {alpha} {yields} 1 is controlled by eigenvalues of the core part of the Google matrix, which are extremely close to unity, leading to large relaxation times as, for example, in spin glasses. (paper)

  20. Comparing classical and quantum PageRanks

    Science.gov (United States)

    Loke, T.; Tang, J. W.; Rodriguez, J.; Small, M.; Wang, J. B.

    2017-01-01

    Following recent developments in quantum PageRanking, we present a comparative analysis of discrete-time and continuous-time quantum-walk-based PageRank algorithms. Relative to classical PageRank and to different extents, the quantum measures better highlight secondary hubs and resolve ranking degeneracy among peripheral nodes for all networks we studied in this paper. For the discrete-time case, we investigated the periodic nature of the walker's probability distribution for a wide range of networks and found that the dominant period does not grow with the size of these networks. Based on this observation, we introduce a new quantum measure using the maximum probabilities of the associated walker during the first couple of periods. This is particularly important, since it leads to a quantum PageRanking scheme that is scalable with respect to network size.

  1. Reliability of journal impact factor rankings

    Science.gov (United States)

    Greenwood, Darren C

    2007-01-01

    Background Journal impact factors and their ranks are used widely by journals, researchers, and research assessment exercises. Methods Based on citations to journals in research and experimental medicine in 2005, Bayesian Markov chain Monte Carlo methods were used to estimate the uncertainty associated with these journal performance indicators. Results Intervals representing plausible ranges of values for journal impact factor ranks indicated that most journals cannot be ranked with great precision. Only the top and bottom few journals could place any confidence in their rank position. Intervals were wider and overlapping for most journals. Conclusion Decisions placed on journal impact factors are potentially misleading where the uncertainty associated with the measure is ignored. This article proposes that caution should be exercised in the interpretation of journal impact factors and their ranks, and specifically that a measure of uncertainty should be routinely presented alongside the point estimate. PMID:18005435

  2. Reliability of journal impact factor rankings

    Directory of Open Access Journals (Sweden)

    Greenwood Darren C

    2007-11-01

    Full Text Available Abstract Background Journal impact factors and their ranks are used widely by journals, researchers, and research assessment exercises. Methods Based on citations to journals in research and experimental medicine in 2005, Bayesian Markov chain Monte Carlo methods were used to estimate the uncertainty associated with these journal performance indicators. Results Intervals representing plausible ranges of values for journal impact factor ranks indicated that most journals cannot be ranked with great precision. Only the top and bottom few journals could place any confidence in their rank position. Intervals were wider and overlapping for most journals. Conclusion Decisions placed on journal impact factors are potentially misleading where the uncertainty associated with the measure is ignored. This article proposes that caution should be exercised in the interpretation of journal impact factors and their ranks, and specifically that a measure of uncertainty should be routinely presented alongside the point estimate.

  3. Cointegration rank testing under conditional heteroskedasticity

    DEFF Research Database (Denmark)

    Cavaliere, Giuseppe; Rahbek, Anders Christian; Taylor, Robert M.

    2010-01-01

    (martingale difference) innovations. We first demonstrate that the limiting null distributions of the rank statistics coincide with those derived by previous authors who assume either independent and identically distributed (i.i.d.) or (strict and covariance) stationary martingale difference innovations. We...... then propose wild bootstrap implementations of the cointegrating rank tests and demonstrate that the associated bootstrap rank statistics replicate the first-order asymptotic null distributions of the rank statistics. We show that the same is also true of the corresponding rank tests based on the i.......i.d. bootstrap of Swensen (2006, Econometrica 74, 1699-1714). The wild bootstrap, however, has the important property that, unlike the i.i.d. bootstrap, it preserves in the resampled data the pattern of heteroskedasticity present in the original shocks. Consistent with this, numerical evidence suggests that...

  4. Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Pootakham, Wirulda; Shearman, Jeremy R; Ruang-Areerate, Panthita; Sonthirod, Chutima; Sangsrakru, Duangjai; Jomchai, Nukoon; Yoocha, Thippawan; Triwitayakorn, Kanokporn; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2014-01-01

    Cassava (Manihot esculenta Crantz) is one of the most important crop species being the main source of dietary energy in several countries. Marker-assisted selection has become an essential tool in plant breeding. Single nucleotide polymorphism (SNP) discovery via transcriptome sequencing is an attractive strategy for genome complexity reduction in organisms with large genomes. We sequenced the transcriptome of 16 cassava accessions using the Illumina HiSeq platform and identified 675,559 EST-derived SNP markers. A subset of those markers was subsequently genotyped by capture-based targeted enrichment sequencing in 100 F1 progeny segregating for starch viscosity phenotypes. A total of 2,110 non-redundant SNP markers were used to construct a genetic map. This map encompasses 1,785 cM and consists of 19 linkage groups. A major quantitative trait locus (QTL) controlling starch pasting properties was identified and shown to coincide with the QTL previously reported for this trait. With a high-density SNP-based linkage map presented here, we also uncovered a novel QTL associated with starch pasting time on LG 10.

  5. PageRank and rank-reversal dependence on the damping factor

    Science.gov (United States)

    Son, S.-W.; Christensen, C.; Grassberger, P.; Paczuski, M.

    2012-12-01

    PageRank (PR) is an algorithm originally developed by Google to evaluate the importance of web pages. Considering how deeply rooted Google's PR algorithm is to gathering relevant information or to the success of modern businesses, the question of rank stability and choice of the damping factor (a parameter in the algorithm) is clearly important. We investigate PR as a function of the damping factor d on a network obtained from a domain of the World Wide Web, finding that rank reversal happens frequently over a broad range of PR (and of d). We use three different correlation measures, Pearson, Spearman, and Kendall, to study rank reversal as d changes, and we show that the correlation of PR vectors drops rapidly as d changes from its frequently cited value, d0=0.85. Rank reversal is also observed by measuring the Spearman and Kendall rank correlation, which evaluate relative ranks rather than absolute PR. Rank reversal happens not only in directed networks containing rank sinks but also in a single strongly connected component, which by definition does not contain any sinks. We relate rank reversals to rank pockets and bottlenecks in the directed network structure. For the network studied, the relative rank is more stable by our measures around d=0.65 than at d=d0.

  6. PageRank and rank-reversal dependence on the damping factor.

    Science.gov (United States)

    Son, S-W; Christensen, C; Grassberger, P; Paczuski, M

    2012-12-01

    PageRank (PR) is an algorithm originally developed by Google to evaluate the importance of web pages. Considering how deeply rooted Google's PR algorithm is to gathering relevant information or to the success of modern businesses, the question of rank stability and choice of the damping factor (a parameter in the algorithm) is clearly important. We investigate PR as a function of the damping factor d on a network obtained from a domain of the World Wide Web, finding that rank reversal happens frequently over a broad range of PR (and of d). We use three different correlation measures, Pearson, Spearman, and Kendall, to study rank reversal as d changes, and we show that the correlation of PR vectors drops rapidly as d changes from its frequently cited value, d_{0}=0.85. Rank reversal is also observed by measuring the Spearman and Kendall rank correlation, which evaluate relative ranks rather than absolute PR. Rank reversal happens not only in directed networks containing rank sinks but also in a single strongly connected component, which by definition does not contain any sinks. We relate rank reversals to rank pockets and bottlenecks in the directed network structure. For the network studied, the relative rank is more stable by our measures around d=0.65 than at d=d_{0}.

  7. A tilting approach to ranking influence

    KAUST Repository

    Genton, Marc G.

    2014-12-01

    We suggest a new approach, which is applicable for general statistics computed from random samples of univariate or vector-valued or functional data, to assessing the influence that individual data have on the value of a statistic, and to ranking the data in terms of that influence. Our method is based on, first, perturbing the value of the statistic by ‘tilting’, or reweighting, each data value, where the total amount of tilt is constrained to be the least possible, subject to achieving a given small perturbation of the statistic, and, then, taking the ranking of the influence of data values to be that which corresponds to ranking the changes in data weights. It is shown, both theoretically and numerically, that this ranking does not depend on the size of the perturbation, provided that the perturbation is sufficiently small. That simple result leads directly to an elegant geometric interpretation of the ranks; they are the ranks of the lengths of projections of the weights onto a ‘line’ determined by the first empirical principal component function in a generalized measure of covariance. To illustrate the generality of the method we introduce and explore it in the case of functional data, where (for example) it leads to generalized boxplots. The method has the advantage of providing an interpretable ranking that depends on the statistic under consideration. For example, the ranking of data, in terms of their influence on the value of a statistic, is different for a measure of location and for a measure of scale. This is as it should be; a ranking of data in terms of their influence should depend on the manner in which the data are used. Additionally, the ranking recognizes, rather than ignores, sign, and in particular can identify left- and right-hand ‘tails’ of the distribution of a random function or vector.

  8. Data mining of public SNP databases for the selection of intragenic SNPs

    NARCIS (Netherlands)

    Aerts, J.; Wetzels, Y.; Cohen, N.; Aerssens, J.

    2002-01-01

    Different strategies to search public single nucleotide polymorphism (SNP) databases for intragenic SNPs were evaluated. First, we assembled a strategy to annotate SNPs onto candidate genes based on a BLAST search of public SNP databases (Intragenic SNP Annotation by BLAST, ISAB). Only BLAST hits

  9. University ranking methodologies. An interview with Ben Sowter about the Quacquarelli Symonds World University Ranking

    Directory of Open Access Journals (Sweden)

    Alberto Baccini

    2015-10-01

    Full Text Available University rankings represent a controversial issue in the debate about higher education policy. One of the best known university ranking is the Quacquarelli Symonds World University Rankings (QS, published annually since 2004 by Quacquarelli Symonds ltd, a company founded in 1990 and headquartered in London. QS provides a ranking based on a score calculated by weighting six different indicators. The 2015 edition, published in October 2015, introduced major methodological innovations and, as a consequence, many universities worldwide underwent major changes of their scores and ranks. Ben Sowter, head of division of intelligence unit of Quacquarelli Symonds, responds to 15 questions about the new QS methodology.

  10. On a common generalization of Shelah's 2-rank, dp-rank, and o-minimal dimension

    OpenAIRE

    Guingona, Vincent; Hill, Cameron Donnay

    2013-01-01

    In this paper, we build a dimension theory related to Shelah's 2-rank, dp-rank, and o-minimal dimension. We call this dimension op-dimension. We exhibit the notion of the n-multi-order property, generalizing the order property, and use this to create op-rank, which generalizes 2-rank. From this we build op-dimension. We show that op-dimension bounds dp-rank, that op-dimension is sub-additive, and op-dimension generalizes o-minimal dimension in o-minimal theories.

  11. Academic rankings: an approach to rank portuguese universities Rankings académicos: un abordaje para clasificar las universidades portuguesas Rankings acadêmicos: uma abordagem ao ranking das universidades portuguesas

    Directory of Open Access Journals (Sweden)

    Pedro Bernardino

    2010-03-01

    Full Text Available The academic rankings are a controversial subject in higher education. However, despite all the criticism, academic rankings are here to stay and more and more different stakeholders use rankings to obtain information about the institutions' performance. The two most well-known rankings, The Times and the Shanghai Jiao Tong University rankings have different methodologies. The Times ranking is based on peer review, whereas the Shanghai ranking has only quantitative indicators and is mainly based on research outputs. In Germany, the CHE ranking uses a different methodology from the traditional rankings, allowing the users to choose criteria and weights. The Portuguese higher education institutions are performing below their European peers, and the Government believes that an academic ranking could improve both performance and competitiveness between institutions. The purpose of this paper is to analyse the advantages and problems of academic rankings and provide guidance to a new Portuguese ranking.Los rankings académicos son un tema muy contradictorio en la enseñanza superior. Todavía, además de todas las críticas los rankings están para quedarse entre nosotros. Y cada vez más, diferentes stakeholders utilizan los rankings para obtener información sobre el desempeño de las instituciones. Dos de los rankings más conocidos, el The Times y el ranking de la universidad de Shangai Jiao Tong tienen métodos distintos. El The Times se basa en la opinión de expertos mientras el ranking de la universidad de Shangai presenta solamente indicadores cuantitativos y mayoritariamente basados en los resultados de actividades de investigación. En Alemania el ranking CHE usa un método distinto permitiendo al utilizador elegir los criterios y su importancia. Las instituciones de enseñanza superior portuguesas tienen un desempeño abajo de las europeas y el gobierno cree que un ranking académico podría contribuir para mejorar su desempeño y

  12. Adiabatic quantum algorithm for search engine ranking.

    Science.gov (United States)

    Garnerone, Silvano; Zanardi, Paolo; Lidar, Daniel A

    2012-06-08

    We propose an adiabatic quantum algorithm for generating a quantum pure state encoding of the PageRank vector, the most widely used tool in ranking the relative importance of internet pages. We present extensive numerical simulations which provide evidence that this algorithm can prepare the quantum PageRank state in a time which, on average, scales polylogarithmically in the number of web pages. We argue that the main topological feature of the underlying web graph allowing for such a scaling is the out-degree distribution. The top-ranked log(n) entries of the quantum PageRank state can then be estimated with a polynomial quantum speed-up. Moreover, the quantum PageRank state can be used in "q-sampling" protocols for testing properties of distributions, which require exponentially fewer measurements than all classical schemes designed for the same task. This can be used to decide whether to run a classical update of the PageRank.

  13. Ranking Adverse Drug Reactions With Crowdsourcing

    KAUST Repository

    Gottlieb, Assaf

    2015-03-23

    Background: There is no publicly available resource that provides the relative severity of adverse drug reactions (ADRs). Such a resource would be useful for several applications, including assessment of the risks and benefits of drugs and improvement of patient-centered care. It could also be used to triage predictions of drug adverse events. Objective: The intent of the study was to rank ADRs according to severity. Methods: We used Internet-based crowdsourcing to rank ADRs according to severity. We assigned 126,512 pairwise comparisons of ADRs to 2589 Amazon Mechanical Turk workers and used these comparisons to rank order 2929 ADRs. Results: There is good correlation (rho=.53) between the mortality rates associated with ADRs and their rank. Our ranking highlights severe drug-ADR predictions, such as cardiovascular ADRs for raloxifene and celecoxib. It also triages genes associated with severe ADRs such as epidermal growth-factor receptor (EGFR), associated with glioblastoma multiforme, and SCN1A, associated with epilepsy. Conclusions: ADR ranking lays a first stepping stone in personalized drug risk assessment. Ranking of ADRs using crowdsourcing may have useful clinical and financial implications, and should be further investigated in the context of health care decision making.

  14. Adiabatic Quantum Algorithm for Search Engine Ranking

    Science.gov (United States)

    Garnerone, Silvano; Zanardi, Paolo; Lidar, Daniel A.

    2012-06-01

    We propose an adiabatic quantum algorithm for generating a quantum pure state encoding of the PageRank vector, the most widely used tool in ranking the relative importance of internet pages. We present extensive numerical simulations which provide evidence that this algorithm can prepare the quantum PageRank state in a time which, on average, scales polylogarithmically in the number of web pages. We argue that the main topological feature of the underlying web graph allowing for such a scaling is the out-degree distribution. The top-ranked log⁡(n) entries of the quantum PageRank state can then be estimated with a polynomial quantum speed-up. Moreover, the quantum PageRank state can be used in “q-sampling” protocols for testing properties of distributions, which require exponentially fewer measurements than all classical schemes designed for the same task. This can be used to decide whether to run a classical update of the PageRank.

  15. Ranking adverse drug reactions with crowdsourcing.

    Science.gov (United States)

    Gottlieb, Assaf; Hoehndorf, Robert; Dumontier, Michel; Altman, Russ B

    2015-03-23

    There is no publicly available resource that provides the relative severity of adverse drug reactions (ADRs). Such a resource would be useful for several applications, including assessment of the risks and benefits of drugs and improvement of patient-centered care. It could also be used to triage predictions of drug adverse events. The intent of the study was to rank ADRs according to severity. We used Internet-based crowdsourcing to rank ADRs according to severity. We assigned 126,512 pairwise comparisons of ADRs to 2589 Amazon Mechanical Turk workers and used these comparisons to rank order 2929 ADRs. There is good correlation (rho=.53) between the mortality rates associated with ADRs and their rank. Our ranking highlights severe drug-ADR predictions, such as cardiovascular ADRs for raloxifene and celecoxib. It also triages genes associated with severe ADRs such as epidermal growth-factor receptor (EGFR), associated with glioblastoma multiforme, and SCN1A, associated with epilepsy. ADR ranking lays a first stepping stone in personalized drug risk assessment. Ranking of ADRs using crowdsourcing may have useful clinical and financial implications, and should be further investigated in the context of health care decision making.

  16. Augmenting the Deliberative Method for Ranking Risks.

    Science.gov (United States)

    Susel, Irving; Lasley, Trace; Montezemolo, Mark; Piper, Joel

    2016-01-01

    The Department of Homeland Security (DHS) characterized and prioritized the physical cross-border threats and hazards to the nation stemming from terrorism, market-driven illicit flows of people and goods (illegal immigration, narcotics, funds, counterfeits, and weaponry), and other nonmarket concerns (movement of diseases, pests, and invasive species). These threats and hazards pose a wide diversity of consequences with very different combinations of magnitudes and likelihoods, making it very challenging to prioritize them. This article presents the approach that was used at DHS to arrive at a consensus regarding the threats and hazards that stand out from the rest based on the overall risk they pose. Due to time constraints for the decision analysis, it was not feasible to apply multiattribute methodologies like multiattribute utility theory or the analytic hierarchy process. Using a holistic approach was considered, such as the deliberative method for ranking risks first published in this journal. However, an ordinal ranking alone does not indicate relative or absolute magnitude differences among the risks. Therefore, the use of the deliberative method for ranking risks is not sufficient for deciding whether there is a material difference between the top-ranked and bottom-ranked risks, let alone deciding what the stand-out risks are. To address this limitation of ordinal rankings, the deliberative method for ranking risks was augmented by adding an additional step to transform the ordinal ranking into a ratio scale ranking. This additional step enabled the selection of stand-out risks to help prioritize further analysis. © 2015 Society for Risk Analysis.

  17. Evaluation of treatment effects by ranking

    DEFF Research Database (Denmark)

    Halekoh, U; Kristensen, K

    2008-01-01

    In crop experiments measurements are often made by a judge evaluating the crops' conditions after treatment. In the present paper an analysis is proposed for experiments where plots of crops treated differently are mutually ranked. In the experimental layout the crops are treated on consecutive...... plots usually placed side by side in one or more rows. In the proposed method a judge ranks several neighbouring plots, say three, by ranking them from best to worst. For the next observation the judge moves on by no more than two plots, such that up to two plots will be re-evaluated again...

  18. SNP interaction detection with Random Forests in high-dimensional genetic data.

    Science.gov (United States)

    Winham, Stacey J; Colby, Colin L; Freimuth, Robert R; Wang, Xin; de Andrade, Mariza; Huebner, Marianne; Biernacka, Joanna M

    2012-07-15

    Identifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF) are a popular data-mining technique that can accommodate a large number of predictor variables and allow for complex models with interactions. RF analysis produces measures of variable importance that can be used to rank the predictor variables. Thus, single nucleotide polymorphism (SNP) analysis using RFs is gaining popularity as a potential filter approach that considers interactions in high-dimensional data. However, the impact of data dimensionality on the power of RF to identify interactions has not been thoroughly explored. We investigate the ability of rankings from variable importance measures to detect gene-gene interaction effects and their potential effectiveness as filters compared to p-values from univariate logistic regression, particularly as the data becomes increasingly high-dimensional. RF effectively identifies interactions in low dimensional data. As the total number of predictor variables increases, probability of detection declines more rapidly for interacting SNPs than for non-interacting SNPs, indicating that in high-dimensional data the RF variable importance measures are capturing marginal effects rather than capturing the effects of interactions. While RF remains a promising data-mining technique that extends univariate methods to condition on multiple variables simultaneously, RF variable importance measures fail to detect interaction effects in high-dimensional data in the absence of a strong marginal component, and therefore may not be useful as a filter technique that allows for interaction effects in genome-wide data.

  19. A novel TCF7L2 type 2 diabetes SNP identified from fine mapping in African American women.

    Directory of Open Access Journals (Sweden)

    Stephen A Haddad

    Full Text Available SNP rs7903146 in the Wnt pathway's TCF7L2 gene is the variant most significantly associated with type 2 diabetes to date, with associations observed across diverse populations. We sought to determine whether variants in other Wnt pathway genes are also associated with this disease. We evaluated 69 genes involved in the Wnt pathway, including TCF7L2, for associations with type 2 diabetes in 2632 African American cases and 2596 controls from the Black Women's Health Study. Tag SNPs for each gene region were genotyped on a custom Affymetrix Axiom Array, and imputation was performed to 1000 Genomes Phase 3 data. Gene-based analyses were conducted using the adaptive rank truncated product (ARTP statistic. The PSMD2 gene was significantly associated with type 2 diabetes after correction for multiple testing (corrected p = 0.016, based on the nine most significant single variants in the +/- 20 kb region surrounding the gene, which includes nearby genes EIF4G1, ECE2, and EIF2B5. Association data on four of the nine variants were available from an independent sample of 8284 African American cases and 15,543 controls; associations were in the same direction, but weak and not statistically significant. TCF7L2 was the only other gene associated with type 2 diabetes at nominal p <0.01 in our data. One of the three variants in the best gene-based model for TCF7L2, rs114770437, was not correlated with the GWAS index SNP rs7903146 and may represent an independent association signal seen only in African ancestry populations. Data on this SNP were not available in the replication sample.

  20. SNP (-617C>A in ARE-like loci of the NRF2 gene: a new biomarker for prognosis of lung adenocarcinoma in Japanese non-smoking women.

    Directory of Open Access Journals (Sweden)

    Yasuko Okano

    Full Text Available The transcription factor NRF2 plays a pivotal role in protecting normal cells from external toxic challenges and oxidative stress, whereas it can also endow cancer cells resistance to anticancer drugs. At present little information is available about the genetic polymorphisms of the NRF2 gene and their clinical relevance. We aimed to investigate the single nucleotide polymorphisms in the NRF2 gene as a prognostic biomarker in lung cancer.We prepared genomic DNA samples from 387 Japanese patients with primary lung cancer and detected SNP (c.-617C>A; rs6721961 in the ARE-like loci of the human NRF2 gene by the rapid genetic testing method we developed in this study. We then analyzed the association between the SNP in the NRF2 gene and patients' overall survival.Patients harboring wild-type (WT homozygous (c.-617C/C, SNP heterozygous (c.-617C/A, and SNP homozygous (c.-617A/A alleles numbered 216 (55.8%, 147 (38.0%, and 24 (6.2%, respectively. Multivariate logistic regression models revealed that SNP homozygote (c.-617A/A was significantly related to gender. Its frequency was four-fold higher in female patients than in males (10.8% female vs 2.7% male and was associated with female non-smokers with adenocarcinoma. Interestingly, lung cancer patients carrying NRF2 SNP homozygous alleles (c.-617A/A and the 309T (WT allele in the MDM2 gene exhibited remarkable survival over 1,700 days after surgical operation (log-rank p = 0.021.SNP homozygous (c.-617A/A alleles in the NRF2 gene are associated with female non-smokers with adenocarcinoma and regarded as a prognostic biomarker for assessing overall survival of patients with lung adenocarcinoma.

  1. SNP based heritability estimation using a Bayesian approach

    DEFF Research Database (Denmark)

    Krag, Kristian; Janss, Luc; Mahdi Shariati, Mohammad

    2013-01-01

    of 0.05, all models had difficulties in estimating the true heritability. The two Bayesian models were compared with a restricted maximum likelihood (REML) approach using a genomic relationship matrix. The comparison showed that the Bayesian approaches performed equally well as the REML approach......Heritability is a central element in quantitative genetics. New molecular markers to assess genetic variance and heritability are continually under development. The availability of molecular single nucleotide polymorphism (SNP) markers can be applied for estimation of variance components....... Differences in family structure were in general not found to influence the estimation of the heritability. For the sample sizes used in this study, a 10-fold increase of SNP density did not improve precision estimates compared with set-ups with a less dense distribution of SNPs. The methods used in this study...

  2. SNP genotyping using single-tube fluorescent bidirectional PCR.

    Science.gov (United States)

    Waterfall, Christy M; Cobb, Benjamin D

    2002-07-01

    SNP genotyping is a well-populatedfield with a large number of assay formats offering accurate allelic discrimination. However, there remains a discord between the ultimate goal of rapid, inexpensive assays that do not require complex design considerations and involved optimization strategies. We describe the first integration of bidirectional allele-specific amplification, SYBR Green I, and rapid-cycle PCR to provide a homogeneous SNP-typing assay. Wild-type, mutant, and heterozygous alleles were easily discriminated in a single tube using melt curve profiling of PCR products alone. We demonstrate the effectiveness and reliability of this assay with a blinded trial using clinical samples from individuals with sickle cell anemia, sickle cell trait, or unaffected individuals. The tests were completed in less than 30 min without expensive fluorogenic probes, prohibiting design rules, or lengthy downstream processing for product analysis.

  3. SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature.

    Science.gov (United States)

    Bokharaeian, Behrouz; Diaz, Alberto; Taghizadeh, Nasrin; Chitsaz, Hamidreza; Chavoshinejad, Ramyar

    2017-04-07

    Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpose of extracting mutations and diseases from texts. However, there is no available corpus, for extracting associations from texts, that is annotated with linguistic-based negation, modality markers, neutral candidates, and confidence level of associations. In this research, different steps were presented so as to produce the SNPPhenA corpus. They include automatic Named Entity Recognition (NER) followed by the manual annotation of SNP and phenotype names, annotation of the SNP-phenotype associations and their level of confidence, as well as modality markers. Moreover, the produced corpus was annotated with negation scopes and cues as well as neutral candidates that play crucial role as far as negation and the modality phenomenon in relation to extraction tasks. The agreement between annotators was measured by Cohen's Kappa coefficient where the resulting scores indicated the reliability of the corpus. The Kappa score was 0.79 for annotating the associations and 0.80 for the confidence degree of associations. Further presented were the basic statistics of the annotated features of the corpus in addition to the results of our first experiments related to the extraction of ranked SNP-Phenotype associations. The prepared guideline documents render the corpus more convenient and facile to use. The corpus, guidelines and inter-annotator agreement analysis are available on the website of the corpus: http://nil.fdi.ucm.es/?q=node/639 . Specifying the confidence degree of SNP-phenotype associations from articles helps identify the strength of associations that could in turn assist genomics scientists in determining phenotypic plasticity and the importance of environmental factors. What is more, our first experiments with the corpus show that linguistic-based confidence

  4. SNPdetector: a software tool for sensitive and accurate SNP detection.

    Directory of Open Access Journals (Sweden)

    Jinghui Zhang

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  5. SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection.

    Directory of Open Access Journals (Sweden)

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozgyosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  6. Robust demographic inference from genomic and SNP data.

    Directory of Open Access Journals (Sweden)

    Laurent Excoffier

    2013-10-01

    Full Text Available We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with ∂a∂i, the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.

  7. Gene-based SNP discovery and genetic mapping in pea.

    Science.gov (United States)

    Sindhu, Anoop; Ramsay, Larissa; Sanderson, Lacey-Anne; Stonehouse, Robert; Li, Rong; Condie, Janet; Shunmugam, Arun S K; Liu, Yong; Jha, Ambuj B; Diapari, Marwan; Burstin, Judith; Aubert, Gregoire; Tar'an, Bunyamin; Bett, Kirstin E; Warkentin, Thomas D; Sharpe, Andrew G

    2014-10-01

    Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.

  8. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

    KAUST Repository

    Coll, Francesc

    2014-09-01

    Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.

  9. A large-scale chromosome-specific SNP discovery guideline.

    Science.gov (United States)

    Akpinar, Bala Ani; Lucas, Stuart; Budak, Hikmet

    2017-01-01

    Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.

  10. Block models and personalized PageRank

    National Research Council Canada - National Science Library

    Kloumann, Isabel M; Ugander, Johan; Kleinberg, Jon

    2017-01-01

    ...? We start from the observation that the most widely used techniques for this problem, personalized PageRank and heat kernel methods, operate in the space of "landing probabilities" of a random walk...

  11. Who's bigger? where historical figures really rank

    CERN Document Server

    Skiena, Steven

    2014-01-01

    Is Hitler bigger than Napoleon? Washington bigger than Lincoln? Picasso bigger than Einstein? Quantitative analysts are rapidly finding homes in social and cultural domains, from finance to politics. What about history? In this fascinating book, Steve Skiena and Charles Ward bring quantitative analysis to bear on ranking and comparing historical reputations. They evaluate each person by aggregating the traces of millions of opinions, just as Google ranks webpages. The book includes a technical discussion for readers interested in the details of the methods, but no mathematical or computational background is necessary to understand the rankings or conclusions. Along the way, the authors present the rankings of more than one thousand of history's most significant people in science, politics, entertainment, and all areas of human endeavor. Anyone interested in history or biography can see where their favorite figures place in the grand scheme of things.

  12. Ranking Forestry Investments With Parametric Linear Programming

    Science.gov (United States)

    Paul A. Murphy

    1976-01-01

    Parametric linear programming is introduced as a technique for ranking forestry investments under multiple constraints; it combines the advantages of simple tanking and linear programming as capital budgeting tools.

  13. Superfund Hazard Ranking System Training Course

    Science.gov (United States)

    The Hazard Ranking System (HRS) training course is a four and ½ day, intermediate-level course designed for personnel who are required to compile, draft, and review preliminary assessments (PAs), site inspections (SIs), and HRS documentation records/packag

  14. A cognitive model for aggregating people's rankings

    National Research Council Canada - National Science Library

    Lee, Michael D; Steyvers, Mark; Miller, Brent

    2014-01-01

    .... Applications of the model to 23 data sets, dealing with general knowledge and prediction tasks, show that the model performs well in producing an aggregate ranking that is often close to the ground...

  15. Block models and personalized PageRank.

    Science.gov (United States)

    Kloumann, Isabel M; Ugander, Johan; Kleinberg, Jon

    2017-01-03

    Methods for ranking the importance of nodes in a network have a rich history in machine learning and across domains that analyze structured data. Recent work has evaluated these methods through the "seed set expansion problem": given a subset [Formula: see text] of nodes from a community of interest in an underlying graph, can we reliably identify the rest of the community? We start from the observation that the most widely used techniques for this problem, personalized PageRank and heat kernel methods, operate in the space of "landing probabilities" of a random walk rooted at the seed set, ranking nodes according to weighted sums of landing probabilities of different length walks. Both schemes, however, lack an a priori relationship to the seed set objective. In this work, we develop a principled framework for evaluating ranking methods by studying seed set expansion applied to the stochastic block model. We derive the optimal gradient for separating the landing probabilities of two classes in a stochastic block model and find, surprisingly, that under reasonable assumptions the gradient is asymptotically equivalent to personalized PageRank for a specific choice of the PageRank parameter [Formula: see text] that depends on the block model parameters. This connection provides a formal motivation for the success of personalized PageRank in seed set expansion and node ranking generally. We use this connection to propose more advanced techniques incorporating higher moments of landing probabilities; our advanced methods exhibit greatly improved performance, despite being simple linear classification rules, and are even competitive with belief propagation.

  16. Rank rigidity for CAT(0) cube complexes

    OpenAIRE

    Caprace, Pierre-Emmanuel; Sageev, Michah

    2010-01-01

    We prove that any group acting essentially without a fixed point at infinity on an irreducible finite-dimensional CAT(0) cube complex contains a rank one isometry. This implies that the Rank Rigidity Conjecture holds for CAT(0) cube complexes. We derive a number of other consequences for CAT(0) cube complexes, including a purely geometric proof of the Tits Alternative, an existence result for regular elements in (possibly non-uniform) lattices acting on cube complexes, and a characterization ...

