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  1. Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens.

    Science.gov (United States)

    Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

    2009-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.

  2. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes

    NARCIS (Netherlands)

    Al-Attar, S.; Westra, E.R.; Oost, van der J.; Brouns, S.J.J.

    2011-01-01

    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences

  3. Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

    Science.gov (United States)

    He, Jiankui; Deem, Michael W.

    2010-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.

  4. Clustered regularly interspaced short palindromic repeats (CRISPRs) analysis of members of the Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Botelho, Ana; Canto, Ana; Leão, Célia; Cunha, Mónica V

    2015-01-01

    Typical CRISPR (clustered, regularly interspaced, short palindromic repeat) regions are constituted by short direct repeats (DRs), interspersed with similarly sized non-repetitive spacers, derived from transmissible genetic elements, acquired when the cell is challenged with foreign DNA. The analysis of the structure, in number and nature, of CRISPR spacers is a valuable tool for molecular typing since these loci are polymorphic among strains, originating characteristic signatures. The existence of CRISPR structures in the genome of the members of Mycobacterium tuberculosis complex (MTBC) enabled the development of a genotyping method, based on the analysis of the presence or absence of 43 oligonucleotide spacers separated by conserved DRs. This method, called spoligotyping, consists on PCR amplification of the DR chromosomal region and recognition after hybridization of the spacers that are present. The workflow beneath this methodology implies that the PCR products are brought onto a membrane containing synthetic oligonucleotides that have complementary sequences to the spacer sequences. Lack of hybridization of the PCR products to a specific oligonucleotide sequence indicates absence of the correspondent spacer sequence in the examined strain. Spoligotyping gained great notoriety as a robust identification and typing tool for members of MTBC, enabling multiple epidemiological studies on human and animal tuberculosis.

  5. Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

    Science.gov (United States)

    Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

    2015-06-01

    In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. [Clustered regularly interspaced short palindromic repeats (CRISPR) site in Bacillus anthracis].

    Science.gov (United States)

    Gao, Zhiqi; Wang, Dongshu; Feng, Erling; Wang, Bingxiang; Hui, Yiming; Han, Shaobo; Jiao, Lei; Liu, Xiankai; Wang, Hengliang

    2014-11-04

    To investigate the polymorphism of clustered regularly interspaced short palindromic repeats (CRISPR) in Bacillu santhracis and the application to molecular typing based on the polymorphism of CRISPR in B. anthracis. We downloaded the whole genome sequence of 6 B. anthracis strains and extracted the CRISPR sites. We designed the primers of CRISPR sites and amplified the CRISPR fragments in 193 B. anthracis strains by PCR and sequenced these fragments. In order to reveal the polymorphism of CRISPR in B. anthracis, wealigned all the extracted sequences and sequenced results by local blasting. At the same time, we also analyzed the CRISPR sites in B. cereus and B. thuringiensis. We did not find any polymorphism of CRISPR in B. anthracis. The molecular typing approach based on CRISPR polymorphism is not suitable for B. anthracis, but it is possible for us to distinguish B. anthracis from B. cereus and B. thuringiensis.

  7. Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR / CRISPR Associated (Cas Systems

    Directory of Open Access Journals (Sweden)

    Peter C. Fineran

    2012-10-01

    Full Text Available Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas proteins, into short interfering RNAs (crRNAs, which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

  8. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems.

    Science.gov (United States)

    Richter, Corinna; Chang, James T; Fineran, Peter C

    2012-10-19

    Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

  9. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats.

    Science.gov (United States)

    Cui, Yujun; Li, Yanjun; Gorgé, Olivier; Platonov, Mikhail E; Yan, Yanfeng; Guo, Zhaobiao; Pourcel, Christine; Dentovskaya, Svetlana V; Balakhonov, Sergey V; Wang, Xiaoyi; Song, Yajun; Anisimov, Andrey P; Vergnaud, Gilles; Yang, Ruifu

    2008-07-09

    Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.

  10. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats.

    Directory of Open Access Journals (Sweden)

    Yujun Cui

    Full Text Available BACKGROUND: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR, an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CONCLUSIONS/SIGNIFICANCE: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.

  11. Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity

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    Briner, Alexandra E.

    2014-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel “spacers” that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5′-AAAA-3′. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri. PMID:24271175

  12. [Molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat in Shigella].

    Science.gov (United States)

    Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Yang, Haiyan; Xi, Yuanlin; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao

    2015-08-01

    To detect the molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in Shigella and to analyze the distribution of CRISPR related to the time of isolation. Of the 52 Shigella strains, 41 were isolated from Henan, 6 from Jiangxi and 5 isolated from Beijing. Both CRISPR locus of S1, S2, S3 and S4 in Shigella were detected by polymerase chain reaction (PCR). The PCR products were sequenced and compared. The positive rates of CRISPR locus in Shigella were 33.69% (S1), 50.00% (S2), 82.69% (S3) and 73.08% (S4), respectively. Two subtypes were discovered in S1 and S3 locus. Three subtypes were discovered in S2 locus. Four different subtypes were discovered in S4 locus. The isolates from Henan strains were divided into two groups by the time of isolation. Distributions of S1 were different, before or after 2004, on Shigella. S1 could not be detected after 2004. There were no statistical differences of S2, S3 and S4 in two groups. Different CRISPR subtypes or Shigella were discovered. A significant correlation was noticed between the CRISPR S1 related to the time of isolation but not between S2, S3 or S4 on the time of isolation.

  13. Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity.

    Science.gov (United States)

    Briner, Alexandra E; Barrangou, Rodolphe

    2014-02-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.

  14. Clustered, regularly interspaced short palindromic repeat (CRISPR) diversity and virulence factor distribution in avian Escherichia coli.

    Science.gov (United States)

    Fu, Qiang; Su, Zhixin; Cheng, Yuqiang; Wang, Zhaofei; Li, Shiyu; Wang, Heng'an; Sun, Jianhe; Yan, Yaxian

    In order to investigate the diverse characteristics of clustered, regularly interspaced short palindromic repeat (CRISPR) arrays and the distribution of virulence factor genes in avian Escherichia coli, 80 E. coli isolates obtained from chickens with avian pathogenic E. coli (APEC) or avian fecal commensal E. coli (AFEC) were identified. Using the multiplex polymerase chain reaction (PCR), five genes were subjected to phylogenetic typing and examined for CRISPR arrays to study genetic relatedness among the strains. The strains were further analyzed for CRISPR loci and virulence factor genes to determine a possible association between their CRISPR elements and their potential virulence. The strains were divided into five phylogenetic groups: A, B1, B2, D and E. It was confirmed that two types of CRISPR arrays, CRISPR1 and CRISPR2, which contain up to 246 distinct spacers, were amplified in most of the strains. Further classification of the isolates was achieved by sorting them into nine CRISPR clusters based on their spacer profiles, which indicates a candidate typing method for E. coli. Several significant differences in invasion-associated gene distribution were found between the APEC isolates and the AFEC isolates. Our results identified the distribution of 11 virulence genes and CRISPR diversity in 80 strains. It was demonstrated that, with the exception of iucD and aslA, there was no sharp demarcation in the gene distribution between the pathogenic (APEC) and commensal (AFEC) strains, while the total number of indicated CRISPR spacers may have a positive correlation with the potential pathogenicity of the E. coli isolates. Copyright © 2016. Published by Elsevier Masson SAS.

  15. Short communication: Determination of Salmonella clustered regularly interspaced short palindromic repeats (CRISPR) diversity on dairy farms in Wisconsin and Minnesota.

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    Wehnes, C A; Rehberger, T G; Barrangou, R; Smith, A H

    2014-10-01

    Salmonella enterica ssp. enterica is a foodborne pathogen able to cause disease in both humans and animals. Diverse serovars of this pathogen exist, some of which are host specific, causing a range of clinical symptoms from asymptomatic infection through morbidity and mortality. According to a 2007 survey by the USDA National Animal Health Monitoring System, fecal shedding of Salmonella from healthy cows occurs on 39.7% of dairy farms in the United States. Certain serovars are frequently isolated from dairy farms and the majority of isolates from the National Animal Health Monitoring System study were represented by 5 serovars; however, genotypic diversity was not examined. The objective of this study was to determine the diversity of clustered regularly interspaced short palindromic repeats (CRISPR) loci in Salmonella collected from 8 dairy farms with a previous history of salmonellosis. None of the cows or calves sampled on 2 of the 8 dairy farms were shedding Salmonella, although Salmonella was detected in a cow bedding sample on 1 of these farms. Salmonella populations were discrete on each farm, according to CRISPR typing, with the exception of an Anatum var. 15+ type on farms 5 and 6 and the Montevideo type on farms 1 and 2. One to 4 distinct CRISPR genotypes were identified per farm. The CRISPR typing differed within serovars, as Montevideo, Anatum var. 15+, and Muenster serovars had no overlap of spacer content, even on the same farm, reflecting between- and within-serovar genetic diversity. The dynamic nature of Salmonella populations was shown in a farm that was sampled longitudinally over 13.5 mo. Changes in serovar from 3,19:-:z27 to Montevideo was observed between the first sampling time and 8 mo later, with concomitant change in CRISPR alleles. The results indicate that Salmonella strains present in smaller dairy herds (<500 head) are specific to that farm and new Salmonella strains may emerge over time. Copyright © 2014 American Dairy Science

  16. [Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

    Science.gov (United States)

    Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

    2009-11-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

  17. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

    DEFF Research Database (Denmark)

    Peng, Xu; Brügger, Kim; Shen, Biao

    2003-01-01

    that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N...... terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

  18. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.

    Science.gov (United States)

    Al-Attar, Sinan; Westra, Edze R; van der Oost, John; Brouns, Stan J J

    2011-04-01

    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' 'immunological memory'. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.

  19. Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

    Science.gov (United States)

    Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

    2013-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

  20. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.

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    Burmistrz, Michal; Rodriguez Martinez, Jose Ignacio; Krochmal, Daniel; Staniec, Dominika; Pyrc, Krzysztof

    2017-12-01

    The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in Porphyromonas gingivalis , a human pathogen associated with periodontitis, rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. We demonstrated the importance of the 5' handle for crRNA recognition by the effector complex and consequently activity, as well as secondary trimming of the 3' handle, which was not affected by modifications of the repeat sequence. IMPORTANCE Porphyromonas gingivalis , a clinically relevant Gram-negative, anaerobic bacterium, is one of the major etiologic agents of periodontitis and has been linked with the development of other clinical conditions, including rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. The presented results on the biogenesis and functions of crRNAs expand our understanding of CRISPR-Cas cellular defenses in P. gingivalis and of horizontal gene transfer in bacteria. Copyright © 2017 American Society for Microbiology.

  1. Recent progress in technological improvement and biomedical applications of the clustered regularly interspaced short palindromic repeats/cas system

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    Yanlan Li

    2017-01-01

    Full Text Available The adaptive immune systems of clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated genes (Cas selectively destroy nonnative DNA and defend almost all archaea and about half of the bacteria against infections. In the past years, the system has been genetically engineered to a powerful genome editing tool for a wide variety of organisms. Recently, many progresses have been made in the CRISPR-Cas systems. These improvements include applications in editing multiple genes, correcting mutation genes with one base difference, targeting nondividing cells, reducing off-target, and editing RNAs. The biomedical applications of the technology are to edit not only cells but also embryos in clinical settings. In this review, we briefly introduce the improvements of CRISPR-Cas9 gene editing methods and summarize the recent advances of this technology.

  2. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora.

    Science.gov (United States)

    Rezzonico, Fabio; Smits, Theo H M; Duffy, Brion

    2011-06-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.

  3. Myotube differentiation in clustered regularly interspaced short palindromic repeat/Cas9-mediated MyoD knockout quail myoblast cells

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    Si Won Kim

    2017-07-01

    Full Text Available Objective In the livestock industry, the regulatory mechanisms of muscle proliferation and differentiation can be applied to improve traits such as growth and meat production. We investigated the regulatory pathway of MyoD and its role in muscle differentiation in quail myoblast cells. Methods The MyoD gene was mutated by the clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 technology and single cell-derived MyoD mutant sublines were identified to investigate the global regulatory mechanism responsible for muscle differentiation. Results The mutation efficiency was 73.3% in the mixed population, and from this population we were able to establish two QM7 MyoD knockout subline (MyoD KO QM7#4 through single cell pick-up and expansion. In the undifferentiated condition, paired box 7 expression in MyoD KO QM7#4 cells was not significantly different from regular QM7 (rQM7 cells. During differentiation, however, myotube formation was dramatically repressed in MyoD KO QM7#4 cells. Moreover, myogenic differentiation-specific transcripts and proteins were not expressed in MyoD KO QM7#4 cells even after an extended differentiation period. These results indicate that MyoD is critical for muscle differentiation. Furthermore, we analyzed the global regulatory interactions by RNA sequencing during muscle differentiation. Conclusion With CRISPR/Cas9-mediated genomic editing, single cell-derived sublines with a specific knockout gene can be adapted to various aspects of basic research as well as in functional genomics studies.

  4. Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.

    Directory of Open Access Journals (Sweden)

    Po-Xing Zheng

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.

  5. Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System*

    Science.gov (United States)

    Stachler, Aris-Edda; Marchfelder, Anita

    2016-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is used by bacteria and archaea to fend off foreign genetic elements. Since its discovery it has been developed into numerous applications like genome editing and regulation of transcription in eukaryotes and bacteria. For archaea currently no tools for transcriptional repression exist. Because molecular biology analyses in archaea become more and more widespread such a tool is vital for investigating the biological function of essential genes in archaea. Here we use the model archaeon Haloferax volcanii to demonstrate that its endogenous CRISPR-Cas system I-B can be harnessed to repress gene expression in archaea. Deletion of cas3 and cas6b genes results in efficient repression of transcription. crRNAs targeting the promoter region reduced transcript levels down to 8%. crRNAs targeting the reading frame have only slight impact on transcription. crRNAs that target the coding strand repress expression only down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%. Repression of an essential gene results in reduction of transcription levels down to 22%. Targeting efficiencies can be enhanced by expressing a catalytically inactive Cas3 mutant. Genes can be targeted on plasmids or on the chromosome, they can be monocistronic or part of a polycistronic operon. PMID:27226589

  6. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein.

    Science.gov (United States)

    Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P; Ke, Ailong

    2012-10-19

    The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.

  7. Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System.

    Science.gov (United States)

    Stachler, Aris-Edda; Marchfelder, Anita

    2016-07-15

    The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is used by bacteria and archaea to fend off foreign genetic elements. Since its discovery it has been developed into numerous applications like genome editing and regulation of transcription in eukaryotes and bacteria. For archaea currently no tools for transcriptional repression exist. Because molecular biology analyses in archaea become more and more widespread such a tool is vital for investigating the biological function of essential genes in archaea. Here we use the model archaeon Haloferax volcanii to demonstrate that its endogenous CRISPR-Cas system I-B can be harnessed to repress gene expression in archaea. Deletion of cas3 and cas6b genes results in efficient repression of transcription. crRNAs targeting the promoter region reduced transcript levels down to 8%. crRNAs targeting the reading frame have only slight impact on transcription. crRNAs that target the coding strand repress expression only down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%. Repression of an essential gene results in reduction of transcription levels down to 22%. Targeting efficiencies can be enhanced by expressing a catalytically inactive Cas3 mutant. Genes can be targeted on plasmids or on the chromosome, they can be monocistronic or part of a polycistronic operon. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.

    Science.gov (United States)

    Zheng, Po-Xing; Chan, Yuen-Chi; Chiou, Chien-Shun; Chiang-Ni, Chuan; Wang, Shu-Ying; Tsai, Pei-Jane; Chuang, Woei-Jer; Lin, Yee-Shin; Liu, Ching-Chuan; Wu, Jiunn-Jong

    2015-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.

  9. Development of a novel molecular detection method for clustered regularly interspaced short palindromic repeats (CRISPRs) in Taylorella organisms.

    Science.gov (United States)

    Hara, Yasushi; Nakajima, Takuya; Akamatsu, Marie; Yahiro, Motoki; Kagawa, Shizuko; Petry, Sandrine; Matsuda, Motoo; Moore, John E

    2015-07-01

    Contagious equine metritis is a bacterial infectious disease of horses caused by Taylorella equigenitalis, a Gram-negative eubacterium. The disease has been described in several continents, including Europe, North America and Asia. A novel molecular method was developed to detect clustered regularly interspaced short palindromic repeats (CRISPRs), which were separated by non-repetitive unique spacer regions (NRUSRs) of similar length, in the Taylorella equigenitalis EQ59 strain using a primer pair, f-/r-TeCRISPR-ladder, by PCR amplification. In total, 31 Taylorella isolates (17 T. equigenitalis and 14 Taylorella asinigenitalis) were examined. The T. equigenitalis isolates came from thoroughbred and cold-blooded horses from nine countries during 1980-1996, whilst the T. asinigenitalis isolates all originated from donkey jacks in France and the USA during 1997-2006. PAGE fractionated all of the 13 CRISPRs separated by 12 NRUSRs in T. equigenitalis EQ59. Permutation examples of CRISPRs, which were separated by NRUSRs for small-sized ladders, consisting of two doublet bands were shown. Putative CRISPRs separated by NRUSRs were amplified with 14/17 (82.4 %) geographically disparate T. equigenitalis isolates using the newly designed primer pair. Approximately 82.4 % of the T. equigenitalis isolates had CRISPRs separated by NRUSRs. The CRISPR locus was also found in the French T. asinigenitalis strain MCE3. Putative CRISPRs separated by NRUSRs were detected similarly in 4/14 (28.6 %) T. asinigenitalis isolates. Overall, a more detailed understanding of the molecular biology of CRISPRs within Taylorella organisms may help elucidate the pathogenic virulence and transmission mechanisms associated with this important equine pathogen.

  10. Characterization of the clustered regularly interspaced short palindromic repeats sites in Streptococcus mutans isolated from early childhood caries patients.

    Science.gov (United States)

    Chen, Jing; Li, Tiancheng; Zhou, Xuedong; Cheng, Lei; Huo, Yuanyuan; Zou, Jing; Li, Yuqing

    2017-11-01

    The aim of this study was to analyze the characteristics of the clustered regularly interspaced short palindromic repeats (CRISPR) sites in 45 clinical Streptococcus mutans strains and their relationship to the clinical manifestations of early childhood caries (ECC). Forty-five S. mutans strains were isolated from the plaque samples taken from sixty-three children. CRISPR sites were sequenced and BLAST was used to compare these sites to those in the CRISPRTarget database. The association between the distribution of CRISPR sites and the manifestation of caries was analyzed by Chi-Square test. Further, biofilm formation (by crystal violet staining) and the synthesis of polysaccharide (by anthrone-sulfuric method) of all clinical isolated S. mutans strains with both CRISPR sites and no CRISPR site were comapared. Finally, acidogenicity and acidurity of two typical strains were determined using pH drop and acid tolerance assays. Biofilm formation and EPS synthesis by two typical strains were compared by 3D CLSM (Confocal Laser Scanning Microscope) assays and the expression of gtf genes were evaluated using qPCR. We found that most of the spacers in the clinical S. mutans strains were derived from Streptococcus phages APCM01 and M102. The number of CRISPR sites in these strains was associated with the clinical manifestations of ECC. Moreover, we found that the biofilm formation and EPS synthesis ability of the S. mutans strains with both CRISPR sites was significant improved. An association was found between the distribution of CRISPR sites and the clinical manifestations of caries. The CRISPR sites might contribute to the cariogenic potential of S. mutans. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC).

    Science.gov (United States)

    Tasaki, E; Hirayama, J; Tazumi, A; Hayashi, K; Hara, Y; Ueno, H; Moore, J E; Millar, B C; Matsuda, M

    2012-02-01

    Novel clustered regularly-interspaced short palindromic repeats (CRISPRs) locus [7,500 base pairs (bp) in length] occurred in the urease-positive thermophilic Campylobacter (UPTC) Japanese isolate, CF89-12. The 7,500 bp gene loci consisted of the 5'-methylaminomethyl-2-thiouridylate methyltransferase gene, putative (P) CRISPR associated (p-Cas), putative open reading frames, Cas1 and Cas2, leader sequence region (146 bp), 12 CRISPRs consensus sequence repeats (each 36 bp) separated by a non-repetitive unique spacer region of similar length (26-31 bp) and the phosphatidyl glycerophosphatase A gene. When the CRISPRs loci in the UPTC CF89-12 and five C. jejuni isolates were compared with one another, these six isolates contained p-Cas, Cas1 and Cas2 within the loci. Four to 12 CRISPRs consensus sequence repeats separated by a non-repetitive unique spacer region occurred in six isolates and the nucleotide sequences of those repeats gave approximately 92-100% similarity with each other. However, no sequence similarity occurred in the unique spacer regions among these isolates. The putative σ(70) transcriptional promoter and the hypothetical ρ-independent terminator structures for the CRISPRs and Cas were detected. No in vivo transcription of p-Cas, Cas1 and Cas2 was confirmed in the UPTC cells.

  12. An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein.

    Science.gov (United States)

    Maier, Lisa-Katharina; Stachler, Aris-Edda; Saunders, Sita J; Backofen, Rolf; Marchfelder, Anita

    2015-02-13

    The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3' handle are still active in triggering an interference reaction. The complete 3' handle could be removed without loss of activity. However, manipulations of the 5' handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. An Active Immune Defense with a Minimal CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA and without the Cas6 Protein*

    Science.gov (United States)

    Maier, Lisa-Katharina; Stachler, Aris-Edda; Saunders, Sita J.; Backofen, Rolf; Marchfelder, Anita

    2015-01-01

    The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3′ handle are still active in triggering an interference reaction. The complete 3′ handle could be removed without loss of activity. However, manipulations of the 5′ handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference. PMID:25512373

  14. Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures.

    Science.gov (United States)

    Kuno, Sotaro; Yoshida, Takashi; Kaneko, Takakazu; Sako, Yoshihiko

    2012-08-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.

  15. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

    DEFF Research Database (Denmark)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...

  16. Disruption of human papillomavirus 16 E6 gene by clustered regularly interspaced short palindromic repeat/Cas system in human cervical cancer cells [Retraction

    Directory of Open Access Journals (Sweden)

    Yu L

    2017-06-01

    Full Text Available Yu L, Wang XL, Zhu D, et al. Disruption of human papillomavirus 16 E6 gene by clustered regularly interspaced short palindromic repeat/Cas system in human cervical cancer cells. OncoTargets and Therapy. 2015;8:37–44 was published subsequent to Hu Z, Yu L, Zhu D, et al. Disruption of HPV16-E7 by CRISPR/Cas system induces apoptosis and growth inhibition in HPV16 positive human cervical cancer cells. BioMed Research International. 2014 (2014, Article ID 612823.When comparing the above papers it becomes apparent that they have an unacceptably high degree of similarity and re-use. Accordingly, the Editor-in-Chief and Publisher have issued this Notice of Retraction.This retraction relates toThis retraction also relates to  

  17. Arrangement and number of clustered regularly interspaced short palindromic repeat spacers are associated with erythromycin susceptibility in emm12, emm75 and emm92 of group A streptococcus.

    Science.gov (United States)

    Zheng, P-X; Chiang-Ni, C; Wang, S-Y; Tsai, P-J; Kuo, C-F; Chuang, W-J; Lin, Y-S; Liu, C-C; Wu, J-J

    2014-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of numerous repeat-spacer units and are considered a prokaryotic defence system against foreign nucleic acids. Since antibiotic-resistant genes are frequently encoded in foreign nucleic acids, the aim of this study was to test whether erythromycin susceptibility in group A streptococcus (Streptococcus pyogenes) is associated with characteristics of CRISPR elements. Erythromycin susceptibility of 330 isolates collected between 1997 and 2003 was analysed. Among 29 emm types, emm12, emm75 and emm92 showed significant changes in erythromycin-resistance rates. By sequencing the spacers from two CRISPR loci, spacer contents in emm12, emm75 and emm92 strains were associated with erythromycin susceptibility. Strains with fewer spacers were more resistant to erythromycin. Moreover, in emm4 strains, which showed no significant change in their annual erythromycin-resistance rate, CRISPR type and number of spacers were not correlated with erythromycin susceptibility. These results highlight a novel association between CRISPR spacer content and erythromycin susceptibility in group A streptococcus. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  18. High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system.

    Science.gov (United States)

    Yosef, Ido; Goren, Moran G; Kiro, Ruth; Edgar, Rotem; Qimron, Udi

    2011-12-13

    Prokaryotic DNA arrays arranged as clustered regularly interspaced short palindromic repeats (CRISPR), along with their associated proteins, provide prokaryotes with adaptive immunity by RNA-mediated targeting of alien DNA or RNA matching the sequences between the repeats. Here, we present a thorough screening system for the identification of bacterial proteins participating in immunity conferred by the Escherichia coli CRISPR system. We describe the identification of one such protein, high-temperature protein G (HtpG), a homolog of the eukaryotic chaperone heat-shock protein 90. We demonstrate that in the absence of htpG, the E. coli CRISPR system loses its suicidal activity against λ prophage and its ability to provide immunity from lysogenization. Transcomplementation of htpG restores CRISPR activity. We further show that inactivity of the CRISPR system attributable to htpG deficiency can be suppressed by expression of Cas3, a protein that is essential for its activity. Accordingly, we also find that the steady-state level of overexpressed Cas3 is significantly enhanced following HtpG expression. We conclude that HtpG is a newly identified positive modulator of the CRISPR system that is essential for maintaining functional levels of Cas3.

  19. Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli.

    Science.gov (United States)

    Toro, Magaly; Cao, Guojie; Ju, Wenting; Allard, Marc; Barrangou, Rodolphe; Zhao, Shaohua; Brown, Eric; Meng, Jianghong

    2014-02-01

    Shiga toxin-producing Escherichia coli (STEC) strains (n = 194) representing 43 serotypes and E. coli K-12 were examined for clustered regularly interspaced short palindromic repeat (CRISPR) arrays to study genetic relatedness among STEC serotypes. A subset of the strains (n = 81) was further analyzed for subtype I-E cas and virulence genes to determine a possible association of CRISPR elements with potential virulence. Four types of CRISPR arrays were identified. CRISPR1 and CRISPR2 were present in all strains tested; 1 strain also had both CRISPR3 and CRISPR4, whereas 193 strains displayed a short, combined array, CRISPR3-4. A total of 3,353 spacers were identified, representing 528 distinct spacers. The average length of a spacer was 32 bp. Approximately one-half of the spacers (54%) were unique and found mostly in strains of less common serotypes. Overall, CRISPR spacer contents correlated well with STEC serotypes, and identical arrays were shared between strains with the same H type (O26:H11, O103:H11, and O111:H11). There was no association identified between the presence of subtype I-E cas and virulence genes, but the total number of spacers had a negative correlation with potential pathogenicity (P CRISPR-cas system and potential virulence needs to be determined on a broader scale, and the biological link will need to be established.

  20. Combination of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 technique with the piggybac transposon system for mouse in utero electroporation to study cortical development.

    Science.gov (United States)

    Cheng, Man; Jin, Xubin; Mu, Lili; Wang, Fangyu; Li, Wei; Zhong, Xiaoling; Liu, Xuan; Shen, Wenchen; Liu, Ying; Zhou, Yan

    2016-09-01

    In utero electroporation (IUE) is commonly used to study cortical development of cerebrum by downregulating or overexpressing genes of interest in neural progenitor cells (NPCs) of small mammals. However, exogenous plasmids are lost or diluted over time. Furthermore, gene knockdown based on short-hairpin RNAs may exert nonspecific effects that lead to aberrant neuronal migration. Genomic engineering by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has great research and therapeutic potentials. Here we integrate the CRISPR/Cas9 components into the piggyBac (PB) transposon system (the CRISPR/Cas9-PB toolkit) for cortical IUEs. The mouse Sry-related HMG box-2 (Sox2) gene was selected as the target for its application. Most transduced cortical NPCs were depleted of SOX2 protein as early as 3 days post-IUE, whereas expressions of SOX1 and PAX6 remained intact. Furthermore, both the WT Cas9 and the D10A nickase mutant Cas9n showed comparable knockout efficiency. Transduced cortical cells were purified with fluorescence-activated cell sorting, and effective gene editing at the Sox2 loci was confirmed. Thus, application of the CRISPR/Cas9-PB toolkit in IUE is a promising strategy to study gene functions in cortical NPCs and their progeny. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  1. The clustered regularly interspaced short palindromic repeats/associated proteins system for the induction of gene mutations and phenotypic changes in Bombyx mori.

    Science.gov (United States)

    Song, Jia; Che, Jiaqian; You, Zhengying; Ye, Xiaogang; Li, Jisheng; Ye, Lupeng; Zhang, Yuyu; Qian, Qiujie; Zhong, Boxiong

    2016-12-01

    To probe the general phenomena of gene mutations, Bombyx mori, the lepidopterous model organism, was chosen as the experimental model. To easily detect phenotypic variations, the piggyBac system was utilized to introduce two marker genes into the silkworm, and 23.4% transposition efficiency aided in easily breeding a new strain for the entire experiment. Then, the clustered regularly interspaced short palindromic repeats/an associated protein (Cas9) system was utilized. The results showed that the Cas9 system can induce efficient gene mutations and the base changes could be detected since the G0 individuals in B. mori; and that the mutation rates on different target sites were diverse. Next, the gRNA2-targeted site that generated higher mutation rate was chosen, and the experimental results were enumerated. First, the mutation proportion in G1 generation was 30.1%, and some gene mutations were not inherited from the G0 generation; second, occasionally, base substitutions did not lead to variation in the amino-acid sequence, which decreased the efficiency of phenotypic changes compared with that of genotypic changes. These results laid the foundation for better use of the Cas9 system in silkworm gene editing. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  3. Disruption of human papillomavirus 16 E6 gene by clustered regularly interspaced short palindromic repeat/Cas system in human cervical cancer cells

    Directory of Open Access Journals (Sweden)

    Yu L

    2014-12-01

    Full Text Available Lan Yu, Xiaoli Wang, Da Zhu, Wencheng Ding, Liming Wang, Changlin Zhang, Xiaohui Jiang, Hui Shen, Shujie Liao, Ding Ma, Zheng Hu, Hui Wang Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China Abstract: High-risk human papillomavirus (HPV, especially HPV16, is considered a main causative agent of cervical cancer. Upon HPV infection, the viral oncoprotein E6 disrupts the host tumor-suppressor protein p53, thus promoting malignant transformation of normal cervical cells. Here, we used the newly developed programmable ribonucleic acid-guided clustered regularly interspaced short palindromic repeat (CRISPR/Cas system to disrupt the HPV16 E6 gene. We showed that HPV16 E6 deoxyribonucleic acid was cleaved at specific sites, leading to apoptosis and growth inhibition of HPV16-positive SiHa and CaSki cells, but not HPV-negative C33A or human embryonic kidney 293 cells. We also observed downregulation of the E6 protein and restoration of the p53 protein. These data proved that the HPV16 E6 ribonucleic acid-guided CRISPR/Cas system might be an effective therapeutic agent in treating HPV infection-related cervical malignancy. Keywords: CRISPR/Cas system, E6, p53, SiHa, CaSki, cervical cancer

  4. Transgenic Clustered Regularly Interspaced Short Palindromic Repeat/Cas9-Mediated Viral Gene Targeting for Antiviral Therapy of Bombyx mori Nucleopolyhedrovirus.

    Science.gov (United States)

    Chen, Shuqing; Hou, Chengxiang; Bi, Honglun; Wang, Yueqiang; Xu, Jun; Li, Muwang; James, Anthony A; Huang, Yongping; Tan, Anjiang

    2017-04-15

    We developed a novel antiviral strategy by combining transposon-based transgenesis and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system for the direct cleavage of Bombyx mori nucleopolyhedrovirus (BmNPV) genome DNA to promote virus clearance in silkworms. We demonstrate that transgenic silkworms constitutively expressing Cas9 and guide RNAs targeting the BmNPV immediate early-1 ( ie-1 ) and me53 genes effectively induce target-specific cleavage and subsequent mutagenesis, especially large (∼7-kbp) segment deletions in BmNPV genomes, and thus exhibit robust suppression of BmNPV proliferation. Transgenic animals exhibited higher and inheritable resistance to BmNPV infection than wild-type animals. Our approach will not only contribute to modern sericulture but also shed light on future antiviral therapy. IMPORTANCE Pathogen genome targeting has shown its potential in antiviral research. However, transgenic CRISPR/Cas9 system-mediated viral genome targeting has not been reported as an antiviral strategy in a natural animal host of a virus. Our data provide an effective approach against BmNPV infection in a real-world biological system and demonstrate the potential of transgenic CRISPR/Cas9 systems in antiviral research in other species. Copyright © 2017 Chen et al.

  5. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    Science.gov (United States)

    Mulepati, Sabin; Bailey, Scott

    2011-09-09

    RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

  6. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    Science.gov (United States)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  7. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells.

    Science.gov (United States)

    Canver, Matthew C; Bauer, Daniel E; Dass, Abhishek; Yien, Yvette Y; Chung, Jacky; Masuda, Takeshi; Maeda, Takahiro; Paw, Barry H; Orkin, Stuart H

    2014-08-01

    The clustered regularly interspaced short [corrected] palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  9. Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

    Science.gov (United States)

    Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

    2011-07-01

    Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

  10. Generation of Hypertension-Associated STK39 Polymorphism Knockin Cell Lines With the Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 System.

    Science.gov (United States)

    Mandai, Shintaro; Mori, Takayasu; Sohara, Eisei; Rai, Tatemitsu; Uchida, Shinichi

    2015-12-01

    Previous genome-wide association studies identified serine threonine kinase 39 (STK39), encoding STE20/SPS1-related proline/alanine-rich kinase, as one of a limited number of hypertension susceptibility genes. A recent meta-analysis confirmed the association of STK39 intronic polymorphism rs3754777 with essential hypertension, among previously reported hypertension-associated STK39 polymorphisms. However, the biochemical function of this polymorphism in the mechanism responsible for hypertension is yet to be clarified. We generated rs3754777G>A knockin human cell lines with clustered regularly interspaced short palindromic repeats-mediated genome engineering. Homozygous (A/A) and heterozygous (G/A) knockin human embryonic kidney cell lines were generated using a double nickase, single-guide RNAs targeting STK39 intron 5 around single-nucleotide polymorphism, and a 100-bp donor single-stranded DNA oligonucleotide. Reverse transcription polymerase chain reaction with sequencing analyses revealed the identical STK39 transcripts among the wild-type and both knockin cell lines. Quantitative reverse transcription polymerase chain reaction showed increased STK39 mRNA expression, and immunoblot analysis revealed increases in total and phosphorylated STE20/SPS1-related proline/alanine-rich kinase with increased phosphorylated Na-K-Cl cotransporter isoform 1 in both knockin cell lines. The largest increases in these molecules were observed in the homozygous cell line. These findings indicated that this intronic polymorphism increases STK39 transcription, leading to activation of the STE20/SPS1-related proline/alanine-rich kinase-solute carrier family 12A signaling cascade. Increased interactions between STE20/SPS1-related proline/alanine-rich kinase and the target cation-chloride cotransporters may be responsible for hypertension susceptibility in individuals with this polymorphism. © 2015 American Heart Association, Inc.

  11. The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition.

    Science.gov (United States)

    Yin, Shuang; Jensen, Mark A; Bai, Jiawei; Debroy, Chitrita; Barrangou, Rodolphe; Dudley, Edward G

    2013-09-01

    The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the "big six" serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity.

  12. Relationship between drug resistance and the clustered, regularly interspaced, short, palindromic repeat-associated protein genes cas1 and cas2 in Shigella from giant panda dung.

    Science.gov (United States)

    Ren, Lu; Deng, Lin-Hua; Zhang, Ri-Peng; Wang, Cheng-Dong; Li, De-Sheng; Xi, Li-Xin; Chen, Zhen-Rong; Yang, Rui; Huang, Jie; Zeng, Yang-Ru; Wu, Hong-Lin; Cao, San-Jie; Wu, Rui; Huang, Yong; Yan, Qi-Gui

    2017-02-01

    To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis. Further, the Kirby-Bauer paper method was used to determine drug sensitivity of the Shigella strains. CRISPR-associated protein genes cas1 and cas2 in Shigella were detected by polymerase chain reaction (PCR), and the PCR products were sequenced and compared. We isolated and identified 17 strains of Shigella from 27 samples, including 14 strains of Shigella flexneri, 2 strains of Shigella sonnei, and 1 strain of Shigella dysenteriae. Further, drug resistance to cefazolin, imipenem, and amoxicillin-clavulanic acid was identified as a serious problem, as multidrug-resistant strains were detected. Further, cas1 and cas2 showed different degrees of point mutations. The CRISPR system widely exists in Shigella and shares homology with that in Escherichia coli. The cas1 and cas 2 mutations contribute to the different levels of resistance. Point mutations at sites 3176455, 3176590, and 3176465 in cas1 (a); sites 3176989, 3176992, and 3176995 in cas1 (b); sites 3176156 and 3176236 in cas2 may affect the resistance of bacteria, cause emergence of multidrug resistance, and increase the types of drug resistance.

  13. Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

    Science.gov (United States)

    Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J Antonio; Castro-Escarpulli, Graciela

    2015-08-04

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes. The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in

  14. Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

    Science.gov (United States)

    Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

    2016-09-01

    The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

  15. Performance Comparisons of Improved Regular Repeat Accumulate (RA and Irregular Repeat Accumulate (IRA Turbo Decoding

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulkadhim Hamad

    2017-08-01

    Full Text Available In this paper, different techniques are used to improve the turbo decoding of regular repeat accumulate (RA and irregular repeat accumulate (IRA codes. The adaptive scaling of a-posteriori information produced by Soft-output Viterbi decoder (SOVA is proposed. The encoded pilots are another scheme that applied for short length RA codes. This work also suggests a simple and a fast method to generate a random interleaver having a free 4 cycle Tanner graph. Progressive edge growth algorithm (PEG is also studied and simulated to create the Tanner graphs which have a great girth.

  16. Automatic detection of regularly repeating vocalizations

    Science.gov (United States)

    Mellinger, David

    2005-09-01

    Many animal species produce repetitive sounds at regular intervals. This regularity can be used for automatic recognition of the sounds, providing improved detection at a given signal-to-noise ratio. Here, the detection of sperm whale sounds is examined. Sperm whales produce highly repetitive ``regular clicks'' at periods of about 0.2-2 s, and faster click trains in certain behavioral contexts. The following detection procedure was tested: a spectrogram was computed; values within a certain frequency band were summed; time windowing was applied; each windowed segment was autocorrelated; and the maximum of the autocorrelation within a certain periodicity range was chosen. This procedure was tested on sets of recordings containing sperm whale sounds and interfering sounds, both low-frequency recordings from autonomous hydrophones and high-frequency ones from towed hydrophone arrays. An optimization procedure iteratively varies detection parameters (spectrogram frame length and frequency range, window length, periodicity range, etc.). Performance of various sets of parameters was measured by setting a standard level of allowable missed calls, and the resulting optimium parameters are described. Performance is also compared to that of a neural network trained using the data sets. The method is also demonstrated for sounds of blue whales, minke whales, and seismic airguns. [Funding from ONR.

  17. A short proof of increased parabolic regularity

    Directory of Open Access Journals (Sweden)

    Stephen Pankavich

    2015-08-01

    Full Text Available We present a short proof of the increased regularity obtained by solutions to uniformly parabolic partial differential equations. Though this setting is fairly introductory, our new method of proof, which uses a priori estimates and an inductive method, can be extended to prove analogous results for problems with time-dependent coefficients, advection-diffusion or reaction diffusion equations, and nonlinear PDEs even when other tools, such as semigroup methods or the use of explicit fundamental solutions, are unavailable.

  18. The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells.

    Science.gov (United States)

    Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A; Zhang, Feng; Lei, Hetian

    2016-07-29

    The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells*

    Science.gov (United States)

    Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A.; Zhang, Feng; Lei, Hetian

    2016-01-01

    The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR. PMID:27246850

  20. A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii*

    Science.gov (United States)

    Brendel, Jutta; Stoll, Britta; Lange, Sita J.; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A.; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

    2014-01-01

    The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA. PMID:24459147

  1. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii.

    Science.gov (United States)

    Brendel, Jutta; Stoll, Britta; Lange, Sita J; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

    2014-03-07

    The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.

  2. Correction of Hirschsprung-Associated Mutations in Human Induced Pluripotent Stem Cells Via Clustered Regularly Interspaced Short Palindromic Repeats/Cas9, Restores Neural Crest Cell Function.

    Science.gov (United States)

    Lai, Frank Pui-Ling; Lau, Sin-Ting; Wong, John Kwong-Leong; Gui, Hongsheng; Wang, Reeson Xu; Zhou, Tingwen; Lai, Wing Hon; Tse, Hung-Fat; Tam, Paul Kwong-Hang; Garcia-Barcelo, Maria-Mercedes; Ngan, Elly Sau-Wai

    2017-07-01

    Hirschsprung disease is caused by failure of enteric neural crest cells (ENCCs) to fully colonize the bowel, leading to bowel obstruction and megacolon. Heterozygous mutations in the coding region of the RET gene cause a severe form of Hirschsprung disease (total colonic aganglionosis). However, 80% of HSCR patients have short-segment Hirschsprung disease (S-HSCR), which has not been associated with genetic factors. We sought to identify mutations associated with S-HSCR, and used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing system to determine how mutations affect ENCC function. We created induced pluripotent stem cell (iPSC) lines from 1 patient with total colonic aganglionosis (with the G731del mutation in RET) and from 2 patients with S-HSCR (without a RET mutation), as well as RET +/- and RET -/- iPSCs. IMR90-iPSC cells were used as the control cell line. Migration and differentiation capacities of iPSC-derived ENCCs were analyzed in differentiation and migration assays. We searched for mutation(s) associated with S-HSCR by combining genetic and transcriptome data from patient blood- and iPSC-derived ENCCs, respectively. Mutations in the iPSCs were corrected using the CRISPR/Cas9 system. ENCCs derived from all iPSC lines, but not control iPSCs, had defects in migration and neuronal lineage differentiation. RET mutations were associated with differentiation and migration defects of ENCCs in vitro. Genetic and transcriptome analyses associated a mutation in the vinculin gene (VCL M209L) with S-HSCR. CRISPR/Cas9 correction of the RET G731del and VCL M209L mutations in iPSCs restored the differentiation and migration capacities of ENCCs. We identified mutations in VCL associated with S-HSCR. Correction of this mutation in iPSC using CRISPR/Cas9 editing, as well as the RET G731del mutation that causes Hirschsprung disease with total colonic aganglionosis, restored ENCC function. Our study demonstrates how human iPSCs can

  3. Modified Suboptimal Iterative Decoding for Regular Repeat- Accumulate Coded Signals

    Directory of Open Access Journals (Sweden)

    Muhammad Thamer Nesr

    2017-05-01

    Full Text Available In this work, two algorithms are suggested in order to improve the performance of systematic Repeat-Accumulate ( decoding. The first one is accomplished by the insertion of pilot symbols among the data stream that entering the encoder. The positions where pilots should be inserted are chosen in such a way that to improve the minimum Hamming distance and/or to reduce the error coefficients of the code. The second proposed algorithm includes the utilization of the inserted pilots to estimate scaling (correction factors. Two-dimensional correction factor was suggested in order to enhance the performance of traditional Minimum-Sum decoding of regular repeat accumulate codes. An adaptive method can be achieved for getting the correction factors by calculating the mean square difference between the values of received pilots and the a-posteriori data of bit and check node related to them which created by the minimum-sum ( decoder

  4. Use of Clustered Regularly Interspaced Short Palindromic Repeat Sequence Polymorphisms for Specific Detection of Enterohemorrhagic Escherichia coli Strains of Serotypes O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 by Real-Time PCR

    OpenAIRE

    Delannoy, Sabine; Beutin, Lothar; Fach, Patrick

    2012-01-01

    We explored the genetic diversity of the clustered regularly interspaced short palindromic repeat (CRISPR) regions of enterohemorrhagic Escherichia coli (EHEC) to design simplex real-time PCR assays for each of the seven most important EHEC serotypes worldwide. A panel of 958 E. coli strains investigated for their CRISPR loci by high-throughput real-time PCR showed that CRISPR polymorphisms in E. coli strongly correlated with both O:H serotypes and the presence of EHEC virulence factors (stx ...

  5. Short-sequence DNA repeats in prokaryotic genomes

    NARCIS (Netherlands)

    A.F. van Belkum (Alex); S. Scherer; L. van Alphen (Loek); H.A. Verbrugh (Henri)

    1998-01-01

    textabstractShort-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or

  6. Y-Chromosome short tandem repeat, typing technology, locus ...

    African Journals Online (AJOL)

    Y-Chromosome short tandem repeat, typing technology, locus information and allele frequency in different population: A review. ... This review will highlight the importance of the Y- Chromosome as a tool for tracing human evolution and describes some details of Y-chromosomal short tandem repeat (STR) analysis. Among ...

  7. Turkish population data on the short tandem repeat locus TPOX

    DEFF Research Database (Denmark)

    Vural, B; Poda, M; Atlioglu, E

    1998-01-01

    Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals.......Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals....

  8. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... 1Department of Biological Sciences, University of Botswana, P/Bag 00704, Gaborone, Botswana. 2Botswana Police Forensic Science Laboratory P/Bag 0012, Gaborone, Botswana. Accepted 15 February, 2008. Allele frequencies for nine short tandem repeat (STR) loci from the AmpFlSTR® Profiler Plus™ ...

  9. X-Chromosome short tandem repeat, advantages and typing ...

    African Journals Online (AJOL)

    Microsatellites of the X-chromosome have been increasingly studied in recent years as a useful tool in forensic analysis. This review describes some details of X-chromosomal short tandem repeat (STR) analysis. Among them are: microsatellites, amplification using polymerase chain reaction (PCR) of STRs, PCR product ...

  10. Genetic Analysis of Eight X-Chromosomal Short Tandem Repeat ...

    African Journals Online (AJOL)

    X-Chromosome short tandem repeat (STR) typing can complement existing DNA profiling protocols and can also offer useful information in cases of complex kinship analysis. This is the first population study of 8 X-linked STRs in Iraq. The purpose of this work was to provide a basic data of allele and haplotype frequency for ...

  11. Repeat-aware modeling and correction of short read errors.

    Science.gov (United States)

    Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

    2011-02-15

    High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors

  12. CRISPR Recognition Tool (CRT): a tool for automatic detection ofclustered regularly interspaced palindromic repeats

    Energy Technology Data Exchange (ETDEWEB)

    Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah; Lowe,Micheal; Brown, Kyndall; Kyrpides, Nikos C.; Hugenholtz, Philip

    2007-05-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT also demonstrated superior performance, especially for genomes containing large numbers of repeats. In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, was shown to be a significant improvement over the current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n) in space and O(nm/l) in time.

