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Sample records for relevant smaller sequence

  1. Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai

    International Nuclear Information System (INIS)

    Nakai, Madoka; Goto, Chie; Kang, Won Kyung; Shikata, Masamitsu; Luque, Teresa; Kunimi, Yasuhisa

    2003-01-01

    Adoxophyes honmai nucleopolyhedrovirus (AdhoNPV) has a distinctive pathology in A. honmai larvae, killing the host more slowly than other NPVs. To further understand the pathology of AdhoNPV, its genome was completely sequenced and compared with those of other baculoviruses. The AdhoNPV genome is 113,220 bp, with a G + C content of 35.6%. It contains 125 putative open reading frames (ORFs), of which 8 are unique to AdhoNPV, and 4 homologous regions. The other 117 ORFs display similarity to previously characterized baculovirus genes involved in early and late gene expression, DNA replication, and structural and auxiliary functions. The phylogenetic position of AdhoNPV, in relation to 15 other baculoviruses whose genomes have been completely sequenced, was assessed by three different analyses: gene sequence, gene order, and gene content. Although gene content analysis failed to support the group II NPVs, phylogenetic trees based on gene sequence and gene order showed AdhoNPV to be closely related to the group II NPVs

  2. Pierre Robin sequence: case report, the relevance of autopsy

    Directory of Open Access Journals (Sweden)

    Cristiano C. Oliveira

    2015-10-01

    Full Text Available ABSTRACTPierre Robin sequence is a neonatal disorder characterized by micrognathism, glossoptosis and cleft palate. We reported an autopsy case of a child whose malformations of the oropharynx were identified only at birth. The child was extremely preterm with severe neonatal depression and poor recovery, and the orofacial alterations prevented the correct treatment. There was facial disorder characterized by micrognathia associated with cleft palate and posterior displacement of the tongue, compressing the vallecula, structurally compatible with glossoptosis. This autopsy surpassed the scientific and epidemiological relevance, allowing the family genetic counseling and close monitoring of a subsequent pregnancy.

  3. Sequencing of the Cheese Microbiome and Its Relevance to Industry

    Directory of Open Access Journals (Sweden)

    Bhagya. R. Yeluri Jonnala

    2018-05-01

    Full Text Available The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

  4. Whole-Exome Sequencing Reveals Clinically Relevant Variants in Family Affected with Autism Spectrum Disorder

    Directory of Open Access Journals (Sweden)

    Jiaxiu Zhou

    2016-10-01

    Full Text Available Chromosomal microarray (CMA has been suggested as a first tier clinical diagnostic test for ASD. High-throughput sequencing (HTS has associated hundreds of genes associated with ASD. Whole Exome Sequencing (WES was used in combination with CMA to identify clinically-relevant ASD variants. In prior work, a trio-based (father, mother, and proband WGS (Whole Genome Sequencing was used to reveal clinically-relevant de novo, or inherited, rare variants in half (16 / 32 of the ASD families in which all probands had normal, or VOUS (Variant of Uncertain Clinical Significance, CMA results. In this study, after CMA screening chromosome structural abnormalities of a proband affected with ASD, a WES was performed on the patient and parents. Some rare de novo, and inherited, variants were detected using trio-based bioinformatics analysis. ASD variants were ranked by SFARI Gene score, HPO (human phenotype ontology, protein function damage, and manual searching PubMed. Sanger sequencing was used to validated some candidate variants in family members. A de novo homozygous mutation in SPG11 (p.C209F, two inherited, compound-heterozygote mutations in SCN9A (p.Q10R and p.R1893H and BEST1 (p.A135V and p.A297V were confirmed. Heterozygous mutations in TSC1 (p.S487C and SHANK2 (p.Arg569His inherited from mother were also confirmed.

  5. PrionHome: a database of prions and other sequences relevant to prion phenomena.

    Directory of Open Access Journals (Sweden)

    Djamel Harbi

    Full Text Available Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions, prionoids (i.e., proteins that propagate like prions between individual cells, and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant, and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments. We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic

  6. PrionHome: a database of prions and other sequences relevant to prion phenomena.

    Science.gov (United States)

    Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M A; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M

    2012-01-01

    Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing

  7. Effects of informed consent for individual genome sequencing on relevant knowledge.

    Science.gov (United States)

    Kaphingst, K A; Facio, F M; Cheng, M-R; Brooks, S; Eidem, H; Linn, A; Biesecker, B B; Biesecker, L G

    2012-11-01

    Increasing availability of individual genomic information suggests that patients will need knowledge about genome sequencing to make informed decisions, but prior research is limited. In this study, we examined genome sequencing knowledge before and after informed consent among 311 participants enrolled in the ClinSeq™ sequencing study. An exploratory factor analysis of knowledge items yielded two factors (sequencing limitations knowledge; sequencing benefits knowledge). In multivariable analysis, high pre-consent sequencing limitations knowledge scores were significantly related to education [odds ratio (OR): 8.7, 95% confidence interval (CI): 2.45-31.10 for post-graduate education, and OR: 3.9; 95% CI: 1.05, 14.61 for college degree compared with less than college degree] and race/ethnicity (OR: 2.4, 95% CI: 1.09, 5.38 for non-Hispanic Whites compared with other racial/ethnic groups). Mean values increased significantly between pre- and post-consent for the sequencing limitations knowledge subscale (6.9-7.7, p benefits knowledge subscale (7.0-7.5, p < 0.0001); increase in knowledge did not differ by sociodemographic characteristics. This study highlights gaps in genome sequencing knowledge and underscores the need to target educational efforts toward participants with less education or from minority racial/ethnic groups. The informed consent process improved genome sequencing knowledge. Future studies could examine how genome sequencing knowledge influences informed decision making. © 2012 John Wiley & Sons A/S.

  8. Preliminary notes on dual relevance of ITS sequences and pigments in Hygrocybe taxonomy .

    NARCIS (Netherlands)

    Babos, M.; Halász, K.; Zagyva, T.; Zöld-Balogh, Á.; Szegö, D.; Bratek, Z.

    2011-01-01

    The relationships based on ITS sequences of 48 Hygrocybe s.l. specimens were studied and compared with previously described taxonomic groups. Our specimens formed two well separated genetic groups. The first one includes the species characterized by vivid yellow and red colours, while species

  9. Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

    Science.gov (United States)

    Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

    2016-01-01

    The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

  10. Preliminary notes on dual relevance of ITS sequences and pigments in Hygrocybe taxonomy.

    Science.gov (United States)

    Babos, M; Halász, K; Zagyva, T; Zöld-Balogh, A; Szegő, D; Bratek, Z

    2011-06-01

    The relationships based on ITS sequences of 48 Hygrocybe s.l. specimens were studied and compared with previously described taxonomic groups. Our specimens formed two well separated genetic groups. The first one includes the species characterized by vivid yellow and red colours, while species belonging to other clades were pallid or pale brown, and in most cases with pink or olive tones. This separation is supported by the presence of muscaflavin pigments among some species referred to Hygrocybe (Bresinsky & Kronawitter 1986). The subgenera distinguished by morphological features can be relatively well recognized on phylogenetic trees, however, the majority of sections were not supported. Variability in the ITS region of Hygrocybe species is unusually high. In some cases sequences differed by more than 25 %, and the lengths of ITS regions also showed large differences. Taxa that were considered as closely related, e.g. the H. conica aggregate, were found to have identical or highly similar sequences. Our results seem to confirm the taxonomic concept of Bresinsky (2008) who proposed the division of the genus Hygrocybe. Hence H. calyptriformis and all examined members of subg. Gliophorus (H. irrigata, H. laeta, H. nitrata, H. psittacina) and subg. Cuphophyllus could be excluded from the genus Hygrocybe s.str. Based on these results further research using DNA markers at the intergeneric level is suggested to revaluate the taxonomy of former Hygrocybe species.

  11. Sequence variation of the feline immunodeficiency virus genome and its clinical relevance.

    Science.gov (United States)

    Stickney, A L; Dunowska, M; Cave, N J

    2013-06-08

    The ongoing evolution of feline immunodeficiency virus (FIV) has resulted in the existence of a diverse continuum of viruses. FIV isolates differ with regards to their mutation and replication rates, plasma viral loads, cell tropism and the ability to induce apoptosis. Clinical disease in FIV-infected cats is also inconsistent. Genomic sequence variation of FIV is likely to be responsible for some of the variation in viral behaviour. The specific genetic sequences that influence these key viral properties remain to be determined. With knowledge of the specific key determinants of pathogenicity, there is the potential for veterinarians in the future to apply this information for prognostic purposes. Genomic sequence variation of FIV also presents an obstacle to effective vaccine development. Most challenge studies demonstrate acceptable efficacy of a dual-subtype FIV vaccine (Fel-O-Vax FIV) against FIV infection under experimental settings; however, vaccine efficacy in the field still remains to be proven. It is important that we discover the key determinants of immunity induced by this vaccine; such data would compliment vaccine field efficacy studies and provide the basis to make informed recommendations on its use.

  12. Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing

    OpenAIRE

    Romero-Hidalgo, Sandra; Ochoa-Leyva, Adrián; Garcíarrubio, Alejandro; Acuña-Alonzo, Victor; Antúnez-Argüelles, Erika; Balcazar-Quintero, Martha; Barquera-Lozano, Rodrigo; Carnevale, Alessandra; Cornejo-Granados, Fernanda; Fernández-López, Juan Carlos; García-Herrera, Rodrigo; García-Ortíz, Humberto; Granados-Silvestre, Ángeles; Granados, Julio; Guerrero-Romero, Fernando

    2017-01-01

    Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained bel...

  13. Synchrotron radiation gives insight in smaller and smaller crystals

    International Nuclear Information System (INIS)

    Hintsches, E.

    1983-01-01

    Scientists from the ''Max-Planck-Institut fuer Festkoerperforschung'' in Stuttgart have extended the method of X-ray analysis to study the structure of very small crystals. For the first time a crystal with 6 μm linear dimension has been successfully analysed using the synchrotron radiation from the DESY electron synchrotron at Hamburg. Thus this important method of analysis has been demonstrated to be usefull for structural studies of crystals, which are smaller by a factor of 20 than hitherto. (orig.) [de

  14. Peripheral blood transcriptome sequencing reveals rejection-relevant genes in long-term heart transplantation.

    Science.gov (United States)

    Chen, Yan; Zhang, Haibo; Xiao, Xue; Jia, Yixin; Wu, Weili; Liu, Licheng; Jiang, Jun; Zhu, Baoli; Meng, Xu; Chen, Weijun

    2013-10-03

    Peripheral blood-based gene expression patterns have been investigated as biomarkers to monitor the immune system and rule out rejection after heart transplantation. Recent advances in the high-throughput deep sequencing (HTS) technologies provide new leads in transcriptome analysis. By performing Solexa/Illumina's digital gene expression (DGE) profiling, we analyzed gene expression profiles of PBMCs from 6 quiescent (grade 0) and 6 rejection (grade 2R&3R) heart transplant recipients at more than 6 months after transplantation. Subsequently, quantitative real-time polymerase chain reaction (qRT-PCR) was carried out in an independent validation cohort of 47 individuals from three rejection groups (ISHLT, grade 0,1R, 2R&3R). Through DGE sequencing and qPCR validation, 10 genes were identified as informative genes for detection of cardiac transplant rejection. A further clustering analysis showed that the 10 genes were not only effective for distinguishing patients with acute cardiac allograft rejection, but also informative for discriminating patients with renal allograft rejection based on both blood and biopsy samples. Moreover, PPI network analysis revealed that the 10 genes were connected to each other within a short interaction distance. We proposed a 10-gene signature for heart transplant patients at high-risk of developing severe rejection, which was found to be effective as well in other organ transplant. Moreover, we supposed that these genes function systematically as biomarkers in long-time allograft rejection. Further validation in broad transplant population would be required before the non-invasive biomarkers can be generally utilized to predict the risk of transplant rejection. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  15. Chernobyl birds have smaller brains.

    Directory of Open Access Journals (Sweden)

    Anders Pape Møller

    2011-02-01

    Full Text Available Animals living in areas contaminated by radioactive material from Chernobyl suffer from increased oxidative stress and low levels of antioxidants. Therefore, normal development of the nervous system is jeopardized as reflected by high frequencies of developmental errors, reduced brain size and impaired cognitive abilities in humans. Alternatively, associations between psychological effects and radiation have been attributed to post-traumatic stress in humans.Here we used an extensive sample of 550 birds belonging to 48 species to test the prediction that even in the absence of post-traumatic stress, there is a negative association between relative brain size and level of background radiation. We found a negative association between brain size as reflected by external head volume and level of background radiation, independent of structural body size and body mass. The observed reduction in brain size in relation to background radiation amounted to 5% across the range of almost a factor 5,000 in radiation level. Species differed significantly in reduction in brain size with increasing background radiation, and brain size was the only morphological character that showed a negative relationship with radiation. Brain size was significantly smaller in yearlings than in older individuals.Low dose radiation can have significant effects on normal brain development as reflected by brain size and therefore potentially cognitive ability. The fact that brain size was smaller in yearlings than in older individuals implies that there was significant directional selection on brain size with individuals with larger brains experiencing a viability advantage.

  16. Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences

    Directory of Open Access Journals (Sweden)

    Ji-Yong An

    2016-01-01

    Full Text Available We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM model and Local Phase Quantization (LPQ to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM, reducing the influence of noise using a Principal Component Analysis (PCA, and using a Relevance Vector Machine (RVM based classifier. We perform 5-fold cross-validation experiments on Yeast and Human datasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM classifier on the Yeast dataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.

  17. Improving irrigation efficiency : the need for a relevant sequence of the management tools

    Science.gov (United States)

    Fayolle, Y.

    2009-04-01

    With 70 % of worldwide withdrawals, irrigation efficiency is a key issue in the overall problem of water resources. Management of water dedicated to agriculture should be improved to secure food production and save water to deal with increasing domestic and industrial demands. This paper is based on the results of a collaborative research project conducted in India with a local NGO (the Aga Khan Rural Support Programme, AKRSP(I)) during which GIS were tested. It is aimed at analyzing the efficiency of water usage in a water development programme conducted by the partner NGO in the semi-arid margins of Gujarat state. The analysis raises the question of the articulation of legal, institutional, economical, and technical tools to improve water efficiency. The NGO supervises the construction of surface water harvesting structures for irrigation purposes. Following a participatory approach, it creates and trains user groups to which the management of dams would then be devolved. User group membership depends on financial contribution to the building costs. A legal vacuum regarding surface water management combined with unequal investment capacities favor the concentration of water resources in the hands of a limited number of farmers. This causes low water use efficiency, irrigation choices being mostly oriented to high water consumptive crops and recipient farmers showing no interest in investing in water saving techniques. Our observations favor equality of access and paying more attention to the sequence in which management tools are articulated. On a national scale, as a prerequisite, water user rights as well as NGO's intervention legal framework should be clarified. On a project scale, before construction, information systems could help to identify all potential beneficiaries and optimize equality of access. It aims at reducing the volume of water per farmer to encourage them to irrigate low water consumptive crops and invest in water saving techniques. Depending

  18. Collage of Saturn's smaller satellites

    Science.gov (United States)

    1981-01-01

    This family portrait shows the smaller satellites of Saturn as viewed by Voyager 2 during its swing through the Saturnian system. The following chart corresponds to this composite photograph (distance from the planet increases from left to right) and lists names, standard numerical designations and approximate dimensions (radii where indicated) in kilometers: 1980S26Outer F-ringshepherd120 X 100 1980S1Leadingco-orbital220 X 160 1980S25TrailingTethys trojanradii: 25 1980S28Outer Ashepherdradii: 20 1980S27Inner F-ringco-orbital145 X 70 1980S3TrailingTethys trojan140 X 100 1980S13LeadingTethys trojanradii: 30 1980S6LeadingDione trojanradii: 30 These images have been scaled to show the satellites in true relative sizes. This set of small objects ranges in size from small asteroidal scales to nearly the size of Saturn's moon Mimas. They are probably fragments of somewhat larger bodies broken up during the bombardment period that followed accretion of the Saturnian system. Scientists believe they may be mostly icy bodies with a mixture of meteorite rock. They are somewhat less reflective than the larger satellites, suggesting that thermal evolution of the larger moons 'cleaned up' their icy surfaces. The Voyager project is managed for NASA by the Jet Propulsion Laboratory, Pasadena, Calif.

