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Sample records for snp multiplex assigning

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

    PubMed Central

    Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon

    2005-01-01

    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 per SNP, though the latter

  2. Multiplex Detection and SNP Genotyping in a Single Fluorescence Channel

    PubMed Central

    Fu, Guoliang; Miles, Andrea; Alphey, Luke

    2012-01-01

    Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4–6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR. PMID:22272339

  3. Multiplex detection and SNP genotyping in a single fluorescence channel.

    PubMed

    Fu, Guoliang; Miles, Andrea; Alphey, Luke

    2012-01-01

    Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4-6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR. PMID:22272339

  4. High-throughput SNP scoring with GAMMArrays: genomic analysis using multiplexed microsphere arrays

    NASA Astrophysics Data System (ADS)

    Green, Lance D.; Cai, Hong; Torney, David C.; Wood, Diane J.; Uribe-Romeo, Francisco J.; Kaderali, Lars; Nolan, John P.; White, P. S.

    2002-06-01

    We have developed a SNP scoring platform, yielding high throughput, inexpensive assays. The basic platform uses fluorescently labeled DNA fragments bound to microspheres, which are analyzed using flow cytometry. SNP scoring is performed using minisequencing primers and fluorescently labeled dideoxynucleotides. Furthermore, multiplexed microspheres make it possible to score hundreds of SNPs simultaneously. Multiplexing, coupled with high throughput rates allow inexpensive scoring of several million SNPs/day. GAMMArrays use universal tags that consist of computer designed, unique DNA tails. These are incorporated into each primer, and the reverse-component is attached to a discrete population of microspheres in a multiplexed set. This enables simultaneous minisequencing of many SNPs in solution, followed by capture onto the appropriate microsphere for multiplexed analysis by flow cytometry. We present results from multiplexed SNP analyses of bacterial pathogens, and human mtDNA variation. Analytes are performed on PCR amplicons, each containing numerous SNPs scored simultaneously. In addition, these assays easily integrate into conventional liquid handling automation, and require no unique instrumentation for setup and analysis. Very high signal-to-noise ratios, ease of setup, flexibility in format and scale, and low cost make these assays extremely versatile and valuable tools for a wide variety of SNP scoring applications.

  5. Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis.

    PubMed

    Bouakaze, Caroline; Keyser, Christine; Crubézy, Eric; Montagnon, Daniel; Ludes, Bertrand

    2009-07-01

    In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers. PMID:19415315

  6. Development of a SNP panel for parentage assignment in sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The construction of accurate pedigrees is important in a variety of animal production systems and research scenarios. For example, the ability to correctly assign the paternity of offspring derived from multi-sire mating is important to producers where lambs show variation in their economic merit at...

  7. A novel three-round multiplex PCR for SNP genotyping with next generation sequencing.

    PubMed

    Chen, Ke; Zhou, Yu-Xun; Li, Kai; Qi, Li-Xin; Zhang, Qi-Fei; Wang, Mao-Chun; Xiao, Jun-Hua

    2016-06-01

    Owing to the high throughput and low cost, next generation sequencing has attracted much attention for SNP genotyping application for researchers. Here, we introduce a new method based on three-round multiplex PCR to precisely genotype SNPs with next generation sequencing. This method can as much as possible consume the equivalent amount of each pair of specific primers to largely eliminate the amplification discrepancy between different loci. After the PCR amplification, the products can be directly subjected to next generation sequencing platform. We simultaneously amplified 37 SNP loci of 757 samples and sequenced all amplicons on ion torrent PGM platform; 90.5 % of the target SNP loci were accurately genotyped (at least 15×) and 90.4 % amplicons had uniform coverage with a variation less than 50-fold. Ligase detection reaction (LDR) was performed to genotype the 19 SNP loci (as part of the 37 SNP loci) with 91 samples randomly selected from the 757 samples, and 99.5 % genotyping data were consistent with the next generation sequencing results. Our results demonstrate that three-round PCR coupled with next generation sequencing is an efficient and economical genotyping approach. Graphical Abstract The schematic diagram of three-round PCR. PMID:27113460

  8. Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua.

    PubMed

    Bradbury, Ian R; Hubert, Sophie; Higgins, Brent; Bowman, Sharen; Paterson, Ian G; Snelgrove, Paul V R; Morris, Corey J; Gregory, Robert S; Hardie, David C; Borza, Tudor; Bentzen, Paul

    2011-03-01

    The increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag-derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (H(e) = 0.36) to eastern (H(e) = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range-wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large-scale assignment studies. PMID:21429176

  9. Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

    PubMed

    Bartram, Jack; Mountjoy, Edward; Brooks, Tony; Hancock, Jeremy; Williamson, Helen; Wright, Gary; Moppett, John; Goulden, Nick; Hubank, Mike

    2016-07-01

    High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. PMID:27183494

  10. Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations.

    PubMed

    Labuschagne, Christiaan; Nupen, Lisa; Kotzé, Antoinette; Grobler, Paul J; Dalton, Desiré L

    2015-10-01

    Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested. PMID:26819703

  11. Application of the ASLP technology to a novel platform for rapid and noise-free multiplexed SNP genotyping.

    PubMed

    Shin, Sung Chul; Kim, Gahee; Yang, Hee-Bum; Park, Kwan Woo; Kang, Byoung-Cheorl; Park, Hyun Gyu

    2014-04-15

    A novel multiplexing method, which relies on universal amplification of separated ligation-dependent probes (ASLP), has been developed to genotype single-nucleotide polymorphisms (SNPs). The ASLP technique employs two allele-specific oligonucleotides (ASO), modified with universal forward primer sequences at the 5'-end and a common locus-specific oligonucleotide (LSO) extended with a universal separation (US) sequence at the 3'-end. In the process, allele-specific ligation first takes place when target genomic DNA is hybridized by perfectly matching the ASO together with the LSO. A separation probe, which consists of a universal reverse primer sequence labeled with biotin at the 5'-end and complementary sequence of US at the 3'-end, is then applied to the resulting ligation product. During the extension reaction of the separation probe, the ligated probes dissociate from target genomic DNA in the form of a double-stranded DNA and are separated from the reaction mixture, which includes genomic DNA and unligated probes, by simply using streptavidin-coated magnetic beads. PCR amplification of the separated ligation products is then carried out by using universal primers and the PCR products are hybridized on a DNA microarray using the RecA protein. The advantageous features of the new method were demonstrated by using it to genotype 15 SNP markers for cultivar identification of pepper in a convenient and correct manner. PMID:24362043

  12. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

    PubMed Central

    2011-01-01

    Background Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe. Results We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation

  13. Development of three multiplex PCR primer sets for ark shell ( Scapharca broughtonii) and their validation in parentage assignment

    NASA Astrophysics Data System (ADS)

    Li, Ning; Li, Qi; Kong, Lingfeng; Yu, Hong

    2016-04-01

    Scapharca broughtonii is a commercially important and over-exploited species. In order to investigate its genetic diversity and population structure, 43 novel polymorphic microsatellites were isolated and characterized. The number of alleles per locus ranged from 3 to 22 with an average of 6.93, and the observed and expected heterozygosities varied between 0.233 and 1.000, and 0.250 and 0.953, with an average of 0.614 and 0.707, respectively. Three highly informative multiplex PCRs were developed from nine of those microsatellites for S. broughtonii. We evaluated and validated these multiplex PCRs in 8 full-sib families. The average polymorphism information content (PIC) was 0.539. The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns. Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets. Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S. broughtonii. The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction, population genetic analysis and brood stock management.

  14. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next-generation sequencing (NGS) technologies are revolutionizing both medical and biological research through generation of massive SNP data sets for identifying heritable genome variation underlying key traits, from rare human diseases to important agronomic phenotypes in crop species. We evaluate...

  15. Combination of Multiplex PCRs for Staphylococcal Cassette Chromosome mec Type Assignment: Rapid Identification System for mec, ccr, and Major Differences in Junkyard Regions▿

    PubMed Central

    Kondo, Yoko; Ito, Teruyo; Ma, Xiao Xue; Watanabe, Shinya; Kreiswirth, Barry N.; Etienne, Jerome; Hiramatsu, Keiichi

    2007-01-01

    Staphylococcal cassette chromosome mec (SCCmec) typing, in combination with genotyping of the Staphylococcus aureus chromosome, has become essential for defining methicillin-resistant S. aureus (MRSA) clones in epidemiological studies. We have developed a convenient system for SCCmec type assignment. The system consists of six multiplex PCRs (M-PCRs) for identifying the ccr gene complex (ccr), the mec gene complex (mec), and specific structures in the junkyard (J) regions: M-PCR with primer set 1 (M-PCR 1) identified five types of ccr genes; M-PCR 2 identified class A to class C mec; M-PCRs 3 and 4 identified specific open reading frames in the J1 regions of type I and IV and of type II, III, and V SCCmec elements, respectively; M-PCR 5 identified the transposons Tn554 and ΨTn554 integrated into the J2 regions of type II and III SCCmec elements; and M-PCR 6 identified plasmids pT181 and pUB110 integrated into J3 regions. The system was validated with 99 MRSA strains carrying SCCmec elements of different types. The SCCmec types of 93 out of the 99 MRSA strains could be assigned. The SCCmec type assignments were identical to those made with a PCR system that uses numerous primer pairs to identify genes or gene alleles. Our system of six M-PCRs is thus a convenient and reliable method for typing SCCmec elements. PMID:17043114

  16. High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiplexed single nucleotide polymorphism (SNP) markers have the potential to increase the speed and cost-effectiveness of genotyping, provided that an optimal SNP density is used for each application. To test the efficiency of multiplexed SNP genotyping for diversity, mapping and breeding applicat...

  17. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.

    PubMed

    Wei, Yi-Liang; Wei, Li; Zhao, Lei; Sun, Qi-Fan; Jiang, Li; Zhang, Tao; Liu, Hai-Bo; Chen, Jian-Gang; Ye, Jian; Hu, Lan; Li, Cai-Xia

    2016-01-01

    A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r (2) < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies. PMID:25833170

  18. Exploration of SNP variants affecting hair colour prediction in Europeans.

    PubMed

    Söchtig, Jens; Phillips, Chris; Maroñas, Olalla; Gómez-Tato, Antonio; Cruz, Raquel; Alvarez-Dios, Jose; de Cal, María-Ángeles Casares; Ruiz, Yarimar; Reich, Kristian; Fondevila, Manuel; Carracedo, Ángel; Lareu, María V

    2015-09-01

    DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes. PMID:26162598

  19. The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

    PubMed Central

    Oh, Chang Seok; Lee, Soong Deok; Kim, Yi-Suk; Shin, Dong Hoon

    2015-01-01

    Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods. PMID:26345190

  20. In-service communication channel sensing based on reflectometry for dynamic wavelength assigned wavelength- and time-division multiplexed passive optical network systems

    NASA Astrophysics Data System (ADS)

    Iida, Daisuke; Kuwano, Shigeru; Terada, Jun

    2015-04-01

    In future radio access systems, base stations will be mainly accommodated in wavelength- and time-division multiplexing passive optical network (PON) based mobile backhaul and fronthaul networks, and in such networks, failed connections in an optical network unit (ONU) wavelength channel will severely degrade mobile system performance. A cost-effective in-service ONU wavelength channel monitor is essential to ensure proper system operation without failed connections. To address this issue, we propose a reflectometry-based remote sensing method that provides ONU wavelength channel information with the optical line terminal-ONU distance. The proposed method enables real-time monitoring of ONU wavelength channels without data signal quality degradation and is also able to determine if the ONUs are connected to the PON. Experimental results show that it achieves wavelength channel distinction with a high distance resolution (˜10 m). Additionally, with the method, the distance resolution for distinguishing the ONUs after the PON splitter is determined by the received signal bandwidth or the test light modulation speed rather than by the pulse width as in conventional optical time-domain reflectometry.

  1. Mononeuritis multiplex

    MedlinePlus

    Mononeuropathy multiplex; Multifocal neuropathy; Peripheral neuropathy - mononeuritis multiplex ... Shy ME. Peripheral neuropathies. In: Goldman L, Ausiello D, eds. Goldman's Cecil Medicine . 23rd ed. Philadelphia, PA: Elsevier Saunders; 2007:chap 446.

  2. 1 + 1 = 3: Development and validation of a SNP-based algorithm to identify genetic contributions from three distinct inbred mouse strains.

    PubMed

    Gorham, James D; Ranson, Matthew S; Smith, Janebeth C; Gorham, Beverly J; Muirhead, Kristen-Ashley

    2012-12-01

    State-of-the-art, genome-wide assessment of mouse genetic background uses single nucleotide polymorphism (SNP) PCR. As SNP analysis can use multiplex testing, it is amenable to high-throughput analysis and is the preferred method for shared resource facilities that offer genetic background assessment of mouse genomes. However, a typical individual SNP query yields only two alleles (A vs. B), limiting the application of this methodology to distinguishing contributions from no more than two inbred mouse strains. By contrast, simple sequence length polymorphism (SSLP) analysis yields multiple alleles but is not amenable to high-throughput testing. We sought to devise a SNP-based technique to identify donor strain origins when three distinct mouse strains potentially contribute to the genetic makeup of an individual mouse. A computational approach was used to devise a three-strain analysis (3SA) algorithm that would permit identification of three genetic backgrounds while still using a binary-output SNP platform. A panel of 15 mosaic mice with contributions from BALB/c, C57Bl/6, and DBA/2 genetic backgrounds was bred and analyzed using a genome-wide SNP panel using 1449 markers. The 3SA algorithm was applied and then validated using SSLP. The 3SA algorithm assigned 85% of 1449 SNPs as informative for the C57Bl/6, BALB/c, or DBA/2 backgrounds, respectively. Testing the panel of 15 F2 mice, the 3SA algorithm predicted donor strain origins genome-wide. Donor strain origins predicted by the 3SA algorithm correlated perfectly with results from individual SSLP markers located on five different chromosomes (n=70 tests). We have established and validated an analysis algorithm based on binary SNP data that can successfully identify the donor strain origins of chromosomal regions in mice that are bred from three distinct inbred mouse strains. PMID:23204929

  3. SNP-VISTA

    SciTech Connect

    Shah, Nameeta; Teplitsky, Michael; Minovitsky, Simon; Dubchak, Inna

    2005-11-07

    SNP-VISTA aids in analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) Mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNPs data.

  4. Steatocystoma multiplex.

    PubMed

    Chu, David H

    2003-10-01

    A 25-year-old man with a 20-year history of asymptomatic nodules on his arms and trunk, which histopathological analysis showed to be consistent with steatocystoma multiplex, is presented. Steatocystoma multiplex is a disorder characterized by multiple, asymptomatic, dermal cysts that usually occur on the trunk and proximal aspects of the extremities. Steatocystoma multiplex with acral predominance has only recently been described. Development of steatocystomas has been hypothesized to be due to alterations in the structure of keratin 17. Treatment for lesions has included surgical excision or drainage, oral retinoids, and liquid nitrogen cryotherapy. PMID:14594591

  5. SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats.

    PubMed

    Brooks, Ashley; Creighton, Erica K; Gandolfi, Barbara; Khan, Razib; Grahn, Robert A; Lyons, Leslie A

    2016-05-01

    Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random-bred domestic cats, focusing on individual and phenotypic identification. Seventy-eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot(®) ). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10(-19) across all Western cat populations and the likelihood ratio was 1.52 × 10(18) . These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications. PMID:27122395

  6. SNP-VISTA

    Energy Science and Technology Software Center (ESTSC)

    2005-11-07

    SNP-VISTA aids in analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) Mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering,more » based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNPs data.« less

  7. Multiplex Pyrosequencing.

    PubMed

    Pourmand, Nader; Elahi, Elahe; Davis, Ronald W; Ronaghi, Mostafa

    2002-04-01

    We describe here the development of a new and simple single-tube multiplex Pyrosequencing assay. Genomic DNA or cDNA was employed to PCR amplify region(s) using biotinylated and normal primer(s). Subsequent to capture of PCR products on streptavidin-coated beads, single-stranded DNA separation and hybridization of multiple sequencing primers, Pyrosequencing was performed. The obtained pyrogram resulted in a unique pattern in which the intensity of the signal determined the number of incorporated nucleotide(s). Here, we demonstrate the use of this multiplex Pyrosequencing for single nucleotide polymorphisms genotyping and microbial typing. PMID:11917037

  8. SNP panels/Imputation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Participants from thirteen countries discussed services that Interbull can perform or recommendations that Interbull can make to promote harmonization and assist member countries in improving their genomic evaluations in regard to SNP panels and imputation. The panel recommended: A mechanism to shar...

  9. Multiple SNP Set Analysis for Genome-Wide Association Studies Through Bayesian Latent Variable Selection.

    PubMed

    Lu, Zhao-Hua; Zhu, Hongtu; Knickmeyer, Rebecca C; Sullivan, Patrick F; Williams, Stephanie N; Zou, Fei

    2015-12-01

    The power of genome-wide association studies (GWAS) for mapping complex traits with single-SNP analysis (where SNP is single-nucleotide polymorphism) may be undermined by modest SNP effect sizes, unobserved causal SNPs, correlation among adjacent SNPs, and SNP-SNP interactions. Alternative approaches for testing the association between a single SNP set and individual phenotypes have been shown to be promising for improving the power of GWAS. We propose a Bayesian latent variable selection (BLVS) method to simultaneously model the joint association mapping between a large number of SNP sets and complex traits. Compared with single SNP set analysis, such joint association mapping not only accounts for the correlation among SNP sets but also is capable of detecting causal SNP sets that are marginally uncorrelated with traits. The spike-and-slab prior assigned to the effects of SNP sets can greatly reduce the dimension of effective SNP sets, while speeding up computation. An efficient Markov chain Monte Carlo algorithm is developed. Simulations demonstrate that BLVS outperforms several competing variable selection methods in some important scenarios. PMID:26515609

  10. Multiple SNP-sets Analysis for Genome-wide Association Studies through Bayesian Latent Variable Selection

    PubMed Central

    Lu, Zhaohua; Zhu, Hongtu; Knickmeyer, Rebecca C; Sullivan, Patrick F.; Stephanie, Williams N.; Zou, Fei

    2015-01-01

    The power of genome-wide association studies (GWAS) for mapping complex traits with single SNP analysis may be undermined by modest SNP effect sizes, unobserved causal SNPs, correlation among adjacent SNPs, and SNP-SNP interactions. Alternative approaches for testing the association between a single SNP-set and individual phenotypes have been shown to be promising for improving the power of GWAS. We propose a Bayesian latent variable selection (BLVS) method to simultaneously model the joint association mapping between a large number of SNP-sets and complex traits. Compared to single SNP-set analysis, such joint association mapping not only accounts for the correlation among SNP-sets, but also is capable of detecting causal SNP-sets that are marginally uncorrelated with traits. The spike-slab prior assigned to the effects of SNP-sets can greatly reduce the dimension of effective SNP-sets, while speeding up computation. An efficient MCMC algorithm is developed. Simulations demonstrate that BLVS outperforms several competing variable selection methods in some important scenarios. PMID:26515609

  11. Evaluation of approaches for identifying population informative markers from high density SNP Chips

    PubMed Central

    2011-01-01

    Background Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a reduced panel containing the most informative markers for these purposes. The objectives of this study were to evaluate methods of marker selection and determine the minimum number of markers from the BovineSNP50 BeadChip required to verify the origin of individuals in European cattle breeds. Delta, Wright's FST, Weir & Cockerham's FST and PCA methods for population differentiation were compared. The level of informativeness of each SNP was estimated from the breed specific allele frequencies. Individual assignment analysis was performed using the ranked informative markers. Stringency levels were applied by log-likelihood ratio to assess the confidence of the assignment test. Results A 95% assignment success rate for the 384 individually genotyped animals was achieved with < 80, < 100, < 140 and < 200 SNP markers (with increasing stringency threshold levels) across all the examined methods for marker selection. No further gain in power of assignment was achieved by sampling in excess of 200 SNP markers. The marker selection method that required the lowest number of SNP markers to verify the animal's breed origin was Wright's FST (60 to 140 SNPs depending on the chosen degree of confidence). Certain breeds required fewer markers (< 100) to achieve 100% assignment success. In contrast, closely related breeds require more markers (~200) to achieve > 95% assignment success. The power of assignment success, and therefore the number of SNP markers required, is dependent on the levels of genetic heterogeneity and pool of samples considered. Conclusions While all SNP selection methods produced marker panels capable of breed identification, the power of assignment varied markedly among

  12. A Bayesian Framework for SNP Identification

    SciTech Connect

    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.

  13. A 48 SNP set for grapevine cultivar identification

    PubMed Central

    2011-01-01

    Background Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification. Results We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification. Conclusions We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP

  14. SNP-VISTA: An interactive SNP visualization tool

    PubMed Central

    Shah, Nameeta; Teplitsky, Michael V; Minovitsky, Simon; Pennacchio, Len A; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L

    2005-01-01

    Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. Results We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. Conclusion The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user. PMID

  15. Linkage mapping bovine EST-based SNP

    PubMed Central

    Snelling, Warren M; Casas, Eduardo; Stone, Roger T; Keele, John W; Harhay, Gregory P; Bennett, Gary L; Smith, Timothy PL

    2005-01-01

    Background Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. Results Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. Conclusion Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and

  16. SNP analysis with duplicated fish genomes: differentiation of SNPs, paralogous sequence variants and multi-site variants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-throughout SNP discovery and genotyping have facilitated genome analyses aimed at identifying factors that affect traits of interest. Platforms that multiplex thousands of SNPs are available for some agricultural species but not yet for aquaculture. Ray-finned fish share an additional (3R) roun...

  17. SNP genotyping by heteroduplex analysis.

    PubMed

    Paniego, Norma; Fusari, Corina; Lia, Verónica; Puebla, Andrea

    2015-01-01

    Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis. PMID:25373754

  18. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

    PubMed

    Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

    2016-07-01

    The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. PMID:27208666

  19. Wavelength division multiplexed fiber optic absolute position encoder

    NASA Technical Reports Server (NTRS)

    Park, Eric D.; Gat, Erann

    1989-01-01

    A wavelength division multiplexing (WDM) method for fiber optic sensors is proposed which uses a broadband light source and narrow bandpass thin film optical filter coatings on cylindrical graded index lenses. In the WDM system described here, all bits are multiplexed onto a single signal return fiber by assigning each bit a unique wavelength. A multielement photodetector array is used as the encoded position information is in parallel. Preliminary prototype test results are presented.

  20. SNP-SNP interactions in breast cancer susceptibility

    PubMed Central

    Onay, Venüs Ümmiye; Briollais, Laurent; Knight, Julia A; Shi, Ellen; Wang, Yuanyuan; Wells, Sean; Li, Hong; Rajendram, Isaac; Andrulis, Irene L; Ozcelik, Hilmi

    2006-01-01

    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(-1082)A]), 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 biological interactions

  1. Negotiating Assignment Pathways: Students and Academic Assignments

    ERIC Educational Resources Information Center

    McDowell, Liz

    2008-01-01

    Existing research identifies that students' approaches to assignments are related to their general approaches to study. It is suggested that students need to better understand the requirements of assignments and acquire new concepts such as "argument". This fine-grained study proposes four qualitatively distinct assignment pathways: gathering,…

  2. Multiplex PageRank.

    PubMed

    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. PMID:24205186

  3. A Microfluidic Device for Multiplex Single-Nucleotide Polymorphism Genotyping

    PubMed Central

    Zhu, Jing; Qiu, Chunmei; Palla, Mirkó; Nguyen, ThaiHuu; Russo, James J.; Ju, Jingyue; Lin, Qiao

    2015-01-01

    Single-nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations; they provide the genetic fingerprint of individuals and are essential for genetic biomarker discoveries. Accurate detection of SNPs is of great significance for disease prevention, diagnosis and prognosis, and for prediction of drug response and clinical outcomes in patients. Nevertheless, conventional SNP genotyping methods are still limited by insufficient accuracy or labor-, time-, and resource-intensive procedures. Microfluidics has been increasingly utilized to improve efficiency; however, the currently available microfluidic genotyping systems still have shortcomings in accuracy, sensitivity, throughput and multiplexing capability. To address these challenges, we developed a multi-step SNP genotyping microfluidic device, which performs single-base extension of SNP specific primers and solid-phase purification of the extension products on a temperature-controlled chip. The products are ready for immediate detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), providing identification of the alleles at the target loci. The integrated device enables efficient and automated operation, while maintaining the high accuracy and sensitivity provided by MS. The multiplex genotyping capability was validated by performing rapid, accurate and simultaneous detection of 4 loci on a synthetic template. The microfluidic device has the potential to perform automatic, accurate, quantitative and high-throughput assays covering a broad spectrum of applications in biological and clinical research, drug development and forensics. PMID:26594354

  4. Multiplex gas chromatography

    NASA Technical Reports Server (NTRS)

    Valentin, Jose R.

    1990-01-01

    The principles of the multiplex gas chromatography (GC) technique, which is a possible candidate for chemical analysis of planetary atmospheres, are discussed. Particular attention is given to the chemical modulators developed by present investigators for multiplex GC, namely, the thermal-desorption, thermal-decomposition, and catalytic modulators, as well as to mechanical modulators. The basic technique of multiplex GC using chemical modulators and a mechanical modulator is demonstrated. It is shown that, with the chemical modulators, only one gas stream consisting of the carrier in combination with the components is being analyzed, resulting in a simplified instrument that requires relatively few consumables. The mechanical modulator demonstrated a direct application of multiplex GC for the analysis of gases in atmosphere of Titan at very low pressures.

  5. The Nifty Assignments Site.

    ERIC Educational Resources Information Center

    Parlante, Nick

    2001-01-01

    Describes a Web site called Nifty Assignments that offers assignments for computer science education. Topics include programming assignments; student appeal; appropriateness for high school classes; and links to other related Web sites. (LRW)

  6. Apollo Multiplexer operations manual

    SciTech Connect

    Miller, M.M.

    1985-04-01

    This report describes the operation of the the Apollo Multiplexer, a microprocessor based communications device designed to process data between an Apollo computer and up to four Gandalf PACXIV data switches. Details are given on overall operation, hardware, and troubleshooting. The reader should gain sufficient knowledge from this report to understand the operation of the multiplexer and effectively analyze and correct any problems that might occur.

  7. Downlink data multiplexer

    NASA Technical Reports Server (NTRS)

    Holland, S. Douglas (Inventor); Steele, Glen F. (Inventor); Romero, Denise M. (Inventor); Koudelka, Robert David (Inventor)

    2008-01-01

    A data multiplexer that accommodates both industry standard CCSDS data packets and bits streams and standard IEEE 1394 data is described. The multiplexer provides a statistical allotment of bandwidth to the channels in turn, preferably four, but expandable in increments of four up to sixteen. A microcontroller determines bandwidth requested by the plurality of channels, as well as the bandwidth available, and meters out the available bandwidth on a statistical basis employing flow control to the input channels.

  8. Multiplexed chirp waveform synthesizer

    DOEpatents

    Dudley, Peter A.; Tise, Bert L.

    2003-09-02

    A synthesizer for generating a desired chirp signal has M parallel channels, where M is an integer greater than 1, each channel including a chirp waveform synthesizer generating at an output a portion of a digital representation of the desired chirp signal; and a multiplexer for multiplexing the M outputs to create a digital representation of the desired chirp signal. Preferably, each channel receives input information that is a function of information representing the desired chirp signal.

  9. BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data.

    PubMed

    Xu, Yanxun; Zheng, Xiaofeng; Yuan, Yuan; Estecio, Marcos R; Issa, Jean-Pierre; Qiu, Peng; Ji, Yuan; Liang, Shoudan

    2014-01-01

    A single-nucleotide polymorphism (SNP) is a sole base change in the DNA sequence and is the most common polymorphism. Detection and annotation of SNPs are among the central topics in biomedical research as SNPs are believed to play important roles on the manifestation of phenotypic events, such as disease susceptibility. To take full advantage of the next-generation sequencing (NGS) technology, we propose a Bayesian approach, BM-SNP, to identify SNPs based on the posterior inference using NGS data. In particular, BM-SNP computes the posterior probability of nucleotide variation at each covered genomic position using the contents and frequency of the mapped short reads. The position with a high posterior probability of nucleotide variation is flagged as a potential SNP. We apply BM-SNP to two cell-line NGS data, and the results show a high ratio of overlap ( >95 percent) with the dbSNP database. Compared with MAQ, BM-SNP identifies more SNPs that are in dbSNP, with higher quality. The SNPs that are called only by BM-SNP but not in dbSNP may serve as new discoveries. The proposed BM-SNP method integrates information from multiple aspects of NGS data, and therefore achieves high detection power. BM-SNP is fast, capable of processing whole genome data at 20-fold average coverage in a short amount of time. PMID:26357041

  10. Coevolution and Correlated Multiplexity in Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Kim, Jung Yeol; Goh, K.-I.

    2013-08-01

    Distinct channels of interaction in a complex networked system define network layers, which coexist and cooperate for the system’s function. Towards understanding such multiplex systems, we propose a modeling framework based on coevolution of network layers, with a class of minimalistic growing network models as working examples. We examine how the entangled growth of coevolving layers can shape the network structure and show analytically and numerically that the coevolution can induce strong degree correlations across layers, as well as modulate degree distributions. We further show that such a coevolution-induced correlated multiplexity can alter the system’s response to the dynamical process, exemplified by the suppressed susceptibility to a social cascade process.

  11. Compact spatial multiplexers for mode division multiplexing.

    PubMed

    Chen, Haoshuo; van Uden, Roy; Okonkwo, Chigo; Koonen, Ton

    2014-12-29

    Spatial multiplexer (SMUX) for mode division multiplexing (MDM) has evolved from mode-selective excitation, multiple-spot and photonic-lantern based solutions in order to minimize both mode-dependent loss (MDL) and coupler insertion loss (CIL). This paper discusses the implementation of all the three solutions by compact components in a small footprint. Moreover, the compact SMUX can be manufactured in mass production and packaged to assure high reliability. First, push-pull scheme and center launch based SMUXes are demonstrated on two mostly-popular photonic integration platforms: Silicon-on-insulator (SOI) and Indium Phosphide (InP) for selectively exciting LP01 and LP11 modes. 2-dimensional (2D) top-coupling by using vertical emitters is explored to provide a coupling interface between a few-mode fiber (FMF) and the photonic integrated SMUX. SOI-based grating couplers and InP-based 45° vertical mirrors are proposed and researched as vertical emitters in each platform. Second, a 3-spot SMUX is realized on an InP-based circuit through employing 45° vertical mirrors. Third, as a newly-emerging photonic integration platform, laser-inscribed 3D waveguide (3DW) technology is applied for a fully-packaged dual-channel 6-mode SMUX including two 6-core photonic lantern structures as mode multiplexer and demultiplexer, respectively. PMID:25607130

  12. Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

    PubMed Central

    Bernardo, Amy; Wang, Shan; St. Amand, Paul; Bai, Guihua

    2015-01-01

    With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat. PMID:26625271

  13. Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography

    PubMed Central

    Cardona-Castro, Nora; Beltrán-Alzate, Juan Camilo; Romero-Montoya, Irma Marcela; Li, Wei; Brennan, Patrick J; Vissa, Varalakshmi

    2013-01-01

    New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined ‘elimination’ status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of M. leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy. PMID:23291420

  14. Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography.

    PubMed

    Cardona-Castro, Nora; Beltrán-Alzate, Juan Camilo; Romero-Montoya, Irma Marcela; Li, Wei; Brennan, Patrick J; Vissa, Varalakshmi

    2013-03-01

    New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined 'elimination' status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of Mycobacterium leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy. PMID:23291420

  15. Spectrally multiplexed chromatic confocal multipoint sensing.

    PubMed

    Hillenbrand, Matthias; Lorenz, Lucia; Kleindienst, Roman; Grewe, Adrian; Sinzinger, Stefan

    2013-11-15

    We present a concept for chromatic confocal distance sensing that employs two levels of spectral multiplexing for the parallelized evaluation of multiple lateral measurement points; at the first level, the chromatic confocal principle is used to encode distance information within the spectral distribution of the sensor signal. For lateral multiplexing, the total spectral bandwidth of the sensor is split into bands. Each band is assigned to a different lateral measurement point by a segmented diffractive element. Based on this concept, we experimentally demonstrate a chromatic confocal three-point sensor that is suitable for harsh production environments, since it works with a single-point spectrometer and does not require scanning functionality. The experimental system has a working distance of more than 50 mm, a measurement range of 9 mm, and an axial resolution of 50 μm. PMID:24322108

  16. Multiplexed Biosensors for Mycotoxins.

    PubMed

    Maragos, Chris M

    2016-07-01

    Significant progress has been made in the development of biosensors that can be used to detect low-MW toxins produced by fungi (mycotoxins). The number of formats that have been investigated is impressive and is an indication of the importance attached to finding easy-to-use, accurate, and rapid methods for detecting these toxins in commodities and foods. This review explores the details of multiplexed biosensors based on many formats, including multiplexed immunoassays, suspension arrays, membrane-based devices (flow-through and immunochromatographic), and planar microarrays. Each assay format has its own strengths and areas that need improvement. Certain formats, such as multiplexed immunochromatographic devices, are well developed and relatively easy to use, and in some cases, commercial products are being sold. Others, such as the suspension arrays and microarrays, are laboratory-based assays that, although more complicated, are also more amenable to a larger scale of multiplexing. The diversity of such efforts and the multitude of formats under investigation suggest that multiple solutions will be found to satisfy the need for multiplexed toxin detection. PMID:27455928

  17. Multiplexed genotyping with sequence-tagged molecular inversion probes.

    PubMed

    Hardenbol, Paul; Banér, Johan; Jain, Maneesh; Nilsson, Mats; Namsaraev, Eugeni A; Karlin-Neumann, George A; Fakhrai-Rad, Hossein; Ronaghi, Mostafa; Willis, Thomas D; Landegren, Ulf; Davis, Ronald W

    2003-06-01

    We report on the development of molecular inversion probe (MIP) genotyping, an efficient technology for large-scale single nucleotide polymorphism (SNP) analysis. This technique uses MIPs to produce inverted sequences, which undergo a unimolecular rearrangement and are then amplified by PCR using common primers and analyzed using universal sequence tag DNA microarrays, resulting in highly specific genotyping. With this technology, multiplex analysis of more than 1,000 probes in a single tube can be done using standard laboratory equipment. Genotypes are generated with a high call rate (95%) and high accuracy (>99%) as determined by independent sequencing. PMID:12730666

  18. Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

    PubMed Central

    2014-01-01

    Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions

  19. Detecting Susceptibility to Breast Cancer with SNP-SNP Interaction Using BPSOHS and Emotional Neural Networks.

    PubMed

    Wang, Xiao; Peng, Qinke; Fan, Yue

    2016-01-01

    Studies for the association between diseases and informative single nucleotide polymorphisms (SNPs) have received great attention. However, most of them just use the whole set of useful SNPs and fail to consider the SNP-SNP interactions, while these interactions have already been proven in biology experiments. In this paper, we use a binary particle swarm optimization with hierarchical structure (BPSOHS) algorithm to improve the effective of PSO for the identification of the SNP-SNP interactions. Furthermore, in order to use these SNP interactions in the susceptibility analysis, we propose an emotional neural network (ENN) to treat SNP interactions as emotional tendency. Different from the normal architecture, just as the emotional brain, this architecture provides a specific path to treat the emotional value, by which the SNP interactions can be considered more quickly and directly. The ENN helps us use the prior knowledge about the SNP interactions and other influence factors together. Finally, the experimental results prove that the proposed BPSOHS_ENN algorithm can detect the informative SNP-SNP interaction and predict the breast cancer risk with a much higher accuracy than existing methods. PMID:27294121

  20. Detecting Susceptibility to Breast Cancer with SNP-SNP Interaction Using BPSOHS and Emotional Neural Networks

    PubMed Central

    Wang, Xiao; Fan, Yue

    2016-01-01

    Studies for the association between diseases and informative single nucleotide polymorphisms (SNPs) have received great attention. However, most of them just use the whole set of useful SNPs and fail to consider the SNP-SNP interactions, while these interactions have already been proven in biology experiments. In this paper, we use a binary particle swarm optimization with hierarchical structure (BPSOHS) algorithm to improve the effective of PSO for the identification of the SNP-SNP interactions. Furthermore, in order to use these SNP interactions in the susceptibility analysis, we propose an emotional neural network (ENN) to treat SNP interactions as emotional tendency. Different from the normal architecture, just as the emotional brain, this architecture provides a specific path to treat the emotional value, by which the SNP interactions can be considered more quickly and directly. The ENN helps us use the prior knowledge about the SNP interactions and other influence factors together. Finally, the experimental results prove that the proposed BPSOHS_ENN algorithm can detect the informative SNP-SNP interaction and predict the breast cancer risk with a much higher accuracy than existing methods. PMID:27294121

  1. A multiplexed quantum memory.

    PubMed

    Lan, S-Y; Radnaev, A G; Collins, O A; Matsukevich, D N; Kennedy, T A; Kuzmich, A

    2009-08-01

    A quantum repeater is a system for long-distance quantum communication that employs quantum memory elements to mitigate optical fiber transmission losses. The multiplexed quantum memory (O. A. Collins, S. D. Jenkins, A. Kuzmich, and T. A. B. Kennedy, Phys. Rev. Lett. 98, 060502 (2007)) has been shown theoretically to reduce quantum memory time requirements. We present an initial implementation of a multiplexed quantum memory element in a cold rubidium gas. We show that it is possible to create atomic excitations in arbitrary memory element pairs and demonstrate the violation of Bell's inequality for light fields generated during the write and read processes. PMID:19654771

  2. Assignments That Work.

    ERIC Educational Resources Information Center

    Hashimoto, I.

    1986-01-01

    Suggests, on a humorous note, a game-plan for assignment justification and elaboration that utilizes, in a constructive and professional manner, the best of what is known about assignment-making. (EL)

  3. SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops

    NASA Astrophysics Data System (ADS)

    Yoshimura, Yoshinaga; Ohtake, Tomoko; Okada, Hajime; Ami, Takehiro; Tsukaguchi, Tadashi; Fujimoto, Kenzo

    2009-06-01

    We describe a simple and inexpensive single-nucleotide polymorphism (SNP) typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.

  4. Time-division SQUID multiplexers

    NASA Astrophysics Data System (ADS)

    Irwin, K. D.; Vale, L. R.; Bergren, N. E.; Deiker, S.; Grossman, E. N.; Hilton, G. C.; Nam, S. W.; Reintsema, C. D.; Rudman, D. A.; Huber, M. E.

    2002-02-01

    SQUID multiplexers make it possible to build arrays of thousands of low-temperature bolometers and microcalorimeters based on superconducting transition-edge sensors with a manageable number of readout channels. We discuss the technical tradeoffs between proposed time-division multiplexer and frequency-division multiplexer schemes and motivate our choice of time division. Our first-generation SQUID multiplexer is now in use in an astronomical instrument. We describe our second-generation SQUID multiplexer, which is based on a new architecture that significantly reduces the dissipation of power at the first stage, allowing thousands of SQUIDs to be operated at the base temperature of a cryostat. .