  13. The Effects of in-Season Repeated Sprint Training Compared to Regular Soccer Training

    Directory of Open Access Journals (Sweden)

    Solberg Nedrehagen Eirik

    2015-12-01

    Full Text Available The aim of this study was to compare the effects of repeated sprints (RSA training and regular soccer training on Yo-Yo IR-1 and RSA performance (6 × 40 m shuttle sprints. Thirteen semi-professional female soccer players and nine amateur male soccer players were randomised into a repeated sprint group (RSG; n = 12 or a regular soccer training group (STG; n = 10. The RSG soccer players executed 3-4 sets of 4-6 repeated sprints (30 m with 180° directional changes weekly during the last eight weeks of the in-season. In parallel, the STG soccer players performed low- to moderate intensity soccer training in form of technical or tactical skills. The RSG showed 15% improvement in Yo-Yo IR-1 (p = 0.04; ES = 1.83 and their mean RSA times were reduced by 1.5% (p = 0.02; ES = 0.89. No significant changes were found for the STG (Yo-Yo IR-1, p = 0.13; RSA, p = 0.49. Comparing the groups, greater improvements were observed in Yo-Yo IR-1 for the RSG (p = 0.02; ES = 1.15, but not for the RSA (p = 0.23; ES = -0.33. Similar training volumes and intensities (% of HFmax were observed between the groups (p = 0.22 and p = 0.79. In conclusion, a weekly RSA session integrated into a regular soccer regime improved in-season RSA and Yo-Yo IR-1 performance compared to regular soccer training.

  14. Short tandem repeat (STR) polymorphisms in Turkish population

    Indian Academy of Sciences (India)

    Keywords. forensic science; population genetics; short tandem repeat; polymorphism; human genetics; Turkey. Author Affiliations. Üner Ülküer1 Melahat Kurtuluş-Ülküer2 Cüneyt Elma1 Tahsin Kesici3 Sevda Menevşe4. General Directory of Security, Criminal Police Laboratories, Biyoloji Bölümü, Aniteppe, Ankara, Turkey ...

  15. CRISPR Recognition Tool (CRT: a tool for automatic detection of clustered regularly interspaced palindromic repeats

    Directory of Open Access Journals (Sweden)

    Brown Kyndall

    2007-06-01

    Full Text Available Abstract Background Clustered Regularly Interspaced Palindromic Repeats (CRISPRs are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. Results CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats. Conclusion In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n in space and O(nm/l in time.

  16. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... DNA fraction. Analysis of STRs is the most widely used method of genotyping used in forensic identification of individuals and for testing paternity. This is because ... Each STR is distinguished by the number of times a sequence is repeated, ... number of copies of the repeat sequence contained within the ...

  17. Exposing Students to Repeat Photography: Increasing Cultural Understanding on a Short-Term Study Abroad

    Science.gov (United States)

    Lemmons, Kelly K.; Brannstrom, Christian; Hurd, Danielle

    2014-01-01

    Traditionally, repeat photography has been used to analyze land cover change. This paper describes how repeat photography may be used as a tool to enhance the short-term study abroad experience by facilitating cultural interaction and understanding. We present evidence from two cases and suggest a five-step repeat photography method for educators…

  18. Short-term Use of Cinacalcet in Children on Regular Hemodialysis ...

    African Journals Online (AJOL)

    Case series: We report here the effect of short term use of cinacalcet on sHPT in two children on regular hemodialysis for CKD stage 5. Both children had very high PTH level which failed to be controlled with vitamin D3 and phosphate binders. We started cinacalcet therapy at a dose of 30 mg/day for both of them for duration ...

  19. Repeated passive stretching : Acute effect on the passive muscle moment and extensibility of short hamstrings

    NARCIS (Netherlands)

    Halbertsma, JPK; Mulder, [No Value; Goeken, LNH; Eisma, WH; Mulder, I.; Göeken, L.N.

    Objective: To examine the response of short hamstring muscles to repeated passive stretching. Design: A repeated measures design. Setting: A university laboratory for human movement analysis in a department of rehabilitation. Subjects: Students (7 men, 10 women) from the Department of Human Movement

  20. Short implant to support maxillary restorations: bone stress analysis using regular and switching platform.

    Science.gov (United States)

    de Carvalho, Nivaldo Antônio; de Almeida, Erika Oliveira; Rocha, Eduardo Passos; Freitas, Amílcar Chagas; Anchieta, Rodolfo Bruniera; Kina, Sidney

    2012-05-01

    The aim of this study was to evaluate stress distribution on peri-implant bone simulating the influence of implants with different lengths on regular and switching platforms in the anterior maxilla by means of three-dimensional finite element analysis. Four mathematical models of a central incisor supported by an external hexagon implant (diameter, 5.0 mm) were created, varying the length (15.0 mm for long implants [L] and 7.0 mm for short implants [S]) and the diameter of the abutment platform (5.0 mm for regular models [R] and 4.1 mm for switching models [S]). The models were created using the Mimics 11.11 (Materialise) and SolidWorks 2010 (Inovart) software. Numerical analysis was performed using ANSYS Workbench 10.0 (Swanson Analysis System). Oblique forces (100 N) were applied to the palatine surface of the central incisor. The bone/implant interface was considered perfectly integrated. Maximum (σ(max)) and minimum (σ(min)) principal stress values were obtained. For the cortical bone, the highest stress values (σ(max)) were observed in the SR (73.7 MPa) followed by LR (65.1 MPa), SS (63.6 MPa), and LS (54.2 MPa). For the trabecular bone, the highest stress values (σ(max)) were observed in the SS (8.87 MPa) followed by the SR (8.32 MPa), LR (7.49 MPa), and LS (7.08 MPa). The influence of switching platform was more evident for the cortical bone in comparison with the trabecular bone for the short and long implants. The long implants showed lower stress values in comparison to the short implants, mainly when the switching platform was used.

  1. Measurement of thermal radiation using regular glass optics and short-wave infrared detectors.

    Science.gov (United States)

    Yoon, H W; Eppeldauer, G P

    2008-01-21

    The measurement of thermal radiation from ambient-temperature objects using short-wave infrared detectors and regular glass optics is described. The detectors are chosen to operate in the 2.0 microm to 2.5 microm atmospheric window. Selection of detectors with high shunt resistance along with the 4-stage thermo-electric cooling of the detectors to -85 degrees C results in detectivity, D*, of 4 x 10(13) cm Hz(1/2)/W which is near the background limited performance at 295 K. Furthermore, the use of regular-glass commercial optics to collect the thermal radiation results in diffraction-limited imaging. The use of a radiation thermometer constructed with these elements for the measurement of a blackbody from 20 degrees C to 50 degrees C results in noise-equivalent temperature difference (NETD) of thermal sensors also leads to lower sensitivity to the emissivity of the object in determining the temperature of the object. These elements are used to construct a calibrator for an infrared collimator, and such a system demonstrates noise-equivalent irradiances of thermal infrared detectors.

  2. 3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

    Directory of Open Access Journals (Sweden)

    Ferenc Matthew T

    2007-07-01

    Full Text Available Abstract Background Short (~5 nucleotides interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes. Description In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR of genes from the Mammalian Gene Collection (MGC. The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder, and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin β4 and two candidate CAG-rich (Sec61α and Syntaxin 1A mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body. Conclusion Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that

  3. Short tandem repeats in CdLS-causing genes: distribution and ...

    Indian Academy of Sciences (India)

    2Birthright Genetic Clinic, Karve Road, Pune 411 007, India. [Bajaj S., Gambhir P. and Ranade S. 2014 Short tandem repeats in CdLS-causing genes: distribution ... (nipped B like) or SMC (structural maintenance of chromo- some) genes (Gillis et al. 2004; Krantz et al. 2004). The major genes involved in causing CdLS are ...

  4. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

    NARCIS (Netherlands)

    K. Ballantyne (Kaye); A. Ralf (Arwin); R. Aboukhalid (Rachid); N.M. Achakzai (Niaz); T. Anjos (Tania); Q. Ayub (Qasim); J. Balažic (Jože); J. Ballantyne (Jack); D.J. Ballard (David); B. Berger (Burkhard); C. Bobillo (Cecilia); M. Bouabdellah (Mehdi); H. Burri (Helen); T. Capal (Tomas); S. Caratti (Stefano); J. Cárdenas (Jorge); F. Cartault (François); E.F. Carvalho (Elizeu); M. de Carvalho (Margarete); B. Cheng (Baowen); M.D. Coble (Michael); D. Comas (David); D. Corach (Daniel); M. D'Amato (Mauro); S. Davison (Sean); P. de Knijff (Peter); M.C.A. de Ungria (Maria Corazon); R. Decorte (Ronny); T. Dobosz (Tadeusz); B.M. Dupuy (Berit); S. Elmrghni (Samir); M. Gliwiński (Mateusz); S.C. Gomes (Sara); L. Grol (Laurens); C. Haas (Cordula); E. Hanson (Erin); J. Henke (Jürgen); L. Henke (Lotte); F. Herrera-Rodríguez (Fabiola); C.R. Hill (Carolyn); G. Holmlund (Gunilla); K. Honda (Katsuya); U.-D. Immel (Uta-Dorothee); S. Inokuchi (Shota); R. Jobling; M. Kaddura (Mahmoud); J.S. Kim (Jong); S.H. Kim (Soon); W. Kim (Wook); T.E. King (Turi); E. Klausriegler (Eva); D. Kling (Daniel); L. Kovačević (Lejla); L. Kovatsi (Leda); P. Krajewski (Paweł); S. Kravchenko (Sergey); M.H.D. Larmuseau (Maarten); E.Y. Lee (Eun Young); R. Lessig (Rüdiger); L.A. Livshits (Ludmila); D. Marjanović (Damir); M. Minarik (Marek); N. Mizuno (Natsuko); H. Moreira (Helena); N. Morling (Niels); M. Mukherjee (Meeta); P. Munier (Patrick); J. Nagaraju (Javaregowda); F. Neuhuber (Franz); S. Nie (Shengjie); P. Nilasitsataporn (Premlaphat); T. Nishi (Takeki); H.H. Oh (Hye); S. Olofsson (Sylvia); V. Onofri (Valerio); J. Palo (Jukka); H. Pamjav (Horolma); W. Parson (Walther); M. Petlach (Michal); C. Phillips (Christopher); R. Ploski (Rafal); S.P.R. Prasad (Samayamantri P.); D. Primorac (Dragan); G.A. Purnomo (Gludhug); J. Purps (Josephine); H. Rangel-Villalobos (Hector); K. Reogonekbała (Krzysztof); B. Rerkamnuaychoke (Budsaba); D.R. Gonzalez (Danel Rey); C. Robino (Carlo); L. Roewer (Lutz); A. de Rosa (Anna); A. Sajantila (Antti); A. Sala (Andrea); J.M. Salvador (Jazelyn); P. Sanz (Paula); C. Schmitt (Christian); A.K. Sharma (Anisha K.); D.A. Silva (Dayse); K.-J. Shin (Kyoung-Jin); T. Sijen (Titia); M. Sirker (Miriam); D. Siváková (Daniela); V. Škaro (Vedrana); C. Solano-Matamoros (Carlos); L. Souto (L.); V. Stenzl (Vlastimil); H. Sudoyo (Herawati); D. Syndercombe-Court (Denise); A. Tagliabracci (Adriano); D. Taylor (Duncan); A. Tillmar (Andreas); I.S. Tsybovsky (Iosif); C. Tyler-Smith (Chris); K. van der Gaag (Kristiaan); D. Vanek (Daniel); A. Völgyi (Antónia); D. Ward (Denise); P. Willemse (Patricia); E.P.H. Yap (Eric); Z-Y. Yong (Ze-Yie); I.Z. Pajnič (Irena Zupanič); M.H. Kayser (Manfred)

    2014-01-01

    textabstractRelevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve

  5. X-Chromosomal short tandem repeat loci in the Turkish population ...

    African Journals Online (AJOL)

    In this study, we aimed to demonstrate the importance and utility of polymorphic short tandem repeat (STR) found on the human X chromosome and to provide the first allelic frequency data of X-STR (X chromosomal) loci in the Turkish population. Blood samples were taken from unrelated individuals (135 males and 129 ...

  6. A study of allelic polymorphism of four short tandem repeats in the population of northwestern Russia

    Energy Technology Data Exchange (ETDEWEB)

    Aseev, M.V.; Skakun, V.N.; Baranov, V.S. [Ott Institute of Obstetrics and Gynecology, St. Petersburg (Russian Federation)

    1995-06-01

    Characteristics of the allelic polymorphisms of the trimeric AGC repeat of the androgen receptor gene (Xq11-12), exon 1 (AR); the tetrameric ATCT repeat of the von Willebrand factor gene (12p12), intron 40 (vWF); the AGAT repeat of the hypoxanthine phosphoribosyltransferase gene (Xq26) (HPRT); and the AGAT repeat of anonymous DNA sequences of the short arm of chromosome X (STRX1) were studied in 160 DNA samples from unrelated inhabitants of northwestern Russia using the method of polymerase chain reaction. Seventeen, ten, eight, and nine alleles were revealed electrophoretically for short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The heterozygosity indices for these repeats were 0.80, 0.70, 0.54, and 0.58, respectively. The values for AR and vWF correlated with those expected according to the Hardy-Weinberg equilibrium, whereas the values for HPRT and STRX1 differed significantly from those theoretically expected. The individualization potentials were 0.045, 0.135, 0.095, and 0.061 for the short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The distribution of genotypes for the set of these four loci in the population studied was determined. The possibilities of using the studied polymorphic marker systems in molecular diagnosis of the corresponding monogenic diseases - spinal and bulbar muscle atrophy (AR), Lesch-Nyhan disease (HPRT), and von Willebrand disease (vWF) - as well as in population human genetics, testing of personal identity, and molecular approaches to the estimation of mutagenic activity are discussed. 17 refs., 2 figs., 6 tabs.

  7. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    Directory of Open Access Journals (Sweden)

    David H. Warshauer

    2015-08-01

    Full Text Available Massively parallel sequencing (MPS technology is capable of determining the sizes of short tandem repeat (STR alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics. The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

  8. Short Tandem Repeats in Human Exons: A Target for Disease Mutations

    Directory of Open Access Journals (Sweden)

    Villesen Palle

    2008-09-01

    Full Text Available Abstract Background In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions, are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats are known to be hypermutable (indel-rich, but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect tandem repeats (STRs which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%, 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp and the limited length of STR regions.

  9. An L₁-regularized logistic model for detecting short-term neuronal interactions.

    Science.gov (United States)

    Zhao, Mengyuan; Batista, Aaron; Cunningham, John P; Chestek, Cynthia; Rivera-Alvidrez, Zuley; Kalmar, Rachel; Ryu, Stephen; Shenoy, Krishna; Iyengar, Satish

    2012-06-01

    Interactions among neurons are a key component of neural signal processing. Rich neural data sets potentially containing evidence of interactions can now be collected readily in the laboratory, but existing analysis methods are often not sufficiently sensitive and specific to reveal these interactions. Generalized linear models offer a platform for analyzing multi-electrode recordings of neuronal spike train data. Here we suggest an L(1)-regularized logistic regression model (L(1)L method) to detect short-term (order of 3 ms) neuronal interactions. We estimate the parameters in this model using a coordinate descent algorithm, and determine the optimal tuning parameter using a Bayesian Information Criterion. Simulation studies show that in general the L(1)L method has better sensitivities and specificities than those of the traditional shuffle-corrected cross-correlogram (covariogram) method. The L(1)L method is able to detect excitatory interactions with both high sensitivity and specificity with reasonably large recordings, even when the magnitude of the interactions is small; similar results hold for inhibition given sufficiently high baseline firing rates. Our study also suggests that the false positives can be further removed by thresholding, because their magnitudes are typically smaller than true interactions. Simulations also show that the L(1)L method is somewhat robust to partially observed networks. We apply the method to multi-electrode recordings collected in the monkey dorsal premotor cortex (PMd) while the animal prepares to make reaching arm movements. The results show that some neurons interact differently depending on task conditions. The stronger interactions detected with our L(1)L method were also visible using the covariogram method.

  10. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)

    This study was carried out to investigate the genetic polymorphism of nine short tandem repeat (STR) loci including D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364 and D22GATA198B05 in Chinese Han population of Henan province and to assess its value in forensic science.

  11. Upstream short sequence repeats regulate expression of the alpha C protein of group B Streptococcus.

    Science.gov (United States)

    Puopolo, Karen M; Madoff, Lawrence C

    2003-11-01

    Group B streptococci (GBS) express a family of repeat-containing surface proteins, the prototype of which is the alpha C protein expressed in type Ia/C strain A909. We have isolated a series of mutant GBS strains by mouse-passage of A909 that do not produce normal levels of the alpha C protein. Polymerase chain reaction amplification and sequencing of the gene encoding the alpha C protein, bca, from four mutant strains revealed the presence of a full-length gene in each strain. However, Northern and RT-PCR analysis revealed greatly reduced levels of RNA encoding the alpha C protein. Sequence analysis of the mutant genes found the coding region unchanged from the wild-type gene in each case, but variation was observed in a specific locus located 110 bp upstream of the start codon. The presence of a 5-nucleotide repeat, AGATT, and a string of adenine residues mark this locus. Both deletion and expansion of the AGATT motif were associated with the complete null phenotype. Deletions in the string of adenine residues were associated with both a decreased-production phenotype and a complete null phenotype. Cloning of this upstream region into a green-fluorescent protein (GFP) reporter system in GBS demonstrated promoter activity that was completely abolished by changes in the pentanucleotide repeat or adenine string. Primer extension studies of the wild-type strain revealed one dominant and two minor transcription start sites. Primer extension studies of the null and low-expression mutant strains revealed that the dominant transcript is completely absent in each mutant. The short sequence repeat locus is located at position - 55 to - 78 relative to the start site of the dominant transcript. We have demonstrated in vitro phase variation in expression of the alpha C protein associated with variation at the pentanucleotide repeat locus. We conclude that this short sequence repeat motif is located upstream of the dominant promoter for the alpha C protein and represents a

  12. Short- and midterm repeatability of magnetic resonance elastography in healthy volunteers at 3.0 T.

    Science.gov (United States)

    Shi, Yu; Guo, Qiyong; Xia, Fei; Sun, Jiaxing; Gao, Yuying

    2014-07-01

    The purpose of this study was to evaluate the short- and midterm repeatability of liver stiffness measurements with magnetic resonance elastography (MRE) in healthy subjects at 3.0T. Twenty-two healthy volunteers were enrolled in this prospective study. The stiffness measurements were obtained from three slices with three repeated acquisitions for each slice (session 1) by two independent raters. After a mean period of 7±2days (session 2) and 195±15days (session 3), each subject was scanned again using the same protocol and MR system. The liver stiffness differences were calculated between sessions or raters. The intraclass correlation coefficient (ICC) was calculated to assess interrater agreement and intersession agreement. The stiffness differences over the short- and midterm intervals was (-0.004±0.086) kPa for sessions 1-2, lower than (-0.055±0.150) kPa for sessions 1-3 and (-0.051±0.173) kPa for sessions 2-3. The liver stiffness was more repeatable for the short-term interval with the mean overall ICC of 0.96 (sessions 1-2) (95% confidence interval [CI]: 0.90-0.98) compared with 0.91 (sessions 1-3) (95% CI: 0.78-0.96) and 0.87 (sessions 2-3) (95% CI: 0.69-0.95) for the midterm intervals. The overall ICC of interrater agreement was excellent at 0.987 (95% CI: 0.983 to 0.990). These results confirm that MRE is a reproducible technique for liver stiffness quantification over short- and midterm intervals up to 6months in a healthy population at 3.0T. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. The effect of a short practical warm-up protocol on repeated sprint performance.

    Science.gov (United States)

    Taylor, Jonathan M; Weston, Matthew; Portas, Matthew D

    2013-07-01

    The aim of our study was to investigate the effect of a short, practical, 2-phase warm-up on repeated sprint performance when compared with more traditional warm-up protocols that contain stretching activities. Eleven subelite male soccer players completed a warm-up protocol that commenced with 5 minutes jogging at approximately 65% of maximal heart rate, followed by no stretching, static stretching, or dynamic stretching and finishing with a task-specific high-intensity activity. Using a crossover design, the 3 warm-up protocols were performed in a counterbalanced order with at least 48 hours between sessions. Repeated sprint performance was measured using a repeated sprint test that consisted of 6 × 40-m maximal sprints interspersed with a 20-second recovery. There were trivial differences in mean sprint time (0.2%) and posttest blood lactate (3.1%) between the 2-phase warm-up and the 3-phase warm-up that included dynamic stretching, whereas the short warm-up had a possibly detrimental effect on fastest sprint time (0.7%). Fastest (-1.1%) and mean (-1.2%) sprint times were quicker and posttest blood lactates were higher (13.2%) after the 2-phase warm-up when compared with the 3-phase warm-up that included static stretching. Although it is not harmful to complete a traditional 3-phase warm-up that includes dynamic stretching, it appears practical for athletes preparing for activities dependent on repeated sprint ability to complete a 2-phase warm-up consisting of a cardiovascular and specific high-intensity activity.

  14. Giant flares in soft gamma-ray repeaters and short GRBs.

    Science.gov (United States)

    Zane, S

    2007-05-15

    Soft gamma-ray repeaters (SGRs) are a peculiar family of bursting neutron stars that, occasionally, have been observed to emit extremely energetic giant flares (GFs), with energy release up to approximately 10(47) ergs(-1). These are exceptional and rare events. It has been recently proposed that GFs, if emitted by extragalactic SGRs, may appear at Earth as short gamma-ray bursts. Here, I will discuss the properties of the GFs observed in SGRs, with particular emphasis on the spectacular event registered from SGR 1806-20 in December 2004. I will review the current scenario for the production of the flare, within the magnetar model, and the observational implications.

  15. Genome-wide identification of human- and primate-specific core promoter short tandem repeats.

    Science.gov (United States)

    Bushehri, A; Barez, M R Mashhoudi; Mansouri, S K; Biglarian, A; Ohadi, M

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Exceptionally long 5' UTR short tandem repeats specifically linked to primates.

    Science.gov (United States)

    Namdar-Aligoodarzi, P; Mohammadparast, S; Zaker-Kandjani, B; Talebi Kakroodi, S; Jafari Vesiehsari, M; Ohadi, M

    2015-09-10

    We have previously reported genome-scale short tandem repeats (STRs) in the core promoter interval (i.e. -120 to +1 to the transcription start site) of protein-coding genes that have evolved identically in primates vs. non-primates. Those STRs may function as evolutionary switch codes for primate speciation. In the current study, we used the Ensembl database to analyze the 5' untranslated region (5' UTR) between +1 and +60 of the transcription start site of the entire human protein-coding genes annotated in the GeneCards database, in order to identify "exceptionally long" STRs (≥5-repeats), which may be of selective/adaptive advantage. The importance of this critical interval is its function as core promoter, and its effect on transcription and translation. In order to minimize ascertainment bias, we analyzed the evolutionary status of the human 5' UTR STRs of ≥5-repeats in several species encompassing six major orders and superorders across mammals, including primates, rodents, Scandentia, Laurasiatheria, Afrotheria, and Xenarthra. We introduce primate-specific STRs, and STRs which have expanded from mouse to primates. Identical co-occurrence of the identified STRs of rare average frequency between 0.006 and 0.0001 in primates supports a role for those motifs in processes that diverged primates from other mammals, such as neuronal differentiation (e.g. APOD and FGF4), and craniofacial development (e.g. FILIP1L). A number of the identified STRs of ≥5-repeats may be human-specific (e.g. ZMYM3 and DAZAP1). Future work is warranted to examine the importance of the listed genes in primate/human evolution, development, and disease. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Mutations of short tandem repeat loci in cases of paternity testing in Chinese.

    Science.gov (United States)

    Sun, Mao; Zhang, XiaoNan; Wu, Dan; Shen, Qi; Wu, YuanMing; Fu, ShanMin

    2016-09-01

    In order to find out the characteristics of genetic mutations in 15 short tandem repeat (STR) loci, 3734 parentage cases were analyzed using AmpFlSTR Sinofiler kit. The allele source, mutation rate, and mutation rule of the STR loci were determined. Seventy mutations were observed in all cases for paternity testing. Among 15 STR loci, the highest mutation rate was observed in D12S391 (0.21 %), but the D5S818 gene mutation rate was relatively low (0.02 %). One-step mutation cases accounted for 95.7 % of all of the cases monitored. And the mutations in this study mainly showed paternal mutation (64/70). The research results are of great significance for identification and paternity tests and for the improvement of genetic studies on Chinese population in the future.

  18. A study on ten short tandem repeat systems: African immigrant and Spanish population data.

    Science.gov (United States)

    Gamero, J J; Romero, J L; Gonzalez, J L; Arufe, M I; Cuesta, M I; Corte-Real, F; Carvalho, M; Anjos, M J; Vieira, D N; Vide, M C

    2000-06-05

    This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.

  19. Allelic polymorphic investigation of 21 autosomal short tandem repeat loci in a Chinese Bai ethnic group.

    Science.gov (United States)

    Shen, Chun-mei; Wang, Hong-dan; Liu, Wen-juan; Fan, Shuan-liang; Yang, Guang; Qin, Hai-Xia; Xie, Tong; Li, Shao-bo; Yan, Jiang-wei; Zhu, Bo-feng

    2013-03-01

    Population genetic data of 21 autosomal short tandem repeats (STRs) were obtained in a sample of 106 unrelated healthy individuals of Bai ethnic minority born in the Dali Bai Autonomous Prefecture in Yunnan Province. We observed 138 alleles with corresponding allelic frequencies ranging from 0.005 to 0.575. The genotypic frequency distributions at those STR loci were consistent with Hardy-Weinberg equilibrium (Bonferroni's correction was used for Hardy-Weinberg equilibrium tests). The combined probability of exclusion, power of discrimination, probability of matching value for all 21 STR loci were 0.9999975729, 0.999999999999999999872 and 1.28×10(-19), respectively. The population data in this study showed significant differences from the previously published population data of Tibetan and Salar groups in some loci. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  20. Mechanical properties of regular porous biomaterials made from truncated cube repeating unit cells: Analytical solutions and computational models.

    Science.gov (United States)

    Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

    2016-03-01

    Additive manufacturing (AM) has enabled fabrication of open-cell porous biomaterials based on repeating unit cells. The micro-architecture of the porous biomaterials and, thus, their physical properties could then be precisely controlled. Due to their many favorable properties, porous biomaterials manufactured using AM are considered as promising candidates for bone substitution as well as for several other applications in orthopedic surgery. The mechanical properties of such porous structures including static and fatigue properties are shown to be strongly dependent on the type of the repeating unit cell based on which the porous biomaterial is built. In this paper, we study the mechanical properties of porous biomaterials made from a relatively new unit cell, namely truncated cube. We present analytical solutions that relate the dimensions of the repeating unit cell to the elastic modulus, Poisson's ratio, yield stress, and buckling load of those porous structures. We also performed finite element modeling to predict the mechanical properties of the porous structures. The analytical solution and computational results were found to be in agreement with each other. The mechanical properties estimated using both the analytical and computational techniques were somewhat higher than the experimental data reported in one of our recent studies on selective laser melted Ti-6Al-4V porous biomaterials. In addition to porosity, the elastic modulus and Poisson's ratio of the porous structures were found to be strongly dependent on the ratio of the length of the inclined struts to that of the uninclined (i.e. vertical or horizontal) struts, α, in the truncated cube unit cell. The geometry of the truncated cube unit cell approaches the octahedral and cube unit cells when α respectively approaches zero and infinity. Consistent with those geometrical observations, the analytical solutions presented in this study approached those of the octahedral and cube unit cells when

  1. Short-term regular aerobic exercise reduces oxidative stress produced by acute in the adipose microvasculature.

    Science.gov (United States)

    Robinson, Austin T; Fancher, Ibra S; Sudhahar, Varadarajan; Bian, Jing Tan; Cook, Marc D; Mahmoud, Abeer M; Ali, Mohamed M; Ushio-Fukai, Masuko; Brown, Michael D; Fukai, Tohru; Phillips, Shane A

    2017-05-01

    High blood pressure has been shown to elicit impaired dilation in the vasculature. The purpose of this investigation was to elucidate the mechanisms through which high pressure may elicit vascular dysfunction and determine the mechanisms through which regular aerobic exercise protects arteries against high pressure. Male C57BL/6J mice were subjected to 2 wk of voluntary running (~6 km/day) for comparison with sedentary controls. Hindlimb adipose resistance arteries were dissected from mice for measurements of flow-induced dilation (FID; with or without high intraluminal pressure exposure) or protein expression of NADPH oxidase II (NOX II) and superoxide dismutase (SOD). Microvascular endothelial cells were subjected to high physiological laminar shear stress (20 dyn/cm2) or static condition and treated with ANG II + pharmacological inhibitors. Cells were analyzed for the detection of ROS or collected for Western blot determination of NOX II and SOD. Resistance arteries from exercised mice demonstrated preserved FID after high pressure exposure, whereas FID was impaired in control mouse arteries. Inhibition of ANG II or NOX II restored impaired FID in control mouse arteries. High pressure increased superoxide levels in control mouse arteries but not in exercise mouse arteries, which exhibited greater ability to convert superoxide to H2O2 Arteries from exercised mice exhibited less NOX II protein expression, more SOD isoform expression, and less sensitivity to ANG II. Endothelial cells subjected to laminar shear stress exhibited less NOX II subunit expression. In conclusion, aerobic exercise prevents high pressure-induced vascular dysfunction through an improved redox environment in the adipose microvasculature.NEW & NOTEWORTHY We describe potential mechanisms contributing to aerobic exercise-conferred protection against high intravascular pressure. Subcutaneous adipose microvessels from exercise mice express less NADPH oxidase (NOX) II and more superoxide dismutase

  2. Finite Element Analysis of Bone Stress in the Posterior Mandible Using Regular and Short Implants, in the Same Context, with Splinted and Nonsplinted Prostheses.

    Science.gov (United States)

    Toniollo, Marcelo Bighetti; Macedo, Ana Paula; Pupim, Denise; Zaparolli, Danilo; da Gloria Chiarello de Mattos, Maria

    The aim of this study was to compare the bone stress generated by rehabilitation using regular and short-length Morse taper implants (11 and 5 mm, respectively) in the same context and allied with splinted (SP) and nonsplinted (NSP) prostheses in the posterior area of the mandible using finite element analysis. Three-dimensional geometric models using regular implants (Ø4 × 11 mm) and short implants (Ø4 × 5 mm) were simulated with a left posterior mandible that had the first premolar tooth and all teeth posterior to that premolar removed. The four experimental groups were as follows: Group 1 NSP (two regular implants and one short implant rehabilitated with nonsplinted prostheses), Group 1 SP (two regular implants and one short implant rehabilitated with splinted prostheses), Group 2 NSP (one regular implant and two short implants rehabilitated with nonsplinted prostheses), and Group 2 SP (one regular implant and two short implants rehabilitated with splinted prostheses). Oblique forces were simulated in molars (365 N) and premolars (200 N). Qualitative and quantitative analyses of the minimum principal stress in bone were performed using the ANSYS Workbench software, version 10.0. The splinted prostheses decreased the stress to the surrounding bone of short implants. Moreover, they also decreased the stress on the surrounding bone adjacent to the tooth. However, the splinted prostheses generated higher stress in the coverage of the surrounding bone for regular intermediate implants and prominently in the bone at the implant cervical region, at the edge crest, compared with the individualized groups. The benefits in the use of splinted prostheses are notable for the preservation of the bone surrounding the short implants and tooth; however, it is necessary to evaluate each clinical situation because, in this context, the regular implants are at higher stress than the individualized implants.

  3. Core promoter short tandem repeats as evolutionary switch codes for primate speciation.

    Science.gov (United States)

    Ohadi, Mina; Valipour, Elaheh; Ghadimi-Haddadan, Saeed; Namdar-Aligoodarzi, Pegah; Bagheri, Abouzar; Kowsari, Ali; Rezazadeh, Maryam; Darvish, Hossein; Kazeminasab, Somayeh

    2015-01-01

    Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥ 6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. © 2014 Wiley Periodicals, Inc.

  4. Short- or long-rest intervals during repeated-sprint training in soccer?

    Directory of Open Access Journals (Sweden)

    F Marcello Iaia

    Full Text Available The present study compared the effects of two repeated-sprint training (RST programs, differing in duration of the between-sprint rest intervals, on various soccer-related exercise performances. For 5 weeks during the competitive season, twenty-nine young trained male soccer players either replaced two of their habitual fitness conditioning sessions with RST characterized by short (5-15; n = 9 or long (5-30; n = 10 rest intervals, or served as control (n = 10. The 5-15 and 5-30 protocols consisted of 6 repetitions of 30-m (~5 s straight-line sprints interspersed with 15 s or 30 s of passive recovery, respectively. 5-15 improved 200-m sprint time (2.0±1.5%; p<0.05 and had a likely positive impact on 20-m sprint performance, whereas 5-30 lowered the 20-m sprint time (2.7±1.6%; p<0.05 but was only possibly effective for enhancing the 200-m sprint performance. The distance covered during the Yo-Yo Intermittent Recovery Test Level 2 increased following 5-15 (11.4±5.0%; p<0.05, which was possibly better than the non-significant 6.5% enhancement observed in 5-30. Improvements in the total time of a repeated-sprint ability test were possibly greater following 5-30 (3.6±0.9%; p<0.05 compared to 5-15 (2.6±1.1%; p<0.05. Both RST interventions led to similar beneficial (p<0.05 reductions in the percentage decrement score (~30% of the repeated-sprint ability test as well as in blood lactate concentration during submaximal exercise (17-18%. No changes occurred in the control group. In soccer players, RST over a 5-week in-season period is an efficient means to simultaneously develop different components of fitness relevant to match performance, with different benefits induced by shorter compared to longer rest intervals.

  5. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    Directory of Open Access Journals (Sweden)

    Seman Ali

    2012-10-01

    Full Text Available Abstract Background Y-Short Tandem Repeats (Y-STR data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH, obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91, k-Modes-RVF (0.81, New Fuzzy k-Modes (0.80, k-Modes (0.76, k-Modes-Hybrid 1 (0.76, k-Modes-Hybrid 2 (0.75, Fuzzy k-Modes (0.74, and k-Modes-UAVM (0.70. Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k and considered to be linear.

  6. A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants.

    Science.gov (United States)

    Niu, Xiangli; Luo, Di; Gao, Shaopei; Ren, Guangjun; Chang, Lijuan; Zhou, Yuke; Luo, Xiaoli; Li, Yuxiang; Hou, Pei; Tang, Wei; Lu, Bao-Rong; Liu, Yongsheng

    2010-01-01

    In several stress responsive gene loci of monocot cereal crops, we have previously identified an unusual posttranscriptional processing mediated by paired presence of short direct repeated (SDR) sequences at 5' and 3' splicing junctions that are distinct from conventional (U2/U12-type) splicing boundaries. By using the known SDR-containing sequences as probes, 24 plant candidate genes involved in diverse functional pathways from both monocots and dicots that potentially possess SDR-mediated posttranscriptional processing were predicted in the GenBank database. The SDRs-mediated posttranscriptional processing events including cis- and trans-actions were experimentally detected in majority of the predicted candidates. Extensive sequence analysis demonstrates several types of SDR-associated splicing peculiarities including partial exon deletion, exon fragment repetition, exon fragment scrambling and trans-splicing that result in either loss of partial exon or unusual exonic sequence rearrangements within or between RNA molecules. In addition, we show that the paired presence of SDR is necessary but not sufficient in SDR-mediated splicing in transient expression and stable transformation systems. We also show prokaryote is incapable of SDR-mediated premRNA splicing. Copyright 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  7. A repeated short educational intervention improves asthma control and quality of life.

    Science.gov (United States)

    Plaza, Vicente; Peiró, Meritxell; Torrejón, Montserrat; Fletcher, Monica; López-Viña, Antolín; Ignacio, José María; Quintano, José Antonio; Bardagí, Santiago; Gich, Ignasi

    2015-11-01

    We assessed the effectiveness of an asthma educational programme based on a repeated short intervention (AEP-RSI) to improve asthma control (symptom control and future risk) and quality of life. A total of 230 adults with mild-to-moderate persistent uncontrolled asthma participated in a 1-year cluster randomised controlled multicentre study. The AEP-RSI was given in four face-to-face sessions at 3-month intervals, and included administration of a written personalised action plan and training on inhaler technique. Centres were randomised to the AEP-RSI (intervention) group or usual clinical practice group. Specialised centres using a standard educational programme were the gold standard group. A significant improvement in the Asthma Control Test score was observed in all three groups (pimprovements were higher in the intervention and gold standard groups than in the usual clinical practice group (p=0.042), which also showed fewer exacerbations (mean±sd; 1.20±2.02 and 0.56±1.5 versus 2.04±2.72, respectively) and greater increases in the Mini Asthma Quality of Life Questionnaire scores (0.95±1.04 and 0.89±0.84 versus 0.52±0.97, respectively). The AEP-RSI was effective in improving asthma symptom control, future risk and quality of life. Copyright ©ERS 2015.

  8. Characterization of two New York City Jewish populations at six short tandem repeat loci.

    Science.gov (United States)

    Medintz, I; Kingston, C; Duran, H; Barry, L; Levine, L; Kobilinsky, L

    2002-02-01

    The Hasidic and non-Hasidic Jewish communities of New York City represent two subpopulations with long-documented histories of restrictive marriage patterns and a high degree of endogamy. As part of a continuing study into their genetic structure, allele frequencies were determined for the six tetrameric short tandem repeat (STR) loci: FESFPS, F13AO1, vWA, CSF1PO, TPOX, and THO1. All loci were tested for Hardy-Weinberg equilibrium (HWE) by three tests: chi-square analysis, Monte Carlo chi-square analysis. and the exact test. The non-Hasidic population failed to meet HWE at the F13A01, FESFPS, and CSF1PO loci by all three tests. The Hasidic population also failed to meet HWE at the same loci by some of the tests. Comparison of the Hasidic to the non-Hasidic population using an R x C contingency table demonstrated a similarity at only the vWA locus. Significant differences exist when comparing the two Jewish populations to a reference Caucasian population.

  9. Effects of a Ten Week Training Programme on Repeated Short Sprints among Football Referees of Malaysia

    Directory of Open Access Journals (Sweden)

    Subramaniam Nathan

    2014-07-01

    Full Text Available The objective of this study was to investigate whether a ten week training programme would improve repeated short sprints of football referees in Malaysia. Sixty national football referees were randomly assigned into 3 groups (n=20 namely the control group, experimental one and experimental two. Experimental one followed a 10 week training programme (duration of training 4 days in a week, each session=90 minutes and time 5 pm supervised by a physical education lecturer and his assistants. Experimental two reported for training at a different venue and trained on their own (duration, frequency and time as for experimental one. Pre-test and post-test results were used to determine whether there was an improvement. SPANOVA results rejected the null hypothesis [F (2, 57 =75.86 p<0.05].  Pillai’s Trace indicated there was a significant difference between pre-test and post-test results and significant interaction effect. Tukey Pair Wise Comparison indicated best performance by experimental one and the control group the poorest. The results indicated that the training programme was acceptable.

  10. Developmental Validation of Short Tandem Repeat Reagent Kit for Forensic DNA Profiling of Canine Biological Materials

    Science.gov (United States)

    Dayton, Melody; Koskinen, Mikko T; Tom, Bradley K; Mattila, Anna-Maria; Johnston, Eric; Halverson, Joy; Fantin, Dennis; DeNise, Sue; Budowle, Bruce; Smith, David Glenn; Kanthaswamy, Sree

    2009-01-01

    Aim To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker. Methods Validation studies to determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species-specificity, case type samples analyses and population studies. Results The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA. In addition, wolf DNA samples could be analyzed with the kit. Conclusion The kit, which produces robust, reliable, and reproducible results, will be made available for the forensic research community after modifications based on this study’s evaluation to comply with the quality standards expected for forensic casework. PMID:19480022

  11. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers.

    Science.gov (United States)

    Asari, Masaru; Okuda, Katsuhiro; Hoshina, Chisato; Omura, Tomohiro; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Shimizu, Keiko

    2016-02-01

    The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. A fully integrated microchip system for automated forensic short tandem repeat analysis.

    Science.gov (United States)

    Han, Junping; Gan, Wupeng; Zhuang, Bin; Sun, Jing; Zhao, Lei; Ye, Jian; Liu, Yao; Li, Cai-Xia; Liu, Peng

    2017-05-30

    We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.

  13. A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis.

    Science.gov (United States)

    Reedy, Carmen R; Hagan, Kristin A; Marchiarullo, Daniel J; Dewald, Alison H; Barron, Annalise; Bienvenue, Joan M; Landers, James P

    2011-02-21

    Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples. Copyright © 2010 Elsevier B.V. All rights reserved.

  14. Population genetic data of eight tetrameric short tandem repeats (STRs) in Casablanca resident population to use in forensic casework.

    Science.gov (United States)

    Chbel, Faiza; Nadifi, Sellama; Martinez-Bouzas, Cristina; Louahlia, Said; Azeddoug, Houssine; Martinez De Pancorbo, Marian

    2003-03-12

    The allele frequencies for eight short tandem repeat (STR) loci HUMvWA, HUMFES/FPS, HUMF13A, HUMF13B, HUMTHO1, HUMTPOX, HUMCSF1P0, HUMLPL included in Geneprint STR kits were obtained from 234 unrelated individuals in Casablanca.

  15. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    Science.gov (United States)

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  16. Short tandem repeat (STR based genetic diversity and relationship of indigenous Niger cattle

    Directory of Open Access Journals (Sweden)

    M. Grema

    2017-11-01

    Full Text Available The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 % was consistently higher than Zebu Arabe (59.3 to 70.4 % and Kuri (80.0 to 83.3 % cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

  17. An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system.

    Directory of Open Access Journals (Sweden)

    Erin K Hanson

    Full Text Available In forensic casework, Y chromosome short tandem repeat markers (Y-STRs are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12-17 loci are currently used in forensic casework (Promega's PowerPlex Y and Applied Biosystems' AmpFlSTR Yfiler. Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used 'core' Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572 indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR Yfiler kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary

  18. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Tomaszkiewicz, Marta; Campos-Sánchez, Rebeca; Eckert, Kristin A; DeGiorgio, Michael; Makova, Kateryna D

    2016-10-01

    Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA-DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea.

    Science.gov (United States)

    Moon, Seo Hyun; Jang, Yoon-Jeong; Han, Myun Soo; Cho, Myung-Haing

    2016-09-30

    Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10(-)⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

  20. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    Science.gov (United States)

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  1. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  2. Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats.

    Science.gov (United States)

    Han, Pu; Deem, Michael W

    2017-02-01

    CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon. © 2017 The Author(s).

  3. Structural Analysis and Anticoagulant Activities of the Novel Sulfated Fucan Possessing a Regular Well-Defined Repeating Unit from Sea Cucumber

    Directory of Open Access Journals (Sweden)

    Mingyi Wu

    2015-04-01

    Full Text Available Sulfated fucans, the complex polysaccharides, exhibit various biological activities. Herein, we purified two fucans from the sea cucumbers Holothuria edulis and Ludwigothurea grisea. Their structures were verified by means of HPGPC, FT-IR, GC–MS and NMR. As a result, a novel structural motif for this type of polymers is reported. The fucans have a unique structure composed of a central core of regular (1→2 and (1→3-linked tetrasaccharide repeating units. Approximately 50% of the units from L. grisea (100% for H. edulis fucan contain sides of oligosaccharides formed by nonsulfated fucose units linked to the O-4 position of the central core. Anticoagulant activity assays indicate that the sea cucumber fucans strongly inhibit human blood clotting through the intrinsic pathways of the coagulation cascade. Moreover, the mechanism of anticoagulant action of the fucans is selective inhibition of thrombin activity by heparin cofactor II. The distinctive tetrasaccharide repeating units contribute to the anticoagulant action. Additionally, unlike the fucans from marine alga, although the sea cucumber fucans have great molecular weights and affluent sulfates, they do not induce platelet aggregation. Overall, our results may be helpful in understanding the structure-function relationships of the well-defined polysaccharides from invertebrate as new types of safer anticoagulants.

  4. Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India.

    Directory of Open Access Journals (Sweden)

    Saroj K Young

    2008-04-01

    Full Text Available Inadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological studies and contribute to our understanding of the disease.Genotyping assays based on variation in the copy number of short tandem repeat sequences were applied to biopsies collected in population-based epidemiological studies of leprosy in northern Malawi, and from members of multi-case households in Hyderabad, India. In the Malawi series, considerable genotypic variability was observed between patients, and also within patients, when isolates were collected at different times or from different tissues. Less within-patient variability was observed when isolates were collected from similar tissues at the same time. Less genotypic variability was noted amongst the closely related Indian patients than in the Malawi series.Lineages of M. leprae undergo changes in their pattern of short tandem repeat sequences over time. Genetic divergence is particularly likely between bacilli inhabiting different (e.g., skin and nerve tissues. Such variability makes short tandem repeat sequences unsuitable as a general tool for population-based strain typing of M. leprae, or for distinguishing relapse from reinfection. Careful use of these markers may provide insights into the development of disease within individuals and for tracking of short transmission chains.

  5. Short-term exposure to repeated chasing stress does not induce habituation in Senegalese sole, Solea senegalensis

    DEFF Research Database (Denmark)

    Conde-Sieira, Marta; Valente, Luisa M.P.; Hernandez-Perez, Juan

    2018-01-01

    Animals can habituate to certain repeated stressors and reduce the physiological response that such stressor evoked initially. Studies related to stress habituation in fish are scarce and the available data differ depending on the species and on the type, duration and severity of the stressor...... for the animals to habituate, indicating that repeated chasing within short periods should be avoided when manipulating fish in order to keep proper welfare conditions in this species........ The main objective of this study was to investigate the stress response of juvenile Senegalese sole (Solea senegalensis) submitted to repeated chasing stress for 3 days previous to the experiment in order to evaluate the occurrence of habituation to those stress conditions in this fish species. Thus, five...

  6. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats

    OpenAIRE

    Seman, Ali; Sapawi, Azizian Mohd; Salleh, Mohd. Zaki

    2015-01-01

    Abstract Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering lar...

  7. Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

    OpenAIRE

    BISWAS, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly dist...

  8. Augmenting short cheap talk scripts with a repeated opt-out reminder in choice experiment surveys

    DEFF Research Database (Denmark)

    Ladenburg, Jacob; Olsen, Søren Bøye

    2014-01-01

    find the OOR to significantly reduce total WTP and to some extent also marginal WTP beyond the capability of the CT applied without the OOR. This suggests that the CT practice should be adapted to fit the potentially different decision processes and repeated choices structure of the Choice Experiment...... format, rather than merely being adopted directly from Contingent Valuation....

  9. Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome.

    Science.gov (United States)

    Odom, Obed W; Baek, Kwang-Hyun; Dani, Radhika N; Herrin, David L

    2008-03-01

    Certain group I introns insert into intronless DNA via an endonuclease that creates a double-strand break (DSB). There are two models for intron homing in phage: synthesis-dependent strand annealing (SDSA) and double-strand break repair (DSBR). The Cr.psbA4 intron homes efficiently from a plasmid into the chloroplast psbA gene in Chlamydomonas, but little is known about the mechanism. Analysis of co-transformants selected using a spectinomycin-resistant 16S gene (16S(spec)) provided evidence for both pathways. We also examined the consequences of the donor DNA having only one-sided or no homology with the psbA gene. When there was no homology with the donor DNA, deletions of up to 5 kb involving direct repeats that flank the psbA gene were obtained. Remarkably, repeats as short as 15 bp were used for this repair, which is consistent with the single-strand annealing (SSA) pathway. When the donor had one-sided homology, the DSB in most co-transformants was repaired using two DNAs, the donor and the 16S(spec) plasmid, which, coincidentally, contained a region that is repeated upstream of psbA. DSB repair using two separate DNAs provides further evidence for the SDSA pathway. These data show that the chloroplast can repair a DSB using short dispersed repeats located proximally, distally, or even on separate molecules relative to the DSB. They also provide a rationale for the extensive repertoire of repeated sequences in this genome.