  17. NUCLEAR POWER PLANTS SAFETY IMPROVEMENT PROJECTS RANKING

    OpenAIRE

    Григорян, Анна Сергеевна; Тигран Георгиевич ГРИГОРЯН; Квасневский, Евгений Анатольевич

    2013-01-01

    The ranking nuclear power plants safety improvement projects is the most important task for ensuring the efficiency of NPP project management office work. Total amount of projects in NPP portfolio may reach more than 400. Features of the nuclear power plants safety improvement projects ranking in NPP portfolio determine the choice of the decision verbal analysis as a method of decision-making, as it allows to quickly compare the number of alternatives that are not available at the time of con...

  18. Ranking Music Data by Relevance and Importance

    DEFF Research Database (Denmark)

    Ruxanda, Maria Magdalena; Nanopoulos, Alexandros; Jensen, Christian Søndergaard

    2008-01-01

    Due to the rapidly increasing availability of audio files on the Web, it is relevant to augment search engines with advanced audio search functionality. In this context, the ranking of the retrieved music is an important issue. This paper proposes a music ranking method capable of flexibly fusing...... the relevance and importance of music. The proposed method may support users with diverse needs when searching for music....

  19. Rank distributions: A panoramic macroscopic outlook

    Science.gov (United States)

    Eliazar, Iddo I.; Cohen, Morrel H.

    2014-01-01

    This paper presents a panoramic macroscopic outlook of rank distributions. We establish a general framework for the analysis of rank distributions, which classifies them into five macroscopic "socioeconomic" states: monarchy, oligarchy-feudalism, criticality, socialism-capitalism, and communism. Oligarchy-feudalism is shown to be characterized by discrete macroscopic rank distributions, and socialism-capitalism is shown to be characterized by continuous macroscopic size distributions. Criticality is a transition state between oligarchy-feudalism and socialism-capitalism, which can manifest allometric scaling with multifractal spectra. Monarchy and communism are extreme forms of oligarchy-feudalism and socialism-capitalism, respectively, in which the intrinsic randomness vanishes. The general framework is applied to three different models of rank distributions—top-down, bottom-up, and global—and unveils each model's macroscopic universality and versatility. The global model yields a macroscopic classification of the generalized Zipf law, an omnipresent form of rank distributions observed across the sciences. An amalgamation of the three models establishes a universal rank-distribution explanation for the macroscopic emergence of a prevalent class of continuous size distributions, ones governed by unimodal densities with both Pareto and inverse-Pareto power-law tails.

  20. Hierarchical Rank Aggregation with Applications to Nanotoxicology.

    Science.gov (United States)

    Patel, Trina; Telesca, Donatello; Rallo, Robert; George, Saji; Xia, Tian; Nel, André E

    2013-06-01

    The development of high throughput screening (HTS) assays in the field of nanotoxicology provide new opportunities for the hazard assessment and ranking of engineered nanomaterials (ENMs). It is often necessary to rank lists of materials based on multiple risk assessment parameters, often aggregated across several measures of toxicity and possibly spanning an array of experimental platforms. Bayesian models coupled with the optimization of loss functions have been shown to provide an effective framework for conducting inference on ranks. In this article we present various loss-function-based ranking approaches for comparing ENM within experiments and toxicity parameters. Additionally, we propose a framework for the aggregation of ranks across different sources of evidence while allowing for differential weighting of this evidence based on its reliability and importance in risk ranking. We apply these methods to high throughput toxicity data on two human cell-lines, exposed to eight different nanomaterials, and measured in relation to four cytotoxicity outcomes. This article has supplementary material online.

  1. snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund

    2012-01-01

    skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can......Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis...... to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic...

  2. ARWU vs. Alternative ARWU Ranking: What are the Consequences for Lower Ranked Universities?

    Directory of Open Access Journals (Sweden)

    Milica Maričić

    2017-05-01

    Full Text Available The ARWU ranking has been a source of academic debate since its development in 2003, but the same does not account for the Alternative ARWU ranking. Namely, the Alternative ARWU ranking attempts to reduce the influence of the prestigious indicators Alumni and Award which are based on the number of received Nobel Prizes and Fields Medals by alumni or university staff. However, the consequences of the reduction of the two indicators have not been scrutinized in detail. Therefore, we propose a statistical approach to the comparison of the two rankings and an in-depth analysis of the Alternative ARWU groups. The obtained results, which are based on the official data, can provide new insights into the nature of the Alternative ARWU ranking. The presented approach might initiate further research on the Alternative ARWU ranking and on the impact of university ranking’s list length. JEL Classification: C10, C38, I23

  3. Efficient Top-k Search for PageRank

    National Research Council Canada - National Science Library

    Fujiwara, Yasuhiro; Nakatsuji, Makoto; Shiokawa, Hiroaki; Mishima, Takeshi; Onizuka, Makoto

    2015-01-01

      In AI communities, many applications utilize PageRank. To obtain high PageRank score nodes, the original approach iteratively computes the PageRank score of each node until convergence from the whole graph...

  4. PageRank as a method to rank biomedical literature by importance.

    Science.gov (United States)

    Yates, Elliot J; Dixon, Louise C

    2015-01-01

    Optimal ranking of literature importance is vital in overcoming article overload. Existing ranking methods are typically based on raw citation counts, giving a sum of 'inbound' links with no consideration of citation importance. PageRank, an algorithm originally developed for ranking webpages at the search engine, Google, could potentially be adapted to bibliometrics to quantify the relative importance weightings of a citation network. This article seeks to validate such an approach on the freely available, PubMed Central open access subset (PMC-OAS) of biomedical literature. On-demand cloud computing infrastructure was used to extract a citation network from over 600,000 full-text PMC-OAS articles. PageRanks and citation counts were calculated for each node in this network. PageRank is highly correlated with citation count (R = 0.905, P PageRank can be trivially computed on commodity cluster hardware and is linearly correlated with citation count. Given its putative benefits in quantifying relative importance, we suggest it may enrich the citation network, thereby overcoming the existing inadequacy of citation counts alone. We thus suggest PageRank as a feasible supplement to, or replacement of, existing bibliometric ranking methods.

  5. RANK/RANK-Ligand/OPG: Ein neuer Therapieansatz in der Osteoporosebehandlung

    Directory of Open Access Journals (Sweden)

    Preisinger E

    2007-01-01

    Full Text Available Die Erforschung der Kopplungsmechanismen zur Osteoklastogenese, Knochenresorption und Remodellierung eröffnete neue mögliche Therapieansätze in der Behandlung der Osteoporose. Eine Schlüsselrolle beim Knochenabbau spielt der RANK- ("receptor activator of nuclear factor (NF- κB"- Ligand (RANKL. Durch die Bindung von RANKL an den Rezeptor RANK wird die Knochenresorption eingeleitet. OPG (Osteoprotegerin sowie der für den klinischen Gebrauch entwickelte humane monoklonale Antikörper (IgG2 Denosumab blockieren die Bindung von RANK-Ligand an RANK und verhindern den Knochenabbau.

  6. Ranking Fuzzy Numbers and Its Application to Products Attributes Preferences

    OpenAIRE

    Abdullah, Lazim; Fauzee, Nor Nashrah Ahmad

    2011-01-01

    Ranking is one of the widely used methods in fuzzy decision making environment. The recent ranking fuzzy numbers proposed by Wang and Li is claimed to be the improved version in ranking. However, the method was never been simplified and tested in real life application. This paper presents a four-step computation of ranking fuzzy numbers and its application in ranking attributes of selected chocolate products. The four steps algorithm was formulated to rank fuzzy numbers and followed by a tes...

  7. Social class rank, essentialism, and punitive judgment.

    Science.gov (United States)

    Kraus, Michael W; Keltner, Dacher

    2013-08-01

    Recent evidence suggests that perceptions of social class rank influence a variety of social cognitive tendencies, from patterns of causal attribution to moral judgment. In the present studies we tested the hypotheses that upper-class rank individuals would be more likely to endorse essentialist lay theories of social class categories (i.e., that social class is founded in genetically based, biological differences) than would lower-class rank individuals and that these beliefs would decrease support for restorative justice--which seeks to rehabilitate offenders, rather than punish unlawful action. Across studies, higher social class rank was associated with increased essentialism of social class categories (Studies 1, 2, and 4) and decreased support for restorative justice (Study 4). Moreover, manipulated essentialist beliefs decreased preferences for restorative justice (Study 3), and the association between social class rank and class-based essentialist theories was explained by the tendency to endorse beliefs in a just world (Study 2). Implications for how class-based essentialist beliefs potentially constrain social opportunity and mobility are discussed.

  8. A network-based dynamical ranking system

    CERN Document Server

    Motegi, Shun

    2012-01-01

    Ranking players or teams in sports is of practical interests. From the viewpoint of networks, a ranking system is equivalent a centrality measure for sports networks, whereby a directed link represents the result of a single game. Previously proposed network-based ranking systems are derived from static networks, i.e., aggregation of the results of games over time. However, the score (i.e., strength) of a player, for example, depends on time. Defeating a renowned player in the peak performance is intuitively more rewarding than defeating the same player in other periods. To account for this factor, we propose a dynamic variant of such a network-based ranking system and apply it to professional men's tennis data. Our ranking system, also interpreted as a centrality measure for directed temporal networks, has two parameters. One parameter represents the exponential decay rate of the past score, and the other parameter controls the effect of indirect wins on the score. We derive a set of linear online update equ...

  9. Global network centrality of university rankings

    Science.gov (United States)

    Guo, Weisi; Del Vecchio, Marco; Pogrebna, Ganna

    2017-10-01

    Universities and higher education institutions form an integral part of the national infrastructure and prestige. As academic research benefits increasingly from international exchange and cooperation, many universities have increased investment in improving and enabling their global connectivity. Yet, the relationship of university performance and its global physical connectedness has not been explored in detail. We conduct, to our knowledge, the first large-scale data-driven analysis into whether there is a correlation between university relative ranking performance and its global connectivity via the air transport network. The results show that local access to global hubs (as measured by air transport network betweenness) strongly and positively correlates with the ranking growth (statistical significance in different models ranges between 5% and 1% level). We also found that the local airport's aggregate flight paths (degree) and capacity (weighted degree) has no effect on university ranking, further showing that global connectivity distance is more important than the capacity of flight connections. We also examined the effect of local city economic development as a confounding variable and no effect was observed suggesting that access to global transportation hubs outweighs economic performance as a determinant of university ranking. The impact of this research is that we have determined the importance of the centrality of global connectivity and, hence, established initial evidence for further exploring potential connections between university ranking and regional investment policies on improving global connectivity.

  10. A Cognitive Model for Aggregating People's Rankings

    Science.gov (United States)

    Lee, Michael D.; Steyvers, Mark; Miller, Brent

    2014-01-01

    We develop a cognitive modeling approach, motivated by classic theories of knowledge representation and judgment from psychology, for combining people's rankings of items. The model makes simple assumptions about how individual differences in knowledge lead to observed ranking data in behavioral tasks. We implement the cognitive model as a Bayesian graphical model, and use computational sampling to infer an aggregate ranking and measures of the individual expertise. Applications of the model to 23 data sets, dealing with general knowledge and prediction tasks, show that the model performs well in producing an aggregate ranking that is often close to the ground truth and, as in the “wisdom of the crowd” effect, usually performs better than most of individuals. We also present some evidence that the model outperforms the traditional statistical Borda count method, and that the model is able to infer people's relative expertise surprisingly well without knowing the ground truth. We discuss the advantages of the cognitive modeling approach to combining ranking data, and in wisdom of the crowd research generally, as well as highlighting a number of potential directions for future model development. PMID:24816733

  11. A Review of Outcomes of Seven World University Ranking Systems

    National Research Council Canada - National Science Library

    Mahmood Khosrowjerdi; Neda Zeraatkar

    2012-01-01

    There are many national and international ranking systems rank the universities and higher education institutions of the world, nationally or internationally, based on the same or different criteria...

  12. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

    Science.gov (United States)

    Guo, Liyuan; Wang, Jing

    2017-11-11

    Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. SNP analysis of follistatin gene associated with polycystic ovarian syndrome

    Directory of Open Access Journals (Sweden)

    et al

    2010-12-01

    Full Text Available Palanisamy Panneerselvam1, Kanakarajan Sivakumari1, Ponmani Jayaprakash1, Ramanathan Srikanth21Department of Zoology, Presidency College, Chennai, Tamil Nadu, India; 2Department of Biotechnology, Sri Venkateswara College of Engineering, Chennai, Tamil Nadu, IndiaAbstract: Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with susceptibility to PCOS. The nucleotide sequence of human follistatin and the protein sequence of human follistatin were retrieved from the NCBI database using Entrez. The follistatin protein of human was retrieved from the Swiss-Prot database. There are 344 amino acids and the molecular weight is 38,007 Da. The ProtParam analysis shows that the isoelectric point is 5.53 and the aliphatic index is 61.25. The hydropathicity is -0.490. The domains in FST protein are as follows: Pfam-B 5005 domain from 1 to 92; EGF-like subdomain from 93 to 116; Kazal 1 domain, occurred in three places, namely, 118–164, 192–239, and 270–316. There are 31 single-nucleotide polymorphisms (SNPs for this gene. Some are nonsynonymous, some occur in the intron region, and some in an untranslated region. Two nonsynonymous SNPs, namely, rs11745088 and rs1127760, were taken for analysis. In the SNP rs11745088, the change is E152Q. Likewise, in rs1127760, the change is C239S. SIFT (Sorting Intolerant from Tolerant showed positions of amino acids and the single letter code of amino acids that can be tolerated or deleterious for each position. There were six SNP results and each result had links to it. The dbSNP id, primary database id, and the type of mutation whether silent and if occurring in coding region are given as phenotype alterations. The FASTA format of protein was given to the nsSNP Analyzer tool, and the variation E152Q and C239S were given

  14. SNP detection for massively parallel whole-genome resequencing.

    Science.gov (United States)

    Li, Ruiqiang; Li, Yingrui; Fang, Xiaodong; Yang, Huanming; Wang, Jian; Kristiansen, Karsten; Wang, Jun

    2009-06-01

    Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36x coverage and assembled a high-quality nonrepetitive consensus sequence for 92.25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered at 99.97% and 99.84% consistency, respectively. At a low sequencing depth, we used prior probability of dbSNP alleles and were able to improve coverage of the dbSNP sites significantly as compared to that obtained using a nonimputation model. Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth.

  15. Ranking schools on external knowledge tests results

    Directory of Open Access Journals (Sweden)

    Gašper Cankar

    2007-01-01

    Full Text Available The paper discusses the use of external knowledge test results for school ranking and the implicit effect of such ranking. A question of validity is raised and a review of research literature and main known problems are presented. In many western countries publication of school results is a common practice and a similar trend can be observed in Slovenia. Experiences of other countries help to predict positive and negative aspects of such publication. Results of external knowledge tests produce very limited information about school quality—if we use other sources of information our ranking of schools can be very different. Nevertheless, external knowledge tests can yield useful information. If we want to improve quality in schools, we must allow schools to use this information themselves and improve from within. Broad public scrutiny is unnecessary and problematic—it moves the focus of school efforts from real improvement of quality to mere improvement of the school public image.

  16. Resolution of ranking hierarchies in directed networks

    Science.gov (United States)

    Barucca, Paolo; Lillo, Fabrizio

    2018-01-01

    Identifying hierarchies and rankings of nodes in directed graphs is fundamental in many applications such as social network analysis, biology, economics, and finance. A recently proposed method identifies the hierarchy by finding the ordered partition of nodes which minimises a score function, termed agony. This function penalises the links violating the hierarchy in a way depending on the strength of the violation. To investigate the resolution of ranking hierarchies we introduce an ensemble of random graphs, the Ranked Stochastic Block Model. We find that agony may fail to identify hierarchies when the structure is not strong enough and the size of the classes is small with respect to the whole network. We analytically characterise the resolution threshold and we show that an iterated version of agony can partly overcome this resolution limit. PMID:29394278

  17. Ranking beta sheet topologies of proteins

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; Helles, Glennie; Winter, Pawel

    2010-01-01

    One of the challenges of protein structure prediction is to identify long-range interactions between amino acids. To reliably predict such interactions, we enumerate, score and rank all beta-topologies (partitions of beta-strands into sheets, orderings of strands within sheets and orientations...... of paired strands) of a given protein. We show that the beta-topology corresponding to the native structure is, with high probability, among the top-ranked. Since full enumeration is very time-consuming, we also suggest a method to deal with proteins with many beta-strands. The results reported...... in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. The top-ranked beta-topologies can be used to find initial conformations from which conformational searches can be started. They can also be used to filter decoys by removing those with poorly...

  18. Low Rank Approximation Algorithms, Implementation, Applications

    CERN Document Server

    Markovsky, Ivan

    2012-01-01

    Matrix low-rank approximation is intimately related to data modelling; a problem that arises frequently in many different fields. Low Rank Approximation: Algorithms, Implementation, Applications is a comprehensive exposition of the theory, algorithms, and applications of structured low-rank approximation. Local optimization methods and effective suboptimal convex relaxations for Toeplitz, Hankel, and Sylvester structured problems are presented. A major part of the text is devoted to application of the theory. Applications described include: system and control theory: approximate realization, model reduction, output error, and errors-in-variables identification; signal processing: harmonic retrieval, sum-of-damped exponentials, finite impulse response modeling, and array processing; machine learning: multidimensional scaling and recommender system; computer vision: algebraic curve fitting and fundamental matrix estimation; bioinformatics for microarray data analysis; chemometrics for multivariate calibration; ...

  19. Adaptive distributional extensions to DFR ranking

    DEFF Research Database (Denmark)

    Petersen, Casper; Simonsen, Jakob Grue; Järvelin, Kalervo

    2016-01-01

    Divergence From Randomness (DFR) ranking models assume that informative terms are distributed in a corpus differently than non-informative terms. Different statistical models (e.g. Poisson, geometric) are used to model the distribution of non-informative terms, producing different DFR models....... An informative term is then detected by measuring the divergence of its distribution from the distribution of non-informative terms. However, there is little empirical evidence that the distributions of non-informative terms used in DFR actually fit current datasets. Practically this risks providing a poor...... separation between informative and non-informative terms, thus compromising the discriminative power of the ranking model. We present a novel extension to DFR, which first detects the best-fitting distribution of non-informative terms in a collection, and then adapts the ranking computation to this best...

  20. Immobilizing silver nanoparticles (SNP) on Musa balbisiana cellulose.

    Science.gov (United States)

    Gogoi, Krishna; Saikia, Jyoti Prasad; Konwar, Bolin Kumar

    2013-02-01

    Cellulose from Musa balbisiana was purified. A part of it was dispersed in distilled water using ultrasonication. The silver nanoparticles (SNP) were synthesized in the colloidal cellulose solution and stability of the nanoparticles was tested using UV-Vis spectrophotometer. Further characterization of the composite was done using spectral analysis by Fourier Transform Infrared Spectroscopy (FTIR) to reveal any bond formation between silver nanoparticles with M. balbisiana cellulose. Here we found that cellulose/silver nanoparticle colloid is stable for 29 days and there is no chemical interaction of cellulose with silver nanoparticles. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. SNP typing on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez Sanchez, Juan Jose; Morling, Niels

    2005-01-01

    at the same time according to a loading protocol generated by the user. Biotinylated deoxyribonucleic acid (DNA) is directed to the pad(s) via the electronic field(s) and bound to streptavidin in the hydrogel layer. Subsequently, fluorescently labeled reporter oligos and a stabilizer oligo are hybridized......We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes...

  2. Computational tradeoffs in multiplex PCR assay design for SNP genotyping

    Directory of Open Access Journals (Sweden)

    Cantor Charles

    2005-07-01

    Full Text Available Abstract Background Multiplex PCR is a key technology for detecting infectious microorganisms, whole-genome sequencing, forensic analysis, and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays requires the consideration of multiple competing objectives and physical constraints, and extensive computational analysis must be performed in order to identify the possible formation of primer-dimers that can negatively impact product yield. Results This paper examines the computational design limits of multiplex PCR in the context of SNP genotyping and examines tradeoffs associated with several key design factors including multiplexing level (the number of primer pairs per tube, coverage (the % of SNP whose associated primers are actually assigned to one of several available tube, and tube-size uniformity. We also examine how design performance depends on the total number of available SNPs from which to choose, and primer stringency criterial. We show that finding high-multiplexing/high-coverage designs is subject to a computational phase transition, becoming dramatically more difficult when the probability of primer pair interaction exceeds a critical threshold. The precise location of this critical transition point depends on the number of available SNPs and the level of multiplexing required. We also demonstrate how coverage performance is impacted by the number of available snps, primer selection criteria, and target multiplexing levels. Conclusion The presence of a phase transition suggests limits to scaling Multiplex PCR performance for high-throughput genomics applications. Achieving broad SNP coverage rapidly transitions from being very easy to very hard as the target multiplexing level (# of primer pairs per tube increases. The onset of a phase transition can be "delayed" by having a larger pool of SNPs, or loosening primer selection constraints so as to increase the number of candidate primer pairs

  3. SNP Discovery In Marine Fish Species By 454 Sequencing

    DEFF Research Database (Denmark)

    Panitz, Frank; Nielsen, Rasmus Ory; van Houdt, Jeroen K J

    2011-01-01

    Based on the 454 Next-Generation-Sequencing technology (Roche) a high throughput screening method was devised in order to generate novel genetic markers (SNPs). SNP discovery was performed for three target species of marine fish: hake (Merluccius merluccius), herring (Clupea harengus) and sole...... (lllumina Golden Gate platform). Successfully genotyped SNPs will be used for studying genetic population structures, with special focus on detecting signatures of divergent selection at functionally important genomic regions. An aim is to compile the most informative markers into a cost-effective tool...... for monitoring fish populations and tracing fish samples...

  4. Ascertainment biases in SNP chips affect measures of population divergence

    DEFF Research Database (Denmark)

    Albrechtsen, Anders; Nielsen, Finn Cilius; Nielsen, Rasmus

    2010-01-01

    on inferences regarding genetic differentiation among populations in one of the common genome-wide genotyping platforms. We generate SNP genotyping data for individuals that previously have been subject to partial genome-wide Sanger sequencing and compare inferences based on genotyping data to inferences based...... on direct sequencing. In addition, we also analyze publicly available genome-wide data. We demonstrate that the ascertainment biases will distort measures of human diversity and possibly change conclusions drawn from these measures in some times unexpected ways. We also show that details of the genotyping...

  5. Sign rank versus Vapnik-Chervonenkis dimension

    Science.gov (United States)

    Alon, N.; Moran, Sh; Yehudayoff, A.

    2017-12-01

    This work studies the maximum possible sign rank of sign (N × N)-matrices with a given Vapnik-Chervonenkis dimension d. For d=1, this maximum is three. For d=2, this maximum is \\widetilde{\\Theta}(N1/2). For d >2, similar but slightly less accurate statements hold. The lower bounds improve on previous ones by Ben-David et al., and the upper bounds are novel. The lower bounds are obtained by probabilistic constructions, using a theorem of Warren in real algebraic topology. The upper bounds are obtained using a result of Welzl about spanning trees with low stabbing number, and using the moment curve. The upper bound technique is also used to: (i) provide estimates on the number of classes of a given Vapnik-Chervonenkis dimension, and the number of maximum classes of a given Vapnik-Chervonenkis dimension--answering a question of Frankl from 1989, and (ii) design an efficient algorithm that provides an O(N/log(N)) multiplicative approximation for the sign rank. We also observe a general connection between sign rank and spectral gaps which is based on Forster's argument. Consider the adjacency (N × N)-matrix of a Δ-regular graph with a second eigenvalue of absolute value λ and Δ ≤ N/2. We show that the sign rank of the signed version of this matrix is at least Δ/λ. We use this connection to prove the existence of a maximum class C\\subseteq\\{+/- 1\\}^N with Vapnik-Chervonenkis dimension 2 and sign rank \\widetilde{\\Theta}(N1/2). This answers a question of Ben-David et al. regarding the sign rank of large Vapnik-Chervonenkis classes. We also describe limitations of this approach, in the spirit of the Alon-Boppana theorem. We further describe connections to communication complexity, geometry, learning theory, and combinatorics. Bibliography: 69 titles.

  6. Pulling Rank: A Plan to Help Students with College Choice in an Age of Rankings

    Science.gov (United States)

    Thacker, Lloyd

    2008-01-01

    Colleges and universities are "ranksteering"--driving under the influence of popular college rankings systems like "U.S. News and World Report's" Best Colleges. This article examines the criticisms of college rankings and describes how a group of education leaders is honing a plan to end the tyranny of the ratings game and better help students and…

  7. When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores

    KAUST Repository

    Wang, Jim Jing-Yan

    2017-06-28

    Sparse coding, which represents a data point as a sparse reconstruction code with regard to a dictionary, has been a popular data representation method. Meanwhile, in database retrieval problems, learning the ranking scores from data points plays an important role. Up to now, these two problems have always been considered separately, assuming that data coding and ranking are two independent and irrelevant problems. However, is there any internal relationship between sparse coding and ranking score learning? If yes, how to explore and make use of this internal relationship? In this paper, we try to answer these questions by developing the first joint sparse coding and ranking score learning algorithm. To explore the local distribution in the sparse code space, and also to bridge coding and ranking problems, we assume that in the neighborhood of each data point, the ranking scores can be approximated from the corresponding sparse codes by a local linear function. By considering the local approximation error of ranking scores, the reconstruction error and sparsity of sparse coding, and the query information provided by the user, we construct a unified objective function for learning of sparse codes, the dictionary and ranking scores. We further develop an iterative algorithm to solve this optimization problem.

  8. Ranking Entities in Networks via Lefschetz Duality

    DEFF Research Database (Denmark)

    Aabrandt, Andreas; Hansen, Vagn Lundsgaard; Poulsen, Bjarne

    2014-01-01

    In the theory of communication it is essential that agents are able to exchange information. This fact is closely related to the study of connected spaces in topology. A communication network may be modelled as a topological space such that agents can communicate if and only if they belong...... then be ranked according to how essential their positions are in the network by considering the effect of their respective absences. Defining a ranking of a network which takes the individual position of each entity into account has the purpose of assigning different roles to the entities, e.g. agents...

  9. Compressed Sensing with Rank Deficient Dictionaries

    DEFF Research Database (Denmark)

    Hansen, Thomas Lundgaard; Johansen, Daniel Højrup; Jørgensen, Peter Bjørn

    2012-01-01

    In compressed sensing it is generally assumed that the dictionary matrix constitutes a (possibly overcomplete) basis of the signal space. In this paper we consider dictionaries that do not span the signal space, i.e. rank deficient dictionaries. We show that in this case the signal-to-noise ratio...... (SNR) in the compressed samples can be increased by selecting the rows of the measurement matrix from the column space of the dictionary. As an example application of compressed sensing with a rank deficient dictionary, we present a case study of compressed sensing applied to the Coarse Acquisition (C...

  10. Research of Subgraph Estimation Page Rank Algorithm for Web Page Rank

    Directory of Open Access Journals (Sweden)

    LI Lan-yin

    2017-04-01

    Full Text Available The traditional PageRank algorithm can not efficiently perform large data Webpage scheduling problem. This paper proposes an accelerated algorithm named topK-Rank,which is based on PageRank on the MapReduce platform. It can find top k nodes efficiently for a given graph without sacrificing accuracy. In order to identify top k nodes,topK-Rank algorithm prunes unnecessary nodes and edges in each iteration to dynamically construct subgraphs,and iteratively estimates lower/upper bounds of PageRank scores through subgraphs. Theoretical analysis shows that this method guarantees result exactness. Experiments show that topK-Rank algorithm can find k nodes much faster than the existing approaches.

  11. Association between CYP19 gene SNP rs2414096 Polymorphism and polycystic ovary syndrome in Chinese women

    OpenAIRE

    Jin, Jia-Li; Sun, Jing; Ge, Hui-Juan; Cao, Yun-Xia; Wu, Xiao-Ke; Liang, Feng-Jing; Sun, Hai-Xiang; Ke, Lu; Yi, Long; Wu, Zhi-Wei; Wang, Yong

    2009-01-01

    Abstract Background Several studies have reported the association of the SNP rs2414096 in the CYP19 gene with hyperandrogenism, which is one of the clinical manifestations of polycystic ovary syndrome (PCOS). These studies suggest that SNP rs2414096 may be involved in the etiopathogenisis of PCOS. To investigate whetherthe CYP19 gene SNP rs2414096 polymorphism is associated with the susceptibility to PCOS, we designed a case-controlled association study including 684 individuals. Methods A ca...

  12. A SNP transferability survey within the genus Vitis

    Science.gov (United States)

    Vezzulli, Silvia; Micheletti, Diego; Riaz, Summaira; Pindo, Massimo; Viola, Roberto; This, Patrice; Walker, M Andrew; Troggio, Michela; Velasco, Riccardo

    2008-01-01

    Background Efforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus. Results This study was performed by genotyping 137 SNPs through the SNPlex™ Genotyping System (Applied Biosystems Inc.) and by comparing the SNPlex sequencing results across 35 (of the 137) regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers. Conclusion Using SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms), but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera. PMID:19087337

  13. Psoriasis prediction from genome-wide SNP profiles

    Directory of Open Access Journals (Sweden)

    Fang Xiangzhong

    2011-01-01

    Full Text Available Abstract Background With the availability of large-scale genome-wide association study (GWAS data, choosing an optimal set of SNPs for disease susceptibility prediction is a challenging task. This study aimed to use single nucleotide polymorphisms (SNPs to predict psoriasis from searching GWAS data. Methods Totally we had 2,798 samples and 451,724 SNPs. Process for searching a set of SNPs to predict susceptibility for psoriasis consisted of two steps. The first one was to search top 1,000 SNPs with high accuracy for prediction of psoriasis from GWAS dataset. The second one was to search for an optimal SNP subset for predicting psoriasis. The sequential information bottleneck (sIB method was compared with classical linear discriminant analysis(LDA for classification performance. Results The best test harmonic mean of sensitivity and specificity for predicting psoriasis by sIB was 0.674(95% CI: 0.650-0.698, while only 0.520(95% CI: 0.472-0.524 was reported for predicting disease by LDA. Our results indicate that the new classifier sIB performs better than LDA in the study. Conclusions The fact that a small set of SNPs can predict disease status with average accuracy of 68% makes it possible to use SNP data for psoriasis prediction.

  14. A SNP uncoupling Mina expression from the TGFβ signaling pathway.

    Science.gov (United States)

    Lian, Shang L; Mihi, Belgacem; Koyanagi, Madoka; Nakayama, Toshinori; Bix, Mark

    2018-03-01

    Mina is a JmjC family 2-oxoglutarate oxygenase with pleiotropic roles in cell proliferation, cancer, T cell differentiation, pulmonary inflammation, and intestinal parasite expulsion. Although Mina expression varies according to cell-type, developmental stage and activation state, its transcriptional regulation is poorly understood. Across inbred mouse strains, Mina protein level exhibits a bimodal distribution, correlating with inheritance of a biallelic haplotype block comprising 21 promoter/intron 1-region SNPs. We previously showed that heritable differences in Mina protein level are transcriptionally regulated. Accordingly, we decided to test the hypothesis that at least one of the promoter/intron 1-region SNPs perturbs a Mina cis-regulatory element (CRE). Here, we have comprehensively scanned for CREs across a Mina locus-spanning 26-kilobase genomic interval. We discovered 8 potential CREs and functionally validated 4 of these, the strongest of which (E2), residing in intron 1, contained a SNP whose BALB/c-but not C57Bl/6 allele-abolished both Smad3 binding and transforming growth factor beta (TGFβ) responsiveness. Our results demonstrate the TGFβ signaling pathway plays a critical role in regulating Mina expression and SNP rs4191790 controls heritable variation in Mina expression level, raising important questions regarding the evolution of an allele that uncouples Mina expression from the TGFβ signaling pathway. © 2017 The Authors. Immunity, Inflammation and Disease Published by John Wiley & Sons Ltd.