  5. The Microwave SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Mates, John Arthur Benson

    2011-12-01

    This thesis describes a multiplexer of Superconducting Quantum Interference Devices (SQUIDs) with low-noise, ultra-low power dissipation, and great scalability. The multiplexer circuit measures the magnetic flux in a large number of unshunted rf SQUIDs by coupling each SQUID to a superconducting microwave resonator tuned to a unique resonance frequency and driving the resonators from a common feedline. A superposition of microwave tones measures each SQUID simultaneously using only two coaxial cables between the cryogenic device and room temperature. This multiplexer will enable the instrumentation of arrays with hundreds of thousands of low-temperature detectors for new applications in cosmology, materials analysis, and nuclear non-proliferation. The driving application of the Microwave SQUID Multiplexer is the readout of large arrays of superconducting transition-edge sensors, by some figures of merit the most sensitive detectors of electromagnetic signals over a span of more than nine orders of magnitude in energy, from 40 GHz microwaves to 200 keV gamma rays. Modern transition-edge sensors have noise-equivalent power as low as 10-20 W / Hz1/2 and energy resolution as good as 2 eV at 6 keV. These per-pixel sensitivities approach theoretical limits set by the underlying signals, motivating a rapid increase in pixel count to access new science. Compelling applications, like the non-destructive assay of nuclear material for treaty verification or the search for primordial gravity waves from inflation use arrays of these detectors to increase collection area or tile a focal plane. We developed three generations of SQUID multiplexers, optimizing the first for flux noise 0.17 muPhi0 / Hz1/2, the second for input current noise 19 pA / Hz1/2, and the last for practical multiplexing of large arrays of cosmic microwave background polarimeters based on transition-edge sensors. Using the last design we demonstrated multiplexed readout of prototype polarimeters with the

  6. SNP Arrays for Species Identification in Salmonids.

    PubMed

    Wenne, Roman; Drywa, Agata; Kent, Matthew; Sundsaasen, Kristil Kindem; Lien, Sigbjørn

    2016-01-01

    The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper. PMID:27460372

  7. Extracting information from multiplex networks.

    PubMed

    Iacovacci, Jacopo; Bianconi, Ginestra

    2016-06-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ̃(S) for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science. PMID:27368796

  8. Extracting information from multiplex networks

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Bianconi, Ginestra

    2016-06-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ ˜ S for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science.

  9. Downlink Data Multiplexer

    NASA Technical Reports Server (NTRS)

    Holland, Douglas; Steele, Glen F.; Romero, Denise M.; Koudelka, Robert David

    2004-01-01

    A multiplexer/demultiplexer system has been developed to enable the transmission, over a single channel, of four data streams generated by a variety of sources at different (including variable) bit rates. In the original intended application, replicas of this multiplexer/demultiplexer system would be incorporated into the spacecraft-to-ground communication systems of the space shuttles. The multiplexer of each system would be installed in the spacecraft, where it would acquire and process data from such sources as commercial digital camcorders, video tape recorders, and the spacecraft telemetry system. The demultiplexer of each system would be installed in a ground station. Purely terrestrial systems of similar design could be attractive for use in situations in which there are requirements to transmit multiple streams of high-quality video data and possibly other data over single channels. The figure is a block diagram of the multiplexer as configured to process data received via three fiber-optic channels like those of the International Space Station and one electrical-cable channel that conforms to the Institute of Electrical and Electronic Engineers (IEEE) 1394 standard. (This standard consists of specifications of a high-speed serial data interface, the physical layer of which includes a cable known in the art as "FireWire." An IEEE 1394 interface can also transfer power between the components to which it is connected.) The fiber-optic channels carry packet and/or bit-stream signals that conform to the standards of the Consultative Committee for Space Data Systems (CCSDS). The IEEE 1394 interface accepts an isochronous signal like that from a digital camcorder or a video tape recorder. The processing of the four input data streams to combine them into one output stream is governed by a statistical multiplexing algorithm that features a flow-control capability and makes it possible to utilize the transmission channel with nearly 100-percent efficiency. This

  10. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  12. Multiplexing oscillatory biochemical signals.

    PubMed

    de Ronde, Wiet; ten Wolde, Pieter Rein

    2014-04-01

    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals. PMID:24685537

  13. Multiplex data bus simulator

    SciTech Connect

    Garbo, D.L.

    1983-01-01

    A multiplex data-bus simulator for analyzing multiprocessor designs is presented. The simulator was designed to be user-friendly, thus allowing a multiprocessor designer to enter various configuration inputs in a concise and orderly fashion through the use of menus. The designer is also provided a method of visualizing a message traffic flow through the use of graphical representation of events. 3 references.

  14. SBE primer : multiplexing minisequencing-based genotyping

    SciTech Connect

    Kaderali, L.; Deshpande, A.; Uribe-Romeo, F. J.; Schliep, A.; Torney, D. C.

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  15. SNP Discovery Using Next Generation Transcriptomic Sequencing.

    PubMed

    De Wit, Pierre

    2016-01-01

    In this chapter, I will guide the user through methods to find new SNP markers from expressed sequence (RNA-Seq) data, focusing on the sample preparation and also on the bioinformatic analyses needed to sort through the immense flood of data from high-throughput sequencing machines. The general steps included are as follows: sample preparation, sequencing, quality control of data, assembly, mapping, SNP discovery, filtering, validation. The first few steps are traditional laboratory protocols, whereas steps following the sequencing are of bioinformatic nature. The bioinformatics described herein are by no means exhaustive, rather they serve as one example of a simple way of analyzing high-throughput sequence data to find SNP markers. Ideally, one would like to run through this protocol several times with a new dataset, while varying software parameters slightly, in order to determine the robustness of the results. The final validation step, although not described in much detail here, is also quite critical as that will be the final test of the accuracy of the assumptions made in silico.There is a plethora of downstream applications of a SNP dataset, not covered in this chapter. For an example of a more thorough protocol also including differential gene expression and functional enrichment analyses, BLAST annotation and downstream applications of SNP markers, a good starting point could be the "Simple Fool's Guide to population genomics via RNA-Seq," which is available at http://sfg.stanford.edu . PMID:27460371

  16. Self-calibrating multiplexer circuit

    DOEpatents

    Wahl, Chris P.

    1997-01-01

    A time domain multiplexer system with automatic determination of acceptable multiplexer output limits, error determination, or correction is comprised of a time domain multiplexer, a computer, a constant current source capable of at least three distinct current levels, and two series resistances employed for calibration and testing. A two point linear calibration curve defining acceptable multiplexer voltage limits may be defined by the computer by determining the voltage output of the multiplexer to very accurately known input signals developed from predetermined current levels across the series resistances. Drift in the multiplexer may be detected by the computer when the output voltage limits, expected during normal operation, are exceeded, or the relationship defined by the calibration curve is invalidated.

  17. Self-calibrating multiplexer circuit

    SciTech Connect

    Wahl, C.P.

    1995-12-31

    A time domain multiplexer system with automatic determination of acceptable multiplexer output limits, error determination, or correction is comprised of a time domain multiplexer, a computer, a constant current source capable of at least three distinct current levels, and two series resistances employed for calibration and testing. A two point linear calibration curve defining acceptable multiplexer voltage limits may be defined by the computer by determining the voltage output of the multiplexer to very accurately known input signals developed from predetermined current levels across the series resistances. Drift in the multiplexer may be detected by the computer when the output voltage limits, expected during normal operation, are exceeded, or the relationship defined by the calibration curve is invalidated.

  18. Linkage Analysis and QTL Mapping Using SNP Dosage Data in a Tetraploid Potato Mapping Population

    PubMed Central

    Hackett, Christine A.; McLean, Karen; Bryan, Glenn J.

    2013-01-01

    New sequencing and genotyping technologies have enabled researchers to generate high density SNP genotype data for mapping populations. In polyploid species, SNP data usually contain a new type of information, the allele dosage, which is not used by current methodologies for linkage analysis and QTL mapping. Here we extend existing methodology to use dosage data on SNPs in an autotetraploid mapping population. The SNP dosages are inferred from allele intensity ratios using normal mixture models. The steps of the linkage analysis (testing for distorted segregation, clustering SNPs, calculation of recombination fractions and LOD scores, ordering of SNPs and inference of parental phase) are extended to use the dosage information. For QTL analysis, the probability of each possible offspring genotype is inferred at a grid of locations along the chromosome from the ordered parental genotypes and phases and the offspring dosages. A normal mixture model is then used to relate trait values to the offspring genotypes and to identify the most likely locations for QTLs. These methods are applied to analyse a tetraploid potato mapping population of parents and 190 offspring, genotyped using an Infinium 8300 Potato SNP Array. Linkage maps for each of the 12 chromosomes are constructed. The allele intensity ratios are mapped as quantitative traits to check that their position and phase agrees with that of the corresponding SNP. This analysis confirms most SNP positions, and eliminates some problem SNPs to give high-density maps for each chromosome, with between 74 and 152 SNPs mapped and between 100 and 300 further SNPs allocated to approximate bins. Low numbers of double reduction products were detected. Overall 3839 of the 5378 polymorphic SNPs can be assigned putative genetic locations. This methodology can be applied to construct high-density linkage maps in any autotetraploid species, and could also be extended to higher autopolyploids. PMID:23704960

  19. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Li, Qingbo; Lu, Xiandan

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  20. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Chang, Huan-Tsang; Fung, Eliza N.; Li, Qingbo; Lu, Xiandan

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  1. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Li, Q.; Lu, X.

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  2. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Chang, H.T.; Fung, E.N.; Li, Q.; Lu, X.

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  3. Hardware Counter Multiplexing

    Energy Science and Technology Software Center (ESTSC)

    2000-10-13

    The Hardware Counter Multiplexer works with the built-in counter registers on computer processors. These counters record various low-level events as software runs, but they can not record all possible events at the same time. This software helps work around that limitation by counting a series of different events in sequence over a period of time. This in turn allows programmers to measure interesting combinations of events, rather than single events. The software is designed tomore » work with multithreaded or single-threaded programs.« less

  4. A Multiple-SNP Approach for Genome-Wide Association Study of Milk Production Traits in Chinese Holstein Cattle

    PubMed Central

    Fang, Ming; Fu, Weixuan; Jiang, Dan; Zhang, Qin; Sun, Dongxiao; Ding, Xiangdong; Liu, Jianfeng

    2014-01-01

    The multiple-SNP analysis has been studied by many researchers, in which the effects of multiple SNPs are simultaneously estimated and tested in a multiple linear regression. The multiple-SNP association analysis usually has higher power and lower false-positive rate for detecting causative SNP(s) than single marker analysis (SMA). Several methods have been proposed to simultaneously estimate and test multiple SNP effects. In this research, a fast method called MEML (Mixed model based Expectation-Maximization Lasso algorithm) was developed for simultaneously estimate of multiple SNP effects. An improved Lasso prior was assigned to SNP effects which were estimated by searching the maximum joint posterior mode. The residual polygenic effect was included in the model to absorb many tiny SNP effects, which is treated as missing data in our EM algorithm. A series of simulation experiments were conducted to validate the proposed method, and the results showed that compared with SMMA, the new method can dramatically decrease the false-positive rate. The new method was also applied to the 50k SNP-panel dataset for genome-wide association study of milk production traits in Chinese Holstein cattle. Totally, 39 significant SNPs and their nearby 25 genes were found. The number of significant SNPs is remarkably fewer than that by SMMA which found 105 significant SNPs. Among 39 significant SNPs, 8 were also found by SMMA and several well-known QTLs or genes were confirmed again; furthermore, we also got some positional candidate gene with potential function of effecting milk production traits. These novel findings in our research should be valuable for further investigation. PMID:25148050

  5. Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

    PubMed Central

    Field, Helen I; Scollen, Serena A; Luccarini, Craig; Baynes, Caroline; Morrison, Jonathan; Dunning, Alison M; Easton, Douglas F; Pharoah, Paul DP

    2009-01-01

    Background In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. Implementation We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design. Conclusion The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5). Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation. Seq4SNPs is available as a service at and , currently for human SNPs, but easily extended to include any species in dbSNP. PMID:19523221

  6. SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus)

    PubMed Central

    Bekkevold, Dorte; Babbucci, Massimiliano; van Houdt, Jeroen; Maes, Gregory E.; Bargelloni, Luca; Nielsen, Rasmus O.; Taylor, Martin I.; Ogden, Rob; Cariani, Alessia; Carvalho, Gary R.; Consortium, FishPopTrace; Panitz, Frank

    2012-01-01

    The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population

  7. SNP Array in Hematopoietic Neoplasms: A Review

    PubMed Central

    Song, Jinming; Shao, Haipeng

    2015-01-01

    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. PMID:27600067

  8. The SNP Consortium website: past, present and future.

    PubMed

    Thorisson, Gudmundur A; Stein, Lincoln D

    2003-01-01

    The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or single nucleotide polymorphism (SNP) keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the data coordinating center (DCC) website (http://snp.cshl.org) are open source. PMID:12519964

  9. Quantitative multiplexed quantum dot immunohistochemistry

    SciTech Connect

    Sweeney, E.; Ward, T.H.; Gray, N.; Womack, C.; Jayson, G.; Hughes, A.; Dive, C.; Byers, R.

    2008-09-19

    Quantum dots are photostable fluorescent semiconductor nanocrystals possessing wide excitation and bright narrow, symmetrical, emission spectra. These characteristics have engendered considerable interest in their application in multiplex immunohistochemistry for biomarker quantification and co-localisation in clinical samples. Robust quantitation allows biomarker validation, and there is growing need for multiplex staining due to limited quantity of clinical samples. Most reported multiplexed quantum dot staining used sequential methods that are laborious and impractical in a high-throughput setting. Problems associated with sequential multiplex staining have been investigated and a method developed using QDs conjugated to biotinylated primary antibodies, enabling simultaneous multiplex staining with three antibodies. CD34, Cytokeratin 18 and cleaved Caspase 3 were triplexed in tonsillar tissue using an 8 h protocol, each localised to separate cellular compartments. This demonstrates utility of the method for biomarker measurement enabling rapid measurement of multiple co-localised biomarkers on single paraffin tissue sections, of importance for clinical trial studies.

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

    PubMed Central

    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. PMID:26236727

  11. Highspeed multiplexed heterodyne interferometry.

    PubMed

    Isleif, Katharina-S; Gerberding, Oliver; Köhlenbeck, Sina; Sutton, Andrew; Sheard, Benjamin; Goßler, Stefan; Shaddock, Daniel; Heinzel, Gerhard; Danzmann, Karsten

    2014-10-01

    Digitally enhanced heterodyne interferometry is a metrology technique that uses pseudo-random noise codes for modulating the phase of the laser light. Multiple interferometric signals from the same beam path can thereby be isolated based on their propagation delay, allowing one to use advantageous optical layouts in comparison to classic laser interferometers. We present here a high speed version of this technique for measuring multiple targets spatially separated by only a few centimetres. This allows measurements of multiplexed signals using free beams, making the technique attractive for several applications requiring compact optical set-ups like for example space-based interferometers. In an experiment using a modulation and sampling rate of 1.25 GHz we are able to demonstrate multiplexing between targets only separated by 36 cm and we achieve a displacement measurement noise floor of <3 pm/√Hz at 10 Hz between them. We identify a limiting excess noise at low frequencies which is unique to this technique and is probably caused by the finite bandwidth in our measurement set-up. Utilising an active clock jitter correction scheme we are also able to reduce this noise in a null measurement configuration by one order of magnitude. PMID:25322043

  12. My Favorite Assignment.

    ERIC Educational Resources Information Center

    Post, Robert E.; Johnson, Jack E.

    1982-01-01

    Presents two assignments that show (1) how George Orwell's "Politics and the English Language" can be applied to business writing and (2) how structured student-teacher conferences can generate enthusiasm for oral expression in a business communication course. (AEA)

  13. Ethnic heterogeneity of IRF6 AP-2α binding site promoter SNP association with nonsyndromic cleft lip and palate

    PubMed Central

    Blanton, Susan H.; Burt, Amber; Garcia, Elizabeth; Mulliken, John B.; Stal, Samuel; Hecht, Jacqueline T.

    2010-01-01

    Objective The goal of this study was to confirm the reported association between a noncoding SNP (rs642961) in IRF6 and nonsyndromic cleft lip and palate (NSCLP). Design, Setting and Participants Two SNPs in IRF6 (rs2235371 and rs64296) were genotyped in Hispanic and nonHispanic white multiplex (122) and simplex (308) NSCLP families. Linkage and family-based association analyses were performed on the individual SNPs as well as the 2-SNP haplotype. Results We find only modest evidence for an association with rs642961 and the 2-SNP haplotype. In contrast, we found strong evidence for association with rs2235371; this was most evident in the nonHispanic white simplex families. Conclusions While we confirm that variation in IRF6 is associated with NSCLP, our results do not support the reported association with SNP rs64296. Importantly, the association varies between ethnic groups. This finding underscores the need for evaluating additional variations in IRF6 across multiple populations to better determine its role in NSCLP. PMID:21039277

  14. Performance of different SNP panels for parentage testing in two East Asian cattle breeds.

    PubMed

    Strucken, E M; Gudex, B; Ferdosi, M H; Lee, H K; Song, K D; Gibson, J P; Kelly, M; Piper, E K; Porto-Neto, L R; Lee, S H; Gondro, C

    2014-08-01

    The International Society for Animal Genetics (ISAG) proposed a panel of single nucleotide polymorphisms (SNPs) for parentage testing in cattle (a core panel of 100 SNPs and an additional list of 100 SNPs). However, markers specific to East Asian taurine cattle breeds were not included, and no information is available as to whether the ISAG panel performs adequately for these breeds. We tested ISAG's core (100 SNP) and full (200 SNP) panels on two East Asian taurine breeds: the Korean Hanwoo and the Japanese Wagyu, the latter from the Australian herd. Even though the power of exclusion was high at 0.99 for both ISAG panels, the core panel performed poorly with 3.01% false-positive assignments in the Hanwoo population and 3.57% in the Wagyu. The full ISAG panel identified all sire-offspring relations correctly in both populations with 0.02% of relations wrongly excluded in the Hanwoo population. Based on these results, we created and tested two population-specific marker panels: one for the Wagyu population, which showed no false-positive assignments with either 100 or 200 SNPs, and a second panel for the Hanwoo, which still had some false-positive assignments with 100 SNPs but no false positives using 200 SNPs. In conclusion, for parentage assignment in East Asian cattle breeds, only the full ISAG panel is adequate for parentage testing. If fewer markers should be used, it is advisable to use population-specific markers rather than the ISAG panel. PMID:24730981

  15. (Multiplex mapping of human cDNAs)

    SciTech Connect

    Nierman, W.C.

    1992-01-01

    We have tested and implemented several protocols to increase productivity for mapping expressed sequence tags EST sequences to human chromosomes. These protocols include adopting PRIMER which permits utilization of batch files, as the standard software for PCR primer design; adding a human 21-only cell line to the NIGMS panel No. 1 to improve discrimination in discordancy analyses involving chromosome 21, adding a monochromosomal hybrid panel to facilitate chromosome assignment of sequences that are amplified from more than 1 chromosome; combining the products of multiple PCR reactions for electrophoretic analysis (pseudoplexing); routinely multiplexing PCR reactions; and automating data entry and analysis as much as possible. We have applied these protocols to assign an overall total of 132 human brain CDNA sequences to individual human chromosomes. PCR primers were designed from ESTS and tested for specific amplification from human genomic DNA. DNA was then amplified using DNA from somatic cell hybrid mapping panels as templates. The amplification products were identified using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis. The localized cDNAs include 2 for known human genes, 2 that map to 2 different human chromosomes, and 25 for cDNAs matching existing database records.

  16. A simple, bead-based assay for multiplex SNP analysis in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism and are highly suitable for automated analysis. These polymorphisms can be used in plants as simple genetic markers for many breeding applications and are useful for cultivar identification, genetic mapping, trait ...

  17. 42 CFR 433.146 - Rights assigned; assignment method.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified...

  18. Development and validation of a SNP panel for parentage assignment in rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In salmonids aquaculture, family-based selective breeding programs rely on accurate pedigree information for estimating genetic merits. The pedigree information can be tracked through the use of Passive Integrated Transponder (PIT) tags. However, PIT tags can be expensive, and cannot be used with sm...

  19. Transcriptome profiling, sequence characterization, and assignment to chromosomes of SNP markers for EXPANSIN genes in cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, leading to turgor-driven cell extension and hence are likely play an important role in determining fiber properties. The objectives of this study were to investigate the expression pro...

  20. Information multiplexing in ptychography.

    PubMed

    Batey, Darren J; Claus, Daniel; Rodenburg, John M

    2014-03-01

    We show for the first time that ptychography (a form of lensless diffractive imaging) can recover the spectral response of an object through simultaneous reconstruction of multiple images that represent the object's response to a particular mode present in the illumination. We solve the phase problem for each mode independently, even though the intensity arriving at every detector pixel is an incoherent superposition of several uncorrelated diffracted waves. Until recently, the addition of incoherent modes has been seen as a nuisance in diffractive imaging: here we show that not only can the difficulties they pose be removed, but that they can also be used to discover much more information about the object. If the illumination function is also mode-specific, we show that we can also solve simultaneously for a multiplicity of such illumination modes. The work opens exciting possibilities for information multiplexing in ptychography over all visible, X-ray and electron wavelengths. PMID:24413077

  1. Portable Multiplex Pathogen Detector

    SciTech Connect

    Visuri, S; McBride, M T; Matthews, D; Rao, R

    2002-07-15

    Tumor marker concentrations in serum provide useful information regarding clinical stage and prognosis of cancer and can thus be used for presymptomatic diagnostic purposes. Currently, detection and identification of soluble analytes in biological fluids is conducted by methods including bioassays, ELISA, PCR, DNA chip or strip tests. While these technologies are generally sensitive and specific, they are time consuming, labor intensive and cannot be multiplexed. Our goal is to develop a simple, point-of-care, portable, liquid array-based immunoassay device capable of simultaneous detection of a variety of cancer markers. Here we describe the development of assays for the detection of Serum Prostate Specific Antigen, and Ovalbumin from a single sample. The multiplexed immunoassays utilize polystyrene microbeads. The beads are imbedded with precise ratios of red and orange fluorescent dyes yielding an array of 100 beads, each with a unique spectral address (Figure 1). Each bead can be coated with capture antibodies specific for a given antigen. After antigen capture, secondary antibodies sandwich the bound antigen and are indirectly labeled by the fluorescent reporter phycoerythrin (PE). Each optically encoded and fluorescently-labeled microbead is then individually interrogated. A red laser excites the dye molecules imbedded inside the bead and classifies the bead to its unique bead set, and a green laser quantifies the assay at the bead surface. This technology has been proven to be comparable to the ELISA in terms of sensitivity and specificity. We also describe the laser-based instrumentation used to acquire fluorescent bead images Following the assay, droplets of bead suspension containing a mixture of bead classes were deposited onto filters held in place by a disposable plexiglass device and the resultant arrays viewed under the fluorescent imaging setup. Using the appropriate filter sets to extract the necessary red, orange and green fluorescence from the

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

    PubMed

    Murk, William; DeWan, Andrew T

    2016-01-01

    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. PMID:27185397

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

    PubMed Central

    Murk, William; DeWan, Andrew T.

    2016-01-01

    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. PMID:27185397

  4. Multiplexer and time duration measuring circuit

    SciTech Connect

    Gray, Jr., James

    1980-01-01

    A multiplexer device is provided for multiplexing data in the form of randomly developed, variable width pulses from a plurality of pulse sources to a master storage. The device includes a first multiplexer unit which includes a plurality of input circuits each coupled to one of the pulse sources, with all input circuits being disabled when one input circuit receives an input pulse so that only one input pulse is multiplexed by the multiplexer unit at any one time.

  5. A 128 Multiplexing Factor Time-Domain SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Prêle, D.; Voisin, F.; Piat, M.; Decourcelle, T.; Perbost, C.; Chapron, C.; Rambaud, D.; Maestre, S.; Marty, W.; Montier, L.

    2016-01-01

    A cryogenic 128:1 Time-Domain Multiplexer (TDM) has been developed for the readout of kilo-pixel Transition Edge Sensor (TES) arrays dedicated to the Q&U Bolometric Interferometer for Cosmology (QUBIC) instrument which aims to measure the B-mode polarization of the Cosmic Microwave Background. Superconducting QUantum Interference Devices (SQUIDs) are usually used to read out TESs. Moreover, SQUIDs are used to build TDM by biasing sequentially the SQUIDs connected together—one for each TES. In addition to this common technique which allows a typical 32 multiplexing factor, a cryogenic integrated circuit provides a 4:1 second multiplexing stage. This cryogenic integrated circuit is one of the original part of our TDM achieving an unprecedented 128 multiplexing factor. We present these two dimension TDM stages: topology of the SQUID multiplexer, operation of the cryogenic integrated circuit, and integration of the full system to read out a TES array dedicated to the QUBIC instrument. Flux-locked loop operation in multiplexed mode is also discussed.

  6. A 128 Multiplexing Factor Time-Domain SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Prêle, D.; Voisin, F.; Piat, M.; Decourcelle, T.; Perbost, C.; Chapron, C.; Rambaud, D.; Maestre, S.; Marty, W.; Montier, L.

    2016-07-01

    A cryogenic 128:1 Time-Domain Multiplexer (TDM) has been developed for the readout of kilo-pixel Transition Edge Sensor (TES) arrays dedicated to the Q&U Bolometric Interferometer for Cosmology (QUBIC) instrument which aims to measure the B-mode polarization of the Cosmic Microwave Background. Superconducting QUantum Interference Devices (SQUIDs) are usually used to read out TESs. Moreover, SQUIDs are used to build TDM by biasing sequentially the SQUIDs connected together—one for each TES. In addition to this common technique which allows a typical 32 multiplexing factor, a cryogenic integrated circuit provides a 4:1 second multiplexing stage. This cryogenic integrated circuit is one of the original part of our TDM achieving an unprecedented 128 multiplexing factor. We present these two dimension TDM stages: topology of the SQUID multiplexer, operation of the cryogenic integrated circuit, and integration of the full system to read out a TES array dedicated to the QUBIC instrument. Flux-locked loop operation in multiplexed mode is also discussed.

  7. METU-SNP: an integrated software system for SNP-complex disease association analysis.

    PubMed

    Ustünkar, Gürkan; Aydın Son, Yeşim

    2011-01-01

    Recently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual’s genetic variability in greatest detail. Genome-wide association studies (GWAS) of SNPs, high-dimensional case-control studies, are among the most promising approaches for identifying disease causing variants. METU-SNP software is a Java based integrated desktop application specifically designed for the prioritization of SNP biomarkers and the discovery of genes and pathways related to diseases via analysis of the GWAS case-control data. Outputs of METU-SNP can easily be utilized for the downstream biomarkers research to allow the prediction and the diagnosis of diseases and other personalized medical approaches. Here, we introduce and describe the system functionality and architecture of the METU-SNP. We believe that the METU-SNP will help researchers with the reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting the development of personalized medicine approaches and targeted drug discoveries. PMID:22156365

  8. Principals Make Assignments Matter

    ERIC Educational Resources Information Center

    Dougherty, Eleanor

    2013-01-01

    The inner-city high school in Washington, DC, that Guillaume Gendre joined as an assistant principal had a modest reputation for achievement but was nevertheless challenged to raise expectations for student work. In other schools, Gendre had used assignments--a specific kind of instructional task in which students are charged to think about an…

  9. Making Effective Assignments.

    ERIC Educational Resources Information Center

    McLeod, Alan M., Ed.

    1982-01-01

    Although the focus of this issue of the "Virginia English Bulletin" is on making effective assignments, most of the articles also emphasize the importance and power of writing. Articles deal with the following topics: (1) the use of I-search (as explained by Kenneth Macrorie in "Searching Writing") as a form of research paper that narrates the…

  10. My Favorite Assignment.

    ERIC Educational Resources Information Center

    Hebert, Margaret; And Others

    1991-01-01

    Contains seven brief articles which offer assignments designed to help students perform job searches, write job application letters, answer difficult questions, write letters of resignation, alleviate fears of public speaking, use the interview effectively in the business communication, and develop listening skills. (PRA)

  11. SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs.

    PubMed

    Do, D N; Janss, L L G; Jensen, J; Kadarmideen, H N

    2015-05-01

    The study investigated genetic architecture and predictive ability using genomic annotation of residual feed intake (RFI) and its component traits (daily feed intake [DFI], ADG, and back fat [BF]). A total of 1,272 Duroc pigs had both genotypic and phenotypic records, and the records were split into a training (968 pigs) and a validation dataset (304 pigs) by assigning records as before and after January 1, 2012, respectively. SNP were annotated by 14 different classes using Ensembl variant effect prediction. Predictive accuracy and prediction bias were calculated using Bayesian Power LASSO, Bayesian A, B, and Cπ, and genomic BLUP (GBLUP) methods. Predictive accuracy ranged from 0.508 to 0.531, 0.506 to 0.532, 0.276 to 0.357, and 0.308 to 0.362 for DFI, RFI, ADG, and BF, respectively. BayesCπ100.1 increased accuracy slightly compared to the GBLUP model and other methods. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP groups. Genomic prediction has accuracy comparable to observed phenotype, and use of genomic prediction can be cost effective by replacing feed intake measurement. Genomic annotation had less impact on predictive accuracy traits considered here but may be different for other traits. It is the first study to provide useful insights into biological classes of SNP driving the whole genomic prediction for complex traits in pigs. PMID:26020301

  12. eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform

    PubMed Central

    Li, Jin; Wang, Limei; Jiang, Tao; Wang, Jizhe; Li, Xue; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Lv, Hongchao; Guo, Maozu

    2016-01-01

    Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs. PMID:27470167

  13. eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.

    PubMed

    Li, Jin; Wang, Limei; Jiang, Tao; Wang, Jizhe; Li, Xue; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Lv, Hongchao; Guo, Maozu

    2016-01-01

    Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs. PMID:27470167

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

    PubMed

    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. PMID:21623652

  15. Gain weighted eigenspace assignment

    NASA Technical Reports Server (NTRS)

    Davidson, John B.; Andrisani, Dominick, II

    1994-01-01

    This report presents the development of the gain weighted eigenspace assignment methodology. This provides a designer with a systematic methodology for trading off eigenvector placement versus gain magnitudes, while still maintaining desired closed-loop eigenvalue locations. This is accomplished by forming a cost function composed of a scalar measure of error between desired and achievable eigenvectors and a scalar measure of gain magnitude, determining analytical expressions for the gradients, and solving for the optimal solution by numerical iteration. For this development the scalar measure of gain magnitude is chosen to be a weighted sum of the squares of all the individual elements of the feedback gain matrix. An example is presented to demonstrate the method. In this example, solutions yielding achievable eigenvectors close to the desired eigenvectors are obtained with significant reductions in gain magnitude compared to a solution obtained using a previously developed eigenspace (eigenstructure) assignment method.

  16. Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay.

    PubMed

    Rotherham, D; Harbison, S A

    2011-04-15

    Cannabis sativa is both an illegal drug and a legitimate crop. The differentiation of illegal drug Cannabis from non-drug forms of Cannabis is relevant in the context of the growth of fibre and seed oil varieties of Cannabis for commercial purposes. This differentiation is currently determined based on the levels of tetrahydrocannabinol (THC) in adult plants. DNA based methods have the potential to assay Cannabis material unsuitable for analysis using conventional means including seeds, pollen and severely degraded material. The purpose of this research was to develop a single nucleotide polymorphism (SNP) assay for the differentiation of "drug" and "non-drug"Cannabis plants. An assay was developed based on four polymorphisms within a 399 bp fragment of the tetrahydrocannabinolic acid (THCA) synthase gene, utilising the snapshot multiplex kit. This SNP assay was tested on 94 Cannabis plants, which included 10 blind samples, and was able to differentiate between "drug" and "non-drug"Cannabis in all cases, while also differentiating between Cannabis and other species. Non-drug plants were found to be homozygous at the four sites assayed while drug Cannabis plants were either homozygous or heterozygous. PMID:21036496

  17. Use of Sequenom Sample ID Plus® SNP Genotyping in Identification of FFPE Tumor Samples

    PubMed Central

    Miller, Jessica K.; Buchner, Nicholas; Timms, Lee; Tam, Shirley; Luo, Xuemei; Brown, Andrew M. K.; Pasternack, Danielle; Bristow, Robert G.; Fraser, Michael; Boutros, Paul C.; McPherson, John D.

    2014-01-01

    Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76–139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework. PMID:24551080

  18. Efficient exploration of multiplex networks

    NASA Astrophysics Data System (ADS)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2016-04-01

    Efficient techniques to navigate networks with local information are fundamental to sample large-scale online social systems and to retrieve resources in peer-to-peer systems. Biased random walks, i.e. walks whose motion is biased on properties of neighbouring nodes, have been largely exploited to design smart local strategies to explore a network, for instance by constructing maximally mixing trajectories or by allowing an almost uniform sampling of the nodes. Here we introduce and study biased random walks on multiplex networks, graphs where the nodes are related through different types of links organised in distinct and interacting layers, and we provide analytical solutions for their long-time properties, including the stationary occupation probability distribution and the entropy rate. We focus on degree-biased random walks and distinguish between two classes of walks, namely those whose transition probability depends on a number of parameters which is extensive in the number of layers, and those whose motion depends on intrinsically multiplex properties of the neighbouring nodes. We analyse the effect of the structure of the multiplex network on the steady-state behaviour of the walkers, and we find that heterogeneous degree distributions as well as the presence of inter-layer degree correlations and edge overlap determine the extent to which a multiplex can be efficiently explored by a biased walk. Finally we show that, in real-world multiplex transportation networks, the trade-off between efficient navigation and resilience to link failure has resulted into systems whose diffusion properties are qualitatively different from those of appropriately randomised multiplex graphs. This fact suggests that multiplexity is an important ingredient to include in the modelling of real-world systems.

  19. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

    PubMed

    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

    2016-03-01

    Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. PMID:26358548

  20. Multiplexed polymer surface plasmon sensor with integrated optical coupler

    NASA Astrophysics Data System (ADS)

    Pyo, Hyeon-Bong; Park, Se Ho; Chung, Kwang Hyo; Choi, Chang Auck

    2005-11-01

    In this paper, we describe a novel multiplexed surface plasmon resonance (SPR) sensor which is made of cyclic olefin copolymers (COCs, TOPAS TM). This material has excellent chemical resistance, low water uptake (< 0.01%), and high refractive index (n He- Ne=1.53) suitable to use as an optical coupler (prism) as well as a sensor substrate. We fabricated a standard slide glass sized, prism integrated, and injection molded COC-SPR sensor which are being applied toward the multiplexed detection of DNA single nucleotide polymorphism (SNP). To evaluate the sensitivity of COC-SPR sensor, we first patterned MgF II on gold-coated COC-SPR sensor and observed the shift of minimum reflectivity (SPR dip) in pixel address. As incident light source we used an expanded, collimated, rectangular shaped He-Ne laser, with a diffuser for beam homogenization. With expanded laser beam we varied incident angle so that the angular shift is expressed as the darkest pixel shift on CCD. For optimized SPR characteristics and sensor configuration, analytical calculations (Fresnel equation) were performed, and the best SPR conditions were found to be d Au~48 nm at wavelength λ=633 nm with respected resonance angle at θ SPR =44.2° for COC-SPR sensor.

  1. Smarter clustering methods for SNP genotype calling

    PubMed Central

    Lin, Yan; Tseng, George C.; Cheong, Soo Yeon; Bean, Lora J. H.; Sherman, Stephanie L.; Feingold, Eleanor

    2008-01-01

    Motivation: Most genotyping technologies for single nucleotide polymorphism (SNP) markers use standard clustering methods to ‘call’ the SNP genotypes. These methods are not always optimal in distinguishing the genotype clusters of a SNP because they do not take advantage of specific features of the genotype calling problem. In particular, when family data are available, pedigree information is ignored. Furthermore, prior information about the distribution of the measurements for each cluster can be used to choose an appropriate model-based clustering method and can significantly improve the genotype calls. One special genotyping problem that has never been discussed in the literature is that of genotyping of trisomic individuals, such as individuals with Down syndrome. Calling trisomic genotypes is a more complicated problem, and the addition of external information becomes very important. Results: In this article, we discuss the impact of incorporating external information into clustering algorithms to call the genotypes for both disomic and trisomic data. We also propose two new methods to call genotypes using family data. One is a modification of the K-means method and uses the pedigree information by updating all members of a family together. The other is a likelihood-based method that combines the Gaussian or beta-mixture model with pedigree information. We compare the performance of these two methods and some other existing methods using simulation studies. We also compare the performance of these methods on a real dataset generated by the Illumina platform (www.illumina.com). Availability: The R code for the family-based genotype calling methods (SNPCaller) is available to be downloaded from the following website: http://watson.hgen.pitt.edu/register. Contact: liny@upmc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18826959

  2. Thermally multiplexed polymerase chain reaction

    PubMed Central

    Phaneuf, Christopher R.; Pak, Nikita; Saunders, D. Curtis; Holst, Gregory L.; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L.; Jerris, Robert; Forest, Craig R.

    2015-01-01

    Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously—each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel. PMID:26339317

  3. Structural measures for multiplex networks

    NASA Astrophysics Data System (ADS)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships.

  4. Structural measures for multiplex networks.

    PubMed

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships. PMID:24730896

  5. Bond Percolation on Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Hackett, A.; Cellai, D.; Gómez, S.; Arenas, A.; Gleeson, J. P.

    2016-04-01

    We present an analytical approach for bond percolation on multiplex networks and use it to determine the expected size of the giant connected component and the value of the critical bond occupation probability in these networks. We advocate the relevance of these tools to the modeling of multilayer robustness and contribute to the debate on whether any benefit is to be yielded from studying a full multiplex structure as opposed to its monoplex projection, especially in the seemingly irrelevant case of a bond occupation probability that does not depend on the layer. Although we find that in many cases the predictions of our theory for multiplex networks coincide with previously derived results for monoplex networks, we also uncover the remarkable result that for a certain class of multiplex networks, well described by our theory, new critical phenomena occur as multiple percolation phase transitions are present. We provide an instance of this phenomenon in a multiplex network constructed from London rail and European air transportation data sets.

  6. pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses.

    PubMed

    Wang, Jingbo; Ronaghi, Mostafa; Chong, Samuel S; Lee, Caroline G L

    2011-01-01

    Currently, >14,000,000 single nucleotide polymorphisms (SNPs) are reported. Identifying phenotype-affecting SNPs among these many SNPs pose significant challenges. Although several Web resources are available that can inform about the functionality of SNPs, these resources are mainly annotation databases and are not very comprehensive. In this article, we present a comprehensive, well-annotated, integrated pfSNP (potentially functional SNPs) Web resource (http://pfs.nus.edu.sg/), which is aimed to facilitate better hypothesis generation through knowledge syntheses mediated by better data integration and a user-friendly Web interface. pfSNP integrates >40 different algorithms/resources to interrogate >14,000,000 SNPs from the dbSNP database for SNPs of potential functional significance based on previous published reports, inferred potential functionality from genetic approaches as well as predicted potential functionality from sequence motifs. Its query interface has the user-friendly "auto-complete, prompt-as-you-type" feature and is highly customizable, facilitating different combination of queries using Boolean-logic. Additionally, to facilitate better understanding of the results and aid in hypotheses generation, gene/pathway-level information with text clouds highlighting enriched tissues/pathways as well as detailed-related information are also provided on the results page. Hence, the pfSNP resource will be of great interest to scientists focusing on association studies as well as those interested to experimentally address the functionality of SNPs. PMID:20672376

  7. KinSNP software for homozygosity mapping of disease genes using SNP microarrays.

    PubMed

    Amir, El-Ad David; Bartal, Ofer; Morad, Efrat; Nagar, Tal; Sheynin, Jony; Parvari, Ruti; Chalifa-Caspi, Vered

    2010-08-01

    Consanguineous families affected with a recessive genetic disease caused by homozygotisation of a mutation offer a unique advantage for positional cloning of rare diseases. Homozygosity mapping of patient genotypes is a powerful technique for the identification of the genomic locus harbouring the causing mutation. This strategy relies on the observation that in these patients a large region spanning the disease locus is also homozygous with high probability. The high marker density in single nucleotide polymorphism (SNP) arrays is extremely advantageous for homozygosity mapping. We present KinSNP, a user-friendly software tool for homozygosity mapping using SNP arrays. The software searches for stretches of SNPs which are homozygous to the same allele in all ascertained sick individuals. User-specified parameters control the number of allowed genotyping 'errors' within homozygous blocks. Candidate disease regions are then reported in a detailed, coloured Excel file, along with genotypes of family members and healthy controls. An interactive genome browser has been included which shows homozygous blocks, individual genotypes, genes and further annotations along the chromosomes, with zooming and scrolling capabilities. The software has been used to identify the location of a mutated gene causing insensitivity to pain in a large Bedouin family. KinSNP is freely available from. PMID:20846928

  8. Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

    PubMed

    Santos, Carla; Phillips, Christopher; Fondevila, Manuel; Daniel, Runa; van Oorschot, Roland A H; Burchard, Esteban G; Schanfield, Moses S; Souto, Luis; Uacyisrael, Jolame; Via, Marc; Carracedo, Ángel; Lareu, Maria V

    2016-01-01

    The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry

  9. Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays.