  19. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection

    Directory of Open Access Journals (Sweden)

    Xin Ma

    2015-01-01

    Full Text Available The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR method, followed by incremental feature selection (IFS. We incorporated features of conjoint triad features and three novel features: binding propensity (BP, nonbinding propensity (NBP, and evolutionary information combined with physicochemical properties (EIPP. The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient. High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

  20. Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors12

    Science.gov (United States)

    Hovelson, Daniel H.; McDaniel, Andrew S.; Cani, Andi K.; Johnson, Bryan; Rhodes, Kate; Williams, Paul D.; Bandla, Santhoshi; Bien, Geoffrey; Choppa, Paul; Hyland, Fiona; Gottimukkala, Rajesh; Liu, Guoying; Manivannan, Manimozhi; Schageman, Jeoffrey; Ballesteros-Villagrana, Efren; Grasso, Catherine S.; Quist, Michael J.; Yadati, Venkata; Amin, Anmol; Siddiqui, Javed; Betz, Bryan L.; Knudsen, Karen E.; Cooney, Kathleen A.; Feng, Felix Y.; Roh, Michael H.; Nelson, Peter S.; Liu, Chia-Jen; Beer, David G.; Wyngaard, Peter; Chinnaiyan, Arul M.; Sadis, Seth; Rhodes, Daniel R.; Tomlins, Scott A.

    2015-01-01

    Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with 95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts. PMID:25925381

  1. Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

    Directory of Open Access Journals (Sweden)

    Marco Scortichini

    2010-11-01

    Full Text Available Forty-five Xanthomonas arboricola pv. juglandis (Xaj strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST, using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity.

  2. RVMAB: Using the Relevance Vector Machine Model Combined with Average Blocks to Predict the Interactions of Proteins from Protein Sequences

    Directory of Open Access Journals (Sweden)

    Ji-Yong An

    2016-05-01

    Full Text Available Protein-Protein Interactions (PPIs play essential roles in most cellular processes. Knowledge of PPIs is becoming increasingly more important, which has prompted the development of technologies that are capable of discovering large-scale PPIs. Although many high-throughput biological technologies have been proposed to detect PPIs, there are unavoidable shortcomings, including cost, time intensity, and inherently high false positive and false negative rates. For the sake of these reasons, in silico methods are attracting much attention due to their good performances in predicting PPIs. In this paper, we propose a novel computational method known as RVM-AB that combines the Relevance Vector Machine (RVM model and Average Blocks (AB to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the AB feature representation on a Position Specific Scoring Matrix (PSSM, reducing the influence of noise using a Principal Component Analysis (PCA, and using a Relevance Vector Machine (RVM based classifier. We performed five-fold cross-validation experiments on yeast and Helicobacter pylori datasets, and achieved very high accuracies of 92.98% and 95.58% respectively, which is significantly better than previous works. In addition, we also obtained good prediction accuracies of 88.31%, 89.46%, 91.08%, 91.55%, and 94.81% on other five independent datasets C. elegans, M. musculus, H. sapiens, H. pylori, and E. coli for cross-species prediction. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM classifier on the yeast dataset. The experimental results demonstrate that our RVM-AB method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool. To facilitate extensive studies for future proteomics research, we developed

  3. 75 FR 35881 - Smaller Learning Communities Program

    Science.gov (United States)

    2010-06-23

    ... Part II Department of Education Smaller Learning Communities Program; Notice #0;#0;Federal... EDUCATION Smaller Learning Communities Program Catalog of Federal Domestic Assistance (CFDA) Number: 84.215L. AGENCY: Office of Elementary and Secondary Education, Department of Education. ACTION: Notice of final...

  4. Storm Sewage Dilution in Smaller Streams

    DEFF Research Database (Denmark)

    Larsen, Torben; Vestergaard, Kristian

    1987-01-01

    A numerical model has been used to show how dilution in smaller streams can be effected by unsteady hydraulic conditions caused by a storm sewage overflow.......A numerical model has been used to show how dilution in smaller streams can be effected by unsteady hydraulic conditions caused by a storm sewage overflow....

  5. Proceedings of the relevance of mass spectrometry to DNA sequence determination: Research needs for the Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    Edmonds, C.G.; Smith, R.D. (Pacific Northwest Lab., Richland, WA (USA)); Smith, L.M. (Wisconsin Univ., Madison, WI (USA))

    1990-11-01

    A workshop was sponsored for the US Department of Energy (DOE), Office of Health and Environmental Research by Pacific Northwest Laboratory, April 4--5, 1990, in Seattle, Washington, to examine the potential role of mass spectrometry in the joint DOE/National Institutes of Health (NIH) Human Genome Program. The workshop was occasioned by recent developments in mass spectrometry that are providing new levels for selectivity, sensitivity, and, in particular, new methods of ionization appropriate for large biopolymers such as DNA. During discussions, three general mass spectrometric approaches to the determination of DNA sequence were considered: (1) the mass spectrometric detection of isotopic labels from DNA sequencing mixtures separated using gel electrophoresis, (2) the direct mass spectrometric analysis from direct ionization of unfractionated sequencing mixtures where the measured mass of the constituents functions to identify and order the base sequence (replacing separation by gel electrophoresis), and (3) an approach in which a single highly charged molecular ion of a large DNA segment produced is rapidly sequenced in an ion cyclotron resonance ion trap. The consensus of the workshop was that, on the basis of the new developments, mass spectrometry has the potential to provide the substantial increases in sequencing speed required for the Human Genome Program. 66 refs., 3 tabs.

  6. Unit size limitations in smaller power systems

    International Nuclear Information System (INIS)

    McConnach, J.S.

    1975-01-01

    The developing nations have generally found it an economic necessity to accept the minimum commercial size limit of 600 MWe. Smaller reactor sizes tendered as 'one off' specials carry high specific cost penalties which considerably weaken the competitiveness of nuclear versus conventional thermal plants. The revised IAEA market survey for nuclear power in developing countries (1974 edition) which takes account of the recent heavy escalation in oil prices, indicates a reasonable market for smaller size reactors in the range 150 MWe to 400 MWe, but until this market is approached seriously by manufacturers, the commercial availability and economic viability of smaller size reactors remains uncertain. (orig.) [de

  7. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

    Science.gov (United States)

    Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

    2017-09-26

    Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

  8. Smaller sized reactors can be economically attractive

    International Nuclear Information System (INIS)

    Carelli, M.D.; Petrovic, B.; Mycoff, C.W.; Trucco, P.; Ricotti, M.E.; Locatelli, G.

    2007-01-01

    Smaller size reactors are going to be an important component of the worldwide nuclear renaissance. However, a misguided interpretation of the economy of scale would label these reactors as not economically competitive with larger plants because of their allegedly higher capital cost (dollar/kWe). Economy of scale does apply only if the considered designs are similar, which is not the case here. This paper identifies and briefly discusses the various factors which, beside size (power produced), contribute to determining the capital cost of smaller reactors and provides a preliminary evaluation for a few of these factors. When they are accounted for, in a set of realistic and comparable configurations, the final capital costs of small and large plants are practically equivalent. The Iris reactor is used as the example of smaller reactors, but the analysis and conclusions are applicable to the whole spectrum of small nuclear plants. (authors)

  9. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

    Directory of Open Access Journals (Sweden)

    Niedzica Camacho

    2017-09-01

    Full Text Available A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA in human cancer. Our study employs Whole Genome DNA Sequence (WGS data from tumor samples (n = 103 to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%, Chr6q27 (16.50% and Chr18q12.3 (17.48%. Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40. We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

  10. Do parents leave a smaller carbon footprint?

    DEFF Research Database (Denmark)

    Nordström, Leif Jonas; Shogren, Jason F.; Thunström, Linda

    Do parents leave a smaller carbon footprint? While becoming a parent is transformational as one focuses more on the future, the time constraints are more binding right now. Using a unique data set that allows us to compare CO2 emissions from Swedish two-adult households with and without children......, we find becoming a Swedish parent causes a person to leave a larger carbon ootprint—due to changes in transportation patterns and food consumption choices....

  11. RNA sequencing analysis of transcriptional change in the freshwater mussel Elliptio complanata after environmentally relevant sodium chloride exposure.

    Science.gov (United States)

    Robertson, Laura S; Galbraith, Heather S; Iwanowicz, Deborah; Blakeslee, Carrie J; Cornman, R Scott

    2017-09-01

    To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled sodium chloride (NaCl) exposures. Ribonucleic acid sequencing (RNA-Seq) of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for 7 d, of which 290 had nonoverlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism. The rate-limiting enzyme for synthesis of taurine, an amino acid frequently linked to osmotic stress in aquatic species, was upregulated, as was the transmembrane ion pump sodium/potassium adenosine 5'-triphosphatase. These patterns confirm a primary transcriptional response to the experimental dose, albeit likely overlapping with nonspecific secondary stress responses. Substantial involvement of the heat shock protein 70 chaperone family and the water-transporting aquaporin family was not detected, however, in contrast to some studies in other bivalves. A subset of the most significantly regulated genes was confirmed by quantitative polymerase chain reaction in an independent sample. Cluster analysis showed separation of mussels exposed to 2 ppt NaCl from control mussels in multivariate space, but mussels exposed to 1 ppt NaCl were largely indistinguishable from controls. Transcriptome-scale analysis of salt exposure under laboratory conditions efficiently identified candidate biomarkers for further functional analysis and field validation. Environ Toxicol Chem 2017;36:2352-2366. © Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. © 2017 SETAC.

  12. Economic characteristics of a smaller, simpler reactor

    International Nuclear Information System (INIS)

    LaBar, M.; Bowers, H.

    1988-01-01

    Reduced load growth and heightened concern with economic risk has led to an expressed utility preference for smaller capacity additions. The Modular High Temperature Reactor (MHTGR) plant has been developed as a small, simple plant that has limited financial risk and is economically competitive with comparatively sized coal plants. Competitive economics is achieved by the simplifications made possible in a small MHTGR, reduction in the quantity of nuclear grade construction and design standardization and certification. Assessments show the MHTGR plant to have an economic advantage over coal plants for plant sizes from 270 MWe to 1080 MWe. Financial risk is limited by small unit sizes and short lead times that allow incremental deployment. Evaluations show the MHTGR incremental deployment capability to reduce negative cash flows by almost a factor of 2 relative to that required by a single large nuclear plant

  13. Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

    Directory of Open Access Journals (Sweden)

    Xiang Li-xin

    2010-08-01

    Full Text Available Abstract Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host

  14. Marketing healthcare: lessons for smaller hospitals.

    Science.gov (United States)

    Chowdhary, N R

    2000-02-01

    Recently, I have noted ubiquitous trends that lead me to conclude that we are on the brink of a fundamental change in the structure of healthcare delivery. Hospitals are changing. The hospital, that enduring and pervasive organization, which for decades has delivered the vast majority of acute care services is being re-conceptualized. Administrators and executives in today's hospitals are beginning to recognize the disaffection of constituents and the necessity to change from placing their own agenda or that of their profession over the needs of the customer. A lesson that is increasingly being heeded, particularly by the leading hospitals, is that a belief in one's own importance or a feeling of invulnerability represents an anachronistic stance. No hospital today can afford to retain a view that it is more important than the patients it serves, or that it is invulnerable. The external pressures are already clear--the actors, factors and forces in the external environment are forcing hospitals to re-evaluate efficiency, effectiveness and delivery arrangements. The rise to prominence of the outcomes movement is part of this trend. The present study was an attempt to assess the practices and trends in the modern smaller hospitals as a part of their strategy to match the competitive pressures.

  15. Development of a Targeted Next-Generation Sequencing Assay to Detect Diagnostically Relevant Mutations of JAK2, CALR, and MPL in Myeloproliferative Neoplasms.

    Science.gov (United States)

    Frawley, Thomas; O'Brien, Cathal P; Conneally, Eibhlin; Vandenberghe, Elisabeth; Percy, Melanie; Langabeer, Stephen E; Haslam, Karl

    2018-02-01

    The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of mutations in these genes has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for mutations in these genes in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms. Polymerase chain reaction (PCR) primers were designed to target mutation hotspots in JAK2 exon 14, JAK2 exon 12, MPL exon 10, and CALR exon 9. Multiplexed PCR conditions were optimized by using qualitative PCR followed by NGS. Diagnostic genomic DNA from 35 MPN patients, known to harbor driver mutations in one of the target genes, was used to validate the assay. One hundred percent concordance was observed between the previously-identified mutations and those detected by NGS, with no false positives, nor any known mutations missed (specificity = 100%, CI = 0.96, sensitivity = 100%, CI = 0.89). Improved resolution of mutation sequences was also revealed by NGS analysis. Detection of diagnostically relevant driver mutations of MPN is enhanced by employing a targeted multiplex NGS approach. This assay presents a robust solution to classical MPN mutation screening, providing an alternative to time-consuming sequential analyses.

  16. Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Steven D.; Klingeman, Dawn M.; Johnson, Courtney M.; Clum, Alicia; Aerts, Andrea; Salamov, Asaf; Sharma, Aditi; Zane, Matthew; Barry, Kerrie; Grigoriev, Igor V.; Davison, Brian H.; Lynd, Lee R.; Gilna, Paul; Hau, Heidi; Hogsett, David A.; Froehlich, Allan C.

    2013-04-19

    Saccharomyces cerevisiae strain M3707 was isolated from a sample of commercial distillers yeast, and its genome sequence together with the genome sequences for the four derived haploid strains M3836, M3837, M3838, and M3839 has been determined. Yeasts have potential for consolidated bioprocessing (CBP) for biofuel production, and access to these genome sequences will facilitate their development.

  17. Biodegradation of hydrocarbon mixtures in surface waters at environmentally relevant levels - Effect of inoculum origin on kinetics and sequence of degradation.

    Science.gov (United States)

    Birch, Heidi; Hammershøj, Rikke; Comber, Mike; Mayer, Philipp

    2017-10-01

    Biodegradation is a dominant removal process for many organic pollutants, and biodegradation tests serve as tools for assessing their environmental fate within regulatory risk assessment. In simulation tests, the inoculum is not standardized, varying in microbial quantity and quality, thereby potentially impacting the observed biodegradation kinetics. In this study we investigated the effect of inoculum origin on the biodegradation kinetics of hydrocarbons for five inocula from surface waters varying in urbanization and thus expected pre-exposure to petroleum hydrocarbons. A new biodegradation method for testing mixtures of hydrophobic chemicals at trace concentrations was demonstrated: Aqueous solutions containing 9 hydrocarbons were generated by passive dosing and diluted with surface water resulting in test systems containing native microorganisms exposed to test substances at ng-μg/L levels. Automated Headspace Solid Phase Microextraction coupled to GC-MS was applied directly to these test systems to determine substrate depletion relative to abiotic controls. Lag phases were generally less than 8 days. First order rate constants were within one order of magnitude for each hydrocarbon in four of the five waters but lower in water from a rural lake. The sequence of degradation between the 9 hydrocarbons showed similar patterns in the five waters indicating the potential for using selected hydrocarbons for benchmarking between biodegradation tests. Degradation half-times were shorter than or within one order of magnitude of BioHCwin predictions for 8 of 9 hydrocarbons. These results showed that location choice is important for biodegradation kinetics and can provide a relevant input to aquatic exposure and fate models. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Ten Indicators of Vitality in Smaller Academic Libraries

    Science.gov (United States)

    Pappas, David

    2009-01-01

    This paper provides a means of quickly ascertaining the relative health of smaller academic libraries by presenting a top ten list of vitality indicators. The list is based on an observational convenience sampling of thirty smaller academic libraries across the United States. The indicators making the list were those which appeared most often in…

  19. 13 CFR 107.710 - Requirement to finance smaller enterprises.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Requirement to finance smaller enterprises. 107.710 Section 107.710 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL... Small Business for Sbic Financing § 107.710 Requirement to finance smaller enterprises. Your Portfolio...

  20. Designing a Smaller Power Inverter: the Google Littlebox Challenge - Text

    Science.gov (United States)

    Version | Energy Systems Integration Facility | NREL Designing a Smaller Power Inverter: the Google Littlebox Challenge - Text Version er Power Inverter: the Google Littlebox Challenge - Text Version Below is the text version for the Designing a Smaller Power Inverter: the Google Littlebox

  1. Trends and patterns in smaller companies: The Danish perspective

    DEFF Research Database (Denmark)

    Ulhøi, John Parm; Madsen, Henning

    2000-01-01

    This paper presents the empirical findings of a recent survey of Danish managers, with a special focus on managers in smaller companies. The survey, called the 'Danish Management Barometer', is part of a joint research programme between the Aarhus School of Business and the Danish Association...