  10. Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure.

    Science.gov (United States)

    Vlassi, Metaxia; Brauns, Katharina; Andrade-Navarro, Miguel A

    2013-10-02

    The human mineralocorticoid receptor (MR) is one of the main components of the renin-angiotensin-aldosterone system (RAAS), the system that regulates the body exchange of water and sodium. The evolutionary origins of this protein predate those of renin and the RAAS; accordingly it has other roles, which are being characterized. The MR has two trans-activating ligand independent domains and one inhibitory domain (ID), which modulates the activity of the former. The structure of the ID is currently unknown. Here we report that the ID contains at least 15 tandem repeats of around 10 amino acids, which we computationally characterize in the human MR and in selected orthologs. This ensemble of repeats seems to have emerged around 450 million years ago, after the divergence of the MR from its close homolog, the glucocorticoid receptor, which does not possess the repeats. The region would have quickly expanded by successive duplication of the repeats stabilizing at its length in human MR shortly after divergence of tetrapoda from bony fishes 400 million years ago. Structural predictions, in combination with molecular dynamics simulations suggest that the repeat ensemble forms a β-solenoid, namely a β-helical fold with a polar core, stabilized by hydrogen-bonded ladders of polar residues. Our 3D-model, in conjunction with previous experimental data, implies a role of the β-helical fold as a scaffold for multiple intra-and inter-molecular interactions and that these interactions are modulated via phosphorylation-dependent conformational changes. We, thus, propose that the structure of the repeat ensemble plays an important role in the coordination and sequential interactions of various MR partners and therefore in the functionality and specificity of MR.

  11. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa.

    Science.gov (United States)

    van Duijn, Esther; Barbu, Ioana M; Barendregt, Arjan; Jore, Matthijs M; Wiedenheft, Blake; Lundgren, Magnus; Westra, Edze R; Brouns, Stan J J; Doudna, Jennifer A; van der Oost, John; Heck, Albert J R

    2012-11-01

    The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.

  12. Effects of Repeated Testing on Short- and Long-Term Memory Performance across Different Test Formats

    Science.gov (United States)

    Stenlund, Tova; Sundström, Anna; Jonsson, Bert

    2016-01-01

    This study examined whether practice testing with short-answer (SA) items benefits learning over time compared to practice testing with multiple-choice (MC) items, and rereading the material. More specifically, the aim was to test the hypotheses of "retrieval effort" and "transfer appropriate processing" by comparing retention…

  13. Augmenting short cheap talk scripts with a repeated opt-out reminder in choice experiment surveys

    DEFF Research Database (Denmark)

    Ladenburg, Jacob; Olsen, Søren Bøye

    Hypothetical bias remains a major problem when valuing non-market goods with stated preference methods. Originally developed for Contingent Valuation studies, Cheap Talk has been found to effectively reduce hypothetical bias in some applications, though empirical results are ambiguous. We discuss......-Out Reminder. This suggests that rather than merely adopting the Cheap Talk practice directly from Contingent Valuation, it should be adapted to fit the potentially different decision processes and repeated choices structure of the Choice Experiment format. Our results further suggest that augmenting Cheap...

  14. Hyperventilation-induced respiratory alkalosis falls short of countering fatigue during repeated maximal isokinetic contractions.

    Science.gov (United States)

    Sakamoto, Akihiro; Naito, Hisashi; Chow, Chin Moi

    2015-07-01

    Hyperventilation, implemented during recovery of repeated maximal sprints, has been shown to attenuate performance decrement. This study evaluated the effects of hyperventilation, using strength exercises, on muscle torque output and EMG amplitude. Fifteen power-trained athletes underwent maximal isokinetic knee extensions consisting of 12 repetitions × 8 sets at 60°/s and 25 repetitions × 8 sets at 300°/s. The inter-set interval was 40 s for both speeds. For the control condition, subjects breathed spontaneously during the interval period. For the hyperventilation condition, subjects hyperventilated for 30 s before each exercise set (50 breaths/min, PETCO2: 20-25 mmHg). EMG was recorded from the vastus medialis and lateralis muscles to calculate the mean amplitude for each contraction. Hyperventilation increased blood pH by 0.065-0.081 and lowered PCO2 by 8.3-10.3 mmHg from the control values (P hyperventilation at 60°/s during the initial repetition phase of the first (P = 0.032) and fourth sets (P = 0.040). EMG amplitude also declined with set number (P hyperventilation. Despite a minor ergogenic effect in peak torque at 60°/s, hyperventilation was not effective in attenuating the decrement in torque output at 300°/s and decrement in EMG amplitude at both speeds during repeated sets of maximal isokinetic knee extensions.

  15. Regularity effect in prospective memory during aging

    Directory of Open Access Journals (Sweden)

    Geoffrey Blondelle

    2016-10-01

    Full Text Available Background: Regularity effect can affect performance in prospective memory (PM, but little is known on the cognitive processes linked to this effect. Moreover, its impacts with regard to aging remain unknown. To our knowledge, this study is the first to examine regularity effect in PM in a lifespan perspective, with a sample of young, intermediate, and older adults. Objective and design: Our study examined the regularity effect in PM in three groups of participants: 28 young adults (18–30, 16 intermediate adults (40–55, and 25 older adults (65–80. The task, adapted from the Virtual Week, was designed to manipulate the regularity of the various activities of daily life that were to be recalled (regular repeated activities vs. irregular non-repeated activities. We examine the role of several cognitive functions including certain dimensions of executive functions (planning, inhibition, shifting, and binding, short-term memory, and retrospective episodic memory to identify those involved in PM, according to regularity and age. Results: A mixed-design ANOVA showed a main effect of task regularity and an interaction between age and regularity: an age-related difference in PM performances was found for irregular activities (older < young, but not for regular activities. All participants recalled more regular activities than irregular ones with no age effect. It appeared that recalling of regular activities only involved planning for both intermediate and older adults, while recalling of irregular ones were linked to planning, inhibition, short-term memory, binding, and retrospective episodic memory. Conclusion: Taken together, our data suggest that planning capacities seem to play a major role in remembering to perform intended actions with advancing age. Furthermore, the age-PM-paradox may be attenuated when the experimental design is adapted by implementing a familiar context through the use of activities of daily living. The clinical

  16. Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

    Science.gov (United States)

    Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community. PMID:25148383

  17. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis.

    Directory of Open Access Journals (Sweden)

    Manosh Kumar Biswas

    Full Text Available Sweet orange (Citrus sinensis is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02% are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21% polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

  18. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).

    Science.gov (United States)

    Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

  19. Investigation of short-term variations in term breast milk composition during repeated breast expression sessions.

    Science.gov (United States)

    Khan, Sadaf; Prime, Danielle K; Hepworth, Anna R; Lai, Ching Tat; Trengove, Naomi J; Hartmann, Peter E

    2013-05-01

    Breast milk composition can be affected by several factors, and it can exhibit short-term (weekly) variations. Investigating variations in breast milk composition is important to accurately estimate nutrient requirements of the infant. To investigate short-term changes in breast milk composition between left and right breasts, over a 3-week period within the first 6 months of lactation. The left and right breasts of the mothers of healthy, term infants (n = 23) were simultaneously expressed with an electric breast pump for 15 minutes, on 3 occasions within 3 weeks. Milk samples (5 mL) were collected from the total expression volume of each breast at each session. The macronutrient contents, total solids, and energy content were determined using a mid-infrared human milk analyzer. Mothers (n = 17) measured their 24-hour milk production, and the average 24-hour fat contents were also determined. Over the 3 weekly sessions, no significant changes were found in macronutrient contents. On average, total solids (P = .04) and energy (P = .04) decreased by week 3 of follow-up sessions from 14 to 13 g/100 mL and from 82 to 76 Kcal/100 mL, respectively; however, these changes became insignificant when expression volume was taken into account. The macronutrient concentration was similar for the left and right breasts; however, milk composition varied markedly between mothers. Furthermore, average 24-hour fat content was significantly lower than the mean fat content from a single expression session (P milk, assuming an average concentration requires caution. The study findings illustrate the importance of using average 24-hour fat content of milk to obtain representative measures of infant energy intake.

  20. A Three-Dimensional Finite Element Analysis of the Stress Distribution Generated by Splinted and Nonsplinted Prostheses in the Rehabilitation of Various Bony Ridges with Regular or Short Morse Taper Implants.

    Science.gov (United States)

    Toniollo, Marcelo Bighetti; Macedo, Ana Paula; Rodrigues, Renata Cristina; Ribeiro, Ricardo Faria; de Mattos, Maria G

    The aim of this study was to compare the biomechanical performance of splinted or nonsplinted prostheses over short- or regular-length Morse taper implants (5 mm and 11 mm, respectively) in the posterior area of the mandible using finite element analysis. Three-dimensional geometric models of regular implants (Ø 4 × 11 mm) and short implants (Ø 4 × 5 mm) were placed into a simulated model of the left posterior mandible that included the first premolar tooth; all teeth posterior to this tooth had been removed. The four experimental groups were as follows: regular group SP (three regular implants were rehabilitated with splinted prostheses), regular group NSP (three regular implants were rehabilitated with nonsplinted prostheses), short group SP (three short implants were rehabilitated with splinted prostheses), and short group NSP (three short implants were rehabilitated with nonsplinted prostheses). Oblique forces were simulated in molars (365 N) and premolars (200 N). Qualitative and quantitative analyses of the minimum principal stress in bone were performed using ANSYS Workbench software, version 10.0. The use of splinting in the short group reduced the stress to the bone surrounding the implants and tooth. The use of NSP or SP in the regular group resulted in similar stresses. The best indication when there are short implants is to use SP. Use of NSP is feasible only when regular implants are present.

  1. Recognition of long-term behaviors by parsing sequences of short-term actions with a stochastic regular grammar

    NARCIS (Netherlands)

    Sanromà, G.; Burghouts, G.J.; Schutte, K.

    2012-01-01

    Human behavior understanding from visual data has applications such as threat recognition. A lot of approaches are restricted to limited time actions, which we call short-term actions. Long-term behaviors are sequences of short-term actions that are more extended in time. Our hypothesis is that they

  2. "New turns from old STaRs": enhancing the capabilities of forensic short tandem repeat analysis.

    Science.gov (United States)

    Phillips, Christopher; Gelabert-Besada, Miguel; Fernandez-Formoso, Luis; García-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Ballard, David; Syndercombe Court, Denise; Carracedo, Angel; Lareu, Maria Victoria

    2014-11-01

    The field of research and development of forensic STR genotyping remains active, innovative, and focused on continuous improvements. A series of recent developments including the introduction of a sixth dye have brought expanded STR multiplex sizes while maintaining sensitivity to typical forensic DNA. New supplementary kits complimenting the core STRs have also helped improve analysis of challenging identification cases such as distant pairwise relationships in deficient pedigrees. This article gives an overview of several recent key developments in forensic STR analysis: availability of expanded core STR kits and supplementary STRs, short-amplicon mini-STRs offering practical options for highly degraded DNA, Y-STR enhancements made from the identification of rapidly mutating loci, and enhanced analysis of genetic ancestry by analyzing 32-STR profiles with a Bayesian forensic classifier originally developed for SNP population data. As well as providing scope for genotyping larger numbers of STRs optimized for forensic applications, the launch of compact next-generation sequencing systems provides considerable potential for genotyping the sizeable proportion of nucleotide variation existing in forensic STRs, which currently escapes detection with CE. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Hybrid Short Term Wind Speed Forecasting Using Variational Mode Decomposition and a Weighted Regularized Extreme Learning Machine

    OpenAIRE

    Nantian Huang; Chong Yuan; Guowei Cai; Enkai Xing

    2016-01-01

    Accurate wind speed forecasting is a fundamental element of wind power prediction. Thus, a new hybrid wind speed forecasting model, using variational mode decomposition (VMD), the partial autocorrelation function (PACF), and weighted regularized extreme learning machine (WRELM), is proposed to improve the accuracy of wind speed forecasting. First, the historic wind speed time series is decomposed into several intrinsic mode functions (IMFs). Second, the partial correlation of each IMF sequenc...

  4. A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

    Science.gov (United States)

    Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

    2011-01-01

    Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

  5. Hybrid Short Term Wind Speed Forecasting Using Variational Mode Decomposition and a Weighted Regularized Extreme Learning Machine

    Directory of Open Access Journals (Sweden)

    Nantian Huang

    2016-11-01

    Full Text Available Accurate wind speed forecasting is a fundamental element of wind power prediction. Thus, a new hybrid wind speed forecasting model, using variational mode decomposition (VMD, the partial autocorrelation function (PACF, and weighted regularized extreme learning machine (WRELM, is proposed to improve the accuracy of wind speed forecasting. First, the historic wind speed time series is decomposed into several intrinsic mode functions (IMFs. Second, the partial correlation of each IMF sequence is analyzed using PACF to select the optimal subfeature set for particular predictors of each IMF. Then, the predictors of each IMF are constructed in order to enhance its strength using WRELM. Finally, wind speed is obtained by adding up all the predictors. The experiment, using real wind speed data, verified the effectiveness and advancement of the new approach.

  6. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

    Science.gov (United States)

    Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

    2015-12-01

    The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Antarctic Ice Sheet Grounding line migration monitoring using COSMO-SkyMed very short repeat-time SAR Interferometry.

    Science.gov (United States)

    Milillo, P.; Rignot, E. J.; Mouginot, J.; Scheuchl, B.; Morlighem, M.; Li, X.; Salzer, J. T.

    2016-12-01

    We employ data from the second generation of SAR systems e.g. the Italian COSMO-SkyMed constellation and the German TanDEM-X formation to monitor the characteristics of grounding line migration using short repeat-time interferometry and accurate InSAR DEM in the Amundsen Sea Embayment (ASE), West Antarctica. The ASE is a marine-based ice sheet with a retrograde bed containing enough ice to raise global sea level by 120 cm. Several studies have inferred the mechanical properties of portions of ASE using observationally constrained numerical models, but these studies offer only temporal snapshots of basal mechanics owing to a dearth of observational time series. Using 1-day CSK repeat pass data and TanDEM-X DEMs, we collected frequent, high-resolution grounding line measurements of Pine Island (PIG), Thwaites, Kohler and Smith glaciers spanning 2015-2016. We compare the results with ERS data spanning 1996-2011, and Sentinel-1a 2014-2015 data. We observe an ongoing, rapid 2km/yr grounding line retreat on Smith, 0.5 km/yr retreat on Pope, ongoing 1 km/yr retreat on Thwaites and PIG and a slight re-advance on Kohler since 2011. On PIG, the data reveal seawater infiltration at high tides over many km along the glacier flanks, significantly more than in 1996/2000. We attribute these infiltrations to the fast retreat of PIG over a rough bed. Such intrusion of warm water fuel the melting of basal ice at the grounding line, which provides an additional positive feedback to the glacier retreat not accounted for in models. We do not observe similar patterns on the other glaciers.

  8. How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study

    Science.gov (United States)

    Schröger, Erich; Grimm, Sabine

    2017-01-01

    The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch. PMID:28472146

  9. How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study.

    Science.gov (United States)

    Bader, Maria; Schröger, Erich; Grimm, Sabine

    2017-01-01

    The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch.

  10. How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study.

    Directory of Open Access Journals (Sweden)

    Maria Bader

    Full Text Available The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm. In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a and for pattern repetitions (repetition positivity, RP revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch.

  11. Short Durations of Static Stretching when Combined with Dynamic Stretching do not Impair Repeated Sprints and Agility

    Science.gov (United States)

    Wong, Del P.; Chaouachi, Anis; Lau, Patrick W.C.; Behm, David G.

    2011-01-01

    This study aimed to compare the effect of different static stretching durations followed by dynamic stretching on repeated sprint ability (RSA) and change of direction (COD). Twenty-five participants performed the RSA and COD tests in a randomized order. After a 5 min aerobic warm up, participants performed one of the three static stretching protocols of 30 s, 60 s or 90 s total duration (3 stretches x 10 s, 20 s or 30 s). Three dynamic stretching exercises of 30 s duration were then performed (90 s total). Sit-and-reach flexibility tests were conducted before the aerobic warm up, after the combined static and dynamic stretching, and post- RSA/COD test. The duration of static stretching had a positive effect on flexibility with 36.3% and 85.6% greater sit-and-reach scores with the 60 s and 90 s static stretching conditions respectively than with the 30 s condition (p ≤ 0.001). However there were no significant differences in RSA and COD performance between the 3 stretching conditions. The lack of change in RSA and COD might be attributed to a counterbalancing of static and dynamic stretching effects. Furthermore, the short duration (≤ 90 s) static stretching may not have provided sufficient stimulus to elicit performance impairments. Key points The duration of combined static and dynamic stretching had a positive effect on flexibility with 36.3% and 85.6% greater sit and reach scores with the 60 s and 90 s static stretching conditions respectively than with the 30 s condition (p ≤ 0.001). No significant differences in RSA and COD between the 3 stretching conditions. The lack of change in RSA and COD might be attributed to a counterbalancing of static and dynamic stretching effects. The short duration (≤ 90 s) static stretching may not have provided sufficient stimulus to elicit performance impairments. PMID:24149890

  12. Association of ECRG2 TCA short tandem repeat polymorphism with the risk of oesophageal cancer in a North Indian population.

    Science.gov (United States)

    Jain, Meenu; Kumar, Shaleen; Ghoshal, Uday C; Mittal, Balraj

    2008-06-01

    Oesophageal cancer-related gene (ECRG2) is a tumour suppressor gene and it has been suggested that a triplet TCA short tandem repeat (STR) in the noncoding region of exon 4 plays a role in genetic susceptibility to oesophageal cancer. In the present study, ECRG2 STR polymorphism was studied in 134 patients with oesophageal cancer and 194 controls, using PCR and polyacrylamide gel electrophoresis. The results showed a higher frequency of the ECRG2 TCA (3)/TCA (4) genotype in cancer patients than in controls (odds ratio 2.6, 95% CI 1.0-6.4, p = 0.03). The association of the ECRG2 TCA (3)/TCA (4) genotype with clinical characteristics showed an increased risk for squamous cell histology (2.8, 95% CI 1.1-7.1, p = 0.03), while no association with tumor location or lymph node involvement was observed. Interaction of tobacco, alcohol and occupational exposure with the ECRG2 genotypes did not show modulation of risk. In conclusion, the ECRG2 TCA (3)/TCA (4) genotype is associated with the risk of oesophageal carcinoma in a North Indian population.

  13. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats.

    Science.gov (United States)

    Seman, Ali; Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-06-01

    Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84-1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data.

  14. SHORT DURATIONS OF STATIC STRETCHING WHEN COMBINED WITH DYNAMIC STRETCHING DO NOT IMPAIR REPEATED SPRINTS AND AGILITY

    Directory of Open Access Journals (Sweden)

    Del P. Wong

    2011-06-01

    Full Text Available This study aimed to compare the effect of different static stretching durations followed by dynamic stretching on repeated sprint ability (RSA and change of direction (COD. Twenty-five participants performed the RSA and COD tests in a randomized order. After a 5 min aerobic warm up, participants performed one of the three static stretching protocols of 30 s, 60 s or 90 s total duration (3 stretches x 10 s, 20 s or 30 s. Three dynamic stretching exercises of 30 s duration were then performed (90 s total. Sit-and-reach flexibility tests were conducted before the aerobic warm up, after the combined static and dynamic stretching, and post- RSA/COD test. The duration of static stretching had a positive effect on flexibility with 36.3% and 85.6% greater sit-and-reach scores with the 60 s and 90 s static stretching conditions respectively than with the 30 s condition (p < 0.001. However there were no significant differences in RSA and COD performance between the 3 stretching conditions. The lack of change in RSA and COD might be attributed to a counterbalancing of static and dynamic stretching effects. Furthermore, the short duration (< 90 s static stretching may not have provided sufficient stimulus to elicit performance impairments

  15. The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

    Science.gov (United States)

    Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

    2015-07-01

    Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  16. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing.

    Science.gov (United States)

    Jin, Bo; Su, Qin; Luo, Haibo; Li, Yingbi; Wu, Jin; Yan, Jing; Hou, Yiping; Liang, Weibo; Zhang, Lin

    2016-07-01

    Mutation rates and 95% CI of 33 short tandem repeat (STR) loci (D1S2142, D2S1338, D2S441, D3S1358, D3S1754, D5S818, D6S1043, D7S3048, D7S820, D8S1132, D8S1179, D10S1248, D11S2368, D12S391, D13S1492, D13S317, D13S325, D14S306, D15S659, D16S539, D18S1364, D18S51, D19S433, D20S161, D21S11, D22GATA198B05, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA) were investigated through more than 424,000 parent-child meiotic transfers obtained from 10636 trios parentage testing cases in southwest Chinese Han population. Overall, 297, including 292 single-step, 4 double-step and 1 triple-step mutation events were observed. The average mutation rate was 0.70×10(-3). Most of the locus-specific mutation rates (varied from 0.20×10(-3) to 1.96×10(-3)) were lower than the other datasets (pstrict inclusion criteria of large-sized parents/child-trio cases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. Allele frequencies and haplotypes of eight Y-short tandem repeats in Bantu population living in Central Africa.

    Science.gov (United States)

    Lecerf, Maxime; Filali, Mounir; Grésenguet, Gérard; Ndjoyi-Mbiguino, Angélique; Le Goff, Jérôme; de Mazancourt, Philippe; Bélec, Laurent

    2007-09-13

    Eight Y chromosome short tandem repeats (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II) were used to assess haplotype distribution in non-selected, unrelated Bantu males living in Central Africa [N. Mathias, M. Bayes, C. Tyler-Smith, Highly informative compound haplotypes for the human Y chromosome, Hum. Mol. Genet. 3 (1994) 115-123; L. Roewer, J. Arnemann, N.K. Spurr, K.H. Grzeschik, J.T. Epplen, Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts, Hum. Genet. 89 (1992) 389-394; P. De Knijff, M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, L. Rower, Chromosome Y microsatellites: population genetic and evolutionary aspects, Int. J. Legal Med. 110 (1997) 134-149; M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, P. de Knijff, L. Rower, Evaluation of Y chromosome STRs: a multicenter study, Int. J. Legal Med. 110 (1997) 125-133, 141-149]. One hundred and sixty-five full haplotypes were obtained from Bantu males. The most common haplotype (DYS19-15, DYS389I-13, DYS389II-30, DYS390-21, DYS391-10, DYS392-11, DYS393-13, DYS385I/II-15,17) was shared by 5.5% of individuals. In the Bantu population in Central Africa, the haplotype diversity and the discrimination capacity of Y-STR may be estimated at 99.14% and 0.5333, respectively.

  18. Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpF lSTR® Yfiler® PCR amplification kit

    NARCIS (Netherlands)

    M.A. Goedbloed (Miriam); M. Vermeulen (Mark); R.N. Fang (Rixun); M. Lembring (Maria); A. Wollstein (Andreas); K. Ballantyne (Kaye); O. Lao Grueso (Oscar); S. Brauer (Silke); C. Krüger (Carmen); L. Roewer (Lutz); R. Lessig (Rüdiger); R. Ploski (Rafal); T. Dobosz (Tadeusz); J. Henke (Jürgen); M.R. Furtado (Manohar); M.H. Kayser (Manfred)

    2009-01-01

    textabstractThe Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpF lSTR® Yfiler® polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data

  19. Cross-cultural adaptation of the Dutch Short Musculoskeletal Function Assessment questionnaire (SMFA-NL) : Internal consistency, validity, repeatability and responsiveness

    NARCIS (Netherlands)

    Reininga, Inge H. F.; El Moumni, Mostafa; Bulstra, Sjoerd K.; Olthof, Maurits G. L.; Wendt, Klaus W.; Stevens, Martin

    The purpose of this study was to translate and culturally adapt the Dutch version of the Short Musculoskeletal Function Assessment questionnaire (SMFA-NL) and to investigate the internal consistency, validity, repeatability and responsiveness of the translated version. The original SMFA was first

  20. Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms

    NARCIS (Netherlands)

    M. Vermeulen (Mark); A. Wollstein (Andreas); K. van der Gaag (Kristiaan); O. Lao Grueso (Oscar); Y. Xue (Yali); Q. Wang (Qiuju); L. Roewer (Lutz); H. Knoblauch (Hans); C. Tyler-Smith (Chris); P. de Knijff (Peter); M.H. Kayser (Manfred)

    2009-01-01

    textabstractWe analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although

  1. Short consensus repeat domains extend the E-selectin structure in order to grab cells out of flow

    KAUST Repository

    Aleisa, Fajr A

    2017-01-08

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. They are composed of an N-terminal extracellular C-type lectin like domain, followed by an Endothelial Growth Factor like domain (EGF), a defined number of short consensus repeats SCR (also called “sushi” domains), a transmembrane domain and a C-terminal cytoplasmic tail. The adhesion of cells (expressing ligands) to the endothelium (expressing the selection i.e., E-selectin) occurs through the interaction between the lectin domain of selectins and sLeX presenting ligands. Structural/function studies to date have mainly focused on investigating the influence of the lectin domain of E-selectin on its ability to bind its ligands while other domains received less atention. We prepared a number of different recombinant E-selectin proteins with changes in the SCR units. Specifically we generated wild-type E-selectin proteins as monomeric or dimeric structures, mutant proteins with varied numbers of SCRs as well as proteins where strategic residues were mutated to change the conformation of the selectin. Using a novel real time immunoprecipitation surface plasmon resonance (SPR)-based in vitro binding study developed in our lab, the interaction of recombinant E-selectin proteins with immunoprecipitated endogenous ligands (i.e. CD44) captured on a CM-5 chip was assessed. These studies provided quantitative binding kinetics with on and off rates of selectin-ligand interactions and suggested that robust binding is dependent on the presence of the SCRs and oligomerization. These results provide significant implications on the functional mechanism of E-selectin binding to its ligands.

  2. Diversity of nuclear short tandem repeat loci in representative sample of North-eastern Bosnian and Herzegovina population

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna

    2012-01-01

    Full Text Available Diversity of nuclear microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia and Herzegovina. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping short tandem repeat (STR loci with PowerPlextm16 kit. Genetic analysis of allelic variants of the 15 STR loci PowerPlextm16 kit detected 17 samples determined as rare allelic variants or microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II. Population genetic analysis of STR loci in a representative sample of the population of northeast Bosnia and Herzegovina included the application of the assessment tests of within-population genetic diversity and interpopulation diversity, as well as genetic differentiation between populations: North-eastern Bosnia and Herzegovina (BH and BH general reference, then the Croatian population, Macedonian, Serbian and Slovenian. Based on the result analysis of specific forensic parameters, it can be assumed that the most informative marker is PENTA E for population genetic analysis and forensic testing in the population of northeast Bosnia and Herzegovina. Research results fit regional STR database of this part of Europe.

  3. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    Science.gov (United States)

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Short term soil erosion dynamics in alpine grasslands - Results from a Fallout Radionuclide repeated-sampling approach

    Science.gov (United States)

    Arata, Laura; Meusburger, Katrin; Zehringer, Markus; Ketterer, Michael E.; Mabit, Lionel; Alewell, Christine

    2016-04-01

    Improper land management and climate change has resulted in accelerated soil erosion rates in Alpine grasslands. To efficiently mitigate and control soil erosion and reduce its environmental impact in Alpine grasslands, reliable and validated methods for comprehensive data generation on its magnitude and spatial extent are mandatory. The use of conventional techniques (e.g. sediment traps, erosion pins or rainfall simulations) may be hindered by the extreme topographic and climatic conditions of the Alps. However, the application of the Fallout Radionuclides (FRNs) as soil tracers has already showed promising results in these specific agro-ecosystems. Once deposited on the ground, FRNs strongly bind to fine particles at the surface soil and move across the landscape primarily through physical processes. As such, they provide an effective track of soil and sediment redistribution. So far, applications of FRN in the Alps include 137Cs (half-life: 30.2 years) and 239+240Pu (239Pu [half-life = 24110 years] and 240Pu [half-life = 6561 years]). To investigate short term (4-5 years) erosion dynamics in the Swiss Alps, the authors applied a FRNs repeated sampling approach. Two study areas in the central Swiss Alps have been investigated: the Urseren Valley (Canton Uri), where significant land use changes occurred in the last centuries, and the Piora Valley (Canton Ticino), where land use change plays a minor role. Soil samples have been collected at potentially erosive sites along the valleys over a period of 4-5 years and measured for 137Cs and 239+240Pu activity. The inventory change between the sampling years indicates high erosion and deposition dynamics at both valleys. High spatial variability of 137Cs activities at all sites has been observed, reflecting the heterogeneous distribution of 137Cs fallout after the Chernobyl power plant accident in 1986. Finally, a new modelling technique to convert the inventory changes to quantitative estimates of soil erosion has

  5. [Analysis on allele frequencies of 7 short tandem repeat loci of Kashing-Beck disease patients on].

    Science.gov (United States)

    Kang, Long-li; Guo, Xiong; Zuo, Hong; Ping, Zhi-guang; Zhang, Bao-di; Lai, Jianghua; Geng, Dong

    2005-10-01

    To analyze the allele frequencies of 7 short tandem repeat (STR) loci (D12S1718, D12S1675, D12S358, D12S367, D12S1638, D12S1646 and D12S1682) on chromosome 12 among Kashing-Beck disease (KBD) patients and the control population living in the KBD areas and non-KBD area. EDTA-blood specimens were collected from 102 unrelated individuals of Chinese Han population in Shaanxi province including 29 KBD patients,30 controls living in the KBD area and 43 living in the non-KBD area. DNA samples were extracted using the Wizard Genomic DNA purification kit (http://www. Promega. com) and were amplified by polymerase chain reaction (PCR) technique. The PCR products were analyzed by ABI 3100 Genetic Analyzer. (1) In KBD patients group, the allele number for 7 STR loci were 4,7,7,8,5,5 and 7, the genotype number were 5,12,13,11,10,9 and 13; (2) In the control population living in KBD area, the allele number for 7 STR loci were 4,9,7,6,6,6 and 8,t he genotype number were 5,10,12,14,12,9 and 13;(3) In the control population living in the non-KBD area, the allele number for 7 STR loci were 7,9,7,7,5,8 and 11, the genotype number were 9,16, 17,16,12,15 and 20;(4) Compared with the allele frequencies among three groups, there were significant differences between KBD patients and the controls living in the KBD area (D12S367: P = 0.034; D12S1638: P = 0.041) and the controls living in the non-KBD area (D12S367: P = 0. 029; D12S1638: P= 0 .028) in the D12S367 and D12S1638 loci; (5) There were significant differences among KBD patients (P = 0.036), controls living in the KBD area (P = 0.039) and controls living in the non-KBD area in the D12S1646. There was significant difference between KBD patients and the controls in the D12S367 and D12S1638 loci.

  6. Regular figures

    CERN Document Server

    Tóth, L Fejes; Ulam, S; Stark, M

    1964-01-01

    Regular Figures concerns the systematology and genetics of regular figures. The first part of the book deals with the classical theory of the regular figures. This topic includes description of plane ornaments, spherical arrangements, hyperbolic tessellations, polyhedral, and regular polytopes. The problem of geometry of the sphere and the two-dimensional hyperbolic space are considered. Classical theory is explained as describing all possible symmetrical groupings in different spaces of constant curvature. The second part deals with the genetics of the regular figures and the inequalities fo

  7. Extension of recovery time from fatigue by repeated rest with short-term sleep during continuous fatigue load: Development of chronic fatigue model.

    Science.gov (United States)

    Kanzaki, Akinori; Okauchi, Takashi; Hu, Di; Shingaki, Tomotaka; Katayama, Yumiko; Koyama, Hidenori; Watanabe, Yasuyoshi; Cui, Yilong

    2016-05-01

    Homeostasis is known to be involved in maintaining the optimal internal environment, helping to achieve the best performance of biological functions. At the same time, a deviation from optimal conditions often attenuates the performance of biological functions, and such restricted performance could be considered as individual fatigue, including physical and mental fatigue. The present study seeks to develop an animal model of chronic or subacute fatigue in which the recovery time is extended through the gradual disruption of homeostasis. We show that repeated short-term rest periods with certain lengths of sleep during continuous fatigue loading extend recovery from spontaneous nighttime activity but not physical performance in comparison with a continuous fatigue-loading procedure. Furthermore, the immobility time in a forced swimming test was extended by repeated short-term rests. These results suggest that repeated short-term rest with certain lengths of sleep during continuous fatigue loading is able to extend the recovery from mental fatigue but not from physical fatigue and that this effect might occur via the disruption of a homeostatic mechanism that is involved in restoring the optimal internal environment. © 2016 Wiley Periodicals, Inc.

  8. Regular icosahedron

    OpenAIRE

    Mihelak, Veronika

    2016-01-01

    Here are collected properties of regular icosahedron which are useful for students of mathematics or mathematics teachers who can prepare exercises for talented students in elementary or middle school. The initial section describes the basic properties of regular polyhedra: tetrahedron, cube, dodecahedron, octahedron and of course icosahedron. We have proven that there are only five regular or platonic solids and have verified Euler's polyhedron formula for them. Then we focused on selected p...

  9. Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model.

    Science.gov (United States)

    Boutrand, Laetitia-Barbollat; Thépot, Amélie; Muther, Charlotte; Boher, Aurélie; Robic, Julie; Guéré, Christelle; Vié, Katell; Damour, Odile; Lamartine, Jérôme

    2017-01-01

    Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to "hot-wet" (40°C, 80% relative humidity [RH]) or "cold-dry" (10°C, 40% RH) climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot-wet and cold-dry) reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold-dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing adaption of human skin to repeated change in its climatic environment.

  10. Invasive Species Management on Military Lands: Clustered Regularly Interspaced Short Palindromic Repeat/ CRISPR associated protein 9 (CRISPR/Cas9) based Gene Drives

    Science.gov (United States)

    2017-06-30

    based technologies to the control of invasive species are emerging as an important area of innovation . As a mechanism to spread the desired genes...ER D C/ EL S R- 17 -2 Center for the Advancement of Sustainability Innovations (CASI) Invasive Species Management on Military Lands...Center (ERDC) solves the nation’s toughest engineering and environmental challenges. ERDC develops innovative solutions in civil and military

  11. Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling.

    Science.gov (United States)

    Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie

    2017-04-01

    Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined c lustered, r egularly i nterspaced s hort p alindromic r epeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Clustured regularly interspersed short palindromic repeats (CRISPR) genetic diversity studies as a mean to reconstruct the evolution of the Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Sola, Christophe

    2015-06-01

    The natural history of tuberculosis may be tackled by various means, among which the record of molecular scars that have been registered by the Mycobacterium tuberculosis complex (MTBC) genomes transmitted from patient to patient for tens of thousands years and possibly more. Recently discovered polymorphic loci, the CRISPR sequences, are indirect witnesses of the historical phage-bacteria struggle, and may be related to the time when the ancestor of today's tubercle bacilli were environmental bacteria, i.e. before becoming intracellular parasites. In this article, we present what are CRISPRs and try to summarize almost 20 years of research results obtained using the genetic diversity of the CRISPR loci in MTBC as a perspective for studying new models. We show that the study of the diversity of CRISPR sequences, thanks to «spoligotyping», has played a great role in our global understanding of the population structure of MTBC. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. A Genome-wide CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Screen Identifies NEK7 as an Essential Component of NLRP3 Inflammasome Activation.

    Science.gov (United States)

    Schmid-Burgk, Jonathan L; Chauhan, Dhruv; Schmidt, Tobias; Ebert, Thomas S; Reinhardt, Julia; Endl, Elmar; Hornung, Veit

    2016-01-01

    Inflammasomes are high molecular weight protein complexes that assemble in the cytosol upon pathogen encounter. This results in caspase-1-dependent pro-inflammatory cytokine maturation, as well as a special type of cell death, known as pyroptosis. The Nlrp3 inflammasome plays a pivotal role in pathogen defense, but at the same time, its activity has also been implicated in many common sterile inflammatory conditions. To this effect, several studies have identified Nlrp3 inflammasome engagement in a number of common human diseases such as atherosclerosis, type 2 diabetes, Alzheimer disease, or gout. Although it has been shown that known Nlrp3 stimuli converge on potassium ion efflux upstream of Nlrp3 activation, the exact molecular mechanism of Nlrp3 activation remains elusive. Here, we describe a genome-wide CRISPR/Cas9 screen in immortalized mouse macrophages aiming at the unbiased identification of gene products involved in Nlrp3 inflammasome activation. We employed a FACS-based screen for Nlrp3-dependent cell death, using the ionophoric compound nigericin as a potassium efflux-inducing stimulus. Using a genome-wide guide RNA (gRNA) library, we found that targeting Nek7 rescued macrophages from nigericin-induced lethality. Subsequent studies revealed that murine macrophages deficient in Nek7 displayed a largely blunted Nlrp3 inflammasome response, whereas Aim2-mediated inflammasome activation proved to be fully intact. Although the mechanism of Nek7 functioning upstream of Nlrp3 yet remains elusive, these studies provide a first genetic handle of a component that specifically functions upstream of Nlrp3. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Maximal ? -regularity

    NARCIS (Netherlands)

    Van Neerven, J.M.A.M.; Veraar, M.C.; Weis, L.

    2015-01-01

    In this paper, we prove maximal regularity estimates in “square function spaces” which are commonly used in harmonic analysis, spectral theory, and stochastic analysis. In particular, they lead to a new class of maximal regularity results for both deterministic and stochastic equations in L p

  15. Short (

    NARCIS (Netherlands)

    Telleman, Gerdien; den Hartog, Laurens

    2013-01-01

    Aim: This systematic review assessed the implant survival rate of short (<10 mm) dental implants installed in partially edentulous patients. A case report of a short implant in the posterior region have been added. Materials and methods: A search was conducted in the electronic databases of MEDLINE

  16. Syncope and hyperCKemia as minimal manifestations of short CTG repeat expansions in myotonic dystrophy type 1.

    Science.gov (United States)

    Finsterer, Josef; Stöllberger, Claudia; Gencik, Martin; Höftberger, Romana; Rahimi, Jasmin; Mokocki, Johannes

    2015-05-01

    Syncope and palpitations as the only initial manifestations of myotonic dystrophy type 1 (MD1) due to a CTG expansion of 50-100 repeats have not been reported. In a 55-year-old female with a family history of MD1 and a personal history of a single syncope, palpitations, and hyperCKemia, 70 CTG repeats were detected in the DMPK gene. Her brother had presented atypical clinical, electromyographic, and muscle biopsy features since the age of 35 but had been diagnosed with MD1 after he later developed typical distal myotonia. He died suddenly during an episode of syncope at the age of 53. A sister with clinical myotonia died suddenly during sleep at the age of 45 and a second sister with quadriparesis died from complications of intestinal rupture at age 52. A third sister committed suicide at age 40 after developing recurrent syncopes, while a fourth sister had hyperCKemia and foot-extensor weakness. The mother of these five affected children died suddenly from myocardial rupture. MD1 with CTG repeats may exclusively manifest cardiologically. Family screening for MD1 is important even in asymptomatic patients. MD1 may initially manifest without typical features, while muscle biopsy may be misleading and indicate glycogenosis. Close cardiac follow-up is important if MD1 manifests cardiologically to prevent syncope or sudden cardiac death. Copyright © 2014 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

  17. Allelic ladder characterization of the short tandem repeat polymorphism located in the 5{prime} flanking region to the human coagulation factor XIII A subunit gene

    Energy Technology Data Exchange (ETDEWEB)

    Puers, C. [Promega Corp., Madison, WI (United States)]|[Institute for Forensic Medicine, Muenster (Germany); Lins, A.M.; Sprecher, C.J. [Promega Corp., Madison, WI (United States)] [and others

    1994-09-01

    The short tandem repeat (STR) polymorphism present within the 5{prime} untranslated region of the human coagulation factor XIII A subunit gene, HUM-F13A01 [AAAG]{sub n}, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population. 27 refs., 2 figs., 1 tab.

  18. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  19. Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model

    Directory of Open Access Journals (Sweden)

    Boutrand LB

    2017-02-01

    Full Text Available Laetitia-Barbollat Boutrand,1 Amélie Thépot,2 Charlotte Muther,3 Aurélie Boher,2 Julie Robic,4 Christelle Guéré,4 Katell Vié,4 Odile Damour,5 Jérôme Lamartine1,3 1Departement de Biologie, Université Claude Bernard Lyon I, 2LabSkinCreations, 3CNRS UMR5305, Laboratoire de Biologie Tissulaire et d’Ingénierie Thérapeutique (LBTI, Lyon, 4Laboratoires Clarins, Cergy-Pontoise, 5Banque de Tissus et Cellules, Hospices Civiles de Lyon, Lyon, France Abstract: Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to “hot–wet” (40°C, 80% relative humidity [RH] or “cold–dry” (10°C, 40% RH climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot–wet and cold–dry reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold–dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing

  20. Regular Boardgames

    OpenAIRE

    Kowalski, Jakub; Sutowicz, Jakub; Szykuła, Marek

    2017-01-01

    We present an initial version of Regular Boardgames general game description language. This stands as an extension of Simplified Boardgames language. Our language is designed to be able to express the rules of a majority of popular boardgames including the complex rules such as promotions, castling, en passant, jump captures, liberty captures, and obligatory moves. The language describes all the above through one consistent general mechanism based on regular expressions, without using excepti...

  1. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

    DEFF Research Database (Denmark)

    Iacolina, Laura; Brajkovic, Vladimir; Canu, Antonio

    2016-01-01

    Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem...... repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five...

  2. Effect of intensified training on muscle ion kinetics, fatigue development and repeated short term performance in endurance trained cyclists

    DEFF Research Database (Denmark)

    Gunnarsson, Thomas Gunnar Petursson; Christensen, Peter Møller; Thomassen, Martin

    2013-01-01

    The effects of intensified training in combination with a reduced training volume on muscle ion kinetics, transporters and work capacity were examined. Eight well-trained cyclists replaced their regular training with speed-endurance training (12x30-s sprints) 2-3 times per wk and aerobic high......-intensity training (4-5x3-4min at 90-100% of maximal heart rate) 1-2 times per wk for 7 wks, and reduced training volume by 70% (intervention period; IP). The duration of an intense exhaustive cycling bout (EX2; 356±6 W), performed 2.5min after a 2-min intense cycle bout (EX1), was longer (p...

  3. Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis.

    Science.gov (United States)

    Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C

    2014-05-01

    Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Effects of short-term repeated exposure to different flooring surfaces on the behavior and physiology of dairy cattle.

    Science.gov (United States)

    Schütz, K E; Cox, N R

    2014-05-01

    Dairy cattle managed in some pasture-based systems such as in New Zealand are predominantly kept outdoors all year around, but are often taken off pasture for periods of time in wet weather to avoid soil damage. It is common to keep cattle on concrete surfaces during such "stand-off" practices and we investigated whether the addition of rubber matting onto concrete areas improves the welfare of dairy cattle. Sixteen groups of 5 cows (4 groups/treatment, 5 cows/group) were allocated to 1 of 4 treatments (concrete, 12-mm-thick rubber mat, 24-mm-thick rubber mat, or deep-bedded wood chips) and kept on these surfaces for 18 h/24h for 4 consecutive days (6h on pasture/24h). Each 4-d stand-off period was repeated 4 times (with 7 d of recovery between periods) to study the accumulated effects of repeated stand-off. Lying behavior was recorded continuously during the experiment. Gait score, stride length, hygiene score, live weight, and blood samples for cortisol analysis were recorded immediately before and after each stand-off period. Cows on wood chips spent the most time lying, and cows on concrete spent the least time lying compared with those on other surfaces [wood chips: 10.8h, 24-mm rubber mat: 7.3h, 12-mm rubber mat: 6.0 h, and concrete: 2.8h/18 h, standard error of the difference (SED): 0.71 h]. Cows on concrete spent more time lying during the 6h on pasture, likely compensating for the reduced lying during the stand-off period. Similarly, cows on concrete spent more time lying on pasture between stand-off periods (concrete: 12.1h, 12-mm rubber mat: 11.1h, 24-mm rubber mat: 11.2h, and wood chips: 10.7h/24h, SED: 0.28 h). Cows on concrete had higher gait score and shorter stride length after the 4-d stand-off period compared with cows on the other surface types, suggesting a change in gait pattern caused by discomfort. Cows on rubber mats were almost 3 times dirtier than cows on concrete or wood chips. Cortisol and live weight decreased for all treatment groups

  5. Analysis of RecA-independent recombination events between short direct repeats related to a genomic island and to a plasmid in Escherichia coli K12

    Directory of Open Access Journals (Sweden)

    María F. Azpiroz

    2017-05-01

    Full Text Available RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, also in the E. coli K12 context. However, it did not encode a site-specific recombinase as mobile genomic islands usually do. It was then deduced that the host cells should provide the recombination function. This latter was searched for by means of a PCR approach to detect the island excision in E. coli K12 mutants affected in a number of recombination functions, including the 16 E. coli K12 site-specific recombinases, the RecET system, and multiple proteins that participate in the RecA-dependent pathways of homologous recombination. None of these appeared to be involved in the island excision. The second model, analyzed in a RecA deficient context, was a plasmid construction containing a short direct repeat proceeding from Saccharomyces cerevisiae, which flanked the cat gene. The excision of this gene by recombination of the DNA repeats was confirmed by PCR and through the detection, recovery and characterization of the plasmid deleted form. In sum, we present new evidence on the occurrence of RecA-independent recombination events in E. coli K12. Although the mechanism underlying these processes is still unknown, their existence suggests that RecA-independent recombination may confer mobility to other genetic elements, thus contributing to genome plasticity.

  6. Adaptive regularization

    DEFF Research Database (Denmark)

    Hansen, Lars Kai; Rasmussen, Carl Edward; Svarer, C.

    1994-01-01

    Regularization, e.g., in the form of weight decay, is important for training and optimization of neural network architectures. In this work the authors provide a tool based on asymptotic sampling theory, for iterative estimation of weight decay parameters. The basic idea is to do a gradient descent...... in the estimated generalization error with respect to the regularization parameters. The scheme is implemented in the authors' Designer Net framework for network training and pruning, i.e., is based on the diagonal Hessian approximation. The scheme does not require essential computational overhead in addition...

  7. Spectrum of short- and long-term brain pathology and long-term behavioral deficits in male repeated hypoxic rats closely resembling human extreme prematurity.

    Science.gov (United States)

    Oorschot, Dorothy E; Voss, Logan; Covey, Matthew V; Goddard, Liping; Huang, William; Birchall, Penny; Bilkey, David K; Kohe, Sarah E

    2013-07-17

    Brain injury in the premature infant is associated with a high risk of neurodevelopmental disability. Previous small-animal models of brain injury attributable to extreme prematurity typically fail to generate a spectrum of pathology and behavior that closely resembles that observed in humans, although they provide initial answers to numerous cellular, molecular, and therapeutic questions. We tested the hypothesis that exposure of rats to repeated hypoxia from postnatal day 1 (P1) to P3 models the characteristic white matter neuropathological injury, gray matter volume loss, and memory deficits seen in children born extremely prematurely. Male Sprague Dawley rats were exposed to repeated hypoxia or repeated normoxia from P1 to P3. The absolute number of pre-oligodendrocytes and mature oligodendrocytes, the surface area and g-ratio of myelin, the absolute volume of cerebral white and gray matter, and the absolute number of cerebral neurons were quantified stereologically. Spatial memory was investigated on a radial arm maze. Rats exposed to repeated hypoxia had a significant loss of (1) pre-oligodendrocytes at P4, (2) cerebral white matter volume and myelin at P14, (3) cerebral cortical and striatal gray matter volume without neuronal loss at P14, and (4) cerebral myelin and memory deficits in adulthood. Decreased myelin was correlated with increased attention deficit hyperactivity disorder-like hyperactivity. This new small-animal model of extreme prematurity generates a spectrum of short- and long-term pathology and behavior that closely resembles that observed in humans. This new rat model provides a clinically relevant tool to investigate numerous cellular, molecular, and therapeutic questions on brain injury attributable to extreme prematurity.