  15. SOUTH AFRICAN ARMY RANKS AND INSIGNIA

    African Journals Online (AJOL)

    major, cap- tain, lieutenant;. Other Ranks : Warrant officer, staff sergeant, sergeant, corporal, lance-cor- poral, private.' We apparently had no need for second lieuten- ants at that time, and they were introduced only .... Army warrant officers can also hold the cmmon serv- ice posts of Sergeant-Major of Special Forces.

  16. Kinesiology Faculty Citations across Academic Rank

    Science.gov (United States)

    Knudson, Duane

    2015-01-01

    Citations to research reports are used as a measure for the influence of a scholar's research line when seeking promotion, grants, and awards. The current study documented the distributions of citations to kinesiology scholars of various academic ranks. Google Scholar Citations was searched for user profiles using five research interest areas…

  17. Biomechanics Scholar Citations across Academic Ranks

    Directory of Open Access Journals (Sweden)

    Knudson Duane

    2015-11-01

    Full Text Available Study aim: citations to the publications of a scholar have been used as a measure of the quality or influence of their research record. A world-wide descriptive study of the citations to the publications of biomechanics scholars of various academic ranks was conducted.

  18. Ranking Workplace Competencies: Student and Graduate Perceptions.

    Science.gov (United States)

    Rainsbury, Elizabeth; Hodges, Dave; Burchell, Noel; Lay, Mark

    2002-01-01

    New Zealand business students and graduates made similar rankings of the five most important workplace competencies: computer literacy, customer service orientation, teamwork and cooperation, self-confidence, and willingness to learn. Graduates placed greater importance on most of the 24 competencies, resulting in a statistically significant…

  19. Subject Gateway Sites and Search Engine Ranking.

    Science.gov (United States)

    Thelwall, Mike

    2002-01-01

    Discusses subject gateway sites and commercial search engines for the Web and presents an explanation of Google's PageRank algorithm. The principle question addressed is the conditions under which a gateway site will increase the likelihood that a target page is found in search engines. (LRW)

  20. Ranking related entities: components and analyses

    NARCIS (Netherlands)

    Bron, M.; Balog, K.; de Rijke, M.

    2010-01-01

    Related entity finding is the task of returning a ranked list of homepages of relevant entities of a specified type that need to engage in a given relationship with a given source entity. We propose a framework for addressing this task and perform a detailed analysis of four core components;

  1. Low-rank coal oil agglomeration

    Science.gov (United States)

    Knudson, C.L.; Timpe, R.C.

    1991-07-16

    A low-rank coal oil agglomeration process is described. High mineral content, a high ash content subbituminous coals are effectively agglomerated with a bridging oil which is partially water soluble and capable of entering the pore structure, and is usually coal-derived.

  2. An evaluation and critique of current rankings

    NARCIS (Netherlands)

    Federkeil, Gero; Westerheijden, Donald F.; van Vught, Franciscus A.; Ziegele, Frank

    2012-01-01

    This chapter raises the question of whether university league tables deliver relevant information to one of their key target groups – students. It examines the inherent biases and weaknesses in the methodologies of the major rankings and argues that the concentration on a single indicator of

  3. World University Ranking Methodologies: Stability and Variability

    Science.gov (United States)

    Fidler, Brian; Parsons, Christine

    2008-01-01

    There has been a steady growth in the number of national university league tables over the last 25 years. By contrast, "World University Rankings" are a more recent development and have received little serious academic scrutiny in peer-reviewed publications. Few researchers have evaluated the sources of data and the statistical…

  4. Alternative Class Ranks Using Z-Scores

    Science.gov (United States)

    Brown, Philip H.; Van Niel, Nicholas

    2012-01-01

    Grades at US colleges and universities have increased precipitously over the last 50 years, suggesting that their signalling power has become attenuated. Moreover, average grades have risen disproportionately in some departments, implying that weak students in departments with high grades may obtain better class ranks than strong students in…

  5. Statistical inference of Minimum Rank Factor Analysis

    NARCIS (Netherlands)

    Shapiro, A; Ten Berge, JMF

    For any given number of factors, Minimum Rank Factor Analysis yields optimal communalities for an observed covariance matrix in the sense that the unexplained common variance with that number of factors is minimized, subject to the constraint that both the diagonal matrix of unique variances and the

  6. City Life: Rankings (Livability) versus Perceptions (Satisfaction)

    Science.gov (United States)

    Okulicz-Kozaryn, Adam

    2013-01-01

    I investigate the relationship between the popular Mercer city ranking (livability) and survey data (satisfactions). Livability aims to capture "objective" quality of life such as infrastructure. Survey items capture "subjective" quality of life such as satisfaction with city. The relationship between objective measures of quality of life and…

  7. Matrices with high completely positive semidefinite rank

    NARCIS (Netherlands)

    de Laat, David; Gribling, Sander; Laurent, Monique

    2017-01-01

    A real symmetric matrix M is completely positive semidefinite if it admits a Gram representation by (Hermitian) positive semidefinite matrices of any size d. The smallest such d is called the (complex) completely positive semidefinite rank of M , and it is an open question whether there exists an

  8. Ranking health between countries in international comparisons

    DEFF Research Database (Denmark)

    Brønnum-Hansen, Henrik

    2014-01-01

    Cross-national comparisons and ranking of summary measures of population health sometimes give rise to inconsistent and diverging conclusions. In order to minimise confusion, international comparative studies ought to be based on well-harmonised data with common standards of definitions...

  9. Comparing survival curves using rank tests

    NARCIS (Netherlands)

    Albers, Willem/Wim

    1990-01-01

    Survival times of patients can be compared using rank tests in various experimental setups, including the two-sample case and the case of paired data. Attention is focussed on two frequently occurring complications in medical applications: censoring and tail alternatives. A review is given of the

  10. Smooth rank one perturbations of selfadjoint operators

    NARCIS (Netherlands)

    Hassi, Seppo; Snoo, H.S.V. de; Willemsma, A.D.I.

    Let A be a selfadjoint operator in a Hilbert space aleph with inner product [.,.]. The rank one perturbations of A have the form A+tau [.,omega]omega, tau epsilon R, for some element omega epsilon aleph. In this paper we consider smooth perturbations, i.e. we consider omega epsilon dom \\A\\(k/2) for

  11. Primate Innovation: Sex, Age and Social Rank

    NARCIS (Netherlands)

    Reader, S.M.; Laland, K.N.

    2001-01-01

    Analysis of an exhaustive survey of primate behavior collated from the published literature revealed significant variation in rates of innovation among individuals of different sex, age and social rank. We searched approximately 1,000 articles in four primatology journals, together with other

  12. An algorithm for ranking assignments using reoptimization

    DEFF Research Database (Denmark)

    Pedersen, Christian Roed; Nielsen, Lars Relund; Andersen, Kim Allan

    2008-01-01

    We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...... technique. Computational results for the new algorithm are presented...

  13. Ouderdom, omvang en citatiescores: rankings nader bekeken

    NARCIS (Netherlands)

    van Rooij, Jules

    2017-01-01

    By comparing the Top-300 lists of four global university rankings (ARWU, THE, QS, Leiden), three hypotheses are tested: 1) position correlates with size in the ARWU more than in the THE and QS; 2) given their strong dependency on reputation scores, position will be correlated more with a

  14. Returns to Tenure: Time or Rank?

    DEFF Research Database (Denmark)

    Buhai, Ioan Sebastian

    -specific investment, efficiency-wages or adverse-selection models. However, rent extracting arguments as suggested by the theory of internal labor markets, indicate that the relative position of the worker in the seniority hierarchy of the firm, her 'seniority rank', may also explain part of the observed returns...

  15. A high-density SNP genotyping array for rice biology and molecular breeding.

    Science.gov (United States)

    Chen, Haodong; Xie, Weibo; He, Hang; Yu, Huihui; Chen, Wei; Li, Jing; Yu, Renbo; Yao, Yue; Zhang, Wenhui; He, Yuqing; Tang, Xiaoyan; Zhou, Fasong; Deng, Xing Wang; Zhang, Qifa

    2014-03-01

    A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

  16. Probabilistic relation between In-Degree and PageRank

    NARCIS (Netherlands)

    Litvak, Nelli; Scheinhardt, Willem R.W.; Volkovich, Y.

    2008-01-01

    This paper presents a novel stochastic model that explains the relation between power laws of In-Degree and PageRank. PageRank is a popularity measure designed by Google to rank Web pages. We model the relation between PageRank and In-Degree through a stochastic equation, which is inspired by the

  17. The effect of new links on Google PageRank

    NARCIS (Netherlands)

    Avrachenkov, Konstatin; Litvak, Nelli

    2004-01-01

    PageRank is one of the principle criteria according to which Google ranks Web pages. PageRank can be interpreted as a frequency of visiting a Web page by a random surfer and thus it reflects the popularity of a Web page. We study the effect of newly created links on Google PageRank. We discuss to

  18. World University Rankings: Take with a Large Pinch of Salt

    Science.gov (United States)

    Cheng, Soh Kay

    2011-01-01

    Equating the unequal is misleading, and this happens consistently in comparing rankings from different university ranking systems, as the NUT saga shows. This article illustrates the problem by analyzing the 2011 rankings of the top 100 universities in the AWUR, QSWUR and THEWUR ranking results. It also discusses the reasons why the rankings…

  19. Generalized Reduced Rank Tests using the Singular Value Decomposition

    NARCIS (Netherlands)

    Kleibergen, F.R.; Paap, R.

    2006-01-01

    We propose a novel statistic to test the rank of a matrix. The rank statistic overcomes deficiencies of existing rank statistics, like: a Kronecker covariance matrix for the canonical correlation rank statistic of Anderson [Annals of Mathematical Statistics (1951), 22, 327-351] sensitivity to the

  20. Some upper and lower bounds on PSD-rank

    NARCIS (Netherlands)

    T. J. Lee (Troy); Z. Wei (Zhaohui); R. M. de Wolf (Ronald)

    2014-01-01

    textabstractPositive semidefinite rank (PSD-rank) is a relatively new quantity with applications to combinatorial optimization and communication complexity. We first study several basic properties of PSD-rank, and then develop new techniques for showing lower bounds on the PSD-rank. All of these

  1. Some upper and lower bounds on PSD-rank

    NARCIS (Netherlands)

    Lee, T.; Wei, Z.; de Wolf, R.

    Positive semidefinite rank (PSD-rank) is a relatively new complexity measure on matrices, with applications to combinatorial optimization and communication complexity. We first study several basic properties of PSD-rank, and then develop new techniques for showing lower bounds on the PSD-rank. All

  2. Biology of RANK, RANKL, and osteoprotegerin

    Science.gov (United States)

    Boyce, Brendan F; Xing, Lianping

    2007-01-01

    The discovery of the receptor activator of nuclear factor-κB ligand (RANKL)/RANK/osteoprotegerin (OPG) system and its role in the regulation of bone resorption exemplifies how both serendipity and a logic-based approach can identify factors that regulate cell function. Before this discovery in the mid to late 1990s, it had long been recognized that osteoclast formation was regulated by factors expressed by osteoblast/stromal cells, but it had not been anticipated that members of the tumor necrosis factor superfamily of ligands and receptors would be involved or that the factors involved would have extensive functions beyond bone remodeling. RANKL/RANK signaling regulates the formation of multinucleated osteoclasts from their precursors as well as their activation and survival in normal bone remodeling and in a variety of pathologic conditions. OPG protects the skeleton from excessive bone resorption by binding to RANKL and preventing it from binding to its receptor, RANK. Thus, RANKL/OPG ratio is an important determinant of bone mass and skeletal integrity. Genetic studies in mice indicate that RANKL/RANK signaling is also required for lymph node formation and mammary gland lactational hyperplasia, and that OPG also protects arteries from medial calcification. Thus, these tumor necrosis factor superfamily members have important functions outside bone. Although our understanding of the mechanisms whereby they regulate osteoclast formation has advanced rapidly during the past 10 years, many questions remain about their roles in health and disease. Here we review our current understanding of the role of the RANKL/RANK/OPG system in bone and other tissues. PMID:17634140

  3. Polymorphisms in the RANK/RANKL Genes and Their Effect on Bone Specific Prognosis in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Alexander Hein

    2014-01-01

    Full Text Available The receptor activator of NF-κB (RANK pathway is involved in bone health as well as breast cancer (BC pathogenesis and progression. Whereas the therapeutic implication of this pathway is established for the treatment of osteoporosis and bone metastases, the application in adjuvant BC is currently investigated. As genetic variants in this pathway have been described to influence bone health, aim of this study was the prognostic relevance of genetic variants in RANK and RANKL. Single nucleotide polymorphisms in RANK(L (rs1054016/rs1805034/rs35211496 were genotyped and analyzed with regard to bone metastasis-free survival (BMFS, disease-free survival, and overall survival for a retrospective cohort of 1251 patients. Cox proportional hazard models were built to examine the prognostic influence in addition to commonly established prognostic factors. The SNP rs1054016 seems to influence BMFS. Patients with two minor alleles had a more favorable prognosis than patients with at least one common allele (HR 0.37 (95% CI: 0.17, 0.84, whereas other outcome parameters remained unaffected. rs1805034 and rs35211496 had no prognostic relevance. The effect of rs1054016(RANKL adds to the evidence that the RANK pathway plays a role in BC pathogenesis and progression with respect to BMFS, emphasizing the connection between BC and bone health.

  4. A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis.

    Science.gov (United States)

    Contreras-Soto, Rodrigo Iván; Mora, Freddy; de Oliveira, Marco Antônio Rott; Higashi, Wilson; Scapim, Carlos Alberto; Schuster, Ivan

    2017-01-01

    Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean cultivars (N = 169) were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes) identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12). The haplotype block 42 on Chr19 (Gm19_Hap42) was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.

  5. Ranked Conservation Opportunity Areas for Region 7 (ECO_RES.RANKED_OAS)

    Science.gov (United States)

    The RANKED_OAS are all the Conservation Opportunity Areas identified by MoRAP that have subsequently been ranked by patch size, landform representation, and the targeted land cover class (highest rank for conservation management = 1 [LFRANK_NOR]). The OAs designate areas with potential for forest or grassland conservation because they are areas of natural or semi-natural land cover that are at least 75 meters away from roads and away from patch edges. The OAs were modeled by creating distance grids using the National Land Cover Database and the Census Bureau's TIGER roads files.

  6. UNIVERSITY RANKINGS BY COST OF LIVING ADJUSTED FACULTY COMPENSATION

    OpenAIRE

    Terrance Jalbert; Mercedes Jalbert; Karla Hayashi

    2010-01-01

    In this paper we rank 574 universities based on compensation paid to their faculty. The analysis examines universities both on a raw basis and on a cost of living adjusted basis. Rankings based on salary data and benefit data are presented. In addition rankings based on total compensation are presented. Separate rankings are provided for universities offering different degrees. The results indicate that rankings of universities based on raw and cost of living adjusted data are markedly differ...

  7. SNP Discovery for mapping alien introgressions in wheat

    Science.gov (United States)

    2014-01-01

    Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and

  8. Molecular cloning and SNP association analysis of chicken PMCH gene.

    Science.gov (United States)

    Sun, Guirong; Li, Ming; Li, Hong; Tian, Yadong; Chen, Qixin; Bai, Yichun; Kang, Xiangtao

    2013-08-01

    The pre-melanin-concentrating hormone (PMCH) gene is an important gene functionally concerning the regulations of body fat content, feeding behavior and energy balance. In this study, the full-length cDNA of chicken PMCH gene was amplified by SMART RACE method. The single nucleotide polymorphisms (SNPs) in the PMCH gene were screened by comparative sequence analysis. The obtained non-synonymous coding SNPs (ncSNPs) were designed for genotyping firstly. Its effects on growth, carcass characteristics and meat quality traits were investigated employing the F2 resource population of Gushi chicken crossed with Anak broiler by AluI CRS-PCR-RFLP. Our results indicated that the cDNA of chicken PMCH shared 67.25 and 66.47% homology with that of human and bovine PMCH, respectively. The deduced amino acid sequence of chicken PMCH (163 amino acids) were 52.07 and 50.89% identical to those of human and bovine PMCH, respectively. The PMCH protein sequence is predicted to have several functional domains, including pro-MCH, CSP, IL7, XPGI and some low complexity sequence. It has 8 phosphorylation sites and no signal peptide sequence. gga-miR-18a, gga-miR-18b, gga-miR-499 microRNA targeting site was predicted in the 3' untranslated region of chicken PMCH mRNA. In addition, a total of seven SNPs including an ncSNP and a synonymous coding SNP, were identified in the PMCH gene. The ncSNP c.81 A>T was found to be in moderate polymorphic state (polymorphic index=0.365), and the frequencies for genotype AA, AB and BB were 0.3648, 0.4682 and 0.1670, respectively. Significant associations between the locus and shear force of breast and leg were observed. This polymorphic site may serve as a useful target for the marker assisted selection of the growth and meat quality traits in chicken.

  9. An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

    Directory of Open Access Journals (Sweden)

    Li-Yeh Chuang

    Full Text Available BACKGROUND: Possible single nucleotide polymorphism (SNP interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR values (1.268 to 0.848; p<0.05 for breast cancer. Based on IPSO algorithm, the jointed effect in terms of SNP barcodes with two to seven SNPs show significantly decreasing OR values (0.84 to 0.57; p<0.05 to 0.001. Using PSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; p<0.05 to 0.001. Based on the results of 20 simulations, medians of the maximum differences for each SNP barcode generated by IPSO are higher than by PSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n = 3∼10 are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification. CONCLUSIONS/SIGNIFICANCE: Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.

  10. Kriging for Simulation Metamodeling: Experimental Design, Reduced Rank Kriging, and Omni-Rank Kriging

    Science.gov (United States)

    Hosking, Michael Robert

    This dissertation improves an analyst's use of simulation by offering improvements in the utilization of kriging metamodels. There are three main contributions. First an analysis is performed of what comprises good experimental designs for practical (non-toy) problems when using a kriging metamodel. Second is an explanation and demonstration of how reduced rank decompositions can improve the performance of kriging, now referred to as reduced rank kriging. Third is the development of an extension of reduced rank kriging which solves an open question regarding the usage of reduced rank kriging in practice. This extension is called omni-rank kriging. Finally these results are demonstrated on two case studies. The first contribution focuses on experimental design. Sequential designs are generally known to be more efficient than "one shot" designs. However, sequential designs require some sort of pilot design from which the sequential stage can be based. We seek to find good initial designs for these pilot studies, as well as designs which will be effective if there is no following sequential stage. We test a wide variety of designs over a small set of test-bed problems. Our findings indicate that analysts should take advantage of any prior information they have about their problem's shape and/or their goals in metamodeling. In the event of a total lack of information we find that Latin hypercube designs are robust default choices. Our work is most distinguished by its attention to the higher levels of dimensionality. The second contribution introduces and explains an alternative method for kriging when there is noise in the data, which we call reduced rank kriging. Reduced rank kriging is based on using a reduced rank decomposition which artificially smoothes the kriging weights similar to a nugget effect. Our primary focus will be showing how the reduced rank decomposition propagates through kriging empirically. In addition, we show further evidence for our

  11. FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases

    Directory of Open Access Journals (Sweden)

    Watson-Haigh Nathan S

    2010-06-01

    Full Text Available Abstract Background Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance. The current challenge is that the information holding the clues to SNP functions is distributed across many different databases. Efficient bioinformatics tools are therefore needed to seamlessly integrate up-to-date functional information on SNPs. Many web services have arisen to meet the challenge but most work only within the framework of human medical research. Although we acknowledge the importance of human research, we identify there is a need for SNP annotation tools for other organisms. Description We introduce an R package called FunctSNP, which is the user interface to custom built species-specific databases. The local relational databases contain SNP data together with functional annotations extracted from online resources. FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies. We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. We illustrate the use of FunctSNP with a livestock example, but the approach and software tools presented here can be applied also to human and other organisms. Conclusions Finding the potential functional significance of SNPs is important when further using the outcomes from whole genome association studies. FunctSNP is unique in that it is the only R

  12. Pulling Rank: Military Rank Affects Hormone Levels and Fairness in an Allocation Experiment

    Directory of Open Access Journals (Sweden)

    Benjamin Siart

    2016-11-01

    Full Text Available Status within social hierarchies has great effects on the lives of socially organized mammals. Its effects on human behavior and related physiology however is relatively little studied. The present study investigated the impact of military rank on fairness and behavior in relation to salivary cortisol (C and testosterone (T levels in male soldiers. For this purpose 180 members of the Austrian Armed Forces belonging to two distinct rank groups participated in two variations of a computer-based guard duty allocation experiment. The rank groups were 1 warrant officers (High Rank, HR and 2 enlisted men (Low Rank, LR. One soldier from each rank group participated in every experiment. At the beginning of the experiment, one participant was assigned to start standing guard and the other participant at rest. The participant who started at rest could choose if and when to relieve his fellow soldier and therefore had control over the experiment. In order to trigger perception of unfair behavior, an additional experiment was conducted which was manipulated by the experimenter. In the manipulated version both soldiers started in the standing guard position and were never relieved, believing that their opponent was at rest, not relieving them. Our aim was to test whether unfair behavior causes a physiological reaction. Saliva samples for hormone analysis were collected at regular intervals throughout the experiment.We found that in the un-manipulated setup high-ranking soldiers spent less time standing guard than lower ranking individuals. Rank was a significant predictor for C but not for T levels during the experiment. C levels in the HR group were higher than in LR group. C levels were also elevated in the manipulated experiment compared to the un-manipulated experiment, especially in LR. We assume that the elevated C levels in HR were caused by HR feeling their status challenged by the situation of having to negotiate with an individual of lower military

  13. Pulling Rank: Military Rank Affects Hormone Levels and Fairness in an Allocation Experiment.

    Science.gov (United States)

    Siart, Benjamin; Pflüger, Lena S; Wallner, Bernard

    2016-01-01

    Status within social hierarchies has great effects on the lives of socially organized mammals. Its effects on human behavior and related physiology, however, is relatively little studied. The present study investigated the impact of military rank on fairness and behavior in relation to salivary cortisol (C) and testosterone (T) levels in male soldiers. For this purpose 180 members of the Austrian Armed Forces belonging to two distinct rank groups participated in two variations of a computer-based guard duty allocation experiment. The rank groups were (1) warrant officers (high rank, HR) and (2) enlisted men (low rank, LR). One soldier from each rank group participated in every experiment. At the beginning of the experiment, one participant was assigned to start standing guard and the other participant at rest. The participant who started at rest could choose if and when to relieve his fellow soldier and therefore had control over the experiment. In order to trigger perception of unfair behavior, an additional experiment was conducted which was manipulated by the experimenter. In the manipulated version both soldiers started in the standing guard position and were never relieved, believing that their opponent was at rest, not relieving them. Our aim was to test whether unfair behavior causes a physiological reaction. Saliva samples for hormone analysis were collected at regular intervals throughout the experiment. We found that in the un-manipulated setup high-ranking soldiers spent less time standing guard than lower ranking individuals. Rank was a significant predictor for C but not for T levels during the experiment. C levels in the HR group were higher than in the LR group. C levels were also elevated in the manipulated experiment compared to the un-manipulated experiment, especially in LR. We assume that the elevated C levels in HR were caused by HR feeling their status challenged by the situation of having to negotiate with an individual of lower military rank

  14. Grouping preprocess for haplotype inference from SNP and CNV data

    Energy Technology Data Exchange (ETDEWEB)

    Shindo, Hiroyuki; Chigira, Hiroshi; Nagaoka, Tomoyo; Inoue, Masato [Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555 (Japan); Kamatani, Naoyuki, E-mail: masato.inoue@eb.waseda.ac.j [Institute of Rheumatology, Tokyo Women' s Medical University, 10-22, Kawada-cho, Shinjuku-ku, Tokyo 162-0054 (Japan)

    2009-12-01

    The method of statistical haplotype inference is an indispensable technique in the field of medical science. The authors previously reported Hardy-Weinberg equilibrium-based haplotype inference that could manage single nucleotide polymorphism (SNP) data. We recently extended the method to cover copy number variation (CNV) data. Haplotype inference from mixed data is important because SNPs and CNVs are occasionally in linkage disequilibrium. The idea underlying the proposed method is simple, but the algorithm for it needs to be quite elaborate to reduce the calculation cost. Consequently, we have focused on the details on the algorithm in this study. Although the main advantage of the method is accuracy, in that it does not use any approximation, its main disadvantage is still the calculation cost, which is sometimes intractable for large data sets with missing values.

  15. Transcriptome sequencing and SNP detection in Phoebe chekiangensis.

    Science.gov (United States)

    He, Bing; Li, Yingang; Ni, Zhouxian; Xu, Li-An

    2017-01-01

    Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level. Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted and 25 were further validated using the Sanger method. The currently available SNP prediction software packages showed low levels of correspondence when compared. The transcriptome and SNPs will contribute to the exploration of P. chekiangensis genetic resources and the understanding of its molecular mechanisms.

  16. Social Bookmarking Induced Active Page Ranking

    Science.gov (United States)

    Takahashi, Tsubasa; Kitagawa, Hiroyuki; Watanabe, Keita

    Social bookmarking services have recently made it possible for us to register and share our own bookmarks on the web and are attracting attention. The services let us get structured data: (URL, Username, Timestamp, Tag Set). And these data represent user interest in web pages. The number of bookmarks is a barometer of web page value. Some web pages have many bookmarks, but most of those bookmarks may have been posted far in the past. Therefore, even if a web page has many bookmarks, their value is not guaranteed. If most of the bookmarks are very old, the page may be obsolete. In this paper, by focusing on the timestamp sequence of social bookmarkings on web pages, we model their activation levels representing current values. Further, we improve our previously proposed ranking method for web search by introducing the activation level concept. Finally, through experiments, we show effectiveness of the proposed ranking method.

  17. Regression Estimator Using Double Ranked Set Sampling

    Directory of Open Access Journals (Sweden)

    Hani M. Samawi

    2002-06-01

    Full Text Available The performance of a regression estimator based on the double ranked set sample (DRSS scheme, introduced by Al-Saleh and Al-Kadiri (2000, is investigated when the mean of the auxiliary variable X is unknown. Our primary analysis and simulation indicates that using the DRSS regression estimator for estimating the population mean substantially increases relative efficiency compared to using regression estimator based on simple random sampling (SRS or ranked set sampling (RSS (Yu and Lam, 1997 regression estimator.  Moreover, the regression estimator using DRSS is also more efficient than the naïve estimators of the population mean using SRS, RSS (when the correlation coefficient is at least 0.4 and DRSS for high correlation coefficient (at least 0.91. The theory is illustrated using a real data set of trees.

  18. Low-rank quadratic semidefinite programming

    KAUST Repository

    Yuan, Ganzhao

    2013-04-01

    Low rank matrix approximation is an attractive model in large scale machine learning problems, because it can not only reduce the memory and runtime complexity, but also provide a natural way to regularize parameters while preserving learning accuracy. In this paper, we address a special class of nonconvex quadratic matrix optimization problems, which require a low rank positive semidefinite solution. Despite their non-convexity, we exploit the structure of these problems to derive an efficient solver that converges to their local optima. Furthermore, we show that the proposed solution is capable of dramatically enhancing the efficiency and scalability of a variety of concrete problems, which are of significant interest to the machine learning community. These problems include the Top-k Eigenvalue problem, Distance learning and Kernel learning. Extensive experiments on UCI benchmarks have shown the effectiveness and efficiency of our proposed method. © 2012.

  19. Classification of rank 2 cluster varieties

    DEFF Research Database (Denmark)

    Mandel, Travis

    We classify rank 2 cluster varieties (those whose corresponding skew-form has rank 2) according to the deformation type of a generic fiber U of their X-spaces, as defined by Fock and Goncharov. Our approach is based on the work of Gross, Hacking, and Keel for cluster varieties and log Calabi......-Yau surfaces. We find, for example, that U is "positive" (i.e., nearly affine) and either finite-type or non-acyclic (in the cluster sense) if and only if the monodromy of the tropicalization of U is one of Kodaira's matrices for the monodromy of an ellpitic fibration. In the positive cases, we also describe...... the action of the cluster modular group on the tropicalization of U....

  20. Deep Impact: Unintended consequences of journal rank

    CERN Document Server

    Brembs, Björn

    2013-01-01

    Much has been said about the increasing bureaucracy in science, stifling innovation, hampering the creativity of researchers and incentivizing misconduct, even outright fraud. Many anecdotes have been recounted, observations described and conclusions drawn about the negative impact of impact assessment on scientists and science. However, few of these accounts have drawn their conclusions from data, and those that have typically relied on a few studies. In this review, we present the most recent and pertinent data on the consequences that our current scholarly communication system has had on various measures of scientific quality (such as utility/citations, methodological soundness, expert ratings and retractions). These data confirm previous suspicions: using journal rank as an assessment tool is bad scientific practice. Moreover, the data lead us to argue that any journal rank (not only the currently-favored Impact Factor) would have this negative impact. Therefore, we suggest that abandoning journals altoge...

  1. Probabilistic Low-Rank Multitask Learning.

    Science.gov (United States)

    Kong, Yu; Shao, Ming; Li, Kang; Fu, Yun

    2017-01-04

    In this paper, we consider the problem of learning multiple related tasks simultaneously with the goal of improving the generalization performance of individual tasks. The key challenge is to effectively exploit the shared information across multiple tasks as well as preserve the discriminative information for each individual task. To address this, we propose a novel probabilistic model for multitask learning (MTL) that can automatically balance between low-rank and sparsity constraints. The former assumes a low-rank structure of the underlying predictive hypothesis space to explicitly capture the relationship of different tasks and the latter learns the incoherent sparse patterns private to each task. We derive and perform inference via variational Bayesian methods. Experimental results on both regression and classification tasks on real-world applications demonstrate the effectiveness of the proposed method in dealing with the MTL problems.

  2. A SNP transferability survey within the genus Vitis

    Directory of Open Access Journals (Sweden)

    Walker M Andrew

    2008-12-01

    Full Text Available Abstract Background Efforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115 genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus. Results This study was performed by genotyping 137 SNPs through the SNPlex™ Genotyping System (Applied Biosystems Inc. and by comparing the SNPlex sequencing results across 35 (of the 137 regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers. Conclusion Using SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms, but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera.

  3. Robust SNP genotyping by multiplex PCR and arrayed primer extension

    Directory of Open Access Journals (Sweden)

    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  4. Hybridization and amplification rate correction for affymetrix SNP arrays

    Directory of Open Access Journals (Sweden)

    Wang Quan

    2012-06-01

    Full Text Available Abstract Background Copy number variation (CNV is essential to understand the pathology of many complex diseases at the DNA level. Affymetrix SNP arrays, which are widely used for CNV studies, significantly depend on accurate copy number (CN estimation. Nevertheless, CN estimation may be biased by several factors, including cross-hybridization and training sample batch, as well as genomic waves of intensities induced by sequence-dependent hybridization rate and amplification efficiency. Since many available algorithms only address one or two of the three factors, a high false discovery rate (FDR often results when identifying CNV. Therefore, we have developed a new CNV detection pipeline which is based on hybridization and amplification rate correction (CNVhac. Methods CNVhac first estimates the allelic concentrations (ACs of target sequences by using the sample independent parameters trained through physicochemical hybridization law. Then the raw CN is estimated by taking the ratio of AC to the corresponding average AC from a reference sample set for one specific site. Finally, a hidden Markov model (HMM segmentation process is implemented to detect CNV regions. Results Based on public HapMap data, the results show that CNVhac effectively smoothes the genomic waves and facilitates more accurate raw CN estimates compared to other methods. Moreover, CNVhac alleviates, to a certain extent, the sample dependence of inference and makes CNV calling with appreciable low FDRs. Conclusion CNVhac is an effective approach to address the common difficulties in SNP array analysis, and the working principles of CNVhac can be easily extended to other platforms.