  2. The Underreported Use of Integrated Marketing Communication by Smaller Businesses.

    Science.gov (United States)

    Johnson, Ed

    This research suggests integrated marketing communication (IMC) is widely used by small business. In a survey of Midwest businesses, it was found that smaller business tend to integrate their marketing communication to the same extent as do larger businesses. Their advertising, P.R., and sales promotion are as likely to present a unified message,…

  3. Healthcare security staffing for smaller facilities: where science meets art.

    Science.gov (United States)

    Warren, Bryan

    2013-01-01

    Obtaining effective security resourcing and staffing for smaller healthcare facilities presents many difficulties, according to the author In this article, he provides guidance to security practitioners on taking existing data and translating it into a language that administration will understand and appreciate.

  4. Library Homepage Design at Smaller Bachelor of Arts Institutions

    Science.gov (United States)

    Jones, Scott L.; Leonard, Kirsten

    2011-01-01

    This study examined the homepages of the libraries of 175 smaller bachelor of arts institutions, coding for the presence of 98 design elements. By reporting and examining the frequency of these features, the authors noted what is and is not common practice at these libraries. They found that only fourteen elements were present on at least half of…

  5. Implementation Study of Smaller Learning Communities. Final Report

    Science.gov (United States)

    Bernstein, Lawrence; Millsap, Mary Ann; Schimmenti, Jennifer; Page, Lindsay

    2008-01-01

    The Smaller Learning Communities (SLC) program was established in response to growing national concerns about students too often lost and alienated in large, impersonal high schools, as well as concerns about school safety and low levels of achievement and graduation for many students. Authorized under the "Elementary and Secondary Education Act,"…

  6. A real-time PCR assay with improved specificity for detection and discrimination of all clinically relevant Bordetella species by the presence and distribution of three Insertion Sequence elements

    Directory of Open Access Journals (Sweden)

    Ossewaarde Jacobus M

    2011-01-01

    Full Text Available Abstract Background In Dutch laboratories molecular detection of B. pertussis and B. parapertussis is commonly based on insertion sequences IS481 and IS1001, respectively. Both IS elements are more widely spread among Bordetella species. Both Bordetella holmesii, and B. bronchiseptica can harbour IS481. Also, IS1001 is found among B. bronchiseptica. IS481, and IS1001 based PCR thus lacks specificity when used for detection of specific Bordetella spp. Findings We designed a PCR based on IS1002, another IS element that is present among Bordetella species, and exploited it as a template in combination with PCR for IS481, and IS1001. In combining the PCRs for IS481, IS1001, and IS1002, and including an inhibition control, we were able to detect and discriminate all clinically relevant Bordetella species. Conclusions We developed an improved PCR method for specific detection of B. pertussis, B. parapertussis, B. holmesii, and B. bronchiseptica.

  7. Smaller superior temporal gyrus volume specificity in schizotypal personality disorder

    Science.gov (United States)

    Goldstein, Kim E.; Hazlett, Erin A.; New, Antonia S.; Haznedar, M. Mehmet; Newmark, Randall E.; Zelmanova, Yuliya; Passarelli, Vincent; Weinstein, Shauna R.; Canfield, Emily L.; Meyerson, David A.; Tang, Cheuk Y.; Buchsbaum, Monte S.; Siever, Larry J.

    2009-01-01

    Background Superior temporal gyrus (STG/BA22) volume is reduced in schizophrenia and to a milder degree in schizotypal personality disorder (SPD), representing a less severe disorder in the schizophrenia-spectrum. SPD and Borderline personality disorder (BPD) are severe personality disorders characterized by social and cognitive dysfunction. However, while SPD is characterized by social withdrawal/anhedonia, BPD is marked by hyper-reactivity to interpersonal stimuli and hyper-emotionality. This is the first morphometric study to directly compare SPD and BPD patients in temporal volume. Methods We compared three age-gender- and education-matched groups: 27 unmedicated SPD individuals with no BPD traits, 52 unmedicated BPD individuals with no SPD traits, and 45 healthy controls. We examined gray matter volume of frontal and temporal lobe Brodmann areas (BAs), and dorsal/ventral amygdala from 3T magnetic resonance imaging. Results In the STG, an auditory association area reported to be dysfunctional in SPD and BPD, the SPD patients had significantly smaller volume than healthy controls and BPD patients. No group differences were found between BPD patients and controls. Smaller BA22 volume was associated with greater symptom severity in SPD patients. Reduced STG volume may be an important endophenotype for schizophrenia-spectrum disorders. SPD is distinct from BPD in terms of STG volume abnormalities which may reflect different underlying pathophysiological mechanisms and could help discriminate between them. PMID:19473820

  8. Forensic age estimation by magnetic resonance imaging of the knee: the definite relevance in bony fusion of the distal femoral- and the proximal tibial epiphyses using closest-to-bone T1 TSE sequence

    Energy Technology Data Exchange (ETDEWEB)

    Ottow, Christian; Heindel, Walter [University Hospital Muenster, Department of Clinical Radiology, Muenster (Germany); Schulz, Ronald; Pfeiffer, Heidi; Schmeling, Andreas [University Hospital Muenster, Institute of Legal Medicine, Muenster (Germany); Vieth, Volker [University Hospital Muenster, Department of Clinical Radiology, Muenster (Germany); Klinikum Ibbenbueren, Clinic for Radiology, Ibbenbueren (Germany)

    2017-12-15

    To clarify the relevance of the bony fusion of the distal femoral and the proximal tibial epiphyses by means of magnetic resonance imaging (MRI), a prospective cross-sectional cohort study was performed with a special focus on a reliable determination of the 14th, 16th and 18th years of life. We scanned 658 German volunteers in the age bracket 12-24 years using a 3.0 T MR-scanner and utilising a T1 turbo spin-echo sequence representing true bone anatomy. Minimum, maximum, mean ± standard deviation and median with lower and upper quartiles were defined. Intra- and interobserver agreements were determined (Cohen's kappa). The statistical relevance of sex-related differences was analysed (Mann-Whitney U test, p < 0.05, exact, two-sided). The bony fusion took place before the 18th year of life in both epiphyses. The Mann-Whitney U test results imply significant sex-related differences for most stages. For both epiphyses, the intra observer (κ femur 0.961; tibia 0.971) and interobserver (κ femur 0.941; tibia 0.951) agreement levels were very good. The 14th and the 16th years of life can be determined in both sexes, but the completion of the 18th year of life cannot solely be determined by the bony fusion, as depicted by closest-to-bone MRI. (orig.)

  9. Forensic age estimation by magnetic resonance imaging of the knee: the definite relevance in bony fusion of the distal femoral- and the proximal tibial epiphyses using closest-to-bone T1 TSE sequence

    International Nuclear Information System (INIS)

    Ottow, Christian; Heindel, Walter; Schulz, Ronald; Pfeiffer, Heidi; Schmeling, Andreas; Vieth, Volker

    2017-01-01

    To clarify the relevance of the bony fusion of the distal femoral and the proximal tibial epiphyses by means of magnetic resonance imaging (MRI), a prospective cross-sectional cohort study was performed with a special focus on a reliable determination of the 14th, 16th and 18th years of life. We scanned 658 German volunteers in the age bracket 12-24 years using a 3.0 T MR-scanner and utilising a T1 turbo spin-echo sequence representing true bone anatomy. Minimum, maximum, mean ± standard deviation and median with lower and upper quartiles were defined. Intra- and interobserver agreements were determined (Cohen's kappa). The statistical relevance of sex-related differences was analysed (Mann-Whitney U test, p < 0.05, exact, two-sided). The bony fusion took place before the 18th year of life in both epiphyses. The Mann-Whitney U test results imply significant sex-related differences for most stages. For both epiphyses, the intra observer (κ femur 0.961; tibia 0.971) and interobserver (κ femur 0.941; tibia 0.951) agreement levels were very good. The 14th and the 16th years of life can be determined in both sexes, but the completion of the 18th year of life cannot solely be determined by the bony fusion, as depicted by closest-to-bone MRI. (orig.)

  10. The Application of Systemic Safety for Smaller Nuclear Installations

    International Nuclear Information System (INIS)

    Ward, J.

    2016-01-01

    This paper will provide an outline of ARPANSA’s approach to systemic safety as applied to smaller hazard nuclear installations. It will describe ARPANSA’s effort to enable licence holders to better understand the principles of systemic safety so that they may make improvements for themselves. In regard to human and organizational factors, inspections are more often used to highlight areas where performance can be improved to meet best practice rather than strictly as a compliance tool. This takes account of a graded, risk informed approach and is undertaken in a collaborative way that places a premium on openness, clarity, reliability and efficiency. The paper will discuss the challenges faced by the approach, and how ARPANSA is currently managing these. It will describe ARPANSA’s regulatory guidance and inspection processes. The significant stages in ARPANSA development of the systemic approach are provided briefly in the following paragraphs.

  11. Automated Polarimetry with Smaller Aperture Telescopes: The ROVOR Observatory

    Directory of Open Access Journals (Sweden)

    Joseph Moody

    2017-10-01

    Full Text Available To better understand possible blazar jet mechanisms and morphologies, brighter prototypical objects are regularly monitored for variability in optical broad-band light. If the monitoring filters are polarized, the position angles and polarization percentages can be measured and their evolution monitored over time. However, building up a statistically significant time base of polarization parameters requires the arduous task of monitoring sources for months or years to catch and follow interesting events such as flares. Fortunately, monitoring an object is easily done using remotely operated or robotic telescopes. The Remote Observatory for Variable Object Research (ROVOR is a small-aperture telescope that has monitored blazars in broad-band Johnson filters since 2009. Calibration data using a set of four plane-polarized filters suggest that it is suitable for polarimetric monitoring as well. We have successfully collected data on CTA 102 and are encouraged at the prospects of monitoring it and other similar objects. Long-term monitoring campaigns are a scientifically and educationally-effective use of underutilized smaller-aperture telescopes.

  12. More, smaller bacteria in response to ocean's warming?

    KAUST Repository

    Moran, Xose Anxelu G.

    2015-06-10

    Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (-1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oligotrophic taxa may severely impact marine foodwebs and carbon fluxes by an overall decrease in the efficiency of the biological pump. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  13. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species.

    Science.gov (United States)

    Arbefeville, S; Harris, A; Ferrieri, P

    2017-09-01

    Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU r

  14. Radiocarbon evidence for a smaller oceanic carbon dioxide sink than previously believed

    Science.gov (United States)

    Hesshaimer, Vago; Heimann, Martin; Levin, Ingeborg

    1994-07-01

    RADIOCARBON produced naturally in the upper atmosphere or arti-ficially during nuclear weapons testing is the main tracer used to validate models of oceanic carbon cycling, in particular the exchange of carbon dioxide with the atmosphere1-3 and the mixing parameters within the ocean itself4-7. Here we test the overall consistency of exchange fluxes between all relevant compartments in a simple model of the global carbon cycle, using measurements of the long-term tropospheric CO2 concentration8 and radiocarbon composition9-12, the bomb 14C inventory in the stratosphere13,14 and a compilation of bomb detonation dates and strengths15. We find that to balance the budget, we must invoke an extra source to account for 25% of the generally accepted uptake of bomb 14C by the oceans3. The strength of this source decreases from 1970 onwards, with a characteristic timescale similar to that of the ocean uptake. Significant radiocarbon transport from the remote high stratosphere and significantly reduced uptake of bomb 14C by the biosphere can both be ruled out by observational constraints. We therefore conclude that the global oceanic bomb 14C inventory should be revised downwards. A smaller oceanic bomb 14C inventory also implies a smaller oceanic radiocarbon penetration depth16, which in turn implies that the oceans take up 25% less anthropogenic CO2 than had previously been believed.

  15. Why relevance theory is relevant for lexicography

    DEFF Research Database (Denmark)

    Bothma, Theo; Tarp, Sven

    2014-01-01

    This article starts by providing a brief summary of relevance theory in information science in relation to the function theory of lexicography, explaining the different types of relevance, viz. objective system relevance and the subjective types of relevance, i.e. topical, cognitive, situational...... that is very important for lexicography as well as for information science, viz. functional relevance. Since all lexicographic work is ultimately aimed at satisfying users’ information needs, the article then discusses why the lexicographer should take note of all these types of relevance when planning a new...... dictionary project, identifying new tasks and responsibilities of the modern lexicographer. The article furthermore discusses how relevance theory impacts on teaching dictionary culture and reference skills. By integrating insights from lexicography and information science, the article contributes to new...

  16. Deep learning relevance

    DEFF Research Database (Denmark)

    Lioma, Christina; Larsen, Birger; Petersen, Casper

    2016-01-01

    train a Recurrent Neural Network (RNN) on existing relevant information to that query. We then use the RNN to "deep learn" a single, synthetic, and we assume, relevant document for that query. We design a crowdsourcing experiment to assess how relevant the "deep learned" document is, compared...... to existing relevant documents. Users are shown a query and four wordclouds (of three existing relevant documents and our deep learned synthetic document). The synthetic document is ranked on average most relevant of all....

  17. Slower gait, slower information processing and smaller prefrontal area in older adults.

    NARCIS (Netherlands)

    Rosano, C.; Studenski, S.A.; Aizenstein, H.J.; Boudreau, R.M.; Longstreth Jr, W.T.; Newman, A.B.

    2012-01-01

    BACKGROUND: Slower gait in older adults is related to smaller volume of the prefrontal area (PFAv). The pathways underlying this association have not yet been explored. Understanding slowing gait could help improve function in older age. We examine whether the association between smaller PFAv and

  18. Smaller Cigarette Pack as a Commitment to Smoke Less? Insights from Behavioral Economics

    Science.gov (United States)

    Marti, Joachim; Sindelar, Jody

    2015-01-01

    Cigarettes are commonly sold in packs of 20 units and therefore little is known about the potential impact of pack size on consumption. Using insights from behavioral economics, we suggest that cigarette packs smaller than the standard size may help some smokers cut back and/or quit, consistent with their long-term goals. Results from an online hypothetical purchase experiment conducted in a sample of US smokers reveal that over a third of smokers are willing to pay a price premium to purchase in smaller quantities. Further, a desire to quit smoking and high self-control is associated with preference for a smaller pack. While we provide some preliminary evidence that smaller packs may be beneficial to certain types of smokers, further research should be conducted to assess whether the smaller pack size should be considered in the arsenal of tobacco control policies to help current smokers quit (JEL: I18; I12; D12) PMID:26356844

  19. Smaller Cigarette Pack as a Commitment to Smoke Less? Insights from Behavioral Economics.

    Directory of Open Access Journals (Sweden)

    Joachim Marti

    Full Text Available Cigarettes are commonly sold in packs of 20 units and therefore little is known about the potential impact of pack size on consumption. Using insights from behavioral economics, we suggest that cigarette packs smaller than the standard size may help some smokers cut back and/or quit, consistent with their long-term goals. Results from an online hypothetical purchase experiment conducted in a sample of US smokers reveal that over a third of smokers are willing to pay a price premium to purchase in smaller quantities. Further, a desire to quit smoking and high self-control is associated with preference for a smaller pack. While we provide some preliminary evidence that smaller packs may be beneficial to certain types of smokers, further research should be conducted to assess whether the smaller pack size should be considered in the arsenal of tobacco control policies to help current smokers quit (JEL: I18; I12; D12.

  20. Validation of rice genome sequence by optical mapping

    Directory of Open Access Journals (Sweden)

    Pape Louise

    2007-08-01

    Full Text Available Abstract Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project and TIGR (The Institute for Genomic Research genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of

  1. High proportion of smaller ranged hummingbird species coincides with ecological specialization across the Americas

    DEFF Research Database (Denmark)

    Sonne, Jesper; Martín González, Ana M.; Maruyama, Pietro K.

    2016-01-01

    Ecological communities that experience stable climate conditions have been speculated to preserve more specialized interspecific associations and have higher proportions of smaller ranged species (SRS). Thus, areas with disproportionally large numbers of SRS are expected to coincide geographicall...

  2. Evidence for smaller right amygdala volumes in posttraumatic stress disorder following childhood trauma

    NARCIS (Netherlands)

    Veer, I.M.; Oei, N.Y.L.; van Buchem, M.A.; Spinhoven, Ph.; Elzinga, B.M.; Rombouts, S.A.R.B.