  8. AB103. A sequence variation of short tandem repeat observed in paternity cases using massively parallel sequencing technology

    Science.gov (United States)

    Sukawutthiya, Poonyapat; Sathirapatyaa, Tikumphorn; Vongpaisarnsina, Kornkiat

    2017-01-01

    Background STR has been regularly used as genetic marker in paternity testing. The current standard procedure of STR allele detection based on DNA fragment analysis using CE. However, the MPS offers the high-throughput sequencing with lower cost per nucleotide. This technology has increase an opportunity for STR allele detection in national database and paternity testing as well. The high degree polymorphism of STR makes them informative that is an influence of their high mutation rate. Moreover, the usefulness even in homozygous alleles is determined by sequence variation in particular STR marker. In this study, we compare a STR allele designation from CE and a STR sequencing from MPS. The sequence variation has observed in particular STR. Methods The DNA of eighteen families were analyzed on a CE using two commercial test kits, while a MPS analysis was performed using MiSeq FG×TM forensic genomics system (Illumina). Results The results from MPS platforms showed totally concordant with CE data and also demonstrated the advantage of sequencing-based method in homozygous alleles. The sequencing variation of STR was detected and identified an inherited pattern even on homozygous alleles. For example, locus D3S1358 of child DNA was typed homozygous allele 16,16 on CE while distinguishable sequence suggested (TCTA)1(TCTG)3(TCTA)12 from father and (TCTA)1(TCTG)2(TCTA)13 from mother, respectively. The variety of STR allele sequences that indicated the allele inherited was detected in 8 of 18 families (44%) in our analysis. The sequence polymorphism was demonstrated in markers, including D2S1338, D3S1358, D4S2408, D5S818, D8S1179, D9S1122 and D21S11. Moreover, the success identification of STR inherited pattern of allele sharing among family also increases a CPI in paternity testing. Conclusions The results from MPS platforms showed totally concordant with CE data. The sequence variation of STR from MPS could be indicated the allele inherited pattern in paternity and

  9. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  10. Short-Term Changes in Anemia and Malaria Parasite Prevalence in Children under 5 Years during One Year of Repeated Cross-Sectional Surveys in Rural Malawi.

    Science.gov (United States)

    Kabaghe, Alinune N; Chipeta, Michael G; Terlouw, Dianne J; McCann, Robert S; van Vugt, Michèle; Grobusch, Martin P; Takken, Willem; Phiri, Kamija S

    2017-11-01

    In stable transmission areas, malaria is the leading cause of anemia in children. Anemia in children is proposed as an added sensitive indicator for community changes in malaria prevalence. We report short-term temporal variations of malaria and anemia prevalence in rural Malawian children. Data from five repeated cross-sectional surveys conducted over 1 year in rural communities in Chikwawa District, Malawi, were analyzed. Different households were sampled per survey; all children, 6-59 months, in sampled household were tested for malaria parasitemia and hemoglobin levels using malaria rapid diagnostic tests (mRDT) and Hemocue 301, respectively. Malaria symptoms, recent treatment (2 weeks) for malaria, anthropometric measurements, and sociodemographic details were recorded. In total, 894 children were included from 1,377 households. The prevalences of mRDT positive and anemia (Hb malaria prevalence, although malaria is an important factor in anemia.

  11. DNA extraction for short tandem repeat typing from mixed samples using anti-human leukocyte CD45 and ABO blood group antibodies.

    Science.gov (United States)

    Yano, Shizue; Honda, Katsuya; Kaminiwa, Junko; Nishi, Takeki; Iwabuchi, Yayoi; Sugano, Yukiko; Kurosu, Akira; Suzuki, Yasuhito

    2014-05-01

    DNA testing from mixed cell samples can be difficult to use successfully in criminal investigations. Here, we present a method for the extraction of DNA from mixed bloodstains involving plural contributors, after antibody-microbead captured cell separation. This method, together with the multiplex short tandem repeat typing presented, has proven highly successful in the recovery of DNA profiles corresponding to the ABO blood type. Methodological steps include magnetic separation using leukocyte specific CD45 antibody-coated microbeads and centrifugal separation of leukocyte agglutination by ABO antibody. The detection results of variable mixed ratio showed that the target DNA was detected accurately as low as 1:512 mixed ratio, regardless of the large amount of the background DNA present. The method presented here is applicable to PCR-based identification for various kinds of mixed samples. Copyright © 2014. Published by Elsevier Ireland Ltd.

  12. A new variant of endemic pemphigus foliaceus in El-Bagre, Colombia: the Hardy-Weinberg-Castle law and linked short tandem repeats.

    Science.gov (United States)

    Abreu-Velez, Ana María; Robles, Edinson Villa; Howard, Michael S

    2009-09-01

    We reported a new variant of endemic pemphigus foliaceus in El Bagre, Colombia. Our study performed Complex Segregation Analysis (CSA) and short tandem repeats to discriminate between environmental and/or genetic factors in this disorder. The CSA analysis was carried out according to the unified model, implemented using the transmission probabilities implemented in the computer program POINTER, and evaluated by using a software package for population genetic data analysis (GDA), Arlequin. We performed pedigree analyses by using Cyrillic 2.1 software, with a total of 30 families with 50 probands (47 males and 3 females) tested. In parallel to the CSA, we tested for the presence of short tandem repeats from HLA class II, DQ alpha 1, involving the gene locus D6S291 by using the Hardy-Weinberg- Castle law. Our results indicate that the best model of inheritance in this disease is a mixed model, with multifactorial effects within a recessive genotype. Two types of possible segregation patterns were found; one with strong recessive penetrance in families whose phenotype is more Amerindian-like, and another of possible somatic mutations. The penetrance of 10% or less in female patients 60 years of age or older indicates that hormones could protect younger females. The greatest risk factor for men being affected by the disorder was the NN genotype. These findings are only possible due to somatic mutations, and/or strong environmental effects. We also found a protective role for two genetic loci (D6S1019 AND D6S439) in the control group.

  13. Regular polytopes

    CERN Document Server

    Coxeter, H S M

    1973-01-01

    Polytopes are geometrical figures bounded by portions of lines, planes, or hyperplanes. In plane (two dimensional) geometry, they are known as polygons and comprise such figures as triangles, squares, pentagons, etc. In solid (three dimensional) geometry they are known as polyhedra and include such figures as tetrahedra (a type of pyramid), cubes, icosahedra, and many more; the possibilities, in fact, are infinite! H. S. M. Coxeter's book is the foremost book available on regular polyhedra, incorporating not only the ancient Greek work on the subject, but also the vast amount of information

  14. Coffee consumption rapidly reduces background DNA strand breaks in healthy humans: Results of a short-term repeated uptake intervention study.

    Science.gov (United States)

    Bakuradze, Tamara; Lang, Roman; Hofmann, Thomas; Schipp, Dorothea; Galan, Jens; Eisenbrand, Gerhard; Richling, Elke

    2016-03-01

    Intervention studies provide evidence that long-term coffee consumption correlates with reduced DNA background damage in healthy volunteers. Here, we report on short-term kinetics of this effect, showing a rapid onset after normal coffee intake. In a short-term human intervention study, we determined the effects of coffee intake on DNA integrity during 8 h. Healthy male subjects ingested coffee in 200 mL aliquots every second hour up to a total volume of 800 mL. Blood samples were taken at baseline, immediately before the first coffee intake and subsequently every 2 h, prior to the respective coffee intake. DNA integrity was assayed by the comet assay. The results show a significant (p coffee intake. Continued coffee intake was associated with further decrements in background DNA damage within the 8 h intervention (p coffee consumption). Repeated coffee consumption was associated with reduced background DNA strand breakage, clearly measurable as early as 2 h after first intake resulting in a cumulative overall reduction by about one-third of the baseline value. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Genetic considerations in human sex-mate selection: partners share human leukocyte antigen but not short-tandem-repeat identity markers.

    Science.gov (United States)

    Israeli, Moshe; Kristt, Don; Nardi, Yuval; Klein, Tirza

    2014-05-01

    Previous studies support a role for MHC on mating preference, yet it remains unsettled as to whether mating occurs preferentially between individuals sharing human leukocyte antigen (HLA) determinants or not. Investigating sex-mate preferences in the contemporary Israeli population is of further curiosity being a population with distinct genetic characteristics, where multifaceted cultural considerations influence mate selection. Pairs of male-female sex partners were evaluated in three groups. Two groups represented unmarried (n = 1002) or married (n = 308) couples and a control group of fictitious male-female couples. HLA and short-tandem-repeat (STR) genetic identification markers were assessed for the frequency of shared antigens and alleles. Human leukocyte antigen results showed that Class I and/ or Class II single antigen as well as double antigen sharing was more common in sex partners than in control group couples (P sex-mates and controls (P = 0.78). Sex partnerships shared HLA determinants more frequently than randomly constituted male-female pairs. The observed phenomenon does not reflect a syngenetic background between sex-mates as STR markers were not selectively shared. Thus, sex-mate selection in man may contravene the evolutionary pressure for genetic diversity in regard to HLA. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Towards improvements in the estimation of the coalescent: implications for the most effective use of Y chromosome short tandem repeat mutation rates.

    Directory of Open Access Journals (Sweden)

    Steven C Bird

    Full Text Available Over the past two decades, many short tandem repeat (STR microsatellite loci on the human Y chromosome have been identified together with mutation rate estimates for the individual loci. These have been used to estimate the coalescent age, or the time to the most recent common ancestor (TMRCA expressed in generations, in conjunction with the average square difference measure (ASD, an unbiased point estimator of TMRCA based upon the average within-locus allele variance between haplotypes. The ASD estimator, in turn, depends on accurate mutation rate estimates to be able to produce good approximations of the coalescent age of a sample. Here, a comparison is made between three published sets of per locus mutation rate estimates as they are applied to the calculation of the coalescent age for real and simulated population samples. A novel evaluation method is developed for estimating the degree of conformity of any Y chromosome STR locus of interest to the strict stepwise mutation model and specific recommendations are made regarding the suitability of thirty-two commonly used Y-STR loci for the purpose of estimating the coalescent. The use of the geometric mean for averaging ASD and û across loci is shown to improve the consistency of the resulting estimates, with decreased sensitivity to outliers and to the number of STR loci compared or the particular set of mutation rates selected.

  17. A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt.

    Science.gov (United States)

    Alfonse, Lauren E; Garrett, Amanda D; Lun, Desmond S; Duffy, Ken R; Grgicak, Catherine M

    2018-01-01

    DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA. The data, generated under 144 laboratory conditions, are classified by total copy number and contributor proportions. For the 70% of samples that were synthetically compromised, we report the level of DNA damage using quantitative and end-point PCR. In addition, we characterize the complexity of the signal by exploring the number of detected alleles in each profile. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Population genetic studies on nine tetrameric short tandem repeat loci using fluorescence dye-labeled primers and capillary electrophoresis in the Austrian population.

    Science.gov (United States)

    Klintschar, M; Ebner, A; Reichenpfader, B

    1999-06-01

    The short tandem repeats (STR) D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and a locus allowing sex discrimination (amelogenin) can be coamplified by the polymerase chain reaction using a commercially available kit, and subsequently typed using capillary electrophoresis. To establish databases for these loci for Austrian Caucasians, 115 unrelated persons were typed. All loci were in Hardy-Weinberg equilibrium. The combined mean paternity exclusion chance (MEC) was 0.999891 and the combined discriminating power (DP) was 3.08 x 10(-11). The allelic distributions showed no differences to those found for other Caucasian populations. Our data differed significantly from an Afro-American population at 5 loci and from a Chinese population at 4 loci. Linkage disequilibrium between any of the coamplified loci was not evident. Thus the combination of multiplex PCR and capillary electrophoresis can save time and yield excellent results for paternity testing and stain analysis.

  19. Short repeats in the spa gene of Staphylococcus aureus are prone to nonsense mutations: stop codons can be found in strains isolated from patients with generalized infection.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Ghaznavi-Rad, Ehsanollah; Neela, Vasanthakumari; Shamsudin, Mariana-Nor; Amouzandeh-Nobaveh, Alireza; Barkovsky, Eugene Victorovich

    2013-11-01

    Fifteen sequences with stop codons have been obtained in the course of standard methicillin-resistant Staphylococcus aureus (MRSA) spa typing. In nine of those sequences, stop codons occurred due to nonsense G-T and A-T transversions. G-T transversions would appear to be frequent in the spa gene, mostly due to symmetric mutational AT-pressure in the whole S. aureus genome and due to replication-associated mutational pressure characteristic of lagging strands of the "chromosome". A-T transversions would appear to be frequent in the spa gene mostly due to transcription-associated mutational pressure. Relative to other S. aureus genes, short repeats in spa are enriched by nonsense sites for G-T and A-T transversions; the probability of being nonsense for A-T transversion is high in that part of spa coding region. 13 out of 15 (87%) of the sequences with stop codons were obtained from strains isolated from patients with generalized S. aureus infection. Truncation of spa at its C-terminus is predicted to result in a protein that possesses functional IgG binding domains unable to be linked to the cell wall. This is discussed in light of the known fact that extracellular spa is a strong virulence factor involved in immune evasion. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  20. Short tandem repeat analysis of host's hepatocellular carcinoma by laser microdissection confirms the validity of safety procedures in liver transplantation: a forensic case.

    Science.gov (United States)

    Ventura, Francesco; Bonsignore, Alessandro; Tettamanti, Camilla; Verdiani, Simonetta; Gianelli Castiglione, Andrea; De Stefano, Francesco

    2013-08-09

    To limit the chimerism typical of transplanted organs, which constantly reveals mixed profiles, laser microdissection (LCM) has been hypothesized as a valid tool in comparison with manual dissection. A 42-year-old man with end-stage HBV/HDV liver cirrhosis and single hepatocellular carcinoma (HCC) underwent liver transplantation. Four months later hepatic nodules were diagnosed. The histological investigation showed an HCC. Despite therapy, the man died as a result of metastatic carcinoma 9 months later. On behalf of the public prosecutor, we performed short tandem repeat analysis on the hepatic nodules to determine whether the carcinoma had originated from the transplanted liver. The manually dissected samples revealed a high degree of chimerism that did not allow a clear diagnosis. Instead, the detected chimerism was very low in the microdissected samples, where the tumor origin was clearly diagnosable as a recurrence of the recipient's primitive HCC. Accordingly, the application of LCM improved the quality of the results leading to an exclusion of medical liability profiles, confirming the high quality safety procedure of the Italian system in solid organ transplantation, and showing at the same time how useful this technique may be in selected forensic cases.

  1. Genetic diversity of 15 autosomal short tandem repeats loci using the AmpFLSTR® Identifiler™ kit in a Bhil Tribe Population from Gujarat state, India

    Science.gov (United States)

    Chaudhari, Ramesh R.; Dahiya, M. S.

    2014-01-01

    MATERIALS AND METHODS: The genetic diversity and forensic parameters based on 15 autosomal short tandem repeats (STR) loci; D8S1179,D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317,D16S539, D2S1338, D19S433, vWA, TPOX, D18S51,D5S818, and FGA in AmpFLSTR® Identifiler™ kit from Applied Biosystems, Foster City, CA, USA were evaluated in saliva samples of 297 unrelated individuals from the Bhil Tribe population of Gujarat state, India to study genetic diversities and relatedness of this population with other national and international populations. RESULTS: Statistical analysis of the data revealed all loci were within Hardy-Weinberg Equilibrium expectations with the exception of the locus vWA (0.019) and locus D18S51 (0.016). The neighbour joining phylogeny tree and Principal Co-ordinate Analysis plot constructed based on Fst distances from autosomal STRs allele frequencies of the present study and other national as well as international populations show clustering of all the South Asian populations in one branch of the tree, while Middle Eastern and African populations cluster in a separate branch. CONCLUSION: Our findings reveal strong genetic affinities seen between the Indo-European (IE) speaking Bhil Tribe of Gujarat and Dravidian groups of South India. PMID:25400342

  2. Genetic diversity of 15 autosomal short tandem repeats loci using the AmpFLSTR(®) Identifiler™ kit in a Bhil Tribe Population from Gujarat state, India.

    Science.gov (United States)

    Chaudhari, Ramesh R; Dahiya, M S

    2014-04-01

    The genetic diversity and forensic parameters based on 15 autosomal short tandem repeats (STR) loci; D8S1179,D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317,D16S539, D2S1338, D19S433, vWA, TPOX, D18S51,D5S818, and FGA in AmpFLSTR® Identifiler™ kit from Applied Biosystems, Foster City, CA, USA were evaluated in saliva samples of 297 unrelated individuals from the Bhil Tribe population of Gujarat state, India to study genetic diversities and relatedness of this population with other national and international populations. Statistical analysis of the data revealed all loci were within Hardy-Weinberg Equilibrium expectations with the exception of the locus vWA (0.019) and locus D18S51 (0.016). The neighbour joining phylogeny tree and Principal Co-ordinate Analysis plot constructed based on Fst distances from autosomal STRs allele frequencies of the present study and other national as well as international populations show clustering of all the South Asian populations in one branch of the tree, while Middle Eastern and African populations cluster in a separate branch. Our findings reveal strong genetic affinities seen between the Indo-European (IE) speaking Bhil Tribe of Gujarat and Dravidian groups of South India.

  3. Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China.

    Science.gov (United States)

    Shi, Yunfang; Li, Xiaozhou; Ju, Duan; Li, Yan; Zhang, Xiuling; Zhang, Ying

    2015-08-01

    Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24-48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome.

  4. Correlation between genotypes of tRNA-linked short tandem repeats in Entamoeba nuttalli isolates and the geographical distribution of host rhesus macaques.

    Science.gov (United States)

    Feng, Meng; Komiyama, Tomoyoshi; Yanagi, Tetsuo; Cheng, Xunjia; Sherchand, Jeevan B; Tachibana, Hiroshi

    2014-01-01

    Several polymorphic markers, including serine-rich protein genes, have been used for the genotyping of isolates from the morphologically indistinguishable protozoan parasites Entamoeba histolytica, Entamoeba dispar, and Entamoeba nuttalli. Genotypes of tRNA-linked short tandem repeats (STRs) are highly polymorphic, but the correlation with geographical distribution is unknown. We have recently isolated 15 E. nuttalli strains from wild rhesus macaques in four locations in Kathmandu Valley, Nepal. The sequences of the serine-rich protein genes of the E. nuttalli strains differed among the four locations. In this study, we analyzed tRNA-linked STRs in six loci of the 15 strains. Two genotypes were found in loci N-K2, R-R, and S(TGA)-D, three in locus S-Q, and five in locus D-A. In locus A-L, one major genotype and ten minor genotypes were found, resulting in mixtures of two to six genotypes in eight strains. By combination of the main genotypes in the six loci, the 15 strains were divided into nine genotypes. The genotypes observed in E. nuttalli strains were quite different from those in E. histolytica and E. dispar. A phylogenetic tree constructed from tRNA-linked STRs in the six loci reflected the different places of isolation. These results suggest that sequence diversity of tRNA-linked STRs in E. nuttalli occurs with relatively high frequency and might be a marker of geographical distribution of host rhesus macaques, even in limited areas.

  5. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

    Science.gov (United States)

    Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

    2011-09-01

    Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

  6. Clustered regulatory interspaced short palindromic repeats (CRISPR)-mediated mutagenesis and phenotype rescue by piggyBac transgenesis in a nonmodel Drosophila species.

    Science.gov (United States)

    Tanaka, R; Murakami, H; Ote, M; Yamamoto, D

    2016-08-01

    How behavioural diversity emerged in evolution is an unexplored subject in biology. To tackle this problem, genes and circuits for a behaviour need to be determined in different species for phylogenetic comparisons. The recently developed clustered regulatory interspaced short palindromic repeats/CRISPR associated protein9 (CRISPR/Cas9) system made such a challenge possible by providing the means to induce mutations in a gene of interest in any organism. Aiming at elucidating diversification in genetic and neural networks for courtship behaviour, we attempted to generate a genetic tool kit in Drosophila subobscura, a nonmodel species distantly related to the genetic model Drosophila melanogaster. Here we report the generation of yellow (y) and white mutations with the aid of the CRISPR/Cas9 system, and the rescue of the y mutant phenotype by germline transformation of the newly established y mutant fly line with a y(+) -marked piggyBac vector. This successful mutagenesis and transformation in D. subobscura open up an avenue for comprehensive genetic analyses of higher functions in this and other nonmodel Drosophila species, representing a key step toward systematic comparisons of genes and circuitries underlying behaviour amongst species. © 2016 The Royal Entomological Society.

  7. Characterization of a functionally important and evolutionarily well-conserved epitope mapped to the short consensus repeats of E-selectin and L-selectin.

    Science.gov (United States)

    Jutila, M A; Watts, G; Walcheck, B; Kansas, G S

    1992-06-01

    Selectins represent a new family of adhesion molecules, expressed by leukocytes and endothelial cells, that are involved in the regulation of leukocyte traffic. Here we have characterized a new monoclonal antibody (mAb) (EL-246) that recognizes both human leukocyte L-selectin (previously called LAM-1, LECAM-1, or gp90MEL-14) and endothelial cell E-selectin (previously called ELAM-1). EL-246 recognized a 110-kD protein expressed on cells transfected with E-selectin cDNA and stained many postcapillary venules in inflamed human tonsil. EL-246 also stained human peripheral blood leukocytes and showed identity with anti-L-selectin mAb in two-color flow cytometric analysis. The expression of the leukocyte EL-246 antigen was regulated in the same manner as L-selectin and EL-246 recognized anti-L-selectin mAb affinity-purified antigen in SDS/PAGE Western blot analysis. Further, L-selectin cDNA transfectants were specifically stained by EL-246. EL-246 blocked greater than 95% of lymphocyte adhesion to peripheral lymph node high endothelial venules and greater than 90% of neutrophil adhesion to E-selectin transfectants. In addition to the EL-246 epitope being expressed on two different human selectins, it was detected on L-selectin from a variety of different animals. Interestingly, domain mapping studies localized the EL-246 epitope to the short consensus repeat (SCR) domains of L-selectin. EL-246 is the first mAb that recognizes two different selectins and potentially defines a functional epitope encoded by the SCR domains. Inhibitors of selectin function targeted to this region would be expected to have the added advantage of simultaneously blocking the activity of two distinct adhesion proteins involved in inflammation.

  8. Fluorescent-based typing of the two short tandem repeat loci HUMTH01 and HUMACTBP2: reproducibility of size measurements and genetic variation in the Swedish population.

    Science.gov (United States)

    Holgersson, S; Karlsson, J A; Kihlgren, A; Rosén, B; Savolainen, P; Gyllensten, U

    1994-07-01

    The aim of this study was to investigate the reproducibility of genetic typing of two tetrameric short tandem repeat (STR) loci and the extent of genetic variation in the Swedish population. An automated, fluorescent-based Applied Biosystems 373A sequencer was used for typing of the HUMTH01 and HUMACTBP2 loci (also named SE33). The former locus has seven alleles in the size range of 154-174 bp, while the latter is a complex locus with more than 32 alleles in the range of 227-316 bp. Using different fluorescent dyes, polymerase chain reaction (PCR) products from the two STR loci were sized in one lane using an internal size standard. In order to compare within- and between-gel reproducibility of fragment size estimates, a control sample was typed three times on each of 20 gels. Within the gel, the standard deviation (SD) of fragment size variability was less than 0.1 bp for four fragment sizes between 158-291 bp. Standard deviations between gels were slightly higher for the two shorter fragment sizes (HUMTH01), while the larger fragments varied between 0.3 and 0.4 bp (HUMACTBP2). The amount of genetic variation was investigated in samples from three Swedish cities (n = 301). Seven alleles were found at HUMTH01 and the observed heterozygosity was 0.77. At the HUMACTBP2 locus more than thirty alleles were found and the observed heterozygosity was 0.96. The observed genotype frequencies at HUMTH01 and HUMACTBP2 did not deviate significantly from Hardy-Weinberg expectations. No indication of a significant excess of homozygotes was found at any of the loci. We conclude that both HUMTH01 and HUMACTBP2 can be reliably typed using the method described. However, the latter locus requires an allelic ladder to be run on each gel.

  9. UNFOLDED REGULAR AND SEMI-REGULAR POLYHEDRA

    Directory of Open Access Journals (Sweden)

    IONIŢĂ Elena

    2015-06-01

    Full Text Available This paper proposes a presentation unfolding regular and semi-regular polyhedra. Regular polyhedra are convex polyhedra whose faces are regular and equal polygons, with the same number of sides, and whose polyhedral angles are also regular and equal. Semi-regular polyhedra are convex polyhedra with regular polygon faces, several types and equal solid angles of the same type. A net of a polyhedron is a collection of edges in the plane which are the unfolded edges of the solid. Modeling and unfolding Platonic and Arhimediene polyhedra will be using 3dsMAX program. This paper is intended as an example of descriptive geometry applications.

  10. An investigative study into the influence of a commercially available carbohydrate-protein-electrolyte beverage on short term repeated exercise performance

    Directory of Open Access Journals (Sweden)

    Roberts Justin D

    2012-03-01

    , respectively; P Conclusions The use of a CPE beverage improves short-term repeated exercise and subsequent performance compared to PL. Higher rates of carbohydrate oxidation, maintenance of plasma glucose, and decreased levels of fatigue may be beneficial for secondary bouts of performance and faster recovery turnover.

  11. Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01[AATG][sub n] and reassignment of alleles in population analysis by using a locus-specific allelic ladder

    Energy Technology Data Exchange (ETDEWEB)

    Puers, C. (Institute for Forensic Medicine, Muenster (Germany)); Schumm, J.W. (Promega Corp., Madison, WI (United States)); Hammond, H.A.; Caskey, C.T.; Jin, L.

    1993-10-01

    An allelic ladder containing amplified sequences of seven alleles of the polymorphic human tyrosine hydroxylase locus, HUMTH01, was constructed and employed as a standard marker. Sequence analysis of each ladder component indicates that fragments differ by integral multiples of the AATG core repeat sequence characteristic of this locus. Individual alles are designated [open quotes]5[close quotes] through [open quotes]11,[close quotes] according to the number of complete reiterations of the core repeat contained within them. Comparison of the HUMTH01 allelic ladder with DNA samples amplified at this locus revealed core repeat length heterogeneity (i.e., deletions or insertions shorter than one core repeat) within the human population. In particular, a common allele was identified which migrates more quickly than allele 10, but more slowly than allele 9, on electrophoresis through a denaturing polyacrylamide gel. Sequence analysis of this allele, designated [open quotes]10-1,[close quotes] reveals lack of a single adenine normally present in the seventh copy of the AATG. The allelic ladder was used to reevaluate previously published population data. Results of testing for Hardy-Weinberg equilibrium and population substructure were not altered significantly by these modifications. 29 refs., 1 fig., 3 tabs.

  12. Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae.

    Science.gov (United States)

    Li, Jia; Gao, Lei; Chen, Shanshan; Tao, Ke; Su, Yingjuan; Wang, Ting

    2016-02-11

    Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data.

  13. Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae

    Science.gov (United States)

    Li, Jia; Gao, Lei; Chen, Shanshan; Tao, Ke; Su, Yingjuan; Wang, Ting

    2016-01-01

    Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data. PMID:26865528

  14. A short-term risk–benefit analysis of occasional and regular use of low-dose aspirin in primary prevention of vascular diseases: a nationwide population-based study

    Science.gov (United States)

    Wu, I-Chen; Hsieh, Hui-Min; Wu, Ming-Tsang

    2015-01-01

    Objective To calculate the short-term risk–benefit effect of occasional and regular use of low-dose aspirin (≤100 mg/day) in primary prevention. Study design Two retrospective cohort studies. Setting Taiwan. Participants 63 788 and 24 910 patients of two nationwide population-based studies were examined. Methods Two databases of 1 000 000 patients were randomly sampled from data of Taiwan's National Health Insurance (NHI) for years 1997–2000 (NHI 2000) and 2005 (NHI 2005). In NHI 2000, 63 788 patients 30–95 years of age were found not to have previously been prescribed aspirin before 1 January 2000, but to have first been prescribed low-dose aspirin after that date. They were also found to be at risk of first hospitalisation for any major vascular diseases including haemorrhage (major gastrointestinal haemorrhage or cerebral haemorrhage) and ischaemia (acute myocardial infarction or ischaemic stroke) after their first prescription. We also applied it to NHI 2005, and the number of eligible patients was 24 910. Patients prescribed low-dose aspirin for aspirin for ≥80% of the days were considered to be regular users. Differences in rate of haemorrhage and ischaemia between these users were used to calculate their net clinical risk. Primary outcome Vascular diseases. Results In NHI 2000, the overall unadjusted rates of haemorrhage and ischaemia were 0.09% and 0.21%, respectively, for occasional users and 0.32% and 2.30%, respectively, for regular users. Adjusted net clinical risk of low-dose aspirin use between the two groups was 2.24% (95% CI 2.03% to 2.48%; paspirin might not be better than occasional use for preventing major vascular diseases in primary prevention. Prescribing regular low-dose aspirin for primary prevention should be done with caution. Future studies should explore the risk–benefit effect of long-term low-dose aspirin use in primary prevention. PMID:25575876

  15. Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree

    OpenAIRE

    Myres, Natalie M.; Ritchie, Kathleen H.; Lin, Alice A.; Hughes, Robert H.; Woodward, Scott R.; Underhill, Peter A.

    2009-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to valuate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 ...

  16. High-Intensity Small-Sided Games versus Repeated Sprint Training in Junior Soccer Players.

    Science.gov (United States)

    Eniseler, Niyazi; Şahan, Çağatay; Özcan, Ilker; Dinler, Kıvanç

    2017-12-01

    The aim of this study was to compare the effects of high-intensity small-sided games training (SSGT) versus repeated-sprint training (RST) on repeated-sprint ability (RSA), soccer specific endurance performance and short passing ability among junior soccer players. The junior soccer players were recruited from of a professional team (age 16.9 ± 1.1 years). The tests included the repeated-shuttle-sprint ability test (RSSAT), Yo-Yo Intermittent Recovery Test level 1 (Yo-Yo IR1) and Loughborough Soccer Passing Test (LSPT). Nineteen participants were randomly assigned to either the small-sided games training (SSGTG) (n = 10) or repeated-sprint training group (RSTG) (n = 9). Small-sided games or repeated-sprint training were added to the regular training sessions for two days of the regular practice week. The Wilcoxon signed-rank and Mann-Whitney U tests were used to examine differences in groups and training effects. A time x training group effect was found in the improvement of short-passing ability for the smallsided games training group which showed significantly better scores than the repeated-sprint training group (p ≤ 0.05). Both groups showed similar improvements in RSAdecrement (p games training can be used as an effective training mode to enhance both repeated sprint ability and short-passing ability.

  17. 5meCpG epigenetic marks neighboring a primate-conserved core promoter short tandem repeat indicate X-chromosome inactivation.

    Directory of Open Access Journals (Sweden)

    Filipe Brum Machado

    Full Text Available X-chromosome inactivation (XCI is the epigenetic transcriptional silencing of an X-chromosome during the early stages of embryonic development in female eutherian mammals. XCI assures monoallelic expression in each cell and compensation for dosage-sensitive X-linked genes between females (XX and males (XY. DNA methylation at the carbon-5 position of the cytosine pyrimidine ring in the context of a CpG dinucleotide sequence (5meCpG in promoter regions is a key epigenetic marker for transcriptional gene silencing. Using computational analysis, we revealed an extragenic tandem GAAA repeat 230-bp from the landmark CpG island of the human X-linked retinitis pigmentosa 2 RP2 promoter whose 5meCpG status correlates with XCI. We used this RP2 onshore tandem GAAA repeat to develop an allele-specific 5meCpG-based PCR assay that is highly concordant with the human androgen receptor (AR exonic tandem CAG repeat-based standard HUMARA assay in discriminating active (Xa from inactive (Xi X-chromosomes. The RP2 onshore tandem GAAA repeat contains neutral features that are lacking in the AR disease-linked tandem CAG repeat, is highly polymorphic (heterozygosity rates approximately 0.8 and shows minimal variation in the Xa/Xi ratio. The combined informativeness of RP2/AR is approximately 0.97, and this assay excels at determining the 5meCpG status of alleles at the Xp (RP2 and Xq (AR chromosome arms in a single reaction. These findings are relevant and directly translatable to nonhuman primate models of XCI in which the AR CAG-repeat is monomorphic. We conducted the RP2 onshore tandem GAAA repeat assay in the naturally occurring chimeric New World monkey marmoset (Callitrichidae and found it to be informative. The RP2 onshore tandem GAAA repeat will facilitate studies on the variable phenotypic expression of dominant and recessive X-linked diseases, epigenetic changes in twins, the physiology of aging hematopoiesis, the pathogenesis of age-related hematopoietic

  18. Automating InDesign with Regular Expressions

    CERN Document Server

    Kahrel, Peter

    2006-01-01

    If you need to make automated changes to InDesign documents beyond what basic search and replace can handle, you need regular expressions, and a bit of scripting to make them work. This Short Cut explains both how to write regular expressions, so you can find and replace the right things, and how to use them in InDesign specifically.

  19. Word regularity affects orthographic learning.

    Science.gov (United States)

    Wang, Hua-Chen; Castles, Anne; Nickels, Lyndsey

    2012-01-01

    Share's self-teaching hypothesis proposes that orthographic representations are acquired via phonological decoding. A key, yet untested, prediction of this theory is that there should be an effect of word regularity on the number and quality of word-specific orthographic representations that children acquire. Thirty-four Grade 2 children were exposed to the sound and meaning of eight novel words and were then presented with those words in written form in short stories. Half the words were assigned regular pronunciations and half irregular pronunciations. Lexical decision and spelling tasks conducted 10 days later revealed that the children's orthographic representations of the regular words appeared to be stronger and more extensive than those of the irregular words.

  20. Repeated Cross-linking After a Short Time Does Not Provide Any Additional Biomechanical Stiffness in the Mouse Cornea In Vivo.

    Science.gov (United States)

    Tabibian, David; Kling, Sabine; Hammer, Arthur; Richoz, Olivier; Hafezi, Farhad

    2017-01-01

    To study whether repeated collagen cross-linking (CXL) performed in vivo in mice shows an additive effect on mechanical corneal stiffness. In this experimental study, epithelium-off CXL was performed in a total of 18 eyes from male C57BL/6 mice, with 0.27%-riboflavin solution applied for 20 minutes, followed by ultraviolet-A (UVA) irradiation (365 nm, 9mW/cm(2)) for 2:50 minutes (fluence 1.53 J/cm(2)). CXL was performed as either a single (1×CXL) or a repeated (2×CXL) treatment. Un-irradiated corneas served as controls. In the 2×CXL group, the procedure was performed on day 1 and day 4 to ensure complete reepithelialization between sessions. Biomechanical analysis was performed on day 7. Corneas were harvested with a small scleral ring and mounted on a customized two-dimensional flap holder. The biomechanical measurement consisted of three parts: (1) pre-conditioned during three cycles from 0.04 to 0.4 N, (2) stress relaxation during 120 seconds following 0.4 N force application, and (3) stress-strain curve until break. After the relaxation period of 120 seconds, highly significant differences (P corneas and 2×CXL corneas. No significant difference (P = .70) was detected between the 1×CXL and 2×CXL groups. The stress remaining after relaxation was 355 ± 25.2 kPa in the control group, 457 ± 34.1 kPa in the 1×CXL group, and 463 ± 22.2 kPa in the 2×CXL group. No significant differences in the stress-strain curves were found between the conditions. Repeated CXL 3 days after the first procedure does not further increase corneal stiffness in mice in vivo. [J Refract Surg. 2017;33(1):56-60.]. Copyright 2017, SLACK Incorporated.

  1. Short-Term Changes in Anemia and Malaria Parasite Prevalence in Children under 5 Years during One Year of Repeated Cross-Sectional Surveys in Rural Malawi

    NARCIS (Netherlands)

    Kabaghe, Alinune N.; Chipeta, Michael G.; Terlouw, Dianne J.; McCann, Robert S.; van Vugt, Michèle; Grobusch, Martin P.; Takken, Willem; Phiri, Kamija S.

    2017-01-01

    In stable transmission areas, malaria is the leading cause of anemia in children. Anemia in children is proposed as an added sensitive indicator for community changes in malaria prevalence. We report short-term temporal variations of malaria and anemia prevalence in rural Malawian children. Data

  2. Short-term changes in anemia and malaria parasite prevalence in children under 5 years during one year of repeated cross-sectional surveys in rural Malawi

    NARCIS (Netherlands)

    Kabaghe, Alinune N.; Chipeta, Michael G.; Terlouw, Dianne J.; McCann, Robert S.; Vugt, Van Michèle; Grobusch, Martin P.; Takken, Willem; Phiri, Kamija S.

    2017-01-01

    In stable transmission areas, malaria is the leading cause of anemia in children. Anemia in children is proposed as an added sensitive indicator for community changes in malaria prevalence. We report short-term temporal variations of malaria and anemia prevalence in rural Malawian children. Data

  3. Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations

    DEFF Research Database (Denmark)

    Meldgaard, Michael; Morling, N

    1997-01-01

    is one repeat unit shorter than the true allele peak. The existence of such artificial peaks is of special importance when the methods are used for forensic investigations because the artificial extra peaks may simulate true alleles when samples containing mixtures of DNA from different individuals...... alleles. Similar results were obtained when the PCR products were analyzed under native conditions. Low-copy genome analysis excluded that somatic heterogeneity of the STR regions caused the extra peaks. The systems HumVWA31A, HumFibra/FGA, and D21S11 were especially affected by low-stringency conditions...

  4. Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree.

    Science.gov (United States)

    Myres, Natalie M; Ritchie, Kathleen H; Lin, Alice A; Hughes, Robert H; Woodward, Scott R; Underhill, Peter A

    2009-06-01

    To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.

  5. Temporal regularity in speech perception: Is regularity beneficial or deleterious?

    Science.gov (United States)

    Geiser, Eveline; Shattuck-Hufnagel, Stefanie

    2012-04-01

    Speech rhythm has been proposed to be of crucial importance for correct speech perception and language learning. This study investigated the influence of speech rhythm in second language processing. German pseudo-sentences were presented to participants in two conditions: 'naturally regular speech rhythm' and an 'emphasized regular rhythm'. Nine expert English speakers with 3.5±1.6 years of German training repeated each sentence after hearing it once over headphones. Responses were transcribed using the International Phonetic Alphabet and analyzed for the number of correct, false and missing consonants as well as for consonant additions. The over-all number of correct reproductions of consonants did not differ between the two experimental conditions. However, speech rhythmicization significantly affected the serial position curve of correctly reproduced syllables. The results of this pilot study are consistent with the view that speech rhythm is important for speech perception.

  6. Effect of biochar addition on short-term N2O and CO2 emissions during repeated drying and wetting of an anthropogenic alluvial soil.

    Science.gov (United States)

    Yang, Fang; Lee, Xinqing; Theng, Benny K G; Wang, Bing; Cheng, Jianzhong; Wang, Qian

    2017-06-01

    Agricultural soils are an important source of greenhouse gases (GHG). Biochar application to such soils has the potential of mitigating global anthropogenic GHG emissions. Under irrigation, the topsoils in arid regions experience repeated drying and wetting during the crop growing season. Biochar incorporation into these soils would change the soil microbial environment and hence affect GHG emissions. Little information, however, is available regarding the effect of biochar addition on carbon dioxide (CO2) and nitrous oxide (N2O) emissions from agricultural soils undergoing repeated drying and wetting. Here, we report the results of a 49-day aerobic incubation experiment, incorporating biochar into an anthropogenic alluvial soil in an arid region of Xinjiang Province, China, and measuring CO2 and N2O emissions. Under both drying-wetting and constantly moist conditions, biochar amendment significantly increased cumulative CO2 emission. At the same time, there was a significant reduction (up to ~20 %) in cumulative N2O emission, indicating that the addition of biochar to irrigated agricultural soils may effectively slow down global warming in arid regions of China.

  7. Effects of in-season short-term aerobic and high-intensity interval training program on repeated sprint ability and jump performance in handball players.

    Science.gov (United States)

    Hermassi, Souhail; Ingebrigtsen, Jørgen; Schwesig, René; Fieseler, Georg; Delank, Karl-Stefan; Chamari, Karim; Shephard, Roy J; Chelly, Mohamed-Souhaiel

    2018-01-01

    This study examined the effects of a 7-week in-season aerobic and high-intensity interval-training program on performance tests linked to successful handball play (e.g., repeated sprint and jumping ability). Thirty participants (age 17.0±1.2 years, body mass 81.1±3.4 kg, height 1.82±0.07 m) performed a Yo-Yo Intermittent Recovery Test level 1 (Yo-Yo IR1), a squat (SJ) and a Countermovement Jump Test (CMJ), as well as a repeated Sprint Ability Test (RSA). From this, maximal aerobic speed (MAS, reached at the end of the Yo-Yo IR1), jumping ability, best time in a single sprint trial (RSAbest), total time (RSATT) and the performance decrement (RSAdec) during all sprints were calculated. Later, subjects were randomly assigned to a control group (CG; N.=15) performing their normal training schedule (5 weekly sessions of ~90 minutes of handball training) or an experimental group (EG; N.=15). The EG performed two 30 min sessions per week of high-intensity aerobic exercises at 100-130% of MAS in addition to their normal training schedule. A significant improvement in MAS (d=4.1), RSAbest (d=1.9), RSATT (d=1.5) and RSAdec (d=2.3) after the training period was demonstrated. Also, significant interaction effects (time x group) were found for all parameters as the EG significantly improved performances in all tests after training. The greatest interaction effects were observed in MAS (η2=0.811) and CMJ (η2=0.759). No relevant changes in test performances were found in the CG (mean d=-0.02). These results indicate that individually speed-controlled aerobic and interval training is effective for improving specific handball performance.

  8. Regular Expression Pocket Reference

    CERN Document Server

    Stubblebine, Tony

    2007-01-01

    This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp

  9. Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

    DEFF Research Database (Denmark)

    Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe

    2013-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...... in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2...

  10. The expression and intranuclear distribution of nucleolin in HL-60 and K-562 cells after repeated, short-term exposition to rotating magnetic fields.

    Science.gov (United States)

    Masiuk, Marek; Rakoczy, Rafal; Masiuk, Stanislaw; Kordas, Marian

    2008-09-01

    The aim of the study was to analyze the influence of rotating magnetic fields (RMF) on the expression and intranuclear distribution of nucleolin, protein involved in ribosome biosynthesis, in HL-60 (acute promyelocytic leukemia) and K-562 (chronic myelogenous leukemia) established human cell lines. Cells were exposed to RMF for two chosen states of the magnetic field induction: B=10 mT and B=20 mT in experimental set-up for 30 min with 24-h intervals for four days. Cytospin slides were prepared and expression of nucleolin was detected using monoclonal antibodies. Parameters of fluorescence related to nucleolin were measured in at least 2000 tumor cells in each slide by a laser scanning cytometer with an argon laser. Percentages of cells in different phases of cell cycle were also analyzed. The repeated exposition of cells to RMF caused significant increase in nucleolin expression in the whole nucleus and in the nucleolin aggregates (NUA). The redistribution of nucleolin measured by changes in number of NUA was also observed. The exposition of both cell lines studied to RMF did not alter the cell cycle. The nucleolin is responsive to RMF in HL-60 and K-562. The increase of its expression may indicate a reaction of cells to RMF and it may influence their other biological properties.

  11. Regular simplex refinement by regular simplices

    NARCIS (Netherlands)

    Casado, L.G.; Tóth, B.G.; Hendrix, E.M.T.; García, I.

    2014-01-01

    A naturalway to define branching in Branch-and-Bound for blending problemis to do bisection. The disadvantage of bisectioning is that partition sets are in general irregular. A regular simplex with fixed orientation can be determined by its center and size, allowing storage savings in a Branchand-

  12. Two Distinct Origins of Long-Term Learning Effects in Verbal Short-Term Memory

    Science.gov (United States)

    Majerus, Steve; Perez, Trecy Martinez; Oberauer, Klaus

    2012-01-01

    Verbal short-term memory (STM) is highly sensitive to learning effects: digit sequences or nonword sequences which have been rendered more familiar via repeated exposure are recalled more accurately. In this study we show that sublist-level, incidental learning of item co-occurrence regularities affects immediate serial recall of words and…

  13. A case report of a cystic fibrosis patient with repeated isolation of Trichosporon mycotoxinivorans identified by a novel short-extraction method.

    Science.gov (United States)

    Goldenberger, Daniel; Hinić, Vladimira; Prince, Spasenija Savic; Tamm, Michael; Balestra, Anna-Maria; Hohler, Doris; Frei, Reno

    2016-10-25

    Trichosporon mycotoxinivorans is a recently described yeast-like fungal organism and its association as a pathogen for patients with cystic fibrosis (CF) was reported previously. We show the clinical course of a CF patient over 9 years as well as the applications of modern molecular and proteomic identification techniques of this rare fungus. We present the case of a 32-year-old male CF patient with sputum cultures continuously positive with the anamorphic yeast T. mycotoxinivorans during 9 years. Furthermore, susceptibility testing of T. mycotoxinivorans to different antifungals were performed. In addition, a rapid identification method of this novel fungal pathogen with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was applied using a simple extraction protocol. Our case presentation confirms T. mycotoxinivorans as a potential emerging pathogen in patients with CF. However, our CF patient showed mild symptoms over a very long time period of 9 years. A short MALDI-TOF MS procedure allows reliable and rapid identification of T. mycotoxinivorans and therefore should facilitate further study on the clinical relevance and epidemiology of this unusual fungal organism.

  14. Regular expressions cookbook

    CERN Document Server

    Goyvaerts, Jan

    2009-01-01

    This cookbook provides more than 100 recipes to help you crunch data and manipulate text with regular expressions. Every programmer can find uses for regular expressions, but their power doesn't come worry-free. Even seasoned users often suffer from poor performance, false positives, false negatives, or perplexing bugs. Regular Expressions Cookbook offers step-by-step instructions for some of the most common tasks involving this tool, with recipes for C#, Java, JavaScript, Perl, PHP, Python, Ruby, and VB.NET. With this book, you will: Understand the basics of regular expressions through a

  15. Regular expression containment

    DEFF Research Database (Denmark)

    Henglein, Fritz; Nielsen, Lasse

    2011-01-01

    * for Kleene-star, and a general coin- duction rule as the only additional rule. Our axiomatization gives rise to a natural computational inter- pretation of regular expressions as simple types that represent parse trees, and of containment proofs as coercions. This gives the axiom- atization a Curry...... to be undecidable. We discuss application of regular expressions as types to bit coding of strings and hint at other applications to the wide-spread use of regular expressions for substring matching, where classical automata-theoretic techniques are a priori inapplicable. Neither regular expressions as types nor...