    PubMed

    Liu, Weiqiang; Zhang, Rui; Wei, Jun; Zhang, Huimin; Yu, Guojiu; Li, Zhihua; Chen, Min; Sun, Xiaofang

    2015-01-01

    Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD. PMID:26184742

  10. SNP marker detection and genotyping in tilapia.

    PubMed

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

    2012-09-01

    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 SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization. PMID:22524158

  11. Helicity multiplexed broadband metasurface holograms

    PubMed Central

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

    2015-01-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

  12. Helicity multiplexed broadband metasurface holograms.

    PubMed

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

    2015-01-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

  13. Pathways to Assignment of Payees

    PubMed Central

    Rosen, Marc I.; Ablondi, Karen; Black, Anne C.; Serowik, Kristin L.; Rowe, Michael

    2013-01-01

    How clients come to be assigned representative payees and/or conservators to manage their funds is not well understood. We compared clients assigned a payee during a clinical trial of a money management-based intervention to those not assigned payees and examined antecedents to payee assignment. One year after randomization, significantly more clients assigned to the ATM money management intervention were assigned payees than participants in the control condition (10 of 47 vs. 2 of 43; p=.02); those assigned payees had lower baseline GAF scores and participated more in study therapies. Several ATM clients were assigned payees after third parties paid more attention to clients’ finances, and others after having negotiated storage of their funds with the ATM money manager during the study. Assignment of payees appears to be influenced by whether third parties critically attend to how clients’ manage funds and by clients’ receptiveness to having a payee. PMID:23765182

  14. Integrated multiplexed capillary electrophoresis system

    SciTech Connect

    Yeung, Edward S.; Tan, Hongdong

    2002-05-14

    The present invention provides an integrated multiplexed capillary electrophoresis system for the analysis of sample analytes. The system integrates and automates multiple components, such as chromatographic columns and separation capillaries, and further provides a detector for the detection of analytes eluting from the separation capillaries. The system employs multiplexed freeze/thaw valves to manage fluid flow and sample movement. The system is computer controlled and is capable of processing samples through reaction, purification, denaturation, pre-concentration, injection, separation and detection in parallel fashion. Methods employing the system of the invention are also provided.

  15. Turing patterns in multiplex networks

    NASA Astrophysics Data System (ADS)

    Asllani, Malbor; Busiello, Daniel M.; Carletti, Timoteo; Fanelli, Duccio; Planchon, Gwendoline

    2014-10-01

    The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The interlayer diffusion constants act as a small parameter in the expansion and the unperturbed state coincides with the limiting setting where the multiplex layers are decoupled. The interaction between adjacent layers can seed the instability of a homogeneous fixed point, yielding self-organized patterns which are instead impeded in the limit of decoupled layers. Patterns on individual layers can also fade away due to cross-talking between layers. Analytical results are compared to direct simulations.

  16. On-chip multiplexing conversion between wavelength division multiplexing-polarization division multiplexing and wavelength division multiplexing-mode division multiplexing.

    PubMed

    Ye, Mengyuan; Yu, Yu; Zou, Jinghui; Yang, Weili; Zhang, Xinliang

    2014-02-15

    A compact silicon-on-insulator device used for conversions between polarization division multiplexing (PDM) and mode division multiplexing (MDM) signals is proposed and experimentally demonstrated by utilizing a structure combining the improved two-dimensional grating coupler and two-mode multiplexer. The detailed design of the proposed device is presented and the results show the extinction ratio of 16 and 20 dB for X- and Y-pol input, respectively. The processing of 40  Gb/s signal is achieved within the C-band with good performance. The proposed converter is capable of handling multiple wavelengths in wavelength division multiplexing (WDM) networks, enabling the conversions between WDM-PDM and WDM-MDM, which is promising to further increase the throughput at the network interface. PMID:24562199

  17. Holographic data storage system combining shift-multiplexing with peristrophic-multiplexing

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Kengo; Tsukamoto, Yu; Okubo, Kaito; Yamamoto, Manabu

    2014-02-01

    Holographic data storage (HDS) is a next-generation optical storage that uses the principles of holography. The multiplex holographic recording method is an important factor that affects the recording capacity of this storage. Various multiplex recording methods have been proposed so far. In this study, we focus on shift multiplexing with spherical waves and propose a method of shift multiplex recording that combines the peristrophic multiplexed recording. Simulation and experimental verification shows that the proposed method is effective in principle.

  18. Large-Scale SNP Marker Development and Genotyping in Oat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, our goals are to develop genome-wide SNP markers using next generation sequencing technologies and to apply a highly parallel SNP genotyping system developed by Illumina for genetics and breeding applications in oat. The large amount of DNA sequence sources generated from cDNAs and Di...

  19. SNPConvert: SNP Array Standardization and Integration in Livestock Species

    PubMed Central

    Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

    2016-01-01

    One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git. PMID:27600083

  20. SNPConvert: SNP Array Standardization and Integration in Livestock Species.

    PubMed

    Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

    2016-01-01

    One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git. PMID:27600083

  1. Accelerating genetic improvement with SNP chips and DNA sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of high-density single nucleotide polymorphism (SNP) assays is expected to have a profound impact on genetic progress in the U.S. dairy industry. In the 16 months since its initial availability, the Illumina BovineSNP50 BeadChip has been used to genotype nearly 20,000 Holsteins. Thes...

  2. Weak percolation on multiplex networks.

    PubMed

    Baxter, Gareth J; Dorogovtsev, Sergey N; Mendes, José F F; Cellai, Davide

    2014-04-01

    Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters. PMID:24827287

  3. Code retrieval via undercover multiplexing

    NASA Astrophysics Data System (ADS)

    Barrera, John Fredy; Henao, Rodrigo; Tebaldi, Myrian; Torroba, Roberto; Bolognini, Nestor

    2008-02-01

    The purpose of this research is to develop an undercover multiplexing technique to give additional protection for optical information encryption. We employ the double random phase mask as our basic optical encryption system. The holographic storage medium of choice is a photorefractive crystal. To achieve the multiplexing we use the aperture size of the pupil in the optical system, as it governs the speckle size. We introduce such variation in order to produce a decorrelation between two consecutively stored speckle patterns. Each stored speckle pattern is associated to an input encrypted image, thus producing a multiplexing of the encrypted information. We implement this operation without altering the setup architecture and the random phase masks. This multiplexing is our undercover operation to encipher a true code behind a fake code. Under this approach, the user can only recover the bulk information stored in the volume hologram. However, he cannot recover the true code without the additional information on the pupil size key, even if accessed in position of the original decoding mask.

  4. Weak percolation on multiplex networks

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Dorogovtsev, Sergey N.; Mendes, José F. F.; Cellai, Davide

    2014-04-01

    Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters.

  5. Atomic Force Microscopy for DNA SNP Identification

    NASA Astrophysics Data System (ADS)

    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.

  6. Structural Case Assignment in Korean

    ERIC Educational Resources Information Center

    Koak, Heeshin

    2012-01-01

    In this dissertation, I aim to provide a theory on the distribution of structural Case in Korean. I propose the following Structural Case Assignment Hypothesis (SCAH) regarding the assignment of structural Case: "Structural Case is assigned by phase heads (C: nominative; v: accusative) to every argument in the c-command domain of the phase…

  7. Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory

    PubMed Central

    Børsting, Claus; Mikkelsen, Martin; Morling, Niels

    2012-01-01

    Background The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. Methods A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. Results It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. Conclusion Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing. PMID:22851935

  8. (Multiplex mapping of human cDNAs)

    SciTech Connect

    Nierman, W.C.

    1991-01-01

    J. Craig Venter, National Institute of Neurological Disorders and Stroke, has begun to identify genes expressed in the human brain by partially sequences cDNA clones. We are collaborating with the Venter group and using their sequence data to develop methods for rapid localization of newly identified cDNAs to human chromosomes. We are applying the ABI automated DNA sequencer to the analysis of fluorescently-tagged PCR products for assigning sequences to individual human chromosomes. The steps in our mapping protocol are (1) to design PCR primers from the Venter laboratory-generated sequence data, (2) to test the primers for specific amplification from human genomic DNA, (3) to use the primers for PCR amplification from a somatic cell hybrid cell mapping panel, (4) to determine the presence or absence of the specific amplification products from each cell line DNA by electrophoretic analysis using the ABI sequencer, and (5) to analyze the pattern of amplification results from the hybrid panel to identify the chromosomal origin of the cDNA sequence. We have demonstrated the principle by mapping 12 sequences or Expressed Sequence Tags'' (ESTs), providing primer sequence data for subsequent subchromosomal localizations. We will now concentrate on developing methodology to allow multiplexing the amplification reactions and analysis of the reaction products, to achieve a high throughput with a minimum allocation of resources. This project will generate a data set from which to evaluate strategies to identify functional primer sequences from cDNA sequence data.

  9. Parallel multiplex laser feedback interferometry

    SciTech Connect

    Zhang, Song; Tan, Yidong; Zhang, Shulian

    2013-12-15

    We present a parallel multiplex laser feedback interferometer based on spatial multiplexing which avoids the signal crosstalk in the former feedback interferometer. The interferometer outputs two close parallel laser beams, whose frequencies are shifted by two acousto-optic modulators by 2Ω simultaneously. A static reference mirror is inserted into one of the optical paths as the reference optical path. The other beam impinges on the target as the measurement optical path. Phase variations of the two feedback laser beams are simultaneously measured through heterodyne demodulation with two different detectors. Their subtraction accurately reflects the target displacement. Under typical room conditions, experimental results show a resolution of 1.6 nm and accuracy of 7.8 nm within the range of 100 μm.

  10. Pattern formation in multiplex networks

    PubMed Central

    Kouvaris, Nikos E.; Hata, Shigefumi; Guilera, Albert Díaz-

    2015-01-01

    The advances in understanding complex networks have generated increasing interest in dynamical processes occurring on them. Pattern formation in activator-inhibitor systems has been studied in networks, revealing differences from the classical continuous media. Here we study pattern formation in a new framework, namely multiplex networks. These are systems where activator and inhibitor species occupy separate nodes in different layers. Species react across layers but diffuse only within their own layer of distinct network topology. This multiplicity generates heterogeneous patterns with significant differences from those observed in single-layer networks. Remarkably, diffusion-induced instability can occur even if the two species have the same mobility rates; condition which can never destabilize single-layer networks. The instability condition is revealed using perturbation theory and expressed by a combination of degrees in the different layers. Our theory demonstrates that the existence of such topology-driven instabilities is generic in multiplex networks, providing a new mechanism of pattern formation. PMID:26042606

  11. Multiplex detection of agricultural pathogens

    DOEpatents

    Siezak, Thomas R.; Gardner, Shea; Torres, Clinton; Vitalis, Elizabeth; Lenhoff, Raymond J.

    2013-01-15

    Described are kits and methods useful for detection of agricultural pathogens in a sample. Genomic sequence information from agricultural pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay and/or an array assay to successfully identify the presence or absence of pathogens in a sample.

  12. Multiplex detection of agricultural pathogens

    DOEpatents

    McBride, Mary Teresa; Slezak, Thomas Richard; Messenger, Sharon Lee

    2010-09-14

    Described are kits and methods useful for detection of seven agricultural pathogens (BPSV; BHV; BVD; FMDV; BTV; SVD; and VESV) in a sample. Genomic sequence information from 7 agricultural pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay to successfully identify the presence or absence of pathogens in a sample.

  13. Lifetime-based tomographic multiplexing

    NASA Astrophysics Data System (ADS)

    Raymond, Scott B.; Boas, David A.; Bacskai, Brian J.; Kumar, Anand T. N.

    2010-07-01

    Near-infrared (NIR) fluorescence tomography of multiple fluorophores has previously been limited by the bandwidth of the NIR spectral regime and the broad emission spectra of most NIR fluorophores. We describe in vivo tomography of three spectrally overlapping fluorophores using fluorescence lifetime-based separation. Time-domain images are acquired using a voltage-gated, intensified charge-coupled device (CCD) in free-space transmission geometry with 750 nm Ti:sapphire laser excitation. Lifetime components are fit from the asymptotic portion of fluorescence decay curve and reconstructed separately with a lifetime-adjusted forward model. We use this system to test the in vivo lifetime multiplexing suitability of commercially available fluorophores, and demonstrate lifetime multiplexing in solution mixtures and in nude mice. All of the fluorophores tested exhibit nearly monoexponential decays, with narrow in vivo lifetime distributions suitable for lifetime multiplexing. Quantitative separation of two fluorophores with lifetimes of 1.1 and 1.37 ns is demonstrated for relative concentrations of 1:5. Finally, we demonstrate tomographic imaging of two and three fluorophores in nude mice with fluorophores that localize to distinct organ systems. This technique should be widely applicable to imaging multiple NIR fluorophores in 3-D.

  14. Balanced input-output assignment

    NASA Technical Reports Server (NTRS)

    Gawronski, W.; Hadaegh, F. Y.

    1989-01-01

    Actuator/sensor locations and balanced representations of linear systems are considered for a given set of controllability and observability grammians. The case of equally controlled and observed states is given special attention. The assignability of grammians is examined, and the conditions for their existence are presented, along with several algorithms for their determination. Although an arbitrary positive semidefinite matrix is not always assignable, the identity grammian is shown to be always assignable. The results are extended to the case of flexible structures.

  15. Automated protein NMR resonance assignments.

    PubMed

    Wan, Xiang; Xu, Dong; Slupsky, Carolyn M; Lin, Guohui

    2003-01-01

    NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use. PMID:16452794

  16. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    PubMed

    Oliver, Rebekah E; Tinker, Nicholas A; Lazo, Gerard R; Chao, Shiaoman; Jellen, Eric N; Carson, Martin L; Rines, Howard W; Obert, Donald E; Lutz, Joseph D; Shackelford, Irene; Korol, Abraham B; Wight, Charlene P; Gardner, Kyle M; Hattori, Jiro; Beattie, Aaron D; Bjørnstad, Åsmund; Bonman, J Michael; Jannink, Jean-Luc; Sorrells, Mark E; Brown-Guedira, Gina L; Mitchell Fetch, Jennifer W; Harrison, Stephen A; Howarth, Catherine J; Ibrahim, Amir; Kolb, Frederic L; McMullen, Michael S; Murphy, J Paul; Ohm, Herbert W; Rossnagel, Brian G; Yan, Weikai; Miclaus, Kelci J; Hiller, Jordan; Maughan, Peter J; Redman Hulse, Rachel R; Anderson, Joseph M; Islamovic, Emir; Jackson, Eric W

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. PMID:23533580

  17. 42 CFR 433.146 - Rights assigned; assignment method.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party...

  18. 42 CFR 433.146 - Rights assigned; assignment method.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party...

  19. 42 CFR 433.146 - Rights assigned; assignment method.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 4 2014-10-01 2014-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party...

  20. 42 CFR 433.146 - Rights assigned; assignment method.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party...

  1. Further development of multiplex single nucleotide polymorphism typing method, the DigiTag2 assay.

    PubMed

    Nishida, Nao; Tanabe, Tetsuya; Takasu, Miwa; Suyama, Akira; Tokunaga, Katsushi

    2007-05-01

    A number of single nucleotide polymorphisms (SNPs) are considered to be candidate susceptibility or resistance genetic factors for multifactorial disease. Genome-wide searches for disease susceptibility regions followed by high-resolution mapping of primary genes require cost-effective and highly reliable technology. To accomplish successful and low-cost typing for candidate SNPs, new technologies must be developed. We previously reported a multiplex SNP typing method, designated the DigiTag assay, that has the potential to analyze nearly any SNP with high accuracy and reproducibility. However, the DigiTag assay requires multiple washing steps in manipulation and uses genotyping probes modified with biotin for each target SNP. Here we describe the next version of the assay, DigiTag2, which works with simple protocols and uses unmodified genotyping probes. We investigated the feasibility of the DigiTag2 assay by genotyping 96 target SNPs spanning a 610-kb region of human chromosome 5. The DigiTag2 assay is suitable for genotyping an intermediate number of SNPs (tens to hundreds of sites) with a high conversion rate (>90%), high accuracy, and low cost. PMID:17359929

  2. Rotation spacing and multiplexing number in angle-peristrophic multiplexing holographic memory

    NASA Astrophysics Data System (ADS)

    Sawada, Masamitsu; Kinoshita, Nobuhiro; Muroi, Tetsuhiko; Motohashi, Mitsuya; Saito, Nobuo

    2015-09-01

    Holographic memory is expected to be the next-generation optical memory with several advantages including high data transfer rate and high recording density. Holographic memory enables the storage of holograms in the same location in a holographic medium typically using the angle multiplexing method. The multiplexing number is an important factor that determines the recording density when using this method. To increase the multiplexing number, it is known as an effective method to combine peristrophic (or rotation) multiplexing with angle multiplexing. We use the k-sphere to describe that the rotation spacing for peristrophic multiplexing depends on both the numerical aperture in the signal beam path and the angle between the reference and signal beams. We then formulate the rotation spacing and compare the results obtained using the theoretical formula with the measured results. Finally, we estimate the maximum multiplexing number for our experimental system using the angle-peristrophic multiplexing method on the basis of the measured results.

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

    PubMed

    Jamshidi, Maral; Fagerholm, Rainer; Khan, Sofia; Aittomäki, Kristiina; Czene, Kamila; Darabi, Hatef; Li, Jingmei; Andrulis, Irene L; Chang-Claude, Jenny; Devilee, Peter; Fasching, Peter A; Michailidou, Kyriaki; Bolla, Manjeet K; Dennis, Joe; Wang, Qin; Guo, Qi; Rhenius, Valerie; Cornelissen, Sten; Rudolph, Anja; Knight, Julia A; Loehberg, Christian R; Burwinkel, Barbara; Marme, Frederik; Hopper, John L; Southey, Melissa C; Bojesen, Stig E; Flyger, Henrik; Brenner, Hermann; Holleczek, Bernd; Margolin, Sara; Mannermaa, Arto; Kosma, Veli-Matti; Van Dyck, Laurien; Nevelsteen, Ines; Couch, Fergus J; Olson, Janet E; Giles, Graham G; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Winqvist, Robert; Pylkäs, Katri; Tollenaar, Rob A E M; García-Closas, Montserrat; Figueroa, Jonine; Hooning, Maartje J; Martens, John W M; Cox, Angela; Cross, Simon S; Simard, Jacques; Dunning, Alison M; Easton, Douglas F; Pharoah, Paul D P; Hall, Per; Blomqvist, Carl; Schmidt, Marjanka K; Nevanlinna, Heli

    2015-11-10

    In breast cancer, constitutive activation of NF-κB has been reported, however, the impact of genetic variation of the pathway on patient prognosis has been little studied. Furthermore, a combination of genetic variants, rather than single polymorphisms, may affect disease prognosis. Here, 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 of SNP pairs without and with an interaction term. We found two interacting pairs associating with prognosis: patients simultaneously homozygous for the rare alleles of rs5996080 and rs7973914 had worse survival (HRinteraction 6.98, 95% CI=3.3-14.4, P=1.42E-07), and patients carrying at least one rare allele for rs17243893 and rs57890595 had better survival (HRinteraction 0.51, 95% CI=0.3-0.6, P = 2.19E-05). Based on in silico functional analyses and literature, we speculate that the rs5996080 and rs7973914 loci may affect the BAFFR and TNFR1/TNFR3 receptors and breast cancer survival, possibly by disturbing both the canonical and non-canonical NF-κB pathways or their dynamics, whereas, rs17243893-rs57890595 interaction on survival may be mediated through TRAF2-TRAIL-R4 interplay. These results warrant further validation and functional analyses. PMID:26317411

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

    PubMed Central

    Jamshidi, Maral; Fagerholm, Rainer; Khan, Sofia; Aittomäki, Kristiina; Czene, Kamila; Darabi, Hatef; Li, Jingmei; Andrulis, Irene L.; Chang-Claude, Jenny; Devilee, Peter; Fasching, Peter A.; Michailidou, Kyriaki; Bolla, Manjeet K.; Dennis, Joe; Wang, Qin; Guo, Qi; Rhenius, Valerie; Cornelissen, Sten; Rudolph, Anja; Knight, Julia A.; Loehberg, Christian R.; Burwinkel, Barbara; Marme, Frederik; Hopper, John L.; Southey, Melissa C.; Bojesen, Stig E.; Flyger, Henrik; Brenner, Hermann; Holleczek, Bernd; Margolin, Sara; Mannermaa, Arto; Kosma, Veli-Matti; Dyck, Laurien Van; Nevelsteen, Ines; Couch, Fergus J.; Olson, Janet E.; Giles, Graham G.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Winqvist, Robert; Pylkäs, Katri; Tollenaar, Rob A.E.M.; García-Closas, Montserrat; Figueroa, Jonine; Hooning, Maartje J.; Martens, John W.M.; Cox, Angela; Cross, Simon S.; Simard, Jacques; Dunning, Alison M.; Easton, Douglas F.; Pharoah, Paul D.P.; Hall, Per; Blomqvist, Carl; Schmidt, Marjanka K.; Nevanlinna, Heli

    2015-01-01

    In breast cancer, constitutive activation of NF-κB has been reported, however, the impact of genetic variation of the pathway on patient prognosis has been little studied. Furthermore, a combination of genetic variants, rather than single polymorphisms, may affect disease prognosis. Here, 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 of SNP pairs without and with an interaction term. We found two interacting pairs associating with prognosis: patients simultaneously homozygous for the rare alleles of rs5996080 and rs7973914 had worse survival (HRinteraction 6.98, 95% CI=3.3-14.4, P = 1.42E-07), and patients carrying at least one rare allele for rs17243893 and rs57890595 had better survival (HRinteraction 0.51, 95% CI=0.3-0.6, P = 2.19E-05). Based on in silico functional analyses and literature, we speculate that the rs5996080 and rs7973914 loci may affect the BAFFR and TNFR1/TNFR3 receptors and breast cancer survival, possibly by disturbing both the canonical and non-canonical NF-κB pathways or their dynamics, whereas, rs17243893-rs57890595 interaction on survival may be mediated through TRAF2-TRAIL-R4 interplay. These results warrant further validation and functional analyses. PMID:26317411

  5. Multiplexing of encrypted data using fractal masks.

    PubMed

    Barrera, John F; Tebaldi, Myrian; Amaya, Dafne; Furlan, Walter D; Monsoriu, Juan A; Bolognini, Néstor; Torroba, Roberto

    2012-07-15

    In this Letter, we present to the best of our knowledge a new all-optical technique for multiple-image encryption and multiplexing, based on fractal encrypting masks. The optical architecture is a joint transform correlator. The multiplexed encrypted data are stored in a photorefractive crystal. The fractal parameters of the key can be easily tuned to lead to a multiplexing operation without cross talk effects. Experimental results that support the potential of the method are presented. PMID:22825170

  6. Multiplex Holograms And Their Applications In Medicine

    NASA Astrophysics Data System (ADS)

    Tsujiuchi, Jumpei

    1988-01-01

    Fundamental properties of reconstructed images from a multiplex hologram are studied, and conditions for compensating distortions and for designing a reconstructing source are proposed. Applications of multiplex hologram to medical objects are reviewed, and a computer-aided hologram synthesizing system is proposed for obtaining better images and wider applications. An example of multiplex holograms synthesized from a series of CT images is also presented.

  7. Measuring and modeling correlations in multiplex networks.

    PubMed

    Nicosia, Vincenzo; Latora, Vito

    2015-09-01

    The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance. PMID:26465526

  8. Measuring and modeling correlations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Latora, Vito

    2015-09-01

    The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance.

  9. 76 FR 55880 - Recording Assignments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-09

    ..., depending on the date they were recorded. The public may also search patent and trademark assignment... United States Patent and Trademark Office Recording Assignments ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its continuing...

  10. The Perils of SNP Microarray Testing: Uncovering Unexpected Consanguinity

    PubMed Central

    Tarini, Beth A.; Konczal, Laura; Goldenberg, Aaron J.; Goldman, Edward B.; McCandless, Shawn E.

    2013-01-01

    Background While single nucleotide polymorphism (SNP) chromosomal microarrays identify areas of small genetic deletions/duplications, they can also reveal regions of homozygosity indicative of consanguinity. As more non-geneticists order SNP microarrays, they must prepare for the potential ethical, legal and social issues that result from revelation of unanticipated consanguinity. Patient An infant with multiple congenital anomalies underwent SNP microarray testing. Results The results of the SNP microarray revealed several large regions of homozygosity that indicated identity by descent most consistent with a second or third degree relative mating (e.g., uncle/ niece, half brother/sister, first cousins). Mother was not aware of the test's potential to reveal consanguinity. When informed of the test results, she reluctantly admitted to being raped by her half-brother around the time of conception. Conclusions During the pre-testing consent process, providers should inform parents that SNP microarray testing could reveal consanguinity. Providers must also understand the psychological implications, as well as the legal and moral obligations, that accompany SNP microarray results that indicate consanguinity. PMID:23827427

  11. Interactive software for spectral assignment

    NASA Technical Reports Server (NTRS)

    Mielke, R. R.; Carraway, P. I.; Marefat, M.

    1985-01-01

    A new interactive computer software package for eigenvalue/eigenvector assignment using constant state feedback is described. The package consists of ten subprograms, each associated with a specific design objective, accessible from a main control program. Using this package, primary design objectives of assigning eigenvalues and approximating eigenvectors are first achieved. Then secondary design objectives, including modification of specific eigenvector components, reduction in specified elements of the feedback gain matrix, and reduction in eigensystem sensitivity to changes in plant parameters, are addressed. These secondary objectives are achieved by a systematic modification of the assigned eigenvectors in a small region about the initial assignment. In addition, the program implements the use of spectral assignment procedures with reduced-order system models. Program modes are described and illustrated by numerical examples.

  12. An Assignment Sequence for Underprepared Writers.

    ERIC Educational Resources Information Center

    Nimmo, Kristi

    2000-01-01

    Presents a sequenced writing assignment on shopping to aid basic writers. Describes a writing assignment focused around online and mail-order shopping. Notes steps in preparing for the assignment, the sequence, and discusses responses to the assignments. (SC)

  13. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes

    PubMed Central

    Krueger, Felix; Andrews, Simon R.

    2016-01-01

    Sequencing reads overlapping polymorphic sites in diploid mammalian genomes may be assigned to one allele or the other. This holds the potential to detect gene expression, chromatin modifications, DNA methylation or nuclear interactions in an allele-specific fashion. SNPsplit is an allele-specific alignment sorter designed to read files in SAM/BAM format and determine the allelic origin of reads or read-pairs that cover known single nucleotide polymorphic (SNP) positions. For this to work libraries must have been aligned to a genome in which all known SNP positions were masked with the ambiguity base 'N' and aligned using a suitable mapping program such as Bowtie2, TopHat, STAR, HISAT2, HiCUP or Bismark. SNPsplit also provides an automated solution to generate N-masked reference genomes for hybrid mouse strains based on the variant call information provided by the Mouse Genomes Project. The unique ability of SNPsplit to work with various different kinds of sequencing data including RNA-Seq, ChIP-Seq, Bisulfite-Seq or Hi-C opens new avenues for the integrative exploration of allele-specific data. PMID:27429743

  14. A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

    PubMed Central

    Kijas, James W.; Townley, David; Dalrymple, Brian P.; Heaton, Michael P.; Maddox, Jillian F.; McGrath, Annette; Wilson, Peter; Ingersoll, Roxann G.; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John; Cockett, Noelle; Oddy, V. Hutton; Nicholas, Frank W.; Raadsma, Herman

    2009-01-01

    The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability. PMID:19270757

  15. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.

    PubMed

    Krueger, Felix; Andrews, Simon R

    2016-01-01

    Sequencing reads overlapping polymorphic sites in diploid mammalian genomes may be assigned to one allele or the other. This holds the potential to detect gene expression, chromatin modifications, DNA methylation or nuclear interactions in an allele-specific fashion. SNPsplit is an allele-specific alignment sorter designed to read files in SAM/BAM format and determine the allelic origin of reads or read-pairs that cover known single nucleotide polymorphic (SNP) positions. For this to work libraries must have been aligned to a genome in which all known SNP positions were masked with the ambiguity base 'N' and aligned using a suitable mapping program such as Bowtie2, TopHat, STAR, HISAT2, HiCUP or Bismark. SNPsplit also provides an automated solution to generate N-masked reference genomes for hybrid mouse strains based on the variant call information provided by the Mouse Genomes Project. The unique ability of SNPsplit to work with various different kinds of sequencing data including RNA-Seq, ChIP-Seq, Bisulfite-Seq or Hi-C opens new avenues for the integrative exploration of allele-specific data. PMID:27429743

  16. Multiplex detection of respiratory pathogens

    DOEpatents

    McBride, Mary; Slezak, Thomas; Birch, James M.

    2012-07-31

    Described are kits and methods useful for detection of respiratory pathogens (influenza A (including subtyping capability for H1, H3, H5 and H7 subtypes) influenza B, parainfluenza (type 2), respiratory syncytial virus, and adenovirus) in a sample. Genomic sequence information from the respiratory pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay to successfully identify the presence or absence of pathogens in a sample.

  17. The PDGF-C regulatory region SNP rs28999109 decreases promoter transcriptional activity and is associated with CL/P

    PubMed Central

    Choi, Sun J; Marazita, Mary L; Hart, P Suzanne; Sulima, Pawel P; Field, L Leigh; McHenry, Toby Goldstein; Govil, Manika; Cooper, Margaret E; Letra, Ariadne; Menezes, Renato; Narayanan, Somnya; Mansilla, Maria Adela; Granjeiro, José M; Vieira, Alexandre R; Lidral, Andrew C; Murray, Jeffrey C; Hart, Thomas C

    2009-01-01

    Human linkage and association studies suggest a gene(s) for nonsyndromic cleft lip with or without cleft palate (CL/P) on chromosome 4q31–q32 at or near the platelet-derived growth factor-C (PDGF-C) locus. The mouse Pdgfc−/− knockout shows that PDGF-C is essential for palatogenesis. To evaluate the role of PDGF-C in human clefting, we performed sequence analysis and SNP genotyping using 1048 multiplex CL/P families and 1000 case–control samples from multiple geographic origins. No coding region mutations were identified, but a novel −986 C>T SNP (rs28999109) was significantly associated with CL/P (P=0.01) in cases from Chinese families yielding evidence of linkage to 4q31–q32. Significant or near-significant association was also seen for this and several other PDGF-C SNPs in families from the United States, Spain, India, Turkey, China, and Colombia, whereas no association was seen in families from the Philippines, and Guatemala, and case–controls from Brazil. The −986T allele abolished six overlapping potential transcription regulatory motifs. Transfection assays of PDGF-C promoter reporter constructs show that the −986T allele is associated with a significant decrease (up to 80%) of PDGF-C gene promoter activity. This functional polymorphism acting on a susceptible genetic background may represent a component of human CL/P etiology. PMID:19092777

  18. Node assignment in heterogeneous computing

    NASA Technical Reports Server (NTRS)

    Som, Sukhamoy

    1993-01-01

    A number of node assignment schemes, both static and dynamic, are explored for the Algorithm to Architecture Mapping Model (ATAMM). The architecture under consideration consists of heterogeneous processors and implements dataflow models of real-time applications. Terminology is developed for heterogeneous computing. New definitions are added to the ATAMM for token and assignment classifications. It is proved that a periodic execution is possible for dataflow graphs. Assignment algorithms are developed and proved. A design procedure is described for satisfying an objective function in an heterogeneous architecture. Several examples are provided for illustration.

  19. System for Multiplexing Acoustic Emission (AE) Instrumentation

    NASA Technical Reports Server (NTRS)

    Prosser, William H. (Inventor); Perey, Daniel F. (Inventor); Gorman, Michael R. (Inventor); Scales, Edgar F. (Inventor)

    2003-01-01

    An acoustic monitoring device has at least two acoustic sensors with a triggering mechanism and a multiplexing circuit. After the occurrence of a triggering event at a sensor, the multiplexing circuit allows a recording component to record acoustic emissions at adjacent sensors. The acoustic monitoring device is attached to a solid medium to detect the occurrence of damage.

  20. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

    PubMed Central

    2013-01-01

    Background Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation

  1. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping.

    PubMed

    McDonough, Caitrin W; Bostrom, Meredith A; Lu, Lingyi; Hicks, Pamela J; Langefeld, Carl D; Divers, Jasmin; Mychaleckyj, Josyf C; Freedman, Barry I; Bowden, Donald W

    2009-12-01

    Genetic studies in Turkish, Native American, European American, and African American (AA) families have linked chromosome 18q21.1-23 to susceptibility for diabetes-associated nephropathy. In this study, we have carried out fine linkage mapping in the 18q region previously linked to diabetic nephropathy in AAs by genotyping both microsatellite and single nucleotide polymorphisms (SNPs) for linkage analysis in an expanded set of 223 AA families multiplexed for type 2 diabetes associated ESRD (T2DM-ESRD). Several approaches were used to evaluate evidence of linkage with the strongest evidence for linkage in ordered subset analysis with an earlier age of T2DM diagnosis compared to the remaining pedigrees (LOD 3.9 at 90.1 cM, ΔP = 0.0161, NPL P value = 0.00002). Overall, the maximum LODs and LOD-1 intervals vary in magnitude and location depending upon analysis. The linkage mapping was followed up by performing a dense SNP map, genotyping 2,814 SNPs in the refined LOD-1 region in 1,029 AA T2DM-ESRD cases and 1,027 AA controls. Of the top 25 most associated SNPs, 10 resided within genic regions. Two candidate genes stood out: NEDD4L and SERPINB7. SNP rs512099, located in intron 1 of NEDD4L, was associated under a dominant model of inheritance [P value = 0.0006; Odds ratio (95% Confidence Interval) OR (95% CI) = 0.70 (0.57-0.86)]. SNP rs1720843, located in intron 2 of SERPINB7, was associated under a recessive model of inheritance [P value = 0.0017; OR (95% CI) = 0.65 (0.50-0.85)]. Collectively, these results suggest that multiple genes in this region may influence diabetic nephropathy susceptibility in AAs. PMID:19690890

  2. A PCR assay for gender assignment in dugong (Dugong dugon) and West Indian manatee (Trichechus manatus).

    PubMed

    McHale, M; Broderick, D; Ovenden, J R; Lanyon, J M

    2008-05-01

    Gender assignment for some aquatic mammals in the field is difficult. Molecular sexing from tissue biopsies is possible as males are heterogametic. Here we describe a multiplex PCR assay that amplifies the male specific SRY gene and differentiates ZFX and ZFY gametologues in two sirenian species, dugong (Dugong dugon) and West Indian manatee (Trichechus manatus). The assay was validated with animals of known gender and proved accurate and robust to experimental failure. PMID:21585866

  3. SQUID Multiplexers for Cryogenic Detector Arrays

    NASA Technical Reports Server (NTRS)

    Irwin, Kent; Beall, James; Deiker, Steve; Doriese, Randy; Duncan, William; Hilton, Gene; Moseley, S. Harvey; Reintsema, Carl; Stahle, Caroline; Ullom, Joel; Vale, Leila

    2004-01-01

    SQUID multiplexers make it possible to build arrays of thousands of cryogenic detectors with a manageable number of readout channels. We are developing time-division SQUID multiplexers based on Nb trilayer SQUIDs to read arrays of superconducting transition-edge sensors. Our first-generation, 8-channel SQUID multiplexer was used in FIBRE, a one-dimensional TES array for submillimeter astronomy. Our second-generation 32-pixel multiplexer, based on an improved architecture, has been developed for instruments including Constellation-X, SCUBA-2, and solar x-ray astronomy missions. SCUBA-2, which is being developed for the James Clerk Maxwell Telescope, will have more than 10,000 pixels. We are now developing a third-generation architecture based on superconducting hot-electron switches. The use of SQUID multiplexers in instruments operating at above 2 K will also be discussed.

  4. A study of East Timor variability using the SNPforID 52-plex SNP panel.

    PubMed

    Santos, C; Phillips, C; Fondevila, M; Porras-Hurtado, L; Carracedo, A; Souto, L; Lareu, M V

    2011-01-01

    A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, A. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713-1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy-Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP. PMID:20457102

  5. Information transport in multiplex networks

    NASA Astrophysics Data System (ADS)

    Pu, Cunlai; Li, Siyuan; Yang, Xianxia; Yang, Jian; Wang, Kai

    2016-04-01

    In this paper, we study information transport in multiplex networks comprised of two coupled subnetworks. The upper subnetwork, called the logical layer, employs the shortest paths protocol to determine the logical paths for packets transmission, while the lower subnetwork acts as the physical layer, in which packets are delivered by the biased random walk mechanism characterized with a parameter α. Through simulation, we obtain the optimal α corresponding to the maximum network lifetime and the maximum number of the arrival packets. Assortative coupling is better than random coupling and disassortative coupling, since it achieves better transmission performance. Generally, the more homogeneous the lower subnetwork is, the better the transmission performance, which is the opposite for the upper subnetwork. Finally, we propose an attack centrality for nodes based on the topological information of both subnetworks, and investigate the transmission performance under targeted attacks. Our work aids in understanding the spread and robustness issues of multiplex networks and provides some clues about the design of more efficient and robust routing architectures in communication systems.

  6. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

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

    PubMed

    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. PMID:25404132

  8. DoGSD: the dog and wolf genome SNP database

    PubMed Central

    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. PMID:25404132

  9. Substantial SNP-based heritability estimates for working memory performance

    PubMed Central

    Vogler, C; Gschwind, L; Coynel, D; Freytag, V; Milnik, A; Egli, T; Heck, A; de Quervain, D J-F; Papassotiropoulos, A

    2014-01-01

    Working memory (WM) is an important endophenotype in neuropsychiatric research and its use in genetic association studies is thought to be a promising approach to increase our understanding of psychiatric disease. As for any genetically complex trait, demonstration of sufficient heritability within the specific study context is a prerequisite for conducting genetic studies of that trait. Recently developed methods allow estimating trait heritability using sets of common genetic markers from genome-wide association study (GWAS) data in samples of unrelated individuals. Here we present single-nucleotide polymorphism (SNP)-based heritability estimates (h2SNP) for a WM phenotype. A Caucasian sample comprising a total of N=2298 healthy and young individuals was subjected to an N-back WM task. We calculated the genetic relationship between all individuals on the basis of genome-wide SNP data and performed restricted maximum likelihood analyses for variance component estimation to derive the h2SNP estimates. Heritability estimates for three 2-back derived WM performance measures based on all autosomal chromosomes ranged between 31 and 41%, indicating a substantial SNP-based heritability for WM traits. These results indicate that common genetic factors account for a prominent part of the phenotypic variation in WM performance. Hence, the application of GWAS on WM phenotypes is a valid method to identify the molecular underpinnings of WM. PMID:25203169

  10. [Multiplex mapping of human cDNAs]. Technical progress report

    SciTech Connect

    Nierman, W.C.