    2015-01-01

    Hippocampus and amygdala volumes in posttraumatic stress disorder (PTSD) related to childhood trauma are relatively understudied, albeit the potential importance to the disorder. Whereas some studies reported smaller hippocampal volumes, little evidence was found for abnormal amygdala volumes. Here

  3. The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

    Science.gov (United States)

    John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.; hide

    2016-01-01

    Human missions to Mars will fundamentally transform how the planet is explored, enabling new scientific discoveries through more sophisticated sample acquisition and processing than can currently be implemented in robotic exploration. The presence of humans also poses new challenges, including ensuring astronaut safety and health and monitoring contamination. Because the capability to transfer materials to Earth will be extremely limited, there is a strong need for in situ diagnostic capabilities. Nucleotide sequencing is a particularly powerful tool because it can be used to: (1) mitigate microbial risks to crew by allowing identification of microbes in water, in air, and on surfaces; (2) identify optimal treatment strategies for infections that arise in crew members; and (3) track how crew members, microbes, and mission-relevant organisms (e.g., farmed plants) respond to conditions on Mars through transcriptomic and genomic changes. Sequencing would also offer benefits for science investigations occurring on the surface of Mars by permitting identification of Earth-derived contamination in samples. If Mars contains indigenous life, and that life is based on nucleic acids or other closely related molecules, sequencing would serve as a critical tool for the characterization of those molecules. Therefore, spaceflight-compatible nucleic acid sequencing would be an important capability for both crew health and astrobiology exploration. Advances in sequencing technology on Earth have been driven largely by needs for higher throughput and read accuracy. Although some reduction in size has been achieved, nearly all commercially available sequencers are not compatible with spaceflight due to size, power, and operational requirements. Exceptions are nanopore-based sequencers that measure changes in current caused by DNA passing through pores; these devices are inherently much smaller and require significantly less power than sequencers using other detection methods

  4. Measurement of smaller colon polyp in CT colonography images using morphological image processing.

    Science.gov (United States)

    Manjunath, K N; Siddalingaswamy, P C; Prabhu, G K

    2017-11-01

    Automated measurement of the size and shape of colon polyps is one of the challenges in Computed tomography colonography (CTC). The objective of this retrospective study was to improve the sensitivity and specificity of smaller polyp measurement in CTC using image processing techniques. A domain knowledge-based method has been implemented with hybrid method of colon segmentation, morphological image processing operators for detecting the colonic structures, and the decision-making system for delineating the smaller polyp-based on a priori knowledge. The method was applied on 45 CTC dataset. The key finding was that the smaller polyps were accurately measured. In addition to 6-9 mm range, polyps of even processing. It takes [Formula: see text] min for measuring the smaller polyp in a dataset of 500 CTC images. With this method, [Formula: see text] and [Formula: see text] were achieved. The domain-based approach with morphological image processing has given good results. The smaller polyps were measured accurately which helps in making right clinical decisions. Qualitatively and quantitatively the results were acceptable when compared to the ground truth at [Formula: see text].

  5. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  6. Poly(3,4-ethylenedioxythiophene) (PEDOT) polymer coatings facilitate smaller neural recording electrodes

    Science.gov (United States)

    Ludwig, Kip A.; Langhals, Nicholas B.; Joseph, Mike D.; Richardson-Burns, Sarah M.; Hendricks, Jeffrey L.; Kipke, Daryl R.

    2011-02-01

    We investigated using poly(3,4-ethylenedioxythiophene) (PEDOT) to lower the impedance of small, gold recording electrodes with initial impedances outside of the effective recording range. Smaller electrode sites enable more densely packed arrays, increasing the number of input and output channels to and from the brain. Moreover, smaller electrode sizes promote smaller probe designs; decreasing the dimensions of the implanted probe has been demonstrated to decrease the inherent immune response, a known contributor to the failure of long-term implants. As expected, chronically implanted control electrodes were unable to record well-isolated unit activity, primarily as a result of a dramatically increased noise floor. Conversely, electrodes coated with PEDOT consistently recorded high-quality neural activity, and exhibited a much lower noise floor than controls. These results demonstrate that PEDOT coatings enable electrode designs 15 µm in diameter.

  7. Wake flow behaviour behind a smaller cylinder oscillating in the wake of an upstream stationary cylinder

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yangyang; Sun, Zhilin [Ocean College, Zhejiang University, Hangzhou 310058 (China); Tan, Danielle S [Maritime Research Centre, Nanyang Technological University, Singapore 639798 (Singapore); Yu, Dingyong [College of Engineering, Ocean University of China, 266100 (China); Tan, Soon Keat, E-mail: yygao@zju.edu.cn [Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 639798 (Singapore)

    2014-04-01

    The flow patterns around a cylinder oscillating freely in the wake of a larger cylinder upstream were investigated using the particle image velocimetry technique. The upstream cylinder was fixed at both ends while the downstream smaller cylinder was held by springs such that it was free to oscillate in the transverse direction. The flow patterns, amplitudes of oscillation and vortex shedding frequencies were compared with those of a single cylinder. In the presence of the upstream cylinder, the three parameters characterizing the oscillation response of the smaller cylinder—amplitude of oscillation, vortex shedding frequency and Reynolds stresses—were greatly reduced. While their magnitude increased with gap ratio, these three parameters were still smaller than the corresponding magnitudes for a single oscillating cylinder. The peak values of turbulence statistics such as Reynolds shear stress and normal stress behind the oscillating downstream cylinder were similarly reduced, and increased with gap ratios. (paper)

  8. Gamma irradiating elm billets reduces their attractancy to the smaller elm bark beetle, Scolytus multistriatus (Marsham)

    International Nuclear Information System (INIS)

    French, J.R.J.; Robinson, P.J.

    1982-01-01

    Irradiating elm billets with gamma rays had a significant effect in reducing the attractancy of these billets to inflight adults of the smaller elm bark beetle Scolytus multistriatus (Marsham). The temperature at which the fresh billets were stored prior to the beetle exposure had little effect. Irradiated billets, irrespective of storage temperature, had significantly fewer holes than the freshly cut billets. There were significant differences associated with the location of the billets in the field, but these differences were smaller than those associated with irradiation. (orig.) [de

  9. Opportunities for smaller engineering companies despite globalization. Chancen kleiner Ingenieurbueros trotz Globalisierung

    Energy Technology Data Exchange (ETDEWEB)

    Lorentzen, P. (IPL Ingenieurbuero Peter Lorentzen, Frankfurt am Main (Germany))

    1999-06-01

    The trend to size is escalating into gigantism. The biggest in the branch merge to become the oversized. In view of this situation, the question which arises is what are the survival chances of the smaller players Will they all drop out of the running The answer to this question does not only concern the future order books of smaller companies, but in conjunction therewith and predominately the social security of employees, type and scope of assignments as well as the competitive situation and the consequences of all these on remuneration. (orig.)

  10. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  11. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  12. Detection of smaller Jc region and damage in YBCO coated conductors by using permanent magnet method

    International Nuclear Information System (INIS)

    Hattori, K.; Saito, A.; Takano, Y.; Suzuki, T.; Yamada, H.; Takayama, T.; Kamitani, A.; Ohshima, S.

    2011-01-01

    We developed a non-destructive method for measuring the critical current density (J c ) in YBCO-coated conductors by using a permanent magnet (Sm 2 Co 17 ). J c could be determined from the repulsive force (F r ) generated between a permanent magnet and a coated conductor where shielding current flows. We also examined the influence of damage to the film on the J c distribution. The measured F r when the permanent magnet approached the cut part was smaller than that of the undamaged area. We developed a non-destructive method for measuring the critical current density (J c ) in YBCO-coated conductors by using a permanent magnet (Sm 2 Co 17 ). J c could be determined from the repulsive force (F r ) generated between a permanent magnet and a coated conductor where shielding current flows. We tried to detect a smaller J c region in the coated conductor by using the system. The J c distribution could be determined without influence from the thick copper film on YBCO thin film. We also examined the influence of damage to the film on the J c distribution. The surface of the coated conductors was cut by using a knife. The measured F r when the permanent magnet approached the cut part was smaller than that of the undamaged area. This J c measurement technique will be useful for detecting smaller J c regions and defects in coated conductors.

  13. An Investigation of Higher-Order Thinking Skills in Smaller Learning Community Social Studies Classrooms

    Science.gov (United States)

    Fischer, Christopher; Bol, Linda; Pribesh, Shana

    2011-01-01

    This study investigated the extent to which higher-order thinking skills are promoted in social studies classes in high schools that are implementing smaller learning communities (SLCs). Data collection in this mixed-methods study included classroom observations and in-depth interviews. Findings indicated that higher-order thinking was rarely…

  14. A nerve stimulation method to selectively recruit smaller motor-units in rat skeletal muscle

    NARCIS (Netherlands)

    van Bolhuis, A.I.; Holsheimer, J.; Savelsberg, H.H.C.M.

    2001-01-01

    Electrical stimulation of peripheral nerve results in a motor-unit recruitment order opposite to that attained by natural neural control, i.e. from large, fast-fatiguing to progressively smaller, fatigue-resistant motor-units. Yet animal studies involving physiological exercise protocols of low

  15. On the Measurements of Particles Smaller than 20 μM by Global Rainbow Refractometry

    Science.gov (United States)

    Saengkaew, S.; Bonin, D.; Gréh, G.

    2007-06-01

    The measurement of the thermo-chemical characteristics of particles under evaporation or cooling is a challenge. Among others techniques, Global Rainbow Refractometry (GRR) is potentially applicable to a large variety of realistic media. This paper is focused on refractive index measurements of particles smaller than 20 μm which are especially important to extract droplet temperature in spray combustion.

  16. Honors Programs at Smaller Colleges. 3rd Edition. National Collegiate Honors Council Monograph Series

    Science.gov (United States)

    Schuman, Samuel

    2011-01-01

    This monograph focuses upon areas of special concern to those working with honors at smaller colleges and universities: mission, recruitment, facilities, administration, budget, and curriculum. In each area, the author makes some general suggestions about overall operating principles, note specific issues that can lead to difficulties, and suggest…

  17. Kicking velocity and effect on match performance when using a smaller, lighter ball in women's football

    DEFF Research Database (Denmark)

    Andersen, Thomas B.; Krustrup, Peter; Bendiksen, Mads

    2016-01-01

    The present study evaluated the effect of a smaller, lighter ball on kicking speed and technical-tactical and physical match performance in high-level adult female footballers. In the laboratory test setting, the peak ball velocity was 6% higher with the new ball (NB) than the standard ball (SB...

  18. Smaller socioeconomic inequalities in health among women: the role of employment status

    NARCIS (Netherlands)

    Stronks, K.; van de Mheen, H.; van den Bos, J.; Mackenbach, J. P.

    1995-01-01

    Socioeconomic inequalities in health are smaller among women than among men. In this paper, it is hypothesized that this is due to a gender difference in employment status. We used data from the baseline of a Dutch longitudinal study. The socioeconomic indicators were educational level of the

  19. 13 CFR 120.215 - What interest rates apply to smaller loans?

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false What interest rates apply to... BUSINESS LOANS Policies Specific to 7(a) Loans Maturities; Interest Rates; Loan and Guarantee Amounts § 120.215 What interest rates apply to smaller loans? For a loan over $25,000 but not exceeding $50,000, the...

  20. Smaller Is More Personal, and the Personal Gets Results. The Editor Reflects.

    Science.gov (United States)

    Erb, Tom

    2001-01-01

    Summarizes growing body of evidence relating small school size at elementary and middle grades to positive student outcomes. Notes that positive outcomes associated with small size relate to teacher commitment and effectiveness as well as student attachment, persistence, and performance. Concludes that smaller, more intimate schools are better…

  1. 75 FR 37779 - Office of Elementary and Secondary Education; Smaller Learning Communities Program; Notice...

    Science.gov (United States)

    2010-06-30

    ... DEPARTMENT OF EDUCATION [CFDA No. 84.215L] Office of Elementary and Secondary Education; Smaller...-Marshall, U.S. Department of Education, 400 Maryland Avenue, SW., room 3E308, Washington, DC 20202-6200..., in text or Adobe Portable Document Format (PDF) on the Internet at the following site: http://www.ed...

  2. Participation of smaller size renewable generation in the electricity market trade in UK: Analyses and approaches

    DEFF Research Database (Denmark)

    Romanovsky, G.; Xydis, G.; Mutale, J.

    2011-01-01

    a number of specific historical, technical and economic reasons that significantly influenced the ability of the smaller size RES/DG to participate in the electricity market and in provision of balancing services in accordance with the UK National Grid requirements. This paper discusses some perspectives...

  3. The role of interpretation in the internationalization of smaller brazilian firms

    NARCIS (Netherlands)

    R.W. Seifert (Ralf); J. Child (John); S.B. Rodrigues (Suzana)

    2012-01-01

    textabstractAbstract This study considers how decision-makers in smaller firms interpret the means and conditions of internationalization, and how different modes of interpretation are likely to inform action choices in this process. Drawing on 58 qualitative interviews with the leaders of

  4. What Research Tells Us about the Impact and Challenges of Smaller Learning Communities

    Science.gov (United States)

    Levine, Thomas H.

    2010-01-01

    In the United States, considerable financial and human resources have been devoted to breaking some large high schools into smaller learning communities (SLCs). This article reviews research that compares SLCs to comprehensive high schools on a variety of measures. Extant research neither supports nor refutes the promise of SLCs to improve…

  5. Smaller hippocampal volume as a vulnerability factor for the persistence of post-traumatic stress disorder

    NARCIS (Netherlands)

    van Rooij, S J H; Kennis, M; Sjouwerman, R; van den Heuvel, M P; Kahn, R S; Geuze, E

    2015-01-01

    BACKGROUND: Smaller hippocampal volume has often been observed in patients with post-traumatic stress disorder (PTSD). However, there is no consensus whether this is a result of stress/trauma exposure, or constitutes a vulnerability factor for the development of PTSD. Second, it is unclear whether

  6. Smaller hippocampal volume as a vulnerability factor for the persistence of post-traumatic stress disorder.

    Science.gov (United States)

    van Rooij, S J H; Kennis, M; Sjouwerman, R; van den Heuvel, M P; Kahn, R S; Geuze, E

    2015-10-01

    Smaller hippocampal volume has often been observed in patients with post-traumatic stress disorder (PTSD). However, there is no consensus whether this is a result of stress/trauma exposure, or constitutes a vulnerability factor for the development of PTSD. Second, it is unclear whether hippocampal volume normalizes with successful treatment of PTSD, or whether a smaller hippocampus is a risk factor for the persistence of PTSD. Magnetic resonance imaging (MRI) scans and clinical interviews were collected from 47 war veterans with PTSD, 25 healthy war veterans (combat controls) and 25 healthy non-military controls. All veterans were scanned a second time with a 6- to 8-month interval, during which PTSD patients received trauma-focused therapy. Based on post-treatment PTSD symptoms, patients were divided into a PTSD group who was in remission (n = 22) and a group in whom PTSD symptoms persisted (n = 22). MRI data were analysed with Freesurfer. Smaller left hippocampal volume was observed in PTSD patients compared with both control groups. Hippocampal volume of the combat controls did not differ from healthy controls. Second, pre- and post-treatment analyses of the PTSD patients and combat controls revealed reduced (left) hippocampal volume only in the persistent patients at both time points. Importantly, hippocampal volume did not change with treatment. Our findings suggest that a smaller (left) hippocampus is not the result of stress/trauma exposure. Furthermore, hippocampal volume does not increase with successful treatment. Instead, we demonstrate for the first time that a smaller (left) hippocampus constitutes a risk factor for the persistence of PTSD.