  5. Ranking agility factors affecting hospitals in Iran

    OpenAIRE

    M. Abdi Talarposht; GH. Mahmodi; MA. Jahani

    2017-01-01

    Background: Agility is an effective response to the changing and unpredictable environment and using these changes as opportunities for organizational improvement. Objective: The aim of the present study was to rank the factors affecting agile supply chain of hospitals of Iran. Methods: This applied study was conducted by cross sectional-descriptive method at some point of 2015 for one year. The research population included managers, administrators, faculty members and experts were sele...

  6. Ranking images based on aesthetic qualities.

    OpenAIRE

    Gaur, Aarushi

    2015-01-01

    The qualitative assessment of image content and aesthetic impression is affected by various image attributes and relations between the attributes. Modelling of such assessments in the form of objective rankings and learning image representations based on them is not a straightforward problem. The criteria can be varied with different levels of complexity for various applications. A highly-complex problem could involve a large number of interrelated attributes and features alongside varied rul...

  7. Homological characterisation of Lambda-ranks

    OpenAIRE

    Howson, Susan

    1999-01-01

    If G is a pro-p, p-adic, Lie group and if $\\Lambda(G)$ denotes the Iwasawa algebra of G then we present a formula for determining the $\\Lambda(G)$-rank of a finitely generated $\\Lambda(G)$-module. This is given in terms of the G homology groups of the module. We explore some consequences of this for the structure of $\\Lambda(G)$-modules.

  8. Citation ranking versus peer evaluation of senior faculty research performance

    DEFF Research Database (Denmark)

    Meho, Lokman I.; Sonnenwald, Diane H.

    2000-01-01

    indicator of research performance of senior faculty members? Citation data, book reviews, and peer ranking were compiled and examined for faculty members specializing in Kurdish studies. Analysis shows that normalized citation ranking and citation content analysis data yield identical ranking results....... Analysis also shows that normalized citation ranking and citation content analysis, book reviews, and peer ranking perform similarly (i.e., are highly correlated) for high-ranked and low-ranked senior scholars. Additional evaluation methods and measures that take into account the context and content......The purpose of this study is to analyze the relationship between citation ranking and peer evaluation in assessing senior faculty research performance. Other studies typically derive their peer evaluation data directly from referees, often in the form of ranking. This study uses two additional...

  9. Estimation of rank correlation for clustered data.

    Science.gov (United States)

    Rosner, Bernard; Glynn, Robert J

    2017-06-30

    It is well known that the sample correlation coefficient (Rxy ) is the maximum likelihood estimator of the Pearson correlation (ρxy ) for independent and identically distributed (i.i.d.) bivariate normal data. However, this is not true for ophthalmologic data where X (e.g., visual acuity) and Y (e.g., visual field) are available for each eye and there is positive intraclass correlation for both X and Y in fellow eyes. In this paper, we provide a regression-based approach for obtaining the maximum likelihood estimator of ρxy for clustered data, which can be implemented using standard mixed effects model software. This method is also extended to allow for estimation of partial correlation by controlling both X and Y for a vector U_ of other covariates. In addition, these methods can be extended to allow for estimation of rank correlation for clustered data by (i) converting ranks of both X and Y to the probit scale, (ii) estimating the Pearson correlation between probit scores for X and Y, and (iii) using the relationship between Pearson and rank correlation for bivariate normally distributed data. The validity of the methods in finite-sized samples is supported by simulation studies. Finally, two examples from ophthalmology and analgesic abuse are used to illustrate the methods. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  10. Higher-rank fields and currents

    Energy Technology Data Exchange (ETDEWEB)

    Gelfond, O.A. [Institute of System Research of Russian Academy of Sciences,Nakhimovsky prospect 36-1, 117218, Moscow (Russian Federation); I.E.Tamm Department of Theoretical Physics, Lebedev Physical Institute,Leninsky prospect 53, 119991, Moscow (Russian Federation); Vasiliev, M.A. [I.E.Tamm Department of Theoretical Physics, Lebedev Physical Institute,Leninsky prospect 53, 119991, Moscow (Russian Federation)

    2016-10-13

    Sp(2M) invariant field equations in the space M{sub M} with symmetric matrix coordinates are classified. Analogous results are obtained for Minkowski-like subspaces of M{sub M} which include usual 4d Minkowski space as a particular case. The constructed equations are associated with the tensor products of the Fock (singleton) representation of Sp(2M) of any rank r. The infinite set of higher-spin conserved currents multilinear in rank-one fields in M{sub M} is found. The associated conserved charges are supported by (rM−((r(r−1))/2))-dimensional differential forms in M{sub M}, that are closed by virtue of the rank-2r field equations. The cohomology groups H{sup p}(σ{sub −}{sup r}) with all p and r, which determine the form of appropriate gauge fields and their field equations, are found both for M{sub M} and for its Minkowski-like subspace.

  11. Association between Metabolic Syndrome and Job Rank.

    Science.gov (United States)

    Mehrdad, Ramin; Pouryaghoub, Gholamreza; Moradi, Mahboubeh

    2018-01-01

    The occupation of the people can influence the development of metabolic syndrome. To determine the association between metabolic syndrome and its determinants with the job rank in workers of a large car factory in Iran. 3989 male workers at a large car manufacturing company were invited to participate in this cross-sectional study. Demographic and anthropometric data of the participants, including age, height, weight, and abdominal circumference were measured. Blood samples were taken to measure lipid profile and blood glucose level. Metabolic syndrome was diagnosed in each participant based on ATPIII 2001 criteria. The workers were categorized based on their job rank into 3 groups of (1) office workers, (2) workers with physical exertion, and (3) workers with chemical exposure. The study characteristics, particularly the frequency of metabolic syndrome and its determinants were compared among the study groups. The prevalence of metabolic syndrome in our study was 7.7% (95% CI 6.9 to 8.5). HDL levels were significantly lower in those who had chemical exposure (p=0.045). Diastolic blood pressure was significantly higher in those who had mechanical exertion (p=0.026). The frequency of metabolic syndrome in the office workers, workers with physical exertion, and workers with chemical exposure was 7.3%, 7.9%, and 7.8%, respectively (p=0.836). Seemingly, there is no association between metabolic syndrome and job rank.

  12. [Ranke and modern surgery in Groningen].

    Science.gov (United States)

    van Gijn, Jan; Gijselhart, Joost P

    2012-01-01

    Hans Rudolph Ranke (1849-1887) studied medicine in Halle, located in the eastern part of Germany, where he also trained as a surgeon under Richard von Volkmann (1830-1889), during which time he became familiar with the new antiseptic technique that had been introduced by Joseph Lister (1827-1912). In 1878 he was appointed head of the department of surgery in Groningen, the Netherlands, where his predecessor had been chronically indisposed and developments were flagging. Within a few months, Ranke had introduced disinfection by using carbolic acid both before and during operations. For the disinfection of wound dressings, he replaced carbolic acid with thymol as this was less pungent and foul-smelling. The rate of postoperative infections dropped to a minimum despite the inadequate housing and living conditions of the patients with infectious diseases. In 1887, at the age of 37, Ranke died after a brief illness - possibly glomerulonephritis - only eight years after he had assumed office. A street in the city of Groningen near its present-day University Medical Centre has been named after him.

  13. Ranking agility factors affecting hospitals in Iran

    Directory of Open Access Journals (Sweden)

    M. Abdi Talarposht

    2017-04-01

    Full Text Available Background: Agility is an effective response to the changing and unpredictable environment and using these changes as opportunities for organizational improvement. Objective: The aim of the present study was to rank the factors affecting agile supply chain of hospitals of Iran. Methods: This applied study was conducted by cross sectional-descriptive method at some point of 2015 for one year. The research population included managers, administrators, faculty members and experts were selected hospitals. A total of 260 people were selected as sample from the health centers. The construct validity of the questionnaire was approved by confirmatory factor analysis test and its reliability was approved by Cronbach's alpha (α=0.97. All data were analyzed by Kolmogorov-Smirnov, Chi-square and Friedman tests. Findings: The development of staff skills, the use of information technology, the integration of processes, appropriate planning, and customer satisfaction and product quality had a significant impact on the agility of public hospitals of Iran (P<0.001. New product introductions had earned the highest ranking and the development of staff skills earned the lowest ranking. Conclusion: The new product introduction, market responsiveness and sensitivity, reduce costs, and the integration of organizational processes, ratings better to have acquired agility hospitals in Iran. Therefore, planners and officials of hospitals have to, through the promotion quality and variety of services customer-oriented, providing a basis for investing in the hospital and etc to apply for agility supply chain public hospitals of Iran.

  14. ASSIsT: An Automatic SNP ScorIng Tool for in- and outbreeding species

    NARCIS (Netherlands)

    Guardo, Di M.; Micheletti, D.; Bianco, L.; Koehorst-van Putten, H.J.J.; Longhi, S.; Costa, F.; Aranzana, M.J.; Velasco, R.; Arus, P.; Troggio, M.; Weg, van de W.E.

    2015-01-01

    ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called

  15. Evaluation of the OvineSNP50 chip for use in four South African ...

    African Journals Online (AJOL)

    Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua ...

  16. Short communication Validation of the 50k Illumina goat SNP chip in ...

    African Journals Online (AJOL)

    Simon

    2015-03-12

    Mar 12, 2015 ... phenotypic variation in two important price-determining traits, namely fibre diameter and fleece weight, were genotyped with the .... Table 2 SNP densities before and after linkage disequilibrium filtering. Minimum gap (bp) Maximum gap (kb) Median gap (kb). SNP density. (average gap). Before LD pruning.

  17. Development and application of a 20K SNP array in potato

    NARCIS (Netherlands)

    Vos, Peter

    2016-01-01

    In this thesis the results are described of investigations of various application of genome wide SNP (single nucleotide polymorphism) markers. The set of SNP markers was identified by GBS (genotyping by sequencing) strategy. The resulting dataset of 129,156 SNPs across 83 tetraploid varieties was

  18. Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm.

    Science.gov (United States)

    Chuang, Li-Yeh; Lane, Hsien-Yuan; Lin, Yu-Da; Lin, Ming-Teng; Yang, Cheng-Hong; Chang, Hsueh-Wei

    2014-01-01

    Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear. This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups). The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance. This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.

  19. Ranking Fuzzy Numbers and Its Application to Products Attributes Preferences

    OpenAIRE

    Lazim Abdullah; Nor Nashrah Ahmad Fauzee

    2011-01-01

    Ranking is one of the widely used methods in fuzzy decision making environment. The recent ranking fuzzy numbers proposed by Wang and Li is claimed to be the improved version in ranking. However, the method was never been simplified and tested in real life application. This paper presents a four-step computation of ranking fuzzy numbers and its application in ranking attributes of selected chocolate products.  The four steps algorithm was formulated to rank fuzzy numbers and followed by a tes...

  20. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

    Directory of Open Access Journals (Sweden)

    Maider Ibarrola-Villava

    Full Text Available As the incidence of Malignant Melanoma (MM reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2 and rs2069398 (SILV/CKD2, were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls. A novel SNP located on the SLC45A2 gene (rs35414 was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001. None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls. Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

  1. Design and characterization of a 52K SNP chip for goats.

    Directory of Open Access Journals (Sweden)

    Gwenola Tosser-Klopp

    Full Text Available The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed: Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes, sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

  2. Design and characterization of a 52K SNP chip for goats.

    Science.gov (United States)

    Tosser-Klopp, Gwenola; Bardou, Philippe; Bouchez, Olivier; Cabau, Cédric; Crooijmans, Richard; Dong, Yang; Donnadieu-Tonon, Cécile; Eggen, André; Heuven, Henri C M; Jamli, Saadiah; Jiken, Abdullah Johari; Klopp, Christophe; Lawley, Cynthia T; McEwan, John; Martin, Patrice; Moreno, Carole R; Mulsant, Philippe; Nabihoudine, Ibouniyamine; Pailhoux, Eric; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Sayre, Brian L; Tircazes, Aurélie; Jun Wang; Wang, Wen; Zhang, Wenguang

    2014-01-01

    The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

  3. Association between MDM2 SNP309 T>G polymorphism and the risk of bladder cancer: new data in a Chinese population and an updated meta-analysis

    Directory of Open Access Journals (Sweden)

    Xie LG

    2015-12-01

    Full Text Available Linguo Xie,1,2,* Yan Sun,2,* Tao Chen,1,2,* Dawei Tian,1,2 Yujuan Li,3 Yu Zhang,1,2 Na Ding,2 Zhonghua Shen,1,2 Hao Xu,1,2 Xuewu Nian,4 Nan Sha,1,2 Ruifa Han,1,2 Hailong Hu,1,2 Changli Wu1,2 Objective: Human murine double minute 2 protein (MDM2 is mainly a negative regulator of p53 tumor suppressor pathway. We aimed to investigate the association between MDM2 SNP309 polymorphism and bladder cancer risk. Methods: A total of 535 bladder cancer patients and 649 health controls were recruited for our study. MDM2 SNP309 T>G polymorphism was genotyped by polymerase chain reaction-ligase detection reaction method. Logistic regression was used to analyze the relationship between the genotype and susceptibility of bladder cancer. Kaplan–Meier estimates and log-rank test were obtained to analyze the association between the genotype and risk of recrudesce in nonmuscle-invasive bladder cancer patients. A multivariable Cox proportional hazards model was fitted to identify independent prognostic factors. To further investigate the association, we conducted a meta-analysis including six studies. Results: The frequency of the MDM2 SNP309 T>G polymorphism showed no significant difference between cases and controls (all P>0.05. In the stratification analysis, the results showed that G allele carriers were prone to have a significant decrease in risk of low-grade bladder cancer (adjusted odds ratio: 0.613, 95% confidence interval: 0.427–0.881, and G variant was associated with a significantly reduced risk of recurrence in nonmuscle-invasive bladder cancer patients with or without chemotherapy (P<0.05. The results of the meta-analysis showed that G allele and GG genotype of MDM2 SNP309 polymorphism were significantly associated with increased risk of bladder cancer in Caucasians (both P<0.05, and no association was observed in total populations and Asians (P>0.05. Conclusion: MDM2 SNP309 T>G polymorphism has no influence on bladder cancer risk in Asians, but

  4. SNP Polymorphism Survey of the Parental Lines of ISRA Sorghum Breeding Program as Part of the Feed the Future

    Data.gov (United States)

    US Agency for International Development — Polymorphism of SNP Markers (single nucleotide polymorphisms) was assessed on 24 parental lines of the ISRA sorghum breeding program . About 1300 SNP have been used...

  5. Ranking U-Sapiens 2010-2

    Directory of Open Access Journals (Sweden)

    Carlos-Roberto Peña-Barrera

    2011-08-01

    Full Text Available Los principales objetivos de esta investigación son los siguientes: (1 que la comunidad científica nacional e internacional y la sociedad en general co-nozcan los resultados del Ranking U-Sapiens Colombia 2010_2, el cual clasifica a cada institución de educación superior colombiana según puntaje, posición y cuartil; (2 destacar los movimientos más importantes al comparar los resultados del ranking 2010_1 con los del 2010_2; (3 publicar las respuestas de algunos actores de la academia nacional con respecto a la dinámica de la investigación en el país; (4 reconocer algunas instituciones, medios de comunicación e investigadores que se han interesado a modo de reflexión, referenciación o citación por esta investigación; y (5 dar a conocer el «Sello Ranking U-Sapiens Colombia» para las IES clasificadas. El alcance de este estudio en cuanto a actores abordó todas y cada una de las IES nacionales (aunque solo algunas lograran entrar al ranking y en cuanto a tiempo, un periodo referido al primer semestre de 2010 con respecto a: (1 los resultados 2010-1 de revistas indexadas en Publindex, (2 los programas de maestrías y doctorados activos durante 2010-1 según el Ministerio de Educación Nacional, y (3 los resultados de grupos de investigación clasificados para 2010 según Colciencias. El método empleado para esta investigación es el mismo que para el ranking 2010_1, salvo por una especificación aún más detallada en uno de los pasos del modelo (las variables α, β, γ; es completamente cuantitativo y los datos de las variables que fundamentan sus resultados provienen de Colciencias y el Ministerio de Educación Nacional; y en esta ocasión se darán a conocer los resultados por variable para 2010_1 y 2010_2. Los resultados más relevantes son estos: (1 entraron 8 IES al ranking y salieron 3; (2 las 3 primeras IES son públicas; (3 en total hay 6 instituciones universitarias en el ranking; (4 7 de las 10 primeras IES son

  6. Ranking the Online Documents Based on Relative Credibility Measures

    Directory of Open Access Journals (Sweden)

    Ahmad Dahlan

    2009-05-01

    Full Text Available Information searching is the most popular activity in Internet. Usually the search engine provides the search results ranked by the relevance. However, for a certain purpose that concerns with information credibility, particularly citing information for scientific works, another approach of ranking the search engine results is required. This paper presents a study on developing a new ranking method based on the credibility of information. The method is built up upon two well-known algorithms, PageRank and Citation Analysis. The result of the experiment that used Spearman Rank Correlation Coefficient to compare the proposed rank (generated by the method with the standard rank (generated manually by a group of experts showed that the average Spearman 0 < rS < critical value. It means that the correlation was proven but it was not significant. Hence the proposed rank does not satisfy the standard but the performance could be improved.

  7. Ranking the Online Documents Based on Relative Credibility Measures

    Directory of Open Access Journals (Sweden)

    Ahmad Dahlan

    2013-09-01

    Full Text Available Information searching is the most popular activity in Internet. Usually the search engine provides the search results ranked by the relevance. However, for a certain purpose that concerns with information credibility, particularly citing information for scientific works, another approach of ranking the search engine results is required. This paper presents a study on developing a new ranking method based on the credibility of information. The method is built up upon two well-known algorithms, PageRank and Citation Analysis. The result of the experiment that used Spearman Rank Correlation Coefficient to compare the proposed rank (generated by the method with the standard rank (generated manually by a group of experts showed that the average Spearman 0 < rS < critical value. It means that the correlation was proven but it was not significant. Hence the proposed rank does not satisfy the standard but the performance could be improved.

  8. On the Nonnegative Rank of Euclidean Distance Matrices.

    Science.gov (United States)

    Lin, Matthew M; Chu, Moody T

    2010-09-01

    The Euclidean distance matrix for n distinct points in ℝ r is generically of rank r + 2. It is shown in this paper via a geometric argument that its nonnegative rank for the case r = 1 is generically n.

  9. Global Low-Rank Image Restoration With Gaussian Mixture Model.

    Science.gov (United States)

    Zhang, Sibo; Jiao, Licheng; Liu, Fang; Wang, Shuang

    2017-06-27

    Low-rank restoration has recently attracted a lot of attention in the research of computer vision. Empirical studies show that exploring the low-rank property of the patch groups can lead to superior restoration performance, however, there is limited achievement on the global low-rank restoration because the rank minimization at image level is too strong for the natural images which seldom match the low-rank condition. In this paper, we describe a flexible global low-rank restoration model which introduces the local statistical properties into the rank minimization. The proposed model can effectively recover the latent global low-rank structure via nuclear norm, as well as the fine details via Gaussian mixture model. An alternating scheme is developed to estimate the Gaussian parameters and the restored image, and it shows excellent convergence and stability. Besides, experiments on image and video sequence datasets show the effectiveness of the proposed method in image inpainting problems.

  10. Algebraic and computational aspects of real tensor ranks

    CERN Document Server

    Sakata, Toshio; Miyazaki, Mitsuhiro

    2016-01-01

    This book provides comprehensive summaries of theoretical (algebraic) and computational aspects of tensor ranks, maximal ranks, and typical ranks, over the real number field. Although tensor ranks have been often argued in the complex number field, it should be emphasized that this book treats real tensor ranks, which have direct applications in statistics. The book provides several interesting ideas, including determinant polynomials, determinantal ideals, absolutely nonsingular tensors, absolutely full column rank tensors, and their connection to bilinear maps and Hurwitz-Radon numbers. In addition to reviews of methods to determine real tensor ranks in details, global theories such as the Jacobian method are also reviewed in details. The book includes as well an accessible and comprehensive introduction of mathematical backgrounds, with basics of positive polynomials and calculations by using the Groebner basis. Furthermore, this book provides insights into numerical methods of finding tensor ranks through...

  11. Implicit Block Diagonal Low-Rank Representation.

    Science.gov (United States)

    Xie, Xingyu; Guo, Xianglin; Liu, Guangcan; Wang, Jun

    2017-10-17

    While current block diagonal constrained subspace clustering methods are performed explicitly on the original data space, in practice it is often more desirable to embed the block diagonal prior into the reproducing kernel Hilbert feature space by kernelization techniques, as the underlying data structure in reality is usually nonlinear. However, it is still unknown how to carry out the embedding and kernelization in the models with block diagonal constraints. In this work, we shall take a step in this direction. First, we establish a novel model termed Implicit Block Diagonal Low-Rank Representation (IBDLR), by incorporating the implicit feature representation and block diagonal prior into the prevalent Low-Rank Representation (LRR) method. Second, mostly important, we show that the model in IBDLR could be kernelized by making use of a smoothed dual representation and the specifics of a proximal gradient based optimization algorithm. Finally, we provide some theoretical analyses for the convergence of our optimization algorithm. Comprehensive experiments on synthetic and realworld datasets demonstrate the superiorities of our IBDLR over state-of-the-art methods.While current block diagonal constrained subspace clustering methods are performed explicitly on the original data space, in practice it is often more desirable to embed the block diagonal prior into the reproducing kernel Hilbert feature space by kernelization techniques, as the underlying data structure in reality is usually nonlinear. However, it is still unknown how to carry out the embedding and kernelization in the models with block diagonal constraints. In this work, we shall take a step in this direction. First, we establish a novel model termed Implicit Block Diagonal Low-Rank Representation (IBDLR), by incorporating the implicit feature representation and block diagonal prior into the prevalent Low-Rank Representation (LRR) method. Second, mostly important, we show that the model in IBDLR could be

  12. Tecer sobe no ranking da Capes

    Directory of Open Access Journals (Sweden)

    José Aparecido

    2013-11-01

    Full Text Available Surpresa ainda maior foi verificar que prosseguimos no rumo da consolidação, crescendo no ranking – chegando a B3 em alguns campos, como pode ser visto no portal de buscas do Qualis Capes http://qualis.capes.gov.br/webqualis/principal.seamhttp://qualis.capes.gov, que apresenta nossa classificação abaixo:   B3 ADMINISTRAÇÃO, CIÊNCIAS CONTÁBEIS E TURISMO B4 CIÊNCIAS SOCIAIS APLICADAS I B4 EDUCAÇÃO B4 INTERDISCIPLINAR B5 DIREITO B5 HISTÓRIA C CIÊNCIA DA COMPUTAÇÃO

  13. On Stein's unbiased risk estimate for reduced rank estimators

    DEFF Research Database (Denmark)

    Hansen, Niels Richard

    2018-01-01

    Stein's unbiased risk estimate (SURE) is considered for matrix valued observables with low rank means. It is shown that SURE is applicable to a class of spectral function estimators including the reduced rank estimator.......Stein's unbiased risk estimate (SURE) is considered for matrix valued observables with low rank means. It is shown that SURE is applicable to a class of spectral function estimators including the reduced rank estimator....

  14. A study of serial ranks via random graphs

    OpenAIRE

    Haeusler, Erich; Mason, David M.; Turova, Tatyana S.

    2000-01-01

    Serial ranks have long been used as the basis for nonparametric tests of independence in time series analysis. We shall study the underlying graph structure of serial ranks. This will lead us to a basic martingale which will allow us to construct a weighted approximation to a serial rank process. To show the applicability of this approximation, we will use it to prove two very general central limit theorems for Wald-Wolfowitz-type serial rank statistics.

  15. Typing of 48 autosomal SNPs and amelogenin with GenPlex SNP genotyping system in forensic genetics

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Stangegaard, Michael; Børsting, Claus

    2008-01-01

    , Somalia and Greenland were investigated with GenPlex using a Biomek 3000 (Beckman Coulter) robot. The results were compared to results obtained with an ISO 17025 accredited SNP typing assay based on single base extension (SBE). With the GenPlex SNP genotyping system, full SNP profiles were obtained in 97...

  16. Do PageRank-based author rankings outperform simple citation counts?

    CERN Document Server

    Fiala, Dalibor; Žitnik, Slavko; Bajec, Marko

    2015-01-01

    The basic indicators of a researcher's productivity and impact are still the number of publications and their citation counts. These metrics are clear, straightforward, and easy to obtain. When a ranking of scholars is needed, for instance in grant, award, or promotion procedures, their use is the fastest and cheapest way of prioritizing some scientists over others. However, due to their nature, there is a danger of oversimplifying scientific achievements. Therefore, many other indicators have been proposed including the usage of the PageRank algorithm known for the ranking of webpages and its modifications suited to citation networks. Nevertheless, this recursive method is computationally expensive and even if it has the advantage of favouring prestige over popularity, its application should be well justified, particularly when compared to the standard citation counts. In this study, we analyze three large datasets of computer science papers in the categories of artificial intelligence, software engineering,...

  17. Rice SNP-seek database update: new SNPs, indels, and queries.

    Science.gov (United States)

    Mansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L; Alexandrov, Nickolai

    2017-01-04

    We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. an investigation into n investigation into index ranking technique for ...

    African Journals Online (AJOL)

    eobe

    The study shows that the utility of the ranking technique may be limited by em. Therefore users of the technique for ranking fuzzy numbers have to maker, risk attitude, critical path, total float ranking s usually faced with a ully managing projects. The th project management is vities in the project have the activity times in the.

  19. Variation in rank abundance replicate samples and impact of clustering

    NARCIS (Netherlands)

    Neuteboom, J.H.; Struik, P.C.

    2005-01-01

    Calculating a single-sample rank abundance curve by using the negative-binomial distribution provides a way to investigate the variability within rank abundance replicate samples and yields a measure of the degree of heterogeneity of the sampled community. The calculation of the single-sample rank

  20. PageRank in scale-free random graphs

    NARCIS (Netherlands)

    Chen, Ningyuan; Litvak, Nelli; Olvera-Cravioto, Mariana; Bonata, Anthony; Chung, Fan; Pralat, Paweł

    2014-01-01

    We analyze the distribution of PageRank on a directed configuration model and show that as the size of the graph grows to infinity, the PageRank of a randomly chosen node can be closely approximated by the PageRank of the root node of an appropriately constructed tree. This tree approximation is in

  1. Tutorial: Calculating Percentile Rank and Percentile Norms Using SPSS

    Science.gov (United States)

    Baumgartner, Ted A.

    2009-01-01

    Practitioners can benefit from using norms, but they often have to develop their own percentile rank and percentile norms. This article is a tutorial on how to quickly and easily calculate percentile rank and percentile norms using SPSS, and this information is presented for a data set. Some issues in calculating percentile rank and percentile…

  2. University Rankings 2.0: New Frontiers in Institutional Comparisons

    Science.gov (United States)

    Usher, Alex

    2009-01-01

    The number of university rankings systems in use around the world has increased dramatically over the last decade. As they have spread, they have mutated; no longer are ranking systems simply clones of the original ranking systems such as "US News" and "World Report". A number of different types of "mutation" have occurred, so that there are now…

  3. Ranking Scholarly Publishers in Political Science: An Alternative Approach

    Science.gov (United States)

    Garand, James C.; Giles, Micheal W.

    2011-01-01

    Previous research has documented how political scientists evaluate and rank scholarly journals, but the evaluation and ranking of scholarly book publishers has drawn less attention. In this article, we use data from a survey of 603 American political scientists to generate a ranking of scholarly publishers in political science. We used open-ended…

  4. Ranking Quality in Higher Education: Guiding or Misleading?

    Science.gov (United States)

    Bergseth, Brita; Petocz, Peter; Abrandt Dahlgren, Madeleine

    2014-01-01

    The study examines two different models of measuring, assessing and ranking quality in higher education. Do different systems of quality assessment lead to equivalent conclusions about the quality of education? This comparative study is based on the rankings of 24 Swedish higher education institutions. Two ranking actors have independently…

  5. Cardinal priority ranking based decision making for economic ...

    African Journals Online (AJOL)

    To access the indifference band, interaction with the decision maker is obtained via cardinal priority ranking (CPR) of the objectives. The cardinal priority ranking is constructed in the functional space and then transformed into the decision space, so the cardinal priority ranking of objectives relate the decision maker's ...

  6. A Fast Algorithm for Generating Permutation Distribution of Ranks in ...

    African Journals Online (AJOL)

    ... function of the distribution of the ranks. This further gives insight into the permutation distribution of a rank statistics. The algorithm is implemented with the aid of the computer algebra system Mathematica. Key words: Combinatorics, generating function, permutation distribution, rank statistics, partitions, computer algebra.

  7. Calibrating Canadian Universities: Rankings for Sale Once Again

    Science.gov (United States)

    Cramer, Kenneth M.; Page, Stewart

    2007-01-01

    A summary and update on recent research by the authors and others concerning rankings of Canadian universities is presented. Some specific data are reported in regard to the 2005 and 2006 ranking data published by "Maclean's" magazine. Some criticisms and difficulties with the use of rank-based data are outlined with regard to the issues…

  8. Higher Education Ranking and Leagues Tables: Lessons Learned from Benchmarking

    Science.gov (United States)

    Proulx, Roland

    2007-01-01

    The paper intends to contribute to the debate on ranking and league tables by adopting a critical approach to ranking methodologies from the point of view of a university benchmarking exercise. The absence of a strict benchmarking exercise in the ranking process has been, in the opinion of the author, one of the major problems encountered in the…

  9. Synthesis of Partial Rankings of Points of Interest Using Crowdsourcing

    DEFF Research Database (Denmark)

    Keles, Ilkcan; Saltenis, Simonas; Jensen, Christian Søndergaard

    2015-01-01

    to the query keywords and the query location. A key challenge in being able to make progress on the design of ranking functions is to be able to assess the quality of the results returned by ranking functions. We propose a model that synthesizes a ranking of points of interest from answers to crowdsourced...

  10. SNP-based typing: a useful tool to study Bordetella pertussis populations.

    Directory of Open Access Journals (Sweden)

    Marjolein van Gent

    Full Text Available To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA. In this study, a single nucleotide polymorphism (SNP typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in The Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.

  11. Fuzzy Multicriteria Ranking of Aluminium Coating Methods

    Science.gov (United States)

    Batzias, A. F.

    2007-12-01

    This work deals with multicriteria ranking of aluminium coating methods. The alternatives used are: sulfuric acid anodization, A1; oxalic acid anodization, A2; chromic acid anodization, A3; phosphoric acid anodization, A4; integral color anodizing, A5; chemical conversion coating, A6; electrostatic powder deposition, A7. The criteria used are: cost of production, f1; environmental friendliness of production process, f2; appearance (texture), f3; reflectivity, f4; response to coloring, f5; corrosion resistance, f6; abrasion resistance, f7; fatigue resistance, f8. Five experts coming from relevant industrial units set grades to the criteria vector and the preference matrix according to a properly modified Delphi method. Sensitivity analysis of the ranked first alternative A1 against the `second best', which was A3 at low and A7 at high resolution levels proved that the solution is robust. The dependence of anodized products quality on upstream processes is presented and the impact of energy price increase on industrial cost is discussed.