    1992-11-01

    We have tested and implemented several protocols to increase productivity for mapping expressed sequence tags EST sequences to human chromosomes. These protocols include adopting PRIMER which permits utilization of batch files, as the standard software for PCR primer design; adding a human 21-only cell line to the NIGMS panel No. 1 to improve discrimination in discordancy analyses involving chromosome 21, adding a monochromosomal hybrid panel to facilitate chromosome assignment of sequences that are amplified from more than 1 chromosome; combining the products of multiple PCR reactions for electrophoretic analysis (pseudoplexing); routinely multiplexing PCR reactions; and automating data entry and analysis as much as possible. We have applied these protocols to assign an overall total of 132 human brain CDNA sequences to individual human chromosomes. PCR primers were designed from ESTS and tested for specific amplification from human genomic DNA. DNA was then amplified using DNA from somatic cell hybrid mapping panels as templates. The amplification products were identified using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis. The localized cDNAs include 2 for known human genes, 2 that map to 2 different human chromosomes, and 25 for cDNAs matching existing database records.

  11. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  12. Whole genome SNP scanning of snow sheep (Ovis nivicola).

    PubMed

    Deniskova, T E; Okhlopkov, I M; Sermyagin, A A; Gladyr', E A; Bagirov, V A; Sölkner, J; Mamaev, N V; Brem, G; Zinov'eva, N A

    2016-07-01

    This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations. PMID:27599514

  13. Detection of copy number variation by SNP-allelotyping.

    PubMed

    Parker, Brett; Alexander, Ryan; Wu, Xingyao; Feely, Shawna; Shy, Michael; Schnetz-Boutaud, Nathalie; Li, Jun

    2015-03-01

    Charcot-Marie-Tooth disease type 1A (CMT1A) is caused by an abnormal copy number variation (CNV) with a trisomy of chromosome 17p12. The increase of the DNA-segment copy number is expected to alter the allele frequency of single nucleotide polymorphism (SNP) within the duplicated region. We tested whether SNP allele frequency determined by a Sequenom MassArray can be used to detect the CMT1A mutation. Our results revealed distinct patterns of SNP allele frequency distribution, which reliably differentiated CMT1A patients from controls. This finding suggests that this technique may serve as an alternative approach to identifying CNV in certain diseases, including CMT1A. PMID:24830919

  14. Conditions for the validity of SNP-based heritability estimation

    PubMed Central

    2014-01-01

    The heritability of a trait (h2) is the proportion of its population variance caused by genetic differences, and estimates of this parameter are important for interpreting the results of genome-wide association studies (GWAS). In recent years, researchers have adopted a novel method for estimating a lower bound on heritability directly from GWAS data that uses realized genetic similarities between nominally unrelated individuals. The quantity estimated by this method is purported to be the contribution to heritability that could in principle be recovered from association studies employing the given panel of SNPs (hSNP2). Thus far, the validity of this approach has mostly been tested empirically. Here, we provide a mathematical explication and show that the method should remain a robust means of obtaining hSNP2 SNP under circumstances wider than those under which it has so far been derived. PMID:24744256

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

    PubMed Central

    Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso; Glynn, Judith R.; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Pain, Arnab; Martin, Nigel; Clark, Taane G.

    2014-01-01

    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. PMID:25176035

  16. Structure of triadic relations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Cozzo, Emanuele; Kivelä, Mikko; De Domenico, Manlio; Solé-Ribalta, Albert; Arenas, Alex; Gómez, Sergio; Porter, Mason A.; Moreno, Yamir

    2015-07-01

    Recent advances in the study of networked systems have highlighted that our interconnected world is composed of networks that are coupled to each other through different ‘layers’ that each represent one of many possible subsystems or types of interactions. Nevertheless, it is traditional to aggregate multilayer networks into a single weighted network in order to take advantage of existing tools. This is admittedly convenient, but it is also extremely problematic, as important information can be lost as a result. It is therefore important to develop multilayer generalizations of network concepts. In this paper, we analyze triadic relations and generalize the idea of transitivity to multiplex networks. By focusing on triadic relations, which yield the simplest type of transitivity, we generalize the concept and computation of clustering coefficients to multiplex networks. We show how the layered structure of such networks introduces a new degree of freedom that has a fundamental effect on transitivity. We compute multiplex clustering coefficients for several real multiplex networks and illustrate why one must take great care when generalizing standard network concepts to multiplex networks. We also derive analytical expressions for our clustering coefficients for ensemble averages of networks in a family of random multiplex networks. Our analysis illustrates that social networks have a strong tendency to promote redundancy by closing triads at every layer and that they thereby have a different type of multiplex transitivity from transportation networks, which do not exhibit such a tendency. These insights are invisible if one only studies aggregated networks.

  17. Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

    PubMed

    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: F(ST), informativeness (I(n)), 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 F(ST), I(n), 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

  18. Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle

    PubMed Central

    Gill, Jennifer L; Bishop, Stephen C; McCorquodale, Caroline; Williams, John L; Wiener, Pamela

    2009-01-01

    Background The purpose of this study was to evaluate the effects of eight single nucleotide polymorphisms (SNP), previously associated with meat and milk quality traits in cattle, in a population of 443 commercial Aberdeen Angus-cross beef cattle. The eight SNP, which were located within five genes: μ-calpain (CAPN1), calpastatin (CAST), leptin (LEP), growth hormone receptor (GHR) and acylCoA:diacylglycerol acyltransferase 1 (DGAT1), are included in various commercial tests for tenderness, fatness, carcass composition and milk yield/quality. Methods A total of 27 traits were examined, 19 relating to carcass quality, such as carcass weight and fatness, one mechanical measure of tenderness, and the remaining seven were sensory traits, such as flavour and tenderness, assessed by a taste panel. Results An SNP in the CAPN1 gene, CAPN316, was significantly associated with tenderness measured by both the tenderometer and the taste panel as well as the weight of the hindquarter, where animals inheriting the CC genotype had more tender meat and heavier hindquarters. An SNP in the leptin gene, UASMS2, significantly affected overall liking, where animals with the TT genotype were assigned higher scores by the panellists. The SNP in the GHR gene was significantly associated with odour, where animals inheriting the AA genotype produced steaks with an intense odour when compared with the other genotypes. Finally, the SNP in the DGAT1 gene was associated with sirloin weight after maturation and fat depth surrounding the sirloin, with animals inheriting the AA genotype having heavier sirloins and more fat. Conclusion The results of this study confirm some previously documented associations. Furthermore, novel associations have been identified which, following validation in other populations, could be incorporated into breeding programmes to improve meat quality. PMID:19555501

  19. Multiwavelength metasurfaces through spatial multiplexing

    PubMed Central

    Arbabi, Ehsan; Arbabi, Amir; Kamali, Seyedeh Mahsa; Horie, Yu; Faraon, Andrei

    2016-01-01

    Metasurfaces are two-dimensional arrangements of optical scatterers rationally arranged to control optical wavefronts. Despite the significant advances made in wavefront engineering through metasurfaces, most of these devices are designed for and operate at a single wavelength. Here we show that spatial multiplexing schemes can be applied to increase the number of operation wavelengths. We use a high contrast dielectric transmittarray platform with amorphous silicon nano-posts to demonstrate polarization insensitive metasurface lenses with a numerical aperture of 0.46, that focus light at 915 and 1550 nm to the same focal distance. We investigate two different methods, one based on large scale segmentation and one on meta-atom interleaving, and compare their performances. An important feature of this method is its simple generalization to adding more wavelengths or new functionalities to a device. Therefore, it provides a relatively straightforward method for achieving multi-functional and multiwavelength metasurface devices. PMID:27597568

  20. Code-multiplexed optical scanner

    NASA Astrophysics Data System (ADS)

    Riza, Nabeel A.; Arain, Muzammil A.

    2003-03-01

    A three-dimensional (3-D) optical-scanning technique is proposed based on spatial optical phase code activation on an input beam. This code-multiplexed optical scanner (C-MOS) relies on holographically stored 3-D beam-forming information. Proof-of-concept C-MOS experimental results by use of a photorefractive crystal as a holographic medium generates eight beams representing a basic 3-D voxel element generated via a binary-code matrix of the Hadamard type. The experiment demonstrates the C-MOS features of no moving parts, beam-forming flexibility, and large centimeter-size apertures. A novel application of the C-MOS as an optical security lock is highlighted.

  1. Cooperative epidemics on multiplex networks

    NASA Astrophysics Data System (ADS)

    Azimi-Tafreshi, N.

    2016-04-01

    The spread of one disease, in some cases, can stimulate the spreading of another infectious disease. Here, we treat analytically a symmetric coinfection model for spreading of two diseases on a two-layer multiplex network. We allow layer overlapping, but we assume that each layer is random and locally loopless. Infection with one of the diseases increases the probability of getting infected with the other. Using the generating function method, we calculate exactly the fraction of individuals infected with both diseases (so-called coinfected clusters) in the stationary state, as well as the epidemic spreading thresholds and the phase diagram of the model. With increasing cooperation, we observe a tricritical point and the type of transition changes from continuous to hybrid. Finally, we compare the coinfected clusters in the case of cooperating diseases with the so-called "viable" clusters in networks with dependencies.

  2. Multiplexed Primer Prediction for PCR

    Energy Science and Technology Software Center (ESTSC)

    2007-07-23

    MPP predicts sets of multiplex-compatible primers for Polymerase Chain Reaction (PCR), finding a near minimal set of primers such that at least one amplicon will be generated from every target sequence in the input file. The code finds highly conserved oligos that are suitable as primers, according to user-specified desired primer characteristics such as length, melting temperature, and amplicon length. The primers are predicted not to form unwanted dimer or hairpin structures. The target sequencesmore » used as input can be diverse, since no multiple sequence alighment is required. The code is scalable, taking up to tens of thousands of sequences as input, and works, for example, to find a "universal primer set" for all viral genomes provided as a single input file. The code generates a periodic check-point file, thus in the event of premature execution termination, the application can be restarted from the last check-point file.« less

  3. Analog bus driver and multiplexer

    NASA Technical Reports Server (NTRS)

    Pain, Bedabrata (Inventor); Hancock, Bruce (Inventor); Cunningham, Thomas J. (Inventor)

    2012-01-01

    For a source-follower signal chain, the ohmic drop in the selection switch causes unacceptable voltage offset, non-linearity, and reduced small signal gain. For an op amp signal chain, the required bias current and the output noise rises rapidly with increasing the array format due to a rapid increase in the effective capacitance caused by the Miller effect boosting up the contribution of the bus capacitance. A new switched source-follower signal chain circuit overcomes limitations of existing op-amp based or source follower based circuits used in column multiplexers and data readout. This will improve performance of CMOS imagers, and focal plane read-out integrated circuits for detectors of infrared or ultraviolet light.

  4. Multiwavelength metasurfaces through spatial multiplexing.

    PubMed

    Arbabi, Ehsan; Arbabi, Amir; Kamali, Seyedeh Mahsa; Horie, Yu; Faraon, Andrei

    2016-01-01

    Metasurfaces are two-dimensional arrangements of optical scatterers rationally arranged to control optical wavefronts. Despite the significant advances made in wavefront engineering through metasurfaces, most of these devices are designed for and operate at a single wavelength. Here we show that spatial multiplexing schemes can be applied to increase the number of operation wavelengths. We use a high contrast dielectric transmittarray platform with amorphous silicon nano-posts to demonstrate polarization insensitive metasurface lenses with a numerical aperture of 0.46, that focus light at 915 and 1550 nm to the same focal distance. We investigate two different methods, one based on large scale segmentation and one on meta-atom interleaving, and compare their performances. An important feature of this method is its simple generalization to adding more wavelengths or new functionalities to a device. Therefore, it provides a relatively straightforward method for achieving multi-functional and multiwavelength metasurface devices. PMID:27597568

  5. Focus issue introduction: space-division multiplexing.

    PubMed

    Li, Guifang; Karlsson, Magnus; Liu, Xiang; Quiquempois, Yves

    2014-12-29

    Since the publication of the first focus issue [Opt. Express 19(11), 2011], single-fiber transmission capacity has eclipsed the 1 Pb/s mark. All aspects related to space-division multiplexing including fiber, passive components [(de)multiplexer, couplers], active components (EDFA and Raman amplifiers), switching and routing elements (ROADM and WSS), as well as transmission and networking have progressed rapidly. This focus issue is intended to bring together the most up-to-date research in space-division multiplexing, including fibers, passive and active components, transmission systems and networking. PMID:25607215

  6. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  7. Expert systems for personnel assignment

    SciTech Connect

    Hardee, J.L.; Liepins, G.

    1986-01-01

    In order to reduce stress on assignment personnel (detailers) and ensure maximum fairness and consistency in the Navy's personnel assignment process, The Navy Military Personnel Command (NMPC) has begun to explore the potential use of expert systems to supplement current manual and computerized distribution methods. The Detailer's Assistant expert system is being developed to improve the detailers' ability to satisfy the needs of their constituents and Navy management. An initial prototype of the Detailer's Assistant is now being evaluated. Numerous upgrades and extensions should lead to an operational system in the near future. Further development to a production system will involve additional research in machine learning, intelligent database methods, and cooperating expert systems.

  8. Equivalence of time-multiplexed and frequency-multiplexed signals in digital communications.

    NASA Technical Reports Server (NTRS)

    Timor, U.

    1972-01-01

    In comparing different techniques for multiplexing N binary data signals into a single channel, time-division multiplexing (TDM) is known to have a theoretic efficiency of 100 percent (neglecting sync power) and thus seems to outperform frequency-division multiplexing systems (FDM). By considering more general FDM systems, we will show that both TDM and FDM are equivalent and have an efficiency of 100 percent. The difference between the systems is in the multiplexing and demultiplexing subsystems, but not in the performance or in the generated waveforms.

  9. Preparing DNA Libraries for Multiplexed Paired-End Deep Sequencing for Illumina GA Sequencers

    PubMed Central

    Son, Mike S.; Taylor, Ronald K.

    2011-01-01

    Whole genome sequencing, also known as deep sequencing, is becoming a more affordable and efficient way to identify SNP mutations, deletions and insertions in DNA sequences across several different strains. Two major obstacles preventing the widespread use of deep sequencers are the costs involved in services used to prepare DNA libraries for sequencing and the overall accuracy of the sequencing data. This Unit describes the preparation of DNA libraries for multiplexed paired-end sequencing using the Illumina GA series sequencer. Self-preparation of DNA libraries can help reduce overall expenses, especially if optimization is required for the different samples, and use of the Illumina GA Sequencer can improve the quality of the data. PMID:21400673

  10. Recent developments in multiplexing techniques for immunohistochemistry

    PubMed Central

    Dixon, Angela R; Bathany, Cédric; Tsuei, Michael; White, Joshua; Barald, Kate F; Takayama, Shuichi

    2016-01-01

    Methods to detect immuno-labelled molecules at increasingly higher resolution, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this mini-review is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods. PMID:26289603

  11. A design for a 32-channel multiplexer

    NASA Astrophysics Data System (ADS)

    Martinson, P. F.

    1981-01-01

    A time scan analog system multiplexer used for recording data during flight trials of unmanned aircraft navigation sensors is described. The 32 inputs are buffered, then multiplexed in groups of 8 onto 4 lines. These four are multiplexed onto one line and the signal passes through the output buffer to the recorder. Aircraft attitude, heading and height are recorded. Signals from a camera and a kinetheodolite tracking system are synchronized. Operating conditions were simulated using a helicopter. Noise and drift are due to the recorder. The multiplexer copes well with signals of several kHz bandwidth (raw data) and signals of a few Hz bandwidth (processed data, test signals). It can be used with any multitrack tape recorder having an FM recording format on at least two tracks. It can be converted for use in a digital telemetry system.

  12. The R2R3-Myb transcription fators of cotton: SNP characterization, chromosomal assignment, and phylogenetic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The R2R3-Myb transcription factors are involved in many plant physiological and biochemical processes including regulation of trichome length and density in Arabidopsis. In cotton, Gossypium spp.,the developmental regulation of some R2R3-Myb transcription factors are related to fiber differentiatio...

  13. "Pique": A Group Dictionary Assignment.

    ERIC Educational Resources Information Center

    Smith, Jane Bowman

    1983-01-01

    THE FOLLOWING IS THE FULL TEXT OF THIS DOCUMENT: This exercise replaces the standard, often boring introductory lecture on using the dictionary with a group assignment that encourages the students to observe and analyze the entry for at least one word very carefully. In doing so, the students discover for themselves both the kinds of information…

  14. Who Benefits from Homework Assignments?

    ERIC Educational Resources Information Center

    Ronning, Marte

    2011-01-01

    Using Dutch data on pupils in elementary school this paper is the first empirical study to analyze whether assigning homework has a heterogeneous impact on pupil achievement. Addressing potential biases by using a difference-in-difference approach, I find that the test score gap is larger in classes where everybody gets homework than in classes…

  15. Managing Large Volumes of Assignments

    ERIC Educational Resources Information Center

    Park, James; Hagen, John, Jr.

    2005-01-01

    In spring 2003, the Distance Education Network (DEN), Viterbi School of Engineering at the University of Southern California (USC), had 860 students and more than 1,000 enrollments in 70 courses toward 10 different degrees. Typically, for assignments in engineering courses, professors require students to show how their answers are derived so that…

  16. Some remarks on assignment maps

    NASA Astrophysics Data System (ADS)

    Masillo, F.; Scolarici, G.; Solombrino, L.

    2011-01-01

    We study the properties of general linear assignment maps, showing that positivity axiom can be suitably relaxed, and propose a new class of dynamical maps (generalized dynamics). A puzzling result, arising in such a context in quantum information theory, is also discussed.

  17. Genetic mapping in grapevine using a SNP microarray: intensity values

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotyping microarrays are widely used for genome wide association studies, but in high-diversity organisms, the quality of SNP calls can be diminished by genetic variation near the assayed nucleotide. To address this limitation in grapevine, we developed a simple heuristic that uses hybridization i...

  18. SNP marker diversity in common bean (Phaseolus vulgaris L.).

    PubMed

    Cortés, Andrés J; Chavarro, Martha C; Blair, Matthew W

    2011-09-01

    Single nucleotide polymorphism (SNP) markers have become a genetic technology of choice because of their automation and high precision of allele calls. In this study, our goal was to develop 94 SNPs and test them across well-chosen common bean (Phaseolus vulgaris L.) germplasm. We validated and accessed SNP diversity at 84 gene-based and 10 non-genic loci using KASPar technology in a panel of 70 genotypes that have been used as parents of mapping populations and have been previously evaluated for SSRs. SNPs exhibited high levels of genetic diversity, an excess of middle frequency polymorphism, and a within-genepool mismatch distribution as expected for populations affected by sudden demographic expansions after domestication bottlenecks. This set of markers was useful for distinguishing Andean and Mesoamerican genotypes but less useful for distinguishing within each gene pool. In summary, slightly greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool but polymorphism rate between genotypes was consistent with genepool and race identity. Our survey results represent a baseline for the choice of SNP markers for future applications because gene-associated SNPs could themselves be causative SNPs for traits. Finally, we discuss that the ideal genetic marker combination with which to carry out diversity, mapping and association studies in common bean should consider a mix of both SNP and SSR markers. PMID:21785951

  19. SNP Discovery through Next-Generation Sequencing and Its Applications

    PubMed Central

    Kumar, Santosh; Banks, Travis W.; Cloutier, Sylvie

    2012-01-01

    The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference. PMID:23227038

  20. Do you really know where this SNP goes?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The release of build 10.2 of the swine genome was a marked improvement over previous builds and has proven extremely useful. However, as most know, there are regions of the genome that this particular build does not accurately represent. For instance, nearly 25% of the 62,162 SNP on the Illumina Por...

  1. Analysis of genetic diversity using SNP markers in oat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A large-scale single nucleotide polymorphism (SNP) discovery was carried out in cultivated oat using Roche 454 sequencing methods. DNA sequences were generated from cDNAs originating from a panel of 20 diverse oat cultivars, and from Diversity Array Technology (DArT) genomic complexity reductions fr...

  2. Software solutions for the livestock genomics SNP array revolution.

    PubMed

    Nicolazzi, E L; Biffani, S; Biscarini, F; Orozco Ter Wengel, P; Caprera, A; Nazzicari, N; Stella, A

    2015-08-01

    Since the beginning of the genomic era, the number of available single nucleotide polymorphism (SNP) arrays has grown considerably. In the bovine species alone, 11 SNP chips not completely covered by intellectual property are currently available, and the number is growing. Genomic/genotype data are not standardized, and this hampers its exchange and integration. In addition, software used for the analyses of these data usually requires not standard (i.e. case specific) input files which, considering the large amount of data to be handled, require at least some programming skills in their production. In this work, we describe a software toolkit for SNP array data management, imputation, genome-wide association studies, population genetics and genomic selection. However, this toolkit does not solve the critical need for standardization of the genotypic data and software input files. It only highlights the chaotic situation each researcher has to face on a daily basis and gives some helpful advice on the currently available tools in order to navigate the SNP array data complexity. PMID:25907889

  3. Correlated edge overlaps in multiplex networks.

    PubMed

    Baxter, Gareth J; Bianconi, Ginestra; da Costa, Rui A; Dorogovtsev, Sergey N; Mendes, José F F

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions. PMID:27575144

  4. Switchable holograms and approaches to storage multiplexing

    NASA Astrophysics Data System (ADS)

    Domash, Lawrence H.; Chen, Yong-Ming; Snowbell, Michael; Gozewski, Conrad M.

    1994-09-01

    Holographic data storage requires reference beam encoding for multiplexing and demultiplexing. Electrically switchable holographic composites (ESHC) based on a Polaroid photopolymer films are being investigated as a basis for several types of reference beam encoding devices. A laboratory demonstration reported here recorded four holograms in a photoresponsive storage medium. Both random phase encoding and angle multiplexing approaches were tested. ESHC encoding devices have much higher diffraction efficiency than spatial light modulators used in many other encoding schemes.

  5. Correlated edge overlaps in multiplex networks

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions.

  6. Allowing for sex differences increases power in a GWAS of multiplex Autism families.

    PubMed

    Lu, A T-H; Cantor, R M

    2012-02-01

    Current genomewide association studies account for only a small fraction of the estimated heritabilities of genetically complex neuropsychiatric disorders, indicating they are likely to result from the small effects of numerous predisposing variants, many of which have gone undetected. The statistical power to detect associations of common variants with small effects is increased by conducting joint association tests of a single nucleotide polymorphism (SNP), an additional risk factor (F), and their interaction. F can represent an environmental exposure, another genotype or any source of genetic heterogeneity. In case and control studies, logistic regression makes joint tests straightforward. This analytic method cannot be employed directly when SNP transmission tests are used to detect associations in parent/affected child trios and multiplex families. However, the method can be implemented using the case/pseudocontrol approach. We applied this approach to analyze data from a genomewide association study of multiplex families ascertained for Autism Spectrum Disorder, where sex was used to define the F. Joint analyses revealed two associations exceeding genomewide significance. One novel gene, Ryandine Receptor 2, implicated in calcium channel defects, was identified with a joint P-value of 3.9E-11. Calcium channel defects have been connected to Autism spectrum disorder (ASD) by Timothy Syndrome, which is Mendelian, and a previous targeted sex-specific association analysis of idiopathic Autism. A second gene, uridine phosphorylase 2, with a joint P-value of 2.3E-9, has been previously linked and associated with Autism in independent samples. These findings highlight two Autism candidate genes for follow-up studies. PMID:21151189

  7. Multiplexing of fiber optic Bragg grating sensors

    NASA Astrophysics Data System (ADS)

    Chan, Kok Cheung Peter

    2000-11-01

    The main objective of this project was to develop a novel technique for multiplexing fiber Bragg grating sensors for strain measurements. Multiplexing is a very important issue for fiber Bragg grating sensors, as it allows them to be used for distributed sensing where their greatest impact is anticipated. Three types of multiplexed fiber Bragg grating sensor system prototypes were developed in this work. Most effort was devoted to a frequency-modulated continuous wave technique for multiplexing fiber Bragg grating sensors. A detailed mathematical analysis of the frequency-modulated continuous wave multiplexing technique was performed. It was identified that the technique can be used to multiplex up to 32 fiber Bragg grating sensors of the same nominal Bragg wavelength with a theoretical crosstalk performance of below -48 dB. This level of crosstalk corresponds to a wavelength detected error of well below 1 pm if fiber Bragg gratings having a bandwidth of around 0.2 nm are used. A few hundreds of sensors could be multiplexed by combining the frequency-modulated continuous wave technique with the well known wavelength-division-multiplexing technique. The practical factors which limit the performance, including the effect of biasing from the optimal working condition and the effect of non-ideal frequency sweeping intensity modulation, were investigated. The system performance, in terms of power budget and inter-sensor crosstalk for a serial and parallel architecture was also determined. A series of experiments were carried out to verify the principle of operation and to study the effects arising from the various practical performance limiting factors and from different network architectures. A three sensor system was experimentally demonstrated with -30 dB crosstalk level and with 2 μɛ resolution in terms of root-mean-square strain value. The system performance was found to be limited by the residual amplitude modulation due to the non-ideal frequency response of

  8. Association of Atherosclerotic Peripheral Arterial Disease with Adiponectin Genes SNP+45 and SNP+276: A Case-Control Study

    PubMed Central

    Gherman, Claudia D.; Bolboacă, Sorana D.

    2013-01-01

    Objectives. We hypothesized that adiponectin gene SNP+45 (rs2241766) and SNP+276 (rs1501299) would be associated with atherosclerotic peripheral arterial disease (PAD). Furthermore, the association between circulating adiponectin levels, fetuin-A, and tumoral necrosis factor-alpha (TNF-α) in patients with atherosclerotic peripheral arterial disease was investigated. Method. Several blood parameters (such as adiponectin, fetuin-A, and TNF-α) were measured in 346 patients, 226 with atherosclerotic peripheral arterial disease (PAD) and 120 without symptomatic PAD (non-PAD). Two common SNPs of the ADIPOQ gene represented by +45T/G 2 and +276G/T were also investigated. Results. Adiponectin concentrations showed lower circulating levels in the PAD patients compared to non-PAD patients (P < 0.001). Decreasing adiponectin concentration was associated with increasing serum levels of fetuin-A in the PAD patients. None of the investigated adiponectin SNPs proved to be associated with the subjects' susceptibility to PAD (P > 0.05). Conclusion. The results of our study demonstrated that neither adiponectin SNP+45 nor SNP+276 is associated with the risk of PAD. PMID:23819115

  9. High throughput SNP discovery and validation in the pig: towards the development of a high density swine SNP chip

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent developments in sequencing technology have allowed the generation of millions of short read sequences in a fast and inexpensive way. This enables the cost effective large scale identification of hundreds of thousands of SNPs needed for the development of high density SNP arrays. Currently, a ...

  10. Large-Scale SNP Discovery through RNA Sequencing and SNP Genotyping by Targeted Enrichment Sequencing in Cassava (Manihot esculenta Crantz)

    PubMed Central

    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. PMID:25551642

  11. Development of Single Nucleotide Polymorphism (SNP) Markers for Use in Commercial Maize (Zea Mays L.) Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of single nucleotide polymorphism (SNP) markers in maize offer the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding, and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and ...

  12. The development and characterization of a 57K SNP array for rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this paper we describe the development and characterization of the first high density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor. The SNP genotyping quality was high and validation rate was close to 90%...

  13. Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy

    PubMed Central

    Neiman, Mårten; Sundling, Simon; Grönberg, Henrik; Hall, Per; Czene, Kamila

    2012-01-01

    During the recent years, rapid development of sequencing technologies and a competitive market has enabled researchers to perform massive sequencing projects at a reasonable cost. As the price for the actual sequencing reactions drops, enabling more samples to be sequenced, the relative price for preparing libraries gets larger and the practical laboratory work becomes complex and tedious. We present a cost-effective strategy for simplified library preparation compatible with both whole genome- and targeted sequencing experiments. An optimized enzyme composition and reaction buffer reduces the number of required clean-up steps and allows for usage of bulk enzymes which makes the whole process cheap, efficient and simple. We also present a two-tagging strategy, which allows for multiplex sequencing of targeted regions. To prove our concept, we have prepared libraries for low-pass sequencing from 100 ng DNA, performed 2-, 4- and 8-plex exome capture and a 96-plex capture of a 500 kb region. In all samples we see a high concordance (>99.4%) of SNP calls when comparing to commercially available SNP-chip platforms. PMID:23139805

  14. Multiplexed modulation of behavioral choice

    PubMed Central

    Palmer, Chris R.; Barnett, Megan N.; Copado, Saul; Gardezy, Fred; Kristan, William B.

    2014-01-01

    Stimuli in the environment, as well as internal states, influence behavioral choice. Of course, animals are often exposed to multiple external and internal factors simultaneously, which makes the ultimate determinants of behavior quite complex. We observed the behavioral responses of European leeches, Hirudo verbana, as we varied one external factor (surrounding water depth) with either another external factor (location of tactile stimulation along the body) or an internal factor (body distention following feeding). Stimulus location proved to be the primary indicator of behavioral response. In general, anterior stimulation produced shortening behavior, midbody stimulation produced local bending, and posterior stimulation usually produced either swimming or crawling but sometimes a hybrid of the two. By producing a systematically measured map of behavioral responses to body stimulation, we found wide areas of overlap between behaviors. When we varied the surrounding water depth, this map changed significantly, and a new feature – rotation of the body along its long axis prior to swimming – appeared. We found additional interactions between water depth and time since last feeding. A large blood meal initially made the animals crawl more and swim less, an effect that was attenuated as water depth increased. The behavioral map returned to its pre-feeding form after approximately 3 weeks as the leeches digested their blood meal. In summary, we found multiplexed impacts on behavioral choice, with the map of responses to tactile stimulation modified by water depth, which itself modulated the impact that feeding had on the decision to swim or crawl. PMID:24902753

  15. Fleet Assignment Using Collective Intelligence

    NASA Technical Reports Server (NTRS)

    Antoine, Nicolas E.; Bieniawski, Stefan R.; Kroo, Ilan M.; Wolpert, David H.

    2004-01-01

    Product distribution theory is a new collective intelligence-based framework for analyzing and controlling distributed systems. Its usefulness in distributed stochastic optimization is illustrated here through an airline fleet assignment problem. This problem involves the allocation of aircraft to a set of flights legs in order to meet passenger demand, while satisfying a variety of linear and non-linear constraints. Over the course of the day, the routing of each aircraft is determined in order to minimize the number of required flights for a given fleet. The associated flow continuity and aircraft count constraints have led researchers to focus on obtaining quasi-optimal solutions, especially at larger scales. In this paper, the authors propose the application of this new stochastic optimization algorithm to a non-linear objective cold start fleet assignment problem. Results show that the optimizer can successfully solve such highly-constrained problems (130 variables, 184 constraints).

  16. Fleet Assignment Using Collective Intelligence

    NASA Technical Reports Server (NTRS)

    Antoine, Nicolas E.; Bieniawski, Stefan R.; Kroo, Ilan M.; Wolpert, David H.

    2004-01-01

    Airline fleet assignment involves the allocation of aircraft to a set of flights legs in order to meet passenger demand, while satisfying a variety of constraints. Over the course of the day, the routing of each aircraft is determined in order to minimize the number of required flights for a given fleet. The associated flow continuity and aircraft count constraints have led researchers to focus on obtaining quasi-optimal solutions, especially at larger scales. In this paper, the authors propose the application of an agent-based integer optimization algorithm to a "cold start" fleet assignment problem. Results show that the optimizer can successfully solve such highly- constrained problems (129 variables, 184 constraints).

  17. Intracavity absorption multiplexed sensor network based on dense wavelength division multiplexing filter.

    PubMed

    Zhang, Haiwei; Lu, Ying; Duan, Liangcheng; Zhao, Zhiqiang; Shi, Wei; Yao, Jianquan

    2014-10-01

    We report the system design and experimental verification of an intracavity absorption multiplexed sensor network with hollow core photonic crystal fiber (HCPCF) sensors and dense wavelength division multiplexing (DWDM) filters. Compared with fiber Bragg grating (FBG), it is easier for the DWDM to accomplish a stable output. We realize the concentration detection of three gas cells filled with acetylene. The sensitivity is up to 100 ppmV at 1536.71 nm. Voltage gradient is firstly used to optimize the intracavity sensor network enhancing the detection efficiency up to 6.5 times. To the best of our knowledge, DWDM is firstly used as a wavelength division multiplexing device to realize intracavity absorption multiplexed sensor network. It make it possible to realize high capacity intracavity sensor network via multiplexed technique. PMID:25322029

  18. Influence of MDM2 SNP309 and SNP285 status on the risk of cancer in the breast, prostate, lung and colon.

    PubMed

    Gansmo, Liv B; Knappskog, Stian; Romundstad, Pål; Hveem, Kristian; Vatten, Lars; Lønning, Per E

    2015-07-01

    MDM2 is a key regulator of the p53 tumor suppressor protein and is overexpressed in many human cancers. Two single nucleotide polymorphisms (SNPs) located in the MDM2 intronic promoter (P2) have been found to exert biological function. The G-allele of SNP309T>G; rs2279744 increases MDM2 transcription and has been linked to increased cancer risk. In contrast, the less frequent SNP285G>C; rs117039649, which is in complete linkage disequilibrium with SNP309 (generating a SNP285C/309G variant haplotype), has been related to reduced MDM2 transcription and to reduced risk of breast, endometrial and ovarian cancer. In this large population-based case-control study, we genotyped SNP309 and SNP285 in 10,830 individuals, including cases with cancer of the breast (n=1,717), colon (n=1,532), lung (n=1,331) and prostate (n=2,501), as well as 3,749 non-cancer controls. We found a slightly reduced risk for lung cancer among individuals harboring the SNP309TG/GG genotypes compared to the SNP309TT genotype (OR= 0.86; CI = 0.67-0.98), but this association was restricted to women (OR = 0.77; CI = 0.63-0.95) and was not present among men (OR = 0.91; CI = 0.77-1.08). Consistent with previous findings, we found a reduced risk for breast cancer among individuals carrying the SNP285GC/309GG genotype versus the SNP285GG/309GG genotype (OR = 0.55; CI = 0.33-0.93). In conclusion, our data support the hypothesis that the effects of both SNP285 and SNP309 status are tissue dependent. PMID:25431177

  19. Model Refinement Using Eigensystem Assignment

    NASA Technical Reports Server (NTRS)

    Maghami, Peiman G.

    2000-01-01

    IA novel approach for the refinement of finite-element-based analytical models of flexible structures is presented. The proposed approach models the possible refinements in the mass, damping, and stiffness matrices of the finite element model in the form of a constant gain feedback with acceleration, velocity, and displacement measurements, respectively. Once the free elements of the structural matrices have been defined, the problem of model refinement reduces to obtaining position, velocity, and acceleration gain matrices with appropriate sparsity that reassign a desired subset of the eigenvalues of the model, along with partial mode shapes, from their baseline values to those obtained from system identification test data. A sequential procedure is used to assign one conjugate pair of eigenvalues at each step using symmetric output feedback gain matrices, and the eigenvectors are partially assigned, while ensuring that the eigenvalues assigned in the previous steps are not disturbed. The procedure can also impose that gain matrices be dissipative to guarantee the stability of the refined model. A numerical example, involving finite element model refinement for a structural testbed at NASA Langley Research Center (Controls-Structures-Interaction Evolutionary model) is presented to demonstrate the feasibility of the proposed approach.

  20. Creating High-Quality Classroom Assignments

    ERIC Educational Resources Information Center

    Matsumura, Lindsay Clare; Gallimore, Ronald

    2005-01-01

    Research indicates that the quality of classroom assignments makes a difference in student learning. Moreover, assignment quality varies between teachers even within the same school and there is room for improvement in many of the assignments that teachers provide to students. Assignment quality, as described in this book, puts into practice…

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

    PubMed Central

    Panneerselvam, Palanisamy; Sivakumari, Kanakarajan; Jayaprakash, Ponmani; Srikanth, Ramanathan

    2010-01-01

    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 as inputs in the SNP data field. E152Q change was neutral and C239S causes disease. Using PANTHER for evolutionary analysis of coding SNPs, the protein sequence was given as input and analyzed for the E152Q and C239S SNPs for deleterious effect on protein function. The genetic association

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

    PubMed

    Panneerselvam, Palanisamy; Sivakumari, Kanakarajan; Jayaprakash, Ponmani; Srikanth, Ramanathan

    2010-01-01

    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 as inputs in the SNP data field. E152Q change was neutral and C239S causes disease. Using PANTHER for evolutionary analysis of coding SNPs, the protein sequence was given as input and analyzed for the E152Q and C239S SNPs for deleterious effect on protein function. The genetic association

  3. A SNP panel for identity and kinship testing using massive parallel sequencing.

    PubMed

    Grandell, Ida; Samara, Raed; Tillmar, Andreas O

    2016-07-01

    Within forensic genetics, there is still a need for supplementary DNA marker typing in order to increase the power to solve cases for both identity testing and complex kinship issues. One major disadvantage with current capillary electrophoresis (CE) methods is the limitation in DNA marker multiplex capability. By utilizing massive parallel sequencing (MPS) technology, this capability can, however, be increased. We have designed a customized GeneRead DNASeq SNP panel (Qiagen) of 140 previously published autosomal forensically relevant identity SNPs for analysis using MPS. One single amplification step was followed by library preparation using the GeneRead Library Prep workflow (Qiagen). The sequencing was performed on a MiSeq System (Illumina), and the bioinformatic analyses were done using the software Biomedical Genomics Workbench (CLC Bio, Qiagen). Forty-nine individuals from a Swedish population were genotyped in order to establish genotype frequencies and to evaluate the performance of the assay. The analyses showed to have a balanced coverage among the included loci, and the heterozygous balance showed to have less than 0.5 % outliers. Analyses of dilution series of the 2800M Control DNA gave reproducible results down to 0.2 ng DNA input. In addition, typing of FTA samples and bone samples was performed with promising results. Further studies and optimizations are, however, required for a more detailed evaluation of the performance of degraded and PCR-inhibited forensic samples. In summary, the assay offers a straightforward sample-to-genotype workflow and could be useful to gain information in forensic casework, for both identity testing and in order to solve complex kinship issues. PMID:26932869

  4. Development and validation of the Axiom(®) Apple480K SNP genotyping array.

    PubMed

    Bianco, Luca; Cestaro, Alessandro; Linsmith, Gareth; Muranty, Hélène; Denancé, Caroline; Théron, Anthony; Poncet, Charles; Micheletti, Diego; Kerschbamer, Emanuela; Di Pierro, Erica A; Larger, Simone; Pindo, Massimo; Van de Weg, Eric; Davassi, Alessandro; Laurens, François; Velasco, Riccardo; Durel, Charles-Eric; Troggio, Michela

    2016-04-01

    Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple. PMID:26919684

  5. Demonstration of 2×ONU 80 Gbps direct detection colorless polarization division multiplexing frequency division multiplexing passive optical network uplink transmission

    NASA Astrophysics Data System (ADS)

    Wang, Zhixin; Xu, Yinfan; Wang, Yanyi; Wang, Yuanquan; Chi, Nan

    2016-04-01

    In this study, we propose and experimentally demonstrate a simple direct detection passive optical network (PON) uplink transmission scheme based on frequency division multiplexing and polarization division multiplexing. Two optical network units (ONUs) are assigned to two different frequency bands at two different orthogonal polarization directions. At the optical line terminal, both ONU signals can be simultaneously detected by a single photodiode without utilizing any polarization control, polarization selection, or complicated polarization demultiplexing algorithms. As a proof-of-concept, the 2×ONU 80 Gbps 32-ary quadrature amplitude modulation Nyquist single carrier signals are successfully transmitted over 2 km standard single mode fiber or 20 km large effective area fiber with the assistance of frequency domain equalization and decision-directed least-mean-square. The measured bit error rate can be below the 7% pre-forward error correction threshold of 3.8×10-3. Meanwhile, this scheme is compatible with the widely used wavelength-division multiplexed PON, which shows the promising potential and feasibility of this proposal.