  7. HIV Distal Neuropathic Pain Is Associated with Smaller Ventral Posterior Cingulate Cortex.

    Science.gov (United States)

    Keltner, John R; Connolly, Colm G; Vaida, Florin; Jenkinson, Mark; Fennema-Notestine, Christine; Archibald, Sarah; Akkari, Cherine; Schlein, Alexandra; Lee, Jisu; Wang, Dongzhe; Kim, Sung; Li, Han; Rennels, Austin; Miller, David J; Kesidis, George; Franklin, Donald R; Sanders, Chelsea; Corkran, Stephanie; Grant, Igor; Brown, Gregory G; Atkinson, J Hampton; Ellis, Ronald J

    2017-03-01

    . Despite modern antiretroviral therapy, HIV-associated neuropathy is one of the most prevalent, disabling and treatment-resistant complications of HIV disease. The presence and intensity of distal neuropathic pain is not fully explained by the degree of peripheral nerve damage. A better understanding of brain structure in HIV distal neuropathic pain may help explain why some patients with HIV neuropathy report pain while the majority does not. Previously, we reported that more intense distal neuropathic pain was associated with smaller total cerebral cortical gray matter volumes. The objective of this study was to determine which parts of the cortex are smaller. . HIV positive individuals with and without distal neuropathic pain enrolled in the multisite (N = 233) CNS HIV Antiretroviral Treatment Effects (CHARTER) study underwent structural brain magnetic resonance imaging. Voxel-based morphometry was used to investigate regional brain volumes in these structural brain images. . Left ventral posterior cingulate cortex was smaller for HIV positive individuals with versus without distal neuropathic pain (peak P  = 0.017; peak t = 5.15; MNI coordinates x = -6, y = -54, z = 20). Regional brain volumes within cortical gray matter structures typically associated with pain processing were also smaller for HIV positive individuals having higher intensity ratings of distal neuropathic pain. . The posterior cingulate is thought to be involved in inhibiting the perception of painful stimuli. Mechanistically a smaller posterior cingulate cortex structure may be related to reduced anti-nociception contributing to increased distal neuropathic pain. © 2016 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  8. Making Deferred Taxes Relevant

    NARCIS (Netherlands)

    Brouwer, Arjan; Naarding, Ewout

    2018-01-01

    We analyse the conceptual problems in current accounting for deferred taxes and provide solutions derived from the literature in order to make International Financial Reporting Standards (IFRS) deferred tax numbers value-relevant. In our view, the empirical results concerning the value relevance of

  9. Parsimonious relevance models

    NARCIS (Netherlands)

    Meij, E.; Weerkamp, W.; Balog, K.; de Rijke, M.; Myang, S.-H.; Oard, D.W.; Sebastiani, F.; Chua, T.-S.; Leong, M.-K.

    2008-01-01

    We describe a method for applying parsimonious language models to re-estimate the term probabilities assigned by relevance models. We apply our method to six topic sets from test collections in five different genres. Our parsimonious relevance models (i) improve retrieval effectiveness in terms of

  10. Desirable airfoil features for smaller-capacity straight-bladed VAWT

    Energy Technology Data Exchange (ETDEWEB)

    Islam, Mazharul; Ting, D.S.-K.; Fartaj, Amir

    2007-05-15

    In the small scale wind turbine market, the simple straight-bladed Darrieus type vertical axis wind turbine (SB-VAWT) is very attractive for its simple blade design. A detailed aerodynamic performance analysis was conducted on a smaller capacity fixed-pitch SB-VAWT. Brief analyses of the main aerodynamic challenges of this type of wind turbine were first discussed and subsequently the authors conducted further literature survey and computational analysis to shortlist aerodynamic characteristics of a desirable airfoil for a self-starting and better performing SB-VAWT. The required geometric features of the desirable airfoil to achieve the short listed characteristics were also discussed. It has been found out that conventionally used NACA symmetric airfoils are not suitable for smaller capacity SB-VAWT. Rather, it is advantageous to utilize a high-lift and low-drag asymmetric thick airfoil suitable for low speed operation typically encountered by SB-VAWT. (author)

  11. How food marketers can sell smaller portions: Consumer insights and product innovation.

    Science.gov (United States)

    Riis, J; Fisher, J O; Rowe, S

    2016-08-01

    Food portion size has been shown to be an important driver of energy intake. Despite the well acknowledged role of portion control in weight management, large portion sizes remain ubiquitous in the marketplace. Moving consumers towards consumption of smaller portion sizes will require changes in consumer behavior as well as changes in products available to consumers in a variety of settings. This special supplement presents cutting edge research aimed at understanding consumer behavior around portion size and innovations in product design that may promote the selection and consumption of smaller portion sizes. We identify further research that will be needed to translate basic behavioral findings into real world settings and to viable product development. Copyright © 2016. Published by Elsevier Ltd.

  12. Effects of a lighter, smaller football on Acute match injuries in adolescent female football

    DEFF Research Database (Denmark)

    Zebis, Mette K.; Thorborg, Kristian; Andersen, Lars L.

    2018-01-01

    BACKGROUND: The high injury incidence during match-play in female adolescent football is a major concern. In football, males and females play matches with the same football size. No studies have investigated the effect of football size on injury incidence in female adolescent football. Thus......, the aim of the present study was to investigate the effects of introducing a lighter, smaller football on the injury pattern in female adolescent football. METHODS We conducted a pilot cluster randomized controlled trial including 26 football teams representing 346 adolescent female football players (age...... 15-18 years). The teams were randomized to a new lighter, smaller football (INT, N.=12 teams) or a traditional FIFA size 5 football (CON, N.=14 teams) during a full match-season. Acute time-loss injuries and football-exposure during match-play were reported weekly by text-message questions...

  13. Media bias under direct and indirect government control: when is the bias smaller?

    OpenAIRE

    Abhra Roy

    2015-01-01

    We present an analytical framework to compare media bias under direct and indirect government control. In this context, we show that direct control can lead to a smaller bias and higher welfare than indirect control. We further show that the size of the advertising market affects media bias only under direct control. Media bias, under indirect control, is not affected by the size of the advertising market.

  14. Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.

    Science.gov (United States)

    Ramírez-Sánchez, Obed; Pérez-Rodríguez, Paulino; Delaye, Luis; Tiessen, Axel

    2016-12-01

    Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  15. Knowledge acquisition for the internationalization of the smaller firm:Content and sources

    OpenAIRE

    Harris, Simon; Fletcher, Margaret

    2012-01-01

    Internationalization process research emphasizes accumulated experience and networks as sources of knowledge for internationalization. Our understanding, however, as to what this knowledge is in practice for smaller firms, the challenges they face in acquiring it, and how they address those challenges is limited. Integrating organizational learning concepts with our theoretical understanding of the small firm internationalization process, we develop a new framework for understanding knowledge...

  16. Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

    Directory of Open Access Journals (Sweden)

    Obed Ramírez-Sánchez

    2016-12-01

    Full Text Available Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt]. Streptophyta have on average only ∼5.7 exons of medium size (∼230 nt. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt. Among subcellular compartments, membrane proteins are the largest (∼520 aa, whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240 aa. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

  17. Trends and patterns in contemporary management in smaller companies: The Danish perspective

    OpenAIRE

    Ulhøi, John Parm; Madsen, Henning

    2001-01-01

    This paper reports empirical findings from a recent survey of Danish managers with a special focus on managers from smaller companies. The survey has been initiated in Denmark and it is called the 'Danish Management Barometer'. The project is a joint research program between the Aarhus School of Business and the Danish Association of Managers and Executives. It is based on a structured, pre-tested questionnaire send out to 1500 pre-notified managers in Denmark aiming at establishing a...

  18. Culturally Relevant Cyberbullying Prevention

    OpenAIRE

    Phillips, Gregory John

    2017-01-01

    In this action research study, I, along with a student intervention committee of 14 members, developed a cyberbullying intervention for a large urban high school on the west coast. This high school contained a predominantly African American student population. I aimed to discover culturally relevant cyberbullying prevention strategies for African American students. The intervention committee selected video safety messages featuring African American actors as the most culturally relevant cyber...

  19. Less Daily Computer Use is Related to Smaller Hippocampal Volumes in Cognitively Intact Elderly.

    Science.gov (United States)

    Silbert, Lisa C; Dodge, Hiroko H; Lahna, David; Promjunyakul, Nutta-On; Austin, Daniel; Mattek, Nora; Erten-Lyons, Deniz; Kaye, Jeffrey A

    2016-01-01

    Computer use is becoming a common activity in the daily life of older individuals and declines over time in those with mild cognitive impairment (MCI). The relationship between daily computer use (DCU) and imaging markers of neurodegeneration is unknown. The objective of this study was to examine the relationship between average DCU and volumetric markers of neurodegeneration on brain MRI. Cognitively intact volunteers enrolled in the Intelligent Systems for Assessing Aging Change study underwent MRI. Total in-home computer use per day was calculated using mouse movement detection and averaged over a one-month period surrounding the MRI. Spearman's rank order correlation (univariate analysis) and linear regression models (multivariate analysis) examined hippocampal, gray matter (GM), white matter hyperintensity (WMH), and ventricular cerebral spinal fluid (vCSF) volumes in relation to DCU. A voxel-based morphometry analysis identified relationships between regional GM density and DCU. Twenty-seven cognitively intact participants used their computer for 51.3 minutes per day on average. Less DCU was associated with smaller hippocampal volumes (r = 0.48, p = 0.01), but not total GM, WMH, or vCSF volumes. After adjusting for age, education, and gender, less DCU remained associated with smaller hippocampal volume (p = 0.01). Voxel-wise analysis demonstrated that less daily computer use was associated with decreased GM density in the bilateral hippocampi and temporal lobes. Less daily computer use is associated with smaller brain volume in regions that are integral to memory function and known to be involved early with Alzheimer's pathology and conversion to dementia. Continuous monitoring of daily computer use may detect signs of preclinical neurodegeneration in older individuals at risk for dementia.

  20. Polymersomes, smaller than you think: ferrocene as a TEM probe to determine core structure

    International Nuclear Information System (INIS)

    Johnston, A. H.; Dalton, P. D.; Newman, T. A.

    2010-01-01

    By incorporating ferrocene into the hydrophobic membrane of PEG-b-PCL polymersome nanoparticles it is possible to selectively visualize their core using Transmission Electron Microscopy (TEM). Two different sizes of ferrocene-loaded polymersomes with mean hydrodynamic diameters of approximately 40 and 90 nm were prepared. Image analysis of TEM pictures of these polymersomes found that the mean diameter of the core was 4-5 times smaller than the mean hydrodynamic diameter. The values obtained also allow the surface diameter and internal volume of the core to be calculated.

  1. Trends and patterns in contemporary management in smaller companies: The Danish perspective

    DEFF Research Database (Denmark)

    Ulhøi, John Parm; Madsen, Henning

    2001-01-01

    This paper reports empirical findings from a recent survey of Danish managers with a special focus on managers from smaller companies. The survey has been initiated in Denmark and it is called the 'Danish Management Barometer'. The project is a joint research program between the Aarhus School...... of Business and the Danish Association of Managers and Executives. It is based on a structured, pre-tested questionnaire send out to 1500 pre-notified managers in Denmark aiming at establishing a data base to further monitor and identify interesting changes and patterns within a broad range of managerial...

  2. Late-night overeating is associated with smaller breakfast, breakfast skipping, and obesity in children: The Healthy Growth Study.

    Science.gov (United States)

    Karatzi, Kalliopi; Moschonis, George; Choupi, Eurikleia; Manios, Yannis

    2017-01-01

    Excessive energy intake during evening hours is associated with several health problems. The aim of this study was to investigate for the first time the possible association of late-night overeating with breakfast habits and obesity in a large sample of Greek children ages 9 to 13 y. In all, 2655 schoolchildren (9-13 y) participated in the Healthy Growth Study, a cross-sectional epidemiologic study conducted in 77 primary schools in four large regions in Greece. The present study presents results on 1912 children having full data regarding anthropometric, dietary, physical activity, and physical examination indices. High-energy intake at dinner and evening snack was associated with higher likelihood of skipping breakfast (odds ratio, 1.85; 95% confidence interval 1.42-2.39) and with lower caloric intake at breakfast (β = 0.14; P overeating is associated with skipping and/or consuming a smaller breakfast. In children with low levels of physical activity, it is associated with increased body mass index. Future relevant studies are essential to further explore and confirm the findings of the present study. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Smaller amygdala volume and reduced anterior cingulate gray matter density associated with history of post-traumatic stress disorder.

    Science.gov (United States)

    Rogers, Mark A; Yamasue, Hidenori; Abe, Osamu; Yamada, Haruyasu; Ohtani, Toshiyuki; Iwanami, Akira; Aoki, Shigeki; Kato, Nobumasa; Kasai, Kiyoto

    2009-12-30

    Although post-traumatic stress disorder (PTSD) may be seen to represent a failure to extinguish learned fear, significant aspects of the pathophysiology relevant to this hypothesis remain unknown. Both the amygdala and hippocampus are necessary for fear extinction occur, and thus both regions may be abnormal in PTSD. Twenty-five people who experienced the Tokyo subway sarin attack in 1995, nine who later developed PTSD and 16 who did not, underwent magnetic resonance imaging (MRI) with manual tracing to determine bilateral amygdala and hippocampus volumes. At the time of scanning, one had PTSD and eight had a history of PTSD. Results indicated that the group with a history of PTSD had significantly smaller mean bilateral amygdala volume than did the group that did not develop PTSD. Furthermore, left amygdala volume showed a significant negative correlation with severity of PTSD symptomatology as well as reduced gray matter density in the left anterior cingulate cortex. To our knowledge, this is the first observation of an association between PTSD and amygdala volume. Furthermore the apparent interplay between amygdala and anterior cingulate cortex represents support at the level of gross brain morphology for the theory of PTSD as a failure of fear extinction.

  4. The Limits to Relevance

    Science.gov (United States)

    Averill, M.; Briggle, A.

    2006-12-01

    Science policy and knowledge production lately have taken a pragmatic turn. Funding agencies increasingly are requiring scientists to explain the relevance of their work to society. This stems in part from mounting critiques of the "linear model" of knowledge production in which scientists operating according to their own interests or disciplinary standards are presumed to automatically produce knowledge that is of relevance outside of their narrow communities. Many contend that funded scientific research should be linked more directly to societal goals, which implies a shift in the kind of research that will be funded. While both authors support the concept of useful science, we question the exact meaning of "relevance" and the wisdom of allowing it to control research agendas. We hope to contribute to the conversation by thinking more critically about the meaning and limits of the term "relevance" and the trade-offs implicit in a narrow utilitarian approach. The paper will consider which interests tend to be privileged by an emphasis on relevance and address issues such as whose goals ought to be pursued and why, and who gets to decide. We will consider how relevance, narrowly construed, may actually limit the ultimate utility of scientific research. The paper also will reflect on the worthiness of research goals themselves and their relationship to a broader view of what it means to be human and to live in society. Just as there is more to being human than the pragmatic demands of daily life, there is more at issue with knowledge production than finding the most efficient ways to satisfy consumer preferences or fix near-term policy problems. We will conclude by calling for a balanced approach to funding research that addresses society's most pressing needs but also supports innovative research with less immediately apparent application.

  5. Relevant Subspace Clustering

    DEFF Research Database (Denmark)

    Müller, Emmanuel; Assent, Ira; Günnemann, Stephan

    2009-01-01

    Subspace clustering aims at detecting clusters in any subspace projection of a high dimensional space. As the number of possible subspace projections is exponential in the number of dimensions, the result is often tremendously large. Recent approaches fail to reduce results to relevant subspace...... clusters. Their results are typically highly redundant, i.e. many clusters are detected multiple times in several projections. In this work, we propose a novel model for relevant subspace clustering (RESCU). We present a global optimization which detects the most interesting non-redundant subspace clusters...... achieves top clustering quality while competing approaches show greatly varying performance....

  6. Simultaneous compared with sequential blood pressure measurement results in smaller inter-arm blood pressure differences.

    Science.gov (United States)

    van der Hoeven, Niels V; Lodestijn, Sophie; Nanninga, Stephanie; van Montfrans, Gert A; van den Born, Bert-Jan H

    2013-11-01

    There are currently few recommendations on how to assess inter-arm blood pressure (BP) differences. The authors compared simultaneous with sequential measurement on mean BP, inter-arm BP differences, and within-visit reproducibility in 240 patients stratified according to age (simultaneous and three sequential BP measurements were taken in each patient. Starting measurement type and starting arm for sequential measurements were randomized. Mean BP and inter-arm BP differences of the first pair and reproducibility of inter-arm BP differences of the first and second pair were compared between both methods. Mean systolic BP was 1.3±7.5 mm Hg lower during sequential compared with simultaneous measurement (Psequential measurement was on average higher than the second, suggesting an order effect. Absolute systolic inter-arm BP differences were smaller on simultaneous (6.2±6.7/3.3±3.5 mm Hg) compared with sequential BP measurement (7.8±7.3/4.6±5.6 mm Hg, PSimultaneous measurement of BP at both arms reduces order effects and results in smaller inter-arm BP differences, thereby potentially reducing unnecessary referral and diagnostic procedures. ©2013 Wiley Periodicals, Inc.