  12. Rank order scaling of pictorial depth.

    Science.gov (United States)

    van Doorn, Andrea; Koenderink, Jan; Wagemans, Johan

    2011-01-01

    We address the topic of "pictorial depth" in cases of pictures that are unlike photographic renderings. The most basic measure of "depth" is no doubt that of depth order. We establish depth order through the pairwise depth-comparison method, involving all pairs from a set of 49 fiducial points. The pictorial space for this study was evoked by a capriccio (imaginary landscape) by Francesco Guardi (1712-1793). In such a drawing pictorial space is suggested by the artist through a small set of conventional depth cues. As a result typical Western observers tend to agree largely in their visual awareness when looking at such art. We rank depths for locations that are not on a single surface and far apart in pictorial space. We find that observers resolve about 40 distinct depth layers and agree largely in this. From a previous experiment we have metrical data for the same observers. The rank correlations between the results are high. Perhaps surprisingly, we find no correlation between the number of distinct depth layers and the total metrical depth range. Thus, the relation between subjective magnitude and discrimination threshold fails to hold for pictorial depth.

  13. Condensing biomedical journal texts through paragraph ranking.

    Science.gov (United States)

    Chiang, Jung-Hsien; Liu, Heng-Hui; Huang, Yi-Ting

    2011-04-15

    The growing availability of full-text scientific articles raises the important issue of how to most efficiently digest full-text content. Although article titles and abstracts provide accurate and concise information on an article's contents, their brevity inevitably entails the loss of detail. Full-text articles provide those details, but require more time to read. The primary goal of this study is to combine the advantages of concise abstracts and detail-rich full-texts to ease the burden of reading. We retrieved abstract-related paragraphs from full-text articles through shared keywords between the abstract and paragraphs from the main text. Significant paragraphs were then recommended by applying a proposed paragraph ranking approach. Finally, the user was provided with a condensed text consisting of these significant paragraphs, allowing the user to save time from perusing the whole article. We compared the performance of the proposed approach with a keyword counting approach and a PageRank-like approach. Evaluation was conducted in two aspects: the importance of each retrieved paragraph and the information coverage of a set of retrieved paragraphs. In both evaluations, the proposed approach outperformed the other approaches. jchiang@mail.ncku.edu.tw.

  14. Rank hypocrisies the insult of the REF

    CERN Document Server

    Sayer, Derek

    2015-01-01

    "The REF is right out of Havel's and Kundera's Eastern Europe: a state-administered exercise to rank academic research like hotel chains dependent on the active collaboration of the UK professoriate. In crystalline text steeped in cold rage, Sayer takes aim at the REF's central claim, that it is a legitimate process of expert peer review. He critiques university and national-level REF processes against actual practices of scholarly review as found in academic journals, university presses, and North American tenure procedures. His analysis is damning. If the REF fails as scholarly review, how can academics and universities continue to participate? And how can government use its rankings as a basis for public policy?" - Tarak Barkawi, Reader in the Department of International Relations, London School of Economics "Many academics across the world have come to see the REF as an arrogant attempt to raise national research standards that has resulted in a variety of self-inflicted wounds to UK higher education. Der...

  15. Using Mendelian inheritance to improve high-throughput SNP discovery.

    Science.gov (United States)

    Chen, Nancy; Van Hout, Cristopher V; Gottipati, Srikanth; Clark, Andrew G

    2014-11-01

    Restriction site-associated DNA sequencing or genotyping-by-sequencing (GBS) approaches allow for rapid and cost-effective discovery and genotyping of thousands of single-nucleotide polymorphisms (SNPs) in multiple individuals. However, rigorous quality control practices are needed to avoid high levels of error and bias with these reduced representation methods. We developed a formal statistical framework for filtering spurious loci, using Mendelian inheritance patterns in nuclear families, that accommodates variable-quality genotype calls and missing data--both rampant issues with GBS data--and for identifying sex-linked SNPs. Simulations predict excellent performance of both the Mendelian filter and the sex-linkage assignment under a variety of conditions. We further evaluate our method by applying it to real GBS data and validating a subset of high-quality SNPs. These results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for GBS loci that is complementary to standard coverage and Hardy-Weinberg filters. The described method, implemented in the software MendelChecker, will improve quality control during SNP discovery in nonmodel as well as model organisms. Copyright © 2014 by the Genetics Society of America.

  16. Comparison of PrASE and Pyrosequencing for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Odeberg Jacob

    2006-11-01

    Full Text Available Abstract Background There is an imperative need for SNP genotyping technologies that are cost-effective per sample with retained high accuracy, throughput and flexibility. We have developed a microarray-based technique and compared it to Pyrosequencing. In the protease-mediated allele-specific extension (PrASE, the protease constrains the elongation reaction and thus prevents incorrect nucleotide incorporation to mismatched 3'-termini primers. Results The assay is automated for 48 genotyping reactions in parallel followed by a tag-microarray detection system. A script automatically visualizes the results in cluster diagrams and assigns the genotypes. Ten polymorphic positions suggested as prothrombotic genetic variations were analyzed with Pyrosequencing and PrASE technologies in 442 samples and 99.8 % concordance was achieved. In addition to accuracy, the robustness and reproducibility of the technique has been investigated. Conclusion The results of this study strongly indicate that the PrASE technology can offer significant improvements in terms of accuracy and robustness and thereof increased number of typeable SNPs.

  17. A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

    Science.gov (United States)

    Talukder, Zahirul I.; Gong, Li; Hulke, Brent S.; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

    2014-01-01

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping. PMID:25014030

  18. Partial Kernelization for Rank Aggregation: Theory and Experiments

    Science.gov (United States)

    Betzler, Nadja; Bredereck, Robert; Niedermeier, Rolf

    Rank Aggregation is important in many areas ranging from web search over databases to bioinformatics. The underlying decision problem Kemeny Score is NP-complete even in case of four input rankings to be aggregated into a "median ranking". We study efficient polynomial-time data reduction rules that allow us to find optimal median rankings. On the theoretical side, we improve a result for a "partial problem kernel" from quadratic to linear size. On the practical side, we provide encouraging experimental results with data based on web search and sport competitions, e.g., computing optimal median rankings for real-world instances with more than 100 candidates within milliseconds.

  19. SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers.

    Directory of Open Access Journals (Sweden)

    Hilal Betul Kaya

    Full Text Available BACKGROUND: The olive tree (Olea europaea L. is a diploid (2n = 2x = 46 outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP discovery in olive. The objectives of this study were (1 to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2 to characterize 96 olive genotypes originating from different regions of Turkey. METHODOLOGY/PRINCIPAL FINDINGS: Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP and simple sequence repeats (SSR markers. CONCLUSIONS/SIGNIFICANCE: This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL analysis, association mapping and map-based gene cloning in the olive. High levels

  20. Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

    Science.gov (United States)

    Scalabrin, Simone; Gilmore, Barbara; Lawley, Cynthia T.; Gasic, Ksenija; Micheletti, Diego; Rosyara, Umesh R.; Cattonaro, Federica; Vendramin, Elisa; Main, Dorrie; Aramini, Valeria; Blas, Andrea L.; Mockler, Todd C.; Bryant, Douglas W.; Wilhelm, Larry; Troggio, Michela; Sosinski, Bryon; Aranzana, Maria José; Arús, Pere; Iezzoni, Amy; Morgante, Michele; Peace, Cameron

    2012-01-01

    Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species. PMID:22536421

  1. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.

    Directory of Open Access Journals (Sweden)

    Dana B Hancock

    Full Text Available Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1, and its ratio to forced vital capacity (FEV(1/FVC. Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA of single nucleotide polymorphism (SNP and SNP-by-smoking (ever-smoking or pack-years associations on FEV(1 and FEV(1/FVC across 19 studies (total N = 50,047. We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = 5.00×10(-11, HLA-DQB1 and HLA-DQA2 (smallest P(JMA = 4.35×10(-9, and KCNJ2 and SOX9 (smallest P(JMA = 1.28×10(-8 were associated with FEV(1/FVC or FEV(1 in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.

  2. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.

    Science.gov (United States)

    Hancock, Dana B; Soler Artigas, María; Gharib, Sina A; Henry, Amanda; Manichaikul, Ani; Ramasamy, Adaikalavan; Loth, Daan W; Imboden, Medea; Koch, Beate; McArdle, Wendy L; Smith, Albert V; Smolonska, Joanna; Sood, Akshay; Tang, Wenbo; Wilk, Jemma B; Zhai, Guangju; Zhao, Jing Hua; Aschard, Hugues; Burkart, Kristin M; Curjuric, Ivan; Eijgelsheim, Mark; Elliott, Paul; Gu, Xiangjun; Harris, Tamara B; Janson, Christer; Homuth, Georg; Hysi, Pirro G; Liu, Jason Z; Loehr, Laura R; Lohman, Kurt; Loos, Ruth J F; Manning, Alisa K; Marciante, Kristin D; Obeidat, Ma'en; Postma, Dirkje S; Aldrich, Melinda C; Brusselle, Guy G; Chen, Ting-hsu; Eiriksdottir, Gudny; Franceschini, Nora; Heinrich, Joachim; Rotter, Jerome I; Wijmenga, Cisca; Williams, O Dale; Bentley, Amy R; Hofman, Albert; Laurie, Cathy C; Lumley, Thomas; Morrison, Alanna C; Joubert, Bonnie R; Rivadeneira, Fernando; Couper, David J; Kritchevsky, Stephen B; Liu, Yongmei; Wjst, Matthias; Wain, Louise V; Vonk, Judith M; Uitterlinden, André G; Rochat, Thierry; Rich, Stephen S; Psaty, Bruce M; O'Connor, George T; North, Kari E; Mirel, Daniel B; Meibohm, Bernd; Launer, Lenore J; Khaw, Kay-Tee; Hartikainen, Anna-Liisa; Hammond, Christopher J; Gläser, Sven; Marchini, Jonathan; Kraft, Peter; Wareham, Nicholas J; Völzke, Henry; Stricker, Bruno H C; Spector, Timothy D; Probst-Hensch, Nicole M; Jarvis, Deborah; Jarvelin, Marjo-Riitta; Heckbert, Susan R; Gudnason, Vilmundur; Boezen, H Marike; Barr, R Graham; Cassano, Patricia A; Strachan, David P; Fornage, Myriam; Hall, Ian P; Dupuis, Josée; Tobin, Martin D; London, Stephanie J

    2012-01-01

    Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1)), and its ratio to forced vital capacity (FEV(1)/FVC). Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA) of single nucleotide polymorphism (SNP) and SNP-by-smoking (ever-smoking or pack-years) associations on FEV(1) and FEV(1)/FVC across 19 studies (total N = 50,047). We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = )5.00×10(-11)), HLA-DQB1 and HLA-DQA2 (smallest P(JMA = )4.35×10(-9)), and KCNJ2 and SOX9 (smallest P(JMA = )1.28×10(-8)) were associated with FEV(1)/FVC or FEV(1) in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years) interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.

  3. Ranking de universidades chilenas: un análisis multivariado

    Directory of Open Access Journals (Sweden)

    Firinguetti Limone, Luis

    2015-06-01

    Full Text Available In this work a ranking of Chilean universities on the basis of publicly available information is developed. This ranking takes into account the multivariate character of these institutions. Also, it is noted that the results are consistent with those of a well-known international ranking that uses a different set of data, as well as with several multivariate analyses of the data considered in this study.En este trabajo se elabora un ranking de las universidades chilenas en base a información pública disponible. Dicho ranking toma en cuenta el carácter multivariado de estas instituciones. Además, se ha comprobado que los resultados del ranking son consistentes con un conocido ranking internacional construido a partir de un conjunto diferente de datos y con varios análisis multivariados realizados de la información tratada en este estudio.

  4. EU Country Rankings' Sensitivity to the Choice of Welfare Indicators

    DEFF Research Database (Denmark)

    Hussain, M. Azhar

    2016-01-01

    are particularly volatile for countries in the middle of the ranking distribution, while countries with either high or low welfare generally have lower volatility. A multidimensional poverty index has the highest correlation with the latent welfare measure. It is concluded that the observed rankings do not tell......Ranking of countries with respect to some welfare measure is highly popular and takes places with high frequency. Ranking of a country can change over time given the same welfare measure is applied. Rankings can also change depending on which welfare measure is applied in a given year. To what...... extent do we see ranking changes and which existing welfare measures best captures an unobserved, yet existing, notion of welfare in society? To investigate this we apply seven welfare indicators for fifteen EU countries covering the years from 2005 until 2011. The results indicate that rankings...

  5. Inhibition of osteoclastogenesis by RNA interference targeting RANK

    Directory of Open Access Journals (Sweden)

    Ma Ruofan

    2012-08-01

    Full Text Available Abstract Background Osteoclasts and osteoblasts regulate bone resorption and formation to allow bone remodeling and homeostasis. The balance between bone resorption and formation is disturbed by abnormal recruitment of osteoclasts. Osteoclast differentiation is dependent on the receptor activator of nuclear factor NF-kappa B (RANK ligand (RANKL as well as the macrophage colony-stimulating factor (M-CSF. The RANKL/RANK system and RANK signaling induce osteoclast formation mediated by various cytokines. The RANK/RANKL pathway has been primarily implicated in metabolic, degenerative and neoplastic bone disorders or osteolysis. The central role of RANK/RANKL interaction in osteoclastogenesis makes RANK an attractive target for potential therapies in treatment of osteolysis. The purpose of this study was to assess the effect of inhibition of RANK expression in mouse bone marrow macrophages on osteoclast differentiation and bone resorption. Methods Three pairs of short hairpin RNAs (shRNA targeting RANK were designed and synthesized. The optimal shRNA was selected among three pairs of shRNAs by RANK expression analyzed by Western blot and Real-time PCR. We investigated suppression of osteoclastogenesis of mouse bone marrow macrophages (BMMs using the optimal shRNA by targeting RANK. Results Among the three shRANKs examined, shRANK-3 significantly suppressed [88.3%] the RANK expression (p Conclusions These findings suggest that retrovirus-mediated shRNA targeting RANK inhibits osteoclast differentiation and osteolysis. It may appear an attractive target for preventing osteolysis in humans with a potential clinical application.

  6. Asynchronous Gossip for Averaging and Spectral Ranking

    Science.gov (United States)

    Borkar, Vivek S.; Makhijani, Rahul; Sundaresan, Rajesh

    2014-08-01

    We consider two variants of the classical gossip algorithm. The first variant is a version of asynchronous stochastic approximation. We highlight a fundamental difficulty associated with the classical asynchronous gossip scheme, viz., that it may not converge to a desired average, and suggest an alternative scheme based on reinforcement learning that has guaranteed convergence to the desired average. We then discuss a potential application to a wireless network setting with simultaneous link activation constraints. The second variant is a gossip algorithm for distributed computation of the Perron-Frobenius eigenvector of a nonnegative matrix. While the first variant draws upon a reinforcement learning algorithm for an average cost controlled Markov decision problem, the second variant draws upon a reinforcement learning algorithm for risk-sensitive control. We then discuss potential applications of the second variant to ranking schemes, reputation networks, and principal component analysis.

  7. Ranking Visualizations of Correlation Using Weber's Law.

    Science.gov (United States)

    Harrison, Lane; Yang, Fumeng; Franconeri, Steven; Chang, Remco

    2014-12-01

    Despite years of research yielding systems and guidelines to aid visualization design, practitioners still face the challenge of identifying the best visualization for a given dataset and task. One promising approach to circumvent this problem is to leverage perceptual laws to quantitatively evaluate the effectiveness of a visualization design. Following previously established methodologies, we conduct a large scale (n=1687) crowdsourced experiment to investigate whether the perception of correlation in nine commonly used visualizations can be modeled using Weber's law. The results of this experiment contribute to our understanding of information visualization by establishing that: (1) for all tested visualizations, the precision of correlation judgment could be modeled by Weber's law, (2) correlation judgment precision showed striking variation between negatively and positively correlated data, and (3) Weber models provide a concise means to quantify, compare, and rank the perceptual precision afforded by a visualization.

  8. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    . These features make Regmex well suited for a range of biological sequence analysis problems related to motif discovery, exemplified by microRNA seed enrichment, but also including enrichment problems involving complex motifs and combinations of motifs. We demonstrate a number of usage scenarios that take......Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  9. Ranking different factors influencing flight delay

    Directory of Open Access Journals (Sweden)

    Meysam Kazemi Asfe

    2014-07-01

    Full Text Available Flight interruption is one of the most important issues in today’s airline industry. Every year, most airlines spend significant amount of money to compensate flight delays. Therefore, it is important to detect important factors influencing on flight delays. This paper presents an empirical investigation to determine important factors on this issue. The study also asks some decision makers to make pairwise comparison and ranks various factors using the art of analytical hierarchy process. The study determines that technical defects and delayed entry were among the most important factors to blame for flight delays. In addition, announcing the postponement, replacement aircraft and path replacement are among the most important decisions facing managers in the aviation industry during the disruption of the flight.

  10. De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

    National Research Council Canada - National Science Library

    Pegadaraju, Venkatramana; Nipper, Rick; Hulke, Brent; Qi, Lili; Schultz, Quentin

    2013-01-01

    Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place...

  11. Evaluation of the OvineSNP50 genotyping array in four South ...

    African Journals Online (AJOL)

    Sandenbergh, Lise

    2016-03-21

    Mar 21, 2016 ... genotyped to determine the utility of the OvineSNP50 chip for these important South ... disequilibrium (LD), population genetic structure, association studies and ..... factor 9 (GDF9) is strongly associated with litter size in sheep.

  12. (SNP) of endothelial nitric oxide synthase gene and serum level of ...

    African Journals Online (AJOL)

    T-786C single-nucleotide polymorphism (SNP) of endothelial nitric oxide synthase gene and serum level of vascular endothelial relaxant factor (VERF) in non-diabetic patients with coronary artery disease.

  13. T-786C single-nucleotide polymorphism (SNP) of endothelial nitric ...

    African Journals Online (AJOL)

    T-786C single-nucleotide polymorphism (SNP) of endothelial nitric oxide synthase gene and serum level of vascular endothelial relaxant factor (VERF) in non-diabetic patients with coronary artery disease.

  14. Citrus (Rutaceae SNP Markers Based on Competitive Allele-Specific PCR; Transferability Across the Aurantioideae Subfamily

    Directory of Open Access Journals (Sweden)

    Andres Garcia-Lor

    2013-04-01

    Full Text Available Premise of the study: Single nucleotide polymorphism (SNP markers based on Competitive Allele-Specific PCR (KASPar were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra- and intergeneric levels and systematic germplasm bank characterization. Methods and Results: Forty-two SNP markers were developed using KASPar technology. Forty-one were successfully genotyped in all of the Citrus germplasm, where intra- and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and should be useful for germplasm fingerprinting at a much broader diversity level.

  15. SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it.

    Science.gov (United States)

    Lachance, Joseph; Tishkoff, Sarah A

    2013-09-01

    Whole genome sequencing and SNP genotyping arrays can paint strikingly different pictures of demographic history and natural selection. This is because genotyping arrays contain biased sets of pre-ascertained SNPs. In this short review, we use comparisons between high-coverage whole genome sequences of African hunter-gatherers and data from genotyping arrays to highlight how SNP ascertainment bias distorts population genetic inferences. Sample sizes and the populations in which SNPs are discovered affect the characteristics of observed variants. We find that SNPs on genotyping arrays tend to be older and present in multiple populations. In addition, genotyping arrays cause allele frequency distributions to be shifted towards intermediate frequency alleles, and estimates of linkage disequilibrium are modified. Since population genetic analyses depend on allele frequencies, it is imperative that researchers are aware of the effects of SNP ascertainment bias. With this in mind, we describe multiple ways to correct for SNP ascertainment bias. © 2013 WILEY Periodicals, Inc.

  16. Lack of association between MDM2 promoter SNP309 and clinical outcome in patients with neuroblastoma.

    Science.gov (United States)

    Rihani, Ali; Van Maerken, Tom; De Wilde, Bram; Zeka, Fjoralba; Laureys, Geneviève; Norga, Koen; Tonini, Gian Paolo; Coco, Simona; Versteeg, Rogier; Noguera, Rosa; Schulte, Johannes H; Eggert, Angelika; Stallings, Raymond L; Speleman, Frank; Vandesompele, Jo

    2014-10-01

    While a polymorphism located within the promoter region of the MDM2 proto-oncogene, SNP309 (T > G), has previously been associated with increased risk and aggressiveness of neuroblastoma and other tumor entities, a protective effect has also been reported in certain other cancers. In this study, we evaluated the association of MDM2 SNP309 with outcome in 496 patients with neuroblastoma and its effect on MDM2 expression. No significant difference in overall or event-free survival was observed among patients with neuroblastoma with or without MDM2 SNP309. The presence of SNP309 does not affect MDM2 expression in neuroblastoma. © 2014 Wiley Periodicals, Inc.

  17. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

  18. Polygenic analysis of genome-wide SNP data identifies common variants on allergic rhinitis

    DEFF Research Database (Denmark)

    Mohammadnejad, Afsaneh; Brasch-Andersen, Charlotte; Haagerup, Annette

    Background: Allergic Rhinitis (AR) is a complex disorder that affects many people around the world. There is a high genetic contribution to the development of the AR, as twins and family studies have estimated heritability of more than 33%. Due to the complex nature of the disease, single SNP...... analysis has limited power in identifying the genetic variations for AR. We combined genome-wide association analysis (GWAS) with polygenic risk score (PRS) in exploring the genetic basis underlying the disease. Methods: We collected clinical data on 631 Danish subjects with AR cases consisting of 434...... sibling pairs and unrelated individuals and control subjects of 197 unrelated individuals. SNP genotyping was done by Affymetrix Genome-Wide Human SNP Array 5.0. SNP imputation was performed using "IMPUTE2". Using additive effect model, GWAS was conducted in discovery sample, the genotypes...

  19. High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors

    DEFF Research Database (Denmark)

    Hansen, Thomas V. O.; Vikesaa, Jonas; Buhl, Sine S

    2015-01-01

    BACKGROUND: Human epidermal growth factor receptor-2 (HER2) overexpression and gene amplification are currently established by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. This study investigates whether high-density single nucleotide polymorphism (SNP......) arrays can provide additional diagnostic power to assess HER2 gene status. METHODS: DNA from 65 breast tumor samples previously diagnosed by HER2 IHC and FISH analysis were blinded and examined for HER2 copy number variation employing SNP array analysis. RESULTS: SNP array analysis identified 24 (37......%) samples with selective amplification or imbalance of the HER2 region in the q-arm of chromosome 17. In contrast, only 15 (23%) tumors were found to have HER2 amplification by IHC and FISH analysis. In total, there was a discrepancy in 19 (29%) samples between SNP array and IHC/FISH analysis. In 12...

  20. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

    Directory of Open Access Journals (Sweden)

    Thomas George H

    2006-01-01

    Full Text Available Abstract Background A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes, microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity. SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. Results We have developed SNPscan, a web-accessible tool to analyze and visualize high density SNP data. It enables researchers (1 to visually and quantitatively assess the quality of user-generated SNP data relative to a benchmark data set derived from a control population, (2 to display SNP intensity and allelic call data in order to detect chromosomal copy number anomalies (duplications and deletions, (3 to display uniparental isodisomy based on loss of heterozygosity (LOH across genomic regions, (4 to compare paired samples (e.g. tumor and normal, and (5 to generate a file type for viewing SNP data in the University of California, Santa Cruz (UCSC Human Genome Browser. SNPscan accepts data exported from Affymetrix Copy Number Analysis Tool as its input. We validated SNPscan using data generated from patients with known deletions, duplications, and uniparental disomy. We also inspected previously generated SNP data from 90 apparently normal individuals from the Centre d'Étude du Polymorphisme Humain (CEPH collection, and identified three cases of uniparental isodisomy, four females having an apparently mosaic X chromosome, two mislabelled SNP data sets, and one microdeletion on chromosome 2 with mosaicism from an apparently normal female. These previously unrecognized abnormalities were all detected using SNPscan. The microdeletion was independently

  1. Evaluation of breast cancer susceptibility using improved genetic algorithms to generate genotype SNP barcodes.

    Science.gov (United States)

    Yang, Cheng-Hong; Lin, Yu-Da; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2013-01-01

    Genetic association is a challenging task for the identification and characterization of genes that increase the susceptibility to common complex multifactorial diseases. To fully execute genetic studies of complex diseases, modern geneticists face the challenge of detecting interactions between loci. A genetic algorithm (GA) is developed to detect the association of genotype frequencies of cancer cases and noncancer cases based on statistical analysis. An improved genetic algorithm (IGA) is proposed to improve the reliability of the GA method for high-dimensional SNP-SNP interactions. The strategy offers the top five results to the random population process, in which they guide the GA toward a significant search course. The IGA increases the likelihood of quickly detecting the maximum ratio difference between cancer cases and noncancer cases. The study systematically evaluates the joint effect of 23 SNP combinations of six steroid hormone metabolisms, and signaling-related genes involved in breast carcinogenesis pathways were systematically evaluated, with IGA successfully detecting significant ratio differences between breast cancer cases and noncancer cases. The possible breast cancer risks were subsequently analyzed by odds-ratio (OR) and risk-ratio analysis. The estimated OR of the best SNP barcode is significantly higher than 1 (between 1.15 and 7.01) for specific combinations of two to 13 SNPs. Analysis results support that the IGA provides higher ratio difference values than the GA between breast cancer cases and noncancer cases over 3-SNP to 13-SNP interactions. A more specific SNP-SNP interaction profile for the risk of breast cancer is also provided.

  2. Direct inference of SNP heterozygosity rates and resolution of LOH detection.

    Directory of Open Access Journals (Sweden)

    Xiaohong Li

    2007-11-01

    Full Text Available Single nucleotide polymorphisms (SNPs have been increasingly utilized to investigate somatic genetic abnormalities in premalignancy and cancer. LOH is a common alteration observed during cancer development, and SNP assays have been used to identify LOH at specific chromosomal regions. The design of such studies requires consideration of the resolution for detecting LOH throughout the genome and identification of the number and location of SNPs required to detect genetic alterations in specific genomic regions. Our study evaluated SNP distribution patterns and used probability models, Monte Carlo simulation, and real human subject genotype data to investigate the relationships between the number of SNPs, SNP HET rates, and the sensitivity (resolution for detecting LOH. We report that variances of SNP heterozygosity rate in dbSNP are high for a large proportion of SNPs. Two statistical methods proposed for directly inferring SNP heterozygosity rates require much smaller sample sizes (intermediate sizes and are feasible for practical use in SNP selection or verification. Using HapMap data, we showed that a region of LOH greater than 200 kb can be reliably detected, with losses smaller than 50 kb having a substantially lower detection probability when using all SNPs currently in the HapMap database. Higher densities of SNPs may exist in certain local chromosomal regions that provide some opportunities for reliably detecting LOH of segment sizes smaller than 50 kb. These results suggest that the interpretation of the results from genome-wide scans for LOH using commercial arrays need to consider the relationships among inter-SNP distance, detection probability, and sample size for a specific study. New experimental designs for LOH studies would also benefit from considering the power of detection and sample sizes required to accomplish the proposed aims.

  3. A 48-plex autosomal SNP GenPlex™ assay for human individualization and relationship testing

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Børsting, Claus; Morling, Niels

    2012-01-01

    SNPs are being increasingly used by forensic laboratories. Different platforms have been developed for SNP typing. We describe the GenPlex™ HID system protocol, a new SNP-typing platform developed by Applied Biosystems where 48 of the 52 SNPforID SNPs and amelogenin are included. The GenPlex™ HID...... system protocol has been successfully tested by a number of forensic laboratories using both ordinary and forensic samples....

  4. SNP and mutation data on the web - hidden treasures for uncovering.

    Science.gov (United States)

    Barnes, Michael R

    2002-01-01

    SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant.

  5. SNP and Mutation Data on the Web – Hidden Treasures for Uncovering

    Science.gov (United States)

    2002-01-01

    SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant. PMID:18628874

  6. Functionally informative tag SNP selection using a Pareto-optimal approach.

    Science.gov (United States)

    Lee, Phil Hyoun; Jung, Jae-Yoon; Shatkay, Hagit

    2010-01-01

    Selecting a representative set of single nucleotide polymorphism (SNP) markers for facilitating association studies is an important step to uncover the genetic basis of human disease. Tag SNP selection and functional SNP selection are the two main approaches for addressing the SNP selection problem. However, little was done so far to effectively combine these distinct and possibly competing approaches. Here, we present a new multiobjective optimization framework for identifying SNPs that are both informative tagging and have functional significance (FS). Our selection algorithm is based on the notion of Pareto optimality, which has been extensively used for addressing multiobjective optimization problems in game theory, economics, and engineering. We applied our method to 34 disease-susceptibility genes for lung cancer and compared the performance with that of other systems which support both tag SNP selection and functional SNP selection methods. The comparison shows that our algorithm always finds a subset of SNPs that improves upon the subset selected by other state-of-the-art systems with respect to both selection objectives.

  7. High-resolution SNP arrays in mental retardation diagnostics: how much do we gain?

    Science.gov (United States)

    Bernardini, Laura; Alesi, Viola; Loddo, Sara; Novelli, Antonio; Bottillo, Irene; Battaglia, Agatino; Digilio, Maria Cristina; Zampino, Giuseppe; Ertel, Adam; Fortina, Paolo; Surrey, Saul; Dallapiccola, Bruno

    2010-02-01

    We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes approximately 900,000 SNP probes and 900,000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number 'neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as 'normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as 'normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms.

  8. Imputation of microsatellite alleles from dense SNP genotypes for parental verification.

    Science.gov (United States)

    McClure, Matthew; Sonstegard, Tad; Wiggans, George; Van Tassell, Curtis P

    2012-01-01

    Microsatellite (MS) markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international interest from producers and research communities, no viable means currently exist to verify parentage for an individual unless all familial connections were analyzed using the same DNA marker type (MS or SNP). A simple and cost-effective method was devised to impute MS alleles from SNP haplotypes within breeds. For some MS, imputation results may allow inference across breeds. A total of 347 dairy cattle representing four dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey) were used to generate reference haplotypes. This approach has been verified (>98% accurate) for imputing the International Society of Animal Genetics recommended panel of 12 MS for cattle parentage verification across a validation set of 1,307 dairy animals. Implementation of this method will allow producers and breed associations to transition to SNP-based parentage verification utilizing MS genotypes from historical data on parents where SNP genotypes are missing. This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP-based parental verification.

  9. Imputation of microsatellite alleles from dense SNP genotypes for parental verification

    Directory of Open Access Journals (Sweden)

    Matthew eMcclure

    2012-08-01

    Full Text Available Microsatellite (MS markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP-based assays. Despite domestic and international interest from producers and research communities, no viable means currently exist to verify parentage for an individual unless all familial connections were analyzed using the same DNA marker type (MS or SNP. A simple and cost-effective method was devised to impute MS alleles from SNP haplotypes within breeds. For some MS, imputation results may allow inference across breeds. A total of 347 dairy cattle representing 4 dairy breeds (Brown Swiss, Guernsey, Holstein, and Jersey were used to generate reference haplotypes. This approach has been verified (>98% accurate for imputing the International Society of Animal Genetics (ISAG recommended panel of 12 MS for cattle parentage verification across a validation set of 1,307 dairy animals.. Implementation of this method will allow producers and breed associations to transition to SNP-based parentage verification utilizing MS genotypes from historical data on parents where SNP genotypes are missing. This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP- based parental verification.