  6. Method and apparatus for multiplexing switch signals

    NASA Technical Reports Server (NTRS)

    Hannaford, Blake (Inventor)

    1989-01-01

    Apparatus for multiplexing switch state signals comprises a plurality of switches and parallel weighted resistors connected in series between circuit ground and a node at a utilization device. The resistors are weighted as a function of a power of the same base, such as the power of the base 2, for coding the multiplexed switch state signals. A constant current source connected between the node and circuit ground drives current over a single cable conductor through the resistor. Each switch may be independently closed to change the switch state voltage signals multiplexed to the node. An analog-to-digital converter connected between the node and circuit ground demultiplexes the switch state signals received at the node and provides a switch state signal at each analog-to-digital output corresponding to the state of the switches at the moment. A potentiometer may replace a resistor and bypass switch combination in a position where the potentiometer has a maximum value of the lowest power of the base in order to multiplex a true analog voltage signal while switch state signals are unambiguously coded and multiplexed. The potentiometer in the least significant position permits the analog value to be in the range from 0 to a maximum corresponding to the least significant position of the switch state encoding. The invention may be used in redundancy systems by duplicating the invention with corresponding switches in each duplication ganged to open and close simultaneously upon operation of a pushbutton switch.

  7. Giant components in directed multiplex networks.

    PubMed

    Azimi-Tafreshi, N; Dorogovtsev, S N; Mendes, J F F

    2014-11-01

    We describe the complex global structure of giant components in directed multiplex networks that generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of m different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, m=2, we define a strongly viable component as a set of vertices in which for each type of edges each two vertices are interconnected by at least two directed paths in both directions, running through the edges of only this type. We show that in this case, a directed multiplex network contains in total nine different giant components including the strongly viable component. In general, the total number of giant components is 3^{m}. For uncorrelated directed multiplex networks, we obtain exactly the size and the emergence point of the strongly viable component and estimate the sizes of other giant components. PMID:25493836

  8. Optical encryption system using quadrature multiplexing

    NASA Astrophysics Data System (ADS)

    Islam, Mohammed Nazrul; Alam, Mohammad S.

    2006-08-01

    Optical security systems have attracted much research interest recently for information security and fraud deterrent applications. A number of encryption techniques have been proposed in the literature, which includes double random-phase encryption, polarization encoding, encryption and verification using a multiplexed minimum average correlation energy phase-encrypted filter. Most of these reports employ a pseudo-random code for each information to be encrypted, where it requires individual storage capacity or transmission channel for further processing of each information. The objective of this paper is to develop an optical encryption system employing quadrature multiplexing to enhance the storage/transmission capacity of the system. Two information signals are encrypted using the same code but employing two orthogonal functions and then they are multiplexed together in the same domain. As the orthogonal functions have zero cross-correlation between them, so the encrypted information are expected to be unaffected by each other. Each encryption and multiplexing process can accommodate two information signals for a single code and a single storage cell or transmission channel. The same process can be performed in multiple steps to increase the multiplexing capability of the system. For decryption purpose, the composite encoded signal is correlated using the appropriate code and the appropriate function. The proposed technique has been found to work excellent in computer simulation with binary as well as gray level images. It has also been verified that the encrypted images remain secure, because no unwanted reproduction is possible without having the appropriate code and function.

  9. Chemically modified primers for improved multiplex PCR

    PubMed Central

    Shum, Jonathan; Paul, Natasha

    2009-01-01

    Multiplexed PCR, the amplification of multiple targets in a single reaction, presents a new set of challenges that further complicate more traditional PCR set-ups. These complications include a greater probability for non-specific amplicon formation and for imbalanced amplification of different targets, each of which can compromise quantification and detection of multiple targets. Despite these difficulties, multiplex PCR is frequently used in such applications as pathogen detection, RNA quantification, mutation analysis and now, next generation DNA sequencing. Herein, we investigate the utility of primers with one or two thermolabile 4-oxo-1-pentyl phosphotriester modifications in improving multiplex PCR performance. Initial endpoint and real-time analyses reveal a decrease in off-target amplification and subsequent increase in amplicon yield. Furthermore, the use of modified primers in multiplex set-ups revealed a greater limit of detection and more uniform amplification of each target as compared to unmodified primers. Overall, the thermolabile modified primers present a novel and exciting avenue in improving multiplex PCR performance. PMID:19258004

  10. Giant components in directed multiplex networks

    NASA Astrophysics Data System (ADS)

    Azimi-Tafreshi, N.; Dorogovtsev, S. N.; Mendes, J. F. F.

    2014-11-01

    We describe the complex global structure of giant components in directed multiplex networks that generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of m different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, m =2 , we define a strongly viable component as a set of vertices in which for each type of edges each two vertices are interconnected by at least two directed paths in both directions, running through the edges of only this type. We show that in this case, a directed multiplex network contains in total nine different giant components including the strongly viable component. In general, the total number of giant components is 3m. For uncorrelated directed multiplex networks, we obtain exactly the size and the emergence point of the strongly viable component and estimate the sizes of other giant components.

  11. Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution.

    PubMed

    Zhao, Zhongming; Fu, Yun-Xin; Hewett-Emmett, David; Boerwinkle, Eric

    2003-07-17

    We investigated the single nucleotide polymorphism (SNP) density across the human genome and in different genic categories using two SNP databases: Celera's CgsSNP, which includes SNPs identified by comparing genomic sequences, and Celera's RefSNP, which includes SNPs from a variety of sources and is biased toward disease-associated genes. Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44, and 8.09 in the human genome, in intergenic regions, and in genic regions, respectively. In genic regions, the SNP density in intronic, exonic and adjoining untranslated regions was 8.21, 5.28, and 7.51 SNPs per 10 kb, respectively. The pattern of SNP density based on RefSNP was different from that based on CgsSNP, emphasizing its utility for genotype-phenotype association studies but not for most population genetic studies. The number of SNPs per chromosome was correlated with chromosome length, but the density of SNPs estimated by CgsSNP was not significantly correlated with the GC content of the chromosome. Based on CgsSNP, the ratio of nonsense to missense mutations (0.027), the ratio of missense to silent mutations (1.15), and the ratio of non-synonymous to synonymous mutations (1.18) was less than half of that expected in a human protein coding sequence under the neutral mutation theory, reflecting a role for natural selection, especially purifying selection. PMID:12909357

  12. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    PubMed

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale. PMID:25476721

  13. Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis.

    PubMed

    Walther, Charles; Mayrhofer, Markus; Nilsson, Jenny; Hofvander, Jakob; Jonson, Tord; Mandahl, Nils; Øra, Ingrid; Gisselsson, David; Mertens, Fredrik

    2016-01-01

    Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents. Alveolar (ARMS) and embryonal (ERMS) histologies predominate, but rare cases are classified as spindle cell/sclerosing (SRMS). For treatment stratification, RMS is further subclassified as fusion-positive (FP-RMS) or fusion-negative (FN-RMS), depending on whether a gene fusion involving PAX3 or PAX7 is present or not. We investigated 19 cases of pediatric RMS using high resolution single-nucleotide polymorphism (SNP) array. FP-ARMS displayed, on average, more structural rearrangements than ERMS; the single FN-ARMS had a genomic profile similar to ERMS. Apart from previously known amplification (e.g., MYCN, CDK4, and MIR17HG) and deletion (e.g., NF1, CDKN2A, and CDKN2B) targets, amplification of ERBB2 and homozygous loss of ASCC3 or ODZ3 were seen. Combining SNP array with cytogenetic data revealed that most cases were polyploid, with at least one case having started as a near-haploid tumor. Further bioinformatic analysis of the SNP array data disclosed genetic heterogeneity, in the form of subclonal chromosomal imbalances, in five tumors. The outcome was worse for patients with FP-ARMS than ERMS or FN-ARMS (6/8 vs. 1/9 dead of disease), and the only children with ERMS showing intratumor diversity or with MYOD1 mutation-positive SRMS also died of disease. High resolution SNP array can be useful in evaluating genomic imbalances in pediatric RMS. PMID:26482321

  14. Introgression browser: high-throughput whole-genome SNP visualization.

    PubMed

    Aflitos, Saulo Alves; Sanchez-Perez, Gabino; de Ridder, Dick; Fransz, Paul; Schranz, Michael E; de Jong, Hans; Peters, Sander A

    2015-04-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (iBrowser), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis iBrowser makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the iBrowser in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of iBrowser makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes iBrowser a valuable breeding tool. PMID:25704554

  15. Detection of homologous horizontal gene transfer in SNP data

    Energy Science and Technology Software Center (ESTSC)

    2012-07-23

    We study the detection of mutations, sequencing errors, and homologous horizontal gene transfers (HGT) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNP's) and break the genomes into blocks to handle the rearrangement problem. Then we apply a synamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HGT.

  16. Robust Demographic Inference from Genomic and SNP Data

    PubMed Central

    Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu

    2013-01-01

    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 , 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. PMID:24204310

  17. PanSNPdb: The Pan-Asian SNP Genotyping Database

    PubMed Central

    Ngamphiw, Chumpol; Assawamakin, Anunchai; Xu, Shuhua; Shaw, Philip J.; Yang, Jin Ok; Ghang, Ho; Bhak, Jong; Liu, Edison; Tongsima, Sissades

    2011-01-01

    The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP. PMID:21731755

  18. How far from the SNP may the causative genes be?

    PubMed

    Brodie, Aharon; Azaria, Johnathan Roy; Ofran, Yanay

    2016-07-27

    While GWAS identify many disease-associated SNPs, using them to decipher disease mechanisms is hindered by the difficulty in mapping SNPs to genes. Most SNPs are in non-coding regions and it is often hard to identify the genes they implicate. To explore how far the SNP may be from the affected genes we used a pathway-based approach. We found that affected genes are often up to 2 Mbps away from the associated SNP, and are not necessarily the closest genes to the SNP. Existing approaches for mapping SNPs to genes leave many SNPs unmapped to genes and reveal only 86 significant phenotype-pathway associations for all known GWAS hits combined. Using the pathway-based approach we propose here allows mapping of virtually all SNPs to genes and reveals 435 statistically significant phenotype-pathway associations. In search for mechanisms that may explain the relationships between SNPs and distant genes, we found that SNPs that are mapped to distant genes have significantly more large insertions/deletions around them than other SNPs, suggesting that these SNPs may sometimes be markers for large insertions/deletions that may affect large genomic regions. PMID:27269582

  19. Development of a forensic identity SNP panel for Indonesia.

    PubMed

    Augustinus, Daniel; Gahan, Michelle E; McNevin, Dennis

    2015-07-01

    Genetic markers included in forensic identity panels must exhibit Hardy-Weinberg and linkage equilibrium (HWE and LE). "Universal" panels designed for global use can fail these tests in regional jurisdictions exhibiting high levels of genetic differentiation such as the Indonesian archipelago. This is especially the case where a single DNA database is required for allele frequency estimates to calculate random match probabilities (RMPs) and associated likelihood ratios (LRs). A panel of 65 single nucleotide polymorphisms (SNPs) and a reduced set of 52 SNPs have been selected from 15 Indonesian subpopulations in the HUGO Pan Asian SNP database using a SNP selection strategy that could be applied to any panel of forensic identity markers. The strategy consists of four screening steps: (1) application of a G test for HWE; (2) ranking for high heterozygosity; (3) selection for LE; and (4) selection for low inbreeding depression. SNPs in our Indonesian panel perform well in comparison to some other universal SNP and short tandem repeat (STR) panels as measured by Fisher's exact test for HWE and LE and Wright's F statistics. PMID:25104323

  20. Population distribution and ancestry of the cancer protective MDM2 SNP285 (rs117039649).

    PubMed

    Knappskog, Stian; Gansmo, Liv B; Dibirova, Khadizha; Metspalu, Andres; Cybulski, Cezary; Peterlongo, Paolo; Aaltonen, Lauri; Vatten, Lars; Romundstad, Pål; Hveem, Kristian; Devilee, Peter; Evans, Gareth D; Lin, Dongxin; Van Camp, Guy; Manolopoulos, Vangelis G; Osorio, Ana; Milani, Lili; Ozcelik, Tayfun; Zalloua, Pierre; Mouzaya, Francis; Bliznetz, Elena; Balanovska, Elena; Pocheshkova, Elvira; Kučinskas, Vaidutis; Atramentova, Lubov; Nymadawa, Pagbajabyn; Titov, Konstantin; Lavryashina, Maria; Yusupov, Yuldash; Bogdanova, Natalia; Koshel, Sergey; Zamora, Jorge; Wedge, David C; Charlesworth, Deborah; Dörk, Thilo; Balanovsky, Oleg; Lønning, Per E

    2014-09-30

    The MDM2 promoter SNP285C is located on the SNP309G allele. While SNP309G enhances Sp1 transcription factor binding and MDM2 transcription, SNP285C antagonizes Sp1 binding and reduces the risk of breast-, ovary- and endometrial cancer. Assessing SNP285 and 309 genotypes across 25 different ethnic populations (>10.000 individuals), the incidence of SNP285C was 6-8% across European populations except for Finns (1.2%) and Saami (0.3%). The incidence decreased towards the Middle-East and Eastern Russia, and SNP285C was absent among Han Chinese, Mongolians and African Americans. Interhaplotype variation analyses estimated SNP285C to have originated about 14,700 years ago (95% CI: 8,300 - 33,300). Both this estimate and the geographical distribution suggest SNP285C to have arisen after the separation between Caucasians and modern day East Asians (17,000 - 40,000 years ago). We observed a strong inverse correlation (r = -0.805; p < 0.001) between the percentage of SNP309G alleles harboring SNP285C and the MAF for SNP309G itself across different populations suggesting selection and environmental adaptation with respect to MDM2 expression in recent human evolution. In conclusion, we found SNP285C to be a pan-Caucasian variant. Ethnic variation regarding distribution of SNP285C needs to be taken into account when assessing the impact of MDM2 SNPs on cancer risk. PMID:25327560

  1. Population distribution and ancestry of the cancer protective MDM2 SNP285 (rs117039649)

    PubMed Central

    Knappskog, Stian; Gansmo, Liv B.; Dibirova, Khadizha; Metspalu, Andres; Cybulski, Cezary; Peterlongo, Paolo; Aaltonen, Lauri; Vatten, Lars; Romundstad, Pål; Hveem, Kristian; Devilee, Peter; Evans, Gareth D.; Lin, Dongxin; Camp, Guy Van; Manolopoulos, Vangelis G.; Osorio, Ana; Milani, Lili; Ozcelik, Tayfun; Zalloua, Pierre; Mouzaya, Francis; Bliznetz, Elena; Balanovska, Elena; Pocheshkova, Elvira; Kučinskas, Vaidutis; Atramentova, Lubov; Nymadawa, Pagbajabyn; Titov, Konstantin; Lavryashina, Maria; Yusupov, Yuldash; Bogdanova, Natalia; Koshel, Sergey; Zamora, Jorge; Wedge, David C.; Charlesworth, Deborah; Dörk, Thilo; Balanovsky, Oleg; Lønning, Per E.

    2014-01-01

    The MDM2 promoter SNP285C is located on the SNP309G allele. While SNP309G enhances Sp1 transcription factor binding and MDM2 transcription, SNP285C antagonizes Sp1 binding and reduces the risk of breast-, ovary- and endometrial cancer. Assessing SNP285 and 309 genotypes across 25 different ethnic populations (>10.000 individuals), the incidence of SNP285C was 6-8% across European populations except for Finns (1.2%) and Saami (0.3%). The incidence decreased towards the Middle-East and Eastern Russia, and SNP285C was absent among Han Chinese, Mongolians and African Americans. Interhaplotype variation analyses estimated SNP285C to have originated about 14,700 years ago (95% CI: 8,300 – 33,300). Both this estimate and the geographical distribution suggest SNP285C to have arisen after the separation between Caucasians and modern day East Asians (17,000 - 40,000 years ago). We observed a strong inverse correlation (r = -0.805; p < 0.001) between the percentage of SNP309G alleles harboring SNP285C and the MAF for SNP309G itself across different populations suggesting selection and environmental adaptation with respect to MDM2 expression in recent human evolution. In conclusion, we found SNP285C to be a pan-Caucasian variant. Ethnic variation regarding distribution of SNP285C needs to be taken into account when assessing the impact of MDM2 SNPs on cancer risk. PMID:25327560

  2. Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies

    PubMed Central

    Pattaro, Cristian; Ruczinski, Ingo; Fallin, Danièle M; Parmigiani, Giovanni

    2008-01-01

    Background Identification of disease-related genes in association studies is challenged by the large number of SNPs typed. To address the dilution of power caused by high dimensionality, and to generate results that are biologically interpretable, it is critical to take into consideration spatial correlation of SNPs along the genome. With the goal of identifying true genetic associations, partitioning the genome according to spatial correlation can be a powerful and meaningful way to address this dimensionality problem. Results We developed and validated an MCMC Algorithm To Identify blocks of Linkage DisEquilibrium (MATILDE) for clustering contiguous SNPs, and a statistical testing framework to detect association using partitions as units of analysis. We compared its ability to detect true SNP associations to that of the most commonly used algorithm for block partitioning, as implemented in the Haploview and HapBlock software. Simulations were based on artificially assigning phenotypes to individuals with SNPs corresponding to region 14q11 of the HapMap database. When block partitioning is performed using MATILDE, the ability to correctly identify a disease SNP is higher, especially for small effects, than it is with the alternatives considered. Advantages can be both in terms of true positive findings and limiting the number of false discoveries. Finer partitions provided by LD-based methods or by marker-by-marker analysis are efficient only for detecting big effects, or in presence of large sample sizes. The probabilistic approach we propose offers several additional advantages, including: a) adapting the estimation of blocks to the population, technology, and sample size of the study; b) probabilistic assessment of uncertainty about block boundaries and about whether any two SNPs are in the same block; c) user selection of the probability threshold for assigning SNPs to the same block. Conclusion We demonstrate that, in realistic scenarios, our adaptive, study

  3. Multiplexed image storage by electromagnetically induced transparency in a solid

    NASA Astrophysics Data System (ADS)

    Heinze, G.; Rentzsch, N.; Halfmann, T.

    2012-11-01

    We report on frequency- and angle-multiplexed image storage by electromagnetically induced transparency (EIT) in a Pr3+:Y2SiO5 crystal. Frequency multiplexing by EIT relies on simultaneous storage of light pulses in atomic coherences, driven in different frequency ensembles of the inhomogeneously broadened solid medium. Angular multiplexing by EIT relies on phase matching of the driving laser beams, which permits simultaneous storage of light pulses propagating under different angles into the crystal. We apply the multiplexing techniques to increase the storage capacity of the EIT-driven optical memory, in particular to implement multiplexed storage of larger two-dimensional amounts of data (images). We demonstrate selective storage and readout of images by frequency-multiplexed EIT and angular-multiplexed EIT, as well as the potential to combine both multiplexing approaches towards further enhanced storage capacities.

  4. An X-band SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Hahn, I.; Bumble, B.; LeDuc, H. G.; Weilert, M.; Day, P.

    2006-09-01

    We are developing a microwave readout multiplexer for arrays of superconducting quantum interference devices (SQUIDs). A series of microwave resonators with frequencies ˜10 GHz are each loaded by a dc SQUID to a degree that depends on the flux state of the SQUID. By using resonators with high quality factors and slightly different resonance frequencies, many of these resonator-coupled SQUIDs may be read out with a single excitation line and cryogenic amplifier. Our multiplexer is similar to the one demonstrated by Irwin and Lehnert except for the use of higher-frequency, fully-lithographed transmission line resonators. We discuss a technique for modulating the SQUID array in series that alleviates the need to individually flux-bias the SQUIDs. The multiplexer has applications to the readout of detector arrays for astronomy as well as medical magnetic imaging.

  5. Superconducting Digital Multiplexers for Sensor Arrays

    NASA Technical Reports Server (NTRS)

    Kadin, Alan M.; Brock, Darren K.; Gupta, Deepnarayan

    2004-01-01

    Arrays of cryogenic microbolometers and other cryogenic detectors are being developed for infrared imaging. If the signal from each sensor is amplified, multiplexed, and digitized using superconducting electronics, then this data can be efficiently read out to ambient temperature with a minimum of noise and thermal load. HYPRES is developing an integrated system based on SQUID amplifiers, a high-resolution analog-to-digital converter (ADC) based on RSFQ (rapid single flux quantum) logic, and a clocked RSFQ multiplexer. The ADC and SQUIDs have already been demonstrated for other projects, so this paper will focus on new results of a digital multiplexer. Several test circuits have been fabricated using Nb Josephson technology and are about to be tested at T = 4.2 K, with a more complete prototype in preparation.

  6. Metric projection for dynamic multiplex networks.

    PubMed

    Jurman, Giuseppe

    2016-08-01

    Evolving multiplex networks are a powerful model for representing the dynamics along time of different phenomena, such as social networks, power grids, biological pathways. However, exploring the structure of the multiplex network time series is still an open problem. Here we propose a two-step strategy to tackle this problem based on the concept of distance (metric) between networks. Given a multiplex graph, first a network of networks is built for each time step, and then a real valued time series is obtained by the sequence of (simple) networks by evaluating the distance from the first element of the series. The effectiveness of this approach in detecting the occurring changes along the original time series is shown on a synthetic example first, and then on the Gulf dataset of political events. PMID:27626089

  7. Using HL7 in hospital staff assignments.

    PubMed

    Unluturk, Mehmet S

    2014-02-01

    Hospital staff assignments are the instructions that allocate the hospital staff members to the hospital beds. Currently, hospital administrators make the assignments without accessing the information regarding the occupancy of the hospital beds and the acuity of the patient. As a result, administrators cannot distinguish between occupied and unoccupied beds, and may therefore assign staff to unoccupied beds. This gives rise to uneven and inefficient staff assignments. In this paper, the hospital admission-discharge-transfer (ADT) system is employed both as a data source and an assignment device to create staff assignments. When the patient data is newly added or modified, the ADT system updates the assignment software client with the relevant data. Based on the relevant data, the assignment software client is able to construct staff assignments in a more efficient way. PMID:24480165

  8. Automated Methods for Multiplexed Pathogen Detection

    SciTech Connect

    Straub, Tim M.; Dockendorff, Brian P.; Quinonez-Diaz, Maria D.; Valdez, Catherine O.; Shutthanandan, Janani I.; Tarasevich, Barbara J.; Grate, Jay W.; Bruckner-Lea, Cindy J.

    2005-09-01

    Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cycler where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides ''live vs. dead'' capabilities. However

  9. Y-chromosome polymorphisms and ethnic group – a combined STR and SNP approach in a population sample from northern Italy

    PubMed Central

    Cortellini, Venusia; Verzeletti, Andrea; Cerri, Nicoletta; Marino, Alberto; De Ferrari, Francesco

    2013-01-01

    Aim To find an association between Y chromosome polymorphisms and some ethnic groups. Methods Short tandem repeats (STR) and single-nucleotide polymorphisms (SNP) on the Y chromosome were typed in 311 unrelated men from four different ethnic groups – Italians from northern Italy, Albanians, Africans from the Maghreb region, and Indo-Pakistanis, using the AmpFlSTR® Yfiler PCR Amplification Kit and the SNaPshot Multiplex Kit. Results STRs analysis found 299 different haplotypes and SNPs analysis 11 different haplogroups. Haplotypes and haplogroups were analyzed and compared between different ethnic groups. Significant differences were found among all the population groups, except between Italians and Indo-Pakistanis and between Albanians and Indo-Pakistanis. Conclusions Typing both STRs and SNPs on the Y chromosome could become useful in determining ethnic origin of a potential suspect. PMID:23771759

  10. Vibrational assignments of 2-iodopyridine

    NASA Astrophysics Data System (ADS)

    Sortur, Veenasangeeta; Yenagi, Jayashree; Tonannavar, J.

    2008-02-01

    A review of the vibrational assignments for 2-iodopyridine has been proposed based on the FT-Raman (3500-50 cm -1) and IR (4000-400 cm -1) spectral measurements. Equilibrium geometries and vibrational frequencies have been computed from a variety of electronic structure methods: the ab initio (RHF), six DFT (BLYP, BP86, B3LYP, B3P86, B3PW91 and SVWN) and MP2 methods using 3-21G*, LANL2DZ and DGDZVP basis sets. A normal coordinate analysis has been carried out: the normal modes and their couplings are characterized in terms of potential energy distributions (PEDs). The comparison of assignments for pyridine and halopyridines shows that several of the normal modes arise from coupled vibrations in 2-iodopyridine. The BP86 and B3LYP methods with LANL2DZ basis set have performed reasonably well in reproducing the observed spectra, demonstrating that the LANL2DZ basis set (with effective core potential representations of electrons near the nuclei for post-third row atoms) is suitable for 2-iodopyridine.

  11. Automatic Assignment of EC Numbers

    PubMed Central

    Egelhofer, Volker; Schomburg, Ida; Schomburg, Dietmar

    2010-01-01

    A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology. When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function, the EC number introduced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) is used. However, each and every one of these applications is critically dependent upon the consistency and reliability of the underlying data for success. We have developed tools for the validation of the EC number classification scheme. In this paper, we present validated data of 3788 enzymatic reactions including 229 sub-subclasses of the EC classification system. Over 80% agreement was found between our assignment and the EC classification. For 61 (i.e., only 2.5%) reactions we found that their assignment was inconsistent with the rules of the nomenclature committee; they have to be transferred to other sub-subclasses. We demonstrate that our validation results can be used to initiate corrections and improvements to the EC number classification scheme. PMID:20126531

  12. Eigenvector centrality of nodes in multiplex networks.

    PubMed

    Solá, Luis; Romance, Miguel; Criado, Regino; Flores, Julio; García del Amo, Alejandro; Boccaletti, Stefano

    2013-09-01

    We extend the concept of eigenvector centrality to multiplex networks, and introduce several alternative parameters that quantify the importance of nodes in a multi-layered networked system, including the definition of vectorial-type centralities. In addition, we rigorously show that, under reasonable conditions, such centrality measures exist and are unique. Computer experiments and simulations demonstrate that the proposed measures provide substantially different results when applied to the same multiplex structure, and highlight the non-trivial relationships between the different measures of centrality introduced. PMID:24089967

  13. Line graphs for a multiplex network.

    PubMed

    Criado, Regino; Flores, Julio; García Del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated. PMID:27368798

  14. Cooperative spreading processes in multiplex networks

    NASA Astrophysics Data System (ADS)

    Wei, Xiang; Chen, Shihua; Wu, Xiaoqun; Ning, Di; Lu, Jun-an

    2016-06-01

    This study is concerned with the dynamic behaviors of epidemic spreading in multiplex networks. A model composed of two interacting complex networks is proposed to describe cooperative spreading processes, wherein the virus spreading in one layer can penetrate into the other to promote the spreading process. The global epidemic threshold of the model is smaller than the epidemic thresholds of the corresponding isolated networks. Thus, global epidemic onset arises in the interacting networks even though an epidemic onset does not arise in each isolated network. Simulations verify the analysis results and indicate that cooperative spreading processes in multiplex networks enhance the final infection fraction.

  15. Multiplexed imaging of intracellular protein networks.

    PubMed

    Grecco, Hernán E; Imtiaz, Sarah; Zamir, Eli

    2016-08-01

    Cellular functions emerge from the collective action of a large number of different proteins. Understanding how these protein networks operate requires monitoring their components in intact cells. Due to intercellular and intracellular molecular variability, it is important to monitor simultaneously multiple components at high spatiotemporal resolution. However, inherent trade-offs narrow the boundaries of achievable multiplexed imaging. Pushing these boundaries is essential for a better understanding of cellular processes. Here the motivations, challenges and approaches for multiplexed imaging of intracellular protein networks are discussed. © 2016 International Society for Advancement of Cytometry. PMID:27183498

  16. Nanowire sensors for multiplexed detection of biomolecules

    PubMed Central

    He, Bo; Morrow, Thomas J; Keating, Christine D

    2009-01-01

    Nanowire-based detection strategies provide promising new routes to bioanalysis that could one day revolutionize the healthcare industry. This review covers recent developments in nanowire sensors for multiplexed detection of biomolecules such as nucleic acids and proteins. We focus on encoded nanowire suspension arrays and semiconductor nanowire-based field-effect transistors. Nanowire assembly and integration with microchip technology is emphasized as a key step toward the ultimate goal of multiplexed detection at the point of care using portable, low power, electronic biosensor chips. PMID:18804551

  17. Multimode fiber optic wavelength division multiplexing

    NASA Technical Reports Server (NTRS)

    Spencer, J. L.

    1982-01-01

    Optical wavelength division multiplexing (WDM) systems, with signals transmitted on different wavelengths through a single optical fiber, can have increased bandwidth and fault isolation properties over single wavelength optical systems. Two WDM system designs that might be used with multimode fibers are considered and a general description of the components which could be used to implement the system are given. The components described are sources, multiplexers, demultiplexers, and detectors. Emphasis is given to the demultiplexer technique which is the major developmental component in the WDM system.

  18. Line graphs for a multiplex network

    NASA Astrophysics Data System (ADS)

    Criado, Regino; Flores, Julio; García del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A.

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated.

  19. Polarization-multiplexed encoding at nanometer scales.

    PubMed

    Macias-Romero, C; Munro, P R T; Török, P

    2014-10-20

    Optical data storage was developed using binary encoding primarily due to signal to noise ratio considerations. We report on a multiplexing method that allows a seven fold storage increase, per storage layer, per side, and propose one that can yield theoretically a 20+ fold increase. Multiplexing is achieved by encoding information in polarization via appropriately oriented nanostructures that emit strongly polarized light when excited by unpolarized light. The storage increase is possible due to the significantly reduced crosstalk that results form using unpolarized light. PMID:25401656

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

    PubMed Central

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

    2016-01-01

    High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species’ genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the ‘ssalar01’ high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. PMID:27194803

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

    PubMed

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

    2016-01-01

    High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. PMID:27194803

  2. Assignment Choice, Effort, and Assignment Completion: Does Work Ethic Predict Those Who Choose Higher-Effort Assignments?

    ERIC Educational Resources Information Center

    Parkhurst, John T.; Fleisher, Matthew S.; Skinner, Christopher H.; Woehr, David J.; Hawthorn-Embree, Meredith L.

    2011-01-01

    After completing the Multidimensional Work-Ethic Profile (MWEP), 98 college students were given a 20-problem math computation assignment and instructed to stop working on the assignment after completing 10 problems. Next, they were allowed to choose to finish either the partially completed assignment that had 10 problems remaining or a new…

  3. 25 CFR 214.18 - Assignments.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., OKLAHOMA, FOR MINING, EXCEPT OIL AND GAS § 214.18 Assignments. Approved leases or any interest therein may... transfer or assignment a satisfactory bond as prescribed in § 214.4 in connection with leases. Any...

  4. Microwave multiplex readout for superconducting sensors

    NASA Astrophysics Data System (ADS)

    Ferri, E.; Becker, D.; Bennett, D.; Faverzani, M.; Fowler, J.; Gard, J.; Giachero, A.; Hays-Wehle, J.; Hilton, G.; Maino, M.; Mates, J.; Puiu, A.; Nucciotti, A.; Reintsema, C.; Schmidt, D.; Swetz, D.; Ullom, J.; Vale, L.

    2016-07-01

    The absolute neutrino mass scale is still an outstanding challenge in both particle physics and cosmology. The calorimetric measurement of the energy released in a nuclear beta decay is a powerful tool to determine the effective electron-neutrino mass. In the last years, the progress on low temperature detector technologies has allowed to design large scale experiments aiming at pushing down the sensitivity on the neutrino mass below 1 eV. Even with outstanding performances in both energy (~ eV on keV) and time resolution (~ 1 μs) on the single channel, a large number of detectors working in parallel is required to reach a sub-eV sensitivity. Microwave frequency domain readout is the best available technique to readout large array of low temperature detectors, such as Transition Edge Sensors (TESs) or Microwave Kinetic Inductance Detectors (MKIDs). In this way a multiplex factor of the order of thousands can be reached, limited only by the bandwidth of the available commercial fast digitizers. This microwave multiplexing system will be used to readout the HOLMES detectors, an array of 1000 microcalorimeters based on TES sensors in which the 163Ho will be implanted. HOLMES is a new experiment for measuring the electron neutrino mass by means of the electron capture (EC) decay of 163Ho. We present here the microwave frequency multiplex which will be used in the HOLMES experiment and the microwave frequency multiplex used to readout the MKID detectors developed in Milan as well.

  5. Highly multiplexed DNA sequencing by capillary electrophoresis

    SciTech Connect

    Yeung, E.S.; Ueno, K.; Chang, H.T.

    1994-12-31

    It is obvious that irrespective of whichever basic technology is eventually selected to sequence the entire human genome there are substantial gains to be made if a high degree of multiplexing of parallel runs can be implemented. Such multiplexing should not involve expensive instrumentation and should not require additional personnel, or else the main objective of cost reduction will not be satisfied even though the total time for sequencing is reduced. In the last two years, several research groups have shown that capillary electrophoresis (CE) is an attractive alternative for DNA sequencing. Part of the improvement in sequencing speed in CE is counteracted by the inherent ability of slab gels for accommodating multiple lanes in a single run. Recently, the authors have developed several excitation schemes for highly multiplexed capillary electrophoresis. Detection at the pM level was demonstrated. The authors report here the use of a novel excitation geometry to simultaneously monitor 100 capillary tubes during electrophoresis. This represents a truly parallel multiplexing scheme for high-speed DNA sequencing.

  6. Moving through a multiplex holographic scene

    NASA Astrophysics Data System (ADS)

    Mrongovius, Martina

    2013-02-01

    This paper explores how movement can be used as a compositional element in installations of multiplex holograms. My holographic images are created from montages of hand-held video and photo-sequences. These spatially dynamic compositions are visually complex but anchored to landmarks and hints of the capturing process - such as the appearance of the photographer's shadow - to establish a sense of connection to the holographic scene. Moving around in front of the hologram, the viewer animates the holographic scene. A perception of motion then results from the viewer's bodily awareness of physical motion and the visual reading of dynamics within the scene or movement of perspective through a virtual suggestion of space. By linking and transforming the physical motion of the viewer with the visual animation, the viewer's bodily awareness - including proprioception, balance and orientation - play into the holographic composition. How multiplex holography can be a tool for exploring coupled, cross-referenced and transformed perceptions of movement is demonstrated with a number of holographic image installations. Through this process I expanded my creative composition practice to consider how dynamic and spatial scenes can be conveyed through the fragmented view of a multiplex hologram. This body of work was developed through an installation art practice and was the basis of my recently completed doctoral thesis: 'The Emergent Holographic Scene — compositions of movement and affect using multiplex holographic images'.

  7. Immunity of multiplex networks via acquaintance vaccination

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Zhao, Da-Wei; Wang, Lin; Sun, Gui-Quan; Jin, Zhen

    2015-11-01

    How to find the effective approach of immunizing a population is one open question in the research of complex systems. Up to now, there have been a great number of works focusing on the efficiency of various immunization strategies. However, the majority of these existing achievements are limited to isolated networks, how immunization affects disease spreading in multiplex networks seems to need further exploration. In this letter, we explore the impact of the acquaintance immunization in multiplex networks, where two kinds of immunization strategies, multiplex node-based acquaintance immunization and layer node-based acquaintance immunization, are proposed. With the generating function method, our theoretical framework is able to accurately calculate the critical immunization threshold which is one of the most important indexes to predict the epidemic regime. Moreover, we further uncover that, with the increment of degree correlation between network layers, the immunization threshold declines for multiplex node-based acquaintance immunization, but slowly increases for layer node-based acquaintance immunization.

  8. Multiplexing schemes for quantum repeater networks

    NASA Astrophysics Data System (ADS)

    Aparicio, Luciano; Van Meter, Rodney

    2011-08-01

    When built, quantum repeaters will allow the distribution of entangled quantum states across large distances, playing a vital part in many proposed quantum technologies. Enabling multiple users to connect through the same network will be key to their real-world deployment. Previous work on repeater technologies has focussed only on simple entanglment production, without considering the issues of resource scarcity and competition that necessarily arise in a network setting. In this paper we simulated a thirteen-node network with up to five flows sharing different parts of the network, measuring the total throughput and fairness for each case. Our results suggest that the Internet-like approach of statistical multiplexing use of a congested link gives the highest aggregate throughput. Time division multiplexing and buffer space multiplexing were slightly less effective, but all three schemes allow the sum of multiple flows to substantially exceed that of any one flow, improving over circuit switching by taking advantage of resources that are forced to remain idle in circuit switching. All three schemes proved to have excellent fairness. The high performance, fairness and simplicity of implementation support a recommendation of statistical multiplexing for shared quantum repeater networks.

  9. Fiber optics wavelength division multiplexing(components)

    NASA Technical Reports Server (NTRS)

    Hendricks, Herbert D.

    1985-01-01

    The long term objectives are to develop optical multiplexers/demultiplexers, different wavelength and modulation stable semiconductor lasers and high data rate transceivers, as well as to test and evaluate fiber optic networks applicable to the Space Station. Progress in each of the above areas is briefly discussed.

  10. 47 CFR 74.802 - Frequency assignment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Frequency assignment. 74.802 Section 74.802... Frequency assignment. (a) Frequencies within the following bands may be assigned for use by low power... MHz. All zones 113 km (70 miles) (c) Specific frequency operation is required when operating...

  11. 47 CFR 80.509 - Frequency assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 false Frequency assignment. 80.509 Section 80.509... MARITIME SERVICES Private Coast Stations and Marine Utility Stations § 80.509 Frequency assignment. Frequencies assignable to private coast stations and marine utility stations are listed in subpart H....

  12. 47 CFR 74.802 - Frequency assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Frequency assignment. 74.802 Section 74.802... Frequency assignment. (a) Frequencies within the following bands may be assigned for use by low power... MHz. All zones 113 km (70 miles) (c) Specific frequency operation is required when operating...

  13. 47 CFR 74.802 - Frequency assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Frequency assignment. 74.802 Section 74.802... Frequency assignment. (a) Frequencies within the following bands may be assigned for use by low power... MHz. All zones 113 km (70 miles) (c) Specific frequency operation is required when operating...

  14. 47 CFR 80.509 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 false Frequency assignment. 80.509 Section 80.509... MARITIME SERVICES Private Coast Stations and Marine Utility Stations § 80.509 Frequency assignment. Frequencies assignable to private coast stations and marine utility stations are listed in subpart H....

  15. 47 CFR 80.509 - Frequency assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 5 2013-10-01 2013-10-01 false Frequency assignment. 80.509 Section 80.509... MARITIME SERVICES Private Coast Stations and Marine Utility Stations § 80.509 Frequency assignment. Frequencies assignable to private coast stations and marine utility stations are listed in subpart H....

  16. 47 CFR 80.509 - Frequency assignment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Frequency assignment. 80.509 Section 80.509... MARITIME SERVICES Private Coast Stations and Marine Utility Stations § 80.509 Frequency assignment. Frequencies assignable to private coast stations and marine utility stations are listed in subpart H....

  17. 47 CFR 74.802 - Frequency assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Frequency assignment. 74.802 Section 74.802... Frequency assignment. (a) Frequencies within the following bands may be assigned for use by low power... MHz. All zones 113 km (70 miles) (c) Specific frequency operation is required when operating...