  16. Deployment Repeatability

    Science.gov (United States)

    2016-08-31

    environment. Zero shift errors  Part replacement after testing  Material damage, including damage to composite fibers and plastic deformation in...of motors or deployment drivers  Loss or redistribution of lubrication Hysteresis errors  Material creep due to time in storage and time in the...measurements can be made with fixed references within the room. The first solution is self -explanatory. The second solution requires regular reference

  17. High-Intensity Small-Sided Games versus Repeated Sprint Training in Junior Soccer Players

    Directory of Open Access Journals (Sweden)

    Eniseler Niyazi

    2017-12-01

    Full Text Available The aim of this study was to compare the effects of high-intensity small-sided games training (SSGT versus repeated-sprint training (RST on repeated-sprint ability (RSA, soccer specific endurance performance and short passing ability among junior soccer players. The junior soccer players were recruited from of a professional team (age 16.9 ± 1.1 years. The tests included the repeated-shuttle-sprint ability test (RSSAT, Yo-Yo Intermittent Recovery Test level 1 (Yo-Yo IR1 and Loughborough Soccer Passing Test (LSPT. Nineteen participants were randomly assigned to either the small-sided games training (SSGTG (n = 10 or repeated-sprint training group (RSTG (n = 9. Small-sided games or repeated-sprint training were added to the regular training sessions for two days of the regular practice week. The Wilcoxon signed-rank and Mann-Whitney U tests were used to examine differences in groups and training effects. A time x training group effect was found in the improvement of short-passing ability for the smallsided games training group which showed significantly better scores than the repeated-sprint training group (p ≤ 0.05. Both groups showed similar improvements in RSAdecrement (p < 0.05. Only the repeated-sprint training group improved in the Yo-Yo IR1 (p < 0.05. This study clearly shows that high-intensity small-sided games training can be used as an effective training mode to enhance both repeated sprint ability and short-passing ability.

  18. Fingerprint enhancement revisited and the effects of blood enhancement chemicals on subsequent profiler Plus fluorescent short tandem repeat DNA analysis of fresh and aged bloody fingerprints.

    Science.gov (United States)

    Frégeau, C J; Germain, O; Fourney, R M

    2000-03-01

    This study was aimed at determining the effect of seven blood enhancement reagents on the subsequent Profiler Plus fluorescent STR DNA analysis of fresh or aged bloody fingerprints deposited on various porous and nonporous surfaces. Amido Black, Crowle's Double Stain. 1,8-diazafluoren-9-one (DFO), Hungarian Red, leucomalachite green, luminol and ninhydrin were tested on linoleum, glass, metal, wood (pine, painted white), clothing (85% polyester/15% cotton, 65% polyester/35% cotton, and blue denim) and paper (Scott 2-ply and Xerox-grade). Preliminary experiments were designed to determine the optimal blood dilutions to use to ensure a DNA typing result following chemical enhancement. A 1:200 blood dilution deposited on linoleum and enhanced with Crowle's Double Stain generated enough DNA for one to two rounds of Profiler Plus PCR amplification. A comparative study of the DNA yields before and after treatment indicated that the quantity of DNA recovered from bloody fingerprints following enhancement was reduced by a factor of 2 to 12. Such a reduction in the DNA yields could potentially compromise DNA typing analysis in the case of small stains. The blood enhancement chemicals selected were also evaluated for their capability to reveal bloodmarks on the various porous and nonporous surfaces chosen in this study. Luminol. Amido Black and Crowle's Double Stain showed the highest sensitivity of all seven chemicals tested and revealed highly diluted (1:200) bloody fingerprints. Both luminol and Amido Black produced excellent results on both porous and nonporous surfaces, but Crowle's Double Stain failed to produce any results on porous substrates. Hungarian Red, DFO, leucomalachite green and ninhydrin showed lower sensitivities. Enhancement of bloodmarks using any of the chemicals selected, and short-term exposure to these same chemicals (i.e., less than 54 days), had no adverse effects on the PCR amplification of the nine STR systems surveyed (D3S 1358, HumvWA, Hum

  19. Impacts of regular and random noise on the behaviour, growth and development of larval Atlantic cod (Gadus morhua).

    Science.gov (United States)

    Nedelec, Sophie L; Simpson, Stephen D; Morley, Erica L; Nedelec, Brendan; Radford, Andrew N

    2015-10-22

    Anthropogenic noise impacts behaviour and physiology in many species, but responses could change with repeat exposures. As repeat exposures can vary in regularity, identifying regimes with less impact is important for regulation. We use a 16-day split-brood experiment to compare effects of regular and random acoustic noise (playbacks of recordings of ships), relative to ambient-noise controls, on behaviour, growth and development of larval Atlantic cod (Gadus morhua). Short-term noise caused startle responses in newly hatched fish, irrespective of rearing noise. Two days of both regular and random noise regimes reduced growth, while regular noise led to faster yolk sac use. After 16 days, growth in all three sound treatments converged, although fish exposed to regular noise had lower body width-length ratios. Larvae with lower body width-length ratios were easier to catch in a predator-avoidance experiment. Our results demonstrate that the timing of acoustic disturbances can impact survival-related measures during development. Much current work focuses on sound levels, but future studies should consider the role of noise regularity and its importance for noise management and mitigation measures. © 2015 The Authors.

  20. Rhythm facilitates the detection of repeating sound patterns

    Directory of Open Access Journals (Sweden)

    Vani G. Rajendran

    2016-01-01

    Full Text Available This study investigates the influence of temporal regularity on human listeners’ ability to detect a repeating noise pattern embedded in statistically identical non-repeating noise. Human listeners were presented with white noise stimuli that either contained a frozen segment of noise that repeated in a temporally regular or irregular manner, or did not contain any repetition at all. Subjects were instructed to respond as soon as they detected any repetition in the stimulus. Pattern detection performance was best when repeated targets occurred in a temporally regular manner, suggesting that temporal regularity plays a facilitative role in pattern detection. A modulation filterbank model could account for these results.

  1. Regularization by External Variables

    DEFF Research Database (Denmark)

    Bossolini, Elena; Edwards, R.; Glendinning, P. A.

    2016-01-01

    Regularization was a big topic at the 2016 CRM Intensive Research Program on Advances in Nonsmooth Dynamics. There are many open questions concerning well known kinds of regularization (e.g., by smoothing or hysteresis). Here, we propose a framework for an alternative and important kind of regula...... of regularization, by external variables that shadow either the state or the switch of the original system. The shadow systems are derived from and inspired by various applications in electronic control, predator-prey preference, time delay, and genetic regulation....

  2. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan

    2015-02-12

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  3. CRISPR Detection From Short Reads Using Partial Overlap Graphs.

    Science.gov (United States)

    Ben-Bassat, Ilan; Chor, Benny

    2016-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

  4. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...

  5. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.

    Science.gov (United States)

    Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine

    2007-05-23

    In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr.

  6. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2007-05-01

    Full Text Available Abstract Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the

  7. Sparse structure regularized ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-04-17

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

  8. Accelerating regular polygon beams.

    Science.gov (United States)

    Barwick, Shane

    2010-12-15

    Beams that possess high-intensity peaks that follow curved paths of propagation under linear diffraction have recently been shown to have a multitude of interesting uses. In this Letter, a family of phase-only masks is derived, and each mask gives rise to multiple accelerating intensity maxima. The curved paths of the peaks can be described by the vertices of a regular polygon that is centered on the optic axis and expands with propagation.

  9. Regular Single Valued Neutrosophic Hypergraphs

    Directory of Open Access Journals (Sweden)

    Muhammad Aslam Malik

    2016-12-01

    Full Text Available In this paper, we define the regular and totally regular single valued neutrosophic hypergraphs, and discuss the order and size along with properties of regular and totally regular single valued neutrosophic hypergraphs. We also extend work on completeness of single valued neutrosophic hypergraphs.

  10. The geometry of continuum regularization

    Energy Technology Data Exchange (ETDEWEB)

    Halpern, M.B.

    1987-03-01

    This lecture is primarily an introduction to coordinate-invariant regularization, a recent advance in the continuum regularization program. In this context, the program is seen as fundamentally geometric, with all regularization contained in regularized DeWitt superstructures on field deformations.

  11. Modular Regularization Algorithms

    DEFF Research Database (Denmark)

    Jacobsen, Michael

    2004-01-01

    an iterative method. The parameter choice method is also used to demonstrate the implementation of the standard-form transformation. We have implemented a simple preconditioner aimed at the preconditioning of the general-form Tikhonov problem and demonstrate its simplicity and effciency. The steps taken...... and used to set up the illposed problems in the toolbox. Hereby, we are able to write regularization algorithms that automatically exploit structure in the ill-posed problem without being rewritten explicitly. We explain how to implement a stopping criteria for a parameter choice method based upon...

  12. The use of Pauli-Villars regularization in string theory

    Science.gov (United States)

    Ambjørn, J.; Makeenko, Y.

    2017-11-01

    The proper-time regularization of bosonic string reproduces the results of canonical quantization in a special scaling limit where the length in target space has to be renormalized. We repeat the analysis for the Pauli-Villars regularization and demonstrate the universality of the results. In the mean-field approximation, we compute the susceptibility anomalous dimension and show it equals 1/2. We discuss the relation with the previously known results on lattice strings.

  13. Two distinct origins of long-term learning effects in verbal short-term memory

    OpenAIRE

    Majerus, Steve; Martinez Perez, Trecy; Oberauer, Klaus

    2012-01-01

    Verbal short-term memory (STM) is highly sensitive to learning effects: digit sequences or nonword sequences which have been rendered more familiar via repeated exposure are recalled more accurately. In this study we show that sublist-level, incidental learning of item co-occurrence regularities affects immediate serial recall of words and nonwords, but not digits. In contrast, list-level chunk learning affects serial recall of digits. In a first series of experiments, participants heard a co...

  14. Regularization and a general linear model for event-related potential estimation.

    Science.gov (United States)

    Kristensen, Emmanuelle; Guerin-Dugué, Anne; Rivet, Bertrand

    2017-12-01

    The usual event-related potential (ERP) estimation is the average across epochs time-locked on stimuli of interest. These stimuli are repeated several times to improve the signal-to-noise ratio (SNR) and only one evoked potential is estimated inside the temporal window of interest. Consequently, the average estimation does not take into account other neural responses within the same epoch that are due to short inter stimuli intervals. These adjacent neural responses may overlap and distort the evoked potential of interest. This overlapping process is a significant issue for the eye fixation-related potential (EFRP) technique in which the epochs are time-locked on the ocular fixations. The inter fixation intervals are not experimentally controlled and can be shorter than the neural response's latency. To begin, the Tikhonov regularization, applied to the classical average estimation, was introduced to improve the SNR for a given number of trials. The generalized cross validation was chosen to obtain the optimal value of the ridge parameter. Then, to deal with the issue of overlapping, the general linear model (GLM), was used to extract all neural responses inside an epoch. Finally, the regularization was also applied to it. The models (the classical average and the GLM with and without regularization) were compared on both simulated data and real datasets from a visual scene exploration in co-registration with an eye-tracker, and from a P300 Speller experiment. The regularization was found to improve the estimation by average for a given number of trials. The GLM was more robust and efficient, its efficiency actually reinforced by the regularization.

  15. Adaptive Regularization of Neural Classifiers

    DEFF Research Database (Denmark)

    Andersen, Lars Nonboe; Larsen, Jan; Hansen, Lars Kai

    1997-01-01

    We present a regularization scheme which iteratively adapts the regularization parameters by minimizing the validation error. It is suggested to use the adaptive regularization scheme in conjunction with optimal brain damage pruning to optimize the architecture and to avoid overfitting. Furthermore......, we propose an improved neural classification architecture eliminating an inherent redundancy in the widely used SoftMax classification network. Numerical results demonstrate the viability of the method...

  16. A Conserved DNA Repeat Promotes Selection of a Diverse Repertoire of Trypanosoma brucei Surface Antigens from the Genomic Archive.

    Directory of Open Access Journals (Sweden)

    Galadriel Hovel-Miner

    2016-05-01

    Full Text Available African trypanosomes are mammalian pathogens that must regularly change their protein coat to survive in the host bloodstream. Chronic trypanosome infections are potentiated by their ability to access a deep genomic repertoire of Variant Surface Glycoprotein (VSG genes and switch from the expression of one VSG to another. Switching VSG expression is largely based in DNA recombination events that result in chromosome translocations between an acceptor site, which houses the actively transcribed VSG, and a donor gene, drawn from an archive of more than 2,000 silent VSGs. One element implicated in these duplicative gene conversion events is a DNA repeat of approximately 70 bp that is found in long regions within each BES and short iterations proximal to VSGs within the silent archive. Early observations showing that 70-bp repeats can be recombination boundaries during VSG switching led to the prediction that VSG-proximal 70-bp repeats provide recombinatorial homology. Yet, this long held assumption had not been tested and no specific function for the conserved 70-bp repeats had been demonstrated. In the present study, the 70-bp repeats were genetically manipulated under conditions that induce gene conversion. In this manner, we demonstrated that 70-bp repeats promote access to archival VSGs. Synthetic repeat DNA sequences were then employed to identify the length, sequence, and directionality of repeat regions required for this activity. In addition, manipulation of the 70-bp repeats allowed us to observe a link between VSG switching and the cell cycle that had not been appreciated. Together these data provide definitive support for the long-standing hypothesis that 70-bp repeats provide recombinatorial homology during switching. Yet, the fact that silent archival VSGs are selected under these conditions suggests the 70-bp repeats also direct DNA pairing and recombination machinery away from the closest homologs (silent BESs and toward the rest of

  17. A Conserved DNA Repeat Promotes Selection of a Diverse Repertoire of Trypanosoma brucei Surface Antigens from the Genomic Archive.

    Science.gov (United States)

    Hovel-Miner, Galadriel; Mugnier, Monica R; Goldwater, Benjamin; Cross, George A M; Papavasiliou, F Nina

    2016-05-01

    African trypanosomes are mammalian pathogens that must regularly change their protein coat to survive in the host bloodstream. Chronic trypanosome infections are potentiated by their ability to access a deep genomic repertoire of Variant Surface Glycoprotein (VSG) genes and switch from the expression of one VSG to another. Switching VSG expression is largely based in DNA recombination events that result in chromosome translocations between an acceptor site, which houses the actively transcribed VSG, and a donor gene, drawn from an archive of more than 2,000 silent VSGs. One element implicated in these duplicative gene conversion events is a DNA repeat of approximately 70 bp that is found in long regions within each BES and short iterations proximal to VSGs within the silent archive. Early observations showing that 70-bp repeats can be recombination boundaries during VSG switching led to the prediction that VSG-proximal 70-bp repeats provide recombinatorial homology. Yet, this long held assumption had not been tested and no specific function for the conserved 70-bp repeats had been demonstrated. In the present study, the 70-bp repeats were genetically manipulated under conditions that induce gene conversion. In this manner, we demonstrated that 70-bp repeats promote access to archival VSGs. Synthetic repeat DNA sequences were then employed to identify the length, sequence, and directionality of repeat regions required for this activity. In addition, manipulation of the 70-bp repeats allowed us to observe a link between VSG switching and the cell cycle that had not been appreciated. Together these data provide definitive support for the long-standing hypothesis that 70-bp repeats provide recombinatorial homology during switching. Yet, the fact that silent archival VSGs are selected under these conditions suggests the 70-bp repeats also direct DNA pairing and recombination machinery away from the closest homologs (silent BESs) and toward the rest of the archive.

  18. Regular-, irregular-, and pseudo-character processing in Chinese: The regularity effect in normal adult readers

    Directory of Open Access Journals (Sweden)

    Dustin Kai Yan Lau

    2014-03-01

    Full Text Available Background Unlike alphabetic languages, Chinese uses a logographic script. However, the pronunciation of many character’s phonetic radical has the same pronunciation as the character as a whole. These are considered regular characters and can be read through a lexical non-semantic route (Weekes & Chen, 1999. Pseudocharacters are another way to study this non-semantic route. A pseudocharacter is the combination of existing semantic and phonetic radicals in their legal positions resulting in a non-existing character (Ho, Chan, Chung, Lee, & Tsang, 2007. Pseudocharacters can be pronounced by direct derivation from the sound of its phonetic radical. Conversely, if the pronunciation of a character does not follow that of the phonetic radical, it is considered as irregular and can only be correctly read through the lexical-semantic route. The aim of the current investigation was to examine reading aloud in normal adults. We hypothesized that the regularity effect, previously described for alphabetical scripts and acquired dyslexic patients of Chinese (Weekes & Chen, 1999; Wu, Liu, Sun, Chromik, & Zhang, 2014, would also be present in normal adult Chinese readers. Method Participants. Thirty (50% female native Hong Kong Cantonese speakers with a mean age of 19.6 years and a mean education of 12.9 years. Stimuli. Sixty regular-, 60 irregular-, and 60 pseudo-characters (with at least 75% of name agreement in Chinese were matched by initial phoneme, number of strokes and family size. Additionally, regular- and irregular-characters were matched by frequency (low and consistency. Procedure. Each participant was asked to read aloud the stimuli presented on a laptop using the DMDX software. The order of stimuli presentation was randomized. Data analysis. ANOVAs were carried out by participants and items with RTs and errors as dependent variables and type of stimuli (regular-, irregular- and pseudo-character as repeated measures (F1 or between subject

  19. Existence of connected regular and nearly regular graphs

    OpenAIRE

    Ganesan, Ghurumuruhan

    2018-01-01

    For integers $k \\geq 2$ and $n \\geq k+1$, we prove the following: If $n\\cdot k$ is even, there is a connected $k$-regular graph on $n$ vertices. If $n\\cdot k$ is odd, there is a connected nearly $k$-regular graph on $n$ vertices.

  20. Strengthening concept learning by repeated testing

    Science.gov (United States)

    Wiklund-Hörnqvist, Carola; Jonsson, Bert; Nyberg, Lars

    2014-01-01

    The aim of this study was to examine whether repeated testing with feedback benefits learning compared to rereading of introductory psychology key-concepts in an educational context. The testing effect was examined immediately after practice, after 18 days, and at a five-week delay in a sample of undergraduate students (n = 83). The results revealed that repeated testing with feedback significantly enhanced learning compared to rereading at all delays, demonstrating that repeated retrieval enhances retention compared to repeated encoding in the short- and the long-term. In addition, the effect of repeated testing was beneficial for students irrespectively of working memory capacity. It is argued that teaching methods involving repeated retrieval are important to consider by the educational system. PMID:24313425

  1. A criterion for regular sequences

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    D P PATIL1, U STORCH2 and J ST ¨UCKRAD3. 1Department of Mathematics, Indian Institute of Science, Bangalore 560 012, India ... For general notations in com- mutative algebra we also refer to [1]. ... Note that every sequence is a strongly regular as well as regular sequence on the zero module. Further, it is clear that a ...

  2. Online co-regularized algorithms

    NARCIS (Netherlands)

    Ruijter, T. de; Tsivtsivadze, E.; Heskes, T.

    2012-01-01

    We propose an online co-regularized learning algorithm for classification and regression tasks. We demonstrate that by sequentially co-regularizing prediction functions on unlabeled data points, our algorithm provides improved performance in comparison to supervised methods on several UCI benchmarks

  3. Natural selection and mechanistic regularity.

    Science.gov (United States)

    DesAutels, Lane

    2016-06-01

    In this article, I address the question of whether natural selection operates regularly enough to qualify as a mechanism of the sort characterized by Machamer, Darden, and Craver (2000). Contrary to an influential critique by Skipper and Millstein (2005), I argue that natural selection can be seen to be regular enough to qualify as an MDC mechanism just fine-as long as we pay careful attention to some important distinctions regarding mechanistic regularity and abstraction. Specifically, I suggest that when we distinguish between process vs. product regularity, mechanism-internal vs. mechanism-external sources of irregularity, and abstract vs. concrete regularity, we can see that natural selection is only irregular in senses that are unthreatening to its status as an MDC mechanism. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Shortness of Breath

    Science.gov (United States)

    ... with obesity hypoventilation syndrome also have sleep apnea. Deconditioning If you are not active or do not exer- cise regularly, as a result of being out of shape and experiencing muscle fatigue, you may develop shortness of breath with physical exertion beyond your customary activity such as when ...

  5. Prognostic significance of repeat biopsy in lupus nephritis: Histopathologic worsening and a short time between biopsies is associated with significantly increased risk for end stage renal disease and death.

    Science.gov (United States)

    Arriens, Cristina; Chen, Sixia; Karp, David R; Saxena, Ramesh; Sambandam, Kamalanathan; Chakravarty, Eliza; James, Judith A; Merrill, Joan T

    2017-12-01

    Approximately half of patients with systemic lupus erythematosus (SLE) develop lupus nephritis (LN), a major cause of morbidity and early mortality in that disease. Prolonged renal inflammation is associated with irreversible kidney damage which confers a 30% risk of end stage renal disease (ESRD), making early, aggressive treatment mandatory. Failure to achieve therapeutic response or recurrence of renal flare often prompts repeat biopsy. However, the role of repeat biopsy in determining long-term renal prognosis remains controversial. For this reason repeat biopsies are usually not utilized unless clinical evidence of refractory or recurrent disease is already present, despite known mismatches between clinical and biopsy findings. The current study quantifies the degree to which histopathologic worsening between first and second biopsies and duration between them predicts ESRD and death. Medical records of 141 LN patients with more than one biopsy were obtained from a single large urban medical center. Cases were attained using billing codes for diagnosis and procedures from 1/1999-1/2015. Biopsy worsening was defined as unfavorable histopathologic classification transitions and/or increased chronicity; if neither were present, the patient was defined as non-worsening. We used Cox proportional hazard models to study the relationship between ESRD and survival adjusting for covariates which included age at first biopsy, gender, race, initial biopsy class, and initial induction therapy. Of 630 patients screened, 141 had more than one biopsy. Advancing chronicity was detected in 48 (34.0%) and a renal class switch to worse grade of pathology was found in 54 (38.3%). At least one of these adverse second biopsy features was reported in 79 (56.0%) patients. Five years following initial biopsy, 28 (35.4%) of those with worsening histopathology on second biopsy developed ESRD, compared to 6 (9.7%) of non-worsening patients and 10 (12.7%) of patients with worsening

  6. Assembly of Repeat Content Using Next Generation Sequencing Data

    Energy Technology Data Exchange (ETDEWEB)

    labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

    2014-03-17

    Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

  7. NONCONVEX REGULARIZATION FOR SHAPE PRESERVATION

    Energy Technology Data Exchange (ETDEWEB)

    CHARTRAND, RICK [Los Alamos National Laboratory

    2007-01-16

    The authors show that using a nonconvex penalty term to regularize image reconstruction can substantially improve the preservation of object shapes. The commonly-used total-variation regularization, {integral}|{del}u|, penalizes the length of the object edges. They show that {integral}|{del}u|{sup p}, 0 < p < 1, only penalizes edges of dimension at least 2-p, and thus finite-length edges not at all. We give numerical examples showing the resulting improvement in shape preservation.

  8. Regularization with a pruning prior

    DEFF Research Database (Denmark)

    Goutte, Cyril; Hansen, Lars Kai

    1997-01-01

    We investigate the use of a regularization priorthat we show has pruning properties. Analyses areconducted both using a Bayesian framework and withthe generalization method, on a simple toyproblem. Results are thoroughly compared withthose obtained with a traditional weight decay.......We investigate the use of a regularization priorthat we show has pruning properties. Analyses areconducted both using a Bayesian framework and withthe generalization method, on a simple toyproblem. Results are thoroughly compared withthose obtained with a traditional weight decay....

  9. Commuting Π-regular rings

    Directory of Open Access Journals (Sweden)

    Shervin Sahebi

    2014-05-01

    Full Text Available ‎$R$ is called commuting regular ring (resp‎. ‎semigroupif‎ for each $x,y\\in R$ there exists $a\\in R$‎ such that$xy=yxayx$‎. ‎In this paper‎, ‎we introduce the concept of‎‎commuting $\\pi$-regular rings (resp‎. ‎semigroups and‎‎study various properties of them.

  10. Implicit Regularization in Deep Learning

    OpenAIRE

    Neyshabur, Behnam

    2017-01-01

    In an attempt to better understand generalization in deep learning, we study several possible explanations. We show that implicit regularization induced by the optimization method is playing a key role in generalization and success of deep learning models. Motivated by this view, we study how different complexity measures can ensure generalization and explain how optimization algorithms can implicitly regularize complexity measures. We empirically investigate the ability of these measures to ...

  11. Chimeric mitochondrial peptides from contiguous regular and swinger RNA

    Directory of Open Access Journals (Sweden)

    Hervé Seligmann

    2016-01-01

    Full Text Available Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A, multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200× rarer than swinger peptides (3/100,000 versus 6/1000. Among 186 peptides with >8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

  12. Regional mapping of short tandem repeats on human chromosome 10: Cytochrome P450 gene CYP2E, D10S196, D10S220, and D10S225

    Energy Technology Data Exchange (ETDEWEB)

    Koelble, K. (Univ. of Oxford (United Kingdom))

    1993-12-01

    Human CYP2E encodes an ethanol-inducible cytochrome P450 monooxygenase that metabolizes various carcinogens and may therefore play a role in cancer susceptibility. An intronic (GGAT)[sub n] [center dot] (CCTA)[sub n] repeat element was found to display limited polymorphism in Caucasoids and was used as a sequence-tagged site for genomic amplification from somatic cell hybrids to localize CYP2E to 10q24.3-qter; using the same panel, three microsatellite markers, D10S196, D10S220, and D10S225, were mapped to 10q21. The close synteny of CYP2E, CYP2C, and CYP17 belonging to two different cytochrome P450 families suggests a central role for the long arm of chromosome 10 in the evolution of this large gene superfamily. 18 refs., 2 figs.

  13. Toric Geometry of the Regular Convex Polyhedra

    Directory of Open Access Journals (Sweden)

    Fiammetta Battaglia

    2017-01-01

    Full Text Available We describe symplectic and complex toric spaces associated with the five regular convex polyhedra. The regular tetrahedron and the cube are rational and simple, the regular octahedron is not simple, the regular dodecahedron is not rational, and the regular icosahedron is neither simple nor rational. We remark that the last two cases cannot be treated via standard toric geometry.

  14. Vertex-deleted subgraphs and regular factors from regular graph☆

    Science.gov (United States)

    Lu, Hongliang; Wang, Wei; Bai, Bing

    2011-01-01

    Let k, m, and r be three integers such that 2≤k≤m≤r. Let G be a 2r-regular, 2m-edge-connected graph of odd order. We obtain some sufficient conditions for G−v to contain a k-factor for all v∈V(G). PMID:21984842

  15. A Pythagoras proof of Szemer\\'edi's regularity lemma

    OpenAIRE

    Schrijver, Alexander

    2012-01-01

    We give a short proof of Szemer\\'edi's regularity lemma, based on elementary Euclidean geometry. The general line of the proof is that of the standard proof (in fact, of Szemer\\'edi's original proof), but most technicalities are swallowed by applying Pythagoras' theorem.

  16. Regularity of laboratory supplies and delivery of histopathology ...

    African Journals Online (AJOL)

    Arun Kumar Agnihotri

    2015-06-23

    Jun 23, 2015 ... Open Access. Short Communication. Mutagubya et al. Arch Med Biomed Res. 2015;2:131-6. doi:10.4314/ambr.v2i4.3. 131. Regularity of laboratory supplies and delivery of histopathology services in the department of Pathology,. Makerere University College of Health. Sciences, Uganda, between January.

  17. Empirical laws, regularity and necessity

    NARCIS (Netherlands)

    Koningsveld, H.

    1973-01-01

    In this book I have tried to develop an analysis of the concept of an empirical law, an analysis that differs in many ways from the alternative analyse's found in contemporary literature dealing with the subject.

    1 am referring especially to two well-known views, viz. the regularity and

  18. Regularization in Matrix Relevance Learning

    NARCIS (Netherlands)

    Schneider, Petra; Bunte, Kerstin; Stiekema, Han; Hammer, Barbara; Villmann, Thomas; Biehl, Michael

    A In this paper, we present a regularization technique to extend recently proposed matrix learning schemes in learning vector quantization (LVQ). These learning algorithms extend the concept of adaptive distance measures in LVQ to the use of relevance matrices. In general, metric learning can

  19. Regularity of conservative inductive limits

    Directory of Open Access Journals (Sweden)

    Jan Kucera

    1999-01-01

    Full Text Available A sequentially complete inductive limit of Fréchet spaces is regular, see [3]. With a minor modification, this property can be extended to inductive limits of arbitrary locally convex spaces under an additional assumption of conservativeness.

  20. Regular Matroids with Graphic Cocircuits

    OpenAIRE

    Papalamprou, Konstantinos; Pitsoulis, Leonidas

    2009-01-01

    We introduce the notion of graphic cocircuits and show that a large class of regular matroids with graphic cocircuits belongs to the class of signed-graphic matroids. Moreover, we provide an algorithm which determines whether a cographic matroid with graphic cocircuits is signed-graphic or not.

  1. Interval matrices: Regularity generates singularity

    Czech Academy of Sciences Publication Activity Database

    Rohn, Jiří; Shary, S.P.

    2018-01-01

    Roč. 540, 1 March (2018), s. 149-159 ISSN 0024-3795 Institutional support: RVO:67985807 Keywords : interval matrix * regularity * singularity * P-matrix * absolute value equation * diagonally singilarizable matrix Subject RIV: BA - General Mathematics Impact factor: 0.973, year: 2016

  2. Regularized Statistical Analysis of Anatomy

    DEFF Research Database (Denmark)

    Sjöstrand, Karl

    2007-01-01

    This thesis presents the application and development of regularized methods for the statistical analysis of anatomical structures. Focus is on structure-function relationships in the human brain, such as the connection between early onset of Alzheimer’s disease and shape changes of the corpus cal...

  3. Regular languages, regular grammars and automata in splicing systems

    Science.gov (United States)

    Mohamad Jan, Nurhidaya; Fong, Wan Heng; Sarmin, Nor Haniza

    2013-04-01

    Splicing system is known as a mathematical model that initiates the connection between the study of DNA molecules and formal language theory. In splicing systems, languages called splicing languages refer to the set of double-stranded DNA molecules that may arise from an initial set of DNA molecules in the presence of restriction enzymes and ligase. In this paper, some splicing languages resulted from their respective splicing systems are shown. Since all splicing languages are regular, languages which result from the splicing systems can be further investigated using grammars and automata in the field of formal language theory. The splicing language can be written in the form of regular languages generated by grammar. Besides that, splicing systems can be accepted by automata. In this research, two restriction enzymes are used in splicing systems namely BfuCI and NcoI.

  4. Regular and conformal regular cores for static and rotating solutions

    Energy Technology Data Exchange (ETDEWEB)

    Azreg-Aïnou, Mustapha

    2014-03-07

    Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

  5. Regular Exercisers Have Stronger Pelvic Floor Muscles than Non-Regular Exercisers at Midpregnancy.

    Science.gov (United States)

    Bø, Kari; Ellstrøm Engh, Marie; Hilde, Gunvor

    2017-12-26

    Today, all healthy pregnant women are encouraged to be physically active throughout pregnancy, with recommendations to participate in at least 30 min of aerobic activity on most days of the week, in addition to perform strength training of the major muscle groups 2-3 days per week, and also pelvic floor muscle training. There is, however, an ongoing debate whether general physical activity enhances or declines pelvic floor muscle function. To compare vaginal resting pressure, pelvic floor muscle strength and endurance in regular exercisers (exercise ≥ 30 minutes ≥ 3 times per week) and non-exercisers at mid-pregnancy. Furthermore, to assess whether regular general exercise or pelvic floor muscle strength was associated with urinary incontinence. This was a cross-sectional study at mean gestational week 20.9 (± 1.4) including 218 nulliparous pregnant women, mean age 28.6 years (range 19-40) and pre-pregnancy body mass index 23.9 kg/m 2 (SD 4.0). Vaginal resting pressure, pelvic floor muscle strength and pelvic floor muscle endurance were measured by a high precision pressure transducer connected to a vaginal balloon. International Consultation on Incontinence Questionnaire Urinary Incontinence Short Form was used to assess urinary incontinence. Differences between groups were analyzed using Independent Sample T-test. Linear regression analysis was conducted to adjust for pre-pregnancy body mass index, age, smoking during pregnancy and regular pelvic floor muscle training during pregnancy. P-value was set to ≤ 0.05. Regular exercisers had statistically significant stronger ( mean 6.4 cm H 2 O (95% CI: 1.7, 11.2)) and more enduring ( mean 39.9 cm H 2 Osec (95% CI: 42.2, 75.7)) pelvic floor muscles. Only pelvic floor muscle strength remained statistically significant, when adjusting for possible confounders. Pelvic floor muscle strength and not regular general exercise was associated with urinary continence (adjusted B: -6.4 (95% CI: -11.5, -1.4)). Regular

  6. Short tandem repeat (STR) haplotypes in HLA: an integrated 50-kb STR/linkage disequilibrium/gene map between the RING3 and HLA-B genes and identification of STR haplotype diversification in the class III region.

    Science.gov (United States)

    Vorechovsky, I; Kralovicova, J; Laycock, M D; Webster, A D; Marsh, S G; Madrigal, A; Hammarström, L

    2001-08-01

    We present a dense STR/linkage disequilibrium(LD)/gene map between the RING3 and HLA-B loci, reference allelic sizes on the most prevalent HLA haplotypes and their allelic frequencies in pedigree founders. This resource will facilitate LD, evolution and gene mapping studies, including comparisons of HLA and STR haplotypes and identification of HLA recombinants. The map was constructed by testing novel and previously reported STRs using a panel of 885 individuals in 211 families and 60 DNA samples from cell lines and bone marrow donors homozygous in the HLA-A, -B and -DR loci selected from over 15 000 entries into the registry of Swedish bone marrow donors. We have also analysed the variability of STR alleles/haplotypes on the most prevalent HLA haplotypes to identify STRs useful for fine mapping of disease genes in the region previously implicated in susceptibility to many disorders. The analysis of 40 HLA-A*01, B*0801, DRB1*03011, DQB1*0201 haplotypes in homozygous donors showed a surprising stability in 23 STRs between the class II recombination hot spot and HLA-B, with the average of 1.9% (16/838) variant alleles. However, 40% variant alleles were found at the D6S2670 locus in intron 19 of the tenascin-X gene both in the families and homozygous donors. The nucleotide sequence analysis of this STR showed a complex polymorphism consisting of tetra- (CTTT)(8-18) and penta-nucleotide (CTTTT)(1-2) repeats, separated by an intervening non-polymorphic sequence of 42 bp. The HLA-A1, B*0801, DRB1*03011, DQB1*0201 haplotypes had five (CTTT)(14-18)/(CTTTT)(2) variants with a predominant (CTTT)(16) allele, implicating the tetranucleotide component as the source of this ancestral haplotype diversification, which may be due to the location of D6S2670 in the region of the highest GC content in the human MHC.

  7. Recursively-regular subdivisions and applications

    Directory of Open Access Journals (Sweden)

    Rafel Jaume

    2016-05-01

    Full Text Available We generalize regular subdivisions (polyhedral complexes resulting from the projection of the lower faces of a polyhedron introducing the class of recursively-regular subdivisions. Informally speaking, a recursively-regular subdivision is a subdivision that can be obtained by splitting some faces of a regular subdivision by other regular subdivisions (and continue recursively. We also define the finest regular coarsening and the regularity tree of a polyhedral complex. We prove that recursively-regular subdivisions are not necessarily connected by flips and that they are acyclic with respect to the in-front relation. We show that the finest regular coarsening of a subdivision can be efficiently computed, and that whether a subdivision is recursively regular can be efficiently decided. As an application, we also extend a theorem known since 1981 on illuminating space by cones and present connections of recursive regularity to tensegrity theory and graph-embedding problems.     

  8. Cognitive, emotional, and social benefits of regular musical activities in early dementia: randomized controlled study.

    Science.gov (United States)

    Särkämö, Teppo; Tervaniemi, Mari; Laitinen, Sari; Numminen, Ava; Kurki, Merja; Johnson, Julene K; Rantanen, Pekka

    2014-08-01

    During aging, musical activities can help maintain physical and mental health and cognitive abilities, but their rehabilitative use has not been systematically explored in persons with dementia (PWDs). Our aim was to determine the efficacy of a novel music intervention based on coaching the caregivers of PWDs to use either singing or music listening regularly as a part of everyday care. Eighty-nine PWD-caregiver dyads were randomized to a 10-week singing coaching group (n = 30), a 10-week music listening coaching group (n = 29), or a usual care control group (n = 30). The coaching sessions consisted primarily of singing/listening familiar songs coupled occasionally with vocal exercises and rhythmic movements (singing group) and reminiscence and discussions (music listening group). In addition, the intervention included regular musical exercises at home. All PWDs underwent an extensive neuropsychological assessment, which included cognitive tests, as well as mood and quality of life (QOL) scales, before and after the intervention period and 6 months later. In addition, the psychological well-being of family members was repeatedly assessed with questionnaires. Compared with usual care, both singing and music listening improved mood, orientation, and remote episodic memory and to a lesser extent, also attention and executive function and general cognition. Singing also enhanced short-term and working memory and caregiver well-being, whereas music listening had a positive effect on QOL. Regular musical leisure activities can have long-term cognitive, emotional, and social benefits in mild/moderate dementia and could therefore be utilized in dementia care and rehabilitation. © The Author 2013. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. From inactive to regular jogger

    DEFF Research Database (Denmark)

    Lund-Cramer, Pernille; Brinkmann Løite, Vibeke; Bredahl, Thomas Viskum Gjelstrup

    to translate intention into regular behavior. TTM: Informants expressed rapid progression from the pre-contemplation to the action stage caused by an early shift in the decisional balance towards advantages overweighing disadvantages. This was followed by a continuous improvement in self-efficacy, which...... jogging-related self-efficacy, and deployment of realistic goal setting was significant in the achievement of regular jogging behavior. Cognitive factors included a positive change in both affective and instrumental beliefs about jogging. Expectations from society and social relations had limited effect...... health, and well-being. An experience-driven change in affective beliefs contributed to the shift in the intention. Informants’ initial expectations to own jogging abilities were realistic and modest, which in combination with a GPS-training watch applied sufficient perceived behavioral control...

  10. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-07

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  11. Physical model of dimensional regularization

    Energy Technology Data Exchange (ETDEWEB)

    Schonfeld, Jonathan F.

    2016-12-15

    We explicitly construct fractals of dimension 4-ε on which dimensional regularization approximates scalar-field-only quantum-field theory amplitudes. The construction does not require fractals to be Lorentz-invariant in any sense, and we argue that there probably is no Lorentz-invariant fractal of dimension greater than 2. We derive dimensional regularization's power-law screening first for fractals obtained by removing voids from 3-dimensional Euclidean space. The derivation applies techniques from elementary dielectric theory. Surprisingly, fractal geometry by itself does not guarantee the appropriate power-law behavior; boundary conditions at fractal voids also play an important role. We then extend the derivation to 4-dimensional Minkowski space. We comment on generalization to non-scalar fields, and speculate about implications for quantum gravity. (orig.)

  12. How to quantify student's regularity?

    OpenAIRE

    Shirvani Boroujeni, Mina; Sharma, Kshitij; Kidzinski, Lukasz; Lucignano, Lorenzo; Dillenbourg, Pierre

    2016-01-01

    Studies carried out in classroom-based learning context, have consistently shown a positive relation between students' conscientiousness and their academic success. We hypothesize that time management and regularity are main constructing blocks of students' conscientiousness in the context of online education. In online education, despite intuitive arguments supporting on-demand courses as more flexible delivery of knowledge, completion rate is higher in the courses with rigid temporal constr...

  13. CRISPR/Cas9-Induced (CTG⋅CAG)nRepeat Instability in the Myotonic Dystrophy Type 1 Locus: Implications for Therapeutic Genome Editing.

    Science.gov (United States)

    van Agtmaal, Ellen L; André, Laurène M; Willemse, Marieke; Cumming, Sarah A; van Kessel, Ingeborg D G; van den Broek, Walther J A A; Gourdon, Geneviève; Furling, Denis; Mouly, Vincent; Monckton, Darren G; Wansink, Derick G; Wieringa, Bé

    2017-01-04

    Myotonic dystrophy type 1 (DM1) is caused by (CTG⋅CAG) n -repeat expansion within the DMPK gene and thought to be mediated by a toxic RNA gain of function. Current attempts to develop therapy for this disease mainly aim at destroying or blocking abnormal properties of mutant DMPK (CUG)n RNA. Here, we explored a DNA-directed strategy and demonstrate that single clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-cleavage in either its 5' or 3' unique flank promotes uncontrollable deletion of large segments from the expanded trinucleotide repeat, rather than formation of short indels usually seen after double-strand break repair. Complete and precise excision of the repeat tract from normal and large expanded DMPK alleles in myoblasts from unaffected individuals, DM1 patients, and a DM1 mouse model could be achieved at high frequency by dual CRISPR/Cas9-cleavage at either side of the (CTG⋅CAG)n sequence. Importantly, removal of the repeat appeared to have no detrimental effects on the expression of genes in the DM1 locus. Moreover, myogenic capacity, nucleocytoplasmic distribution, and abnormal RNP-binding behavior of transcripts from the edited DMPK gene were normalized. Dual sgRNA-guided excision of the (CTG⋅CAG)n tract by CRISPR/Cas9 technology is applicable for developing isogenic cell lines for research and may provide new therapeutic opportunities for patients with DM1. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Germ-line CAG repeat instability causes extreme CAG repeat expansion with infantile-onset spinocerebellar ataxia type 2.

    Science.gov (United States)

    Vinther-Jensen, Tua; Ek, Jakob; Duno, Morten; Skovby, Flemming; Hjermind, Lena E; Nielsen, Jørgen E; Nielsen, Troels Tolstrup

    2013-06-01

    The spinocerebellar ataxias (SCA) are a genetically and clinically heterogeneous group of diseases, characterized by dominant inheritance, progressive cerebellar ataxia and diverse extracerebellar symptoms. A subgroup of the ataxias is caused by unstable CAG-repeat expansions in their respective genes leading to pathogenic expansions of polyglutamine stretches in the encoded proteins. In general, unstable CAG repeats have an uninterrupted CAG repeat, whereas stable CAG repeats are either short or interrupted by CAA codons, which - like CAG codons - code for glutamine. Here we report on an infantile SCA2 patient who, due to germ-line CAG repeat instability in her father, inherited an extremely expanded CAG repeat in the SCA2 locus. Surprisingly, the expanded allele of the father was an interrupted CAG repeat sequence. Furthermore, analyses of single spermatozoa showed a high frequency of paternal germ-line repeat sequence instability of the expanded SCA2 locus.

  15. Honesty through repeated interactions.

    Science.gov (United States)

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Tree games with regular objectives

    Directory of Open Access Journals (Sweden)

    Marcin Przybyłko

    2014-08-01

    Full Text Available We study tree games developed recently by Matteo Mio as a game interpretation of the probabilistic μ-calculus. With expressive power comes complexity. Mio showed that tree games are able to encode Blackwell games and, consequently, are not determined under deterministic strategies. We show that non-stochastic tree games with objectives recognisable by so-called game automata are determined under deterministic, finite memory strategies. Moreover, we give an elementary algorithmic procedure which, for an arbitrary regular language L and a finite non-stochastic tree game with a winning objective L decides if the game is determined under deterministic strategies.

  17. Academic Training Lecture - Regular Programme

    CERN Multimedia

    PH Department

    2011-01-01

    Regular Lecture Programme 9 May 2011 ACT Lectures on Detectors - Inner Tracking Detectors by Pippa Wells (CERN) 10 May 2011 ACT Lectures on Detectors - Calorimeters (2/5) by Philippe Bloch (CERN) 11 May 2011 ACT Lectures on Detectors - Muon systems (3/5) by Kerstin Hoepfner (RWTH Aachen) 12 May 2011 ACT Lectures on Detectors - Particle Identification and Forward Detectors by Peter Krizan (University of Ljubljana and J. Stefan Institute, Ljubljana, Slovenia) 13 May 2011 ACT Lectures on Detectors - Trigger and Data Acquisition (5/5) by Dr. Brian Petersen (CERN) from 11:00 to 12:00 at CERN ( Bldg. 222-R-001 - Filtration Plant )

  18. Regular nanofabrics in emerging technologies

    CERN Document Server

    Jamaa, M Haykel Ben

    2011-01-01

    ""Regular Nanofabrics in Emerging Technologies"" gives a deep insight into both fabrication and design aspects of emerging semiconductor technologies, that represent potential candidates for the post-CMOS era. Its approach is unique, across different fields, and it offers a synergetic view for a public of different communities ranging from technologists, to circuit designers, and computer scientists. The book presents two technologies as potential candidates for future semiconductor devices and systems and it shows how fabrication issues can be addressed at the design level and vice versa. The

  19. Regularization methods in Banach spaces

    CERN Document Server

    Schuster, Thomas; Hofmann, Bernd; Kazimierski, Kamil S

    2012-01-01

    Regularization methods aimed at finding stable approximate solutions are a necessary tool to tackle inverse and ill-posed problems. Usually the mathematical model of an inverse problem consists of an operator equation of the first kind and often the associated forward operator acts between Hilbert spaces. However, for numerous problems the reasons for using a Hilbert space setting seem to be based rather on conventions than on an approprimate and realistic model choice, so often a Banach space setting would be closer to reality. Furthermore, sparsity constraints using general Lp-norms or the B

  20. Regular capacities on metrizable spaces

    Directory of Open Access Journals (Sweden)

    T. M. Cherkovskyi

    2014-07-01

    Full Text Available It is proved that for a (not necessarily compact metric space: the metrics on the space of capacities in the sense of Zarichnyi and Prokhorov are equal; completeness of the space of capacities is equivalent to completeness of the original space. It is shown that for the capacities on metrizable spaces the properties of $\\omega$-smoothness and of $\\tau$-smoothness are equivalent precisely on the separable spaces, and the properties of $\\omega$-smoothness and of regularity w.r.t. some (then w.r.t. any admissible metric are equivalent precisely on the compact spaces.

  1. The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiying; Zheng, Han; Preamplume, Gan; Shao, Yaming; Li, Hong [FSU

    2012-03-15

    The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of a noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.

  2. Repeated Infections in Children

    Science.gov (United States)

    ... he/she have ear tubes?What are the dangers of my child’s repeated infections?Should my child ... affect you or your baby through your breast milk.December 2017December 2017familydoctor.org editorial staffHip Problems in ...

  3. Modeling polycrystals with regular polyhedra

    Directory of Open Access Journals (Sweden)

    Paulo Rangel Rios

    2006-06-01

    Full Text Available Polycrystalline structure is of paramount importance to materials science and engineering. It provides an important example of a space-filling irregular network structure that also occurs in foams as well as in certain biological tissues. Therefore, seeking an accurate description of the characteristics of polycrystals is of fundamental importance. Recently, one of the authors (MEG published a paper in which a method was devised of representation of irregular networks by regular polyhedra with curved faces. In Glicksman's method a whole class of irregular polyhedra with a given number of faces, N, is represented by a single symmetrical polyhedron with N curved faces. This paper briefly describes the topological and metric properties of these special polyhedra. They are then applied to two important problems of irregular networks: the dimensionless energy 'cost' of irregular networks, and the derivation of a 3D analogue of the von Neumann-Mullins equation for the growth rate of grains in a polycrystal.