  10. Involvement of Sodium Nitroprusside (SNP in the Mechanism That Delays Stem Bending of Different Gerbera Cultivars

    Directory of Open Access Journals (Sweden)

    Aung H. Naing

    2017-11-01

    Full Text Available Longevity of cut flowers of many gerbera cultivars (Gerbera jamesonii is typically short because of stem bending; hence, stem bending that occurs during the early vase life period is a major problem in gerbera. Here, we investigated the effects of sodium nitroprusside (SNP on the delay of stem bending in the gerbera cultivars, Alliance, Rosalin, and Bintang, by examining relative fresh weight, bacterial density in the vase solution, transcriptional analysis of a lignin biosynthesis gene, antioxidant activity, and xylem blockage. All three gerbera cultivars responded to SNP by delaying stem bending, compared to the controls; however, the responses were dose- and cultivar-dependent. Among the treatments, SNP at 20 mg L-1 was the best to delay stem bending in Alliance, while dosages of 10 and 5 mg L-1 were the best for Rosalin and Bintang, respectively. However, stem bending in Alliance and Rosalin was faster than in Bintang, indicating a discrepancy influenced by genotype. According to our analysis of the role of SNP in the delay of stem bending, the results revealed that SNP treatment inhibited bacterial growth and xylem blockage, enhanced expression levels of a lignin biosynthesis gene, and maintained antioxidant activities. Therefore, it is suggested that the cause of stem bending is associated with the above-mentioned parameters and SNP is involved in the mechanism that delays stem bending in the different gerbera cultivars.

  11. Construction of a versatile SNP array for pyramiding useful genes of rice.

    Science.gov (United States)

    Kurokawa, Yusuke; Noda, Tomonori; Yamagata, Yoshiyuki; Angeles-Shim, Rosalyn; Sunohara, Hidehiko; Uehara, Kanako; Furuta, Tomoyuki; Nagai, Keisuke; Jena, Kshirod Kumar; Yasui, Hideshi; Yoshimura, Atsushi; Ashikari, Motoyuki; Doi, Kazuyuki

    2016-01-01

    DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  12. Image Registration based on Low Rank Matrix: Rank-Regularized SSD.

    Science.gov (United States)

    Ghaffari, Aboozar; Fatemizadeh, Emad

    2017-08-25

    Similarity measure is a main core of image registration algorithms. Spatially varying intensity distortion is an important challenge which affects the performance of similarity measures. Correlation among pixels is the main characteristic of this distortion. Similarity measures such as sum-of-squareddifferences (SSD) and mutual information (MI) ignore this correlation; Hence, perfect registration cannot be achieved in the presence of this distortion. In this paper, we model this correlation with the aid of the low rank matrix theory. Based on this model, we compensate this distortion analytically and introduce Rank-Regularized SSD (RRSSD). This new similarity measure is a modified SSD based on singular values of difference image in mono-modal imaging. In fact, image registration and distortion correction are performed simultaneously in the proposed model. Based on our experiments, the RRSSD similarity measure achieves clinically acceptable registration results, and outperforms other state-of-the-art similarity measures such as the well-known method of residual complexity.

  13. Rankings matter: nurse graduates from higher-ranked institutions have higher productivity.

    Science.gov (United States)

    Yakusheva, Olga; Weiss, Marianne

    2017-02-13

    Increasing demand for baccalaureate-prepared nurses has led to rapid growth in the number of baccalaureate-granting programs, and to concerns about educational quality and potential effects on productivity of the graduating nursing workforce. We examined the association of individual productivity of a baccalaureate-prepared nurse with the ranking of the degree-granting institution. For a sample of 691 nurses from general medical-surgical units at a large magnet urban hospital between 6/1/2011-12/31/2011, we conducted multivariate regression analysis of nurse productivity on the ranking of the degree-granting institution, adjusted for age, hospital tenure, gender, and unit-specific effects. Nurse productivity was coded as "top"/"average"/"bottom" based on a computation of individual nurse value-added to patient outcomes. Ranking of the baccalaureate-granting institution was derived from the US News and World Report Best Colleges Rankings' categorization of the nurse's institution as the "first tier" or the "second tier", with diploma or associate degree as the reference category. Relative to diploma or associate degree nurses, nurses who had attended first-tier universities had three-times the odds of being in the top productivity category (OR = 3.18, p productivity (OR = 1.73, p = 0.11). Being in the bottom productivity category was not associated with having a baccalaureate degree or the quality tier. The productivity boost from a nursing baccalaureate degree depends on the quality of the educational institution. Recognizing differences in educational outcomes, initiatives to build a baccalaureate-educated nursing workforce should be accompanied by improved access to high-quality educational institutions.

  14. Optimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications.

    Directory of Open Access Journals (Sweden)

    Xiao-Lin Wu

    Full Text Available Low-density (LD single nucleotide polymorphism (SNP arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO algorithm was developed for design of optimal LD SNP chips that can be imputed accurately to medium-density (MD or high-density (HD SNP genotypes for genomic prediction. The objective function facilitates maximization of non-gap map length and system information for the SNP chip, and the latter is computed either as locus-averaged (LASE or haplotype-averaged Shannon entropy (HASE and adjusted for uniformity of the SNP distribution. HASE performed better than LASE with ≤1,000 SNPs, but required considerably more computing time. Nevertheless, the differences diminished when >5,000 SNPs were selected. Optimization was accomplished conditionally on the presence of SNPs that were obligated to each chromosome. The frame location of SNPs on a chip can be either uniform (evenly spaced or non-uniform. For the latter design, a tunable empirical Beta distribution was used to guide location distribution of frame SNPs such that both ends of each chromosome were enriched with SNPs. The SNP distribution on each chromosome was finalized through the objective function that was locally and empirically maximized. This MOLO algorithm was capable of selecting a set of approximately evenly-spaced and highly-informative SNPs, which in turn led to increased imputation accuracy compared with selection solely of evenly-spaced SNPs. Imputation accuracy increased with LD chip size, and imputation error rate was extremely low for chips with ≥3,000 SNPs. Assuming that genotyping or imputation error occurs at random, imputation error rate can be viewed as the upper limit for genomic prediction error. Our results show that about 25% of imputation error rate was propagated to genomic prediction in an Angus

  15. Using incomplete citation data for MEDLINE results ranking.

    Science.gov (United States)

    Herskovic, Jorge R; Bernstam, Elmer V

    2005-01-01

    Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.

  16. Improving the Incoherence of a Learned Dictionary via Rank Shrinkage.

    Science.gov (United States)

    Ubaru, Shashanka; Seghouane, Abd-Krim; Saad, Yousef

    2017-01-01

    This letter considers the problem of dictionary learning for sparse signal representation whose atoms have low mutual coherence. To learn such dictionaries, at each step, we first update the dictionary using the method of optimal directions (MOD) and then apply a dictionary rank shrinkage step to decrease its mutual coherence. In the rank shrinkage step, we first compute a rank 1 decomposition of the column-normalized least squares estimate of the dictionary obtained from the MOD step. We then shrink the rank of this learned dictionary by transforming the problem of reducing the rank to a nonnegative garrotte estimation problem and solving it using a path-wise coordinate descent approach. We establish theoretical results that show that the rank shrinkage step included will reduce the coherence of the dictionary, which is further validated by experimental results. Numerical experiments illustrating the performance of the proposed algorithm in comparison to various other well-known dictionary learning algorithms are also presented.

  17. LogDet Rank Minimization with Application to Subspace Clustering.

    Science.gov (United States)

    Kang, Zhao; Peng, Chong; Cheng, Jie; Cheng, Qiang

    2015-01-01

    Low-rank matrix is desired in many machine learning and computer vision problems. Most of the recent studies use the nuclear norm as a convex surrogate of the rank operator. However, all singular values are simply added together by the nuclear norm, and thus the rank may not be well approximated in practical problems. In this paper, we propose using a log-determinant (LogDet) function as a smooth and closer, though nonconvex, approximation to rank for obtaining a low-rank representation in subspace clustering. Augmented Lagrange multipliers strategy is applied to iteratively optimize the LogDet-based nonconvex objective function on potentially large-scale data. By making use of the angular information of principal directions of the resultant low-rank representation, an affinity graph matrix is constructed for spectral clustering. Experimental results on motion segmentation and face clustering data demonstrate that the proposed method often outperforms state-of-the-art subspace clustering algorithms.

  18. RANK/RANK-L/OPG in Patients with Bone Metastases Treated with Anticancer Agents and Zoledronic Acid: A Prospective Study

    Directory of Open Access Journals (Sweden)

    Laura Mercatali

    2013-05-01

    Full Text Available Patients with solid cancer frequently develop bone metastases (BM. Zoledronic acid (Zometa®, ZA, routinely used to treat patients with BM, acts on osteoclasts and also has antitumor properties. We aimed to assess the effect of ZA over time in novel bone turnover markers (RANK/receptor activator of nuclear factor-k B ligand (RANK-L/ Osteoprotegerin (OPG and to correlate these with serum N-terminal telopeptide (NTX. The study prospectively evaluated levels of RANK, RANK-L and OPG transcripts by real-time PCR and NTX expression by ELISA in the peripheral blood of 49 consecutive patients with advanced breast, lung or prostate cancer. All patients received the standard ZA schedule and were monitored for 12 months. Median baseline values of RANK, RANK-L and OPG were 78.28 (range 7.34–620.64, 319.06 (21.42–1884.41 and 1.52 (0.10–58.02, respectively. At 12 months, the median RANK-L value had decreased by 22% with respect to the baseline, whereas median OPG levels had increased by about 96%. Consequently, the RANK-L/OPG ratio decreased by 56% from the baseline. Median serum NTX levels decreased over the 12-month period, reaching statistical significance (p < 0.0001. Our results would seem to indicate that ZA modulates RANK, RANK-L and OPG expression, thus decreasing osteoclast activity.

  19. RANK/RANKL/OPG Signalization Implication in Periodontitis: New Evidence from a RANK Transgenic Mouse Model

    Directory of Open Access Journals (Sweden)

    Bouchra Sojod

    2017-05-01

    Full Text Available Periodontitis is based on a complex inflammatory over-response combined with possible genetic predisposition factors. The RANKL/RANK/OPG signaling pathway is implicated in bone resorption through its key function in osteoclast differentiation and activation, as well as in the inflammatory response. This central element of osteo-immunology has been suggested to be perturbed in several diseases, including periodontitis, as it is a predisposing factor for this disease. The aim of the present study was to validate this hypothesis using a transgenic mouse line, which over-expresses RANK (RTg and develops a periodontitis-like phenotype at 5 months of age. RTg mice exhibited severe alveolar bone loss, an increased number of TRAP positive cells, and disorganization of periodontal ligaments. This phenotype was more pronounced in females. We also observed dental root resorption lacunas. Hyperplasia of the gingival epithelium, including Malassez epithelial rests, was visible as early as 25 days, preceding any other symptoms. These results demonstrate that perturbations of the RANKL/RANK/OPG system constitute a core element of periodontitis, and more globally, osteo-immune diseases.

  20. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  1. Photo Aesthetics Ranking Network with Attributes and Content Adaptation

    OpenAIRE

    Kong, Shu; Shen, Xiaohui; Lin, Zhe; Mech, Radomir; Fowlkes, Charless

    2016-01-01

    Real-world applications could benefit from the ability to automatically generate a fine-grained ranking of photo aesthetics. However, previous methods for image aesthetics analysis have primarily focused on the coarse, binary categorization of images into high- or low-aesthetic categories. In this work, we propose to learn a deep convolutional neural network to rank photo aesthetics in which the relative ranking of photo aesthetics are directly modeled in the loss function. Our model incorpor...

  2. A Review of Ranking Models in Data Envelopment Analysis

    OpenAIRE

    Hosseinzadeh Lotfi, F.; Jahanshahloo, G.R.; M. Khodabakhshi; Rostamy-Malkhlifeh, M.; Moghaddas, Z.; Vaez-Ghasemi, M.

    2013-01-01

    In the course of improving various abilities of data envelopment analysis (DEA) models, many investigations have been carried out for ranking decision-making units (DMUs). This is an important issue both in theory and practice. There exist a variety of papers which apply different ranking methods to a real data set. Here the ranking methods are divided into seven groups. As each of the existing methods can be viewed from different aspects, it is possible that somewhat these groups have an ove...

  3. International ranking systems for universities and institutions: a critical appraisal

    Science.gov (United States)

    Ioannidis, John PA; Patsopoulos, Nikolaos A; Kavvoura, Fotini K; Tatsioni, Athina; Evangelou, Evangelos; Kouri, Ioanna; Contopoulos-Ioannidis, Despina G; Liberopoulos, George

    2007-01-01

    Background Ranking of universities and institutions has attracted wide attention recently. Several systems have been proposed that attempt to rank academic institutions worldwide. Methods We review the two most publicly visible ranking systems, the Shanghai Jiao Tong University 'Academic Ranking of World Universities' and the Times Higher Education Supplement 'World University Rankings' and also briefly review other ranking systems that use different criteria. We assess the construct validity for educational and research excellence and the measurement validity of each of the proposed ranking criteria, and try to identify generic challenges in international ranking of universities and institutions. Results None of the reviewed criteria for international ranking seems to have very good construct validity for both educational and research excellence, and most don't have very good construct validity even for just one of these two aspects of excellence. Measurement error for many items is also considerable or is not possible to determine due to lack of publication of the relevant data and methodology details. The concordance between the 2006 rankings by Shanghai and Times is modest at best, with only 133 universities shared in their top 200 lists. The examination of the existing international ranking systems suggests that generic challenges include adjustment for institutional size, definition of institutions, implications of average measurements of excellence versus measurements of extremes, adjustments for scientific field, time frame of measurement and allocation of credit for excellence. Conclusion Naïve lists of international institutional rankings that do not address these fundamental challenges with transparent methods are misleading and should be abandoned. We make some suggestions on how focused and standardized evaluations of excellence could be improved and placed in proper context. PMID:17961208

  4. Asian top universities in six world university ranking systems

    OpenAIRE

    Mahmood Khosrowjerdi; Zahra Seif Kashani

    2013-01-01

    There are a variety of ranking systems for universities throughout the different continents of the world. The majority of the world ranking systems have paid special attention toward evaluation of universities and higher education institutions at the national and international level. This paper tries to study the similarities and status of top Asian universities in the list of top 200 universities by these world ranking systems. Findings show that there are some parallelisms among the...

  5. International ranking systems for universities and institutions: a critical appraisal

    Directory of Open Access Journals (Sweden)

    Tatsioni Athina

    2007-10-01

    Full Text Available Abstract Background Ranking of universities and institutions has attracted wide attention recently. Several systems have been proposed that attempt to rank academic institutions worldwide. Methods We review the two most publicly visible ranking systems, the Shanghai Jiao Tong University 'Academic Ranking of World Universities' and the Times Higher Education Supplement 'World University Rankings' and also briefly review other ranking systems that use different criteria. We assess the construct validity for educational and research excellence and the measurement validity of each of the proposed ranking criteria, and try to identify generic challenges in international ranking of universities and institutions. Results None of the reviewed criteria for international ranking seems to have very good construct validity for both educational and research excellence, and most don't have very good construct validity even for just one of these two aspects of excellence. Measurement error for many items is also considerable or is not possible to determine due to lack of publication of the relevant data and methodology details. The concordance between the 2006 rankings by Shanghai and Times is modest at best, with only 133 universities shared in their top 200 lists. The examination of the existing international ranking systems suggests that generic challenges include adjustment for institutional size, definition of institutions, implications of average measurements of excellence versus measurements of extremes, adjustments for scientific field, time frame of measurement and allocation of credit for excellence. Conclusion Naïve lists of international institutional rankings that do not address these fundamental challenges with transparent methods are misleading and should be abandoned. We make some suggestions on how focused and standardized evaluations of excellence could be improved and placed in proper context.

  6. Ranking agricultural, environmental and natural resource economics journals: A note

    OpenAIRE

    Halkos, George; Tzeremes, Nickolaos

    2012-01-01

    This paper by applying Data Envelopment Analysis (DEA) ranks for the first time Economics journals in the field of Agricultural, Environmental and Natural Resource. Specifically, by using one composite input and one composite output the paper ranks 32 journals. In addition for the first time three different quality ranking reports have been incorporated to the DEA modelling problem in order to classify the journals into four categories (‘A’ to ‘D’). The results reveal that the journals with t...

  7. Reduced Rank Adaptive Filtering in Impulsive Noise Environments

    KAUST Repository

    Soury, Hamza

    2014-01-06

    An impulsive noise environment is used in this paper. A new aspect of signal truncation is deployed to reduce the harmful effect of the impulsive noise to the signal. A full rank direct solution is derived followed by an iterative solution. The reduced rank adaptive filter is presented in this environment by using two methods for rank reduction. The minimized objective function is defined using the Lp norm. The results are presented and the efficiency of each algorithm is discussed.

  8. Diffusion of scientific credits and the ranking of scientists

    OpenAIRE

    Radicchi, Filippo; Fortunato, Santo; Markines, Benjamin; Vespignani, Alessandro

    2009-01-01

    Recently, the abundance of digital data enabled the implementation of graph based ranking algorithms that provide system level analysis for ranking publications and authors. Here we take advantage of the entire Physical Review publication archive (1893-2006) to construct authors' networks where weighted edges, as measured from opportunely normalized citation counts, define a proxy for the mechanism of scientific credit transfer. On this network we define a ranking method based on a diffusion ...

  9. Social ranking effects on tooth-brushing behaviour

    OpenAIRE

    Maltby, John; Paterson, Kevin; Day, Liz; Jones, Ceri; Kinnear, Hayley; Buchanan, Heather

    2016-01-01

    Objective: A tooth-brushing social rank hypothesis is tested suggesting tooth-brushing duration is influenced when individuals position their behaviour in a rank when comparing their behaviour with other individuals.\\ud Design: Study 1 used a correlation design, Study 2 used a semi-experimental design, and Study 3 used a randomized intervention design to examine the tooth-brushing social rank hypothesis in terms of self-reported attitudes, cognitions, and behaviour towards tooth-brushing dura...

  10. A scale for ranking volcanoes by risk

    Science.gov (United States)

    Scandone, Roberto; Bartolini, Stefania; Martí, Joan

    2016-01-01

    We propose a simple volcanic risk coefficient (VRC) useful for comparing the degree of risk arising from different volcanoes, which may be used by civil protection agencies and volcano observatories to rapidly allocate limited resources even without a detailed knowledge of each volcano. Volcanic risk coefficient is given by the sum of the volcanic explosivity index (VEI) of the maximum expected eruption from the volcano, the logarithm of the eruption rate, and the logarithm of the population that may be affected by the maximum expected eruption. We show how to apply the method to rank the risk using as examples the volcanoes of Italy and in the Canary Islands. Moreover, we demonstrate that the maximum theoretical volcanic risk coefficient is 17 and pertains to the large caldera-forming volcanoes like Toba or Yellowstone that may affect the life of the entire planet. We develop also a simple plugin for a dedicated Quantum Geographic Information System (QGIS) software to graphically display the VRC of different volcanoes in a region.

  11. Relevancy Ranking of Satellite Dataset Search Results

    Science.gov (United States)

    Lynnes, Christopher; Quinn, Patrick; Norton, James

    2017-01-01

    As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

  12. Multirelational Social Recommendations via Multigraph Ranking.

    Science.gov (United States)

    Mao, Mingsong; Lu, Jie; Zhang, Guangquan; Zhang, Jinlong

    2017-12-01

    Recommender systems aim to identify relevant items for particular users in large-scale online applications. The historical rating data of users is a valuable input resource for many recommendation models such as collaborative filtering (CF), but these models are known to suffer from the rating sparsity problem when the users or items under consideration have insufficient rating records. With the continued growth of online social networks, the increased user-to-user relationships are reported to be helpful and can alleviate the CF rating sparsity problem. Although researchers have developed a range of social network-based recommender systems, there is no unified model to handle multirelational social networks. To address this challenge, this paper represents different user relationships in a multigraph and develops a multigraph ranking model to identify and recommend the nearest neighbors of particular users in high-order environments. We conduct empirical experiments on two real-world datasets: 1) Epinions and 2) Last.fm, and the comprehensive comparison with other approaches demonstrates that our model improves recommendation performance in terms of both recommendation coverage and accuracy, especially when the rating data are sparse.

  13. Grades and Ranking: When Tenure Affects Assessment

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    Jean Filetti

    2010-10-01

    Full Text Available This article examines how a faculty member's status-'either tenured or tenure-track-'might affect the grades assigned to students in a writing class. We begin with a brief review of the research surrounding faculty to student assessment practices and follow with specific controversies regarding faculty motivation pertaining to grading practices. We interpret the grade distributions of tenured and tenure-track faculty members teaching a sophomore-level writing course in an English Department at a small, public liberal arts university in Virginia, examine the relationship between grade distributions and faculty rank, and conclude that tenure-track faculty grade more leniently than their tenured colleagues, primarily in the number of - A- grades assigned. The results of this study suggest that tenured professors tend to award fewer - As- than tenure-track professors. We posit that at universities where emphasis is placed upon teaching, two specific patterns emerge: reciprocity may be an unspoken agreement between some faculty and students with regard to the exchange of good grades for good evaluations, or with experience comes rigor.

  14. Improving CBIR Systems Using Automated Ranking

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    B. D. Reljin

    2012-11-01

    Full Text Available The most common way of searching images on the Internet and in private collections is based on a similarity measuring of a series of text words that are assigned to each image with users query series. This method imposes strong constraints (the number of words to describe the image, the time necessary to thoroughly describe the subjective experience of images, the level of details in the picture, language barrier, etc., and is therefore very inefficient. Modern researches in this area are focused on the contentbased searching images (CBIR. In this way, all described disadvantages are overcome and the quality of searching results is improved. This paper presents a solution for CBIR systems where the search procedure is enhanced using sophisticated extraction and ranking of extracted images. The searching procedure is based on extraction and preprocessing of a large number of low level image features. Thus, when the user defines a query image, the proposed algorithm based on artificial intelligence, shows to the user a group of images which are most similar to a query image by content. The proposed algorithm is iterative, so the user can direct the searching procedure to an expected outcome and get a set of images that are more similar to the query one.

  15. Rank diversity of languages: generic behavior in computational linguistics.

    Science.gov (United States)

    Cocho, Germinal; Flores, Jorge; Gershenson, Carlos; Pineda, Carlos; Sánchez, Sergio

    2015-01-01

    Statistical studies of languages have focused on the rank-frequency distribution of words. Instead, we introduce here a measure of how word ranks change in time and call this distribution rank diversity. We calculate this diversity for books published in six European languages since 1800, and find that it follows a universal lognormal distribution. Based on the mean and standard deviation associated with the lognormal distribution, we define three different word regimes of languages: "heads" consist of words which almost do not change their rank in time, "bodies" are words of general use, while "tails" are comprised by context-specific words and vary their rank considerably in time. The heads and bodies reflect the size of language cores identified by linguists for basic communication. We propose a Gaussian random walk model which reproduces the rank variation of words in time and thus the diversity. Rank diversity of words can be understood as the result of random variations in rank, where the size of the variation depends on the rank itself. We find that the core size is similar for all languages studied.

  16. Econophysics of a ranked demand and supply resource allocation problem

    Science.gov (United States)

    Priel, Avner; Tamir, Boaz

    2018-01-01

    We present a two sided resource allocation problem, between demands and supplies, where both parties are ranked. For example, in Big Data problems where a set of different computational tasks is divided between a set of computers each with its own resources, or between employees and employers where both parties are ranked, the employees by their fitness and the employers by their package benefits. The allocation process can be viewed as a repeated game where in each iteration the strategy is decided by a meta-rule, based on the ranks of both parties and the results of the previous games. We show the existence of a phase transition between an absorbing state, where all demands are satisfied, and an active one where part of the demands are always left unsatisfied. The phase transition is governed by the ratio between supplies and demand. In a job allocation problem we find positive correlation between the rank of the workers and the rank of the factories; higher rank workers are usually allocated to higher ranked factories. These all suggest global emergent properties stemming from local variables. To demonstrate the global versus local relations, we introduce a local inertial force that increases the rank of employees in proportion to their persistence time in the same factory. We show that such a local force induces non trivial global effects, mostly to benefit the lower ranked employees.

  17. Proceedings of the sixteenth biennial low-rank fuels symposium

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    Low-rank coals represent a major energy resource for the world. The Low-Rank Fuels Symposium, building on the traditions established by the Lignite Symposium, focuses on the key opportunities for this resource. This conference offers a forum for leaders from industry, government, and academia to gather to share current information on the opportunities represented by low-rank coals. In the United States and throughout the world, the utility industry is the primary user of low-rank coals. As such, current experiences and future opportunities for new technologies in this industry were the primary focuses of the symposium.

  18. Multidimensional ranking the design and development of U-Multirank

    CERN Document Server

    Ziegele, Frank

    2012-01-01

    During the last decades ranking has become one of the most controversial issues in higher education and research. It is widely recognized now that, although some of the current rankings can be severely criticized, they seem to be here to stay. In addition, rankings appear to have a great impact on decision-makers at all levels of higher education and research systems worldwide, including in universities. Rankings reflect a growing international competition among universities for talent and resources; at the same time they reinforce competition by their very results. Yet major concerns remain a

  19. Quantum probability ranking principle for ligand-based virtual screening.

    Science.gov (United States)

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-04-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  20. Quantum probability ranking principle for ligand-based virtual screening

    Science.gov (United States)

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-04-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  1. A Modification on the Hesitant Fuzzy Set Lexicographical Ranking Method

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    Xiaodi Liu

    2016-12-01

    Full Text Available Recently, a novel hesitant fuzzy set (HFS ranking technique based on the idea of lexicographical ordering is proposed and an example is presented to demonstrate that the proposed ranking method is invariant with multiple occurrences of any element of a hesitant fuzzy element (HFE. In this paper, we show by examples that the HFS lexicographical ordering method is sometimes invalid, and a modified ranking method is presented. In comparison with the HFS lexicographical ordering method, the modified ranking method is more reasonable in more general cases.

  2. Extreme learning machine for ranking: generalization analysis and applications.

    Science.gov (United States)

    Chen, Hong; Peng, Jiangtao; Zhou, Yicong; Li, Luoqing; Pan, Zhibin

    2014-05-01

    The extreme learning machine (ELM) has attracted increasing attention recently with its successful applications in classification and regression. In this paper, we investigate the generalization performance of ELM-based ranking. A new regularized ranking algorithm is proposed based on the combinations of activation functions in ELM. The generalization analysis is established for the ELM-based ranking (ELMRank) in terms of the covering numbers of hypothesis space. Empirical results on the benchmark datasets show the competitive performance of the ELMRank over the state-of-the-art ranking methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. fcGENE: a versatile tool for processing and transforming SNP datasets.

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    Nab Raj Roshyara

    Full Text Available Modern analysis of high-dimensional SNP data requires a number of biometrical and statistical methods such as pre-processing, analysis of population structure, association analysis and genotype imputation. Software used for these purposes often rely on specific and incompatible input and output data formats. Therefore extensive data management including multiple format conversions is necessary during analyses.In order to support fast and efficient management and bio-statistical quality control of high-dimensional SNP data, we developed the publically available software fcGENE using C++ object-oriented programming language. This software simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses.fcGENE transforms SNP data and imputation results into different formats required for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, EIGENSOFT, GenABEL and tools used for genotype imputation such as MaCH, IMPUTE, BEAGLE and others. Data Management tasks like merging, splitting, extracting SNP and pedigree information can be performed. fcGENE also supports a number of bio-statistical quality control processes and quality based filtering processes at SNP- and sample-wise level. The tool also generates templates of commands required to run specific software packages, especially those required for genotype imputation. We demonstrate the functionality of fcGENE by example workflows of SNP data analyses and provide a comprehensive manual of commands, options and applications.We have developed a user-friendly open-source software fcGENE, which comprehensively supports SNP data management, quality control and analysis workflows. Download statistics and corresponding feedbacks indicate that software is highly recognised and extensively applied by the scientific community.

  4. Severe language effect in university rankings: particularly Germany and France are wronged in citation-based rankings.

    Science.gov (United States)

    van Raan, Anthony F J; van Leeuwen, Thed N; Visser, Martijn S

    2011-08-01

    We applied a set of standard bibliometric indicators to monitor the scientific state-of-arte of 500 universities worldwide and constructed a ranking on the basis of these indicators (Leiden Ranking 2010). We find a dramatic and hitherto largely underestimated language effect in the bibliometric, citation-based measurements of research performance when comparing the ranking based on all Web of Science (WoS) covered publications and on only English WoS covered publications, particularly for Germany and France.

  5. Effect of Doximity Residency Rankings on Residency Applicants’ Program Choices

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    Aimee M. Rolston

    2015-11-01

    Full Text Available Introduction: Choosing a residency program is a stressful and important decision. Doximity released residency program rankings by specialty in September 2014. This study sought to investigate the impact of those rankings on residency application choices made by fourth year medical students. Methods: A 12-item survey was administered in October 2014 to fourth year medical students at three schools. Students indicated their specialty, awareness of and perceived accuracy of the rankings, and the rankings’ impact on the programs to which they chose to apply. Descriptive statistics were reported for all students and those applying to Emergency Medicine (EM. Results: A total of 461 (75.8% students responded, with 425 applying in one of the 20 Doximity ranked specialties. Of the 425, 247 (58% were aware of the rankings and 177 looked at them. On a 1-100 scale (100=very accurate, students reported a mean ranking accuracy rating of 56.7 (SD 20.3. Forty-five percent of students who looked at the rankings modified the number of programs to which they applied. The majority added programs. Of the 47 students applying to EM, 18 looked at the rankings and 33% changed their application list with most adding programs. Conclusion: The Doximity rankings had real effects on students applying to residencies as almost half of students who looked at the rankings modified their program list. Additionally, students found the rankings to be moderately accurate. Graduating students might benefit from emphasis on more objective characterization of programs to assess in light of their own interests and personal/career goals

  6. SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

    Directory of Open Access Journals (Sweden)

    Carlborg Örjan

    2010-11-01

    Full Text Available Abstract Background Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight. Results Genotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55 and 38 kb (correlation 0.45, respectively. Conclusions Genome resequencing with limited coverage (~5X using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the

  7. Transcriptome sequencing for SNP discovery across Cucumis melo

    Directory of Open Access Journals (Sweden)

    Blanca José

    2012-06-01

    and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes. Conclusions This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

  8. Development of an automated SNP analysis method using a paramagnetic beads handling robot.

    Science.gov (United States)

    Hagiwara, Hiroko; Sawakami-Kobayashi, Kazumi; Yamamoto, Midori; Iwasaki, Shoji; Sugiura, Mika; Abe, Hatsumi; Kunihiro-Ohashi, Sumiko; Takase, Kumiko; Yamane, Noriko; Kato, Kaoru; Son, Renkon; Nakamura, Michihiro; Segawa, Osamu; Yoshida, Mamiko; Yohda, Masafumi; Tajima, Hideji; Kobori, Masato; Takahama, Yousuke; Itakura, Mitsuo; Machida, Masayuki

    2007-10-01

    Biological and medical importance of the single nucleotide polymorphism (SNP) has led to development of a wide variety of methods for SNP typing. Aiming for establishing highly reliable and fully automated SNP typing, we have developed the adapter ligation method in combination with the paramagnetic beads handling technology, Magtration(R). The method utilizes sequence specific ligation between the fluorescently labeled adapter and the sample DNAs at the cohesive end produced by a type IIS restriction enzyme. Evaluation of the method using human genomic DNA showed clear discrimination of the three genotypes without ambiguity using the same reaction condition for any SNPs examined. The operations following PCR amplification were automatically performed by the Magtration(R)-based robot that we have previously developed. Multiplex typing of two SNPs in a single reaction by using four fluorescent dyes was successfully preformed at the almost same sensitivity and reliability as the single typing. These results demonstrate that the automated paramagnetic beads handling technology, Magtration(R), is highly adaptable to the automated SNP analysis and that our method best fits to an automated in-house SNP typing for laboratory and medical uses. (c) 2007 Wiley Periodicals, Inc.

  9. Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.

    Science.gov (United States)

    Hwang, Michael T; Landon, Preston B; Lee, Joon; Choi, Duyoung; Mo, Alexander H; Glinsky, Gennadi; Lal, Ratnesh

    2016-06-28

    Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.

  10. Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method.