  18. 47 CFR 74.802 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Frequency assignment. 74.802 Section 74.802... Frequency assignment. (a) Frequencies within the following bands may be assigned for use by low power... MHz. All zones 113 km (70 miles) (c) Specific frequency operation is required when operating...

  19. 47 CFR 80.509 - Frequency assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Frequency assignment. 80.509 Section 80.509... MARITIME SERVICES Private Coast Stations and Marine Utility Stations § 80.509 Frequency assignment. Frequencies assignable to private coast stations and marine utility stations are listed in subpart H....

  20. 28 CFR 548.17 - Work assignments.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Work assignments. 548.17 Section 548.17... PROGRAMS Religious Beliefs and Practices of Committed Offenders § 548.17 Work assignments. When the religious tenets of an inmate's faith are violated or jeopardized by a particular work assignment,...

  1. 28 CFR 548.17 - Work assignments.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Work assignments. 548.17 Section 548.17... PROGRAMS Religious Beliefs and Practices of Committed Offenders § 548.17 Work assignments. When the religious tenets of an inmate's faith are violated or jeopardized by a particular work assignment,...

  2. 28 CFR 548.17 - Work assignments.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 28 Judicial Administration 2 2013-07-01 2013-07-01 false Work assignments. 548.17 Section 548.17... PROGRAMS Religious Beliefs and Practices of Committed Offenders § 548.17 Work assignments. When the religious tenets of an inmate's faith are violated or jeopardized by a particular work assignment,...

  3. 28 CFR 548.17 - Work assignments.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Work assignments. 548.17 Section 548.17... PROGRAMS Religious Beliefs and Practices of Committed Offenders § 548.17 Work assignments. When the religious tenets of an inmate's faith are violated or jeopardized by a particular work assignment,...

  4. 28 CFR 548.17 - Work assignments.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 2 2014-07-01 2014-07-01 false Work assignments. 548.17 Section 548.17... PROGRAMS Religious Beliefs and Practices of Committed Offenders § 548.17 Work assignments. When the religious tenets of an inmate's faith are violated or jeopardized by a particular work assignment,...

  5. 7 CFR 1437.104 - Assigned production.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Assigned production. 1437.104 Section 1437.104... Determining Yield Coverage Using Actual Production History § 1437.104 Assigned production. (a) When determining losses under this section, assigned production will be used to offset the loss of production...

  6. 24 CFR 221.255 - Assignment option.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    .... (b) The mortgagee may exercise its assignment option within 1 year following the twentieth anniversary of the date the mortgage was endorsed for insurance. (c) Upon the exercise of the assignment... the assignment, plus accrued interest to such date. (d) The debentures issued pursuant to the...

  7. 24 CFR 221.255 - Assignment option.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    .... (b) The mortgagee may exercise its assignment option within 1 year following the twentieth anniversary of the date the mortgage was endorsed for insurance. (c) Upon the exercise of the assignment... the assignment, plus accrued interest to such date. (d) The debentures issued pursuant to the...

  8. 24 CFR 221.255 - Assignment option.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    .... (b) The mortgagee may exercise its assignment option within 1 year following the twentieth anniversary of the date the mortgage was endorsed for insurance. (c) Upon the exercise of the assignment... the assignment, plus accrued interest to such date. (d) The debentures issued pursuant to the...

  9. 25 CFR 215.20 - Assignment.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assignment. 215.20 Section 215.20 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEAD AND ZINC MINING OPERATIONS AND LEASES, QUAPAW AGENCY § 215.20 Assignment. Leases granted or approved under the regulations in this part may be assigned and the leased premises may...

  10. Lexical Stress Assignment in Italian Developmental Dyslexia

    ERIC Educational Resources Information Center

    Paizi, Despina; Zoccolotti, Pierluigi; Burani, Cristina

    2011-01-01

    Stress assignment to Italian polysyllabic words is unpredictable, because stress is neither marked nor predicted by rule. Stress assignment, especially to low frequency words, has been reported to be a function of stress dominance and stress neighbourhood. Two experiments investigate stress assignment in sixth-grade, skilled and dyslexic, readers.…

  11. 12 CFR 563e.28 - Assigned ratings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) and(c) of this section, the OTS assigns to a savings association a rating of “outstanding... service tests. The OTS assigns a rating for a savings association assessed under the lending, investment... an “outstanding” rating on the lending test receives an assigned rating of at least...

  12. 12 CFR 563e.28 - Assigned ratings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) and(c) of this section, the OTS assigns to a savings association a rating of “outstanding... service tests. The OTS assigns a rating for a savings association assessed under the lending, investment... an “outstanding” rating on the lending test receives an assigned rating of at least...

  13. 12 CFR 563e.28 - Assigned ratings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...) and(c) of this section, the OTS assigns to a savings association a rating of “outstanding... service tests. The OTS assigns a rating for a savings association assessed under the lending, investment... an “outstanding” rating on the lending test receives an assigned rating of at least...

  14. 7 CFR 1437.104 - Assigned production.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assigned production. 1437.104 Section 1437.104... Determining Yield Coverage Using Actual Production History § 1437.104 Assigned production. (a) When determining losses under this section, assigned production will be used to offset the loss of production...

  15. 43 CFR 2521.3 - Assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Procedures § 2521.3 Assignment...), assignments of desert-land entries were recognized, the Department of the Interior, largely for administrative reasons, held that a desert-land entry might be assigned as a whole or in its entirety, but refused...

  16. 43 CFR 2521.3 - Assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Procedures § 2521.3 Assignment...), assignments of desert-land entries were recognized, the Department of the Interior, largely for administrative reasons, held that a desert-land entry might be assigned as a whole or in its entirety, but refused...

  17. 43 CFR 2521.3 - Assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Procedures § 2521.3 Assignment...), assignments of desert-land entries were recognized, the Department of the Interior, largely for administrative reasons, held that a desert-land entry might be assigned as a whole or in its entirety, but refused...

  18. 43 CFR 2521.3 - Assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Procedures § 2521.3 Assignment...), assignments of desert-land entries were recognized, the Department of the Interior, largely for administrative reasons, held that a desert-land entry might be assigned as a whole or in its entirety, but refused...

  19. Antibody-Based Protein Multiplex Platforms: Technical and Operational Challenges

    PubMed Central

    Ellington, Allison A.; Kullo, Iftikhar J.; Bailey, Kent R.; Klee, George G.

    2010-01-01

    BACKGROUND The measurement of multiple protein biomarkers may refine risk stratification in clinical settings. This concept has stimulated development of multiplexed immunoassay platforms that provide multiple, parallel protein measurements on the same specimen. CONTENT We provide an overview of antibody-based multiplexed immunoassay platforms and discuss technical and operational challenges. Multiplexed immunoassays use traditional immunoassay principles in which high-affinity capture ligands are immobilized in parallel arrays in either planar format or on microspheres in suspension. Development of multiplexed immunoassays requires rigorous validation of assay configuration and analytical performance to minimize assay imprecision and inaccuracy. Challenges associated with multiplex configuration include selection and immobilization of capture ligands, calibration, interference between antibodies and proteins and assay diluents, and compatibility of assay limits of quantification. We discuss potential solutions to these challenges. Criteria for assessing analytical multiplex assay performance include the range of linearity, analytical specificity, recovery, and comparison to a quality reference method. Quality control materials are not well developed for multiplexed protein immunoassays, and algorithms for interpreting multiplex quality control data are needed. SUMMARY Technical and operational challenges have hindered implementation of multiplexed assays in clinical settings. Formal procedures that guide multiplex assay configuration, analytical validation, and quality control are needed before broad application of multiplexed arrays can occur in the in vitro diagnostic market. PMID:19959625

  20. TES Detector Noise Limited Readout Using SQUID Multiplexers

    NASA Technical Reports Server (NTRS)

    Staguhn, J. G.; Benford, D. J.; Chervenak, J. A.; Khan, S. A.; Moseley, S. H.; Shafer, R. A.; Deiker, S.; Grossman, E. N.; Hilton, G. C.; Irwin, K. D.

    2004-01-01

    The availability of superconducting Transition Edge Sensors (TES) with large numbers of individual detector pixels requires multiplexers for efficient readout. The use of multiplexers reduces the number of wires needed between the cryogenic electronics and the room temperature electronics and cuts the number of required cryogenic amplifiers. We are using an 8 channel SQUID multiplexer to read out one-dimensional TES arrays which are used for submillimeter astronomical observations. We present results from test measurements which show that the low noise level of the SQUID multiplexers allows accurate measurements of the TES Johnson noise, and that in operation, the readout noise is dominated by the detector noise. Multiplexers for large number of channels require a large bandwidth for the multiplexed readout signal. We discuss the resulting implications for the noise performance of these multiplexers which will be used for the readout of two dimensional TES arrays in next generation instruments.

  1. Capacity limits of spatially multiplexed free-space communication

    NASA Astrophysics Data System (ADS)

    Zhao, Ningbo; Li, Xiaoying; Li, Guifang; Kahn, Joseph M.

    2015-12-01

    Increasing the information capacity per unit bandwidth has been a perennial goal of scientists and engineers. Multiplexing of independent degrees of freedom, such as wavelength, polarization and more recently space, has been a preferred method to increase capacity in both radiofrequency and optical communication. Orbital angular momentum, a physical property of electromagnetic waves discovered recently, has been proposed as a new degree of freedom for multiplexing to achieve capacity beyond conventional multiplexing techniques, and has generated widespread and significant interest in the scientific community. However, the capacity of orbital angular momentum multiplexing has not been established or compared to other multiplexing techniques. Here, we show that orbital angular momentum multiplexing is not an optimal technique for realizing the capacity limits of a free-space communication channel and is outperformed by both conventional line-of-sight multi-input multi-output transmission and spatial-mode multiplexing.

  2. Integrated assignment and path planning

    NASA Astrophysics Data System (ADS)

    Murphey, Robert A.

    2005-11-01

    A surge of interest in unmanned systems has exposed many new and challenging research problems across many fields of engineering and mathematics. These systems have the potential of transforming our society by replacing dangerous and dirty jobs with networks of moving machines. This vision is fundamentally separate from the modern view of robotics in that sophisticated behavior is realizable not by increasing individual vehicle complexity, but instead through collaborative teaming that relies on collective perception, abstraction, decision making, and manipulation. Obvious examples where collective robotics will make an impact include planetary exploration, space structure assembly, remote and undersea mining, hazardous material handling and clean-up, and search and rescue. Nonetheless, the phenomenon driving this technology trend is the increasing reliance of the US military on unmanned vehicles, specifically, aircraft. Only a few years ago, following years of resistance to the use of unmanned systems, the military and civilian leadership in the United States reversed itself and have recently demonstrated surprisingly broad acceptance of increasingly pervasive use of unmanned platforms in defense surveillance, and even attack. However, as rapidly as unmanned systems have gained acceptance, the defense research community has discovered the technical pitfalls that lie ahead, especially for operating collective groups of unmanned platforms. A great deal of talent and energy has been devoted to solving these technical problems, which tend to fall into two categories: resource allocation of vehicles to objectives, and path planning of vehicle trajectories. An extensive amount of research has been conducted in each direction, yet, surprisingly, very little work has considered the integrated problem of assignment and path planning. This dissertation presents a framework for studying integrated assignment and path planning and then moves on to suggest an exact

  3. SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.)

    PubMed Central

    2013-01-01

    Background Field pea (Pisum sativum L.) is a self-pollinating, diploid, cool-season food legume. Crop production is constrained by multiple biotic and abiotic stress factors, including salinity, that cause reduced growth and yield. Recent advances in genomics have permitted the development of low-cost high-throughput genotyping systems, allowing the construction of saturated genetic linkage maps for identification of quantitative trait loci (QTLs) associated with traits of interest. Genetic markers in close linkage with the relevant genomic regions may then be implemented in varietal improvement programs. Results In this study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and used to generate comprehensive linkage maps for field pea. From a set of 36,188 variant nucleotide positions detected through in silico analysis, 768 were selected for genotyping of a recombinant inbred line (RIL) population. A total of 705 SNPs (91.7%) successfully detected segregating polymorphisms. In addition to SNPs, genomic and EST-derived simple sequence repeats (SSRs) were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Sequences associated with the mapped molecular markers were used for comparative genomic analysis with other legume species. Higher levels of conserved synteny were observed with the genomes of Medicago truncatula Gaertn. and chickpea (Cicer arietinum L.) than with soybean (Glycine max [L.] Merr.), Lotus japonicus L. and pigeon pea (Cajanus cajan [L.] Millsp.). Parents and RIL progeny were screened at the seedling growth stage for responses to salinity stress, imposed by addition of NaCl in the watering solution at a concentration of 18 dS m-1. Salinity-induced symptoms showed normal distribution, and the severity of the symptoms increased over time. QTLs for salinity tolerance were identified on linkage groups Ps III and VII, with flanking SNP markers suitable for

  4. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

    PubMed

    Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh

    2016-01-20

    The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and

  5. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

    PubMed

    Colella, Stefano; Yau, Christopher; Taylor, Jennifer M; Mirza, Ghazala; Butler, Helen; Clouston, Penny; Bassett, Anne S; Seller, Anneke; Holmes, Christopher C; Ragoussis, Jiannis

    2007-01-01

    Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to disease susceptibility. We developed, and experimentally validated, a novel computational framework (QuantiSNP) for detecting regions of copy number variation from BeadArray SNP genotyping data using an Objective Bayes Hidden-Markov Model (OB-HMM). Objective Bayes measures are used to set certain hyperparameters in the priors using a novel re-sampling framework to calibrate the model to a fixed Type I (false positive) error rate. Other parameters are set via maximum marginal likelihood to prior training data of known structure. QuantiSNP provides probabilistic quantification of state classifications and significantly improves the accuracy of segmental aneuploidy identification and mapping, relative to existing analytical tools (Beadstudio, Illumina), as demonstrated by validation of breakpoint boundaries. QuantiSNP identified both novel and validated CNVs. QuantiSNP was developed using BeadArray SNP data but it can be adapted to other platforms and we believe that the OB-HMM framework has widespread applicability in genomic research. In conclusion, QuantiSNP is a novel algorithm for high-resolution CNV/aneuploidy detection with application to clinical genetics, cancer and disease association studies. PMID:17341461

  6. PCR amplification of SNP loci from crude DNA for large-scale genotyping of oomycetes.

    PubMed

    Hu, Jian; Lyon, Rebecca; Zhou, Yuxin; Lamour, Kurt

    2014-01-01

    Similar to other eukaryotes, single nucleotide polymorphism (SNP) markers are abundant in many oomycete plant pathogen genomes. High resolution DNA melting analysis (HR-DMA) is a cost-effective method for SNP genotyping, but like many SNP marker technologies, is limited by the amount and quality of template DNA. We describe PCR preamplification of Phytophthora and Peronospora SNP loci from crude DNA extracted from a small amount of mycelium and/or infected plant tissue to produce sufficient template to genotype at least 10 000 SNPs. The approach is fast, inexpensive, requires minimal biological material and should be useful for many organisms in a variety of contexts. PMID:24871597

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

    PubMed Central

    2010-01-01

    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 for young bulls

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

    PubMed

    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. PMID:24391119

  9. Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

    PubMed Central

    2012-01-01

    Background A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an alternative strategy must be used. We previously reported the development of a pipeline (AGSNP) for genome-wide SNP discovery in coding sequences and other single-copy DNA without a complete genome sequence in self-pollinating (autogamous) plants. Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.). Results The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-copy sequences in it. To identify single-copy sequences, multiple genome equivalents of short SOLiD reads of another individual were mapped to shallow genome coverage of long Sanger or Roche 454 reads making up the reference sequence. The relative depth of SOLiD reads was used to filter out repeated sequences from single-copy sequences in the reference sequence. The second step was a search for SNPs between SOLiD reads and the reference sequence. Polymorphism within the mapped SOLiD reads would have precluded SNP discovery; hence both individuals had to be homozygous. The AGSNP pipeline was updated here for using SOLiD or other type of short reads of a heterozygous individual for these two principal steps. A total of 32.6X walnut genome equivalents of SOLiD reads of vegetatively propagated walnut scion cultivar ‘Chandler’ were mapped to 48,661 ‘Chandler’ bacterial artificial chromosome (BAC) end sequences (BESs) produced by Sanger sequencing during the construction of a walnut physical map. A total of 22,799 putative SNPs were initially identified. A total of 6,000 Infinium II type SNPs evenly distributed along the walnut physical map were selected for the construction of an Infinium Bead

  10. An Investigation of the Partial-Assignment Completion Effect on Students' Assignment Choice Behavior

    ERIC Educational Resources Information Center

    Hawthorn-Embree, Meredith L.; Skinner, Christopher H.; Parkhurst, John; Conley, Elisha

    2011-01-01

    This study was designed to investigate the partial assignment completion effect. Seventh-grade students were given a math assignment. After working for 5 min, they were interrupted and their partially completed assignments were collected. About 20 min later, students were given their partially completed assignment and a new, control assignment…

  11. RNASEL and MIR146A SNP-SNP Interaction as a Susceptibility Factor for Non-Melanoma Skin Cancer

    PubMed Central

    Farzan, Shohreh F.; Karagas, Margaret R.; Christensen, Brock C.; Li, Zhongze; Kuriger, Jacquelyn K.; Nelson, Heather H.

    2014-01-01

    Immunity and inflammatory pathways are important in the genesis of non-melanoma skin cancers (NMSC). Functional genetic variation in immune modulators has the potential to affect disease etiology. We investigated associations between common variants in two key regulators, MIR146A and RNASEL, and their relation to NMSCs. Using a large population-based case-control study of basal cell (BCC) and squamous cell carcinoma (SCC), we investigated the impact of MIR146A SNP rs2910164 on cancer risk, and interaction with a SNP in one of its putative targets (RNASEL, rs486907). To examine associations between genotype and BCC and SCC, occurrence odds ratios (OR) and 95% confidence intervals (95%CI) were calculated using unconditional logistic regression, accounting for multiple confounding factors. We did not observe an overall change in the odds ratios for SCC or BCC among individuals carrying either of the RNASEL or MIR146A variants compared with those who were wild type at these loci. However, there was a sex-specific association between BCC and MIR146A in women (ORGC = 0.73, [95%CI = 0.52–1.03]; ORCC = 0.29, [95% CI = 0.14–0.61], p-trend<0.001), and a reduction in risk, albeit not statistically significant, associated with RNASEL and SCC in men (ORAG = 0.88, [95%CI = 0.65–1.19]; ORAA = 0.68, [95%CI = 0.43–1.08], p-trend = 0.10). Most striking was the strong interaction between the two genes. Among individuals carrying variant alleles of both rs2910164 and rs486907, we observed inverse relationships with SCC (ORSCC = 0.56, [95%CI = 0.38–0.81], p-interaction = 0.012) and BCC (ORBCC = 0.57, [95%CI = 0.40–0.80], p-interaction = 0.005). Our results suggest that genetic variation in immune and inflammatory regulators may influence susceptibility to NMSC, and novel SNP-SNP interaction for a microRNA and its target. These data suggest that RNASEL, an enzyme involved in RNA turnover, is controlled by miR-146a

  12. RNASEL and MIR146A SNP-SNP interaction as a susceptibility factor for non-melanoma skin cancer.

    PubMed

    Farzan, Shohreh F; Karagas, Margaret R; Christensen, Brock C; Li, Zhongze; Kuriger, Jacquelyn K; Nelson, Heather H

    2014-01-01

    Immunity and inflammatory pathways are important in the genesis of non-melanoma skin cancers (NMSC). Functional genetic variation in immune modulators has the potential to affect disease etiology. We investigated associations between common variants in two key regulators, MIR146A and RNASEL, and their relation to NMSCs. Using a large population-based case-control study of basal cell (BCC) and squamous cell carcinoma (SCC), we investigated the impact of MIR146A SNP rs2910164 on cancer risk, and interaction with a SNP in one of its putative targets (RNASEL, rs486907). To examine associations between genotype and BCC and SCC, occurrence odds ratios (OR) and 95% confidence intervals (95%CI) were calculated using unconditional logistic regression, accounting for multiple confounding factors. We did not observe an overall change in the odds ratios for SCC or BCC among individuals carrying either of the RNASEL or MIR146A variants compared with those who were wild type at these loci. However, there was a sex-specific association between BCC and MIR146A in women (ORGC = 0.73, [95%CI = 0.52-1.03]; ORCC = 0.29, [95% CI = 0.14-0.61], p-trend<0.001), and a reduction in risk, albeit not statistically significant, associated with RNASEL and SCC in men (ORAG = 0.88, [95%CI = 0.65-1.19]; ORAA = 0.68, [95%CI = 0.43-1.08], p-trend = 0.10). Most striking was the strong interaction between the two genes. Among individuals carrying variant alleles of both rs2910164 and rs486907, we observed inverse relationships with SCC (ORSCC = 0.56, [95%CI = 0.38-0.81], p-interaction = 0.012) and BCC (ORBCC = 0.57, [95%CI = 0.40-0.80], p-interaction = 0.005). Our results suggest that genetic variation in immune and inflammatory regulators may influence susceptibility to NMSC, and novel SNP-SNP interaction for a microRNA and its target. These data suggest that RNASEL, an enzyme involved in RNA turnover, is controlled by miR-146a and may be important in NMSC etiology. PMID:24699816

  13. SNP Markers and Their Impact on Plant Breeding

    PubMed Central

    Mammadov, Jafar; Aggarwal, Rajat; Buyyarapu, Ramesh; Kumpatla, Siva

    2012-01-01

    The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact. PMID:23316221

  14. Eigenanalysis of SNP data with an identity by descent interpretation.

    PubMed

    Zheng, Xiuwen; Weir, Bruce S

    2016-02-01

    Principal component analysis (PCA) is widely used in genome-wide association studies (GWAS), and the principal component axes often represent perpendicular gradients in geographic space. The explanation of PCA results is of major interest for geneticists to understand fundamental demographic parameters. Here, we provide an interpretation of PCA based on relatedness measures, which are described by the probability that sets of genes are identical-by-descent (IBD). An approximately linear transformation between ancestral proportions (AP) of individuals with multiple ancestries and their projections onto the principal components is found. In addition, a new method of eigenanalysis "EIGMIX" is proposed to estimate individual ancestries. EIGMIX is a method of moments with computational efficiency suitable for millions of SNP data, and it is not subject to the assumption of linkage equilibrium. With the assumptions of multiple ancestries and their surrogate ancestral samples, EIGMIX is able to infer ancestral proportions (APs) of individuals. The methods were applied to the SNP data from the HapMap Phase 3 project and the Human Genome Diversity Panel. The APs of individuals inferred by EIGMIX are consistent with the findings of the program ADMIXTURE. In conclusion, EIGMIX can be used to detect population structure and estimate genome-wide ancestral proportions with a relatively high accuracy. PMID:26482676

  15. Identification of Salmonella enterica Serovar Typhi Genotypes by Use of Rapid Multiplex Ligation-Dependent Probe Amplification

    PubMed Central

    Pham Thanh, Duy; Tran Vu Thieu, Nga; Tran Thuy, Chau; Lodén, Martin; Tuin, Kiki; Campbell, James I.; Van Minh Hoang, Nguyen; Voong Vinh, Phat; Farrar, Jeremy J.; Holt, Kathryn E.; Dougan, Gordon

    2013-01-01

    Salmonella enterica serovar Typhi, the causative agent of typhoid fever, is highly clonal and genetically conserved, making isolate subtyping difficult. We describe a standardized multiplex ligation-dependent probe amplification (MLPA) genotyping scheme targeting 11 key phylogenetic markers of the S. Typhi genome. The MLPA method demonstrated 90% concordance with single nucleotide polymorphism (SNP) typing, the gold standard for S. Typhi genotyping, and had the ability to identify isolates of the H58 haplotype, which is associated with resistance to multiple antimicrobials. Additionally, the assay permitted the detection of fluoroquinolone resistance-associated mutations in the DNA gyrase-encoding gene gyrA and the topoisomerase gene parC with a sensitivity of 100%. The MLPA methodology is simple and reliable, providing phylogenetically and phenotypically relevant genotyping information. This MLPA scheme offers a more-sensitive and interpretable alternative to the nonphylogenetic subgrouping methodologies that are currently used in reference and research laboratories in areas where typhoid is endemic. PMID:23824765

  16. [Multiplex mapping of human cDNAs]. Technical progress report

    SciTech Connect

    Nierman, W.C.

    1991-12-31

    J. Craig Venter, National Institute of Neurological Disorders and Stroke, has begun to identify genes expressed in the human brain by partially sequences cDNA clones. We are collaborating with the Venter group and using their sequence data to develop methods for rapid localization of newly identified cDNAs to human chromosomes. We are applying the ABI automated DNA sequencer to the analysis of fluorescently-tagged PCR products for assigning sequences to individual human chromosomes. The steps in our mapping protocol are (1) to design PCR primers from the Venter laboratory-generated sequence data, (2) to test the primers for specific amplification from human genomic DNA, (3) to use the primers for PCR amplification from a somatic cell hybrid cell mapping panel, (4) to determine the presence or absence of the specific amplification products from each cell line DNA by electrophoretic analysis using the ABI sequencer, and (5) to analyze the pattern of amplification results from the hybrid panel to identify the chromosomal origin of the cDNA sequence. We have demonstrated the principle by mapping 12 sequences or ``Expressed Sequence Tags`` (ESTs), providing primer sequence data for subsequent subchromosomal localizations. We will now concentrate on developing methodology to allow multiplexing the amplification reactions and analysis of the reaction products, to achieve a high throughput with a minimum allocation of resources. This project will generate a data set from which to evaluate strategies to identify functional primer sequences from cDNA sequence data.

  17. Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum.

    PubMed

    Fu, Yong-Bi; Dong, Yibo; Yang, Mo-Hua

    2016-08-01

    A genome-wide detection of phylogenetic signals by next generation sequencing (NGS) has recently emerged as a promising genomic approach for phylogenetic analysis of non-model organisms. Here we explored the use of a multiplexed shotgun sequencing method to assess the phylogenetic relationships of 18 Linum samples representing 16 species within four botanical sections of the flax genus Linum. The whole genome DNAs of 18 Linum samples were fragmented, tagged, and sequenced using an Illumina MiSeq. Acquired sequencing reads per sample were further separated into chloroplast, mitochondrial and nuclear sequence reads. SNP calls upon genome-specific sequence data sets revealed 6143 chloroplast, 2673 mitochondrial, and 19,562 nuclear SNPs. Phylogenetic analyses based on three-genome SNP data sets with and without missing observations showed congruent three-genome phylogenetic signals for four botanical sections of the Linum genus. Specifically, two major lineages showing a separation of Linum-Dasylinum sections and Linastrum-Syllinum sections were confirmed. The Linum section displayed three major branches representing two major evolutionary stages leading to cultivated flax. Cultivated flax and its immediate progenitor were formed as its own branch, genetically more closely related to L. decumbens and L. grandiflorum with chromosome count of eight, and distantly apart from six other species with chromosome count of nine. Five species of the Linastrum and Syllinum sections were genetically more distant from cultivated flax, but they appeared to be more closely related to each other, even with variable chromosome counts. These findings not only provide the first evidence of congruent three-genome phylogenetic pathways within the Linum genus, but also demonstrate the utility of the multiplexed shotgun sequencing in acquisition of three-genome phylogenetic signals of non-model organisms. PMID:27165939

  18. Time slot assignment in TDM multicast switching systems

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Tsuen; Sheu, Pi-Rong; Yu, Jiunn-Hwa

    1994-01-01

    The time slot assignment problem in time-division multiplexed switching systems which can support multicast transmissions is studied. It is shown that this problem is NP-complete, i.e., computationally intractable. Two effective heuristic algorithms are proposed, and computer simulations are also performed to evaluate the performance of both algorithms. The results of the simulations indicate that the solutions generated by these heuristic algorithms are very close to the optimal on the average. In addition, this problem is also examined under a more restrictive condition that the destination sets of any two multicast packets are either identical or disjoint, a situation often encountered in many practical applications. It is proved that this special problem is still NP-complete. Two fast heuristic algorithms are given which can find solutions not greater than twice the optimal solution. Computer simulations for evaluating these two heuristic algorithms are also performed. Experimental results demonstrate that the solutions of the two algorithms are almost equal to the optimal.

  19. Integrated mode converter for mode division multiplexing

    NASA Astrophysics Data System (ADS)

    Perez-Galacho, Diego; Alonso-Ramos, Carlos Alberto; Marris-Morini, Delphine; Vakarin, Vladyslav; Le Roux, Xavier; Ortega-Moñux, Alejandro; Wangüemert-Perez, Juan Gonzalo; Vivien, Laurent

    2016-05-01

    The ever growing demands of bandwidth in optical communication systems are making traditional Wavelength Division Multiplexing (WDM) based systems to reach its limit. In order to cope with future bandwidth demand is necessary to use new levels of orthogonality, such as the waveguide mode or the polarization state. Mode Division Multiplexing (MDM) has recently attracted attention as a possible solution to increase aggregate bandwidth. In this work we discuss the proposition a of mode converter that can cover the whole C-Band of optical communications. The Mode Converter is based on two Multimode Interference (MMI) couplers and a phase shifter. Insertion loss (IL) below 0.2 dB and Extinction ratio (ER) higher than 20 dB in a broad bandwidth range of 1.5 μm to 1.6 μm have been estimated. The total length of the device is less than 30 μm.

  20. Tunable lifetime multiplexing using luminescent nanocrystals

    NASA Astrophysics Data System (ADS)

    Lu, Yiqing; Zhao, Jiangbo; Zhang, Run; Liu, Yujia; Liu, Deming; Goldys, Ewa M.; Yang, Xusan; Xi, Peng; Sunna, Anwar; Lu, Jie; Shi, Yu; Leif, Robert C.; Huo, Yujing; Shen, Jian; Piper, James A.; Robinson, J. Paul; Jin, Dayong

    2014-01-01

    Optical multiplexing plays an important role in applications such as optical data storage, document security, molecular probes and bead assays for personalized medicine. Conventional fluorescent colour coding is limited by spectral overlap and background interference, restricting the number of distinguishable identities. Here, we show that tunable luminescent lifetimes τ in the microsecond region can be exploited to code individual upconversion nanocrystals. In a single colour band, one can generate more than ten nanocrystal populations with distinct lifetimes ranging from 25.6 µs to 662.4 µs and decode their well-separated lifetime identities, which are independent of both colour and intensity. Such `τ-dots' potentially suit multichannel bioimaging, high-throughput cytometry quantification, high-density data storage, as well as security codes to combat counterfeiting. This demonstration extends the optical multiplexing capability by adding the temporal dimension of luminescent signals, opening new opportunities in the life sciences, medicine and data security.

  1. Spin and wavelength multiplexed nonlinear metasurface holography

    PubMed Central

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-01-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam–Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption. PMID:27306147

  2. Multiplexed Energy Coupler for Rotating Equipment

    NASA Technical Reports Server (NTRS)

    Zhao, Xiaoliang

    2011-01-01

    A multiplexing antenna assembly can efficiently couple AC signal/energy into, or out of, rotating equipment. The unit only passes AC energy while blocking DC energy. Concentric tubes that are sliced into multiple pieces are assembled together so that, when a piece from an outer tube aligns well with an inner tube piece, efficient energy coupling is achieved through a capacitive scheme. With N outer pieces and M inner pieces, an effective N x M combination can be achieved in a multiplexed manner. The energy coupler is non-contact, which is useful if isolation from rotating and stationary parts is required. Additionally, the innovation can operate in high temperatures. Applications include rotating structure sensing, non-contact energy transmission, etc.

  3. Optimal estimator for tomographic fluorescence lifetime multiplexing

    PubMed Central

    Hou, Steven S.; Bacskai, Brian J.; Kumar, Anand T. N.

    2016-01-01

    We use the model resolution matrix to analytically derive an optimal Bayesian estimator for multiparameter inverse problems that simultaneously minimizes inter-parameter cross talk and the total reconstruction error. Application of this estimator to time-domain diffuse fluorescence imaging shows that the optimal estimator for lifetime multiplexing is identical to a previously developed asymptotic time-domain (ATD) approach, except for the inclusion of a diagonal regularization term containing decay amplitude uncertainties. We show that, while the optimal estimator and ATD provide zero cross talk, the optimal estimator provides lower reconstruction error, while ATD results in superior relative quantitation. The framework presented here is generally applicable to other multiplexing problems where the simultaneous and accurate relative quantitation of multiple parameters is of interest. PMID:27192234

  4. Dual phase multiplex polymerase chain reaction

    DOEpatents

    Pemov, Alexander; Bavykin, Sergei

    2008-10-07

    Highly specific and sensitive methods were developed for multiplex amplification of nucleic acids on supports such as microarrays. Based on a specific primer design, methods include five types of amplification that proceed in a reaction chamber simultaneously. These relate to four types of multiplex amplification of a target DNA on a solid support, directed by forward and reverse complex primers immobilized to the support and a fifth type--pseudo-monoplex polymerase chain reaction (PCR) of multiple targets in solution, directed by a single pair of unbound universal primers. The addition of the universal primers in the reaction mixture increases the yield over the traditional "bridge" amplification on a solid support by approximately ten times. Methods that provide multitarget amplification and detection of as little as 0.45-4.5.times.10.sup.-12 g (equivalent to 10.sup.2-10.sup.3 genomes) of a bacterial genomic DNA are disclosed.

  5. Spin and wavelength multiplexed nonlinear metasurface holography

    NASA Astrophysics Data System (ADS)

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-06-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam-Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption.

  6. Spin and wavelength multiplexed nonlinear metasurface holography.

    PubMed

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-01-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam-Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption. PMID:27306147

  7. Multiplexing Short Primers for Viral Family PCR

    SciTech Connect

    Gardner, S N; Hiddessen, A L; Hara, C A; Williams, P L; Wagner, M; Colston, B W

    2008-06-26

    We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets for large, diverse, and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ({approx}3700 18-mers or {approx}2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus, hemagglutinin and neuraminidase segments of influenza A virus, Norwalk virus, and HIV-1.

  8. Optimal distributions for multiplex logistic networks.

    PubMed

    Solá Conde, Luis E; Used, Javier; Romance, Miguel

    2016-06-01

    This paper presents some mathematical models for distribution of goods in logistic networks based on spectral analysis of complex networks. Given a steady distribution of a finished product, some numerical algorithms are presented for computing the weights in a multiplex logistic network that reach the equilibrium dynamics with high convergence rate. As an application, the logistic networks of Germany and Spain are analyzed in terms of their convergence rates. PMID:27368801

  9. Physicians' Attitudes About Multiplex Tumor Genomic Testing

    PubMed Central

    Gray, Stacy W.; Hicks-Courant, Katherine; Cronin, Angel; Rollins, Barrett J.; Weeks, Jane C.

    2014-01-01

    Purpose Although predictive multiplex somatic genomic tests hold the potential to transform care by identifying targetable alterations in multiple cancer genes, little is known about how physicians will use such tests in practice. Participants and Methods Before the initiation of enterprise-wide multiplex testing at a major cancer center, we surveyed all clinically active adult cancer physicians to assess their current use of somatic testing, their attitudes about multiplex testing, and their genomic confidence. Results A total of 160 physicians participated (response rate, 61%): 57% were medical oncologists; 29%, surgeons; 14% radiation oncologists; 37%, women; and 83%, research principal investigators. Twenty-two percent of physicians reported low confidence in their genomic knowledge. Eighteen percent of physicians anticipated testing patients infrequently (≤ 10%), whereas 25% anticipate testing most patients (≥ 90%). Higher genomic confidence was associated with wanting to test a majority of patients (adjusted odds ratio [OR], 6.09; 95% CI, 2.1 to 17.5) and anticipating using actionable (adjusted OR, 2.46; 95% CI, 1.2 to 5.2) or potentially actionable (adjusted OR, 2.89; 95% CI, 1.1 to 7.9) test results to inform treatment recommendations. Forty-two percent of physicians endorsed disclosure of uncertain genomic findings to patients. Conclusion Physicians at a tertiary-care National Cancer Institute–designated comprehensive cancer center varied considerably in how they planned to incorporate predictive multiplex somatic genomic tests into practice and in their attitudes about the disclosure of genomic information of uncertain significance. Given that many physicians reported low genomic confidence, evidence-based guidelines and enhanced physician genomic education efforts may be needed to ensure that genomically guided cancer care is adequately delivered. PMID:24663044

  10. Space division multiplexing in access networks

    NASA Astrophysics Data System (ADS)

    Effenberger, Frank J.

    2015-01-01

    Space division multiplexing (SDM) has received a lot of attention in the past years, as it is seen as the final frontier of fiber optic capacity improvement for long haul transmission. Its use in access networks is even more interesting, due to the different design optimization goals in access versus transport. This paper explores some of the applications of SDM in access that have the potential for early adoption.

  11. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, Edward S.; Taylor, John A.

    1994-06-28

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

  12. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, Edward S.; Taylor, John A.

    1996-03-12

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

  13. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, E.S.; Taylor, J.A.

    1994-06-28

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figures.

  14. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, E.S.; Taylor, J.A.

    1996-03-12

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figs.

  15. Selecting optimal oligonucleotide primers for multiplex PCR.

    PubMed

    Nicodème, P; Steyaert, J M

    1997-01-01

    We investigate the problem of designing efficient multiplex PCR for medical applications. We show that the problem is NP-complete by transformation to the Multiple Choice Matching problem and give an efficient approximation algorithm. We developed this algorithm in a computer program that predicts which genomic regions may be simultaneously amplified by PCR. Practical use of the software shows that the method can treat 250 non-polymorphic loci with less than 5 simultaneous experiments. PMID:9322038

  16. Broadband Hybrid Holographic Multiplexing with Geometric Metasurfaces.

    PubMed

    Huang, Lingling; Mühlenbernd, Holger; Li, Xiaowei; Song, Xu; Bai, Benfeng; Wang, Yongtian; Zentgraf, Thomas

    2015-11-01

    An effective way for broadband holographic multiplexing based on geometric metasurfaces is demonstrated by the integration of several recording channels into a single device. Each image can be individually addressed with a unique set of parameters, such as circular polarization, position, and angle. Such a technique paves the way for a wide range of applications related to optical patterning, encryption, and information processing. PMID:26398589

  17. Microgels for multiplex and direct fluorescence detection

    NASA Astrophysics Data System (ADS)

    Causa, Filippo; Aliberti, Anna; Cusano, Angela M.; Battista, Edmondo; Netti, Paolo A.

    2015-05-01

    Blood borne oligonucleotides fragments contain useful clinical information whose detection and monitoring represent the new frontier in liquid biopsy as they can transform the current diagnosis procedure. For instance, recent studies have identified a new class of circulating biomarkers such as s miRNAs, and demonstrated that changes in their concentration are closely associated with the development of cancer and other pathologies. However, direct detection of miRNAs in body fluids is particularly challenging and demands high sensitivity -concentration range between atto to femtomolarspecificity, and multiplexing Here we report on engineered multifunctional microgels and innovative probe design for a direct and multiplex detection of relevant clinical miRNAs in fluorescence by single particle assay. Polyethyleneglycol-based microgels have a coreshell architecture with two spectrally encoded fluorescent dyes for multiplex analyses and are endowed with fluorescent probes for miRNA detection. Encoding and detection fluorescence signals are distinguishable by not overlapping emission spectra. Tuneable fluorescence probe conjugation and corresponding emission confinement on single microgel allows for enhanced target detection. Such suspension array has indeed high selectivity and sensitivity with a detection limit of 10-15 M and a dynamic range from 10-9 to 10-15 M. We believe that sensitivity in the fM concentration range, signal background minimization, multiplexed capability and direct measurement of such microgels will translate into diagnostic benefits opening up new roots toward liquid biopsy in the context of point-of-care testing through an easy and fast detection of sensitive diagnostic biomarkers directly in serum.