  4. Regularity of Dual Gabor Windows

    Directory of Open Access Journals (Sweden)

    Ole Christensen

    2013-01-01

    Full Text Available We present a construction of dual windows associated with Gabor frames with compactly supported windows. The size of the support of the dual windows is comparable to that of the given window. Under certain conditions, we prove that there exist dual windows with higher regularity than the canonical dual window. On the other hand, there are cases where no differentiable dual window exists, even in the overcomplete case. As a special case of our results, we show that there exists a common smooth dual window for an interesting class of Gabor frames. In particular, for any value of K∈ℕ, there is a smooth function h which simultaneously is a dual window for all B-spline generated Gabor frames {EmbTnBN(x/2}m,n∈ℕ for B-splines BN of order N=1,…,2K+1 with a fixed and sufficiently small value of b.

  5. Bayesian regularization of neural networks.

    Science.gov (United States)

    Burden, Frank; Winkler, Dave

    2008-01-01

    Bayesian regularized artificial neural networks (BRANNs) are more robust than standard back-propagation nets and can reduce or eliminate the need for lengthy cross-validation. Bayesian regularization is a mathematical process that converts a nonlinear regression into a "well-posed" statistical problem in the manner of a ridge regression. The advantage of BRANNs is that the models are robust and the validation process, which scales as O(N2) in normal regression methods, such as back propagation, is unnecessary. These networks provide solutions to a number of problems that arise in QSAR modeling, such as choice of model, robustness of model, choice of validation set, size of validation effort, and optimization of network architecture. They are difficult to overtrain, since evidence procedures provide an objective Bayesian criterion for stopping training. They are also difficult to overfit, because the BRANN calculates and trains on a number of effective network parameters or weights, effectively turning off those that are not relevant. This effective number is usually considerably smaller than the number of weights in a standard fully connected back-propagation neural net. Automatic relevance determination (ARD) of the input variables can be used with BRANNs, and this allows the network to "estimate" the importance of each input. The ARD method ensures that irrelevant or highly correlated indices used in the modeling are neglected as well as showing which are the most important variables for modeling the activity data. This chapter outlines the equations that define the BRANN method plus a flowchart for producing a BRANN-QSAR model. Some results of the use of BRANNs on a number of data sets are illustrated and compared with other linear and nonlinear models.

  6. Generalization performance of regularized neural network models

    DEFF Research Database (Denmark)

    Larsen, Jan; Hansen, Lars Kai

    1994-01-01

    Architecture optimization is a fundamental problem of neural network modeling. The optimal architecture is defined as the one which minimizes the generalization error. This paper addresses estimation of the generalization performance of regularized, complete neural network models. Regularization...

  7. EXPRESSÃO REGULAR NUMÉRICA

    Directory of Open Access Journals (Sweden)

    Bruno Vier Hoffmeister

    2014-06-01

    Full Text Available This article defines the formal definition of the computer program language Numeric Regular Expression. A language concept inspired by Regular Expression syntax, applying your power and flexibility to numeric chains are describe.

  8. Comment on "Construction of regular black holes in general relativity"

    Science.gov (United States)

    Bronnikov, Kirill A.

    2017-12-01

    We claim that the paper by Zhong-Ying Fan and Xiaobao Wang on nonlinear electrodynamics coupled to general relativity [Phys. Rev. D 94,124027 (2016)], although correct in general, in some respects repeats previously obtained results without giving proper references. There is also an important point missing in this paper, which is necessary for understanding the physics of the system: in solutions with an electric charge, a regular center requires a non-Maxwell behavior of Lagrangian function L (f ) , (f =Fμ νFμ ν) at small f . Therefore, in all electric regular black hole solutions with a Reissner-Nordström asymptotic, the Lagrangian L (f ) is different in different parts of space, and the electromagnetic field behaves in a singular way at surfaces where L (f ) suffers branching.

  9. Allowing repeat winners

    OpenAIRE

    Marco D. Huesch; Richard Brady

    2010-01-01

    Unbiased lotteries seem the least unfair and simplest procedures to allocate scarce indivisible resources to those with equal claims. But, when lotteries are repeated, it is not immediately obvious whether prior winners should be included or excluded. As in design questions surrounding single-shot lotteries, considerations of self-interest and distributive social preferences may interact. We investigate preferences for allowing participation of earlier winners in sequential lotteries. We foun...

  10. Y-Chromosome short tandem repeat, typing technology, locus ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-07-08

    Jul 8, 2015 ... Chromosome Y microsatellites seem to be ideal markers to delineate differences between human populations. They are transmitted in uniparental and they are very sensitive for genetic drift. This review will highlight the importance of the Y- Chromosome as a tool for tracing human evolution and describes.

  11. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    Matching probability was below 0.2 hence power of discrimination was high, indicating that the alleles from the five subpopulations can be used in human identifications. The present study is the first reported attempt at determining allele frequencies of subpopulations in Botswana and could possibly be used in developing a ...

  12. Short tandem repeat (STR) polymorphisms in Turkish population

    Indian Academy of Sciences (India)

    Administrator

    AmpFlSTR Profiler Plus PCR products were analyzed on ABI PrismTM 377 DNA sequencer. The. GeneScan-500 (ROX) internal lane size standard was used. Statistical analysis. The exact test was used to verify whether the genotypic dis- tribution at each locus was in conformity with Hardy-. Weinberg equilibrium (Guo et al.

  13. Split Dimensional Regularization for the Temporal Gauge

    OpenAIRE

    Chen, Yaw-Hwang; Hsieh, Ron-Jou; Lin, Chilong

    1996-01-01

    A split dimensional regularization, which was introduced for the Coulomb gauge by Leibbrandt and Williams, is used to regularize the spurious singularities of Yang-Mills theory in the temporal gauge. Typical one-loop split dimensionally regularized temporal gauge integrals, and hence the renormalization structure of the theory are shown to be the same as those calculated with some nonprincipal-value prescriptions.

  14. Supervised scale-regularized linear convolutionary filters

    DEFF Research Database (Denmark)

    Loog, Marco; Lauze, Francois Bernard

    2017-01-01

    benefit from some form of regularization and, secondly, arguing that the problem of scale has not been taken care of in a very satis- factory manner, we come to a combined resolution of both of these shortcomings by proposing a technique that we coin scale regularization. This regularization problem can...

  15. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  16. Interactive facades analysis and synthesis of semi-regular facades

    KAUST Repository

    AlHalawani, Sawsan

    2013-05-01

    Urban facades regularly contain interesting variations due to allowed deformations of repeated elements (e.g., windows in different open or close positions) posing challenges to state-of-the-art facade analysis algorithms. We propose a semi-automatic framework to recover both repetition patterns of the elements and their individual deformation parameters to produce a factored facade representation. Such a representation enables a range of applications including interactive facade images, improved multi-view stereo reconstruction, facade-level change detection, and novel image editing possibilities. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and Blackwell Publishing Ltd.

  17. Slimming and regularization of cozero maps

    Directory of Open Access Journals (Sweden)

    Mohamad Mehdi Ebrahimi

    2017-01-01

    Full Text Available Cozero maps are generalized forms of cozero elements. Two particular cases of cozero maps, slim and regular cozero maps, are significant. In this paper we present methods to construct slim and regular cozero maps from a given cozero map. The construction of the slim and the regular cozero map from a cozero map are called slimming and regularization of the cozero map, respectively. Also, we prove that the slimming and regularization create reflector functors, and so we may say that they are the best method of constructing slim and regular cozero maps, in the sense of category theory. Finally, we give slim regularization for a cozero map c:M→L in the general case where A is not a Q-algebra. We use the ring and module of fractions, in this construction process.

  18. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  19. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-12-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five Glenn Research Center (GRC) provided coupons with 25 layers was shown to be +/- 8.4% whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0%. A second group of 10 coupons has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  20. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-08-01

    The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques for duct leakage using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards. The three duct leak measurement methods assessed in this report are the two duct pressurization methods that are commonly used by many practitioners and the DeltaQ technique. These are methods B, C and A, respectively of the ASTM E1554 standard. Although it would be useful to evaluate other duct leak test methods, this study focused on those test methods that are commonly used and are required in various test standards, such as BPI (2010), RESNET (2014), ASHRAE 62.2 (2013), California Title 24 (CEC 2012), DOE Weatherization and many other energy efficiency programs.

  1. Regularity extraction from non-adjacent sounds.

    Science.gov (United States)

    Bendixen, Alexandra; Schröger, Erich; Ritter, Walter; Winkler, István

    2012-01-01

    The regular behavior of sound sources helps us to make sense of the auditory environment. Regular patterns may, for instance, convey information on the identity of a sound source (such as the acoustic signature of a train moving on the rails). Yet typically, this signature overlaps in time with signals emitted from other sound sources. It is generally assumed that auditory regularity extraction cannot operate upon this mixture of signals because it only finds regularities between adjacent sounds. In this view, the auditory environment would be grouped into separate entities by means of readily available acoustic cues such as separation in frequency and location. Regularity extraction processes would then operate upon the resulting groups. Our new experimental evidence challenges this view. We presented two interleaved sound sequences which overlapped in frequency range and shared all acoustic parameters. The sequences only differed in their underlying regular patterns. We inserted deviants into one of the sequences to probe whether the regularity was extracted. In the first experiment, we found that these deviants elicited the mismatch negativity (MMN) component. Thus the auditory system was able to find the regularity between the non-adjacent sounds. Regularity extraction was not influenced by sequence cohesiveness as manipulated by the relative duration of tones and silent inter-tone-intervals. In the second experiment, we showed that a regularity connecting non-adjacent sounds was discovered only when the intervening sequence also contained a regular pattern, but not when the intervening sounds were randomly varying. This suggests that separate regular patterns are available to the auditory system as a cue for identifying signals coming from distinct sound sources. Thus auditory regularity extraction is not necessarily confined to a processing stage after initial sound grouping, but may precede grouping when other acoustic cues are unavailable.

  2. Slimming and regularization of cozero maps

    Directory of Open Access Journals (Sweden)

    Mohamad Mehdi Ebrahimi

    2017-01-01

    Full Text Available Cozero maps are generalized forms of cozero elements. Two particular cases of cozero maps, slim and regular cozero maps, are significant. In this paper we present methods to construct slim and regular cozero maps from a given  cozero map. The construction of the slim and the regular cozero map from a cozero map are called slimming and regularization of the cozero map, respectively. Also, we prove that the slimming and regularization create reflector functors, and so we may say that they are the best method of constructing slim and regular cozero maps, in the sense of category theory. Finally, we give slim regularizationfor a cozero map $c:Mrightarrow L$ in the general case where $A$is not a ${Bbb Q}$-algebra. We use the ring and module offractions, in this construction process.

  3. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  4. Short tunnels.

    NARCIS (Netherlands)

    Schreuder, D.A.

    1965-01-01

    Before dealing with the question of lighting short tunnels, it is necessary define what is meant by a tunnel and when it should be called 'short'. Confined to motorized road traffic the following is the most apt definition of a tunnel: every form of roofing-over a road section, irrespective of it

  5. The regularization of Old English weak verbs

    OpenAIRE

    Marta Tío Sáenz

    2015-01-01

    [EN] This article deals with the regularization of non-standard spellings of the verbal forms extracted from a corpus. It addresses the question of what the limits of regularization are when lemmatizing Old English weak verbs. The purpose of such regularization, also known as normalization, is to carry out lexicological analysis or lexicographical work. The analysis concentrates on weak verbs from the second class and draws on the lexical database of Old English Nerthus, which has incorporate...

  6. Repeated judgment sampling: Boundaries

    Directory of Open Access Journals (Sweden)

    Johannes Muller-Trede

    2011-06-01

    Full Text Available This paper investigates the boundaries of the recent result that eliciting more than one estimate from the same person and averaging these can lead to accuracy gains in judgment tasks. It first examines its generality, analysing whether the kind of question being asked has an effect on the size of potential gains. Experimental results show that the question type matters. Previous results reporting potential accuracy gains are reproduced for year-estimation questions, and extended to questions about percentage shares. On the other hand, no gains are found for general numerical questions. The second part of the paper tests repeated judgment sampling's practical applicability by asking judges to provide a third and final answer on the basis of their first two estimates. In an experiment, the majority of judges do not consistently average their first two answers. As a result, they do not realise the potential accuracy gains from averaging.

  7. Allowing repeat winners

    Directory of Open Access Journals (Sweden)

    Marco D. Huesch

    2010-08-01

    Full Text Available Unbiased lotteries seem the least unfair and simplest procedures to allocate scarce indivisible resources to those with equal claims. But, when lotteries are repeated, it is not immediately obvious whether prior winners should be included or excluded. As in design questions surrounding single-shot lotteries, considerations of self-interest and distributive social preferences may interact. We investigate preferences for allowing participation of earlier winners in sequential lotteries. We found a strong preference for exclusion, both in settings where subjects were involved, and those where they were not. Subjects who answered questions about both settings did not differ in their tendency to prefer exclusion. Stated rationales significantly predicted choice but did not predict switching of choices between the two settings.

  8. Iterative regularization with minimum-residual methods

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Hansen, Per Christian

    2006-01-01

    subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES - their success......We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... as regularization methods is highly problem dependent....

  9. Iterative Regularization with Minimum-Residual Methods

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Hansen, Per Christian

    2007-01-01

    subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES their success......We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... as regularization methods is highly problem dependent....

  10. Bit-coded regular expression parsing

    DEFF Research Database (Denmark)

    Nielsen, Lasse; Henglein, Fritz

    2011-01-01

    Regular expression parsing is the problem of producing a parse tree of a string for a given regular expression. We show that a compact bit representation of a parse tree can be produced efficiently, in time linear in the product of input string size and regular expression size, by simplifying...... the DFA-based parsing algorithm due to Dub ´e and Feeley to emit the bits of the bit representation without explicitly materializing the parse tree itself. We furthermore show that Frisch and Cardelli’s greedy regular expression parsing algorithm can be straightforwardly modified to produce bit codings...

  11. Adaptive regularization using the entire solution surface.

    Science.gov (United States)

    Wu, S; Shen, X; Geyer, C J

    2009-09-01

    Several sparseness penalties have been suggested for delivery of good predictive performance in automatic variable selection within the framework of regularization. All assume that the true model is sparse. We propose a penalty, a convex combination of the L1- and L∞-norms, that adapts to a variety of situations including sparseness and nonsparseness, grouping and nongrouping. The proposed penalty performs grouping and adaptive regularization. In addition, we introduce a novel homotopy algorithm utilizing subgradients for developing regularization solution surfaces involving multiple regularizers. This permits efficient computation and adaptive tuning. Numerical experiments are conducted using simulation. In simulated and real examples, the proposed penalty compares well against popular alternatives.

  12. More than words: fast acquisition and generalization of orthographic regularities during novel word learning in adults.

    Science.gov (United States)

    Laine, Matti; Polonyi, Tünde; Abari, Kálmán

    2014-08-01

    In literates, reading is a fundamental channel for acquiring new vocabulary both in the mother tongue and in foreign languages. By using an artificial language learning task, we examined the acquisition of novel written words and their embedded regularities (an orthographic surface feature and a syllabic feature) in three groups of university students with different exposures (Group 1 saw 2 words once, Group 2 saw 20 words once, Group 3 saw 20 words three times). Recognition memory results for Groups 2 and 3 indicated that adults can learn novel written words even with just a single exposure, albeit repeated exposure improved target detection. A generalization task revealed that even the minimal exposure in Group 1 was enough for acquisition of the two embedded regularities. More exemplars and repeated exposure provided more robust effects for the syllable regularity. Finally, post-test interview showed that repeated exposure was needed to become aware of the regularities. The present results show that adults learn novel written words and their inherent regularities in a fast and effective fashion.

  13. Short Communication

    African Journals Online (AJOL)

    Mike MacNeil

    All genotypes were collected on a LiCor 4200 DNA. Analysis System (Lincoln, NE, USA). Genotypes were independently scored by two individuals. PCR was repeated for discrepancies that could not be resolved. Anomalous genotypes were detected using GenoProb. (Thallman et al., 2001a,b). Genetic linkage maps were ...

  14. A regularized stationary mean-field game

    KAUST Repository

    Yang, Xianjin

    2016-04-19

    In the thesis, we discuss the existence and numerical approximations of solutions of a regularized mean-field game with a low-order regularization. In the first part, we prove a priori estimates and use the continuation method to obtain the existence of a solution with a positive density. Finally, we introduce the monotone flow method and solve the system numerically.

  15. Regular Event Structures and Finite Petri Nets

    DEFF Research Database (Denmark)

    Nielsen, M.; Thiagarajan, P.S.

    2002-01-01

    We present the notion of regular event structures and conjecture that they correspond exactly to finite 1-safe Petri nets. We show that the conjecture holds for the conflict-free case. Even in this restricted setting, the proof is non-trivial and involves a natural subclass of regular event...

  16. On infinite regular and chiral maps

    OpenAIRE

    Arredondo, John A.; Valdez, Camilo Ramírez y Ferrán

    2015-01-01

    We prove that infinite regular and chiral maps take place on surfaces with at most one end. Moreover, we prove that an infinite regular or chiral map on an orientable surface with genus can only be realized on the Loch Ness monster, that is, the topological surface of infinite genus with one end.

  17. Impact of eight weeks of repeated ischaemic preconditioning on brachial artery and cutaneous microcirculatory function in healthy males.

    Science.gov (United States)

    Jones, Helen; Nyakayiru, Jean; Bailey, Tom G; Green, Daniel J; Cable, N Timothy; Sprung, Victoria S; Hopkins, Nicola D; Thijssen, Dick H J

    2015-08-01

    Ischaemic preconditioning has well-established cardiac and vascular protective effects. Short interventions (one week) of daily ischaemic preconditioning episodes improve conduit and microcirculatory function. This study examined whether a longer (eight weeks) and less frequent (three per week) protocol of repeated ischaemic preconditioning improves vascular function. Eighteen males were randomly allocated to either ischaemic preconditioning (22.4 ± 2.3 years, 23.7 ± 3.1 kg/m(2)) or a control intervention (26.0 ± 4.8 years, 26.4 ± 1.9 kg/m(2)). Brachial artery endothelial-dependent (FMD), forearm cutaneous microvascular function and cardiorespiratory fitness were assessed at zero, two and eight weeks. A greater improvement in FMD was evident following ischaemic preconditioning training compared with control at weeks 2 (2.24% (0.40, 4.08); p=0.02) and 8 (1.11% (0.13, 2.10); p=0.03). Repeated ischaemic preconditioning did not change cutaneous microcirculatory function or fitness. These data indicate that a feasible and practical protocol of regular ischaemic preconditioning episodes improves endothelial function in healthy individuals within two weeks, and these effects persist following repeated ischaemic preconditioning for eight weeks. © The European Society of Cardiology 2014.

  18. Visual mismatch negativity reveals automatic detection of sequential regularity violation.

    Science.gov (United States)

    Stefanics, Gábor; Kimura, Motohiro; Czigler, István

    2011-01-01

    Sequential regularities are abstract rules based on repeating sequences of environmental events, which are useful to make predictions about future events. Here, we tested whether the visual system is capable to detect sequential regularity in unattended stimulus sequences. The visual mismatch negativity (vMMN) component of the event-related potentials is sensitive to the violation of complex regularities (e.g., object-related characteristics, temporal patterns). We used the vMMN component as an index of violation of conditional (if, then) regularities. In the first experiment, to investigate emergence of vMMN and other change-related activity to the violation of conditional rules, red and green disk patterns were delivered in pairs. The majority of pairs comprised of disk patterns with identical colors, whereas in deviant pairs the colors were different. The probabilities of the two colors were equal. The second member of the deviant pairs elicited a vMMN with longer latency and more extended spatial distribution to deviants with lower probability (10 vs. 30%). In the second (control) experiment the emergence of vMMN to violation of a simple, feature-related rule was studied using oddball sequences of stimulus pairs where deviant colors were presented with 20% probabilities. Deviant colored patterns elicited a vMMN, and this component was larger for the second member of the pair, i.e., after a shorter inter-stimulus interval. This result corresponds to the SOA/(v)MMN relationship, expected on the basis of a memory-mismatch process. Our results show that the system underlying vMMN is sensitive to abstract, conditional rules. Representation of such rules implicates expectation of a subsequent event, therefore vMMN can be considered as a correlate of violated predictions about the characteristics of environmental events.

  19. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  20. Regular Simple Queues of Protein Contact Maps.

    Science.gov (United States)

    Guo, Qiang-Hui; Sun, Lisa Hui; Wang, Jian

    2017-01-01

    A protein fold can be viewed as a self-avoiding walk in certain lattice model, and its contact map is a graph that represents the patterns of contacts in the fold. Goldman, Istrail, and Papadimitriou showed that a contact map in the 2D square lattice can be decomposed into at most two stacks and one queue. In the terminology of combinatorics, stacks and queues are noncrossing and nonnesting partitions, respectively. In this paper, we are concerned with 2-regular and 3-regular simple queues, for which the degree of each vertex is at most one and the arc lengths are at least 2 and 3, respectively. We show that 2-regular simple queues are in one-to-one correspondence with hill-free Motzkin paths, which have been enumerated by Barcucci, Pergola, Pinzani, and Rinaldi by using the Enumerating Combinatorial Objects method. We derive a recurrence relation for the generating function of Motzkin paths with [Formula: see text] peaks at level i, which reduces to the generating function for hill-free Motzkin paths. Moreover, we show that 3-regular simple queues are in one-to-one correspondence with Motzkin paths avoiding certain patterns. Then we obtain a formula for the generating function of 3-regular simple queues. Asymptotic formulas for 2-regular and 3-regular simple queues are derived based on the generating functions.

  1. Multiple graph regularized protein domain ranking

    Directory of Open Access Journals (Sweden)

    Wang Jim

    2012-11-01

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

  2. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-11-19

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

  3. To Repeat or Not to Repeat a Course

    Science.gov (United States)

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  4. Completeness and regularity of generalized fuzzy graphs.

    Science.gov (United States)

    Samanta, Sovan; Sarkar, Biswajit; Shin, Dongmin; Pal, Madhumangal

    2016-01-01

    Fuzzy graphs are the backbone of many real systems like networks, image, scheduling, etc. But, due to some restriction on edges, fuzzy graphs are limited to represent for some systems. Generalized fuzzy graphs are appropriate to avoid such restrictions. In this study generalized fuzzy graphs are introduced. In this study, matrix representation of generalized fuzzy graphs is described. Completeness and regularity are two important parameters of graph theory. Here, regular and complete generalized fuzzy graphs are introduced. Some properties of them are discussed. After that, effective regular graphs are exemplified.

  5. J-regular rings with injectivities

    OpenAIRE

    Shen, Liang

    2010-01-01

    A ring $R$ is called a J-regular ring if R/J(R) is von Neumann regular, where J(R) is the Jacobson radical of R. It is proved that if R is J-regular, then (i) R is right n-injective if and only if every homomorphism from an $n$-generated small right ideal of $R$ to $R_{R}$ can be extended to one from $R_{R}$ to $R_{R}$; (ii) R is right FP-injective if and only if R is right (J, R)-FP-injective. Some known results are improved.

  6. Lattice-Valued Convergence Spaces: Weaker Regularity and p-Regularity

    Directory of Open Access Journals (Sweden)

    Lingqiang Li

    2014-01-01

    Full Text Available By using some lattice-valued Kowalsky’s dual diagonal conditions, some weaker regularities for Jäger’s generalized stratified L-convergence spaces and those for Boustique et al’s stratified L-convergence spaces are defined and studied. Here, the lattice L is a complete Heyting algebra. Some characterizations and properties of weaker regularities are presented. For Jäger’s generalized stratified L-convergence spaces, a notion of closures of stratified L-filters is introduced and then a new p-regularity is defined. At last, the relationships between p-regularities and weaker regularities are established.

  7. Occupational concerns associated with regular use of microscope.

    Science.gov (United States)

    Jain, Garima; Shetty, Pushparaja

    2014-08-01

    Microscope work can be strenuous both to the visual system and the musculoskeletal system. Lack of awareness or indifference towards health issues may result in microscope users becoming victim to many occupational hazards. Our objective was to understand the occupational problems associated with regular use of microscope, awareness regarding the hazards, attitude and practice of microscope users towards the problems and preventive strategies. a questionnaire based survey done on 50 professionals and technicians who used microscope regularly in pathology, microbiology, hematology and cytology laboratories. Sixty two percent of subjects declared that they were suffering from musculoskeletal problems, most common locations being neck and back. Maximum prevalence of musculoskeletal problems was noted in those using microscope for 11-15 years and for more than 30 h/week. Sixty two percent of subjects were aware of workplace ergonomics. Fifty six percent of microscope users took regular short breaks for stretching exercises and 58% took visual breaks every 15-30 min in between microscope use sessions. As many as 94% subjects reported some form of visual problem. Fourty four percent of microscope users felt stressed with long working hours on microscope. The most common occupational concerns of microscope users were musculoskeletal problems of neck and back regions, eye fatigue, aggravation of ametropia, headache, stress due to long working hours and anxiety during or after microscope use. There is an immediate need for increasing awareness about the various occupational hazards and their irreversible effects to prevent them.

  8. Regularity of optimal transport maps and applications

    CERN Document Server

    Philippis, Guido

    2013-01-01

    In this thesis, we study the regularity of optimal transport maps and its applications to the semi-geostrophic system. The first two chapters survey the known theory, in particular there is a self-contained proof of Brenier’ theorem on existence of optimal transport maps and of Caffarelli’s Theorem on Holder continuity of optimal maps. In the third and fourth chapter we start investigating Sobolev regularity of optimal transport maps, while in Chapter 5 we show how the above mentioned results allows to prove the existence of Eulerian solution to the semi-geostrophic equation. In Chapter 6 we prove partial regularity of optimal maps with respect to a generic cost functions (it is well known that in this case global regularity can not be expected). More precisely we show that if the target and source measure have smooth densities the optimal map is always smooth outside a closed set of measure zero.

  9. Mixed-norm regularization for brain decoding.

    Science.gov (United States)

    Flamary, R; Jrad, N; Phlypo, R; Congedo, M; Rakotomamonjy, A

    2014-01-01

    This work investigates the use of mixed-norm regularization for sensor selection in event-related potential (ERP) based brain-computer interfaces (BCI). The classification problem is cast as a discriminative optimization framework where sensor selection is induced through the use of mixed-norms. This framework is extended to the multitask learning situation where several similar classification tasks related to different subjects are learned simultaneously. In this case, multitask learning helps in leveraging data scarcity issue yielding to more robust classifiers. For this purpose, we have introduced a regularizer that induces both sensor selection and classifier similarities. The different regularization approaches are compared on three ERP datasets showing the interest of mixed-norm regularization in terms of sensor selection. The multitask approaches are evaluated when a small number of learning examples are available yielding to significant performance improvements especially for subjects performing poorly.

  10. Iterative regularization method in generalized inverse beamforming

    Science.gov (United States)

    Zhang, Zhifei; Chen, Si; Xu, Zhongming; He, Yansong; Li, Shu

    2017-05-01

    Beamforming based on microphone array is a method to identify sound sources. It can visualize the sound field of the source plane and reveal interesting acoustic information. Generalized inverse beamforming (GIB) is one important branch of beamforming techniques due to its high identification accuracy and computational efficiency. However, in real testing situation, errors caused by measurement noise and configuration problems may seriously reduce the beamforming accuracy. As an inverse problem, the stability of GIB can be improved with regularization methods. We proposed a new iterative regularization method for GIB by iteratively redefining the form of regularization matrix and calculating the corresponding solution. Moreover, the new method is applied to functional beamforming and double-layer antenna beamforming respectively. Numerical simulations and experiments are implemented. The results show that the proposed regularization method leads to more robust beamforming output and higher accuracy in both the two applications.

  11. The regularization of Old English weak verbs

    Directory of Open Access Journals (Sweden)

    Marta Tío Sáenz

    2015-07-01

    Full Text Available This article deals with the regularization of non-standard spellings of the verbal forms extracted from a corpus. It addresses the question of what the limits of regularization are when lemmatizing Old English weak verbs. The purpose of such regularization, also known as normalization, is to carry out lexicological analysis or lexicographical work. The analysis concentrates on weak verbs from the second class and draws on the lexical database of Old English Nerthus, which has incorporated the texts of the Dictionary of Old English Corpus. As regards the question of the limits of normalization, the solution adopted are, in the first place, that when it is necessary to regularize, normalization is restricted to correspondences based on dialectal and diachronic variation and, secondly, that normalization has to be unidirectional.

  12. Mixed-Norm Regularization for Brain Decoding

    Directory of Open Access Journals (Sweden)

    R. Flamary

    2014-01-01

    Full Text Available This work investigates the use of mixed-norm regularization for sensor selection in event-related potential (ERP based brain-computer interfaces (BCI. The classification problem is cast as a discriminative optimization framework where sensor selection is induced through the use of mixed-norms. This framework is extended to the multitask learning situation where several similar classification tasks related to different subjects are learned simultaneously. In this case, multitask learning helps in leveraging data scarcity issue yielding to more robust classifiers. For this purpose, we have introduced a regularizer that induces both sensor selection and classifier similarities. The different regularization approaches are compared on three ERP datasets showing the interest of mixed-norm regularization in terms of sensor selection. The multitask approaches are evaluated when a small number of learning examples are available yielding to significant performance improvements especially for subjects performing poorly.

  13. Regularization of B-Spline Objects.

    Science.gov (United States)

    Xu, Guoliang; Bajaj, Chandrajit

    2011-01-01

    By a d-dimensional B-spline object (denoted as ), we mean a B-spline curve (d = 1), a B-spline surface (d = 2) or a B-spline volume (d = 3). By regularization of a B-spline object we mean the process of relocating the control points of such that they approximate an isometric map of its definition domain in certain directions and is shape preserving. In this paper we develop an efficient regularization method for , d = 1, 2, 3 based on solving weak form L(2)-gradient flows constructed from the minimization of certain regularizing energy functionals. These flows are integrated via the finite element method using B-spline basis functions. Our experimental results demonstrate that our new regularization method is very effective.

  14. On Comparison of Adaptive Regularization Methods

    DEFF Research Database (Denmark)

    Sigurdsson, Sigurdur; Larsen, Jan; Hansen, Lars Kai

    2000-01-01

    at the expense of introducing extra bias. The overall objective of adaptive regularization is to tune the amount of regularization ensuring minimal generalization error. Regularization is a supplement to direct model selection techniques like step-wise selection and one would prefer a hybrid scheme; however...... different criteria, e.g., the Bayesian evidence. The evidence expresses basically the probability of the model, which is conceptually different from generalization error; however, asymptotically for large training data sets they will converge. First the basic model definition, training and generalization......Modeling with flexible models, such as neural networks, requires careful control of the model complexity and generalization ability of the resulting model which finds expression in the ubiquitous bias-variance dilemma. Regularization is a tool for optimizing the model structure reducing variance...

  15. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  16. Fast and compact regular expression matching

    DEFF Research Database (Denmark)

    Bille, Philip; Farach-Colton, Martin

    2008-01-01

    We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how to ...... to improve the space and/or remove a dependency on the alphabet size for each problem using either an improved tabulation technique of an existing algorithm or by combining known algorithms in a new way....

  17. Regularity of Tor for weakly stable ideals

    Directory of Open Access Journals (Sweden)

    Katie Ansaldi

    2015-05-01

    Full Text Available It is proved that if I and J are weakly stable ideals in a polynomial ring R = k[x_1, . . ., x_n], with k a field, then the regularity of Tor^R_i (R/I, R/J has the expected upper bound. We also give a bound for the regularity of Ext^i_R (R/I, R for I a weakly stable ideal.

  18. Deterministic automata for extended regular expressions

    Directory of Open Access Journals (Sweden)

    Syzdykov Mirzakhmet

    2017-12-01

    Full Text Available In this work we present the algorithms to produce deterministic finite automaton (DFA for extended operators in regular expressions like intersection, subtraction and complement. The method like “overriding” of the source NFA(NFA not defined with subset construction rules is used. The past work described only the algorithm for AND-operator (or intersection of regular languages; in this paper the construction for the MINUS-operator (and complement is shown.

  19. Short Communication

    African Journals Online (AJOL)

    ... et al., 1999). The assay represents a rapid, inexpensive and simple bioassay for testing plant extracts bioactivity which in most cases correlates reasonably well with cytotoxic and anti-tumor properties. The brine shrimp lethality assay is based on the ability of the extract to show lethality in laboratory. Short Communication ...

  20. Short Report

    African Journals Online (AJOL)

    Bioline

    Short Report. Waiting time among acute abdominal emergencies in a Nigerian teaching hospital: causes of delay and consequences. N .Mbah, W. Ek. Opara and N. P. Agwu ... admitted with acute surgical abdomen are most commonly due to financial difficulties. ... private, general and primary health institutions within.

  1. SHORT COMMUNICATION

    African Journals Online (AJOL)

    Tanzania Health Research Bulletin (2005), Vol. 7, No. 2. SHORT COMMUNICATION. Palliative care in Tanzania: a needs assessment study of family caregivers in urban setting. T. NGOMA. Ocean Road Cancer Institute, PO. Box 3592 Dar es Salaam, Tanzania;. Email: ngoma@uccmail.co.tz. Tanzania, with a population of ...

  2. Short communications

    African Journals Online (AJOL)

    2015-05-23

    May 23, 2015 ... the majority of birds in one image (Fig. 2). Figure 2. Partial stack of 100+ Levant Sparrowhawks over the Mara North Conservancy, 23 February 2014. Photo: M. Mockler. Short communications. 33. Figure 1. Photographs confirming the identification of Levant Sparrowhawk. Accipiter brevipes. Photos: M.

  3. Short Comm.

    African Journals Online (AJOL)

    E-LIBRARY

    economic stability. Industrialization according to Britannica Encyclopedia is, “The process of converting to a socio-economic or development in which industry is ... and even secondary schools. Furthermore, disciplines such as Library and Information Science have over the years been. Short Comm. Information Impact:.

  4. Short Communication

    African Journals Online (AJOL)

    Nigerian Journal of Basic and Applied Science (2011), 19(2): 304-307. ISSN 0794-5698. Short Communication. Lead and Cadmium Levels of Five Commonly and Widely Consumed Leafy Vegetables in. Kano State, Nigeria. *M.I. Mohammed and ... the agreed international requirements. This is particularly important for farm ...

  5. Short communication

    African Journals Online (AJOL)

    UPuser

    Short communication. Polymorphisms of the CAST gene in the Meishan and five other pig populations in China. Q.S. Wang. 1. , Y.C. Pan. 1#. , L.B. Sun. 2 and H. Meng. 1. 1 Department of Animal Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai. 201101, P.R. China. 2 Shanghai Institute of ...

  6. All-photonic quantum repeaters

    Science.gov (United States)

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  7. Quantum key distribution with two-segment quantum repeaters

    Energy Technology Data Exchange (ETDEWEB)

    Kampermann, Hermann; Abruzzo, Silvestre; Bruss, Dagmar [Theoretische Physik III, Heinrich-Heine-Universitaet Duesseldorf (Germany)

    2014-07-01

    Quantum repeaters represent one possible way to achieve long-distance quantum key distribution. One way of improving the repeater rate and decreasing the memory coherence time is the usage of multiplexing. Motivated by the experimental fact that long-range connections are practically demanding, we extend the analysis of the quantum repeater multiplexing protocol to the case of short-range connections. We derive formulas for the repeater rate and we show that short-range connections lead to most of the benefits of a full-range multiplexing protocol. A less demanding QKD-protocol without quantum memories was recently introduced by Lo et al. We generalize this measurement-device-independent quantum key Distribution protocol to the scenario where the repeater Station contains also heralded quantum memories. We assume either single-photon sources or weak coherent pulse sources plus decay states. We show that it is possible to significantly outperform the original proposal, even in presence of decoherence of the quantum memory. We give formulas in terms of device imperfections i.e., the quantum bit error rate and the repeater rate.

  8. Short Stature

    DEFF Research Database (Denmark)

    Christesen, Henrik Boye Thybo; Pedersen, Birgitte Tønnes; Pournara, Effie

    2016-01-01

    -scale, non-interventional, multinational study. The patient cohort consisted of 5996 short pediatric patients diagnosed with growth hormone deficiency (GHD), Turner syndrome (TS) or born small for gestational age (SGA). The proportions of children with baseline height standard deviation score (SDS) below...... clinical cut-off values (-2 SDS for GHD and TS; -2.5 SDS for SGA) based on national growth references and WHO growth standards/references were compared for children aged ....0001), TS (21%; PSGA (32%; P

  9. Conservative regularization of ideal hydrodynamics and magnetohydrodynamics

    Science.gov (United States)

    Thyagaraja, A.

    2010-03-01

    Inviscid, incompressible hydrodynamics and incompressible ideal magnetohydrodynamics (MHD) share many properties such as time-reversal invariance of equations, conservation laws, and certain topological features. In three dimensions, these systems may lead to singular solutions (involving vortex and current sheets). While dissipative (viscoresistive) effects can regularize the equations leading to bounded solutions to the initial-boundary value (Cauchy) problem which presumably exist uniquely, the time-reversal symmetry and associated conservation properties are certainly destroyed. The present work is analogous to (and suggested by) the Korteweg-de Vries regularization of the one-dimensional, nonlinear kinematic wave equation. Thus the regularizations applied to the original equations of hydrodynamics and ideal MHD retain conservation properties and the symmetries of the original equations. Integral invariants which generalize those known for the original systems are shown to imply bounded enstrophy. The regularization developed can also be applied to the corresponding dissipative models (such as the Navier-Stokes equations and the viscoresistive MHD equations) and may imply interesting regularity properties for the solutions of the latter as well. The models developed thus have intrinsic mathematical interest as well as possible applications to large-scale numerical simulations in systems where dissipative effects are extremely small or even absent.

  10. Regularities, Natural Patterns and Laws of Nature

    Directory of Open Access Journals (Sweden)

    Stathis Psillos

    2014-02-01

    Full Text Available  The goal of this paper is to sketch an empiricist metaphysics of laws of nature. The key idea is that there are regularities without regularity-enforcers. Differently put, there are natural laws without law-makers of a distinct metaphysical kind. This sketch will rely on the concept of a natural pattern and more significantly on the existence of a network of natural patterns in nature. The relation between a regularity and a pattern will be analysed in terms of mereology.  Here is the road map. In section 2, I will briefly discuss the relation between empiricism and metaphysics, aiming to show that an empiricist metaphysics is possible. In section 3, I will offer arguments against stronger metaphysical views of laws. Then, in section 4 I will motivate nomic objectivism. In section 5, I will address the question ‘what is a regularity?’ and will develop a novel answer to it, based on the notion of a natural pattern. In section 6, I will raise the question: ‘what is a law of nature?’, the answer to which will be: a law of nature is a regularity that is characterised by the unity of a natural pattern.

  11. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul

    2017-01-01

    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  12. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S.K.

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  13. Fractional Regularization Term for Variational Image Registration

    Directory of Open Access Journals (Sweden)

    Rafael Verdú-Monedero

    2009-01-01

    Full Text Available Image registration is a widely used task of image analysis with applications in many fields. Its classical formulation and current improvements are given in the spatial domain. In this paper a regularization term based on fractional order derivatives is formulated. This term is defined and implemented in the frequency domain by translating the energy functional into the frequency domain and obtaining the Euler-Lagrange equations which minimize it. The new regularization term leads to a simple formulation and design, being applicable to higher dimensions by using the corresponding multidimensional Fourier transform. The proposed regularization term allows for a real gradual transition from a diffusion registration to a curvature registration which is best suited to some applications and it is not possible in the spatial domain. Results with 3D actual images show the validity of this approach.

  14. Stream Processing Using Grammars and Regular Expressions

    DEFF Research Database (Denmark)

    Rasmussen, Ulrik Terp

    In this dissertation we study regular expression based parsing and the use of grammatical specifications for the synthesis of fast, streaming string-processing programs. In the first part we develop two linear-time algorithms for regular expression based parsing with Perl-style greedy...... disambiguation. The first algorithm operates in two passes in a semi-streaming fashion, using a constant amount of working memory and an auxiliary tape storage which is written in the first pass and consumed by the second. The second algorithm is a single-pass and optimally streaming algorithm which outputs...... as much of the parse tree as is semantically possible based on the input prefix read so far, and resorts to buffering as many symbols as is required to resolve the next choice. Optimality is obtained by performing a PSPACE-complete pre-analysis on the regular expression. In the second part we present...

  15. Surface counterterms and regularized holographic complexity

    Science.gov (United States)

    Yang, Run-Qiu; Niu, Chao; Kim, Keun-Young

    2017-09-01

    The holographic complexity is UV divergent. As a finite complexity, we propose a "regularized complexity" by employing a similar method to the holographic renor-malization. We add codimension-two boundary counterterms which do not contain any boundary stress tensor information. It means that we subtract only non-dynamic back-ground and all the dynamic information of holographic complexity is contained in the regularized part. After showing the general counterterms for both CA and CV conjectures in holographic spacetime dimension 5 and less, we give concrete examples: the BTZ black holes and the four and five dimensional Schwarzschild AdS black holes. We propose how to obtain the counterterms in higher spacetime dimensions and show explicit formulas only for some special cases with enough symmetries. We also compute the complexity of formation by using the regularized complexity.

  16. REX XML shallow parsing with regular expressions

    CERN Document Server

    Cameron, R D

    1999-01-01

    The syntax of XML is simple enough that it is possible to parse an XML document into a list of its markup and text items using a single regular expression. Such a shallow parse of an XML document can be very useful for the construction of a variety of lightweight XML processing tools. However, complex regular expressions can be difficult to construct and even more difficult to read. Using a form of literate programming for regular expressions, this paper documents a set of XML shallow parsing expressions that can be used a basis for simple, correct, efficient, robust and language-independent XML shallow parsing. Complete shallow parser implementations of less than 50 lines each in Perl, JavaScript and Lex/Flex are also given. (0 refs).

  17. Contour Propagation With Riemannian Elasticity Regularization

    DEFF Research Database (Denmark)

    Bjerre, Troels; Hansen, Mads Fogtmann; Sapru, W.

    2011-01-01

    guided corrections. This study compares manual delineations in replanning CT scans of head-and-neck patients to automatic contour propagation using deformable registration with Riemannian regularization. The potential benefit of locally assigned regularization parameters according to tissue type...... is investigated. Materials/Methods: Planning PET-CT scans plus 2 - 4 subsequent replanning CTs for five head-and-neck cancer patients were obtained. The Gross Tumor Volume (GTV) was manually delineated on the planning CT by an experienced clinician and manually propagated by pasting the set of contours from...... the planning CT onto the rescans and correcting to reflect actual anatomical changes. For deformable registration, a free-form, multi-level, B-spline deformation model with Riemannian elasticity, penalizing non-rigid local deformations, and volumetric changes, was used. Regularization parameters was defined...

  18. Generalized inverse beamforming with optimized regularization strategy

    Science.gov (United States)

    Zavala, P. A. G.; De Roeck, W.; Janssens, K.; Arruda, J. R. F.; Sas, P.; Desmet, W.

    2011-04-01

    A promising recent development on acoustic source localization and source strength estimation is the generalized inverse beamforming, which is based on the microphone array cross-spectral matrix eigenstructure. This method presents several advantages over the conventional beamforming, including a higher accuracy on the source center localization and strength estimation even with distributed coherent sources. This paper aims to improve the strength estimation of the generalized inverse beamforming method with an automated regularization factor definition. Also in this work, a virtual target grid is introduced, and source mapping and strength estimation are obtained disregarding, as much as possible, the reflections influence. Two simple problems are used to compare the generalized inverse performance with fixed regularization factor to performance obtained using the optimized regularization strategy. Numerical and experimental data are used, and two other strength estimation methods are also evaluated for reference.

  19. Regularization and Migration Policy in Europe

    Directory of Open Access Journals (Sweden)

    Philippe de Bruycker

    2001-05-01

    Full Text Available The following pages present, in a general way, the contents of Regularization of illegal immigrants in the European Union, which includes a comparative synthesis and statistical information for each of the eight countries involved; a description of actions since the beginning of the year 2000; and a systematic analysis of the different categories of foreigners, the types of regularization carried out, and the rules that have governed these actions.In relation to regularization, the author considers the political coherence of the actions taken by the member states as well as how they relate to two ever more crucial aspects of immigration policy –the integration of legal resident immigrants and the fight againstillegal immigration in the context of a control of migratory flows.

  20. The repeatability of behaviour: a meta-analysis

    Science.gov (United States)

    Bell, Alison M.; Hankison, Shala J.; Laskowski, Kate L.

    2014-01-01

    There is increasing interest in individual differences in animal behaviour. Recent research now suggests that an individual’s behaviour, once considered to be plastic, may be more predictable than previously thought. Here, we take advantage of the large number of studies that have estimated the repeatability of various behaviours to evaluate whether there is good evidence for consistent individual differences in behaviour and to answer some outstanding questions about possible factors that can influence repeatability. Specifically, we use meta-analysis to ask whether different types of behaviours were more repeatable than others, and if repeatability estimates depended on taxa, sex, age, field versus laboratory, the number of measures and the interval between measures. Some of the overall patterns that were revealed by this analysis were that repeatability estimates were higher in the field compared to the laboratory and repeatability was higher when the interval between observations was short. Mate preference behaviour was one of the best studied but least repeatable behaviours. Our findings prompt new insights into the relative flexibility of different types of behaviour and offer suggestions for the design and analysis of future research. PMID:24707058

  1. A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

    Directory of Open Access Journals (Sweden)

    Shuaibin Lian

    2014-01-01

    Full Text Available Background. Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses. Up to now, the performances of assembling repeats of these current assemblers are very poor. Results. To improve this problem, we proposed a new genome assembly algorithm, named SWA, which has four properties: (1 assembling repeats and nonrepeats; (2 adopting a new overlapping extension strategy to extend each seed; (3 adopting sliding window to filter out the sequencing bias; and (4 proposing a compensational mechanism for low coverage datasets. SWA was evaluated and validated in both simulations and real sequencing datasets. The accuracy of assembling repeats and estimating the copy numbers is up to 99% and 100%, respectively. Finally, the extensive comparisons with other eight leading assemblers show that SWA outperformed others in terms of completeness and correctness of assembling repeats and nonrepeats. Conclusions. This paper proposed a new de novo genome assembly method for resolving complex repeats. SWA not only can detect where repeats or nonrepeats are but also can assemble them completely from NGS data, especially for assembling repeats. This is the advantage over other assemblers.

  2. Short esophagus.

    Science.gov (United States)

    Kunio, Nicholas R; Dolan, James P; Hunter, John G

    2015-06-01

    In the presence of long-standing and severe gastroesophageal reflux disease, patients can develop various complications, including a shortened esophagus. Standard preoperative testing in these patients should include endoscopy, esophagography, and manometry, whereas the objective diagnosis of a short esophagus must be made intraoperatively following adequate mediastinal mobilization. If left untreated, it is a contributing factor to the high recurrence rate following fundoplications or repair of large hiatal hernias. A laparoscopic Collis gastroplasty combined with an antireflux procedure offers safe and effective therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Regular-fat dairy and human health

    DEFF Research Database (Denmark)

    Astrup, Arne; Bradley, Beth H Rice; Brenna, J Thomas

    2016-01-01

    to disseminate, explore and discuss the state of the science on the relationship between regular fat dairy products and health, symposia were programmed by dairy industry organizations in Europe and North America at The Eurofed Lipids Congress (2014) in France, The Dairy Nutrition Annual Symposium (2014......) in Canada, The American Society for Nutrition Annual Meeting held in conjunction with Experimental Biology (2015) in the United States, and The Federation of European Nutrition Societies (2015) in Germany. This synopsis of these symposia describes the complexity of dairy fat and the effects regular...