    Science.gov (United States)

    Kenta, T; Gratten, J; Haigh, N S; Hinten, G N; Slate, J; Butlin, R K; Burke, T

    2008-11-01

    We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  11. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation

    Directory of Open Access Journals (Sweden)

    Aldred Micheala A

    2007-07-01

    Full Text Available Abstract Background The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no longer always be accurately assigned one of three genotypes in an individual. In the presence of copy number variability, the individual may theoretically harbor any number of copies of each of the two SNP alleles. Results To address this issue, we have developed a method to infer a "generalized genotype" from raw SNP microarray data. Here we apply our approach to data from 48 individuals and uncover thousands of aberrant SNPs, most in regions that were previously unreported as copy number variants. We show that our allele-specific copy numbers follow Mendelian inheritance patterns that would be obscured in the absence of SNP allele information. The interplay between duplication and point mutation in our data shed light on the relative frequencies of these events in human history, showing that at least some of the duplication events were recurrent. Conclusion This new multi-allelic view of SNPs has a complicated role in disease association studies, and further work will be necessary in order to accurately assess its importance. Software to perform generalized genotyping from SNP array data is freely available online 1.

  12. Single Nucleotide Polymorphism (SNP) Arrays and Unexpected Consanguinity: Considerations for Clinicians When Returning Results to Families

    Science.gov (United States)

    Delgado, Fernanda; Tabor, Holly K.; Chow, Penny M.; Conta, Jessie H.; Feldman, Kenneth W.; Tsuchiya, Karen D.; Beck, Anita E.

    2014-01-01

    Purpose The broad use of SNP microarrays has increased identification of unexpected consanguinity. Therefore, guidelines to address reporting of consanguinity have been published for clinical laboratories. Because no such guidelines exist for clinicians, we describe a case and present recommendations for clinicians to disclose unexpected consanguinity to families. Methods In a boy with multiple endocrine abnormalities and structural birth defects, SNP array analysis revealed ~23% autosomal homozygosity suggestive of a 1st-degree parental relationship. We assembled an interdisciplinary healthcare team, planned the most appropriate way to discuss results of the SNP array with the adult mother including the possibility of multiple autosomal recessive disorders in her child, and finally met with her as a team. Results From these discussions, we developed four major considerations for clinicians returning results of unexpected consanguinity, all guided by the child’s best interests: 1) ethical and legal obligations for reporting possible abuse, 2) preservation of the clinical relationship, 3) attention to justice and psychosocial challenges, and 4) utilization of the SNP array results to guide further testing. Conclusion As SNP arrays become a common clinical diagnostic tool, clinicians can use this framework to return results of unexpected consanguinity to families in a supportive and productive manner. PMID:25232848

  13. Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes.

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    Sven Stringer

    Full Text Available Complex diseases are often highly heritable. However, for many complex traits only a small proportion of the heritability can be explained by observed genetic variants in traditional genome-wide association (GWA studies. Moreover, for some of those traits few significant SNPs have been identified. Single SNP association methods test for association at a single SNP, ignoring the effect of other SNPs. We show using a simple multi-locus odds model of complex disease that moderate to large effect sizes of causal variants may be estimated as relatively small effect sizes in single SNP association testing. This underestimation effect is most severe for diseases influenced by numerous risk variants. We relate the underestimation effect to the concept of non-collapsibility found in the statistics literature. As described, continuous phenotypes generated with linear genetic models are not affected by this underestimation effect. Since many GWA studies apply single SNP analysis to dichotomous phenotypes, previously reported results potentially underestimate true effect sizes, thereby impeding identification of true effect SNPs. Therefore, when a multi-locus model of disease risk is assumed, a multi SNP analysis may be more appropriate.

  14. MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression.

    Science.gov (United States)

    He, Jingwu; Zelikovsky, Alexander

    2006-10-15

    The search for the association between complex diseases and single nucleotide polymorphisms (SNPs) or haplotypes has recently received great attention. For these studies, it is essential to use a small subset of informative SNPs accurately representing the rest of the SNPs. Informative SNP selection can achieve (1) considerable budget savings by genotyping only a limited number of SNPs and computationally inferring all other SNPs or (2) necessary reduction of the huge SNP sets (obtained, e.g. from Affymetrix) for further fine haplotype analysis. A novel informative SNP selection method for unphased genotype data based on multiple linear regression (MLR) is implemented in the software package MLR-tagging. This software can be used for informative SNP (tag) selection and genotype prediction. The stepwise tag selection algorithm (STSA) selects positions of the given number of informative SNPs based on a genotype sample population. The MLR SNP prediction algorithm predicts a complete genotype based on the values of its informative SNPs, their positions among all SNPs, and a sample of complete genotypes. An extensive experimental study on various datasets including 10 regions from HapMap shows that the MLR prediction combined with stepwise tag selection uses fewer tags than the state-of-the-art method of Halperin et al. (2005). MLR-Tagging software package is publicly available at http://alla.cs.gsu.edu/~software/tagging/tagging.html

  15. A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Fang, David D; Xiao, Jinhua; Canci, Paulo C; Cantrell, Roy G

    2010-03-01

    Resistance to cotton blue disease (CBD) was evaluated in 364 F(2.3) families of three populations derived from resistant variety 'Delta Opal'. The CBD resistance in 'Delta Opal' was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resides at the telomere region of chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 diploid species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) was identified at the 136 th position by sequence alignment analysis. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. A strong association between a haplotype based on four SNP markers and Cbd was developed. This demonstrates one of the first examples in cotton where SNP markers were used to effectively tag a trait enabling marker-assisted selection for high levels of CBD resistance in breeding programs.

  16. Leveraging ethnic group incidence variation to investigate genetic susceptibility to glioma: A novel candidate SNP approach

    Directory of Open Access Journals (Sweden)

    Daniel Ian Jacobs

    2012-10-01

    Full Text Available Objectives: Using a novel candidate SNP approach, we aimed to identify a possible genetic basis for the higher glioma incidence in Whites relative to East Asians and African-Americans. Methods: We hypothesized that genetic regions containing SNPs with extreme differences in allele frequencies across ethnicities are most likely to harbor susceptibility variants. We used International HapMap Project data to identify 3,961 candidate SNPs with the largest allele frequency differences in Whites compared to East Asians and Africans and tested these SNPs for association with glioma risk in a set of White cases and controls. Top SNPs identified in the discovery dataset were tested for association with glioma in five independent replication datasets. Results: No SNP achieved statistical significance in either the discovery or replication datasets after accounting for multiple testing. However, the most strongly associated SNP, rs879471, was found to be in linkage disequilibrium with a previously identified risk SNP, rs6010620, in RTEL1. We estimate rs6010620 to account for a glioma incidence rate ratio of 1.34 for Whites relative to East Asians. Conclusions: We explored genetic susceptibility to glioma using a novel candidate SNP method which may be applicable to other diseases with appropriate epidemiologic patterns.

  17. Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework.

    Science.gov (United States)

    Venables, Samantha J; Mehta, Bhavik; Daniel, Runa; Walsh, Simon J; van Oorschot, Roland A H; McNevin, Dennis

    2014-11-01

    High resolution melting (HRM) analysis is a simple, cost effective, closed tube SNP genotyping technique with high throughput potential. The effectiveness of HRM for forensic SNP genotyping was assessed with five commercially available HRM kits evaluated on the ViiA™ 7 Real Time PCR instrument. Four kits performed satisfactorily against forensically relevant criteria. One was further assessed to determine the sensitivity, reproducibility, and accuracy of HRM SNP genotyping. The manufacturer's protocol using 0.5 ng input DNA and 45 PCR cycles produced accurate and reproducible results for 17 of the 19 SNPs examined. Problematic SNPs had GC rich flanking regions which introduced additional melting domains into the melting curve (rs1800407) or included homozygotes that were difficult to distinguish reliably (rs16891982; a G to C SNP). A proof of concept multiplexing experiment revealed that multiplexing a small number of SNPs may be possible after further investigation. HRM enables genotyping of a number of SNPs in a large number of samples without extensive optimization. However, it requires more genomic DNA as template in comparison to SNaPshot®. Furthermore, suitably modifying pre-existing forensic intelligence SNP panels for HRM analysis may pose difficulties due to the properties of some SNPs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data.

    Directory of Open Access Journals (Sweden)

    Davoud Torkamaneh

    Full Text Available Genotyping-by-sequencing (GBS represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%, the resulting SNP datasets were of uniformly high accuracy (96-98%. We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K. We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%. Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis, 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at ≤20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more

  19. Adiponectin gene SNP 276G ? T, nutrient intakes, and cardiovascular disease risk in Korean type 2 DM patients

    OpenAIRE

    Yu, So Young; Ryu, Han Kyoung; Park, Hee Jung; Choi, Young Ju; Huh, Kap Bum; Kim, Wha Young

    2007-01-01

    Single nucleotide polymorphism (SNP) in adiponectin gene has been associated with insulin resistance, diabetes, and cardiovascular disease (CVD). This study was performed to investigate the association of SNP 276G?T at adiponectin gene with CVD risk factors in Korean type 2 diabetes mellitus (DM) patients. The subjects were 351 type 2 DM patients visited a DM clinic in Seoul, and the patients with known CVD were excluded. The adiponectin SNP 276G?T was analyzed and dietary intakes were assess...

  20. Ranking production units according to marginal efficiency contribution

    DEFF Research Database (Denmark)

    Ghiyasi, Mojtaba; Hougaard, Jens Leth

    League tables associated with various forms of service activities from schools to hospitals illustrate the public need for ranking institutions by their productive performance. We present a new method for ranking production units which is based on each units marginal contribution to the technical...

  1. WISER ranking of the African national libraries' websites | Gupta ...

    African Journals Online (AJOL)

    Data collection has been done with the help of Google search engine and Check Page Rank tool. This study highlighted the fact that the ranking based on web impact factor was not much reliable and it is biased towards the small number of webpages and in-links. In the present study WISER, a combined web indicator was ...

  2. Monte Carlo methods of PageRank computation

    NARCIS (Netherlands)

    Litvak, Nelli

    2004-01-01

    We describe and analyze an on-line Monte Carlo method of PageRank computation. The PageRank is being estimated basing on results of a large number of short independent simulation runs initiated from each page that contains outgoing hyperlinks. The method does not require any storage of the hyperlink

  3. Co-integration Rank Testing under Conditional Heteroskedasticity

    DEFF Research Database (Denmark)

    Cavaliere, Guiseppe; Rahbæk, Anders; Taylor, A.M. Robert

    null distributions of the rank statistics coincide with those derived by previous authors who assume either i.i.d. or (strict and covariance) stationary martingale difference innovations. We then propose wild bootstrap implementations of the co-integrating rank tests and demonstrate that the associated...

  4. The Ranking Phenomenon and the Experience of Academics in Taiwan

    Science.gov (United States)

    Lo, William Yat Wai

    2014-01-01

    The primary aim of the paper is to examine how global university rankings have influenced the higher education sector in Taiwan from the perspective of academics. A qualitative case study method was used to examine how university ranking influenced the Taiwanese higher education at institutional and individual levels, respectively, thereby…

  5. Relying on topic subsets for system ranking estimation

    NARCIS (Netherlands)

    Hauff, C.; Hiemstra, Djoerd; de Jong, Franciska M.G.; Azzopardi, Leif

    2009-01-01

    Ranking a number of retrieval systems according to their retrieval effectiveness without relying on costly relevance judgments was first explored by Soboroff et al [6]. Over the years, a number of alternative approaches have been proposed. We perform a comprehensive analysis of system ranking

  6. Who Should Rank Our Journals...And Based on What?

    Science.gov (United States)

    Cherkowski, Sabre; Currie, Russell; Hilton, Sandy

    2012-01-01

    Purpose: This study aims to establish the use of active scholar assessment (ASA) in the field of education leadership as a new methodology in ranking administration and leadership journals. The secondary purpose of this study is to respond to the paucity of research on journal ranking in educational administration and leadership.…

  7. A Comparative Analysis of Higher Education Ranking Systems in Europe

    Science.gov (United States)

    Hendel, Darwin D.; Stolz, Ingo

    2008-01-01

    According to Altbach in 2004, "everyone wants a world-class university". Corresponding developmental efforts undertaken by higher education institutions are very often referenced to improvements in ranking results. Surprisingly, there is relatively little analysis of variations in higher education ranking systems across countries…

  8. International University Ranking Systems and the Idea of University Excellence

    Science.gov (United States)

    Taylor, Paul; Braddock, Richard

    2007-01-01

    We look at some of the theoretical and methodological issues underlying international university ranking systems and, in particular, their conceptual connection with the idea of excellence. We then turn to a critical examination of the two best-known international university ranking systems--the "Times Higher Education Supplement (THES)" World…

  9. How Do European Pharmacy Students Rank Competences for Practice?

    NARCIS (Netherlands)

    Atkinson, Jeffrey; De Paepe, Kristien; Sánchez Pozo, Antonio; Rekkas, Dimitrios; Volmer, Daisy; Hirvonen, Jouni; Bozic, Borut; Skowron, Agnieska; Mircioiu, Constantin; Marcincal, Annie; Koster, Andries; Wilson, Keith; van Schravendijk, Chris; Hočevar, Sandra

    2016-01-01

    European students (n = 370), academics (n = 241) and community pharmacists (n = 258) ranked 13 clusters of 68 personal and patient care competences for pharmacy practice. The results show that ranking profiles for all three groups as a rule were similar. This was especially true of the comparison

  10. The Distribution of the Sum of Signed Ranks

    Science.gov (United States)

    Albright, Brian

    2012-01-01

    We describe the calculation of the distribution of the sum of signed ranks and develop an exact recursive algorithm for the distribution as well as an approximation of the distribution using the normal. The results have applications to the non-parametric Wilcoxon signed-rank test.

  11. Online learning to rank for information retrieval: SIGIR 2016 tutorial

    NARCIS (Netherlands)

    Grotov, A.; de Rijke, M.

    2016-01-01

    During the past 10--15 years offline learning to rank has had a tremendous influence on information retrieval, both scientifically and in practice. Recently, as the limitations of offline learning to rank for information retrieval have become apparent, there is increased attention for online

  12. A generative language modeling approach for ranking entities

    NARCIS (Netherlands)

    Weerkamp, W.; Balog, K.; Meij, E.

    2009-01-01

    We describe our participation in the INEX 2008 Entity Ranking track. We develop a generative language modeling approach for the entity ranking and list completion tasks. Our framework comprises the following components: (i) entity and (ii) query language models, (iii) entity prior, (iv) the

  13. Estimating Independent Locally Shifted Random Utility Models for Ranking Data

    Science.gov (United States)

    Lam, Kar Yin; Koning, Alex J.; Franses, Philip Hans

    2011-01-01

    We consider the estimation of probabilistic ranking models in the context of conjoint experiments. By using approximate rather than exact ranking probabilities, we avoided the computation of high-dimensional integrals. We extended the approximation technique proposed by Henery (1981) in the context of the Thurstone-Mosteller-Daniels model to any…

  14. A Global Comparison of Business Journal Ranking Systems

    Science.gov (United States)

    Alexander, Jennifer K.; Scherer, Robert F.; Lecoutre, Marc

    2007-01-01

    The authors compared business journal ranking systems from 6 countries. Results revealed a low degree of agreement among the systems, and a low to moderate relationship between pairs of systems. In addition, the French and United Kingdom ranking systems were different from each other and from the systems in Australia, Germany, Hong Kong, and the…

  15. Trachomatous Scar Ranking: A Novel Outcome for Trachoma Studies.

    Science.gov (United States)

    Baldwin, Angela; Ryner, Alexander M; Tadesse, Zerihun; Shiferaw, Ayalew; Callahan, Kelly; Fry, Dionna M; Zhou, Zhaoxia; Lietman, Thomas M; Keenan, Jeremy D

    2017-06-01

    AbstractWe evaluated a new trachoma scarring ranking system with potential use in clinical research. The upper right tarsal conjunctivas of 427 individuals from Ethiopian villages with hyperendemic trachoma were photographed. An expert grader first assigned a scar grade to each photograph using the 1981 World Health Organization (WHO) grading system. Then, all photographs were ranked from least (rank = 1) to most scarring (rank = 427). Photographic grading found 79 (18.5%) conjunctivae without scarring (C0), 191 (44.7%) with minimal scarring (C1), 105 (24.6%) with moderate scarring (C2), and 52 (12.2%) with severe scarring (C3). The ranking method demonstrated good internal validity, exhibiting a monotonic increase in the median rank across the levels of the 1981 WHO grading system. Intrarater repeatability was better for the ranking method (intraclass correlation coefficient = 0.84, 95% CI = 0.74-0.94). Exhibiting better internal and external validity, this ranking method may be useful for evaluating the difference in scarring between groups of individuals.

  16. Combining Document-and Paragraph-Based Entity Ranking

    NARCIS (Netherlands)

    Rode, H.; Serdyukov, Pavel; Hiemstra, Djoerd

    2008-01-01

    We study entity ranking on the INEX entity track and pro- pose a simple graph-based ranking approach that enables to combine scores on document and paragraph level. The com- bined approach improves the retrieval results not only on the INEX testset, but similarly on TREC’s expert finding task.

  17. University Rankings: How Well Do They Measure Library Service Quality?

    Science.gov (United States)

    Jackson, Brian

    2015-01-01

    University rankings play an increasingly large role in shaping the goals of academic institutions and departments, while removing universities themselves from the evaluation process. This study compares the library-related results of two university ranking publications with scores on the LibQUAL+™ survey to identify if library service quality--as…

  18. What Parameters Do Students Value in Business School Rankings?

    Science.gov (United States)

    Mårtensson, Pär; Richtnér, Anders

    2015-01-01

    The starting point of this paper is the question: Which issues do students think are important when choosing a higher education institution, and how are they related to the factors taken into consideration in ranking institutions? The aim is to identify and rank the parameters students perceive as important when choosing their place of education.…

  19. Positioning Open Access Journals in a LIS Journal Ranking

    Science.gov (United States)

    Xia, Jingfeng

    2012-01-01

    This research uses the h-index to rank the quality of library and information science journals between 2004 and 2008. Selected open access (OA) journals are included in the ranking to assess current OA development in support of scholarly communication. It is found that OA journals have gained momentum supporting high-quality research and…

  20. Information Theoretic Bounds for Low-Rank Matrix Completion

    CERN Document Server

    Vishwanath, Sriram

    2010-01-01

    This paper studies the low-rank matrix completion problem from an information theoretic perspective. The completion problem is rephrased as a communication problem of an (uncoded) low-rank matrix source over an erasure channel. The paper then uses achievability and converse arguments to present order-wise optimal bounds for the completion problem.

  1. Balancing exploration and exploitation in learning to rank online

    NARCIS (Netherlands)

    Hofmann, K.; Whiteson, S.; de Rijke, M.

    2011-01-01

    As retrieval systems become more complex, learning to rank approaches are being developed to automatically tune their parameters. Using online learning to rank approaches, retrieval systems can learn directly from implicit feedback, while they are running. In such an online setting, algorithms need

  2. On the classification of complex vector bundles of stable rank

    Indian Academy of Sciences (India)

    According to previous observations, this would imply (under the above torsion conditions) a classification of all rank r complex vector bundles on X, for stable rank r ≥ n/2. A few partial answers to this question are known. For instance, a classical result of. Wu asserts that any couple of cohomology classes (c1,c2) ∈ H2(X, ...

  3. Economic Research at National Liberal Arts Colleges: School Rankings.

    Science.gov (United States)

    Hartley, James E.; Robinson, Michael D.

    1997-01-01

    Presents a comprehensive ranking of all national liberal arts colleges based on publications cataloged by the "Journal of Economic Literature" (JEL) from 1989-1994. Concludes that, although economics research is important at the highest ranked colleges, it remains a secondary consideration at the rest. Briefly discusses previous rankings…

  4. Rank range test for equality of dispersion | Odiase | Journal of ...

    African Journals Online (AJOL)

    This paper exploits the computational simplicity of the range of a set of data to formulate a twosample scale test called the Rank Range test. The performance of the test statistic is compared with other tests of scale. The exact distribution of the Rank Range test statistic is generated empirically through the unconditional ...

  5. Social ranking effects on tooth-brushing behaviour.

    Science.gov (United States)

    Maltby, John; Paterson, Kevin; Day, Liz; Jones, Ceri; Kinnear, Hayley; Buchanan, Heather

    2016-05-01

    A tooth-brushing social rank hypothesis is tested suggesting tooth-brushing duration is influenced when individuals position their behaviour in a rank when comparing their behaviour with other individuals. Study 1 used a correlation design, Study 2 used a semi-experimental design, and Study 3 used a randomized intervention design to examine the tooth-brushing social rank hypothesis in terms of self-reported attitudes, cognitions, and behaviour towards tooth-brushing duration. Study 1 surveyed participants to examine whether the perceived health benefits of tooth-brushing duration could be predicted from the ranking of each person's tooth-brushing duration. Study 2 tested whether manipulating the rank position of the tooth-brushing duration influenced participant-perceived health benefits of tooth-brushing duration. Study 3 used a longitudinal intervention method to examine whether messages relating to the rank positions of tooth-brushing durations causally influenced the self-report tooth-brushing duration. Study 1 demonstrates that perceptions of the health benefits from tooth-brushing duration are predicted by the perceptions of how that behaviour ranks in comparison to other people's behaviour. Study 2 demonstrates that the perceptions of the health benefits of tooth-brushing duration can be manipulated experimentally by changing the ranked position of a person's tooth-brushing duration. Study 3 experimentally demonstrates the possibility of increasing the length of time for which individuals clean their teeth by focusing on how they rank among their peers in terms of tooth-brushing duration. The effectiveness of interventions using social-ranking methods relative to those that emphasize comparisons made against group averages or normative guidelines are discussed. What is already known on this subject? Individual make judgements based on social rank information. Social rank information has been shown to influence positive health behaviours such as exercise

  6. Forensic typing of autosomal SNPs with a 29 SNP-multiplex--results of a collaborative EDNAP exercise

    DEFF Research Database (Denmark)

    Sanchez, Juan Jose; Børsting, C; Balogh, K

    2008-01-01

    We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised...... sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP...

  7. PageRank model of opinion formation on social networks

    Science.gov (United States)

    Kandiah, Vivek; Shepelyansky, Dima L.

    2012-11-01

    We propose the PageRank model of opinion formation and investigate its rich properties on real directed networks of the Universities of Cambridge and Oxford, LiveJournal, and Twitter. In this model, the opinion formation of linked electors is weighted with their PageRank probability. Such a probability is used by the Google search engine for ranking of web pages. We find that the society elite, corresponding to the top PageRank nodes, can impose its opinion on a significant fraction of the society. However, for a homogeneous distribution of two opinions, there exists a bistability range of opinions which depends on a conformist parameter characterizing the opinion formation. We find that the LiveJournal and Twitter networks have a stronger tendency to a totalitarian opinion formation than the university networks. We also analyze the Sznajd model generalized for scale-free networks with the weighted PageRank vote of electors.

  8. CNN-based ranking for biomedical entity normalization.

    Science.gov (United States)

    Li, Haodi; Chen, Qingcai; Tang, Buzhou; Wang, Xiaolong; Xu, Hua; Wang, Baohua; Huang, Dong

    2017-10-03

    Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical entity normalization as a ranking problem and benefits from semantic information of biomedical entities. The CNN-based ranking method first generates candidates using handcrafted rules, and then ranks the candidates according to their semantic information modeled by CNN as well as their morphological information. Experiments on two benchmark datasets for biomedical entity normalization show that our proposed CNN-based ranking method outperforms traditional rule-based method with state-of-the-art performance. We propose a CNN architecture that regards biomedical entity normalization as a ranking problem. Comparison results show that semantic information is beneficial to biomedical entity normalization and can be well combined with morphological information in our CNN architecture for further improvement.

  9. Rankings Scientists, Journals and Countries using h-Index

    Directory of Open Access Journals (Sweden)

    Gyula Mester

    2016-01-01

    Full Text Available Indexes in scientometrics are based on citations. However, in contrast to the journal impact factor, which gives only the ranking of the scientific journals, ordered by impact factor, indexes in scientometrics are suitable for ranking of scientists, scientific journals and countries. In this paper the h-index, h5-index, the World ranking the top of 25 Highly Cited Researchers (h > 100 and the ranking of 25 scientists in Hungarian Institutions according to their Google Scholar Citations public profiles are considered. These indexes (h5-index are applied for making of the list of top 20 publications (journals and proceedings in the field of Robotics. The World ranking is done of the best 50 countries according to h-index in year 2014. Data are obtained from the portal Scimago.

  10. Sensitivity ranking for freshwater invertebrates towards hydrocarbon contaminants.

    Science.gov (United States)

    Gerner, Nadine V; Cailleaud, Kevin; Bassères, Anne; Liess, Matthias; Beketov, Mikhail A

    2017-11-01

    Hydrocarbons have an utmost economical importance but may also cause substantial ecological impacts due to accidents or inadequate transportation and use. Currently, freshwater biomonitoring methods lack an indicator that can unequivocally reflect the impacts caused by hydrocarbons while being independent from effects of other stressors. The aim of the present study was to develop a sensitivity ranking for freshwater invertebrates towards hydrocarbon contaminants, which can be used in hydrocarbon-specific bioindicators. We employed the Relative Sensitivity method and developed the sensitivity ranking S hydrocarbons based on literature ecotoxicological data supplemented with rapid and mesocosm test results. A first validation of the sensitivity ranking based on an earlier field study has been conducted and revealed the S hydrocarbons ranking to be promising for application in sensitivity based indicators. Thus, the first results indicate that the ranking can serve as the core component of future hydrocarbon-specific and sensitivity trait based bioindicators.

  11. Rank Protein Immunolabeling during Bone-Implant Interface Healing Process

    Directory of Open Access Journals (Sweden)

    Francisley Ávila Souza

    2010-01-01

    Full Text Available The purpose of this paper was to evaluate the expression of RANK protein during bone-healing process around machined surface implants. Twenty male Wistar rats, 90 days old, after having had a 2 mm diameter and 6 mm long implant inserted in their right tibias, were evaluated at 7, 14, 21, and 42 days after healing. After obtaining the histological samples, slides were subjected to RANK immunostaining reaction. Results were quantitatively evaluated. Results. Immunolabeling analysis showed expressions of RANK in osteoclast and osteoblast lineage cells. The statistical analysis showed an increase in the expression of RANK in osteoblasts at 7 postoperative days and a gradual decrease during the chronology of the healing process demonstrated by mild cellular activity in the final stage (P<.05. Conclusion. RANK immunolabeling was observed especially in osteoclast and osteoblast cells in primary bone during the initial periods of bone-healing/implant interface.

  12. Rank Protein Immunolabeling during Bone-Implant Interface Healing Process

    Science.gov (United States)

    Ávila Souza, Francisley; Pereira Queiroz, Thallita; Rodrigues Luvizuto, Eloá; Nishioka, Renato Sussumu; Garcia-JR, Idelmo Rangel; de Carvalho, Paulo Sérgio Perri; Okamoto, Roberta

    2010-01-01

    The purpose of this paper was to evaluate the expression of RANK protein during bone-healing process around machined surface implants. Twenty male Wistar rats, 90 days old, after having had a 2 mm diameter and 6 mm long implant inserted in their right tibias, were evaluated at 7, 14, 21, and 42 days after healing. After obtaining the histological samples, slides were subjected to RANK immunostaining reaction. Results were quantitatively evaluated. Results. Immunolabeling analysis showed expressions of RANK in osteoclast and osteoblast lineage cells. The statistical analysis showed an increase in the expression of RANK in osteoblasts at 7 postoperative days and a gradual decrease during the chronology of the healing process demonstrated by mild cellular activity in the final stage (P < .05). Conclusion. RANK immunolabeling was observed especially in osteoclast and osteoblast cells in primary bone during the initial periods of bone-healing/implant interface. PMID:20706673

  13. Beyond Zipf's Law: The Lavalette Rank Function and its Properties

    CERN Document Server

    Fontanelli, Oscar; Yang, Yaning; Cocho, Germinal; Li, Wentian

    2016-01-01

    Although Zipf's law is widespread in natural and social data, one often encounters situations where one or both ends of the ranked data deviate from the power-law function. Previously we proposed the Beta rank function to improve the fitting of data which does not follow a perfect Zipf's law. Here we show that when the two parameters in the Beta rank function have the same value, the Lavalette rank function, the probability density function can be derived analytically. We also show both computationally and analytically that Lavalette distribution is approximately equal, though not identical, to the lognormal distribution. We illustrate the utility of Lavalette rank function in several datasets. We also address three analysis issues on the statistical testing of Lavalette fitting function, comparison between Zipf's law and lognormal distribution through Lavalette function, and comparison between lognormal distribution and Lavalette distribution.

  14. Large Scale Association Analysis for Drug Addiction: Results from SNP to Gene

    Directory of Open Access Journals (Sweden)

    Xiaobo Guo

    2012-01-01

    Full Text Available Many genetic association studies used single nucleotide polymorphisms (SNPs data to identify genetic variants for complex diseases. Although SNP-based associations are most common in genome-wide association studies (GWAS, gene-based association analysis has received increasing attention in understanding genetic etiologies for complex diseases. While both methods have been used to analyze the same data, few genome-wide association studies compare the results or observe the connection between them. We performed a comprehensive analysis of the data from the Study of Addiction: Genetics and Environment (SAGE and compared the results from the SNP-based and gene-based analyses. Our results suggest that the gene-based method complements the individual SNP-based analysis, and conceptually they are closely related. In terms of gene findings, our results validate many genes that were either reported from the analysis of the same dataset or based on animal studies for substance dependence.

  15. Multiplex SNP analysis on whole genome amplified DNA from archived dried bloodspots, a validation study

    DEFF Research Database (Denmark)

    Tvedegaard, Kristine C.; Parner, Erik; Hooper, Craig W.

    on whole genome amplified (WGA) DNA from archived dried bloodspots. METHODS AND MATERIAL: The chemically synthesized new base pair (isoC and isoG) allow for the creation of new DNA strands that provide superior specificity and allow development of assays with greater sensitivity than conventional methods...... is a further development of allele specific primer extension (ASPE) for multiplex SNP analysis based on the Luminex 100 IS platform. It uses isobases (isoC and isoG) and the software MultiCode-PLx platform for data analysis and data handling. We validate the EraGen multicode system in two 6-plex assays used....... To validate the method 900 WGA DNA samples were genotyped in duplets. 10-20 % of all samples were sequenced to be used as reference. Accuracy and repeatability was estimated for each SNP. Robustness was estimated as rate of conclusive outcomes for each SNP. RESULTS: The accuracy ranged from 98...

  16. SNP calling using genotype model selection on high-throughput sequencing data

    KAUST Repository

    You, Na

    2012-01-16

    Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers. © The Author 2012. Published by Oxford University Press. All rights reserved.

  17. VisualRank: applying PageRank to large-scale image search.

    Science.gov (United States)

    Jing, Yushi; Baluja, Shumeet

    2008-11-01

    Because of the relative ease in understanding and processing text, commercial image-search systems often rely on techniques that are largely indistinguishable from text-search. Recently, academic studies have demonstrated the effectiveness of employing image-based features to provide alternative or additional signals. However, it remains uncertain whether such techniques will generalize to a large number of popular web queries, and whether the potential improvement to search quality warrants the additional computational cost. In this work, we cast the image-ranking problem into the task of identifying "authority" nodes on an inferred visual similarity graph and propose VisualRank to analyze the visual link structures among images. The images found to be "authorities" are chosen as those that answer the image-queries well. To understand the performance of such an approach in a real system, we conducted a series of large-scale experiments based on the task of retrieving images for 2000 of the most popular products queries. Our experimental results show significant improvement, in terms of user satisfaction and relevancy, in comparison to the most recent Google Image Search results. Maintaining modest computational cost is vital to ensuring that this procedure can be used in practice; we describe the techniques required to make this system practical for large scale deployment in commercial search engines.