  7. Fluid cognitive ability is associated with greater exposure and smaller reactions to daily stressors.

    Science.gov (United States)

    Stawski, Robert S; Almeida, David M; Lachman, Margie E; Tun, Patricia A; Rosnick, Christopher B

    2010-06-01

    The authors of this study investigated whether fluid cognitive ability predicts exposure and emotional reactivity to daily stressors. A national sample of adults from the Midlife in the United States study and the National Study of Daily Experiences (N = 1,202) who had a mean age of 57 years (SD = 12; 56% women, 44% men) completed positive and negative mood reports as well as a stressor diary on 8 consecutive evenings via telephone. Participants also completed a telephone-based battery of tests measuring fluid cognitive ability. Higher levels of fluid cognitive ability were associated with greater exposure to work- and home-related overload stressors. Possessing higher levels of fluid cognitive ability was associated with smaller stressor-related increases in negative mood, primarily for interpersonal tensions and network stressors, and smaller stressor-related decreases in positive mood for interpersonal tensions. Furthermore, fluid cognitive ability was unrelated to subjective severity ratings of the stressors reported. Discussion focuses on the role of fluid cognitive ability in daily stress processes. (c) 2010 APA, all rights reserved).

  8. Order of Magnitude Smaller Limit on the Electron's Electron Dipole Moment

    Science.gov (United States)

    Gabrielse, Gerald

    2014-05-01

    Proposed extensions to the Standard Model of particle physics typically predict that the electron would naturally have a small but potentially measurable electric dipole moment (EDM). The Standard Model, known to be incomplete, instead predicts that the electron EDM is much too small to measure. The ACME collaboration used the enormous electric field that electrons experience within a ThO molecule, the unique structure of this molecule, and a cryogenic buffer gas beam of molecules to search for an electron EDM. The new search was sensitive enough to detect an EDM that is ten times smaller than the previously measured upper limit - well within the range of predictions from various proposed extensions to the Standard Model. We did not detect such an EDM, however. Instead, we set a new upper limit on the electron EDM at a 90% confidence limit, | de | < 8 . 7 × 10-29 , making use of the effective electric field calculated for ThO. The new limit stringently constrains the parameters of proposed extensions to the Standard Model to values that predict an electron EDM smaller than the new limit. The TeV energy scale being probed is comparable to that being investigated at CERN's Large Hadron Collider (LHC). Supported by the AMO program of the NSF.

  9. Use of precracked Charpy and smaller specimens to establish the master curve

    International Nuclear Information System (INIS)

    Sokolov, M.A.; McCabe, D.E.; Nanstad, R.K.; Davidov, Y.A.

    1997-01-01

    The current provisions used in the U.S. Code of Federal Regulations for the determination of the fracture toughness of reactor pressure vessel steels employs an assumption that there is a direct correlation between K Ic lower-bound toughness and the Charpy V-notch transition curve. Such correlations are subject to scatter from both approaches which weakens the reliability of fracture mechanics-based analyses. In this study, precracked Charpy and smaller size specimens are used in three-point static bend testing to develop fracture mechanics based K k values. The testing is performed under carefully controlled conditions such that the values can be used to predict the fracture toughness performance of large specimens. The concept of a universal transition curve (master curve) is applied. Data scatter that is characteristic of commercial grade steels and their weldments is handled by Weibull statistical modeling. The master curve is developed to describe the median K Jc fracture toughness for 1T size compact specimens. Size effects are modeled using weakest-link theory and are studied for different specimen geometries. It is shown that precracked Charpy specimens when tested within their confined validity limits follow the weakest-link size-adjustment trend and predict the fracture toughness of larger specimens. Specimens of smaller than Charpy sizes (5 mm thick) exhibit some disparities in results relative to weakest-link size adjustment prediction suggesting that application of such adjustment to very small specimens may have some limitations

  10. Smaller self-inflating bags produce greater guideline consistent ventilation in simulated cardiopulmonary resuscitation.

    Science.gov (United States)

    Nehme, Ziad; Boyle, Malcolm J

    2009-02-20

    Suboptimal bag ventilation in cardiopulmonary resuscitation (CPR) has demonstrated detrimental physiological outcomes for cardiac arrest patients. In light of recent guideline changes for resuscitation, there is a need to identify the efficacy of bag ventilation by prehospital care providers. The objective of this study was to evaluate bag ventilation in relation to operator ability to achieve guideline consistent ventilation rate, tidal volume and minute volume when using two different capacity self-inflating bags in an undergraduate paramedic cohort. An experimental study using a mechanical lung model and a simulated adult cardiac arrest to assess the ventilation ability of third year Monash University undergraduate paramedic students. Participants were instructed to ventilate using 1600 ml and 1000 ml bags for a length of two minutes at the correct rate and tidal volume for a patient undergoing CPR with an advanced airway. Ventilation rate and tidal volume were recorded using an analogue scale with mean values calculated. Ethics approval was granted. Suboptimal ventilation with the use of conventional 1600 ml bag was common, with 77% and 97% of participants unable to achieve guideline consistent ventilation rates and tidal volumes respectively. Reduced levels of suboptimal ventilation arouse from the use of the smaller bag with a 27% reduction in suboptimal tidal volumes (p = 0.015) and 23% reduction in suboptimal minute volumes (p = 0.045). Smaller self-inflating bags reduce the incidence of suboptimal tidal volumes and minute volumes and produce greater guideline consistent results for cardiac arrest patients.

  11. A nerve stimulation method to selectively recruit smaller motor-units in rat skeletal muscle.

    Science.gov (United States)

    van Bolhuis, A I; Holsheimer, J; Savelberg, H H

    2001-05-30

    Electrical stimulation of peripheral nerve results in a motor-unit recruitment order opposite to that attained by natural neural control, i.e. from large, fast-fatiguing to progressively smaller, fatigue-resistant motor-units. Yet animal studies involving physiological exercise protocols of low intensity and long duration require minimal fatigue. The present study sought to apply a nerve stimulation method to selectively recruit smaller motor-units in rat skeletal muscle. Two pulse generators were used, independently supplying short supramaximal cathodal stimulating pulses (0.5 ms) and long subthreshold cathodal inactivating pulses (1.5 s) to the sciatic nerve. Propagation of action potentials was selectively blocked in nerve fibres of different diameter by adjusting the strength of the inactivating current. A tensile-testing machine was used to gauge isometric muscle force of the plantaris and both heads of the gastrocnemius muscle. The order of motor-unit recruitment was estimated from twitch characteristics, i.e. peak force and relaxation time. The results showed prolonged relaxation at lower twitch peak forces as the intensity of the inactivating current increased, indicating a reduction of the number of large motor-units to force production. It is shown that the nerve stimulation method described is effective in mimicking physiological muscle control.

  12. Is Information Still Relevant?

    Science.gov (United States)

    Ma, Lia

    2013-01-01

    Introduction: The term "information" in information science does not share the characteristics of those of a nomenclature: it does not bear a generally accepted definition and it does not serve as the bases and assumptions for research studies. As the data deluge has arrived, is the concept of information still relevant for information…

  13. Opportunities and barriers for smaller portions in food service: lessons from marketing and behavioral economics.

    Science.gov (United States)

    Riis, J

    2014-07-01

    This paper uses the frameworks and evidence from marketing and behavioral economics to highlight the opportunities and barriers for portion control in food service environments. Applying Kahneman's 'thinking fast and slow' concepts, it describes 10 strategies that can be effective in 'tricking' the consumer's fast cognitive system to make better decisions and in triggering the slow cognitive system to help prevent the fast system from making bad decisions. These strategies include shrinking defaults, elongating packages, increasing the visibility of small portions, offering more mixed virtue options, adding more small sizes, offering 'right-sized' standard portions, using meaningful size labels, adopting linear pricing, using temporal landmarks to push smaller portions and facilitating pre-commitment. For each of these strategies, I discuss the specific cost and revenue barriers that a food service operator would face if the strategy were adopted.

  14. TouchGrid: Touchpad pointing by recursively mapping taps to smaller display regions

    DEFF Research Database (Denmark)

    Hertzum, Morten; Hornbæk, Kasper

    2005-01-01

    Touchpad devices are widely used but lacking in pointing efficiency. The TouchGrid, an instance of what we term cell cursors, replaces moving the cursor through dragging the finger on a touchpad with tapping in different regions of the touchpad. The touchpad regions are recursively mapped...... to smaller display regions and thereby enable high-precision pointing without requiring high tapping precision. In an experiment, six subjects used the TouchGrid and a standard touchpad across different numbers of targets, distances to targets, and target widths. Whereas standard touchpad operation follows...... Fitts’ law, target selection time with the TouchGrid is a linear function of the required number of taps. The TouchGrid was significantly faster for small targets and for tasks requiring one tap, and marginally faster for two-tap tasks. Error rates tended to be higher with the TouchGrid than...

  15. Benefits of research activities incorporation into the core business of smaller TSOs

    International Nuclear Information System (INIS)

    Rovny, J.

    2007-01-01

    Much has been done to develop the nuclear safety technology to the current level. Nevertheless, incremental development of this knowledge based on demand-pull innovation only seems not to satisfy the future needs of nuclear industry. In order to cope with technical challenges faced by TSOs in the context of nuclear renaissance, the technology-push innovation has to be done in certain amount as well to ensure that brand-new ideas, technologies and attitudes will be implemented in order to enhance nuclear safety. For the reasons described, the technology-push innovation is accessible mainly for larger organizations. In order to cross the entrance barrier for smaller organizations, a cooperation among several TSOs is needed. Uncertainties related to investments in research can be optimalized by creating a research project portfolio. According to the traditional innovation management theory, technological innovation is a driver of competition and profitability and, therefore, the motivation is supported by economical benefits. (author)

  16. Opportunities and barriers for smaller portions in food service: lessons from marketing and behavioral economics

    Science.gov (United States)

    Riis, J

    2014-01-01

    This paper uses the frameworks and evidence from marketing and behavioral economics to highlight the opportunities and barriers for portion control in food service environments. Applying Kahneman's ‘thinking fast and slow' concepts, it describes 10 strategies that can be effective in ‘tricking' the consumer's fast cognitive system to make better decisions and in triggering the slow cognitive system to help prevent the fast system from making bad decisions. These strategies include shrinking defaults, elongating packages, increasing the visibility of small portions, offering more mixed virtue options, adding more small sizes, offering ‘right-sized' standard portions, using meaningful size labels, adopting linear pricing, using temporal landmarks to push smaller portions and facilitating pre-commitment. For each of these strategies, I discuss the specific cost and revenue barriers that a food service operator would face if the strategy were adopted. PMID:25033960

  17. Economic potential of smaller-sized nuclear plants in today's economy

    International Nuclear Information System (INIS)

    Behrens, C.E.

    1984-01-01

    In this study, the cost of producing power was modelled for a utility with specified financial and production parameters. Two reference cases were considered: in one, it was assumed that the utility would build 400-megawatt nuclear units as necessary to meet its growth in load; in the second, that it would meet its load growth by building 1200-MW units. The smaller plants were assumed to cost 12 percent more per kilowatt than the larger units. The object was to see if the lower financing costs of the 400-megawatt units were enough to overcome the larger plants' economies of scale. In addition to the reference cases, the sensitivity of the cost measurement to changes in various parameters was modelled. The parameters tested included interest rates, fuel mix, cost differential between the 400-megawatt and 1200-megawatt plants, and the rate of growth in load. The results of these cases indicate strongly that small nuclear power plants could have a market

  18. An atlas of the smaller maps in orientable and nonorientable surfaces

    CERN Document Server

    Jackson, David

    2000-01-01

    Maps are beguilingly simple structures with deep and ubiquitous properties. They arise in an essential way in many areas of mathematics and mathematical physics, but require considerable time and computational effort to generate. Few collected drawings are available for reference, and little has been written, in book form, about their enumerative aspects. An Atlas of the Smaller Maps in Orientable and Nonorientable Surfaces is the first book to provide complete collections of maps along with their vertex and face partitions, number of rootings, and an index number for cross referencing. It provides an explanation of axiomatization and encoding, and serves as an introduction to maps as a combinatorial structure. The Atlas lists the maps first by genus and number of edges, and gives the embeddings of all graphs with at most five edges in orientable surfaces, thus presenting the genus distribution for each graph. Exemplifying the use of the Atlas, the authors explore two substantial conjectures with origins in ...

  19. The Problem with Big Data: Operating on Smaller Datasets to Bridge the Implementation Gap.

    Science.gov (United States)

    Mann, Richard P; Mushtaq, Faisal; White, Alan D; Mata-Cervantes, Gabriel; Pike, Tom; Coker, Dalton; Murdoch, Stuart; Hiles, Tim; Smith, Clare; Berridge, David; Hinchliffe, Suzanne; Hall, Geoff; Smye, Stephen; Wilkie, Richard M; Lodge, J Peter A; Mon-Williams, Mark

    2016-01-01

    Big datasets have the potential to revolutionize public health. However, there is a mismatch between the political and scientific optimism surrounding big data and the public's perception of its benefit. We suggest a systematic and concerted emphasis on developing models derived from smaller datasets to illustrate to the public how big data can produce tangible benefits in the long term. In order to highlight the immediate value of a small data approach, we produced a proof-of-concept model predicting hospital length of stay. The results demonstrate that existing small datasets can be used to create models that generate a reasonable prediction, facilitating health-care delivery. We propose that greater attention (and funding) needs to be directed toward the utilization of existing information resources in parallel with current efforts to create and exploit "big data."

  20. Usefulness of CT-guided automatic needle biopsy of solitary pulmonary nodule smaller than 15 mm

    International Nuclear Information System (INIS)

    Jin, Gong Yong; Lim, Yeong Su

    2004-01-01

    To evaluate the usefulness of the CT-guided percutaneous lung biopsy for the solitary pulmonary nodules smaller than 15 mm in diameter. Between April 2002 and May 2003, we evaluated twenty-five patients (11 men, 14 women, mean ages: 52.5 years) who had solitary pulmonary nodules, which we could not discriminate as being benign or malignant on the CT findings. All the subjects had CT-guided percutaenous cutting needle biopsy (PCNB) performed on them at our institution. A definitive diagnosis of benignity or malignancy was established to retrospectively analyze the patient's records. We evaluated the accuracy, sensitivity, specificity and complications of PCNB for the definitive diagnosis of benignity or malignancy. The sensitivity and specificity of PCNB were determined using the Chi-square test, and the correlations with pneumothorax and emphysema after biopsy were analyzed using Spearman's rank correlation coefficient. In two nodules of the twenty-five nodules, no definitive diagnosis could be established. Of the remaining twenty-three nodules, 7 (30.4%) were malignant and 16 (69.6%) were benign. Twenty (87%) of the twenty-three definitively diagnosed nodules were correctly diagnosed with PCNB. Of the twenty nodules, 6 (30%) were malignant and 14 (70%) were benign. The sensitivity and specificity of the malignant nodules were 85.7% (6/7) and 100% (16/16), respectively. The sensitivity and specificity of the benign nodules were 87.5% (14/16) and 85.7% (6/7), respectively. Post-biopsy complication occurred in nine patients (36%): Hemoptysis (n=4, 16%) and pneumothorax (n=5, 20%). However, there was not a statistical significance between pneumothorax and emphysema after biopsy (r=0.3, p=0.15). When CT-guided percutaneous lung biopsy of the solitary pulmonary nodules smaller than 15 mm in diameter was performed without an on-site cytopathologist, we know that PCNB can yield high diagnostic accuracy and very few complications

  1. New algorithm for detecting smaller retinal blood vessels in fundus images

    Science.gov (United States)

    LeAnder, Robert; Bidari, Praveen I.; Mohammed, Tauseef A.; Das, Moumita; Umbaugh, Scott E.