  4. Deconvolution and Regularization with Toeplitz Matrices

    DEFF Research Database (Denmark)

    Hansen, Per Christian

    2002-01-01

    treatment requires the use of regularization methods. The corresponding computational problem takes the form of structured matrix problem with a Toeplitz or block Toeplitz coefficient matrix. The aim of this paper is to present a tutorial survey of numerical algorithms for the practical treatment...... of these discretized deconvolution problems, with emphasis on methods that take the special structure of the matrix into account. Wherever possible, analogies to classical DFT-based deconvolution problems are drawn. Among other things, we present direct methods for regularization with Toeplitz matrices, and we show...

  5. On a correspondence between regular and non-regular operator monotone functions

    DEFF Research Database (Denmark)

    Gibilisco, P.; Hansen, Frank; Isola, T.

    2009-01-01

    We prove the existence of a bijection between the regular and the non-regular operator monotone functions satisfying a certain functional equation. As an application we give a new proof of the operator monotonicity of certain functions related to the Wigner-Yanase-Dyson skew information....

  6. Evolution Analysis of Simple Sequence Repeats in Plant Genome.

    Science.gov (United States)

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

  7. Orientating Children in Regular Schools towards Impairments.

    Science.gov (United States)

    Gorman, P. P.

    1979-01-01

    The author discusses audio-visual material and other education techniques which eventually may facilitate the integration of children with mental, physical, and sensory impairments in the regular classroom. Films, radio texts, theater plays, and books are considered. Emphasis is on the introduction of impairments to the nonhandicapped population.…

  8. Regular ultrafilters and finite square principles

    NARCIS (Netherlands)

    Kennedy, J.; Shelah, S.; Väänänen, J.

    2008-01-01

    We show that many singular cardinals lambda above a strongly compact cardinal have regular ultrafilters D that violate the finite square principle square(fin)(lambda,D) introduced in [3]. For such ultrafilters D and cardinals lambda there are models of size lambda for which M-lambda/D is not

  9. Broad temperature range antiferroelectric regular mixtures

    Science.gov (United States)

    Dabrowski, Roman; Czuprynski, Krzysztof; Gasowska, J.; Oton, Jose; Quintana, Xabier; Castillo, P. L.; Bennis, N.

    2004-09-01

    Tristate regular mixtures with different electro-optical properties such as threshold voltage, saturation voltage, holding ratio and response time are presented. The relation of properties with the structure of compounds is discussed. All of mixtures show only moderate dynamic and static contrast but big gray level scale without hysteresis for positive and negative field driving.

  10. Regular matrix transformation on triple sequence spaces

    Directory of Open Access Journals (Sweden)

    Shyamal Debnath

    2017-10-01

    Full Text Available The main aim of this paper is to introduce the necessary and sufficient condition for a particular type of transformation of the form A: (a......  be regular from a triple sequence space to another triple sequence space.

  11. Regular and context-free nominal traces

    DEFF Research Database (Denmark)

    Degano, Pierpaolo; Ferrari, Gian-Luigi; Mezzetti, Gianluca

    2017-01-01

    Two kinds of automata are presented, for recognising new classes of regular and context-free nominal languages. We compare their expressive power with analogous proposals in the literature, showing that they express novel classes of languages. Although many properties of classical languages hold ...

  12. On bigraded regularities of Rees algebra

    Indian Academy of Sciences (India)

    Ramakrishna Nanduri

    2017-08-03

    Aug 3, 2017 ... K-algebra were defined in terms of syzygies [18, Definition 5.4] (also see [10, Defini- tion 1.1.3]). Since R(I) ... way (see Definition 2.3). We also define the Tor bigraded regularities of R; see ...... referee for a thorough reading of the manuscript and suggesting some improvements. References. [1] Aramova A ...

  13. From recreational to regular drug use

    DEFF Research Database (Denmark)

    Järvinen, Margaretha; Ravn, Signe

    2011-01-01

    to extricate themselves from this pattern. Hence, when regular drug users talk about their future, it is not a future characterised by total abstinence from illegal drugs but a future where they have rolled back their drug use career to the recreational drug use pattern they started out with. Empirically...

  14. On regular riesz operators | Raubenheimer | Quaestiones ...

    African Journals Online (AJOL)

    The r-asymptotically quasi finite rank operators on Banach lattices are examples of regular Riesz operators. We characterise Riesz elements in a subalgebra of a Banach algebra in terms of Riesz elements in the Banach algebra. This enables us to characterise r-asymptotically quasi finite rank operators in terms of adjoint ...

  15. Regular Sleep Makes for Happier College Students

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_166856.html Regular Sleep Makes for Happier College Students When erratic snoozers improve shut-eye habits, ... Health and Human Services. More Health News on College Health Healthy Sleep Recent Health News Related MedlinePlus Health Topics College ...

  16. 28 CFR 540.44 - Regular visitors.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Regular visitors. 540.44 Section 540.44... and if there exists no reason to exclude them. (c) Friends and associates. The visiting privilege ordinarily will be extended to friends and associates having an established relationship with the inmate...

  17. Neural Classifier Construction using Regularization, Pruning

    DEFF Research Database (Denmark)

    Hintz-Madsen, Mads; Hansen, Lars Kai; Larsen, Jan

    1998-01-01

    In this paper we propose a method for construction of feed-forward neural classifiers based on regularization and adaptive architectures. Using a penalized maximum likelihood scheme, we derive a modified form of the entropic error measure and an algebraic estimate of the test error. In conjunction...

  18. Regularization algorithms based on total least squares

    DEFF Research Database (Denmark)

    Hansen, Per Christian; O'Leary, Dianne P.

    1996-01-01

    or truncated {\\em SVD}, are not designed for problems in which both the coefficient matrix and the right-hand side are known only approximately. For this reason, we develop {\\em TLS}\\/-based regularization methods that take this situation into account. Here, we survey two different approaches to incorporation...

  19. Stabilization, pole placement, and regular implementability

    NARCIS (Netherlands)

    Belur, MN; Trentelman, HL

    In this paper, we study control by interconnection of linear differential systems. We give necessary and sufficient conditions for regular implementability of a-given linear, differential system. We formulate the problems of stabilization and pole placement as problems of finding a suitable,

  20. Stabilization, Pole Placement, and Regular Implementability

    NARCIS (Netherlands)

    Belur, Madhu N.; Trentelman, H.L.

    2002-01-01

    In this paper, we study control by interconnection of linear differential systems. We give necessary and sufficient conditions for regular implementability of a given linear differential system. We formulate the problems of stabilization and pole placement as problems of finding a suitable,

  1. A Sim(2 invariant dimensional regularization

    Directory of Open Access Journals (Sweden)

    J. Alfaro

    2017-09-01

    Full Text Available We introduce a Sim(2 invariant dimensional regularization of loop integrals. Then we can compute the one loop quantum corrections to the photon self energy, electron self energy and vertex in the Electrodynamics sector of the Very Special Relativity Standard Model (VSRSM.

  2. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  3. Quantification of fetal heart rate regularity using symbolic dynamics

    Science.gov (United States)

    van Leeuwen, P.; Cysarz, D.; Lange, S.; Geue, D.; Groenemeyer, D.

    2007-03-01

    Fetal heart rate complexity was examined on the basis of RR interval time series obtained in the second and third trimester of pregnancy. In each fetal RR interval time series, short term beat-to-beat heart rate changes were coded in 8bit binary sequences. Redundancies of the 28 different binary patterns were reduced by two different procedures. The complexity of these sequences was quantified using the approximate entropy (ApEn), resulting in discrete ApEn values which were used for classifying the sequences into 17 pattern sets. Also, the sequences were grouped into 20 pattern classes with respect to identity after rotation or inversion of the binary value. There was a specific, nonuniform distribution of the sequences in the pattern sets and this differed from the distribution found in surrogate data. In the course of gestation, the number of sequences increased in seven pattern sets, decreased in four and remained unchanged in six. Sequences that occurred less often over time, both regular and irregular, were characterized by patterns reflecting frequent beat-to-beat reversals in heart rate. They were also predominant in the surrogate data, suggesting that these patterns are associated with stochastic heart beat trains. Sequences that occurred more frequently over time were relatively rare in the surrogate data. Some of these sequences had a high degree of regularity and corresponded to prolonged heart rate accelerations or decelerations which may be associated with directed fetal activity or movement or baroreflex activity. Application of the pattern classes revealed that those sequences with a high degree of irregularity correspond to heart rate patterns resulting from complex physiological activity such as fetal breathing movements. The results suggest that the development of the autonomic nervous system and the emergence of fetal behavioral states lead to increases in not only irregular but also regular heart rate patterns. Using symbolic dynamics to

  4. Repeated mild lateral fluid percussion brain injury in the rat causes cumulative long-term behavioral impairments, neuroinflammation, and cortical loss in an animal model of repeated concussion.

    Science.gov (United States)

    Shultz, Sandy R; Bao, Feng; Omana, Vanessa; Chiu, Charlotte; Brown, Arthur; Cain, Donald Peter

    2012-01-20

    There is growing evidence that repeated brain concussion can result in cumulative and long-term behavioral symptoms, neuropathological changes, and neurodegeneration. Little is known about the factors and mechanisms that contribute to these effects. The current study addresses the need to investigate and better understand the effects of repeated concussion through the development of an animal model. Male Long-Evans rats received 1, 3, or 5 mild lateral fluid percussion injuries or sham injuries spaced 5 days apart. After the final injury, rats received either a short (24 h) or long (8 weeks) post-injury recovery period, followed by a detailed behavioral analysis consisting of tests for rodent anxiety-like behavior, cognition, social behavior, sensorimotor function, and depression-like behavior. Brains were examined immunohistochemically to assess neuroinflammation and cortical damage. Rats given 1, 3, or 5 mild percussion injuries displayed significant short-term cognitive impairments. Rats given repeated mild percussion injuries displayed significantly worse short- and long-term cognitive impairments. Rats given 5 mild percussion injuries also displayed increased anxiety- and depression-like behaviors. Neuropathological analysis revealed short-term neuroinflammation in 3-injury rats, and both short- and long-term neuroinflammation in 5-injury rats. There was also evidence that repeated injuries induced short- and long-term cortical damage. These cumulative and long-term changes are consistent with findings in human patients suffering repeated brain concussion, provide support for the use of repeated mild lateral fluid percussion injuries to study repeated concussion in the rat, and suggest that neuroinflammation may be important for understanding the cumulative and chronic effects of repeated concussion.

  5. Spatially regularized multifractal analysis for fMRI data.

    Science.gov (United States)

    Ciuciu, Philippe; Wendt, Herwig; Combrexelle, Sebastien; Abry, Patrice

    2017-07-01

    Scale-free dynamics is nowadays a massively used paradigm to model infraslow macroscopic brain activity. Multifractal analysis is becoming the standard tool to characterize scale-free dynamics. It is commonly used on various modalities of neuroimaging data to evaluate whether arrhythmic fluctuations in ongoing or evoked brain activity are related to pathologies (Alzheimer, epilepsy) or task performance. The success of multifractal analysis in neurosciences remains however so far contrasted: While it lead to relevant findings on M/EEG data, less clear impact was shown when applied to fMRI data. This is mostly due to their poor time resolution and very short duration as well as to the fact that analysis remains performed voxelwise. To take advantage of the large amount of voxels recorded jointly in fMRI, the present contribution proposes the use of a recently introduced Bayesian formalism for multifractal analysis, that regularizes the estimation of the multifractality parameter of a given voxel using information from neighbor voxels. The benefits of this regularized multifractal analysis are illustrated by comparison against classical multifractal analysis on fMRI data collected on one subject, at rest and during a working memory task: Though not yet statistically significant, increased multifractality is observed in task-negative and task-positive networks, respectively.

  6. TERRA: telomeric repeat-containing RNA.

    Science.gov (United States)

    Luke, Brian; Lingner, Joachim

    2009-09-02

    Telomeres, the physical ends of eukaryotic chromosomes, consist of tandem arrays of short DNA repeats and a large set of specialized proteins. A recent analysis has identified telomeric repeat-containing RNA (TERRA), a large non-coding RNA in animals and fungi, which forms an integral component of telomeric heterochromatin. TERRA transcription occurs at most or all chromosome ends and it is regulated by RNA surveillance factors and in response to changes in telomere length. TERRA functions that are emerging suggest important roles in the regulation of telomerase and in orchestrating chromatin remodelling throughout development and cellular differentiation. The accumulation of TERRA at telomeres can also interfere with telomere replication, leading to a sudden loss of telomere tracts. Such a phenotype can be observed upon impairment of the RNA surveillance machinery or in cells from ICF (Immunodeficiency, Centromeric region instability, Facial anomalies) patients, in which TERRA is upregulated because of DNA methylation defects in the subtelomeric region. Thus, TERRA may mediate several crucial functions at the telomeres, a region of the genome that had been considered to be transcriptionally silent.

  7. Regular Magnetic Black Hole Gravitational Lensing

    Science.gov (United States)

    Liang, Jun

    2017-05-01

    The Bronnikov regular magnetic black hole as a gravitational lens is studied. In nonlinear electrodynamics, photons do not follow null geodesics of background geometry, but move along null geodesics of a corresponding effective geometry. To study the Bronnikov regular magnetic black hole gravitational lensing in the strong deflection limit, the corresponding effective geometry should be obtained firstly. This is the most important and key step. We obtain the deflection angle in the strong deflection limit, and further calculate the angular positions and magnifications of relativistic images as well as the time delay between different relativistic images. The influence of the magnetic charge on the black hole gravitational lensing is also discussed. Supported by the Natural Science Foundation of Education Department of Shannxi Province under Grant No 15JK1077, and the Doctorial Scientific Research Starting Fund of Shannxi University of Science and Technology under Grant No BJ12-02.

  8. Exploring the structural regularities in networks

    CERN Document Server

    Shen, Hua-Wei; Guo, Jia-Feng

    2011-01-01

    In this paper, we consider the problem of exploring structural regularities of networks by dividing the nodes of a network into groups such that the members of each group have similar patterns of connections to other groups. Specifically, we propose a general statistical model to describe network structure. In this model, group is viewed as hidden or unobserved quantity and it is learned by fitting the observed network data using the expectation-maximization algorithm. Compared with existing models, the most prominent strength of our model is the high flexibility. This strength enables it to possess the advantages of existing models and overcomes their shortcomings in a unified way. As a result, not only broad types of structure can be detected without prior knowledge of what type of intrinsic regularities exist in the network, but also the type of identified structure can be directly learned from data. Moreover, by differentiating outgoing edges from incoming edges, our model can detect several types of stru...

  9. Regularized algorithm for Raman lidar data processing.

    Science.gov (United States)

    Shcherbakov, Valery

    2007-08-01

    A regularized algorithm that has the potential to improve the quality of Raman lidar data processing is presented. Compared to the conventional scheme, the proposed algorithm has the advantage, which results from the fact that it is based on a well-posed procedure. That is, the profile of the aerosol backscatter coefficient is computed directly, using the explicit relationships, without numerical differentiation. Thereafter, the profile of the lidar ratio is retrieved as a regularized solution of a first-kind Volterra integral equation. Once these two steps have been completed, the profile of the aerosol extinction coefficient is computed by a straightforward multiplication. The numerical simulations demonstrated that the proposed algorithm provides good accuracy and resolution of aerosol profile retrievals. The error analysis showed that the retrieved profiles are continuous functions of the measurement errors and of the a priori information uncertainties.

  10. Modeling Regular Replacement for String Constraint Solving

    Science.gov (United States)

    Fu, Xiang; Li, Chung-Chih

    2010-01-01

    Bugs in user input sanitation of software systems often lead to vulnerabilities. Among them many are caused by improper use of regular replacement. This paper presents a precise modeling of various semantics of regular substitution, such as the declarative, finite, greedy, and reluctant, using finite state transducers (FST). By projecting an FST to its input/output tapes, we are able to solve atomic string constraints, which can be applied to both the forward and backward image computation in model checking and symbolic execution of text processing programs. We report several interesting discoveries, e.g., certain fragments of the general problem can be handled using less expressive deterministic FST. A compact representation of FST is implemented in SUSHI, a string constraint solver. It is applied to detecting vulnerabilities in web applications

  11. Effort variation regularization in sound field reproduction

    DEFF Research Database (Denmark)

    Stefanakis, Nick; Jacobsen, Finn; Sarris, Ioannis

    2010-01-01

    . Specifically, it is suggested that the phase differential of the source driving signals should be in agreement with the phase differential of the desired sound pressure field. The performance of the suggested method is compared with that of conventional effort regularization, wave field synthesis (WFS......In this paper, active control is used in order to reproduce a given sound field in an extended spatial region. A method is proposed which minimizes the reproduction error at a number of control positions with the reproduction sources holding a certain relation within their complex strengths......), and adaptive wave field synthesis (AWFS), both under free-field conditions and in reverberant rooms. It is shown that effort variation regularization overcomes the problems associated with small spaces and with a low ratio of direct to reverberant energy, improving thus the reproduction accuracy...

  12. Basic analysis of regularized series and products

    CERN Document Server

    Jorgenson, Jay A

    1993-01-01

    Analytic number theory and part of the spectral theory of operators (differential, pseudo-differential, elliptic, etc.) are being merged under amore general analytic theory of regularized products of certain sequences satisfying a few basic axioms. The most basic examples consist of the sequence of natural numbers, the sequence of zeros with positive imaginary part of the Riemann zeta function, and the sequence of eigenvalues, say of a positive Laplacian on a compact or certain cases of non-compact manifolds. The resulting theory is applicable to ergodic theory and dynamical systems; to the zeta and L-functions of number theory or representation theory and modular forms; to Selberg-like zeta functions; andto the theory of regularized determinants familiar in physics and other parts of mathematics. Aside from presenting a systematic account of widely scattered results, the theory also provides new results. One part of the theory deals with complex analytic properties, and another part deals with Fourier analys...

  13. Chiral Perturbation Theory With Lattice Regularization

    CERN Document Server

    Ouimet, P P A

    2005-01-01

    In this work, alternative methods to regularize chiral perturbation theory are discussed. First, Long Distance Regularization will be considered in the presence of the decuplet of the lightest spin 32 baryons for several different observables. This serves motivation and introduction to the use of the lattice regulator for chiral perturbation theory. The mesonic, baryonic and anomalous sectors of chiral perturbation theory will be formulated on a lattice of space time points. The consistency of the lattice as a regulator will be discussed in the context of the meson and baryon masses. Order a effects will also be discussed for the baryon masses, sigma terms and magnetic moments. The work will close with an attempt to derive an effective Wess-Zumino-Witten Lagrangian for Wilson fermions at non-zero a. Following this discussion, there will be a proposal for a phenomenologically useful WZW Lagrangian at non-zero a.

  14. Testing the Equivalence of Regular Languages

    Directory of Open Access Journals (Sweden)

    Marco Almeida

    2009-07-01

    Full Text Available The minimal deterministic finite automaton is generally used to determine regular languages equality. Antimirov and Mosses proposed a rewrite system for deciding regular expressions equivalence of which Almeida et al. presented an improved variant. Hopcroft and Karp proposed an almost linear algorithm for testing the equivalence of two deterministic finite automata that avoids minimisation. In this paper we improve the best-case running time, present an extension of this algorithm to non-deterministic finite automata, and establish a relationship between this algorithm and the one proposed in Almeida et al. We also present some experimental comparative results. All these algorithms are closely related with the recent coalgebraic approach to automata proposed by Rutten.

  15. Extreme values, regular variation and point processes

    CERN Document Server

    Resnick, Sidney I

    1987-01-01

    Extremes Values, Regular Variation and Point Processes is a readable and efficient account of the fundamental mathematical and stochastic process techniques needed to study the behavior of extreme values of phenomena based on independent and identically distributed random variables and vectors It presents a coherent treatment of the distributional and sample path fundamental properties of extremes and records It emphasizes the core primacy of three topics necessary for understanding extremes the analytical theory of regularly varying functions; the probabilistic theory of point processes and random measures; and the link to asymptotic distribution approximations provided by the theory of weak convergence of probability measures in metric spaces The book is self-contained and requires an introductory measure-theoretic course in probability as a prerequisite Almost all sections have an extensive list of exercises which extend developments in the text, offer alternate approaches, test mastery and provide for enj...

  16. Regularization in Orbital Mechanics; Theory and Practice

    Science.gov (United States)

    Roa, Javier

    2017-09-01

    Regularized equations of motion can improve numerical integration for the propagation of orbits, and simplify the treatment of mission design problems. This monograph discusses standard techniques and recent research in the area. While each scheme is derived analytically, its accuracy is investigated numerically. Algebraic and topological aspects of the formulations are studied, as well as their application to practical scenarios such as spacecraft relative motion and new low-thrust trajectories.

  17. Implementing regularization implicitly via approximate eigenvector computation

    OpenAIRE

    Mahoney, Michael W.; Orecchia, Lorenzo

    2010-01-01

    Regularization is a powerful technique for extracting useful information from noisy data. Typically, it is implemented by adding some sort of norm constraint to an objective function and then exactly optimizing the modified objective function. This procedure often leads to optimization problems that are computationally more expensive than the original problem, a fact that is clearly problematic if one is interested in large-scale applications. On the other hand, a large body of empirical work...

  18. Regular black hole in three dimensions

    OpenAIRE

    Myung, Yun Soo; Yoon, Myungseok

    2008-01-01

    We find a new black hole in three dimensional anti-de Sitter space by introducing an anisotropic perfect fluid inspired by the noncommutative black hole. This is a regular black hole with two horizons. We compare thermodynamics of this black hole with that of non-rotating BTZ black hole. The first-law of thermodynamics is not compatible with the Bekenstein-Hawking entropy.

  19. Bifurcations in the regularized Ericksen bar model

    OpenAIRE

    Grinfeld, M.; Lord, G. J. (Gabriel J.)

    2007-01-01

    We consider the regularized Ericksen model of an elastic bar on an elastic foundation on an interval with Dirichlet boundary conditions as a two-parameter bifurcation problem. We explore, using local bifurcation analysis and continuation methods, the structure of bifurcations from double zero eigenvalues. Our results provide evidence in support of M\\"uller's conjecture \\cite{Muller} concerning the symmetry of local minimizers of the associated energy functional and describe in detail the stru...

  20. On bigraded regularities of Rees algebra

    Indian Academy of Sciences (India)

    For any homogeneous ideal I in K [ x 1 , . . . , x n ] of analytic spread ℓ , we show that for the Rees algebra R ( I ) , r e g ( 0 , 1 ) s y z \\sl ( R ( I ) ) = r e g ( 0 , 1 ) T \\sl ( R ( I ) ) . We compute a formula for the (0, 1)-regularity of R ( I ) , which is a bigraded analog of Theorem1.1 of Aramova and Herzog ( A m . J . M a t h . 122 ( 4 ) ...

  1. Preconditioners for regularized saddle point matrices

    Czech Academy of Sciences Publication Activity Database

    Axelsson, Owe

    2011-01-01

    Roč. 19, č. 2 (2011), s. 91-112 ISSN 1570-2820 Institutional research plan: CEZ:AV0Z30860518 Keywords : saddle point matrices * preconditioning * regularization * eigenvalue clustering Subject RIV: BA - General Mathematics Impact factor: 0.533, year: 2011 http://www.degruyter.com/view/j/jnma.2011.19.issue-2/jnum.2011.005/jnum.2011.005. xml

  2. Regularity bounds on Zakharov system evolutions

    Directory of Open Access Journals (Sweden)

    James Colliander

    2002-08-01

    Full Text Available Spatial regularity properties of certain global-in-time solutions of the Zakharov system are established. In particular, the evolving solution $u(t$ is shown to satisfy an estimate $|u(t|_{H^s} leq C |t|^{(s-1+}$, where $H^s$ is the standard spatial Sobolev norm. The proof is an adaptation of earlier work on the nonlinear Schrodinger equation which reduces matters to bilinear estimates.

  3. Efficiency of repeated network interactions

    NARCIS (Netherlands)

    Timmer, Judith B.; Mandjes, M.R.H.

    2009-01-01

    In this paper we consider a network with interactions by two users. Each of them repeatedly issues download requests on the network. These requests may be unsuccessful due to congestion or non-congestion related errors. A user decides when to cancel a request (that is, what his impatience threshold

  4. Hyperspectral Image Recovery via Hybrid Regularization.

    Science.gov (United States)

    Arablouei, Reza; de Hoog, Frank

    2016-09-27

    Natural images tend to mostly consist of smooth regions with individual pixels having highly correlated spectra. This information can be exploited to recover hyperspectral images of natural scenes from their incomplete and noisy measurements. To perform the recovery while taking full advantage of the prior knowledge, we formulate a composite cost function containing a square-error data-fitting term and two distinct regularization terms pertaining to spatial and spectral domains. The regularization for the spatial domain is the sum of total-variation of the image frames corresponding to all spectral bands. The regularization for the spectral domain is the ��������-norm of the coefficient matrix obtained by applying a suitable sparsifying transform to the spectra of the pixels. We use an accelerated proximal-subgradient method to minimize the formulated cost function. We analyse the performance of the proposed algorithm and prove its convergence. Numerical simulations using real hyperspectral images exhibit that the proposed algorithm offers an excellent recovery performance with a number of measurements that is only a small fraction of the hyperspectral image data size. Simulation results also show that the proposed algorithm significantly outperforms an accelerated proximal-gradient algorithm that solves the classical basis-pursuit denoising problem to recover the hyperspectral image.

  5. Pentapeptide Repeat Proteins and Cyanobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  6. Bypassing the Limits of Ll Regularization: Convex Sparse Signal Processing Using Non-Convex Regularization

    Science.gov (United States)

    Parekh, Ankit

    Sparsity has become the basis of some important signal processing methods over the last ten years. Many signal processing problems (e.g., denoising, deconvolution, non-linear component analysis) can be expressed as inverse problems. Sparsity is invoked through the formulation of an inverse problem with suitably designed regularization terms. The regularization terms alone encode sparsity into the problem formulation. Often, the ℓ1 norm is used to induce sparsity, so much so that ℓ1 regularization is considered to be `modern least-squares'. The use of ℓ1 norm, as a sparsity-inducing regularizer, leads to a convex optimization problem, which has several benefits: the absence of extraneous local minima, well developed theory of globally convergent algorithms, even for large-scale problems. Convex regularization via the ℓ1 norm, however, tends to under-estimate the non-zero values of sparse signals. In order to estimate the non-zero values more accurately, non-convex regularization is often favored over convex regularization. However, non-convex regularization generally leads to non-convex optimization, which suffers from numerous issues: convergence may be guaranteed to only a stationary point, problem specific parameters may be difficult to set, and the solution is sensitive to the initialization of the algorithm. The first part of this thesis is aimed toward combining the benefits of non-convex regularization and convex optimization to estimate sparse signals more effectively. To this end, we propose to use parameterized non-convex regularizers with designated non-convexity and provide a range for the non-convex parameter so as to ensure that the objective function is strictly convex. By ensuring convexity of the objective function (sum of data-fidelity and non-convex regularizer), we can make use of a wide variety of convex optimization algorithms to obtain the unique global minimum reliably. The second part of this thesis proposes a non-linear signal

  7. Replacement of the myotonic dystrophy type 1 CTG repeat with 'non-CTG repeat' insertions in specific tissues.

    Science.gov (United States)

    Axford, Michelle M; López-Castel, Arturo; Nakamori, Masayuki; Thornton, Charles A; Pearson, Christopher E

    2011-07-01

    Recently, curious mutations have been reported to occur within the (CTG)n repeat tract of the myotonic dystrophy type 1 (DM1) locus. For example, the repeat, long presumed to be a pure repeat sequence, has now been revealed to often contain interruption motifs in a proportion of cases with expansions. Similarly, a few de novo somatic CTG expansions have been reported to arise from non-expanded DM1 alleles with 5-37 units, thought to be genetically stable. This study has characterised a novel mutation configuration at the DM1 CTG repeat that arose as somatic mosaicism in a juvenile onset DM1 patient with a non-expanded allele of (CTG)12 and tissue specific expansions ranging from (CTG)1100 to 6000. The mutation configuration replaced the CTG tract with a non-CTG repeat insertion of 43 or 60 nucleotides, precisely placed in the position of the CTG tract with proper flanking sequences. The inserts appeared to arise from a longer human sequence on chromosome 4q12, and may have arisen through DNA structure mediated somatic inter-gene recombination or replication/repair template switching errors. De novo insertions were detected in cerebral cortex and skeletal muscle, but not in heart or liver. Repeat tracts with -1 or -2 CTG units were also detected in cerebellum, which may have arisen by contractions of the short (CTG)12 allele. This non-CTG configuration expands current understanding of the sequence variations that can arise at this hypermutable site.

  8. Automated detection of repeated structures in building facades

    Directory of Open Access Journals (Sweden)

    M. Previtali

    2013-10-01

    Full Text Available Automatic identification of high-level repeated structures in 3D point clouds of building façades is crucial for applications like digitalization and building modelling. Indeed, in many architectural styles building façades are governed by arrangements of objects into repeated patterns. In particular, façades are generally designed as the repetition of some few basic objects organized into interlaced and\\or concatenated grid structures. Starting from this key observation, this paper presents an algorithm for Repeated Structure Detection (RSD in 3D point clouds of building façades. The presented methodology consists of three main phases. First, in the point cloud segmentation stage (i the building façade is decomposed into planar patches which are classified by means of some weak prior knowledge of urban buildings formulated in a classification tree. Secondly (ii, in the element clustering phase detected patches are grouped together by means of a similarity function and pairwise transformations between patches are computed. Eventually (iii, in the structure regularity estimation step the parameters of repeated grid patterns are calculated by using a Least- Squares optimization. Workability of the presented approach is tested using some real data from urban scenes.

  9. Attempted suicide in Denmark. III. Assessment of repeated suicidal behaviour

    DEFF Research Database (Denmark)

    Wang, A G; Nielsen, B; Bille-Brahe, U

    1985-01-01

    features for the repeaters were previous suicidal behaviour and suicidal behaviour among relatives. Many had a psychiatric record and expressed chronic somatic complaints. Around the time of the attempt, many expressed hopelessness, isolation and suicidal ideation. Pierce's Suicide Intent Scale performed......Ninety-nine patients, randomly chosen among hospital admitted suicide attempters, were initially interviewed at the Department of Psychiatry, Odense University Hospital, Denmark, and then followed up for a period of about 3 years. Half of the patients repeated the attempt in the follow-up period......, mostly in the first year. Ten patients committed suicide, half of them in the first 3 months after the interview, shortly after discharge from hospital. The majority of the repeaters were living alone, while those that committed suicide were mostly married women aged 50-60 years. Other characteristic...

  10. Convergence and Fluctuations of Regularized Tyler Estimators

    Science.gov (United States)

    Kammoun, Abla; Couillet, Romain; Pascal, Ferderic; Alouini, Mohamed-Slim

    2016-02-01

    This article studies the behavior of regularized Tyler estimators (RTEs) of scatter matrices. The key advantages of these estimators are twofold. First, they guarantee by construction a good conditioning of the estimate and second, being a derivative of robust Tyler estimators, they inherit their robustness properties, notably their resilience to the presence of outliers. Nevertheless, one major problem that poses the use of RTEs in practice is represented by the question of setting the regularization parameter $\\rho$. While a high value of $\\rho$ is likely to push all the eigenvalues away from zero, it comes at the cost of a larger bias with respect to the population covariance matrix. A deep understanding of the statistics of RTEs is essential to come up with appropriate choices for the regularization parameter. This is not an easy task and might be out of reach, unless one considers asymptotic regimes wherein the number of observations $n$ and/or their size $N$ increase together. First asymptotic results have recently been obtained under the assumption that $N$ and $n$ are large and commensurable. Interestingly, no results concerning the regime of $n$ going to infinity with $N$ fixed exist, even though the investigation of this assumption has usually predated the analysis of the most difficult $N$ and $n$ large case. This motivates our work. In particular, we prove in the present paper that the RTEs converge to a deterministic matrix when $n\\to\\infty$ with $N$ fixed, which is expressed as a function of the theoretical covariance matrix. We also derive the fluctuations of the RTEs around this deterministic matrix and establish that these fluctuations converge in distribution to a multivariate Gaussian distribution with zero mean and a covariance depending on the population covariance and the parameter $\\rho$.

  11. Convergence and fluctuations of Regularized Tyler estimators

    KAUST Repository

    Kammoun, Abla

    2015-10-26

    This article studies the behavior of regularized Tyler estimators (RTEs) of scatter matrices. The key advantages of these estimators are twofold. First, they guarantee by construction a good conditioning of the estimate and second, being a derivative of robust Tyler estimators, they inherit their robustness properties, notably their resilience to the presence of outliers. Nevertheless, one major problem that poses the use of RTEs in practice is represented by the question of setting the regularization parameter p. While a high value of p is likely to push all the eigenvalues away from zero, it comes at the cost of a larger bias with respect to the population covariance matrix. A deep understanding of the statistics of RTEs is essential to come up with appropriate choices for the regularization parameter. This is not an easy task and might be out of reach, unless one considers asymptotic regimes wherein the number of observations n and/or their size N increase together. First asymptotic results have recently been obtained under the assumption that N and n are large and commensurable. Interestingly, no results concerning the regime of n going to infinity with N fixed exist, even though the investigation of this assumption has usually predated the analysis of the most difficult N and n large case. This motivates our work. In particular, we prove in the present paper that the RTEs converge to a deterministic matrix when n → ∞ with N fixed, which is expressed as a function of the theoretical covariance matrix. We also derive the fluctuations of the RTEs around this deterministic matrix and establish that these fluctuations converge in distribution to a multivariate Gaussian distribution with zero mean and a covariance depending on the population covariance and the parameter.

  12. Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.

    Science.gov (United States)

    Kiliszek, Agnieszka; Kierzek, Ryszard; Krzyzosiak, Wlodzimierz J; Rypniewski, Wojciech

    2010-12-01

    CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to pathogenesis in addition to the well-known pathogenic effects of mutant proteins. We have analysed two crystal forms of RNA duplexes containing CAG repeats: (GGCAGCAGCC)(2). One of the structures has been determined at atomic resolution (0.95 Å) and the other at 1.9 Å. The duplexes include non-canonical A-A pairs that fit remarkably well within a regular A-helix. All the adenosines are in the anti-conformation and the only interaction within each A-A pair is a single C2-H2···N1 hydrogen bond. Both adenosines in each A-A pair are shifted towards the major groove, although to different extents; the A which is the H-bond donor stands out more (the 'thumbs-up' conformation). The main effect on the helix conformation is a local unwinding. The CAG repeats and the previously examined CUG structures share a similar pattern of electrostatic charge distribution in the minor groove, which could explain their affinity for the pathogenesis-related MBNL1 protein.

  13. A repeating fast radio burst

    Science.gov (United States)

    Spitler, L. G.; Scholz, P.; Hessels, J. W. T.; Bogdanov, S.; Brazier, A.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J.; Ferdman, R. D.; Freire, P. C. C.; Kaspi, V. M.; Lazarus, P.; Lynch, R.; Madsen, E. C.; McLaughlin, M. A.; Patel, C.; Ransom, S. M.; Seymour, A.; Stairs, I. H.; Stappers, B. W.; van Leeuwen, J.; Zhu, W. W.

    2016-03-01

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  14. Two-pass greedy regular expression parsing

    DEFF Research Database (Denmark)

    Grathwohl, Niels Bjørn Bugge; Henglein, Fritz; Nielsen, Lasse

    2013-01-01

    We present new algorithms for producing greedy parses for regular expressions (REs) in a semi-streaming fashion. Our lean-log algorithm executes in time O(mn) for REs of size m and input strings of size n and outputs a compact bit-coded parse tree representation. It improves on previous algorithms...... by: operating in only 2 passes; using only O(m) words of random-access memory (independent of n); requiring only kn bits of sequentially written and read log storage, where k

  15. Multichannel image regularization using anisotropic geodesic filtering

    Energy Technology Data Exchange (ETDEWEB)

    Grazzini, Jacopo A [Los Alamos National Laboratory

    2010-01-01

    This paper extends a recent image-dependent regularization approach introduced in aiming at edge-preserving smoothing. For that purpose, geodesic distances equipped with a Riemannian metric need to be estimated in local neighbourhoods. By deriving an appropriate metric from the gradient structure tensor, the associated geodesic paths are constrained to follow salient features in images. Following, we design a generalized anisotropic geodesic filter; incorporating not only a measure of the edge strength, like in the original method, but also further directional information about the image structures. The proposed filter is particularly efficient at smoothing heterogeneous areas while preserving relevant structures in multichannel images.

  16. Regular and Chaotic Dynamics of Flexible Plates

    Directory of Open Access Journals (Sweden)

    J. Awrejcewicz

    2014-01-01

    Full Text Available Nonlinear dynamics of flexible rectangular plates subjected to the action of longitudinal and time periodic load distributed on the plate perimeter is investigated. Applying both the classical Fourier and wavelet analysis we illustrate three different Feigenbaum type scenarios of transition from a regular to chaotic dynamics. We show that the system vibrations change with respect not only to the change of control parameters, but also to all fixed parameters (system dynamics changes when the independent variable, time, increases. In addition, we show that chaotic dynamics may appear also after the second Hopf bifurcation. Curves of equal deflections (isoclines lose their previous symmetry while transiting into chaotic vibrations.

  17. Spherical Averages on Regular and Semiregular Graphs

    OpenAIRE

    Douma, Femke

    2008-01-01

    In 1966, P. Guenther proved the following result: Given a continuous function f on a compact surface M of constant curvature -1 and its periodic lift g to the universal covering, the hyperbolic plane, then the averages of the lift g over increasing spheres converge to the average of the function f over the surface M. In this article, we prove similar results for functions on the vertices and edges of regular and semiregular graphs, with special emphasis on the convergence rate. We also consid...

  18. Equivariant semidefinite lifts of regular polygons

    OpenAIRE

    Fawzi, Hamza; Saunderson, James; Parrilo, Pablo A.

    2014-01-01

    Given a polytope P in $\\mathbb{R}^n$, we say that P has a positive semidefinite lift (psd lift) of size d if one can express P as the linear projection of an affine slice of the positive semidefinite cone $\\mathbf{S}^d_+$. If a polytope P has symmetry, we can consider equivariant psd lifts, i.e. those psd lifts that respect the symmetry of P. One of the simplest families of polytopes with interesting symmetries are regular polygons in the plane, which have played an important role in the stud...

  19. Equivariant semidefinite lifts of regular polygons

    OpenAIRE

    Fawzi, Hamza; Saunderson, J.; Parrilo, PA

    2017-01-01

    Given a polytope P in $\\mathbb{R}^n$, we say that P has a positive semidefinite lift (psd lift) of size d if one can express P as the linear projection of an affine slice of the positive semidefinite cone $\\mathbf{S}^d_+$. If a polytope P has symmetry, we can consider equivariant psd lifts, i.e. those psd lifts that respect the symmetry of P. One of the simplest families of polytopes with interesting symmetries are regular polygons in the plane, which have played an importan...

  20. Foaming behaviour of organic and regular milk

    OpenAIRE

    Pijnenburg, J.; Sala, G.; Valenberg, van, H.J.F.; Meinders, M.B.J.

    2012-01-01

    Organic milk is used more and more by consumers to froth milk that is used e.g. for the preparation of a capuccino. Frequently, organic milk turns out not to foam properly. This report describes a study to find the main couse of this bad foamability of organic milk. The focus of the research was to get insight in the foaming behaviour of a specific brand, indicated as A. The foamability and stability of different milk, both organic and regular, as well as skimmed, semi-skimmed, and full fat, ...

  1. Wave regularity in curve integrable spacetimes

    CERN Document Server

    Sanchez, Yafet Sanchez

    2015-01-01

    The idea of defining a gravitational singularity as an obstruction to the dynamical evolution of a test field (described by a PDE) rather than the dynamical evolution of a particle (described by a geodesics) is explored. In particular, the concept of wave regularity is introduced which serves to show that the classical singularities in curve integrable spacetimes do not interrupt the well-posedness of the wave equation. The techniques used also provide arguments that can be extended to establish when a classically singular spacetime remains singular in a semi-classical picture.

  2. Electronic Structure of Regular Bacterial Surface Layers

    Science.gov (United States)

    Vyalikh, Denis V.; Danzenbächer, Steffen; Mertig, Michael; Kirchner, Alexander; Pompe, Wolfgang; Dedkov, Yuriy S.; Molodtsov, Serguei L.

    2004-12-01

    We report photoemission and near-edge x-ray absorption fine structure measurements of the occupied and unoccupied valence electronic states of the regular surface layer of Bacillus sphaericus, which is widely used as the protein template for the fabrication of metallic nanostructures. The two-dimensional protein crystal shows a semiconductorlike behavior with a gap value of ˜3.0 eV and the Fermi energy close to the bottom of the lowest unoccupied molecular orbital. We anticipate that these results will open up new possibilities for the electric addressability of biotemplated low-dimensional hybrid structures.

  3. Strategies for regular segmented reductions on GPU

    DEFF Research Database (Denmark)

    Larsen, Rasmus Wriedt; Henriksen, Troels

    2017-01-01

    We present and evaluate an implementation technique for regular segmented reductions on GPUs. Existing techniques tend to be either consistent in performance but relatively inefficient in absolute terms, or optimised for specific workloads and thereby exhibiting bad performance for certain input...... is in the context of the Futhark compiler, the implementation technique is applicable to any library or language that has a need for segmented reductions. We evaluate the technique on four microbenchmarks, two of which we also compare to implementations in the CUB library for GPU programming, as well as on two...

  4. Predicting regular breast cancer screening in African-American women with a family history of breast cancer.

    Science.gov (United States)

    Laing, Sharon S; Makambi, Kepher

    2008-11-01

    To evaluate the impact of socioeconomic, personal and affective factors on regular breast cancer screening in at-risk African-American women. The study was a cross-sectional analysis assessing socioeconomic and affective predictors of breast cancer screening practices. Unaffected African-American women ages 40-64 with a family history of breast cancer were recruited from community settings. The main outcome measures were recent mammography, regular mammography and regular breast self-examinations. The majority of women reported having a recent mammogram (73%) and yearly mammograms (71%). More than half (56%) reported monthly breast self-examinations (BSEs). Available health insurance and risk perception had significant independent associations with regular mammography screening so that women having a mammogram every 6-12 months were more likely to have health insurance [odds ratio (OR)=4.99, 95% confidence interval (CI): 1.05-23.52], and women not engaged in regular screenings were less likely to perceive future breast cancer risk (OR=0.10, 95% CI: 0.01-0.96). Access to regular healthcare had a significant independent association with recent mammography so that women having a mammogram in the past 12 months were more likely to have access to regular healthcare (OR=6.59, 95% CI: 1.01-42.79). A significant majority of this subset of African-American women engage in repeat mammography screenings with cognitive and economic factors predicting noncompliance. Additional research with repeat mammography users is required so that regular screening practices can be encouraged among all at-risk women.

  5. Effect of proximal versus distal 50% enterectomy on nutritional parameters in rats preconditioned with a high-fat diet or regular chow

    OpenAIRE

    Ujwal R. Yanala; Roger D. Reidelberger; Jon S. Thompson; Valerie K. Shostrom; Mark A. Carlson

    2015-01-01

    Obesity may protect against the nutritional consequences of short bowel syndrome. We hypothesized that rats preconditioned with an obesogenic diet would have better outcomes after surgical induction of short bowel syndrome compared to rats on regular chow. Rats were fed a high-fat diet or regular rat chow for six months, and then underwent 50% proximal, 50% distal, or sham enterectomy. Food intake, weight, and body composition were monitored before and for 4 weeks after surgery. The high-fat ...

  6. Supporting Regularized Logistic Regression Privately and Efficiently.

    Science.gov (United States)

    Li, Wenfa; Liu, Hongzhe; Yang, Peng; Xie, Wei

    2016-01-01

    As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc.

  7. Multiple graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2013-10-01

    Non-negative matrix factorization (NMF) has been widely used as a data representation method based on components. To overcome the disadvantage of NMF in failing to consider the manifold structure of a data set, graph regularized NMF (GrNMF) has been proposed by Cai et al. by constructing an affinity graph and searching for a matrix factorization that respects graph structure. Selecting a graph model and its corresponding parameters is critical for this strategy. This process is usually carried out by cross-validation or discrete grid search, which are time consuming and prone to overfitting. In this paper, we propose a GrNMF, called MultiGrNMF, in which the intrinsic manifold is approximated by a linear combination of several graphs with different models and parameters inspired by ensemble manifold regularization. Factorization metrics and linear combination coefficients of graphs are determined simultaneously within a unified object function. They are alternately optimized in an iterative algorithm, thus resulting in a novel data representation algorithm. Extensive experiments on a protein subcellular localization task and an Alzheimer\\'s disease diagnosis task demonstrate the effectiveness of the proposed algorithm. © 2013 Elsevier Ltd. All rights reserved.

  8. Supporting Regularized Logistic Regression Privately and Efficiently.

    Directory of Open Access Journals (Sweden)

    Wenfa Li

    Full Text Available As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc.

  9. Maze navigation by honeybees: learning path regularity.

    Science.gov (United States)

    Zhang, S; Mizutani, A; Srinivasan, M V

    2000-01-01

    We investigated the ability of honeybees to learn mazes of four types: constant-turn mazes, in which the appropriate turn is always in the same direction in each decision chamber; zig-zag mazes, in which the appropriate turn is alternately left and right in successive decision chambers; irregular mazes, in which there is no readily apparent pattern to the turns; and variable irregular mazes, in which the bees were trained to learn several irregular mazes simultaneously. The bees were able to learn to navigate all four types of maze. Performance was best in the constant-turn mazes, somewhat poorer in the zig-zag mazes, poorer still in the irregular mazes, and poorest in the variable irregular mazes. These results demonstrate that bees do not navigate such mazes simply by memorizing the entire sequence of appropriate turns. Rather, performance in the various configurations depends on the existence of regularity in the structure of the maze and on the ease with which this regularity is recognized and learned.

  10. Handicap Labelings of 4-Regular Graphs

    Directory of Open Access Journals (Sweden)

    Petr Kovar

    2017-01-01

    Full Text Available Let G be a simple graph, let f : V(G→{1,2,...,|V(G|} be a bijective mapping. The weight of v ∈ V(G is the sum of labels of all vertices adjacent to v. We say that f is a distance magic labeling of G if the weight of every vertex is the same constant k and we say that f is a handicap magic labeling of G if the weight of every vertex v is l + f(v for some constant l. Graphs that allow such labelings are called distance magic or handicap, respectively. Distance magic and handicap labelings of regular graphs are used for scheduling incomplete tournaments. While distance magic labelings correspond to so called equalized tournaments, handicap labelings can be used to schedule incomplete tournaments that are more challenging to stronger teams or players, hence they increase competition and yield attractive schemes in which every games counts. We summarize known results on distance magic and handicap labelings and construct a new infinite class of 4-regular handicap graphs.

  11. From Regular to Strictly Locally Testable Languages

    Directory of Open Access Journals (Sweden)

    Stefano Crespi Reghizzi

    2011-08-01

    Full Text Available A classical result (often credited to Y. Medvedev states that every language recognized by a finite automaton is the homomorphic image of a local language, over a much larger so-called local alphabet, namely the alphabet of the edges of the transition graph. Local languages are characterized by the value k=2 of the sliding window width in the McNaughton and Papert's infinite hierarchy of strictly locally testable languages (k-slt. We generalize Medvedev's result in a new direction, studying the relationship between the width and the alphabetic ratio telling how much larger the local alphabet is. We prove that every regular language is the image of a k-slt language on an alphabet of doubled size, where the width logarithmically depends on the automaton size, and we exhibit regular languages for which any smaller alphabetic ratio is insufficient. More generally, we express the trade-off between alphabetic ratio and width as a mathematical relation derived from a careful encoding of the states. At last we mention some directions for theoretical development and application.