  18. Wireless Multiplexed Surface Acoustic Wave Sensors Project

    NASA Technical Reports Server (NTRS)

    Youngquist, Robert C.

    2014-01-01

    Wireless Surface Acoustic Wave (SAW) Sensor is a new technology for obtaining multiple, real-time measurements under extreme environmental conditions. This project plans to develop a wireless multiplexed sensor system that uses SAW sensors, with no batteries or semiconductors, that are passive and rugged, can operate down to cryogenic temperatures and up to hundreds of degrees C, and can be used to sense a wide variety of parameters over reasonable distances (meters).

  19. Optimal distributions for multiplex logistic networks

    NASA Astrophysics Data System (ADS)

    Solá Conde, Luis E.; Used, Javier; Romance, Miguel

    2016-06-01

    This paper presents some mathematical models for distribution of goods in logistic networks based on spectral analysis of complex networks. Given a steady distribution of a finished product, some numerical algorithms are presented for computing the weights in a multiplex logistic network that reach the equilibrium dynamics with high convergence rate. As an application, the logistic networks of Germany and Spain are analyzed in terms of their convergence rates.

  20. Emergence of Multiplex Communities in Collaboration Networks

    PubMed Central

    Nicosia, Vincenzo; Bianconi, Ginestra; Latora, Vito

    2016-01-01

    Community structures in collaboration networks reflect the natural tendency of individuals to organize their work in groups in order to better achieve common goals. In most of the cases, individuals exploit their connections to introduce themselves to new areas of interests, giving rise to multifaceted collaborations which span different fields. In this paper, we analyse collaborations in science and among movie actors as multiplex networks, where the layers represent respectively research topics and movie genres, and we show that communities indeed coexist and overlap at the different layers of such systems. We then propose a model to grow multiplex networks based on two mechanisms of intra and inter-layer triadic closure which mimic the real processes by which collaborations evolve. We show that our model is able to explain the multiplex community structure observed empirically, and we infer the strength of the two underlying social mechanisms from real-world systems. Being also able to correctly reproduce the values of intra-layer and inter-layer assortativity correlations, the model contributes to a better understanding of the principles driving the evolution of social networks. PMID:26815700

  1. Emergence of Multiplex Communities in Collaboration Networks.

    PubMed

    Battiston, Federico; Iacovacci, Jacopo; Nicosia, Vincenzo; Bianconi, Ginestra; Latora, Vito

    2016-01-01

    Community structures in collaboration networks reflect the natural tendency of individuals to organize their work in groups in order to better achieve common goals. In most of the cases, individuals exploit their connections to introduce themselves to new areas of interests, giving rise to multifaceted collaborations which span different fields. In this paper, we analyse collaborations in science and among movie actors as multiplex networks, where the layers represent respectively research topics and movie genres, and we show that communities indeed coexist and overlap at the different layers of such systems. We then propose a model to grow multiplex networks based on two mechanisms of intra and inter-layer triadic closure which mimic the real processes by which collaborations evolve. We show that our model is able to explain the multiplex community structure observed empirically, and we infer the strength of the two underlying social mechanisms from real-world systems. Being also able to correctly reproduce the values of intra-layer and inter-layer assortativity correlations, the model contributes to a better understanding of the principles driving the evolution of social networks. PMID:26815700

  2. Multiplex congruence network of natural numbers

    NASA Astrophysics Data System (ADS)

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-03-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations.

  3. Multiplexed Holographic Data Storage in Bacteriorhodopsin

    NASA Technical Reports Server (NTRS)

    Mehrl, David J.; Krile, Thomas F.

    1997-01-01

    High density optical data storage, driven by the information revolution, remains at the forefront of current research areas. Much of the current research has focused on photorefractive materials (SBN and LiNbO3) and polymers, despite various problems with expense, durability, response time and retention periods. Photon echo techniques, though promising, are questionable due to the need for cryogenic conditions. Bacteriorhodopsin (BR) films are an attractive alternative recording medium. Great strides have been made in refining BR, and materials with storage lifetimes as long as 100 days have recently become available. The ability to deposit this robust polycrystalline material as high quality optical films suggests the use of BR as a recording medium for commercial optical disks. Our own recent research has demonstrated the suitability of BR films for real time spatial filtering and holography. We propose to fully investigate the feasibility of performing holographic mass data storage in BR. Important aspects of the problem to be investigated include various data multiplexing techniques (e.g. angle- amplitude- and phase-encoded multiplexing, and in particular shift-multiplexing), multilayer recording techniques, SLM selection and data readout using crossed polarizers for noise rejection. Systems evaluations of storage parameters, including access times, memory refresh constraints, erasure, signal-to-noise ratios and bit error rates, will be included in our investigations.

  4. Emergence of Chimera in Multiplex Network

    NASA Astrophysics Data System (ADS)

    Ghosh, Saptarshi; Jalan, Sarika

    2016-06-01

    Chimera is a relatively new emerging phenomenon where coexistence of synchronous and asynchronous states is observed in symmetrically coupled dynamical units. We report the observation of the chimera state in multiplex networks where individual layer is represented by 1-d lattice with nonlocal interactions. While, multiplexing does not change the type of the chimera state and retains the multi-chimera state displayed by the isolated networks, it changes the regions of the incoherence. We investigate the emergence of coherent-incoherent bifurcation upon varying the control parameters, namely, the coupling strength and the network size. Additionally, we investigate the effect of initial condition on the dynamics of the chimera state. Using a measure based on the differences between the neighboring nodes which distinguishes smooth and nonsmooth spatial profiles, we find the critical coupling strength for the transition to the chimera state. Observing chimera in a multiplex network with one-to-one inter layer coupling is important to gain insight to many real world complex systems which inherently posses multilayer architecture.

  5. Multiplex congruence network of natural numbers.

    PubMed

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-01-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations. PMID:27029650

  6. Multiplex congruence network of natural numbers

    PubMed Central

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-01-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations. PMID:27029650

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

    PubMed Central

    2010-01-01

    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 package that links SNPs to

  8. SNP Discovery for mapping alien introgressions in wheat

    PubMed Central

    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

  9. Time division multiplexed orbital angular momentum access system

    NASA Astrophysics Data System (ADS)

    Shi, Jianyang; Fang, Yuan; Chi, Nan

    2016-03-01

    We propose and experimentally demonstrate time division multiplexed orbital angular momentum (OAM) access system to increase transmission capacity and spectral efficiency. In this system, data carried on different time tributaries share the same OAM mode. Multiple time division multiplexed OAM modes are multiplexed to realize two-dimensional (time dimension and OAM dimension) multiplexing. Therefore, the capacity and spectral efficiency of the access system will increase. The orthogonality between optical time division multiplexing (OTDM) and OAM techniques is also verified in our experiment. In a proof-of-concept experiment, 2×5-Gbps return-to-zero signal over OAM mode +4 is transmitted and investigated. The bit error ratio performance after transmission in this system can be smaller than 1×10-9. Results show that the proposed time division multiplexed OAM access system is suitable for future broadband access network.

  10. Multiplex PCR for rapid diagnosis of tuberculous meningitis.

    PubMed

    Kusum, Sharma; Aman, Sharma; Pallab, Ray; Kumar, Sharma Shiv; Manish, Modi; Sudesh, Prabhakar; Subhash, Varma; Meera, Sharma

    2011-10-01

    Rapid and specific diagnosis of tubercular meningitis is of paramount importance to decrease morbidity and mortality. The aim of the study was to evaluate multiplex PCR using protein b, MPB 64, and IS6110 primers directed against M. tuberculosis complex for the diagnosis of tuberculous meningitis (TBM). Multiplex PCR was performed on 18 TBM confirmed cases (culture was positive), 92 clinically suspected TBM cases and 100 non-TBM (control group) patients. Multiplex PCR had a sensitivity of 94.4% for confirmed cases and specificity of 100% for confirmed TBM cases. In 92 clinically diagnosed but unconfirmed TBM cases, multiplex PCR was positive in 84.78% cases. The overall sensitivity of microscopy, culture and multiplex cases were 1.81, 16.73, and 86.63% and specificity was 100, 100, and 100% respectively. Multiplex PCR using protein b, MPB 64, and IS6110 primers has a high sensitivity and specificity in diagnosis of tubercular meningitis. PMID:21455603

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

    PubMed Central

    2014-01-01

    Background 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. Methods 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). Results 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. Conclusions This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion. PMID:24955105

  12. Demonstration of hybrid orbital angular momentum multiplexing and time-division multiplexing passive optical network.

    PubMed

    Wang, Andong; Zhu, Long; Liu, Jun; Du, Cheng; Mo, Qi; Wang, Jian

    2015-11-16

    Mode-division multiplexing passive optical network (MDM-PON) is a promising scheme for next-generation access networks to further increase fiber transmission capacity. In this paper, we demonstrate the proof-of-concept experiment of hybrid mode-division multiplexing (MDM) and time-division multiplexing (TDM) PON architecture by exploiting orbital angular momentum (OAM) modes. Bidirectional transmissions with 2.5-Gbaud 4-level pulse amplitude modulation (PAM-4) downstream and 2-Gbaud on-off keying (OOK) upstream are demonstrated in the experiment. The observed optical signal-to-noise ratio (OSNR) penalties for downstream and upstream transmissions at a bit-error rate (BER) of 2 × 10(-3) are less than 2.0 dB and 3.0 dB, respectively. PMID:26698429

  13. A new SNP panel for evaluating genetic diversity in a composite cattle breed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A custom 60K SNP panel, extracted from Bovine HD SNP chip was used to evaluate genotypic frequency changes in Braford (BF, a composite breed) when compared to progenitor breeds: Hereford (HF), Brahman (BR), and Nelore (NE). Samples from both the U. S. and Brazil were used. The new panel differentiat...

  14. A Coordinated Approach to Peach SNP Discovery in RosBREED

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the USDA-funded multi-institutional and trans-disciplinary project, “RosBREED”, crop-specific SNP genome scan platforms are being developed for peach, apple, strawberry, and cherry at a resolution of at least one polymorphic SNP marker every 5 cM in any random cross, for use in Pedigree-Based Ana...

  15. A genome-wide SNP panel for genetic diversity, mapping and breeding studies in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genome-wide SNP resource was developed for rice using the GoldenGate assay and used to genotype 400 landrace accessions of O. sativa. SNPs were originally discovered using Perlegen re-sequencing technology in 20 diverse landraces of O. sativa as part of OryzaSNP project (http://irfgc.irri.org). An...

  16. Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A Bovine 50K Illumina™ iSelect SNP chip (51,386 polymorphic SNP markers) was designed using a combination of publicly available SNPs along with highly informative novel SNPs discovered using a reduced representation and next-generation sequencing technology strategy. A total of 576 animals (426 mal...

  17. Strategies to build high-density linkage maps of the porcine 60k SNP chip

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present here two different strategies to compute high-density linkage maps based on the porcine 60k SNP chip that was genotyped on 4 different pedigrees with a total of 5600 animals. The first strategy uses the draft sequence as a reference order, the SNP being first mapped to it. The second stra...

  18. Development and Applications of a Bovine 50,000 SNP Chip

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To develop an Illumina iSelect high density single nucleotide polymorphism (SNP) assay for cattle, the collaborative iBMC (Illumina, USDA ARS Beltsville, University of Missouri, USDA ARS Clay Center) Consortium first performed a de novo SNP discovery project in which genomic reduced representation l...

  19. The development and characterization of a 60K SNP chip for chicken

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In livestock species like the chicken, high throughput SNP genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). We describe the design of a moderate density (60K) Illumina SNP BeadChip in chicken consisting o...

  20. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome projects routinely produce draft sequences for species from diverse evolutionary clades, but generally do not create single nucleotide polymorphism (SNP) resources. We present an approach for de novo SNP discovery based on short-read sequencing of reduced representation libraries (RRL) to ge...

  1. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales.

    PubMed

    Smith, Matt J; Pascal, Carita E; Grauvogel, Zac; Habicht, Christopher; Seeb, James E; Seeb, Lisa W

    2011-03-01

    Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA. PMID:21429180

  2. SNP-VISTA: An Interactive SNPs Visualization Tool

    SciTech Connect

    Shah, Nameeta; Teplitsky, Michael V.; Pennacchio, Len A.; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L.

    2005-07-05

    Recent advances in sequencing technologies promise better diagnostics for many diseases as well as better understanding of evolution of microbial populations. Single Nucleotide Polymorphisms(SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it is possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease and then screen for causative mutations.In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples makes possible more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista.

  3. SNP and haplotype mapping for genetic analysis in the rat.

    PubMed

    Saar, Kathrin; Beck, Alfred; Bihoreau, Marie-Thérèse; Birney, Ewan; Brocklebank, Denise; Chen, Yuan; Cuppen, Edwin; Demonchy, Stephanie; Dopazo, Joaquin; Flicek, Paul; Foglio, Mario; Fujiyama, Asao; Gut, Ivo G; Gauguier, Dominique; Guigo, Roderic; Guryev, Victor; Heinig, Matthias; Hummel, Oliver; Jahn, Niels; Klages, Sven; Kren, Vladimir; Kube, Michael; Kuhl, Heiner; Kuramoto, Takashi; Kuroki, Yoko; Lechner, Doris; Lee, Young-Ae; Lopez-Bigas, Nuria; Lathrop, G Mark; Mashimo, Tomoji; Medina, Ignacio; Mott, Richard; Patone, Giannino; Perrier-Cornet, Jeanne-Antide; Platzer, Matthias; Pravenec, Michal; Reinhardt, Richard; Sakaki, Yoshiyuki; Schilhabel, Markus; Schulz, Herbert; Serikawa, Tadao; Shikhagaie, Medya; Tatsumoto, Shouji; Taudien, Stefan; Toyoda, Atsushi; Voigt, Birger; Zelenika, Diana; Zimdahl, Heike; Hubner, Norbert

    2008-05-01

    The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies. PMID:18443594

  4. TcSNP: a database of genetic variation in Trypanosoma cruzi

    PubMed Central

    Ackermann, Alejandro A.; Carmona, Santiago J.; Agüero, Fernán

    2009-01-01

    The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms and mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas disease. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs and genomic sequences); multiple sequence alignments obtained from these sequences; and single-nucleotide polymorphisms and small indels identified by scanning these multiple sequence alignments. Information in TcSNP can be readily interrogated to arrive at gene sets, or SNP sets of interest based on a number of attributes. Sequence similarity searches using BLAST are also supported. This first release of TcSNP contains nearly 170 000 high-confidence candidate SNPs, derived from the analysis of annotated coding sequences. As new sequence data become available, TcSNP will incorporate these data, mapping new candidate SNPs onto the reference genome sequences. PMID:18974180

  5. Genotyping NAT2 with only two SNPs (rs1041983 and rs1801280) outperforms the tagging SNP rs1495741 and is equivalent to the conventional 7-SNP NAT2 genotype.

    PubMed

    Selinski, Silvia; Blaszkewicz, Meinolf; Lehmann, Marie-Louise; Ovsiannikov, Daniel; Moormann, Oliver; Guballa, Christoph; Kress, Alexander; Truss, Michael C; Gerullis, Holger; Otto, Thomas; Barski, Dimitri; Niegisch, Günter; Albers, Peter; Frees, Sebastian; Brenner, Walburgis; Thüroff, Joachim W; Angeli-Greaves, Miriam; Seidel, Thilo; Roth, Gerhard; Dietrich, Holger; Ebbinghaus, Rainer; Prager, Hans M; Bolt, Hermann M; Falkenstein, Michael; Zimmermann, Anna; Klein, Torsten; Reckwitz, Thomas; Roemer, Hermann C; Löhlein, Dietrich; Weistenhöfer, Wobbeke; Schöps, Wolfgang; Hassan Rizvi, Syed Adibul; Aslam, Muhammad; Bánfi, Gergely; Romics, Imre; Steffens, Michael; Ekici, Arif B; Winterpacht, Andreas; Ickstadt, Katja; Schwender, Holger; Hengstler, Jan G; Golka, Klaus

    2011-10-01

    Genotyping N-acetyltransferase 2 (NAT2) is of high relevance for individualized dosing of antituberculosis drugs and bladder cancer epidemiology. In this study we compared a recently published tagging single nucleotide polymorphism (SNP) (rs1495741) to the conventional 7-SNP genotype (G191A, C282T, T341C, C481T, G590A, A803G and G857A haplotype pairs) and systematically analysed if novel SNP combinations outperform the latter. For this purpose, we studied 3177 individuals by PCR and phenotyped 344 individuals by the caffeine test. Although the tagSNP and the 7-SNP genotype showed a high degree of correlation (R=0.933, P<0.0001) the 7-SNP genotype nevertheless outperformed the tagging SNP with respect to specificity (1.0 vs. 0.9444, P=0.0065). Considering all possible SNP combinations in a receiver operating characteristic analysis we identified a 2-SNP genotype (C282T, T341C) that outperformed the tagging SNP and was equivalent to the 7-SNP genotype. The 2-SNP genotype predicted the correct phenotype with a sensitivity of 0.8643 and a specificity of 1.0. In addition, it predicted the 7-SNP genotype with sensitivity and specificity of 0.9993 and 0.9880, respectively. The prediction of the NAT2 genotype by the 2-SNP genotype performed similar in populations of Caucasian, Venezuelan and Pakistani background. A 2-SNP genotype predicts NAT2 phenotypes with similar sensitivity and specificity as the conventional 7-SNP genotype. This procedure represents a facilitation in individualized dosing of NAT2 substrates without losing sensitivity or specificity. PMID:21750470

  6. Communicability reveals a transition to coordinated behavior in multiplex networks

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Gómez-Gardeñes, Jesús

    2014-04-01

    We analyze the flow of information in multiplex networks by means of the communicability function. First, we generalize this measure from its definition from simple graphs to multiplex networks. Then, we study its relevance for the analysis of real-world systems by studying a social multiplex where information flows using formal-informal channels and an air transportation system where the layers represent different air companies. Accordingly, the communicability, which is essential for the good performance of these complex systems, emerges at a systemic operation point in the multiplex where the performance of the layers operates in a coordinated way very differently from the state represented by a collection of unconnected networks.

  7. Diffraction model of peristrophic multiplexing with spherical reference wave.

    PubMed

    Yoshida, Shuhei; Takahata, Yosuke; Horiuchi, Shuma; Yamamoto, Manabu

    2015-02-01

    Multiplexing recording is a primary contributor to determining the recording density in holographic data storage. Therefore, many different kinds of recording methods have been proposed. Among them, the method that utilizes spherical waves as reference waves is characterized by the ability to enable multiplexing recording only by moving (shifting or rotating) the recording medium. In our research, we propose a theoretical diffraction model of peristrophic multiplexing with a spherical reference wave and evaluate the diffraction efficiency; this multiplexing recording method has incorporated spherical reference waves in rotation of the media. Additionally, we verify the effectiveness of the model by comparing it with experimental results. PMID:26366593

  8. Shift-peristrophic multiplexing for holographic data storage

    NASA Astrophysics Data System (ADS)

    Kurata, Hiroyuki; Mori, Jun; Tsukamoto, Yu; Yamamoto, Keiko; Yoshida, Shuhei; Yamamoto, Manabu

    2014-09-01

    Holographic data storage (HDS) is a promising technology that has huge capacity. A multiplexing method plays a significant role in increasing the data capacity. Various multiplexing methods have been researched so far. In this paper, we proposed shift-peristrophic multiplexing using spherical reference wave and experimentally verified that this method is efficiently increase the data capacity. A series of holograms was recorded with shift multiplexing and rotating recording material with the axis of rotation being perpendicular to the material's surface. This method can realize more than 1 Tbits/inch2 data density recording. Furthermore if we maximize the performance of a recording medium, several TB per disk capacity would be available.

  9. Multiplex PCR Tests for Detection of Pathogens Associated with Gastroenteritis

    PubMed Central

    Zhang, Hongwei; Morrison, Scott; Tang, Yi-Wei

    2016-01-01

    Synopsis A wide range of enteric pathogens can cause infectious gastroenteritis. Conventional diagnostic algorithms including culture, biochemical identification, immunoassay and microscopic examination are time consuming and often lack sensitivity and specificity. Advances in molecular technology have as allowed its use as clinical diagnostic tools. Multiplex PCR based testing has made its way to gastroenterology diagnostic arena in recent years. In this article we present a review of recent laboratory developed multiplex PCR tests and current commercial multiplex gastrointestinal pathogen tests. We will focus on two FDA cleared commercial syndromic multiplex tests: Luminex xTAG GPP and Biofire FimArray GI test. These multiplex tests can detect and identify multiple enteric pathogens in one test and provide results within hours. Multiplex PCR tests have shown superior sensitivity to conventional methods for detection of most pathogens. The high negative predictive value of these multiplex tests has led to the suggestion that they be used as screening tools especially in outbreaks. Although the clinical utility and benefit of multiplex PCR test are to be further investigated, implementing these multiplex PCR tests in gastroenterology diagnostic algorithm has the potential to improve diagnosis of infectious gastroenteritis. PMID:26004652

  10. Design and Characterization of a 52K SNP Chip for Goats

    PubMed Central

    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. PMID:24465974

  11. 25 CFR 214.18 - Assignments.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Assignments. 214.18 Section 214.18 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF OSAGE RESERVATION LANDS, OKLAHOMA, FOR MINING, EXCEPT OIL AND GAS § 214.18 Assignments. Approved leases or any interest therein...

  12. 25 CFR 214.18 - Assignments.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Assignments. 214.18 Section 214.18 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF OSAGE RESERVATION LANDS, OKLAHOMA, FOR MINING, EXCEPT OIL AND GAS § 214.18 Assignments. Approved leases or any interest therein...

  13. 25 CFR 214.18 - Assignments.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Assignments. 214.18 Section 214.18 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF OSAGE RESERVATION LANDS, OKLAHOMA, FOR MINING, EXCEPT OIL AND GAS § 214.18 Assignments. Approved leases or any interest therein...

  14. 25 CFR 214.18 - Assignments.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Assignments. 214.18 Section 214.18 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF OSAGE RESERVATION LANDS, OKLAHOMA, FOR MINING, EXCEPT OIL AND GAS § 214.18 Assignments. Approved leases or any interest therein...

  15. 7 CFR 625.18 - Assignments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 6 2014-01-01 2014-01-01 false Assignments. 625.18 Section 625.18 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE WATER RESOURCES HEALTHY FORESTS RESERVE PROGRAM § 625.18 Assignments. Any person entitled to...

  16. 47 CFR 74.1202 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Frequency assignment. 74.1202 Section 74.1202... FM Broadcast Booster Stations § 74.1202 Frequency assignment. (a) An applicant for a new FM broadcast... stations. The application must be specific with regard to the frequency requested. Only one output...

  17. 33 CFR 401.61 - Assigned frequencies.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Assigned frequencies. 401.61 Section 401.61 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT... frequencies. The Seaway stations operate on the following assigned VHF frequencies: 156.8 MHz—(channel...

  18. 47 CFR 74.502 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Frequency assignment. 74.502 Section 74.502... § 74.502 Frequency assignment. (a) Except as provided in NG30, broadcast auxiliary stations licensed as... Frequency Allocations. These stations will be protected from possible interference caused by new users...

  19. 47 CFR 74.1202 - Frequency assignment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Frequency assignment. 74.1202 Section 74.1202... FM Broadcast Booster Stations § 74.1202 Frequency assignment. (a) An applicant for a new FM broadcast... stations. The application must be specific with regard to the frequency requested. Only one output...

  20. 33 CFR 401.61 - Assigned frequencies.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Assigned frequencies. 401.61 Section 401.61 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT... frequencies. The Seaway stations operate on the following assigned VHF frequencies: 156.8 MHz—(channel...

  1. 47 CFR 74.1202 - Frequency assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Frequency assignment. 74.1202 Section 74.1202... FM Broadcast Booster Stations § 74.1202 Frequency assignment. (a) An applicant for a new FM broadcast... stations. The application must be specific with regard to the frequency requested. Only one output...

  2. 47 CFR 74.103 - Frequency assignment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Frequency assignment. 74.103 Section 74.103....103 Frequency assignment. (a) Frequencies allocated to broadcasting and the various categories of auxiliary stations, in the FCC's Table of Frequency Allocations (Part 2 of this chapter), may be...

  3. 47 CFR 74.103 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Frequency assignment. 74.103 Section 74.103....103 Frequency assignment. (a) Frequencies allocated to broadcasting and the various categories of auxiliary stations, in the FCC's Table of Frequency Allocations (Part 2 of this chapter), may be...

  4. 33 CFR 401.61 - Assigned frequencies.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Assigned frequencies. 401.61 Section 401.61 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT... frequencies. The Seaway stations operate on the following assigned VHF frequencies: 156.8 MHz—(channel...

  5. 47 CFR 74.1202 - Frequency assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Frequency assignment. 74.1202 Section 74.1202... FM Broadcast Booster Stations § 74.1202 Frequency assignment. (a) An applicant for a new FM broadcast... stations. The application must be specific with regard to the frequency requested. Only one output...

  6. 47 CFR 74.502 - Frequency assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Frequency assignment. 74.502 Section 74.502... § 74.502 Frequency assignment. (a) Except as provided in NG30, broadcast auxiliary stations licensed as... Frequency Allocations. These stations will be protected from possible interference caused by new users...

  7. 7 CFR 247.21 - Caseload assignment.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE CHILD NUTRITION PROGRAMS COMMODITY SUPPLEMENTAL FOOD PROGRAM § 247.21 Caseload assignment. (a) How does.... Caseload assignments for the previous caseload cycle will remain in effect, subject to the availability...

  8. 47 CFR 74.502 - Frequency assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Frequency assignment. 74.502 Section 74.502... § 74.502 Frequency assignment. (a) Except as provided in NG30, broadcast auxiliary stations licensed as... Frequency Allocations. These stations will be protected from possible interference caused by new users...

  9. 47 CFR 74.502 - Frequency assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Frequency assignment. 74.502 Section 74.502... § 74.502 Frequency assignment. (a) Except as provided in NG30, broadcast auxiliary stations licensed as... Frequency Allocations. These stations will be protected from possible interference caused by new users...

  10. 47 CFR 74.103 - Frequency assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Frequency assignment. 74.103 Section 74.103....103 Frequency assignment. (a) Frequencies allocated to broadcasting and the various categories of auxiliary stations, in the FCC's Table of Frequency Allocations (Part 2 of this chapter), may be...

  11. 33 CFR 401.61 - Assigned frequencies.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Assigned frequencies. 401.61 Section 401.61 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT... frequencies. The Seaway stations operate on the following assigned VHF frequencies: 156.8 MHz—(channel...

  12. 47 CFR 74.502 - Frequency assignment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Frequency assignment. 74.502 Section 74.502... § 74.502 Frequency assignment. (a) Except as provided in NG30, broadcast auxiliary stations licensed as... Frequency Allocations. These stations will be protected from possible interference caused by new users...

  13. 47 CFR 74.1202 - Frequency assignment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Frequency assignment. 74.1202 Section 74.1202... FM Broadcast Booster Stations § 74.1202 Frequency assignment. (a) An applicant for a new FM broadcast... stations. The application must be specific with regard to the frequency requested. Only one output...

  14. 33 CFR 401.61 - Assigned frequencies.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Assigned frequencies. 401.61 Section 401.61 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT... frequencies. The Seaway stations operate on the following assigned VHF frequencies: 156.8 MHz—(channel...

  15. 7 CFR 247.21 - Caseload assignment.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 4 2011-01-01 2011-01-01 false Caseload assignment. 247.21 Section 247.21 Agriculture Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE CHILD NUTRITION PROGRAMS COMMODITY SUPPLEMENTAL FOOD PROGRAM § 247.21 Caseload assignment. (a) How...

  16. 47 CFR 74.702 - Channel assignments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.702 Channel assignments. (a) An applicant for a new low power TV or TV translator... standard VHF Channels (2 to 13 inclusive) may be assigned to a VHF low power TV or TV translator...

  17. 47 CFR 74.702 - Channel assignments.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.702 Channel assignments. (a) An applicant for a new low power TV or TV translator... standard VHF Channels (2 to 13 inclusive) may be assigned to a VHF low power TV or TV translator...

  18. 47 CFR 74.702 - Channel assignments.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.702 Channel assignments. (a) An applicant for a new low power TV or TV translator... standard VHF Channels (2 to 13 inclusive) may be assigned to a VHF low power TV or TV translator...

  19. 47 CFR 74.702 - Channel assignments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.702 Channel assignments. (a) An applicant for a new low power TV or TV translator... standard VHF Channels (2 to 13 inclusive) may be assigned to a VHF low power TV or TV translator...

  20. 47 CFR 74.702 - Channel assignments.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.702 Channel assignments. (a) An applicant for a new low power TV or TV translator... standard VHF Channels (2 to 13 inclusive) may be assigned to a VHF low power TV or TV translator...

  1. Gapminder: An AP Human Geography Lab Assignment

    ERIC Educational Resources Information Center

    Keller, Kenneth H.

    2012-01-01

    This lesson is designed as a lab assignment for Advanced Placement (AP) Human Geography students wherein they use the popular Gapminder web site to compare levels of development in countries from different world regions. For this lesson, it is important for the teacher to practice with Gapminder before giving the assignment to students. (Contains…

  2. 7 CFR 625.17 - Assignments.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Assignments. 625.17 Section 625.17 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE WATER RESOURCES HEALTHY FORESTS RESERVE PROGRAM § 625.17 Assignments. Any person entitled to...

  3. 7 CFR 623.19 - Assignments.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Assignments. 623.19 Section 623.19 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE WATER RESOURCES EMERGENCY WETLANDS RESERVE PROGRAM § 623.19 Assignments. Any participant...

  4. Using Cognitive Science to Assign Test Weights.

    ERIC Educational Resources Information Center

    Bhaskar, R.; Dillard, Jesse F.

    1983-01-01

    Description of an objective method for assigning weights to questions on examinations includes discussions of classical test theory, knowledge organization, and how task analysis can be used to identify knowledge elements required to solve specific problems, rank them, and assign objective weights to exam questions using a Pareto distribution (7…

  5. Scaling Preference Data for Program Assignments.

    ERIC Educational Resources Information Center

    Carifio, James

    The present study devised a computerized assignment-by-preference algorithm for a ninth-grade exploratory curriculum. The problem addressed was one of maximally mapping all students into 8 of 12 vocational programs in terms of their preferences for studying each of the programs and the assignment restrictions established by the school. To minimize…

  6. Effects of Individualized Assignments on Biology Achievement.

    ERIC Educational Resources Information Center

    Kremer, Philip L.

    1983-01-01

    Compared detailed (favoring field dependence and induction) and nondetailed (favoring field dependence and deduction) assignments on biology achievement of grade 10 male students (N=95) over a seven-month period. Detailed assignments, employing pictorial and verbal block diagrams and high structure, significantly enhanced learning among some…

  7. Integrating Online Assignments Checking in Introductory Courses

    ERIC Educational Resources Information Center

    Pundak, David; Shacham, Miri; Herscovitz, Orit

    2013-01-01

    Web technology offers lecturers the option of checking students' assignments online. Several systems have evolved to deliver personal assignments to each student in a multi-participant course. These systems provide students with immediate feedback, allowing them to correct erroneous answers and referring them to relevant literary sources that…

  8. Detecting Plagiarism in MS Access Assignments

    ERIC Educational Resources Information Center

    Singh, Anil

    2013-01-01

    Assurance of individual effort from students in computer-based assignments is a challenge. Due to digitization, students can easily use a copy of their friend's work and submit it as their own. Plagiarism in assignments puts students who cheat at par with those who work honestly and this compromises the learning evaluation process. Using a…

  9. Absolute Points for Multiple Assignment Problems

    ERIC Educational Resources Information Center

    Adlakha, V.; Kowalski, K.

    2006-01-01

    An algorithm is presented to solve multiple assignment problems in which a cost is incurred only when an assignment is made at a given cell. The proposed method recursively searches for single/group absolute points to identify cells that must be loaded in any optimal solution. Unlike other methods, the first solution is the optimal solution. The…

  10. 47 CFR 74.602 - Frequency assignment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Frequency assignment. 74.602 Section 74.602 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES EXPERIMENTAL RADIO, AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Television Broadcast Auxiliary Stations § 74.602 Frequency assignment....

  11. 47 CFR 74.602 - Frequency assignment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Frequency assignment. 74.602 Section 74.602 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES EXPERIMENTAL RADIO, AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Television Broadcast Auxiliary Stations § 74.602 Frequency assignment....

  12. Stress Assignment in Reading Italian Polysyllabic Pseudowords

    ERIC Educational Resources Information Center

    Sulpizio, Simone; Arduino, Lisa S.; Paizi, Despina; Burani, Cristina

    2013-01-01

    In 4 naming experiments we investigated how Italian readers assign stress to pseudowords. We assessed whether participants assign stress following distributional information such as stress neighborhood (the proportion and number of existent words sharing orthographic ending and stress pattern) and whether such distributional information affects…

  13. 7 CFR 1415.16 - Assignments.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assignments. 1415.16 Section 1415.16 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRASSLANDS RESERVE PROGRAM § 1415.16 Assignments. (a)...

  14. 7 CFR 1415.16 - Assignments.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Assignments. 1415.16 Section 1415.16 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRASSLANDS RESERVE PROGRAM § 1415.16 Assignments. (a)...

  15. 7 CFR 1415.16 - Assignments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Assignments. 1415.16 Section 1415.16 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRASSLANDS RESERVE PROGRAM § 1415.16 Assignments. (a)...

  16. 7 CFR 1415.16 - Assignments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Assignments. 1415.16 Section 1415.16 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRASSLANDS RESERVE PROGRAM § 1415.16 Assignments. (a)...

  17. 7 CFR 1415.16 - Assignments.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Assignments. 1415.16 Section 1415.16 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS GRASSLANDS RESERVE PROGRAM § 1415.16 Assignments. (a)...

  18. 47 CFR 101.147 - Frequency assignments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Frequency assignments. 101.147 Section 101.147 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES FIXED MICROWAVE SERVICES Technical Standards § 101.147 Frequency assignments. Link to an amendment published at 76 FR 59573, Sept. 27, 2011....

  19. 12 CFR 345.28 - Assigned ratings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    .... Subject to paragraphs (b) and (c) of this section, the FDIC assigns to a bank a rating of “outstanding... FDIC assigns a rating for a bank assessed under the lending, investment, and service tests in accordance with the following principles: (1) A bank that receives an “outstanding” rating on the...

  20. 12 CFR 228.28 - Assigned ratings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based on the..., and service tests. The Board assigns a rating for a bank assessed under the lending, investment, and...” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A bank...

  1. 12 CFR 345.28 - Assigned ratings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    .... Subject to paragraphs (b) and (c) of this section, the FDIC assigns to a bank a rating of “outstanding... FDIC assigns a rating for a bank assessed under the lending, investment, and service tests in accordance with the following principles: (1) A bank that receives an “outstanding” rating on the...

  2. 12 CFR 345.28 - Assigned ratings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    .... Subject to paragraphs (b) and (c) of this section, the FDIC assigns to a bank a rating of “outstanding... FDIC assigns a rating for a bank assessed under the lending, investment, and service tests in accordance with the following principles: (1) A bank that receives an “outstanding” rating on the...

  3. 12 CFR 345.28 - Assigned ratings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    .... Subject to paragraphs (b) and (c) of this section, the FDIC assigns to a bank a rating of “outstanding... FDIC assigns a rating for a bank assessed under the lending, investment, and service tests in accordance with the following principles: (1) A bank that receives an “outstanding” rating on the...

  4. 12 CFR 345.28 - Assigned ratings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    .... Subject to paragraphs (b) and (c) of this section, the FDIC assigns to a bank a rating of “outstanding... FDIC assigns a rating for a bank assessed under the lending, investment, and service tests in accordance with the following principles: (1) A bank that receives an “outstanding” rating on the...

  5. 12 CFR 228.28 - Assigned ratings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... bank a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance...) Lending, investment, and service tests. The Board assigns a rating for a bank assessed under the lending... “outstanding” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A...

  6. 12 CFR 25.28 - Assigned ratings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based..., investment, and service tests. The OCC assigns a rating for a bank assessed under the lending, investment... “outstanding” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A...

  7. 12 CFR 228.28 - Assigned ratings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based on the..., and service tests. The Board assigns a rating for a bank assessed under the lending, investment, and...” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A bank...

  8. 12 CFR 228.28 - Assigned ratings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... bank a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance...) Lending, investment, and service tests. The Board assigns a rating for a bank assessed under the lending... “outstanding” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A...

  9. 12 CFR 25.28 - Assigned ratings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based..., investment, and service tests. The OCC assigns a rating for a bank assessed under the lending, investment... “outstanding” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A...

  10. 12 CFR 25.28 - Assigned ratings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based..., investment, and service tests. The OCC assigns a rating for a bank assessed under the lending, investment... “outstanding” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A...

  11. 12 CFR 228.28 - Assigned ratings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based on the..., and service tests. The Board assigns a rating for a bank assessed under the lending, investment, and...” rating on the lending test receives an assigned rating of at least “satisfactory”; (2) A bank...

  12. Individualized Assignments in an Experimental Psychology Course.

    ERIC Educational Resources Information Center

    Hovancik, John R.

    1984-01-01

    A computer is used to individualize student assignments in statistics. The principal benefit of individualized activities is that they emphasize decision-making processes rather than correct answers. Students in an individualized assignment group scored higher on an examination than those in a comparison group. (RM)

  13. 7 CFR 623.19 - Assignments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 6 2013-01-01 2013-01-01 false Assignments. 623.19 Section 623.19 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE WATER RESOURCES EMERGENCY WETLANDS RESERVE PROGRAM § 623.19 Assignments. Any participant...

  14. 7 CFR 1467.17 - Assignments.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Assignments. 1467.17 Section 1467.17 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS WETLANDS RESERVE PROGRAM § 1467.17 Assignments. Any...

  15. 47 CFR 74.402 - Frequency assignment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Frequency assignment. 74.402 Section 74.402 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES EXPERIMENTAL RADIO, AUXILIARY, SPECIAL BROADCAST AND OTHER PROGRAM DISTRIBUTIONAL SERVICES Remote Pickup Broadcast Stations § 74.402 Frequency assignment....

  16. Online Discussion Assignments Improve Students' Class Preparation

    ERIC Educational Resources Information Center

    Lineweaver, Tara T.

    2010-01-01

    To increase the number of students who read the text before class and to promote student interaction centering on text material, I developed an online discussion assignment as a required component of a cognitive psychology course. Across 2 studies, this assignment had a limited effect on examination performance, but students completing online…

  17. Development of a multiplex real-time PCR assay for identification of members of the Anopheles gambiae species complex.

    PubMed

    Bass, Chris; Williamson, Martin S; Field, Linda M

    2008-07-01

    Two high-throughput assays for the identification of members of the Anopheles gambiae sensu lato species complex have recently been reported. These methods, are based on TaqMan single nucleotide polymorphism (SNP) genotyping that enables rapid scoring of mosquito DNA samples in real-time PCR reactions. Unfortunately, both assays are restricted in the number of species that they can identify and a combination of the two assays may be required to identify all possible species in certain regions. To overcome this limitation, and thereby further increase throughput while reducing costs, we have developed a new multiplex real-time PCR assay for identifying members of the An. gambiae complex. The new method uses three probes labelled with fluorophores with distinct emission and excitation spectra, allowing simultaneous detection of the two main malaria vectors from the non-vector sibling species, and can be used on single mosquito legs from silica-dried specimens. A genotyping trial of over 450 specimens collected from 13 countries in sub-Saharan Africa showed the multiplex assay to be highly specific and sensitive and it compared well against the two previously reported TaqMan assays and standard allele-specific PCR. PMID:18490000

  18. Low DSP complexity mid-haul mode-division multiplexing links utilizing wideband modal dispersion compensated two-mode fibers

    NASA Astrophysics Data System (ADS)

    Diamantopoulos, N. P.; Nakazawa, M.; Yoshida, Y.; Maruta, A.; Maruyama, R.; Kuwaki, N.; Matsuo, S.; Kitayama, K.