    2010-03-01

    About 4.1 million Americans suffer from diabetic retinopathy. To help automatically diagnose various stages of the disease, a new blood-vessel-segmentation algorithm based on spatial high-pass filtering was developed to automatically segment blood vessels, including the smaller ones, with low noise. Methods: Image database: Forty, 584 x 565-pixel images were collected from the DRIVE image database. Preprocessing: Green-band extraction was used to obtain better contrast, which facilitated better visualization of retinal blood vessels. A spatial highpass filter of mask-size 11 was applied. A histogram stretch was performed to enhance contrast. A median filter was applied to mitigate noise. At this point, the gray-scale image was converted to a binary image using a binary thresholding operation. Then, a NOT operation was performed by gray-level value inversion between 0 and 255. Postprocessing: The resulting image was AND-ed with its corresponding ring mask to remove the outer-ring (lens-edge) artifact. At this point, the above algorithm steps had extracted most of the major and minor vessels, with some intersections and bifurcations missing. Vessel segments were reintegrated using the Hough transform. Results: After applying the Hough transform, both the average peak SNR and the RMS error improved by 10%. Pratt's Figure of Merit (PFM) was decreased by 6%. Those averages were better than [1] by 10-30%. Conclusions: The new algorithm successfully preserved the details of smaller blood vessels and should prove successful as a segmentation step for automatically identifying diseases that affect retinal blood vessels.

  2. Smaller self-inflating bags produce greater guideline consistent ventilation in simulated cardiopulmonary resuscitation

    Directory of Open Access Journals (Sweden)

    Boyle Malcolm J

    2009-02-01

    Full Text Available Abstract Background Suboptimal bag ventilation in cardiopulmonary resuscitation (CPR has demonstrated detrimental physiological outcomes for cardiac arrest patients. In light of recent guideline changes for resuscitation, there is a need to identify the efficacy of bag ventilation by prehospital care providers. The objective of this study was to evaluate bag ventilation in relation to operator ability to achieve guideline consistent ventilation rate, tidal volume and minute volume when using two different capacity self-inflating bags in an undergraduate paramedic cohort. Methods An experimental study using a mechanical lung model and a simulated adult cardiac arrest to assess the ventilation ability of third year Monash University undergraduate paramedic students. Participants were instructed to ventilate using 1600 ml and 1000 ml bags for a length of two minutes at the correct rate and tidal volume for a patient undergoing CPR with an advanced airway. Ventilation rate and tidal volume were recorded using an analogue scale with mean values calculated. Ethics approval was granted. Results Suboptimal ventilation with the use of conventional 1600 ml bag was common, with 77% and 97% of participants unable to achieve guideline consistent ventilation rates and tidal volumes respectively. Reduced levels of suboptimal ventilation arouse from the use of the smaller bag with a 27% reduction in suboptimal tidal volumes (p = 0.015 and 23% reduction in suboptimal minute volumes (p = 0.045. Conclusion Smaller self-inflating bags reduce the incidence of suboptimal tidal volumes and minute volumes and produce greater guideline consistent results for cardiac arrest patients.

  3. Clinical Relevance of Adipokines

    Directory of Open Access Journals (Sweden)

    Matthias Blüher

    2012-10-01

    Full Text Available The incidence of obesity has increased dramatically during recent decades. Obesity increases the risk for metabolic and cardiovascular diseases and may therefore contribute to premature death. With increasing fat mass, secretion of adipose tissue derived bioactive molecules (adipokines changes towards a pro-inflammatory, diabetogenic and atherogenic pattern. Adipokines are involved in the regulation of appetite and satiety, energy expenditure, activity, endothelial function, hemostasis, blood pressure, insulin sensitivity, energy metabolism in insulin sensitive tissues, adipogenesis, fat distribution and insulin secretion in pancreatic β-cells. Therefore, adipokines are clinically relevant as biomarkers for fat distribution, adipose tissue function, liver fat content, insulin sensitivity, chronic inflammation and have the potential for future pharmacological treatment strategies for obesity and its related diseases. This review focuses on the clinical relevance of selected adipokines as markers or predictors of obesity related diseases and as potential therapeutic tools or targets in metabolic and cardiovascular diseases.

  4. Information Needs/Relevance

    OpenAIRE

    Wildemuth, Barbara M.

    2009-01-01

    A user's interaction with a DL is often initiated as the result of the user experiencing an information need of some kind. Aspects of that experience and how it might affect the user's interactions with the DL are discussed in this module. In addition, users continuously make decisions about and evaluations of the materials retrieved from a DL, relative to their information needs. Relevance judgments, and their relationship to the user's information needs, are discussed in this module. Draft

  5. Sequencing chess

    Science.gov (United States)

    Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas

    2016-10-01

    We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.

  6. Fleet view of electrified transportation reveals smaller potential to reduce GHG emissions

    International Nuclear Information System (INIS)

    Meinrenken, Christoph J.; Lackner, Klaus S.

    2015-01-01

    Highlights: • Novel framework compares GHG of plugins vs. hybrids for any vehicle type/performance. • Fleet GHG can be compared without forecasting market penetrations of vehicle sizes. • GHG/km for pure electrics must account for limited range using novel, modified Utility Factor. • Applied to the US, this points to smaller GHG reduction at fleet level than traditional fleet analyses. - Abstract: Plugin and hybrid vehicles have been shown to offer possible reductions in greenhouse gas (GHG) emissions, depending on grid-carbon-intensity, range and thus life-cycle battery emissions and vehicle weight, and on trip patterns. We present a framework that enables GHG comparisons (well-to-wheel plus storage manufacturing) for three drivetrains (pure-electric, gasoline-hybrid, and plugin-hybrid), both for individual vehicles and for fleets. The framework captures effects of grid- versus vehicle-based electricity generation, grid transmission and charging losses, and manufacturing and carrying batteries. In contrast to previous work, GHG comparisons can be obtained for heterogeneous fleets of varying vehicle sizes (cars, vans, buses, trucks) and performances, without requiring forecasting of such vehicle specs and their respective market penetrations. Further, we show how a novel adaptation of the Utility Factor concept from plug-in-hybrids to mixed fleets of battery-only and gasoline-hybrids is crucial to quantifying battery-only-vehicles’ impact on fleet-wide GHG. To account for regional variations and possible future technology improvements, we show scenarios over a wide spectrum of grid-carbon-intensities (50–1200 g CO 2 e/kW h at wall), vehicle range (∼5–500 km), battery energy densities, and battery life-cycle GHG. Model uncertainties are quantified via sensitivity tests. Applying the framework to trip patterns of US passenger transportation, we find that owing to the interplay of GHG/km, battery size, all-electric range, and trip patterns, GHG

  7. IRIS: A Comprehensive Approach to Implementing Nuclear Power in Countries with Smaller Electric Grids

    International Nuclear Information System (INIS)

    Petrovic, B.; Carelli, M. D.; Sandell, L.; Storrick, G. D.; Cavlina, N.

    2008-01-01

    Many emerging markets and smaller size countries are considering the nuclear option and the deployment of their first nuclear reactor(s). However, some of their requirements and available infrastructure are quite different from those of larger countries currently employing nuclear power. Specific considerations might include: a small size electrical grid, in some cases on the order of a few GWe; limited financial resources; no nuclear experience; inadequate availability of necessary material and people infrastructure. Large nuclear power plants of 1000 MWe or greater do not provide best fit. The IRIS (International Reactor Innovative and Secure) reactor, under development by an international team of eighteen organizations from nine countries led by Westinghouse specifically addresses these needs. IRIS is an advanced PWR with integral configuration that yields a simple design with enhanced safety. The IRIS size is 335 MWe and may be deployed in single or multiple modules. It can fit almost any grid, or a small utility within a larger grid; moreover, it allows incremental power additions as needed. The capital outlay is of the order of hundreds of millions rather than a few billions dollars. Successive construction and operation of multiple modules significantly reduces the required capital resources and capital at risk with generation income from earlier plants offsetting the construction outlays of subsequent ones. This is highly desirable in both developed and emerging markets, but it may be of critical importance to the latter. IRIS safety characteristics allow for licensing with a significantly reduced size of emergency zone, a critical feature for small countries and when cogeneration is desired. In fact, IRIS is designed to produce steam for district heating, water desalination and bio-fuel generation in addition to electricity. The U.S. Department of Energy (DOE) has announced in February 2008 its intention to contribute to funding the licensing of a 'Grid

  8. Any effects of social orientation priming on object-location memory are smaller than initially reported.

    Science.gov (United States)

    Drouin, Héloïse; Davidson, Patrick S R

    2015-12-01

    It has previously been reported that priming a collectivistic social orientation (compared with an individualistic one) boosts object-location memory (Kühnen & Oyserman, 2002; Oyserman, Sorensen, Reber, & Chen, 2009). We conducted 4 experiments to replicate this reported effect, using the same methods as in those initial reports. In Experiment 1 (n = 145), we found a hint of a priming effect on object-location memory, but also an unanticipated interaction between priming and gender. In Experiment 2 (n = 90), we included gender as a formal factor and doubled the "dosage" of the priming, yet did not see any priming effects on memory. In Experiment 3 (n = 101), we octupled the priming "dosage" and again saw no significant effects on memory. Finally, in Experiment 4 (n = 102), we performed an exact replication of the methods of the original reports and again found no priming effects on memory. Any effects of this type of social orientation priming on object-location memory appear to be smaller and/or less robust than initially thought. (c) 2015 APA, all rights reserved).

  9. A heterodyne interferometer with periodic nonlinearities smaller than ±10 pm

    International Nuclear Information System (INIS)

    Weichert, C; Köchert, P; Köning, R; Flügge, J; Andreas, B; Kuetgens, U; Yacoot, A

    2012-01-01

    The PTB developed a new optical heterodyne interferometer in the context of the European joint research project ‘Nanotrace’. A new optical concept using plane-parallel plates and spatially separated input beams to minimize the periodic nonlinearities was realized. Furthermore, the interferometer has the resolution of a double-path interferometer, compensates for possible angle variations between the mirrors and the interferometer optics and offers a minimal path difference between the reference and the measurement arm. Additionally, a new heterodyne phase evaluation based on an analogue to digital converter board with embedded field programmable gate arrays was developed, providing a high-resolving capability in the single-digit picometre range. The nonlinearities were characterized by a comparison with an x-ray interferometer, over a measurement range of 2.2 periods of the optical interferometer. Assuming an error-free x-ray interferometer, the nonlinearities are considered to be the deviation of the measured displacement from a best-fit line. For the proposed interferometer, nonlinearities smaller than ±10 pm were observed without any quadrature fringe correction. (paper)

  10. A heterodyne interferometer with periodic nonlinearities smaller than ±10 pm

    Science.gov (United States)

    Weichert, C.; Köchert, P.; Köning, R.; Flügge, J.; Andreas, B.; Kuetgens, U.; Yacoot, A.

    2012-09-01

    The PTB developed a new optical heterodyne interferometer in the context of the European joint research project ‘Nanotrace’. A new optical concept using plane-parallel plates and spatially separated input beams to minimize the periodic nonlinearities was realized. Furthermore, the interferometer has the resolution of a double-path interferometer, compensates for possible angle variations between the mirrors and the interferometer optics and offers a minimal path difference between the reference and the measurement arm. Additionally, a new heterodyne phase evaluation based on an analogue to digital converter board with embedded field programmable gate arrays was developed, providing a high-resolving capability in the single-digit picometre range. The nonlinearities were characterized by a comparison with an x-ray interferometer, over a measurement range of 2.2 periods of the optical interferometer. Assuming an error-free x-ray interferometer, the nonlinearities are considered to be the deviation of the measured displacement from a best-fit line. For the proposed interferometer, nonlinearities smaller than ±10 pm were observed without any quadrature fringe correction.

  11. Why droplet dimension can be larger than, equal to, or smaller than the nanowire dimension

    Science.gov (United States)

    Mohammad, S. Noor

    2009-11-01

    Droplets play central roles in the nanowire (NW) growth by vapor phase mechanisms. These mechanisms include vapor-liquid-solid (VLS), vapor-solid-solid or vapor-solid (VSS), vapor-quasisolid-solid or vapor-quasiliquid-solid (VQS), oxide-assisted growth (OAG), and self-catalytic growth (SCG) mechanisms. Fundamentals of the shape, size, characteristics, and dynamics of droplets and the impacts of them on the NW growth, have been studied. The influence of growth techniques, growth parameters (e.g., growth temperature, partial pressure, gas flow rates, etc.), thermodynamic conditions, surface and interface energy, molar volume, chemical potentials, etc. have been considered on the shapes and sizes of droplets. A model has been presented to explain why droplets can be larger than, equal to, or smaller than the associated NWs. Various growth techniques have been analyzed to understand defects created in NWs. Photoluminescence characteristics have been presented to quantify the roles of droplets in the creation of NW defects. The study highlights the importance of the purity of the droplet material. It attests to the superiority of the SCG mechanism, and clarifies the differences between the VSS, VQS, VLS, and SCG mechanisms. It explains why droplets produced by some mechanisms are visible but droplets produced by some other mechanisms are not visible. It elucidates the formation mechanisms of very large and very small droplets, and discusses the ground rules for droplets creating necked NWs. It puts forth reasons to demonstrate that very large droplets may not behave as droplets.

  12. Multiple Smaller Missions as a Direct Pathway to Mars Sample Return

    Science.gov (United States)

    Niles, P. B.; Draper, D. S.; Evans, C. A.; Gibson, E. K.; Graham, L. D.; Jones, J. H.; Lederer, S. M.; Ming, D.; Seaman, C. H.; Archer, P. D.; hide

    2012-01-01

    Recent discoveries by the Mars Exploration Rovers, Mars Express, Mars Odyssey, and Mars Reconnaissance Orbiter spacecraft include multiple, tantalizing astrobiological targets representing both past and present environments on Mars. The most desirable path to Mars Sample Return (MSR) would be to collect and return samples from that site which provides the clearest examples of the variety of rock types considered a high priority for sample return (pristine igneous, sedimentary, and hydrothermal). Here we propose an MSR architecture in which the next steps (potentially launched in 2018) would entail a series of smaller missions, including caching, to multiple landing sites to verify the presence of high priority sample return targets through in situ analyses. This alternative architecture to one flagship-class sample caching mission to a single site would preserve a direct path to MSR as stipulated by the Planetary Decadal Survey, while permitting investigation of diverse deposit types and providing comparison of the site of returned samples to other aqueous environments on early Mars

  13. The Effect of Introducing a Smaller and Lighter Basketball on Female Basketball Players’ Shot Accuracy

    Science.gov (United States)

    Podmenik, Nadja; Leskošek, Bojan; Erčulj, Frane

    2012-01-01

    Our study examined whether the introduction of a smaller and lighter basketball (no. 6) affected the accuracy of female basketball players’ shots at the basket. The International Basketball Federation (FIBA) introduced a size 6 ball in the 2004/2005 season to improve the efficiency and accuracy of technical elements, primarily shots at the basket. The sample for this study included 573 European female basketball players who were members of national teams that had qualified for the senior women’s European championships in 2001, 2003, 2005 and 2007. A size 7 (larger and heavier) basketball was used by 286 players in 1,870 matches, and a size 6 basketball was used by 287 players in 1,966 matches. The players were categorised into three playing positions: guards, forwards and centres. The results revealed that statistically significant changes by year occurred only in terms of the percentage of successful free throws. With the size 6 basketball, this percentage decreased. Statistically significant differences between the playing positions were observed in terms of the percentage of field goals worth three points (between guards and forwards) and two points (between guards and centres). The results show that the introduction of the size 6 basketball did not lead to improvement in shooting accuracy (the opposite was found for free throws), although the number of three-point shots increased. PMID:23486286

  14. The Role of Interpretation in the Internationalization of Smaller Brazilian Firms

    Directory of Open Access Journals (Sweden)

    Rene Eugenio Seifert

    2012-10-01

    Full Text Available This study considers how decision-makers in smaller firms interpret the means and conditions of internationalization, and how different modes of interpretation are likely to inform action choices in this process. Drawing on 58 qualitative interviews with the leaders of Brazilian small and medium-sized enterprises (SMEsin the clothing industry located in the state of Paraná, the results support the contention that different understandings given to the means/conditions of internationalization are associated with different action choices. More specifically, the results indicate that: (a interpretation changes the criteria and parameters by which rational choices on internationalization are made; (b a comprehensive explanation of internationalization on the basis of situational characteristics is likely to be inconclusive without taking into account decision-makers’ interpretations; (c particular meanings given to internationalization are likely to inform choice in different ways, (d managers act on the basis of their inter-subjectively negotiated, shared and sustained reality; and (e investigative proximity with practitioners is pivotal in order to comprehensively account for their interpretations.