  18. Association between CYP19 gene SNP rs2414096 Polymorphism and polycystic ovary syndrome in Chinese women

    Directory of Open Access Journals (Sweden)

    Yi Long

    2009-12-01

    Full Text Available Abstract Background Several studies have reported the association of the SNP rs2414096 in the CYP19 gene with hyperandrogenism, which is one of the clinical manifestations of polycystic ovary syndrome (PCOS. These studies suggest that SNP rs2414096 may be involved in the etiopathogenisis of PCOS. To investigate whetherthe CYP19 gene SNP rs2414096 polymorphism is associated with the susceptibility to PCOS, we designed a case-controlled association study including 684 individuals. Methods A case-controlled association study including 684 individuals (386 PCOS patients and 298 controls was performed to assess the association of SNP rs2414096 with PCOS. Genotyping of SNP rs2414096 was conducted by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method that was performed on genomic DNA isolated from blood leucocytes. Results were analyzed in respect to clinical test results. Results The genotypic distributions of rs2414096 (GG, AG, AA in the CYP19 gene (GG, AG, AA in women with PCOS (0.363, 0.474, 0.163, respectively were significantly different from that in controls (0.242, 0.500, 0.258, respectively (P = 0.001. E2/T was different between the AA and GG genotypes. Age at menarche (AAM and FSH were also significantly different among the GG, AG, and AA genotypes in women with PCOS (P = 0.0391 and 0.0118, respectively. No differences were observed in body mass index (BMI and other serum hormone concentrations among the three genotypes, either in the PCOS patients or controls. Conclusions Our data suggest that SNP rs2414096 in the CYP19 gene is associated with susceptibility to PCOS.

  19. An integrated SNP mining and utilization (ISMU pipeline for next generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Sarwar Azam

    Full Text Available Open source single nucleotide polymorphism (SNP discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2, SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a

  20. Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data.

    Directory of Open Access Journals (Sweden)

    Rosemary Braun

    2011-06-01

    Full Text Available Genome-wide association studies (GWAS have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP alleles that are associated with diseases. However, while typical GWAS analysis techniques treat markers individually, complex diseases (cancers, diabetes, and Alzheimers, amongst others are unlikely to have a single causative gene. Thus, there is a pressing need for multi-SNP analysis methods that can reveal system-level differences in cases and controls. Here, we present a novel multi-SNP GWAS analysis method called Pathways of Distinction Analysis (PoDA. The method uses GWAS data and known pathway-gene and gene-SNP associations to identify pathways that permit, ideally, the distinction of cases from controls. The technique is based upon the hypothesis that, if a pathway is related to disease risk, cases will appear more similar to other cases than to controls (or vice versa for the SNPs associated with that pathway. By systematically applying the method to all pathways of potential interest, we can identify those for which the hypothesis holds true, i.e., pathways containing SNPs for which the samples exhibit greater within-class similarity than across classes. Importantly, PoDA improves on existing single-SNP and SNP-set enrichment analyses, in that it does not require the SNPs in a pathway to exhibit independent main effects. This permits PoDA to reveal pathways in which epistatic interactions drive risk. In this paper, we detail the PoDA method and apply it to two GWAS: one of breast cancer and the other of liver cancer. The results obtained strongly suggest that there exist pathway-wide genomic differences that contribute to disease susceptibility. PoDA thus provides an analytical tool that is complementary to existing techniques and has the power to enrich our understanding of disease genomics at the systems-level.

  1. SNP markers-based map construction and genome-wide linkage analysis in Brassica napus.

    Science.gov (United States)

    Raman, Harsh; Dalton-Morgan, Jessica; Diffey, Simon; Raman, Rosy; Alamery, Salman; Edwards, David; Batley, Jacqueline

    2014-09-01

    An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  2. Journal Rankings by Health Management Faculty Members: Are There Differences by Rank, Leadership Status, or Area of Expertise?

    Science.gov (United States)

    Menachemi, Nir; Hogan, Tory H; DelliFraine, Jami L

    2015-01-01

    Health administration (HA) faculty members publish in a variety of journals, including journals focused on management, economics, policy, and information technology. HA faculty members are evaluated on the basis of the quality and quantity of their journal publications. However, it is unclear how perceptions of these journals vary by subdiscipline, department leadership role, or faculty rank. It is also not clear how perceptions of journals may have changed over the past decade since the last evaluation of journal rankings in the field was published. The purpose of the current study is to examine how respondents rank journals in the field of HA, as well as the variation in perception by academic rank, department leadership status, and area of expertise. Data were drawn from a survey of HA faculty members at U.S. universities, which was completed in 2012. Different journal ranking patterns were noted for faculty members of different subdisciplines. The health management-oriented journals (Health Care Management Review and Journal of Healthcare Management) were ranked higher than in previous research, suggesting that journal ranking perceptions may have changed over the intervening decade. Few differences in perceptions were noted by academic rank, but we found that department chairs were more likely than others to select Health Affairs in their top three most prestigious journals (β = 0.768; p different disciplines, and this perceived difference could have implications for promotion and tenure decisions.

  3. The Times Higher Education Supplement and Quacquarelli Symonds (THES - QS) World University Rankings: New Developments in Ranking Methodology

    Science.gov (United States)

    Sowter, Ben

    2008-01-01

    This paper presents key new developments in the THES - QS World University Rankings in 2007, related to enhancements to the "Peer Review", "Data Collection" and "Statistical Aggregation" utilised in this ranking as well as discussing the decision to utilise Full-Time Equivalent (FTE) figures for personnel statistics. Indicator correlation is also…

  4. The structure of completely positive matrices according to their CP-rank and CP-plus-rank

    NARCIS (Netherlands)

    Dickinson, Peter James Clair; Bomze, Immanuel M.; Still, Georg J.

    2015-01-01

    We study the topological properties of the cp-rank operator $\\mathrm{cp}(A)$ and the related cp-plus-rank operator $\\mathrm{cp}^+(A)$ (which is introduced in this paper) in the set $\\mathcal{S}^n$ of symmetric $n\\times n$-matrices. For the set of completely positive matrices, $\\mathcal{CP}^n$, we

  5. BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters.

    Science.gov (United States)

    Huang, Hailiang; Tata, Sandeep; Prill, Robert J

    2013-01-01

    Computational workloads for genome-wide association studies (GWAS) are growing in scale and complexity outpacing the capabilities of single-threaded software designed for personal computers. The BlueSNP R package implements GWAS statistical tests in the R programming language and executes the calculations across computer clusters configured with Apache Hadoop, a de facto standard framework for distributed data processing using the MapReduce formalism. BlueSNP makes computationally intensive analyses, such as estimating empirical p-values via data permutation, and searching for expression quantitative trait loci over thousands of genes, feasible for large genotype-phenotype datasets. http://github.com/ibm-bioinformatics/bluesnp

  6. Using SNP markers to estimate additive, dominance and imprinting genetic variance

    DEFF Research Database (Denmark)

    Lopes, M S; Bastiaansen, J W M; Janss, Luc

    .01 to 0.02. Dominance effects make an important contribution to the genetic variation of NT in the two lines evaluated. Imprinting effects appeared less important for NT than additive and dominance effects. The SNP random regression model presented and evaluated in this study is a feasible approach......The contributions of additive, dominance and imprinting effects to the variance of number of teats (NT) were evaluated in two purebred pig populations using SNP markers. Three different random regression models were evaluated, accounting for the mean and: 1) additive effects (MA), 2) additive...

  7. AptRank: an adaptive PageRank model for protein function prediction on   bi-relational graphs.

    Science.gov (United States)

    Jiang, Biaobin; Kloster, Kyle; Gleich, David F; Gribskov, Michael

    2017-06-15

    Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function-function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model. We first construct a Bi-relational graph (Birg) model comprised of both protein-protein association and function-function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training. The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank . gribskov@purdue.edu. Supplementary data are available at Bioinformatics online.

  8. Highlighting Entanglement of Cultures via Ranking of Multilingual Wikipedia Articles

    Science.gov (United States)

    Eom, Young-Ho; Shepelyansky, Dima L.

    2013-01-01

    How different cultures evaluate a person? Is an important person in one culture is also important in the other culture? We address these questions via ranking of multilingual Wikipedia articles. With three ranking algorithms based on network structure of Wikipedia, we assign ranking to all articles in 9 multilingual editions of Wikipedia and investigate general ranking structure of PageRank, CheiRank and 2DRank. In particular, we focus on articles related to persons, identify top 30 persons for each rank among different editions and analyze distinctions of their distributions over activity fields such as politics, art, science, religion, sport for each edition. We find that local heroes are dominant but also global heroes exist and create an effective network representing entanglement of cultures. The Google matrix analysis of network of cultures shows signs of the Zipf law distribution. This approach allows to examine diversity and shared characteristics of knowledge organization between cultures. The developed computational, data driven approach highlights cultural interconnections in a new perspective. Dated: June 26, 2013 PMID:24098338

  9. SRS: Site ranking system for hazardous chemical and radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Rechard, R.P.; Chu, M.S.Y.; Brown, S.L.

    1988-05-01

    This report describes the rationale and presents instructions for a site ranking system (SRS). SRS ranks hazardous chemical and radioactive waste sites by scoring important and readily available factors that influence risk to human health. Using SRS, sites can be ranked for purposes of detailed site investigations. SRS evaluates the relative risk as a combination of potentially exposed population, chemical toxicity, and potential exposure of release from a waste site; hence, SRS uses the same concepts found in a detailed assessment of health risk. Basing SRS on the concepts of risk assessment tends to reduce the distortion of results found in other ranking schemes. More importantly, a clear logic helps ensure the successful application of the ranking procedure and increases its versatility when modifications are necessary for unique situations. Although one can rank sites using a detailed risk assessment, it is potentially costly because of data and resources required. SRS is an efficient approach to provide an order-of-magnitude ranking, requiring only readily available data (often only descriptive) and hand calculations. Worksheets are included to make the system easier to understand and use. 88 refs., 19 figs., 58 tabs.

  10. Highlighting entanglement of cultures via ranking of multilingual Wikipedia articles.

    Directory of Open Access Journals (Sweden)

    Young-Ho Eom

    Full Text Available How different cultures evaluate a person? Is an important person in one culture is also important in the other culture? We address these questions via ranking of multilingual Wikipedia articles. With three ranking algorithms based on network structure of Wikipedia, we assign ranking to all articles in 9 multilingual editions of Wikipedia and investigate general ranking structure of PageRank, CheiRank and 2DRank. In particular, we focus on articles related to persons, identify top 30 persons for each rank among different editions and analyze distinctions of their distributions over activity fields such as politics, art, science, religion, sport for each edition. We find that local heroes are dominant but also global heroes exist and create an effective network representing entanglement of cultures. The Google matrix analysis of network of cultures shows signs of the Zipf law distribution. This approach allows to examine diversity and shared characteristics of knowledge organization between cultures. The developed computational, data driven approach highlights cultural interconnections in a new perspective. Dated: June 26, 2013.

  11. Highlighting entanglement of cultures via ranking of multilingual Wikipedia articles.

    Science.gov (United States)

    Eom, Young-Ho; Shepelyansky, Dima L

    2013-01-01

    How different cultures evaluate a person? Is an important person in one culture is also important in the other culture? We address these questions via ranking of multilingual Wikipedia articles. With three ranking algorithms based on network structure of Wikipedia, we assign ranking to all articles in 9 multilingual editions of Wikipedia and investigate general ranking structure of PageRank, CheiRank and 2DRank. In particular, we focus on articles related to persons, identify top 30 persons for each rank among different editions and analyze distinctions of their distributions over activity fields such as politics, art, science, religion, sport for each edition. We find that local heroes are dominant but also global heroes exist and create an effective network representing entanglement of cultures. The Google matrix analysis of network of cultures shows signs of the Zipf law distribution. This approach allows to examine diversity and shared characteristics of knowledge organization between cultures. The developed computational, data driven approach highlights cultural interconnections in a new perspective. Dated: June 26, 2013.

  12. Ranking the dermatology programs based on measurements of academic achievement.

    Science.gov (United States)

    Wu, Jashin J; Ramirez, Claudia C; Alonso, Carol A; Berman, Brian; Tyring, Stephen K

    2007-07-13

    The only dermatology rankings in the past were based on National Institutes of Health (NIH) funding and journal citations. To determine the highest ranking academic dermatology programs based on 5 outcome measures and on an overall ranking scale. To the best of our knowledge, this is the first report to rank the dermatology programs on 4 of the following outcome measures of academic achievement and with an overall ranking. We collected extensive 2001 to 2004 data ranging from total publications to grant funding on 107 U.S. dermatology programs and their full-time faculty. Data from part-time and volunteer faculty were not used. Publications in 2001 to 2004; NIH funding in 2004; Dermatology Foundation grants in 2001 to 2004; faculty lectures in 2004 delivered at national conferences; number of full-time faculty members who were on the editorial boards of the top 3 U.S. dermatology journals and the top 4 subspecialty journals We used the 5 outcome measures to tabulate the highest ranking programs in each category. Using a weighted ranking system, we also tabulated the overall top 30 dermatology programs based on these 5 outcome measures. We were not able to determine the total amount of NIH funding in dollars of the dermatology divisions. The impact factors of the journal in which these publications appeared was not factored into our calculations. Since faculty members may collaborate on the same publication, some publications may have been double-counted. In descending order, the 5 highest ranked academic programs are the University of Pennsylvania; University of California, San Francisco; Yale-New Haven Medical Center; New York University; and University of Michigan. This ranking system may allow residents and faculty to improve the academic achievements at their respective programs.

  13. Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing.

    Science.gov (United States)

    Børsting, Claus; Fordyce, Sarah L; Olofsson, Jill; Mogensen, Helle Smidt; Morling, Niels

    2014-09-01

    The Ion Torrent™ HID SNP assay amplified 136 autosomal SNPs and 33 Y-chromosome markers in one PCR and the markers were subsequently typed using the Ion PGM™ second generation sequencing platform. A total of 51 of the autosomal SNPs were selected from the SNPforID panel that is routinely used in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent™ HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent™ HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals were previously identified by typing 45 Y-chromosome SNPs. Full concordance between the assays were obtained except for the SNP genotypes of two SNPs. These SNPs were among the eight SNPs (rs2399332, rs1029047, rs10776839, rs4530059, rs8037429, rs430046, rs1031825 and rs1523537) with inconsistent allele balance among samples. These SNPs should be excluded from the panel. The optimal amount of DNA in the PCR seemed to be ≥0.5ng. Allele drop-outs were rare and only seen in experiments with <0.5ng input DNA and with a coverage of <50reads. No allele drop-in was observed. The great majority of the heterozygote allele balances were between 0.6 and 1.6, which is comparable to the heterozygote balances of STRs typed with PCR-CE. The number of reads with base calls that differed from the genotype call was typically less than five. This allowed detection of 1:100 mixtures with a high degree of certainty in experiments with a high total depth of coverage. In conclusion, the Ion PGM™ is a very promising platform for forensic genetics. However, the secondary sequence analysis software made wrong genotype calls from correctly sequenced alleles. These types of errors must be corrected before the platform can be used in case work. Furthermore, the sequence analysis software should be further developed and include quality settings for each SNP based on validation studies. Copyright

  14. Effect of the MDM2 promoter polymorphisms SNP309T>G and SNP285G>C on the risk of ovarian cancer in BRCA1 mutation carriers

    Directory of Open Access Journals (Sweden)

    Bjørnslett Merete

    2012-10-01

    Full Text Available Abstract Background While BRCA mutation carriers possess a 20-40% lifetime risk of developing ovarian cancer, knowledge about genetic modifying factors influencing the phenotypic expression remains obscure. We explored the distribution of the MDM2 polymorphisms SNP309T>G and the recently discovered SNP285G>C in Norwegian patients with BRCA related ovarian cancer. Methods 221 BRCA related ovarian cancer cases (BRCA1; n = 161 and BRCA2; n = 60 were tested for the MDM2 polymorphisms. Results were compared to healthy controls (n = 2,465. Results The SNP309G allele was associated with elevated OR for ovarian cancer in BRCA1 mutation carriers (SNP309TG: OR 1.53; CI 1.07-2.19; p = 0.020; SNP309GG: OR 1.92; CI 1.19-3.10; p = 0.009; SNP309TG+GG combined: OR 1.61; CI 1.15-2.27; p = 0.005. In contrast, the SNP285C allele reduced risk of BRCA1 related ovarian cancer in carriers of the SNP309G allele (OR 0.50; CI 0.24-1.04; p = 0.057. Censoring individuals carrying the SNP285C/309G haplotype from the analysis elevated the OR related to the SNP309G allele (OR 1.73; CI 1.23-2.45; p = 0.002. The mean age at disease onset was 3.1 years earlier in carriers of SNP309TG+GG as compared to carriers of SNP309TT (p = 0.068. No such associations were found in BRCA2 related ovarian cancer. Conclusions Our results indicate the SNP309G allele to increase and the SNP285C allele to reduce the risk of BRCA1 related ovarian cancer. If confirmed in independent studies, this finding may have implications to counseling and decision-making regarding risk reducing measures in BRCA1 mutation carriers.

  15. An Efficient PageRank Approach for Urban Traffic Optimization

    Directory of Open Access Journals (Sweden)

    Florin Pop

    2012-01-01

    to determine optimal decisions for each traffic light, based on the solution given by Larry Page for page ranking in Web environment (Page et al. (1999. Our approach is similar with work presented by Sheng-Chung et al. (2009 and Yousef et al. (2010. We consider that the traffic lights are controlled by servers and a score for each road is computed based on efficient PageRank approach and is used in cost function to determine optimal decisions. We demonstrate that the cumulative contribution of each car in the traffic respects the main constrain of PageRank approach, preserving all the properties of matrix consider in our model.

  16. The art of living in Otto Rank's Will Therapy.

    Science.gov (United States)

    Wadlington, Will

    2012-12-01

    Otto Rank's approach to psychotherapy, developed after his separation from Freud, encourages living life fully in spite of death and limitation. In his emphasis on the here and now, new experience in the therapeutic relationship, and collaboration and creativity in the therapy process, Rank was ahead of his time. As a theorist of personality and of creativity, his work is well known, but his influence on the practices of humanistic, existential, and post-psychoanalytic relational therapists is largely unacknowledged. Rank's creative legacy is an approach to psychotherapy that calls forth artistry and collaboration between therapist and client.

  17. Who's #1? The Science of Rating and Ranking

    CERN Document Server

    Langville, Amy N

    2012-01-01

    A website's ranking on Google can spell the difference between success and failure for a new business. NCAA football ratings determine which schools get to play for the big money in postseason bowl games. Product ratings influence everything from the clothes we wear to the movies we select on Netflix. Ratings and rankings are everywhere, but how exactly do they work? Who's #1? offers an engaging and accessible account of how scientific rating and ranking methods are created and applied to a variety of uses. Amy Langville and Carl Meyer provide the first comprehensive overview of the mathemat

  18. Reduced rank adaptive filtering in impulsive noise environments

    KAUST Repository

    Soury, Hamza

    2014-11-01

    An impulsive noise environment is considered in this paper. A new aspect of signal truncation is deployed to reduce the harmful effect of the impulsive noise to the signal. A full rank direct solution is derived followed by an iterative solution. The reduced rank adaptive filter is presented in this environment by using two methods for rank reduction, while the minimized objective function is defined using the Lp norm. The results are presented and the efficiency of each method is discussed. © 2014 IEEE.

  19. Google's pagerank and beyond the science of search engine rankings

    CERN Document Server

    Langville, Amy N

    2006-01-01

    Why doesn't your home page appear on the first page of search results, even when you query your own name? How do other Web pages always appear at the top? What creates these powerful rankings? And how? The first book ever about the science of Web page rankings, Google's PageRank and Beyond supplies the answers to these and other questions and more. The book serves two very different audiences: the curious science reader and the technical computational reader. The chapters build in mathematical sophistication, so that the first five are accessible to the general academic reader. While other cha

  20. SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa

    Directory of Open Access Journals (Sweden)

    Locedie Mansueto

    2016-11-01

    In this paper, we discuss the datasets stored in SNP-Seek, architecture of the database and web application, interoperability methodologies in place, and discuss a few use cases demonstrating the utility of SNP-Seek for diversity analysis and molecular breeding.

  1. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

    Science.gov (United States)

    Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to ...

  2. SNP high-throughput screening in grapevine using the SNPlex genotyping system.

    Science.gov (United States)

    Pindo, Massimo; Vezzulli, Silvia; Coppola, Giuseppina; Cartwright, Dustin A; Zharkikh, Andrey; Velasco, Riccardo; Troggio, Michela

    2008-01-28

    Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods. Herein we report the first application of the SNPlexgenotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah x Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay. Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.

  3. SNP high-throughput screening in grapevine using the SNPlex™ genotyping system

    Science.gov (United States)

    Pindo, Massimo; Vezzulli, Silvia; Coppola, Giuseppina; Cartwright, Dustin A; Zharkikh, Andrey; Velasco, Riccardo; Troggio, Michela

    2008-01-01

    Background Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods. Results Herein we report the first application of the SNPlex™ genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay. Conclusion Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories. PMID:18226250

  4. High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Han, Yuanhong; Khu, Dong-Man; Monteros, Maria J

    2012-02-01

    Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic polymorphism in plant genomes. SNP markers are valuable tools for genetic analysis of complex traits of agronomic importance, linkage and association mapping, genome-wide selection, map-based cloning, and marker-assisted selection. Current challenges for SNP genotyping in polyploid outcrossing species include multiple alleles per loci and lack of high-throughput methods suitable for variant detection. In this study, we report on a high-resolution melting (HRM) analysis system for SNP genotyping and mapping in outcrossing tetraploid genotypes. The sensitivity and utility of this technology is demonstrated by identification of the parental genotypes and segregating progeny in six alfalfa populations based on unique melting curve profiles due to differences in allelic composition at one or multiple loci. HRM using a 384-well format is a fast, consistent, and efficient approach for SNP discovery and genotyping, useful in polyploid species with uncharacterized genomes. Possible applications of this method include variation discovery, analysis of candidate genes, genotyping for comparative and association mapping, and integration of genome-wide selection in breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9566-x) contains supplementary material, which is available to authorized users.

  5. Evaluation of the OvineSNP50 genotyping array in four South

    African Journals Online (AJOL)

    Sandenbergh, Lise

    2016-03-21

    Mar 21, 2016 ... The OvineSNP50 chip was developed by Illumina in collaboration with the International Sheep. Genomics Consortium (ISGC) and became commercially available in 2009. This microarray-based system is designed to determine the genotype of approximately 54 000 single nucleotide polymorphisms (SNPs).

  6. A one-degree-of-freedom test for supra-multiplicativity of SNP effects.

    Directory of Open Access Journals (Sweden)

    Christine Herold

    Full Text Available Deviation from multiplicativity of genetic risk factors is biologically plausible and might explain why Genome-wide association studies (GWAS so far could unravel only a portion of disease heritability. Still, evidence for SNP-SNP epistasis has rarely been reported, suggesting that 2-SNP models are overly simplistic. In this context, it was recently proposed that the genetic architecture of complex diseases could follow limiting pathway models. These models are defined by a critical risk allele load and imply multiple high-dimensional interactions. Here, we present a computationally efficient one-degree-of-freedom "supra-multiplicativity-test" (SMT for SNP sets of size 2 to 500 that is designed to detect risk alleles whose joint effect is fortified when they occur together in the same individual. Via a simulation study we show that the SMT is powerful in the presence of threshold models, even when only about 30-45% of the model SNPs are available. In addition, we demonstrate that the SMT outperforms standard interaction analysis under recessive models involving just a few SNPs. We apply our test to 10 consensus Alzheimer's disease (AD susceptibility SNPs that were previously identified by GWAS and obtain evidence for supra-multiplicativity ([Formula: see text] that is not attributable to either two-way or three-way interaction.

  7. A novel SNP of Chemerin gene in cattle and its association with ...

    African Journals Online (AJOL)

    User

    2012-04-26

    Apr 26, 2012 ... SNP 2692C>T. It was shown that associations do exist between chemerin gene and carcass and meat quality traits. As a result of the small sample size of this study, it is ..... HW, Hardy-Weinberg equilibrium; QC, Qinchuan cattle breed; CYR, Caoyuan red cattle breed; JR, Jiaxian red cattle breed; LX, Luxi.

  8. Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA.

    Directory of Open Access Journals (Sweden)

    Aubrey E Hill

    Full Text Available Like many other ancient genes, the cystic fibrosis transmembrane conductance regulator (CFTR has survived for hundreds of millions of years. In this report, we consider whether such prodigious longevity of an individual gene--as opposed to an entire genome or species--should be considered surprising in the face of eons of relentless DNA replication errors, mutagenesis, and other causes of sequence polymorphism. The conventions that modern human SNP patterns result either from purifying selection or random (neutral drift were not well supported, since extant models account rather poorly for the known plasticity and function (or the established SNP distributions found in a multitude of genes such as CFTR. Instead, our analysis can be taken as a polemic indicating that SNPs in CFTR and many other mammalian genes may have been generated--and continue to accrue--in a fundamentally more organized manner than would otherwise have been expected. The resulting viewpoint contradicts earlier claims of 'directional' or 'intelligent design-type' SNP formation, and has important implications regarding the pace of DNA adaptation, the genesis of conserved non-coding DNA, and the extent to which eukaryotic SNP formation should be viewed as adaptive.

  9. Design and Characterization of a 52K SNP Chip for Goats

    NARCIS (Netherlands)

    Tosser-klopp, G.; Bardou, P.; Bouchez, O.; Cabau, C.; Crooijmans, R.P.M.A.; Dong, Y.; Donnadieu-Tonon, C.; Eggen, A.; Heuven, H.C.M.; Jamli, S.; Jiken, A.J.; Klopp, C.; Lawley, C.T.; McEwen, J.; Martin, P.; Moreno, C.R.; Mulsant, P.; Nabihoudine, I.; Pailhoux, E.; Palhiere, I.; Rupp, R.; Sarry, J.; Sayre, B.L.; Tircazes, A.; Wang, J.; Wang, W.; Zhang, W.G.

    2014-01-01

    The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a

  10. Cloning and SNP screening of TLR4 gene and the association ...

    African Journals Online (AJOL)

    huis

    Thirty-one single nucleotide polymorphisms (SNPs) were detected by sequencing polymerase chain reaction (PCR) products from 15 cattle, consisting of five randomly selected individuals from Chinese Simmental, Holstein and. Sanhe cattle breeds each. Sixteen of these SNPs were in coding regions (cSNP). However, the.

  11. Identification of Mendelian inconsistencies between SNP and pedigree Information of Sibs

    NARCIS (Netherlands)

    Calus, M.P.L.; Mulder, H.A.; Bastiaansen, J.W.M.

    2011-01-01

    Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype

  12. Cloning and SNP screening of the TLR4 gene and the association ...

    African Journals Online (AJOL)

    Cloning and SNP screening of the TLR4 gene and the association between its polymorphism and somatic cell score in dairy cattle. ... Human models, in particular, suggest TLR4 to be a candidate gene associated with resistance to sepsis, immunodeficiencies, atherosclerosis and asthma. In this study the bovine TLR4 ...

  13. Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians

    Directory of Open Access Journals (Sweden)

    Sumiko Anno

    2007-01-01

    Full Text Available This study was undertaken to clarify the molecular basis for human skin color variation and the environmental adaptability to ultraviolet irradiation, with the ultimate goal of predicting the impact of changes in future environments on human health risk. One hundred twenty-two Caucasians living in Toledo, Ohio participated. Back and cheek skin were assayed for melanin as a quantitative trait marker. Buccal cell samples were collected and used for DNA extraction. DNA was used for SNP genotyping using the Masscode™ system, which entails two-step PCR amplification and a platform chemistry which allows cleavable mass spectrometry tags. The results show gene-gene interaction between SNP alleles at multiple loci (not necessarily on the same chromosome contributes to inter-individual skin color variation while suggesting a high probability of linkage disequilibrium. Confirmation of these findings requires further study with other ethic groups to analyze the associations between SNP alleles at multiple loci and human skin color variation. Our overarching goal is to use remote sensing data to clarify the interaction between atmospheric environments and SNP allelic frequency and investigate human adaptability to ultraviolet irradiation. Such information should greatly assist in the prediction of the health effects of future environmental changes such as ozone depletion and increased ultraviolet exposure. If such health effects are to some extent predictable, it might be possible to prepare for such changes in advance and thus reduce the extent of their impact.

  14. The use of SNP data for the monitoring of genetic diversity in cattle breeds

    Science.gov (United States)

    LD between SNPs contains information about effective population size. In this study, we investigate the use of genome-wide SNP data for marker based estimation of effective population size for two taurine cattle breeds of Africa and two local cattle breeds of Switzerland. Estimated recombination rat...

  15. SNP-based genotyping in lentil: linking sequence information with phenotypes

    Science.gov (United States)

    Lentil (Lens culinaris) has been late to enter the world of high throughput molecular analysis due to a general lack of genomic resources. Using a 454 sequencing-based approach, SNPs have been identified in genes across the lentil genome. Several hundred have been turned into single SNP KASP assay...

  16. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.)).

    Science.gov (United States)

    Hu, Xin; Ren, Jing; Ren, Xifeng; Huang, Sisi; Sabiel, Salih A I; Luo, Mingcheng; Nevo, Eviatar; Fu, Chunjie; Peng, Junhua; Sun, Dongfa

    2015-01-01

    Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.

  17. Development of gene-tagged SNP markers for gland morphogenesis in cotton

    Science.gov (United States)

    Cotton (Gossypium spp.) plants, including cottonseed, have small, pigmented glands containing gossypol and other terpenoid compounds that are toxic to humans and non-ruminant animals. Single nucleotide polymorphism (SNP) markers involved in gland morphogenesis are useful for the discovery of candid...

  18. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

    DEFF Research Database (Denmark)

    Schubert, Mikkel; Ermini, Luca; Der Sarkissian, Clio

    2014-01-01

    -generation sequencing reads, PALEOMIX carries out adapter removal, mapping against reference genomes, PCR duplicate removal, characterization of and compensation for postmortem damage, SNP calling and maximum-likelihood phylogenomic inference, and it profiles the metagenomic contents of the samples. As such, PALEOMIX...

  19. Assessing the Clinical Utility of SNP Microarray for Prader-Willi Syndrome due to Uniparental Disomy.

    Science.gov (United States)

    Santoro, Stephanie L; Hashimoto, Sayaka; McKinney, Aimee; Mihalic Mosher, Theresa; Pyatt, Robert; Reshmi, Shalini C; Astbury, Caroline; Hickey, Scott E

    2017-01-01

    Maternal uniparental disomy (UPD) 15 is one of the molecular causes of Prader-Willi syndrome (PWS), a multisystem disorder which presents with neonatal hypotonia and feeding difficulty. Current diagnostic algorithms differ regarding the use of SNP microarray to detect PWS. We retrospectively examined the frequency with which SNP microarray could identify regions of homozygosity (ROH) in patients with PWS. We determined that 7/12 (58%) patients with previously confirmed PWS by methylation analysis and microsatellite-positive UPD studies had ROH (>10 Mb) by SNP microarray. Additional assessment of 5,000 clinical microarrays, performed from 2013 to present, determined that only a single case of ROH for chromosome 15 was not caused by an imprinting disorder or identity by descent. We observed that ROH for chromosome 15 is rarely incidental and strongly associated with hypotonic infants having features of PWS. Although UPD microsatellite studies remain essential to definitively establish the presence of UPD, SNP microarray has important utility in the timely diagnostic algorithm for PWS. © 2017 S. Karger AG, Basel.

  20. Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana

    Science.gov (United States)

    In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation wa...