  12. Words cluster phonetically beyond phonotactic regularities.

    Science.gov (United States)

    Dautriche, Isabelle; Mahowald, Kyle; Gibson, Edward; Christophe, Anne; Piantadosi, Steven T

    2017-06-01

    Recent evidence suggests that cognitive pressures associated with language acquisition and use could affect the organization of the lexicon. On one hand, consistent with noisy channel models of language (e.g., Levy, 2008), the phonological distance between wordforms should be maximized to avoid perceptual confusability (a pressure for dispersion). On the other hand, a lexicon with high phonological regularity would be simpler to learn, remember and produce (e.g., Monaghan et al., 2011) (a pressure for clumpiness). Here we investigate wordform similarity in the lexicon, using measures of word distance (e.g., phonological neighborhood density) to ask whether there is evidence for dispersion or clumpiness of wordforms in the lexicon. We develop a novel method to compare lexicons to phonotactically-controlled baselines that provide a null hypothesis for how clumpy or sparse wordforms would be as the result of only phonotactics. Results for four languages, Dutch, English, German and French, show that the space of monomorphemic wordforms is clumpier than what would be expected by the best chance model according to a wide variety of measures: minimal pairs, average Levenshtein distance and several network properties. This suggests a fundamental drive for regularity in the lexicon that conflicts with the pressure for words to be as phonologically distinct as possible. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Flanking Variation Influences Rates of Stutter in Simple Repeats

    Directory of Open Access Journals (Sweden)

    August E. Woerner

    2017-11-01

    Full Text Available It has been posited that the longest uninterrupted stretch (LUS of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL. While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.

  14. Computer Simulation Studies of CTG Triplet Repeat Sequences

    Science.gov (United States)

    Rasaiah, Jayendran. C.; Lynch, Joshua

    1998-03-01

    Long segments of CTG trinucleotide repeats in human DNA are correlated with a class of neurological diseases (myotonic dystrophy, fragile-X syndrome, and Kenndy's disease). These diseases are characterized by genetic anticipation and are thought to arise from replication errors caused by unusual conformations of CTG repeat segments. We have studied the properties of a single short segment of double starnded DNA with CTG repeats in 0.5 M sodium chloride solution with molecular dynamics simulations. The simulations are carried out in the micro canonical ensemble using an all-atom force field with CHARMM parameters. The TIPS3 water model is used to simulate a molecular solvent. Electrostatic interactions are calculated by Ewald summation and the equations of motion integrated using a Verlet algorithm in conjunction with SHAKE constrained dynamics to maintain bond lengths. The simulation of CTG repeat sequence is compared with a control system containing CAG triplet repeats to determine possible differencesin the conformation and elasticity of the two sequences.

  15. Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

    Science.gov (United States)

    Järve, Mari; Zhivotovsky, Lev A.; Rootsi, Siiri; Help, Hela; Rogaev, Evgeny I.; Khusnutdinova, Elza K.; Kivisild, Toomas; Sanchez, Juan J.

    2009-01-01

    Background Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used. Principal Findings In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups. Conclusions Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies. PMID:19789645

  16. The Existence of Quasi Regular and Bi-Regular Self-Complementary 3-Uniform Hypergraphs

    Directory of Open Access Journals (Sweden)

    Kamble Lata N.

    2016-05-01

    Full Text Available A k-uniform hypergraph H = (V ;E is called self-complementary if there is a permutation σ : V → V , called a complementing permutation, such that for every k-subset e of V , e ∈ E if and only if σ(e ∉ E. In other words, H is isomorphic with H′ = (V ; V(k − E. In this paper we define a bi-regular hypergraph and prove that there exists a bi-regular self-complementary 3-uniform hypergraph on n vertices if and only if n is congruent to 0 or 2 modulo 4. We also prove that there exists a quasi regular self-complementary 3-uniform hypergraph on n vertices if and only if n is congruent to 0 modulo 4.

  17. Drug-drug interaction of microdose and regular-dose omeprazole with a CYP2C19 inhibitor and inducer.

    Science.gov (United States)

    Park, Gab-Jin; Bae, Soo Hyeon; Park, Wan-Su; Han, Seunghoon; Park, Min-Ho; Shin, Seok-Ho; Shin, Young G; Yim, Dong-Seok

    2017-01-01

    A microdose drug-drug interaction (DDI) study may be a valuable tool for anticipating drug interaction at therapeutic doses. This study aimed to compare the magnitude of DDIs at microdoses and regular doses to explore the applicability of a microdose DDI study. Six healthy male volunteer subjects were enrolled into each DDI study of omeprazole (victim) and known perpetrators: fluconazole (inhibitor) and rifampin (inducer). For both studies, the microdose (100 μg, cold compound) and the regular dose (20 mg) of omeprazole were given at days 0 and 1, respectively. On days 2-9, the inhibitor or inducer was given daily, and the microdose and regular dose of omeprazole were repeated at days 8 and 9, respectively. Full omeprazole pharmacokinetic samplings were performed at days 0, 1, 8, and 9 of both studies for noncompartmental analysis. The magnitude of the DDI, the geometric mean ratios (with perpetrator/omeprazole only) of maximum concentration (C max ) and area under the curve to the last measurement (AUC t ) of the microdose and the regular dose were compared. The geometric mean ratios in the inhibition study were: 2.17 (micro) and 2.68 (regular) for C max , and 4.07 (micro), 4.33 (regular) for AUC t . For the induction study, they were 0.26 (micro) and 0.21 (regular) for C max , and 0.16 (micro) and 0.15 (regular) for AUC t . There were no significant statistical differences in the magnitudes of DDIs between microdose and regular-dose conditions, regardless of induction or inhibition. Our results may be used as partial evidence that microdose DDI studies may replace regular-dose studies, or at least be used for DDI-screening purposes.

  18. Improving repeated sprint ability in young elite soccer players: repeated shuttle sprints vs. explosive strength training.

    Science.gov (United States)

    Buchheit, Martin; Mendez-Villanueva, Alberto; Delhomel, Gregory; Brughelli, Matt; Ahmaidi, Said

    2010-10-01

    To compare the effects of explosive strength (ExpS) vs. repeated shuttle sprint (RS) training on repeated sprint ability (RSA) in young elite soccer players, 15 elite male adolescents (14.5 ± 0.5 years) performed, in addition to their soccer training program, RS (n = 7) or ExpS (n = 8) training once a week for a total of 10 weeks. RS training consisted of 2-3 sets of 5-6 × 15- to 20-m repeated shuttle sprints interspersed with 14 seconds of passive or 23 seconds of active recovery (≈2 m·s⁻¹); ExpS training consisted of 4-6 series of 4-6 exercises (e.g., maximal unilateral countermovement jumps (CMJs), calf and squat plyometric jumps, and short sprints). Before and after training, performance was assessed by 10 and 30 m (10 and 30 m) sprint times, best (RSAbest) and mean (RSAmean) times on a repeated shuttle sprint ability test, a CMJ, and a hopping (Hop) test. After training, except for 10 m (p = 0.22), all performances were significantly improved in both groups (all p's < 0.05). Relative changes in 30 m (-2.1 ± 2.0%) were similar for both groups (p = 0.45). RS training induced greater improvement in RSAbest (-2.90 ± 2.1 vs. -0.08 ± 3.3%, p = 0.04) and tended to enhance RSAmean more (-2.61 ± 2.8 vs. -0.75 ± 2.5%, p = 0.10, effect size [ES] = 0.70) than ExpS. In contrast, ExpS tended to induce greater improvements in CMJ (14.8 ± 7.7 vs. 6.8 ± 3.7%, p = 0.02) and Hop height (27.5 ± 19.2 vs. 13.5 ± 13.2%, p = 0.08, ES = 0.9) compared with RS. Improvements in the repeated shuttle sprint test were only observed after RS training, whereas CMJ height was only increased after ExpS. Because RS and ExpS were equally efficient at enhancing maximal sprinting speed, RS training-induced improvements in RSA were likely more related to progresses in the ability to change direction.

  19. Analysis of bubble plume spacing produced by regular breaking waves

    Science.gov (United States)

    Phaksopa, J.; Haller, M. C.

    2012-12-01

    The breaking wave process in the ocean is a significant mechanism for energy dissipation, splash, and entrainment of air. The relationship between breaking waves and bubble plume characteristics is still a mystery because of the complexity of the breaking wave mechanism. This study takes a unique approach to quantitatively analyze bubble plumes produced by regular breaking waves. Various previous studies have investigated the formation and the characteristics of bubble plumes using either field observations, laboratory experiments, or numerical modeling However, in most observational work the plume characteristics have been studied from the underneath the water surface. In addition, though numerical simulations are able to include much of the important physics, the computational costs are high and bubble plume events are only simulated for short times. Hence, bubble plume evolution and generation throughout the surf zone is not yet computationally feasible. In the present work we take a unique approach to analyzing bubble plumes. These data may be of use for model/data comparisons as numerical simulations become more tractable. The remotely sensed video data from freshwater breaking waves in the OSU Large Wave Flume (Catalan and Haller, 2008) are analyzed. The data set contains six different regular wave conditions and the video intensity data are used to estimate the spacing of plume events (wavenumber spectrum), to calculate the spectral width (i.e. the range of plume spacing), and to relate these with the wave conditions. The video intensity data capture the evolution of the wave passage over a fixed bed arranged in a bar-trough morphology. Bright regions represent the moving path or trajectory coincident with bubble plume of each wave. It also shows the bubble foam were generated and released from wave crest shown in the form of bubble tails with almost regular spacing for each wave. The bubble tails show that most bubbles did not move along with wave. For the

  20. Coordinated hybrid automatic repeat request

    KAUST Repository

    Makki, Behrooz

    2014-11-01

    We develop a coordinated hybrid automatic repeat request (HARQ) approach. With the proposed scheme, if a user message is correctly decoded in the first HARQ rounds, its spectrum is allocated to other users, to improve the network outage probability and the users\\' fairness. The results, which are obtained for single- and multiple-antenna setups, demonstrate the efficiency of the proposed approach in different conditions. For instance, with a maximum of M retransmissions and single transmit/receive antennas, the diversity gain of a user increases from M to (J+1)(M-1)+1 where J is the number of users helping that user.

  1. Improving repeatability by improving quality

    Energy Technology Data Exchange (ETDEWEB)

    Ronen, Shuki; Ackers, Mark; Schlumberger, Geco-Prakla; Brink, Mundy

    1998-12-31

    Time lapse (4-D) seismic is a promising tool for reservoir characterization and monitoring. The method is apparently simple: to acquire data repeatedly over the same reservoir, process and interpret the data sets, then changes between the data sets indicate changes in the reservoir. A problem with time lapse seismic data is that reservoirs are a relatively small part of the earth and important reservoir changes may cause very small differences to the time lapse data. The challenge is to acquire and process economical time lapse data such that reservoir changes can be detected above the noise of varying acquisition and environment. 7 refs., 9 figs.

  2. The use of adomian decomposition method for solving the regularized long-wave equation

    Energy Technology Data Exchange (ETDEWEB)

    El-Danaf, Talaat S. [Department of Mathematics, Faculty of Science, Menoufia University, Shiben El-Kom (Egypt); Ramadan, Mohamed A. [Department of Mathematics, Faculty of Science, Menoufia University, Shiben El-Kom (Egypt)] e-mail: mramadan@mailer.eun.eg; Abd Alaal, Faysal E.I. [Department of Mathematics, Faculty of Science, Menoufia University, Shiben El-Kom (Egypt)

    2005-11-01

    In this paper, an accurate method to obtain an approximate numerical solution for the nonlinear regularized long-wave (in short RLW) equation is considered. The theoretical analysis of the method is investigated. The performance and the accuracy of the algorithm are illustrated by solving two test examples of the problem. The obtained results are presented and compared with the analytical solutions. It is observed that only few terms of the series expansion are required to obtain approximate solutions with good accuracy.

  3. Thermodynamics of regular accelerating black holes

    Science.gov (United States)

    Astorino, Marco

    2017-03-01

    Using the covariant phase space formalism, we compute the conserved charges for a solution, describing an accelerating and electrically charged Reissner-Nordstrom black hole. The metric is regular provided that the acceleration is driven by an external electric field, in spite of the usual string of the standard C-metric. The Smarr formula and the first law of black hole thermodynamics are fulfilled. The resulting mass has the same form of the Christodoulou-Ruffini irreducible mass. On the basis of these results, we can extrapolate the mass and thermodynamics of the rotating C-metric, which describes a Kerr-Newman-(A)dS black hole accelerated by a pulling string.

  4. Explicit formulas for regularized products and series

    CERN Document Server

    Jorgenson, Jay; Goldfeld, Dorian

    1994-01-01

    The theory of explicit formulas for regularized products and series forms a natural continuation of the analytic theory developed in LNM 1564. These explicit formulas can be used to describe the quantitative behavior of various objects in analytic number theory and spectral theory. The present book deals with other applications arising from Gaussian test functions, leading to theta inversion formulas and corresponding new types of zeta functions which are Gaussian transforms of theta series rather than Mellin transforms, and satisfy additive functional equations. Their wide range of applications includes the spectral theory of a broad class of manifolds and also the theory of zeta functions in number theory and representation theory. Here the hyperbolic 3-manifolds are given as a significant example.

  5. Generalized equations of state and regular universes

    CERN Document Server

    Contreras, Felipe; González, Esteban

    2015-01-01

    We found non singular solutions for universes filled with a fluid which obey a Generalized Equation of State of the form $P(\\rho)=-A\\rho+\\gamma\\rho^{\\lambda}$. An emergent universe is obtained if $A=1$ and $\\lambda =1/2$. If the matter source is reinterpret as that of a scalar matter field with some potential, the corresponding potential is derived. For a closed universe, an exact bounce solution is found for $A=1/3$ and the same $\\lambda $. We also explore how the composition of theses universes can be interpreted in terms of known fluids. It is of interest to note that accelerated solutions previously found for the late time evolution also represent regular solutions at early times.

  6. Regularity and Complexity in Dynamical Systems

    CERN Document Server

    Luo, Albert C J

    2012-01-01

    Regularity and Complexity in Dynamical Systems describes periodic and chaotic behaviors in dynamical systems, including continuous, discrete, impulsive,discontinuous, and switching systems. In traditional analysis, the periodic and chaotic behaviors in continuous, nonlinear dynamical systems were extensively discussed even if unsolved. In recent years, there has been an increasing amount of interest in periodic and chaotic behaviors in discontinuous dynamical systems because such dynamical systems are prevalent in engineering. Usually,the smoothening of discontinuous dynamical system is adopted in order to use the theory of continuous dynamical systems. However, such technique cannot provide suitable results in such discontinuous systems. In this book, an alternative way is presented to discuss the periodic and chaotic behaviors in discontinuous dynamical systems. This book also: Illustrates new concepts and methodology in discontinuous dynamical systems Uses different ideas to describe complicated dynamical...

  7. Regularization destriping of remote sensing imagery

    Directory of Open Access Journals (Sweden)

    R. Basnayake

    2017-07-01

    Full Text Available We illustrate the utility of variational destriping for ocean color images from both multispectral and hyperspectral sensors. In particular, we examine data from a filter spectrometer, the Visible Infrared Imaging Radiometer Suite (VIIRS on the Suomi National Polar Partnership (NPP orbiter, and an airborne grating spectrometer, the Jet Population Laboratory's (JPL hyperspectral Portable Remote Imaging Spectrometer (PRISM sensor. We solve the destriping problem using a variational regularization method by giving weights spatially to preserve the other features of the image during the destriping process. The target functional penalizes the neighborhood of stripes (strictly, directionally uniform features while promoting data fidelity, and the functional is minimized by solving the Euler–Lagrange equations with an explicit finite-difference scheme. We show the accuracy of our method from a benchmark data set which represents the sea surface temperature off the coast of Oregon, USA. Technical details, such as how to impose continuity across data gaps using inpainting, are also described.

  8. Regularization destriping of remote sensing imagery

    Science.gov (United States)

    Basnayake, Ranil; Bollt, Erik; Tufillaro, Nicholas; Sun, Jie; Gierach, Michelle

    2017-07-01

    We illustrate the utility of variational destriping for ocean color images from both multispectral and hyperspectral sensors. In particular, we examine data from a filter spectrometer, the Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi National Polar Partnership (NPP) orbiter, and an airborne grating spectrometer, the Jet Population Laboratory's (JPL) hyperspectral Portable Remote Imaging Spectrometer (PRISM) sensor. We solve the destriping problem using a variational regularization method by giving weights spatially to preserve the other features of the image during the destriping process. The target functional penalizes the neighborhood of stripes (strictly, directionally uniform features) while promoting data fidelity, and the functional is minimized by solving the Euler-Lagrange equations with an explicit finite-difference scheme. We show the accuracy of our method from a benchmark data set which represents the sea surface temperature off the coast of Oregon, USA. Technical details, such as how to impose continuity across data gaps using inpainting, are also described.

  9. Regularization of Instantaneous Frequency Attribute Computations

    Science.gov (United States)

    Yedlin, M. J.; Margrave, G. F.; Van Vorst, D. G.; Ben Horin, Y.

    2014-12-01

    We compare two different methods of computation of a temporally local frequency:1) A stabilized instantaneous frequency using the theory of the analytic signal.2) A temporally variant centroid (or dominant) frequency estimated from a time-frequency decomposition.The first method derives from Taner et al (1979) as modified by Fomel (2007) and utilizes the derivative of the instantaneous phase of the analytic signal. The second method computes the power centroid (Cohen, 1995) of the time-frequency spectrum, obtained using either the Gabor or Stockwell Transform. Common to both methods is the necessity of division by a diagonal matrix, which requires appropriate regularization.We modify Fomel's (2007) method by explicitly penalizing the roughness of the estimate. Following Farquharson and Oldenburg (2004), we employ both the L curve and GCV methods to obtain the smoothest model that fits the data in the L2 norm.Using synthetic data, quarry blast, earthquakes and the DPRK tests, our results suggest that the optimal method depends on the data. One of the main applications for this work is the discrimination between blast events and earthquakesFomel, Sergey. " Local seismic attributes." , Geophysics, 72.3 (2007): A29-A33.Cohen, Leon. " Time frequency analysis theory and applications." USA: Prentice Hall, (1995).Farquharson, Colin G., and Douglas W. Oldenburg. "A comparison of automatic techniques for estimating the regularization parameter in non-linear inverse problems." Geophysical Journal International 156.3 (2004): 411-425.Taner, M. Turhan, Fulton Koehler, and R. E. Sheriff. " Complex seismic trace analysis." Geophysics, 44.6 (1979): 1041-1063.

  10. The repeatability of sonographic measures of functional pelvic floor anatomy.

    Science.gov (United States)

    Tan, Li; Shek, Ka Lai; Atan, Ixora Kamisan; Rojas, Rodrigo Guzman; Dietz, Hans Peter

    2015-11-01

    Translabial 3D/4D ultrasound is increasingly being used in the diagnostic evaluation of pelvic floor dysfunction. The result of the assessment is influenced by a number of confounders that are generally unrecognised. The aim of this study was to determine the short- to medium-term repeatability of translabial ultrasound measures of female pelvic organ support and pelvic floor anatomy. This is a retrospective study analyzing archived ultrasound volume datasets of 106 patients with pelvic floor dysfunction. Every subject was assessed twice at an average interval of 73 days. Outcome measures including hiatal area on Valsalva, descent of the bladder neck, bladder, uterus and rectal ampulla, rectocele depth, diagnosis of true rectocele, and levator integrity (avulsion) were compared at the first and second appointments. All parameters of organ descent demonstrated good to excellent reliability (ICC 0.73-0.93) except for rectocele descent, which showed moderate reliability (ICC 0.44, CI 0.26-0.58). The most highly repeatable measure was hiatal area on Valsalva or "ballooning" (ICC 0.93, CI 0.90-0.95). For the diagnosis of levator avulsion and true rectocele, agreement was very high (kappa 0.91 for avulsion (CI 0.77-0.94) and kappa 0.73 (CI 0.56-0.84) for true rectocele). The short- to medium-term repeatability of translabial ultrasound measures of functional pelvic floor anatomy seems to be high. Hiatal area on Valsalva (ballooning) and diagnosis of levator avulsion were the most repeatable measures. The least repeatable measures related to the posterior compartment.

  11. Learning what from where: Effects of spatial regularity on nonspatial sequence learning and updating.

    Science.gov (United States)

    Filipowicz, Alex; Anderson, Britt; Danckert, James

    2014-01-01

    The current study examined the influence of redundant stimulus features on our ability to build and update representations of our environment. We hypothesized that our ability to process redundant spatial features would speed our ability to adapt to changing nonspatial regularities. Using a computerized version of the children's game "rock-paper-scissors", undergraduates were instructed to win as often as possible against a computer opponent. The computer's plays were repeating sequences of five choices that were presented either with spatial regularity (i.e., "rock" would always appear on the left, "paper" in the middle, and "scissors" on the right) or without spatial regularity (i.e., the items were equally likely to appear in any of the three locations). Once participants learned a sequence, the computer switched to a different sequence without participants being informed that a switch had occurred. Redundant spatial regularity improved a participant's ability both to learn sequences of plays and to update their plays to reflect new computer sequences. Our results suggest that our perceptual system is sensitive to redundant spatial stimulus features and that this information can improve learning and updating.

  12. Morphisms on infinite alphabets, countable states automata and regular sequences

    Science.gov (United States)

    Zhang, Jie-Meng; Chen, Jin; Guo, Ying-Jun; Wen, Zhi-Xiong

    2017-06-01

    In this paper, we prove that a class of regular sequences can be viewed as projections of fixed points of uniform morphisms on a countable alphabet, and also can be generated by countable states automata. Moreover, we prove that the regularity of some regular sequences is invariant under some codings.

  13. Exclusion of children with intellectual disabilities from regular ...

    African Journals Online (AJOL)

    Study investigated why teachers exclude children with intellectual disability from the regular classrooms in Nigeria. Participants were, 169 regular teachers randomly selected from Oyo and Ogun states. Questionnaire was used to collect data result revealed that 57.4% regular teachers could not cope with children with ID ...

  14. Solid-state power converter repeatability analysis

    CERN Document Server

    Dal Gobbo, Anthony; Aguglia, Davide

    2015-01-01

    This paper presents a method for evaluating power converter repeatability. The focus is on solid-state switch mode power converter for which the most problematic non-repeatability sources are the jitter of the drivers and of the switches leading to output voltage pulses bad repeatability. Both driver and switch turn-on and turn-off delay dispersion have been measured. These measurements confirm that the delay is Gaussian distributed and that the repeatability prediction method is valid.

  15. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  16. Contraceptive use among women seeking repeat abortion in Addis Ababa, Ethiopia.

    Science.gov (United States)

    Prata, Ndola; Holston, Martine; Fraser, Ashley; Melkamu, Yilma

    2013-12-01

    Limited access to modern contraceptives in populations that desire smaller families can lead to repeat unintended pregnancy and repeat abortions. We conducted an analysis of the medical records of 1,200 women seeking abortion-related services in public and private facilities in Addis Ababa, Ethiopia from October 2008 to February 2009. We examined the characteristics of initial and repeat abortion clients including prior contraceptive use and subsequent method selection. The incidence of repeat abortion was 30%. Compared with women seeking their first abortion, significantly more repeat abortion clients had ever used contraceptives and they were nearly twice as likely to leave the facility with a method. However, repeat abortion clients were significantly more likely to have ever used short-term reversible methods and to choose short-term methods post-abortion. Contraceptive counseling services for repeat abortion clients' should address reasons for previous contraceptive failure, discontinuation, or non-use. Post-abortion family planning services should be strengthened to help decrease repeat abortion.

  17. Repeated expansion in burn sequela.

    Science.gov (United States)

    Pitanguy, Ivo; Gontijo de Amorim, Natale Ferreira; Radwanski, Henrique N; Lintz, José Eduardo

    2002-08-01

    This paper presents a retrospective study of the use of 346 expanders in 132 patients operated at the Ivo Pitanguy Clinic, between the period of 1985 and 2000. The expanders were used in the treatment of burn sequela. In the majority of cases, more than one expander was used at the same time. In 42 patients, repeated tissue expansion was done. The re-expanded flaps demonstrated good distension and viability. With the increase in area at each new expansion, larger volume expanders were employed, achieving an adequate advancement of the flaps to remove the injured tissue. The great advantage of using tissue re-expansion in the burned patient is the reconstruction of extensive areas with the same color and texture of neighboring tissues, without the addition of new scars.

  18. Dynamically self-regular quantum harmonic black holes

    Directory of Open Access Journals (Sweden)

    Euro Spallucci

    2015-04-01

    Full Text Available The recently proposed UV self-complete quantum gravity program is a new and very interesting way to envision Planckian/trans-Planckian physics. In this new framework, high energy scattering is dominated by the creation of micro black holes, and it is experimentally impossible to probe distances shorter than the horizon radius. In this letter we present a model which realizes this idea through the creation of self-regular quantum black holes admitting a minimal size extremal configuration. Their radius provides a dynamically generated minimal length acting as a universal short-distance cutoff. We propose a quantization scheme for this new kind of microscopic objects based on a Bohr-like approach, which does not require a detailed knowledge of quantum gravity. The resulting black hole quantum picture resembles the energy spectrum of a quantum harmonic oscillator. The mass of the extremal configuration plays the role of zero-point energy. Large quantum number re-establishes the classical black hole description. Finally, we also formulate a “quantum hoop conjecture” which is satisfied by all the mass eigenstates and sustains the existence of quantum black holes sourced by Gaussian matter distributions.

  19. Iron status of regular voluntary blood donors

    Directory of Open Access Journals (Sweden)

    Mahida Vilsu

    2008-01-01

    Full Text Available Background: Our blood bank is a regional blood transfusion centre, which accepts blood only from voluntary donors. Aim: The aim is to study iron status of regular voluntary donors who donated their blood at least twice in a year. Materials and Methods: Prior to blood donation, blood samples of 220 male and 30 female voluntary donors were collected. Control included 100 each male and female healthy individuals in the 18- to 60-year age group, who never donated blood and did not have any chronic infection. In the study and control groups, about 10% subjects consumed non-vegetarian diet. After investigation, 85 males and 56 females having haemoglobin (Hb levels above 12.5 g/dl were selected as controls. Donors were divided into ≤10, 11-20, 21-50 and> 50 blood donation categories. Majority of the donors in> 50 donation category donated blood four times in a year, whereas the remaining donors donated two to three times per year. Haematological parameters were measured on fully automatic haematology analyzer, serum iron and total iron-binding capacity (TIBC by biochemical methods, ferritin using ELISA kits and transferrin using immunoturbidometry kits. Iron/TIBC ratio x 100 gave percentage of transferrin saturation value. Statistical Analysis: Statistical evaluation was done by mean, standard deviation, pair t -test, χ2 and anova ( F -test. Results: Preliminary analysis revealed that there was no significant difference in the iron profile of vegetarian and non-vegetarian subjects or controls and the donors donating < 20 times. Significant increase or decrease was observed in mean values of various haematological and iron parameters in donors who donated blood for> 20 times ( P < 0.001, compared to controls. Anaemia, iron deficiency and depletion of iron stores were more prevalent in female donors ( P < 0.05 compared to males and especially in those male donors who donated their blood for more than 20 times. Conclusion: Regular voluntary blood

  20. Accreting fluids onto regular black holes via Hamiltonian approach

    Energy Technology Data Exchange (ETDEWEB)

    Jawad, Abdul [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); Shahzad, M.U. [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); University of Central Punjab, CAMS, UCP Business School, Lahore (Pakistan)

    2017-08-15

    We investigate the accretion of test fluids onto regular black holes such as Kehagias-Sfetsos black holes and regular black holes with Dagum distribution function. We analyze the accretion process when different test fluids are falling onto these regular black holes. The accreting fluid is being classified through the equation of state according to the features of regular black holes. The behavior of fluid flow and the existence of sonic points is being checked for these regular black holes. It is noted that the three-velocity depends on critical points and the equation of state parameter on phase space. (orig.)

  1. Multiconductor Short/Open Cable Tester

    Science.gov (United States)

    Eichenberg, Dennis

    1994-01-01

    Frequent or regular testing of multiconductor cables terminated in multipin conductors tedious, if not impossible, task. This inexpensive circuit simplifies open/short testing and is amenable to automation. In operation, pair of connectors selected to match pair of connectors installed on each of cables to be tested. As many connectors accommodated as required, and each can have as many conductors as required. Testing technique implemented with this circuit automated easily with electronic controls and computer interface. Printout provides status of each conductor in cable, indicating which, if any, of conductors has open or short circuit.

  2. Acute effects of strength exercises and effects of regular strength training on cell free DNA concentrations in blood plasma

    Science.gov (United States)

    Tross, Anna-Katharina; Hegen, Patrick; Neuberger, Elmo Wanja Immanuel; Helmig, Susanne; Schöllhorn, Wolfgang; Simon, Perikles

    2017-01-01

    Creatine kinase (CK) is a marker for muscle cell damage with limited potential as marker for training load in strength training. Recent exercise studies identified cell free DNA (cfDNA) as a marker for aseptic inflammation and cell damage. Here we overserved in a pilot study the acute effects during strength exercise and chronic effects of regular strength training on cfDNA concentrations over a period of four weeks in three training groups applying conservation training (CT) at 60% of the 1 repetition maximum, high intensity-low repetition training (HT) at 90% of the 1 repetition maximum and differential training (DT) at 60% of the 1 repetition maximum. EDTA-plasma samples were collected before every training session, and on the first and last training day repeatedly after every set of exercises. CfDNA increased significantly by 1.62-fold (mean (±SD) before first exercise: 8.31 (2.84) ng/ml, after last exercise 13.48 (4.12) ng/ml) across all groups within a single training session (ptraining session only at day two with a subsequent return to baseline (ptraining procedures did not cause any alterations in CK. Our results suggest that during strength exercise short-fragmented cfDNA is released, reflecting a fast, aseptic inflammatory response, while elevation of longer fragments at baseline on day two seemed to reflect mild cellular damage due to a novel training regime. We critically discuss the implications of our findings for future evaluations of cfDNA as a marker for training load in strength training. PMID:28910365

  3. A regularity-based modeling of oil borehole logs

    Science.gov (United States)

    Gaci, Said; Zaourar, Naima

    2013-04-01

    Multifractional Brownian motions (mBms) are successfully used to describe borehole logs behavior. These local fractal models allow to investigate the depth-evolution of regularity of the logs, quantified by the Hölder exponent (H). In this study, a regularity analysis is carried out on datasets recorded in Algerian oil boreholes located in different geological settings. The obtained regularity profiles show a clear correlation with lithology. Each lithological discontinuity corresponds to a jump in H value. Moreover, for a given borehole, all the regularity logs are significantly correlated and lead to similar lithological segmentations. Therefore, the Hölderian regularity is a robust property which can be used to characterize lithological heterogeneities. However, this study does not draw any relation between the recorded physical property and its estimated regularity degree for all the analyzed logs. Keywords: well logs, regularity, Hölder exponent, multifractional Brownian motion

  4. Regularities and irregularities in order flow data

    Science.gov (United States)

    Theissen, Martin; Krause, Sebastian M.; Guhr, Thomas

    2017-11-01

    We identify and analyze statistical regularities and irregularities in the recent order flow of different NASDAQ stocks, focusing on the positions where orders are placed in the order book. This includes limit orders being placed outside of the spread, inside the spread and (effective) market orders. Based on the pairwise comparison of the order flow of different stocks, we perform a clustering of stocks into groups with similar behavior. This is useful to assess systemic aspects of stock price dynamics. We find that limit order placement inside the spread is strongly determined by the dynamics of the spread size. Most orders, however, arrive outside of the spread. While for some stocks order placement on or next to the quotes is dominating, deeper price levels are more important for other stocks. As market orders are usually adjusted to the quote volume, the impact of market orders depends on the order book structure, which we find to be quite diverse among the analyzed stocks as a result of the way limit order placement takes place.

  5. Flip to Regular Triangulation and Convex Hull.

    Science.gov (United States)

    Gao, Mingcen; Cao, Thanh-Tung; Tan, Tiow-Seng

    2017-02-01

    Flip is a simple and local operation to transform one triangulation to another. It makes changes only to some neighboring simplices, without considering any attribute or configuration global in nature to the triangulation. Thanks to this characteristic, several flips can be independently applied to different small, non-overlapping regions of one triangulation. Such operation is favored when designing algorithms for data-parallel, massively multithreaded hardware, such as the GPU. However, most existing flip algorithms are designed to be executed sequentially, and usually need some restrictions on the execution order of flips, making them hard to be adapted to parallel computation. In this paper, we present an in depth study of flip algorithms in low dimensions, with the emphasis on the flexibility of their execution order. In particular, we propose a series of provably correct flip algorithms for regular triangulation and convex hull in 2D and 3D, with implementations for both CPUs and GPUs. Our experiment shows that our GPU implementation for constructing these structures from a given point set achieves up to two orders of magnitude of speedup over other popular single-threaded CPU implementation of existing algorithms.

  6. Regularities development of entrepreneurial structures in regions

    Directory of Open Access Journals (Sweden)

    Julia Semenovna Pinkovetskaya

    2012-12-01

    Full Text Available Consider regularities and tendencies for the three types of entrepreneurial structures — small enterprises, medium enterprises and individual entrepreneurs. The aim of the research was to confirm the possibilities of describing indicators of aggregate entrepreneurial structures with the use of normal law distribution functions. Presented proposed by the author the methodological approach and results of construction of the functions of the density distribution for the main indicators for the various objects: the Russian Federation, regions, as well as aggregates ofentrepreneurial structures, specialized in certain forms ofeconomic activity. All the developed functions, as shown by the logical and statistical analysis, are of high quality and well-approximate the original data. In general, the proposed methodological approach is versatile and can be used in further studies of aggregates of entrepreneurial structures. The received results can be applied in solving a wide range of problems justify the need for personnel and financial resources at the federal, regional and municipal levels, as well as the formation of plans and forecasts of development entrepreneurship and improvement of this sector of the economy.

  7. Toroidal regularization of the guiding center Lagrangian

    Science.gov (United States)

    Burby, J. W.; Ellison, C. L.

    2017-11-01

    In the Lagrangian theory of guiding center motion, an effective magnetic field B*=B +(m /e )v∥∇× b appears prominently in the equations of motion. Because the parallel component of this field can vanish, there is a range of parallel velocities where the Lagrangian guiding center equations of motion are either ill-defined or very badly behaved. Moreover, the velocity dependence of B* greatly complicates the identification of canonical variables and therefore the formulation of symplectic integrators for guiding center dynamics. This letter introduces a simple coordinate transformation that alleviates both these problems simultaneously. In the new coordinates, the Liouville volume element is equal to the toroidal contravariant component of the magnetic field. Consequently, the large-velocity singularity is completely eliminated. Moreover, passing from the new coordinate system to canonical coordinates is extremely simple, even if the magnetic field is devoid of flux surfaces. We demonstrate the utility of this approach in regularizing the guiding center Lagrangian by presenting a new and stable one-step variational integrator for guiding centers moving in arbitrary time-dependent electromagnetic fields.

  8. Identifying Cognitive States Using Regularity Partitions.

    Science.gov (United States)

    Pappas, Ioannis; Pardalos, Panos

    2015-01-01

    Functional Magnetic Resonance (fMRI) data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality.

  9. Identifying Cognitive States Using Regularity Partitions.

    Directory of Open Access Journals (Sweden)

    Ioannis Pappas

    Full Text Available Functional Magnetic Resonance (fMRI data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality.

  10. Regularity and approximability of electronic wave functions

    CERN Document Server

    Yserentant, Harry

    2010-01-01

    The electronic Schrödinger equation describes the motion of N-electrons under Coulomb interaction forces in a field of clamped nuclei. The solutions of this equation, the electronic wave functions, depend on 3N variables, with three spatial dimensions for each electron. Approximating these solutions is thus inordinately challenging, and it is generally believed that a reduction to simplified models, such as those of the Hartree-Fock method or density functional theory, is the only tenable approach. This book seeks to show readers that this conventional wisdom need not be ironclad: the regularity of the solutions, which increases with the number of electrons, the decay behavior of their mixed derivatives, and the antisymmetry enforced by the Pauli principle contribute properties that allow these functions to be approximated with an order of complexity which comes arbitrarily close to that for a system of one or two electrons. The text is accessible to a mathematical audience at the beginning graduate level as...

  11. Multiparametric tissue abnormality characterization using manifold regularization

    Science.gov (United States)

    Batmanghelich, Kayhan; Wu, Xiaoying; Zacharaki, Evangelia; Markowitz, Clyde E.; Davatzikos, Christos; Verma, Ragini

    2008-03-01

    Tissue abnormality characterization is a generalized segmentation problem which aims at determining a continuous score that can be assigned to the tissue which characterizes the extent of tissue deterioration, with completely healthy tissue being one end of the spectrum and fully abnormal tissue such as lesions, being on the other end. Our method is based on the assumptions that there is some tissue that is neither fully healthy or nor completely abnormal but lies in between the two in terms of abnormality; and that the voxel-wise score of tissue abnormality lies on a spatially and temporally smooth manifold of abnormality. Unlike in a pure classification problem which associates an independent label with each voxel without considering correlation with neighbors, or an absolute clustering problem which does not consider a priori knowledge of tissue type, we assume that diseased and healthy tissue lie on a manifold that encompasses the healthy tissue and diseased tissue, stretching from one to the other. We propose a semi-supervised method for determining such as abnormality manifold, using multi-parametric features incorporated into a support vector machine framework in combination with manifold regularization. We apply the framework towards the characterization of tissue abnormality to brains of multiple sclerosis patients.

  12. One-dimensional QCD in thimble regularization

    Science.gov (United States)

    Di Renzo, F.; Eruzzi, G.

    2018-01-01

    QCD in 0 +1 dimensions is numerically solved via thimble regularization. In the context of this toy model, a general formalism is presented for S U (N ) theories. The sign problem that the theory displays is a genuine one, stemming from a (quark) chemical potential. Three stationary points are present in the original (real) domain of integration, so that contributions from all the thimbles associated to them are to be taken into account: we show how semiclassical computations can provide hints on the regions of parameter space where this is absolutely crucial. Known analytical results for the chiral condensate and the Polyakov loop are correctly reproduced: this is in particular trivial at high values of the number of flavors Nf. In this regime we notice that the single thimble dominance scenario takes place (the dominant thimble is the one associated to the identity). At low values of Nf computations can be more difficult. It is important to stress that this is not at all a consequence of the original sign problem (not even via the residual phase). The latter is always under control, while accidental, delicate cancelations of contributions coming from different thimbles can be in place in (restricted) regions of the parameter space.

  13. ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

    NARCIS (Netherlands)

    Luo, H.; Lin, K.; David, A.; Nijveen, H.; Leunissen, J.A.M.

    2012-01-01

    ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85

  14. Repeated high-intensity running and sprinting in elite women’s soccer competition

    OpenAIRE

    Gabbett, Tim J.; Wiig, Håvard; Spencer, Matt

    2013-01-01

    Background: To the authors’ knowledge, no study has investigated the concurrent repeated, high-intensity (RHIA) and repeated-sprint activity (RSA) of intermittent team-sport competition. Purpose: In this study, they report on the RSA of elite women’s football competition. In addition, they describe the nature of RHIA (eg, striding and sprinting activities) that involve a high energy cost and are associated with short (ie, ≤20 s) recovery periods. Methods: Thirteen elite women soccer players u...

  15. Suppression of Repeat-Intensive False Targets Based on Temporal Pulse Diversity

    OpenAIRE

    Lu, Gang; Chen, Yongqiang; Lei, Yu; Gui, Guan

    2013-01-01

    This paper considers the problem of suppressing the repeat-intensive false targets produced by a deception electronic attack (EA) system equipped with a Digital Radio Frequency Memory (DRFM) device. Different from a conventional repeat jammer, this type of jamming intensively retransmits the intercepted signal stored in a DRFM to the victim radar in a very short time-delay interval relative to a radar pulse wide. A multipeak matched-filtering output is then produced other than the merely expe...

  16. Elementary Particle Spectroscopy in Regular Solid Rewrite

    Science.gov (United States)

    Trell, Erik

    2008-10-01

    The Nilpotent Universal Computer Rewrite System (NUCRS) has operationalized the radical ontological dilemma of Nothing at All versus Anything at All down to the ground recursive syntax and principal mathematical realisation of this categorical dichotomy as such and so governing all its sui generis modalities, leading to fulfilment of their individual terms and compass when the respective choice sequence operations are brought to closure. Focussing on the general grammar, NUCRS by pure logic and its algebraic notations hence bootstraps Quantum Mechanics, aware that it "is the likely keystone of a fundamental computational foundation" also for e.g. physics, molecular biology and neuroscience. The present work deals with classical geometry where morphology is the modality, and ventures that the ancient regular solids are its specific rewrite system, in effect extensively anticipating the detailed elementary particle spectroscopy, and further on to essential structures at large both over the inorganic and organic realms. The geodetic antipode to Nothing is extension, with natural eigenvector the endless straight line which when deployed according to the NUCRS as well as Plotelemeian topographic prescriptions forms a real three-dimensional eigenspace with cubical eigenelements where observed quark-skewed quantum-chromodynamical particle events self-generate as an Aristotelean phase transition between the straight and round extremes of absolute endlessness under the symmetry- and gauge-preserving, canonical coset decomposition SO(3)×O(5) of Lie algebra SU(3). The cubical eigen-space and eigen-elements are the parental state and frame, and the other solids are a range of transition matrix elements and portions adapting to the spherical root vector symmetries and so reproducibly reproducing the elementary particle spectroscopy, including a modular, truncated octahedron nano-composition of the Electron which piecemeal enter into molecular structures or compressed to each

  17. Chaos and Regularity in the Doubly Magic Nucleus 208Pb

    Science.gov (United States)

    Dietz, B.; Heusler, A.; Maier, K. H.; Richter, A.; Brown, B. A.

    2017-01-01

    High-resolution experiments have recently lead to a complete identification (energy, spin, and parity) of 151 nuclear levels up to an excitation energy of Ex=6.20 MeV in 208Pb [Heusler et al., Phys. Rev. C 93, 054321 (2016), 10.1103/PhysRevC.93.054321]. We present a thorough study of the fluctuation properties in the energy spectra of the unprecedented set of nuclear bound states. In a first approach, we group states with the same spin and parity into 14 subspectra, analyze standard statistical measures for short- and long-range correlations, i.e., the nearest-neighbor spacing distribution, the number variance Σ2, the Dyson-Mehta Δ3 statistics, and the novel distribution of the ratios of consecutive spacings of adjacent energy levels in each energy sequence, and then compute their ensemble average. Their comparison with a random matrix ensemble which interpolates between Poisson statistics expected for regular systems and the Gaussian orthogonal ensemble (GOE) predicted for chaotic systems shows that the data are well described by the GOE. In a second approach, following an idea of Rosenzweig and Porter [Phys. Rev. 120, 1698 (1960), 10.1103/PhysRev.120.1698], we consider the complete spectrum composed of the independent subspectra. We analyze their fluctuation properties using the method of Bayesian inference involving a quantitative measure, called the chaoticity parameter f , which also interpolates between Poisson (f =0 ) and GOE statistics (f =1 ). It turns out to be f ≈0.9 . This is so far the closest agreement with a GOE observed in the spectra of bound states in a nucleus. The same analysis is also performed with spectra computed on the basis of shell model calculations with different interactions (surface-delta interaction, Kuo-Brown, Michigan-three-Yukawa). While the simple surface-delta interaction exhibits features typical for nuclear many-body systems with regular dynamics, the other, more realistic interactions yield chaoticity parameters f close

  18. Repeated Maxima of Sunspot Cycles

    Science.gov (United States)

    Krivodubskij, V.

    2015-12-01

    The explanation for the observed phenomenon of repeated maxima of sunspot cycles is proposed. Key roles in the proposed scenarioplay two tides of toroidal field from the lower base of the solar convection zone (SCZ) to the surface. Deep toroidal field is excited due to Ω-effectnear the bottom of the SCZ at the beginning of the cycle. Then this field is transported to the surface due to combined acting of magnetic buoyancy,magnetic ∇ρ-flow and turbulent diamagnetism in the equatorial domain. Over time the magnetic fragments can be seen as bipolar spots in themiddle latitudes in the "royal zone". This first wave of toroidal field, which is directed up, gives the main maximum activity spots. However, theunderlying toroidal field in the high-latitude polar domains at the beginning of the cycle is blocked by directed downward magnetic∇ρ-pumping and turbulent diamagnetism. Directed to the equator deep meridional flow replaces this field to the low latitudes (the equatorialdomain) during about 1 - 2 years. After that the turn of floating this "retarded" field to surface (second tide of toroidal field). Coming to the surfaceat low latitudes this second portion of toroidal field leads to second sunspot maximum.

  19. Repeats and EST analysis for new organisms

    Directory of Open Access Journals (Sweden)

    Jonassen Inge

    2008-01-01

    Full Text Available Abstract Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms. There are few studies that investigate the effectiveness of this approach, or attempt to evaluate the different methods for identifying and masking repeats. Results Using zebrafish and medaka as example organisms, we show that accurate repeat masking is an important factor for obtaining a high quality clustering. Furthermore, we show that masking with standard repeat libraries based on curated genomic information from other species has little or no positive effect on the quality of the resulting EST clustering. Library based repeat masking which often constitutes a computational bottleneck in the EST analysis pipeline can therefore be reduced to species specific repeat libraries, or perhaps eliminated entirely. In contrast, substantially improved results can be achived by applying a repeat library derived from a partial reference clustering (e.g., from mapping sequences against a partially sequenced genome. Conclusion Of the methods explored, we find that the best EST clustering is achieved after masking with repeat libraries that are species specific. In the absence of such libraries, library-less masking gives results superior to the current practice of using cross-species, genome-based libraries.

  20. Highly specific contractions of a single CAG/CTG trinucleotide repeat by TALEN in yeast.

    Science.gov (United States)

    Richard, Guy-Franck; Viterbo, David; Khanna, Varun; Mosbach, Valentine; Castelain, Lauriane; Dujon, Bernard

    2014-01-01

    Trinucleotide repeat expansions are responsible for more than two dozens severe neurological disorders in humans. A double-strand break between two short CAG/CTG trinucleotide repeats was formerly shown to induce a high frequency of repeat contractions in yeast. Here, using a dedicated TALEN, we show that induction of a double-strand break into a CAG/CTG trinucleotide repeat in heterozygous yeast diploid cells results in gene conversion of the repeat tract with near 100% efficacy, deleting the repeat tract. Induction of the same TALEN in homozygous yeast diploids leads to contractions of both repeats to a final length of 3-13 triplets, with 100% efficacy in cells that survived the double-strand breaks. Whole-genome sequencing of surviving yeast cells shows that the TALEN does not increase mutation rate. No other CAG/CTG repeat of the yeast genome showed any length alteration or mutation. No large genomic rearrangement such as aneuploidy, segmental duplication or translocation was detected. It is the first demonstration that induction of a TALEN in an eukaryotic cell leads to shortening of trinucleotide repeat tracts to lengths below pathological thresholds in humans, with 100% efficacy and very high specificity.