    2015-11-01

    Mode-division multiplexing (MDM) over wavelength division multiplexed (WDM) networks is studied, particularly for the deployment of metro area networks (MAN) using two-mode fibers (TMF). Full C-band differential mode group delay (DMGD)-compensated TMF links are adopted for decreasing the computational complexity of real-time multiple-input multiple-output (MIMO) signal processing. The effect of modal crosstalk to the maximum delay spread of the channel is validated through numerical simulations. Finally, the 2×2 MIMO channel state information (CSI) of a 102.6-km DMGD-compensated TMF link is experimentally estimated for mode path provisioning based upon routing and mode assignment (RMA) in MDM networks. The results confirm close-to-zero total DMGD value over the entire C-band.

  19. A novel scheme of SONET/SDH label assignment in GMPLS-controlled MSTN network

    NASA Astrophysics Data System (ADS)

    Zhao, Mingzhi; Wang, Yan; Wang, Jun; Xie, Guowu; Jin, Yaohui; Sun, Weiqiang; Guo, Wei; Hu, Weisheng

    2007-11-01

    Because SONET/SDH technology which includes contiguous concatenation and virtual concatenation is used in GMPLS-Controlled Multi-services Transport Platform (MSTP) Network, it is more complex when we consider the label assignment when setting up a Label Switch Path (LSP). It is very imperative to use a method which could use the limited labels effectively. In this paper, we study the structure of the label space and different label algorithm to allocate SONET/SDH labels, which include virtual concatenation labels and contiguous concatenation labels in GMPLS-Controlled MSTP Network. We proposed a minimum Contiguous Labels Algorithm (min-CLA) to solve the problem of using the limited label space on each interface at the most degree. Different from the previous schemes worked on Route Wavelength Assignment (RWA) in the Wavelength-Division-Multiplex (WDM) networks, our scheme finds out the primary and easy method based on SONET/SDH label which has virtual concatenation labels and contiguous concatenation labels used for different kinds of needs. Because of taking the multiple services requirements into account, the proposed algorithm finds out more efficient feasible solution requiring less network resources and even find a feasible solution which will enable some label assignment failed in other label assignment algorithm and we will compare our scheme and the Fist Fit Scheme.

  20. A Customized Pigmentation SNP Array Identifies a Novel SNP Associated with Melanoma Predisposition in the SLC45A2 Gene

    PubMed Central

    Alonso, Santos; Boyano, M. Dolores; Peña-Chilet, Maria; Pita, Guillermo; Aviles, Jose A.; Mayor, Matias; Gomez-Fernandez, Cristina; Casado, Beatriz; Martin-Gonzalez, Manuel; Izagirre, Neskuts; De la Rua, Concepcion; Asumendi, Aintzane; Perez-Yarza, Gorka; Arroyo-Berdugo, Yoana; Boldo, Enrique; Lozoya, Rafael; Torrijos-Aguilar, Arantxa; Pitarch, Ana; Pitarch, Gerard; Sanchez-Motilla, Jose M.; Valcuende-Cavero, Francisca; Tomas-Cabedo, Gloria; Perez-Pastor, Gemma; Diaz-Perez, Jose L.; Gardeazabal, Jesus; de Lizarduy, Iñigo Martinez; Sanchez-Diez, Ana; Valdes, Carlos; Pizarro, Angel; Casado, Mariano; Carretero, Gregorio; Botella-Estrada, Rafael; Nagore, Eduardo; Lazaro, Pablo; Lluch, Ana; Benitez, Javier; Martinez-Cadenas, Conrado; Ribas, Gloria

    2011-01-01

    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. PMID:21559390

  1. Sibship analysis of associations between SNP haplotypes and a continuous trait with application to mammographic density.

    PubMed

    Stone, J; Gurrin, L C; Hayes, V M; Southey, M C; Hopper, J L; Byrnes, G B

    2010-05-01

    Haplotype-based association studies have been proposed as a powerful comprehensive approach to identify causal genetic variation underlying complex diseases. Data comparisons within families offer the additional advantage of dealing naturally with complex sources of noise, confounding and population stratification. Two problems encountered when investigating associations between haplotypes and a continuous trait using data from sibships are (i) the need to define within-sibship comparisons for sibships of size greater than two and (ii) the difficulty of resolving the joint distribution of haplotype pairs within sibships in the absence of parental genotypes. We therefore propose first a method of orthogonal transformation of both outcomes and exposures that allow the decomposition of between- and within-sibship regression effects when sibship size is greater than two. We conducted a simulation study, which confirmed analysis using all members of a sibship is statistically more powerful than methods based on cross-sectional analysis or using subsets of sib-pairs. Second, we propose a simple permutation approach to avoid errors of inference due to the within-sibship correlation of any errors in haplotype assignment. These methods were applied to investigate the association between mammographic density (MD), a continuously distributed and heritable risk factor for breast cancer, and single nucleotide polymorphisms (SNPs) and haplotypes from the VDR gene using data from a study of 430 twins and sisters. We found evidence of association between MD and a 4-SNP VDR haplotype. In conclusion, our proposed method retains the benefits of the between- and within-pair analysis for pairs of siblings and can be implemented in standard software. PMID:19918759

  2. A novel multiplex pyrosequencing assay for genotyping functionally relevant CTLA-4 polymorphisms: potential applications in autoimmunity and cancer.

    PubMed

    Banelli, Barbara; Morabito, Anna; Laurent, Stefania; Piccioli, Patrizia; Dozin, Beatrice; Ghio, Massimo; Ascierto, Paolo Antonio; Monteghirfo, Stefano; Marasco, Antonella; Ottaviano, Vincenzo; Queirolo, Paola; Romani, Massimo; Pistillo, Maria Pia

    2014-08-01

    CTLA-4 expression/function can be affected by single nucleotide polymorphisms (SNPs) of CTLA-4 gene, which have been widely associated with susceptibility or progression to autoimmune diseases and cancer development. In this study, we analyzed six CTLA-4 SNPs (-1661A>G, -1577G>A, -658C>T, -319C>T, +49A>G, CT60G>A) in 197 DNA samples from 43 B-lymphoblastoid cell lines (B-LCLs), 40 systemic sclerosis (SSc) patients, 14 pre-analyzed melanoma patients and 100 Italian healthy subjects. Genotyping of -1661A>G, -1577G>A, -658C>T and CT60G>A was performed by newly developed multiplex pyrosequencing (PSQ) assays, whereas -319C>T and +49A>G by T-ARMS PCR and direct sequencing. Genotype/allele frequency were analyzed using χ(2) or Fisher exact test. Our study provides the first multiplex PSQ method that allows simultaneous genotyping of two CTLA-4 SNP pairs (i.e. -1661A>G/-658C>T and -1577G>A/CT60G>A) by two multiplex PSQ reactions. Herein, we show the CTLA-4 genotype distribution in the B-LCLs providing the first and best characterized cell line panel typed for functionally relevant CTLA-4 SNPs. We also report the significant association of the -1661A/G genotype, -1661 & -319 AC-GT diplotype and -319 & CT60 TG haplotype with susceptibility to SSc without Hashimoto's thyroiditis occurrence. Furthermore, we confirmed previous genotyping data referred to melanoma patients and provided new genotyping data for Italian healthy subjects. PMID:24801647

  3. High thickness acrylamide photopolymer for peristrophic multiplexing

    NASA Astrophysics Data System (ADS)

    Ortuño, M.; Fernández, E.; Márquez, A.; Gallego, S.; Neipp, C.; Pascual, I.

    2006-05-01

    The acrylamide photolymers are considered interesting materials for holographic media. They have high diffraction efficiency (ratio of the intensities of the diffracted and the incident beams), an intermediate energetic sensitivity among other materials and post-processing steps are not necessary, therefore the media is not altered. The layers of these materials, about 1 mm thick, are a suitable media for recording many diffraction gratings in the same volume of photopolymer using peristrophic multiplexing technique, with great practical importance in the field of holographic memories type WORM (write once read many). In this work we study the recording of diffraction gratings by peristrophic multiplexing with axis of rotation perpendicular to the recording media. The photopolymer is composed of acrylamide as the polymerizable monomer, triethanolamine as radical generator, yellowish eosin as sensitizer and a binder of polyvinyl alcohol. We analyze the holographic behaviour of the material during recording and reconstruction of diffraction gratings using a continuous Nd:YAG laser (532 nm) at an intensity of 5 mW/cm2 as recording laser. The response of the material is monitored after recording with an He-Ne laser. We study the recording process of unslanted diffraction gratings of 1125 lines/mm. The diffraction efficiency of each hologram is seen to decrease as the number of holograms recorded increases, due to consumption of the available dynamic range, in a constant exposure scheduling. It can be seen that the photopolymer works well with high energy levels, without excessive dispersion of light by noise gratings. In order to homogenize the diffraction efficiency of each hologram we use the method proposed by Pu. This method is designed to share all or part of the avaliable dynamic range of the recording material among the holograms to be multiplexed. Using exposure schedules derived from this method we have used 3 scheduling recordings from the algorithm used

  4. Multiplexed Western Blotting Using Microchip Electrophoresis.

    PubMed

    Jin, Shi; Furtaw, Michael D; Chen, Huaxian; Lamb, Don T; Ferguson, Stephen A; Arvin, Natalie E; Dawod, Mohamed; Kennedy, Robert T

    2016-07-01

    Western blotting is a commonly used protein assay that combines the selectivity of electrophoretic separation and immunoassay. The technique is limited by long time, manual operation with mediocre reproducibility, and large sample consumption, typically 10-20 μg per assay. Western blots are also usually used to measure only one protein per assay with an additional housekeeping protein for normalization. Measurement of multiple proteins is possible; however, it requires stripping membranes of antibody and then reprobing with a second antibody. Miniaturized alternatives to Western blot based on microfluidic or capillary electrophoresis have been developed that enable higher-throughput, automation, and greater mass sensitivity. In one approach, proteins are separated by electrophoresis on a microchip that is dragged along a polyvinylidene fluoride membrane so that as proteins exit the chip they are captured on the membrane for immunoassay. In this work, we improve this method to allow multiplexed protein detection. Multiple injections made from the same sample can be deposited in separate tracks so that each is probed with a different antibody. To further enhance multiplexing capability, the electrophoresis channel dimensions were optimized for resolution while keeping separation and blotting times to less than 8 min. Using a 15 μm deep × 50 μm wide × 8.6 cm long channel, it is possible to achieve baseline resolution of proteins that differ by 5% in molecular weight, e.g., ERK1 (44 kDa) from ERK2 (42 kDa). This resolution allows similar proteins detected by cross-reactive antibodies in a single track. We demonstrate detection of 11 proteins from 9 injections from a single Jurkat cell lysate sample consisting of 400 ng of total protein using this procedure. Thus, multiplexed Western blots are possible without cumbersome stripping and reprobing steps. PMID:27270033

  5. Optimal processor assignment for pipeline computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Simha, Rahul; Choudhury, Alok N.; Narahari, Bhagirath

    1991-01-01

    The availability of large scale multitasked parallel architectures introduces the following processor assignment problem for pipelined computations. Given a set of tasks and their precedence constraints, along with their experimentally determined individual responses times for different processor sizes, find an assignment of processor to tasks. Two objectives are of interest: minimal response given a throughput requirement, and maximal throughput given a response time requirement. These assignment problems differ considerably from the classical mapping problem in which several tasks share a processor; instead, it is assumed that a large number of processors are to be assigned to a relatively small number of tasks. Efficient assignment algorithms were developed for different classes of task structures. For a p processor system and a series parallel precedence graph with n constituent tasks, an O(np2) algorithm is provided that finds the optimal assignment for the response time optimization problem; it was found that the assignment optimizing the constrained throughput in O(np2log p) time. Special cases of linear, independent, and tree graphs are also considered.

  6. Automated Assignment of Proposals to Reviewers

    NASA Technical Reports Server (NTRS)

    Kantak, Anil; Kantak, Anil

    2006-01-01

    A computer program automates the process of selecting unbiased peer reviewers of research proposals submitted to NASA. Heretofore, such selection has been performed by manual searching of two large databases subject to a set of assignment rules. One database lists proposals and proposers; the other database lists potential reviewers. The manual search takes an average of several weeks per proposal. In contrast, the present software can perform the selection in seconds. The program begins by selecting one entry from each database, then applying the assignment rules to this pair of entries. If and only if all the assignment rules are satisfied, the chosen reviewer is assigned to the chosen proposal. The assignment rules enforced by the program are (1) a maximum allowable number of proposals assigned to a single reviewer; (2) a maximum allowable number of reviewers assigned to a single proposal; (3) if the proposing team includes a member affiliated with an industry, then the reviewer must not be affiliated with any industry; and (4) the reviewer must not be a member of the proposing team or affiliated with the same institution as that of a member of the proposing team.

  7. Hardware Counter Multiplexing V1.2

    Energy Science and Technology Software Center (ESTSC)

    2000-10-13

    The Hardware Counter Multiplexer works with the built-in counter registers on computer processors. These counters record varius low-level events as software runs, but they can cannot record all possible events at the same time. This software helps work around that limitation by counting a series of different events in sequence over a period of time. This in turn allows programmers to measure interesting combinations of events, rather than single events. The software is designed tomore » work with multithreaded or single-threaded programs.« less

  8. Multiplexed microsatellite markers for seven Metarhizium species.

    PubMed

    Mayerhofer, Johanna; Lutz, Andy; Widmer, Franco; Rehner, Stephen A; Leuchtmann, Adrian; Enkerli, Jürg

    2015-11-01

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium strains including all 54 used in a recent phylogenetic revision of the genus were characterized. Between 15 and 34 polymorphic SSR markers produced scorable PCR amplicons in seven species, including M. anisopliae, M. brunneum, M. guizhouense, M. lepidiotae, M. majus, M. pingshaense, and M. robertsii. To provide genotyping tools for concurrent analysis of these seven species fifteen markers grouped in five multiplex pools were selected based on high allelic diversity and easy scorability of SSR chromatograms. PMID:26407949

  9. Two wavelength division multiplexing WAN trials

    SciTech Connect

    Lennon, W.J.; Thombley, R.L.

    1995-01-20

    Lawrence Livermore National Laboratory, as a super-user, supercomputer, and super-application site, is anticipating the future bandwidth and protocol requirements necessary to connect to other such sites as well as to connect to remote-sited control centers and experiments. In this paper the authors discuss their vision of the future of Wide Area Networking, describe the plans for a wavelength division multiplexed link connecting Livermore with the University of California at Berkeley and describe plans for a transparent, {approx} 10 Gb/s ring around San Francisco Bay.

  10. Replicator dynamics with diffusion on multiplex networks

    NASA Astrophysics Data System (ADS)

    Requejo, R. J.; Díaz-Guilera, A.

    2016-08-01

    In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies.

  11. Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima.

    PubMed

    Jones, David B; Jerry, Dean R; Forêt, Sylvain; Konovalov, Dmitry A; Zenger, Kyall R

    2013-12-01

    Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima, is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF)≥ 0.15, read depth  ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 %; mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry. PMID:23715808

  12. Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp.

    PubMed

    Garcés-Claver, Ana; Fellman, Shanna Moore; Gil-Ortega, Ramiro; Jahn, Molly; Arnedo-Andrés, María S

    2007-11-01

    A single nucleotide polymorphism (SNP) associated with pungency was detected within an expressed sequence tag (EST) of 307 bp. This fragment was identified after expression analysis of the EST clone SB2-66 in placenta tissue of Capsicum fruits. Sequence alignments corresponding to this new fragment allowed us to identify an SNP between pungent and non-pungent accessions. Two methods were chosen for the development of the SNP marker linked to pungency: tetra-primer amplification refractory mutation system-PCR (tetra-primer ARMS-PCR) and cleaved amplified polymorphic sequence. Results showed that both methods were successful in distinguishing genotypes. Nevertheless, tetra-primer ARMS-PCR was chosen for SNP genotyping because it was more rapid, reliable and less cost-effective. The utility of this SNP marker for pungency was demonstrated by the ability to distinguish between 29 pungent and non-pungent cultivars of Capsicum annuum. In addition, the SNP was also associated with phenotypic pungent character in the tested genotypes of C. chinense, C. baccatum, C. frutescens, C. galapagoense, C. eximium, C. tovarii and C. cardenasi. This SNP marker is a faster, cheaper and more reproducible method for identifying pungent peppers than other techniques such as panel tasting, and allows rapid screening of the trait in early growth stages. PMID:17882396

  13. Target assignment of simultaneous arrival for UAVs

    NASA Astrophysics Data System (ADS)

    Xia, Jie; Gao, Jinyuan

    2003-09-01

    The Extend Hungary Method (EHM) is presented to solve the assignment problem that the number of UAVs is larger than that of targets. The target assignment is modeling and the motivations are minimize the distance of the UAV fleet, maximize the survivability of the UAV fleet, maximize the number of UAVs assigned to each target and maximize the number of target attacked. An algorithm for arriving simultaneously is presented by combination of the EHM. Simulation results demonstrating the feasibility of the approach are presented. The approach could be easily applied into other multi-robot cooperative mission.

  14. A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees

    PubMed Central

    Silberstein, Mark; Weissbrod, Omer; Otten, Lars; Tzemach, Anna; Anisenia, Andrei; Shtark, Oren; Tuberg, Dvir; Galfrin, Eddie; Gannon, Irena; Shalata, Adel; Borochowitz, Zvi U.; Dechter, Rina; Thompson, Elizabeth; Geiger, Dan

    2013-01-01

    Motivation: The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis of large pedigrees is impeded by significant technical, methodological and computational challenges. Here we describe Superlink-Online SNP, a new powerful online system that streamlines the linkage analysis of SNP data. It features a fully integrated flexible processing workflow comprising both well-known and novel data analysis tools, including SNP clustering, erroneous data filtering, exact and approximate LOD calculations and maximum-likelihood haplotyping. The system draws its power from thousands of CPUs, performing data analysis tasks orders of magnitude faster than a single computer. By providing an intuitive interface to sophisticated state-of-the-art analysis tools coupled with high computing capacity, Superlink-Online SNP helps geneticists unleash the potential of SNP data for detecting disease genes. Results: Computations performed by Superlink-Online SNP are automatically parallelized using novel paradigms, and executed on unlimited number of private or public CPUs. One novel service is large-scale approximate Markov Chain–Monte Carlo (MCMC) analysis. The accuracy of the results is reliably estimated by running the same computation on multiple CPUs and evaluating the Gelman–Rubin Score to set aside unreliable results. Another service within the workflow is a novel parallelized exact algorithm for inferring maximum-likelihood haplotyping. The reported system enables genetic analyses that were previously infeasible. We demonstrate the system capabilities through a study of a large complex pedigree affected with metabolic syndrome. Availability: Superlink-Online SNP is freely available for researchers at http://cbl-hap.cs.technion.ac.il/superlink-snp. The system source code can also be downloaded from the system website. Contact: omerw@cs.technion.ac.il Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23162081

  15. Preliminary study of visual effect of multiplex hologram

    NASA Astrophysics Data System (ADS)

    Fu, Huaiping; Xiong, Bingheng; Yang, Hong; Zhang, Xueguo

    2004-06-01

    The process of any movement of real object can be recorded and displayed by a multiplex holographic stereogram. An embossing multiplex holographic stereogram and a multiplex rainbow holographic stereogram have been made by us, the multiplex rainbow holographic stereogram reconstructs the dynamic 2D line drawing of speech organs, the embossing multiplex holographic stereogram reconstructs the process of an old man drinking water. In this paper, we studied the visual result of an embossing multiplex holographic stereogram made with 80 films of 2-D pictures. Forty-eight persons of aged from 13 to 67 were asked to see the hologram and then to answer some questions about the feeling of viewing. The results indicate that this kind of holograms could be accepted by human visual sense organ without any problem. This paper also discusses visual effect of the multiplex holography stereograms base on visual perceptual psychology. It is open out that the planar multiplex holograms can be recorded and present the movement of real animal and object. Not only have the human visual perceptual constancy for shape, just as that size, color, etc... but also have visual perceptual constancy for binocular parallax.

  16. 47 CFR 73.319 - FM multiplex subcarrier technical standards.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false FM multiplex subcarrier technical standards. 73.319 Section 73.319 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES FM Broadcast Stations § 73.319 FM multiplex subcarrier technical standards. (a) The technical specifications in...

  17. 47 CFR 73.319 - FM multiplex subcarrier technical standards.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false FM multiplex subcarrier technical standards. 73.319 Section 73.319 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES FM Broadcast Stations § 73.319 FM multiplex subcarrier technical standards. (a) The technical specifications in...

  18. Multiplex Allele-Specific Amplification from Whole Blood for Detecting Multiple Polymorphisms Simultaneously

    PubMed Central

    Zhu, Jianjie; Chen, Lanxin; Mao, Yong; Zhou, Huan

    2013-01-01

    Allele-specific amplification on the basis of polymerase chain reaction (PCR) has been widely used for single-nucleotide polymorphism (SNP) genotyping. However, the extraction of PCR-compatible genomic DNA from whole blood is usually required. This process is complicated and tedious, and is prone to cause cross-contamination between samples. To facilitate direct PCR amplification from whole blood without the extraction of genomic DNA, we optimized the pH value of PCR solution and the concentrations of magnesium ions and facilitator glycerol. Then, we developed multiplex allele-specific amplifications from whole blood and applied them to a case–control study. In this study, we successfully established triplex, five-plex, and eight-plex allele-specific amplifications from whole blood for determining the distribution of genotypes and alleles of 14 polymorphisms in 97 gastric cancer patients and 141 healthy controls. Statistical analysis results showed significant association of SNPs rs9344, rs1799931, and rs1800629 with the risk of gastric cancer. This method is accurate, time-saving, cost-effective, and easy-to-do, especially suitable for clinical prediction of disease susceptibility. PMID:23072573

  19. Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping.

    PubMed

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

    2013-03-15

    Many drug or single nucleotide polymorphism (SNP)-related resources and tools have been developed, but connecting and integrating them is still a challenge. Here, we describe a user-friendly web-based software package, named Drug-SNPing, which provides a platform for the integration of drug information (DrugBank and PharmGKB), protein-protein interactions (STRING), tagSNP selection (HapMap) and genotyping information (dbSNP, REBASE and SNP500Cancer). DrugBank-based inputs include the following: (i) common name of the drug, (ii) synonym or drug brand name, (iii) gene name (HUGO) and (iv) keywords. PharmGKB-based inputs include the following: (i) gene name (HUGO), (ii) drug name and (iii) disease-related keywords. The output provides drug-related information, metabolizing enzymes and drug targets, as well as protein-protein interaction data. Importantly, tagSNPs of the selected genes are retrieved for genotyping analyses. All drug-based and protein-protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes. Thus, users can enter any drug keywords/brand names to obtain immediate information that is highly relevant to genotyping for pharmacogenomics research. PMID:23418190

  20. Flexible wavelength de-multiplexer for elastic optical networking.

    PubMed

    Zhou, Rui; Gutierrez Pascual, M Deseada; Anandarajah, Prince M; Shao, Tong; Smyth, Frank; Barry, Liam P

    2016-05-15

    We report an injection locked flexible wavelength de-multiplexer (de-mux) that shows 24-h frequency stability of 1 kHz for optical comb-based elastic optical networking applications. We demonstrate 50 GHz, 87.5 GHz equal spacing and 6.25G-25G-50 GHz, 75G-50G-100 GHz unequal spacing for the de-multiplexer outputs. We also implement an unequally spaced (75G-50G-100 GHz), mixed symbol rate (12.5 GBaud and 40 GBaud) and modulation format (polarization division multiplexed quadrature phase shift keying and on-off keying) wavelength division multiplexed transmission system using the de-multiplexer outputs. The results show 0.6 dB receiver sensitivity penalty, at 7% hard decision forward error correction coding limit, of the 100 km transmitted de-mux outputs when compared to comb source seeding laser back-to-back. PMID:27176972

  1. Cascading processes on multiplex networks: Impact of weak layers

    NASA Astrophysics Data System (ADS)

    Lee, Kyu-Min; Goh, Kwang-Il

    Many real-world complex systems such as biological and socio-technological systems consist of manifold layers in multiplex networks. The multiple network layers give rise to the nonlinear effect for the emergent dynamics of systems. Especially, the weak layers plays the significant role in nonlinearity of multiplex networks, which can be neglected in single-layer network framework overlaying all layers. Here we present a simple model of cascades on multiplex networks of heterogeneous layers. The model is simulated on the multiplex network of international trades. We found that the multiplex model produces more catastrophic cascading failures which were the result of collective behaviors from coupling layers rather than the simple summation effect. Therefore risks can be systematically underestimated in simply overlaid network system because the impact of weak layers is overlooked. Our simple theoretical model would have some implications to investigate and design optimal real-world complex systems.

  2. Wavelength division multiplexing WDM, CWDM and DWDM applications

    NASA Astrophysics Data System (ADS)

    Vasile, Irina Bristena; Vasile, Alexandru; Luciana, Stan; Tache, Mihaela

    2007-05-01

    The fiber optics has become the most preferred media for this very large data traffic. TDM (Time Division Multiplexing) has been the most practical method to divide the significant capacity of a single fiber optics into several communication channels. This technology is still limited by the large complexity of high-flow modulation and multiplexing equipment. Presently, a complementary approach proves its potential: Wavelength-Division Multiplexing (WDM). The evolution of WDM allows now a very small spacing between channels wavelength, in nm, generating DWDM (Dense Wavelength Division Multiplexing). The networks with individual fibers including more than 100 independent optic channels, as well as those with bidirectional flow are already available on the market. CWDM (Coarse Wavelength Division Multiplexing) represents an economical application of a mature technology which may provide options where the capacity of fibers is limited.

  3. Quantum probability assignment limited by relativistic causality.

    PubMed

    Han, Yeong Deok; Choi, Taeseung

    2016-01-01

    Quantum theory has nonlocal correlations, which bothered Einstein, but found to satisfy relativistic causality. Correlation for a shared quantum state manifests itself, in the standard quantum framework, by joint probability distributions that can be obtained by applying state reduction and probability assignment that is called Born rule. Quantum correlations, which show nonlocality when the shared state has an entanglement, can be changed if we apply different probability assignment rule. As a result, the amount of nonlocality in quantum correlation will be changed. The issue is whether the change of the rule of quantum probability assignment breaks relativistic causality. We have shown that Born rule on quantum measurement is derived by requiring relativistic causality condition. This shows how the relativistic causality limits the upper bound of quantum nonlocality through quantum probability assignment. PMID:26971717

  4. Quantum probability assignment limited by relativistic causality

    PubMed Central

    Han, Yeong Deok; Choi, Taeseung

    2016-01-01

    Quantum theory has nonlocal correlations, which bothered Einstein, but found to satisfy relativistic causality. Correlation for a shared quantum state manifests itself, in the standard quantum framework, by joint probability distributions that can be obtained by applying state reduction and probability assignment that is called Born rule. Quantum correlations, which show nonlocality when the shared state has an entanglement, can be changed if we apply different probability assignment rule. As a result, the amount of nonlocality in quantum correlation will be changed. The issue is whether the change of the rule of quantum probability assignment breaks relativistic causality. We have shown that Born rule on quantum measurement is derived by requiring relativistic causality condition. This shows how the relativistic causality limits the upper bound of quantum nonlocality through quantum probability assignment. PMID:26971717

  5. A New Gimmick for Assigning Absolute Configuration.

    ERIC Educational Resources Information Center

    Ayorinde, F. O.

    1983-01-01

    A five-step procedure is provided to help students in making the assignment absolute configuration less bothersome. Examples for both single (2-butanol) and multi-chiral carbon (3-chloro-2-butanol) molecules are included. (JN)

  6. Multiplexed Colorimetric Solid-Phase Extraction

    NASA Technical Reports Server (NTRS)

    Gazda, Daniel B.; Fritz, James S.; Porter, Marc D.

    2009-01-01

    Multiplexed colorimetric solid-phase extraction (MC-SPE) is an extension of colorimetric solid-phase extraction (C-SPE) an analytical platform that combines colorimetric reagents, solid phase extraction, and diffuse reflectance spectroscopy to quantify trace analytes in water. In CSPE, analytes are extracted and complexed on the surface of an extraction membrane impregnated with a colorimetric reagent. The analytes are then quantified directly on the membrane surface using a handheld diffuse reflectance spectrophotometer. Importantly, the use of solid-phase extraction membranes as the matrix for impregnation of the colorimetric reagents creates a concentration factor that enables the detection of low concentrations of analytes in small sample volumes. In extending C-SPE to a multiplexed format, a filter holder that incorporates discrete analysis channels and a jig that facilitates the concurrent operation of multiple sample syringes have been designed, enabling the simultaneous determination of multiple analytes. Separate, single analyte membranes, placed in a readout cartridge create unique, analyte-specific addresses at the exit of each channel. Following sample exposure, the diffuse reflectance spectrum of each address is collected serially and the Kubelka-Munk function is used to quantify each water quality parameter via calibration curves. In a demonstration, MC-SPE was used to measure the pH of a sample and quantitate Ag(I) and Ni(II).

  7. Multiplexed quantification for data-independent acquisition.

    PubMed

    Minogue, Catherine E; Hebert, Alexander S; Rensvold, Jarred W; Westphall, Michael S; Pagliarini, David J; Coon, Joshua J

    2015-03-01

    Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS(2) spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS(1)-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches. PMID:25621425

  8. Multiplexed protein profiling by sequential affinity capture.

    PubMed

    Ayoglu, Burcu; Birgersson, Elin; Mezger, Anja; Nilsson, Mats; Uhlén, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2016-04-01

    Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off-target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi-automated sequential capture assay. This novel bead-based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read-out by a secondary capture bead array. We demonstrate in a proof-of-concept setting that target detection via two sequential affinity interactions reduced off-target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA-based signal amplification, and demonstrate the applicability of the dual capture bead-based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond. PMID:26935855

  9. Multiplexing holograms in an acrylamide photopolymer

    NASA Astrophysics Data System (ADS)

    Fernández, Elena; Ortuño, Manuel; Márquez, Andrés; Gallego, Sergi; Pascual, Inmaculada

    2006-04-01

    A peristrophic multiplexing method is used to store various diffraction gratings at the same spot in the material. This material is formed of acrylamide photopolymers which are considered interesting materials for recording holographic memories. They have high diffraction efficiency (ratio between diffracted and incident beams), high energetic sensitivity and optical quality, and developing processes are not necessary. In this work, the photopolymer is composed of acrylamide (AA) as the polymerizable monomer, triethanolamine (TEA) as radical generator, N,N'methylene-bis-acrylamide (BMA) as crosslinker, yellowish eosin (YE) as sensitizer and a binder of polyvinyl alcohol (PVA). The layers of material obtained are approximately 1 mm thick. Using holographic recording schedules, the exposure energy each hologram should receive in order to achieve uniform diffraction efficiency is optimized. The purpose of these recording schedules is to enable full advantage to be taken of the whole dynamic range of the material and to share it between the individual holograms. The Scheduled Exposure Method (SEM) and the Incremental Exposure Method (IEM) are the two multiplexing schedules used to determine the recording times. Having determined these times, the results obtained with both methods are compared to ascertain which method enables the greatest number of holograms to be recorded with the highest, most uniform diffraction efficiencies.

  10. Mesoscopic quantum multiplex for channeling bunches

    NASA Astrophysics Data System (ADS)

    Shen, Jing

    1998-09-01

    (1) Bogacz-Cline channeling is an interesting idea that can transform a bunch of low particle intensity to a collider of high luminosity but it was maintained as impossible to carry out because of three technical problems. (2) The first of which is discussed in this paper, and it is how to get billions particles from each bunch to enter into and channel through a single crystal channel. (3) Two basic difficulties of entrance are discussed in this paper. The first is due to the Heisenberg's uncertainty, and the second is the dimension reduction of a beam bunch in crystal from 3D to 1D. (4) To overcome these difficulties, a hybrid device named Mesoscopic Quantum Multiplex (MQM) is designed to achieve entrance and channeling. It is a quantum generalization of classical multiplex in detector readout electronics for the classical-quantum interface. It is made by nano-crystalline technology. (5) The MQM can channel the Richter-Kimura-Takada flat e± beams of NLC-JLC, and low emittance p or heavy ion beams as well as the Bogacz-Cline μ± beams, and the Nagamine-Chu cool μ± beams.

  11. Pneumatic Valve Operated by Multiplex Pneumatic Transmission

    NASA Astrophysics Data System (ADS)

    Nishioka, Yasutaka; Suzumori, Koichi; Kanda, Takefumi; Wakimoto, Shuichi

    A pneumatic system has several advantages, which are cheapness, lightweight, and reliability to human and environment. These advantages are adapted to some research areas, such as industrial lines, medical and nursing cares, and rehabilitation tools. However, the pneumatic system needs several devices; compressor, air tube, and control valve. This research aim to downsize pneumatic system. In this paper, a new method of multiplex pneumatic transmission for multi-pneumatic servo system is proposed. The valve for this system consists of two vibrators supported by springs, which was designed with simple and cheap structure. The working principle of the valve is vibrators resonance from multiplex pneumatic transmission and it is possible to work as ON/OFF valves without electric wire. Dynamic simulation was used to confirm the working principle of the resonance driving system. A prototype device confirming the principle was designed and developed based on the simulation. The experiments show that this new control system works very well to control two separated valves through single pneumatic tube.

  12. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  13. Controllability of asynchronous Boolean multiplex control networks

    NASA Astrophysics Data System (ADS)

    Luo, Chao; Wang, Xingyuan; Liu, Hong

    2014-09-01

    In this article, the controllability of asynchronous Boolean multiplex control networks (ABMCNs) is studied. First, the model of Boolean multiplex control networks under Harvey' asynchronous update is presented. By means of semi-tensor product approach, the logical dynamics is converted into linear representation, and a generalized formula of control-depending network transition matrices is achieved. Second, a necessary and sufficient condition is proposed to verify that only control-depending fixed points of ABMCNs can be controlled with probability one. Third, using two types of controls, the controllability of system is studied and formulae are given to show: (a) when an initial state is given, the reachable set at time s under a group of specified controls; (b) the reachable set at time s under arbitrary controls; (c) the specific probability values from a given initial state to destination states. Based on the above formulae, an algorithm to calculate overall reachable states from a specified initial state is presented. Moreover, we also discuss an approach to find the particular control sequence which steers the system between two states with maximum probability. Examples are shown to illustrate the feasibility of the proposed scheme.

  14. Multiplexed Quantification for Data-Independent Acquisition

    PubMed Central

    Minogue, Catherine E.; Hebert, Alexander S.; Rensvold, Jarred W.; Westphall, Michael S.; Pagliarini, David J.; Coon, Joshua J.

    2015-01-01

    Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS2 spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS1-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches. PMID:25621425

  15. Dispersion-reduction technique using subcarrier multiplexing

    SciTech Connect

    Sargis, P.D.; Haigh, R.E.; McCammon, K.G.

    1995-10-18

    We have developed a novel dispersion-reduction technique using subcarrier multiplexing (SCM) which permits the transmission of multiple 2.5 Gbit/s data channels over hundreds of kilometers of conventional fiber-optic cable with negligible dispersion. Using a lithium niobate external modulator having a modulation bandwidth of 20 GHz, we are able to multiplex several high-speed data channels at a single wavelength. At the receiving end, we demultiplex the data and detect each channel using a 2-GHz bandwidth optical detector. All of the hardware in our system consists of off-the-shelf components and can be integrated to reduce the overall cost. We demonstrated our dispersion-reduction technique in a recent field trial by transmitting two 2.5 Gbit/s data channels over 90 km of commercially-installed single-mode fiber, followed by 210 km of spooled fiber. For comparison, we substituted the 300 km of fiber with equivalent optical attenuation. We also ran computer simulations to evaluate link behavior. Technical details and field trial results will be presented.

  16. SNP Markers as Additional Information to Resolve Complex Kinship Cases

    PubMed Central

    Pontes, M. Lurdes; Fondevila, Manuel; Laréu, Maria Victoria; Medeiros, Rui

    2015-01-01

    Summary Background DNA profiling with sets of highly polymorphic autosomal short tandem repeat (STR) markers has been applied in various aspects of human identification in forensic casework for nearly 20 years. However, in some cases of complex kinship investigation, the information provided by the conventionally used STR markers is not enough, often resulting in low likelihood ratio (LR) calculations. In these cases, it becomes necessary to increment the number of loci under analysis to reach adequate LRs. Recently, it has been proposed that single nucleotide polymorphisms (SNPs) could be used as a supportive tool to STR typing, eventually even replacing the methods/markers now employed. Methods In this work, we describe the results obtained in 7 revised complex paternity cases when applying a battery of STRs, as well as 52 human identification SNPs (SNPforID 52plex identification panel) using a SNaPshot methodology followed by capillary electrophoresis. Results Our results show that the analysis of SNPs, as complement to STR typing in forensic casework applications, would at least increase by a factor of 4 total PI values and correspondent Essen-Möller's W value. Conclusions We demonstrated that SNP genotyping could be a key complement to STR information in challenging casework of disputed paternity, such as close relative individualization or complex pedigrees subject to endogamous relations. PMID:26733770

  17. Imputation of KIR Types from SNP Variation Data.

    PubMed

    Vukcevic, Damjan; Traherne, James A; Næss, Sigrid; Ellinghaus, Eva; Kamatani, Yoichiro; Dilthey, Alexander; Lathrop, Mark; Karlsen, Tom H; Franke, Andre; Moffatt, Miriam; Cookson, William; Trowsdale, John; McVean, Gil; Sawcer, Stephen; Leslie, Stephen

    2015-10-01

    Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed investigation of the role of KIRs in human disease. PMID:26430804

  18. Imputation of KIR Types from SNP Variation Data

    PubMed Central

    Vukcevic, Damjan; Traherne, James A.; Næss, Sigrid; Ellinghaus, Eva; Kamatani, Yoichiro; Dilthey, Alexander; Lathrop, Mark; Karlsen, Tom H.; Franke, Andre; Moffatt, Miriam; Cookson, William; Trowsdale, John; McVean, Gil; Sawcer, Stephen; Leslie, Stephen

    2015-01-01

    Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed investigation of the role of KIRs in human disease. PMID:26430804

  19. Porcine colonization of the Americas: a 60k SNP story

    PubMed Central

    Burgos-Paz, W; Souza, C A; Megens, H J; Ramayo-Caldas, Y; Melo, M; Lemús-Flores, C; Caal, E; Soto, H W; Martínez, R; Álvarez, L A; Aguirre, L; Iñiguez, V; Revidatti, M A; Martínez-López, O R; Llambi, S; Esteve-Codina, A; Rodríguez, M C; Crooijmans, R P M A; Paiva, S R; Schook, L B; Groenen, M A M; Pérez-Enciso, M

    2013-01-01

    The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level. PMID:23250008

  20. Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.

    PubMed

    Ogden, R; Gharbi, K; Mugue, N; Martinsohn, J; Senn, H; Davey, J W; Pourkazemi, M; McEwing, R; Eland, C; Vidotto, M; Sergeev, A; Congiu, L

    2013-06-01

    Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. PMID:23473098