  15. IRIS-50. A 50 MWe advanced PWR design for smaller, regional grids and specialized applications

    International Nuclear Information System (INIS)

    Petrovic, Bojan; Carelli, Mario; Conway, Larry; Hundal, Rolv; Barbaso, Enrico; Gamba, Federica; Centofante, Mario

    2009-01-01

    IRIS is an advanced, medium-power (1000 MWt or ∼335 MWe) advanced PWR design of integral configuration, that has gained wide recognition due to its innovative 'safety-by-design' safety approach. In spite of its smaller size compared to large monolithic nuclear power plants, it is economically competitive due to its simplicity and advantages of modular deployment. However, the optimum power level for a class of specific applications (e.g., power generation in small regional isolated grids; water desalination and biodiesel production at remote locations; autonomous power source for special applications, etc.) may be even lower, of the order of tens rather than hundreds of MWe. The simple and robust IRIS 335 MWe design provides a solid basis for establishing a 20-100 MWe design, utilizing the same safety and economics principles, so that it will retain economic attractiveness compared to other alternatives of the same power level. A conceptual 50 MWe design, IRIS-50, was initially developed and then assessed in a 2001 report to the US Congress on small and medium reactors, as a design mature enough to have deployment potential within a decade. In the meantime, while the main efforts have focused on the 335 MWe design completion and licensing, parallel efforts have progressed toward the preliminary design of IRIS-50. This paper summarizes the main IRIS-50 features and presents an update on its design status. (author)

  16. Retinal Nerve Fiber Layer Converges More Convexly on Normal Smaller Optic Nerve Head.

    Science.gov (United States)

    Jung, Kyoung In; Shin, Jeong Ah; Park, Hae-Young Lopilly; Park, Chan Kee

    2015-08-01

    To investigate retinal nerve fiber layer (RNFL) configuration in the optic nerve head (ONH) and peripapillary area according to disc size and to determine whether it explains cup discrepancy among eyes with different disc sizes. Horizontal and vertical RNFL curvature and mean thickness were measured using confocal scanning laser ophthalmoscopy (Heidelberg Retina Tomograph) in 63 normal subjects grouped by disc size. Average and quadrant RNFL thickness, disc size, average cup-to-disc ratio (CDR), and convergence angle at the optic disc were also measured using Cirrus HD-optical coherence tomography. The relationships between disc size and RNFL curvature, thickness, angle at optic disc, and CDR were evaluated. RNFL curvature and convergence angle reflects convexity "on" and "into" the optic disc, respectively. CDR was smaller for small discs and was positively correlated with disc size (Poptic disc were positively correlated with disc size (POptic disc area was negatively correlated with mean RNFL thickness at the optic disc margin measured by HRT (P=0.002), but not in the peripapillary area by optical coherence tomography. Using imaging techniques, we demonstrated that the shape of the RNFLs converging "on" and entering "into" the optic disc was more convex for small optic discs compared with large discs. A low CDR for small discs could be mediated by these RNFL profiles at the ONH, which may guide the clinical evaluation of glaucomatous ONH damage.

  17. Similar representations of sequence knowledge in young and older adults: A study of effector independent transfer

    Directory of Open Access Journals (Sweden)

    Jonathan Sebastiaan Barnhoorn

    2016-08-01

    Full Text Available Older adults show reduced motor performance and changes in motor skill development. To better understand these changes, we studied differences in sequence knowledge representations between young and older adults using a transfer task. Transfer, or the ability to apply motor skills flexibly, is highly relevant in day-to-day motor activity and facilitates generalization of learning to new contexts. By using movement types that are completely unrelated in terms of muscle activation and response location, we focused on transfer facilitated by the early, visuospatial system.We tested 32 right-handed older adults (65 – 74 and 32 young adults (18 – 30. During practice of a discrete sequence production task, participants learned two 6-element sequences using either unimanual key-presses (KPs or by moving a lever with lower arm flexion-extension (FE movements. Each sequence was performed 144 times. They then performed a test phase consisting of familiar and random sequences performed with the type of movements not used during practice. Both age groups displayed transfer from FE to KP movements as indicated by faster performance on the familiar sequences in the test phase. Only young adults transferred their sequence knowledge from KP to FE movements. In both directions, the young showed higher transfer than older adults. These results suggest that the older participants, like the young, represented their sequences in an abstract visuospatial manner. Transfer was asymmetric in both age groups: there was more transfer from FE to KP movements than vice versa. This similar asymmetry is a further indication that the types of representations that older adults develop are comparable to those that young adults develop. We furthermore found that older adults improved less during FE practice, gained less explicit knowledge, displayed a smaller visuospatial working memory capacity and had lower processing speed than young adults. Despite the many differences

  18. [Relevant public health enteropathogens].

    Science.gov (United States)

    Riveros, Maribel; Ochoa, Theresa J

    2015-01-01

    Diarrhea remains the third leading cause of death in children under five years, despite recent advances in the management and prevention of this disease. It is caused by multiple pathogens, however, the prevalence of each varies by age group, geographical area and the scenario where cases (community vs hospital) are recorded. The most relevant pathogens in public health are those associated with the highest burden of disease, severity, complications and mortality. In our country, norovirus, Campylobacter and diarrheagenic E. coli are the most prevalent pathogens at the community level in children. In this paper we review the local epidemiology and potential areas of development in five selected pathogens: rotavirus, norovirus, Shiga toxin-producing E. coli (STEC), Shigella and Salmonella. Of these, rotavirus is the most important in the pediatric population and the main agent responsible for child mortality from diarrhea. The introduction of rotavirus vaccination in Peru will have a significant impact on disease burden and mortality from diarrhea. However, surveillance studies are needed to determine the impact of vaccination and changes in the epidemiology of diarrhea in Peru following the introduction of new vaccines, as well as antibiotic resistance surveillance of clinical relevant bacteria.

  19. Behavioral inhibition in childhood predicts smaller hippocampal volume in adolescent offspring of parents with panic disorder

    Science.gov (United States)

    Schwartz, C E; Kunwar, P S; Hirshfeld-Becker, D R; Henin, A; Vangel, M G; Rauch, S L; Biederman, J; Rosenbaum, J F

    2015-01-01

    Behavioral inhibition (BI) is a genetically influenced behavioral profile seen in 15–20% of 2-year-old children. Children with BI are timid with people, objects and situations that are novel or unfamiliar, and are more reactive physiologically to these challenges as evidenced by higher heart rate, pupillary dilation, vocal cord tension and higher levels of cortisol. BI predisposes to the later development of anxiety, depression and substance abuse. Reduced hippocampal volumes have been observed in anxiety disorders, depression and posttraumatic stress disorder. Animal models have demonstrated that chronic stress can damage the hippocampal formation and implicated cortisol in these effects. We, therefore, hypothesized that the hippocampi of late adolescents who had been behaviorally inhibited as children would be smaller compared with those who had not been inhibited. Hippocampal volume was measured with high-resolution structural magnetic resonance imaging in 43 females and 40 males at 17 years of age who were determined to be BI+ or BI− based on behaviors observed in the laboratory as young children. BI in childhood predicted reduced hippocampal volumes in the adolescents who were offspring of parents with panic disorder, or panic disorder with comorbid major depression. We discuss genetic and environmental factors emanating from both child and parent that may explain these findings. To the best of our knowledge, this is the first study to demonstrate a relationship between the most extensively studied form of temperamentally based human trait anxiety, BI, and hippocampal structure. The reduction in hippocampal volume, as reported by us, suggests a role for the hippocampus in human trait anxiety and anxiety disorder that warrants further investigation. PMID:26196438

  20. S175. AMOTIVATION IS ASSOCIATED WITH SMALLER VENTRAL STRIATUM VOLUMES IN OLDER PATIENTS WITH SCHIZOPHRENIA

    Science.gov (United States)

    Caravaggio, Fernando; Fervaha, Gagan; Iwata, Yusuke; Plitman, Eric; Chung, Jun Ku; Nakajima, Shinichiro; Mar, Wanna; Gerretsen, Philip; Kim, Julia; Chakravarty, Mallar; Mulsant, Benoit; Pollock, Bruce; Mamo, David; Remington, Gary; Graff-Guerrero, Ariel

    2018-01-01

    Abstract Background Motivational deficits are prevalent in patients with schizophrenia, persist despite antipsychotic treatment, and predict long‐term outcomes. Evidence suggests that patients with greater amotivation have smaller ventral striatum (VS) volumes. We wished to replicate this finding in a sample of older, chronically medicated patients with schizophrenia. Using structural imaging and positron emission tomography, we examined whether amotivation uniquely predicted VS volumes beyond the effects of striatal dopamine D2/3 receptor (D2/3R) blockade by antipsychotics. Methods Data from 41 older schizophrenia patients (mean age: 60.2 ± 6.7; 11 female) were reanalysed from previously published imaging data. We constructed multivariate linear stepwise regression models with VS volumes as the dependent variable and various sociodemographic and clinical variables as the initial predictors: age, gender, total brain volume, and antipsychotic striatal D2/3R occupancy. Amotivation was included as a subsequent step to determine any unique relationships with VS volumes beyond the contribution of the covariates. In a reduced sample (n = 36), general cognition was also included as a covariate. Results Amotivation uniquely explained 8% and 6% of the variance in right and left VS volumes, respectively (right: β = -.38, t = -2.48, P = .01; left: β = -.31, t = -2.17, P = .03). Considering cognition, amotivation levels uniquely explained 9% of the variance in right VS volumes (β = -.43, t = -0.26, P = .03). Discussion We replicate and extend the finding of reduced VS volumes with greater amotivation. We demonstrate this relationship uniquely beyond the potential contributions of striatal D2/3R blockade by antipsychotics. Elucidating the structural correlates of amotivation in schizophrenia may help develop treatments for this presently irremediable deficit.

  1. Amotivation is associated with smaller ventral striatum volumes in older patients with schizophrenia.

    Science.gov (United States)

    Caravaggio, Fernando; Fervaha, Gagan; Iwata, Yusuke; Plitman, Eric; Chung, Jun Ku; Nakajima, Shinichiro; Mar, Wanna; Gerretsen, Philip; Kim, Julia; Chakravarty, M Mallar; Mulsant, Benoit; Pollock, Bruce; Mamo, David; Remington, Gary; Graff-Guerrero, Ariel

    2018-03-01

    Motivational deficits are prevalent in patients with schizophrenia, persist despite antipsychotic treatment, and predict long-term outcomes. Evidence suggests that patients with greater amotivation have smaller ventral striatum (VS) volumes. We wished to replicate this finding in a sample of older, chronically medicated patients with schizophrenia. Using structural imaging and positron emission tomography, we examined whether amotivation uniquely predicted VS volumes beyond the effects of striatal dopamine D 2/3 receptor (D 2/3 R) blockade by antipsychotics. Data from 41 older schizophrenia patients (mean age: 60.2 ± 6.7; 11 female) were reanalysed from previously published imaging data. We constructed multivariate linear stepwise regression models with VS volumes as the dependent variable and various sociodemographic and clinical variables as the initial predictors: age, gender, total brain volume, and antipsychotic striatal D 2/3 R occupancy. Amotivation was included as a subsequent step to determine any unique relationships with VS volumes beyond the contribution of the covariates. In a reduced sample (n = 36), general cognition was also included as a covariate. Amotivation uniquely explained 8% and 6% of the variance in right and left VS volumes, respectively (right: β = -.38, t = -2.48, P = .01; left: β = -.31, t = -2.17, P = .03). Considering cognition, amotivation levels uniquely explained 9% of the variance in right VS volumes (β = -.43, t = -0.26, P = .03). We replicate and extend the finding of reduced VS volumes with greater amotivation. We demonstrate this relationship uniquely beyond the potential contributions of striatal D 2/3 R blockade by antipsychotics. Elucidating the structural correlates of amotivation in schizophrenia may help develop treatments for this presently irremediable deficit. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Faster diffraction-based overlay measurements with smaller targets using 3D gratings

    Science.gov (United States)

    Li, Jie; Kritsun, Oleg; Liu, Yongdong; Dasari, Prasad; Volkman, Catherine; Hu, Jiangtao

    2012-03-01

    Diffraction-based overlay (DBO) technologies have been developed to address the overlay metrology challenges for 22nm technology node and beyond. Most DBO technologies require specially designed targets that consist of multiple measurement pads, which consume too much space and increase measurement time. The traditional empirical approach (eDBO) using normal incidence spectroscopic reflectometry (NISR) relies on linear response of the reflectance with respect to overlay displacement within a small range. It offers convenience of quick recipe setup since there is no need to establish a model. However it requires three or four pads per direction (x or y) which adds burden to throughput and target size. Recent advances in modeling capability and computation power enabled mDBO, which allows overlay measurement with reduced number of pads, thus reducing measurement time and DBO target space. In this paper we evaluate the performance of single pad mDBO measurements using two 3D targets that have different grating shapes: squares in boxes and L-shapes in boxes. Good overlay sensitivities are observed for both targets. The correlation to programmed shifts and image-based overlay (IBO) is excellent. Despite the difference in shapes, the mDBO results are comparable for square and L-shape targets. The impact of process variations on overlay measurements is studied using a focus and exposure matrix (FEM) wafer. Although the FEM wafer has larger process variations, the correlation of mDBO results with IBO measurements is as good as the normal process wafer. We demonstrate the feasibility of single pad DBO measurements with faster throughput and smaller target size, which is particularly important in high volume manufacturing environment.

  3. Birds and Roads: Reduced Transit for Smaller Species over Roads within an Urban Environment

    Directory of Open Access Journals (Sweden)

    Christopher D. Johnson

    2017-05-01

    important role in determining species presence and crossing likelihood. Dense vegetation is known to benefit smaller species due to the provision of foraging resources and shelter from larger, more aggressive species.

  4. Fewer but not smaller schools in declining fish and krill populations.

    Science.gov (United States)

    Brierley, Andrew S; Cox, Martin J

    2015-01-05

    Many pelagic species (species that live in the water column), including herring and krill, aggregate to form schools, shoals, or swarms (hereafter simply "schools," although the words are not synonyms). Schools provide benefits to individual members, including locomotory economy and protection from predators that prey on individuals, but paradoxically make schooling species energetically viable and commercially attractive targets for predators of groups and for fishers. Large schools are easier to find and yield greater prey/catch than small schools, and there is a requirement from fields as diverse as theoretical ecology and fisheries management to understand whether and how aggregation sizes change with changing population size. We collated data from vertical echosounder surveys of taxonomically diverse pelagic stocks from geographically diverse ecosystems. The data contain common significant positive linear stock-biomass to school-number relationships. They show that the numbers of schools in the stocks change with changing stock biomass and suggest that the distributions of school sizes do not change with stock biomass. New data that we collected using a multibeam sonar, which can image entire schools, contained the same stock-biomass to school-number relationship and confirm that the distribution of school sizes is not related to changing stock size: put simply, as stocks decline, individuals are distributed among fewer schools, not smaller schools. Since school characteristics affect catchability (the ease or difficulty with which fishers can capture target species) and availability of prey to predators, our findings have commercial and ecological implications, particularly within the aspirational framework of ecosystem-based management of marine systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Other relevant biological papers

    International Nuclear Information System (INIS)

    Shimizu, M.

    1989-01-01

    A considerable number of CRESP-relevant papers concerning deep-sea biology and radioecology have been published. It is the purpose of this study to call attention to them. They fall into three general categories. The first is papers of general interest. They are mentioned only briefly, and include text references to the global bibliography at the end of the volume. The second are papers that are not only mentioned and referenced, but for various reasons are described in abstract form. The last is a list of papers compiled by H.S.J. Roe specifically for this volume. They are listed in bibliographic form, and are also included in the global bibliography at the end of the volume

  6. The moving minimum audible angle is smaller during self motion than during source motion.

    Directory of Open Access Journals (Sweden)

    W. Owen eBrimijoin

    2014-09-01

    Full Text Available We are rarely perfectly still: our heads rotate in three axes and move in three dimensions, constantly varying the spectral and binaural cues at the ear drums. In spite of this motion, static sound sources in the world are typically perceived as stable objects. This argues that the auditory system – in a manner not unlike the vestibulo-ocular reflex – works to compensate for self motion and stabilize our sensory representation of the world. We tested a prediction arising from this postulate: that self motion should be processed more accurately than source motion.We used an infrared motion tracking system to measure head angle, and real-time interpolation of head related impulse responses to create head-stabilized signals that appeared to remain fixed in space as the head turned. After being presented with pairs of simultaneous signals consisting of a man and a woman speaking a snippet of speech, normal and hearing impaired listeners were asked to report whether the female voice was to the left or the right of the male voice. In this way we measured the moving minimum audible angle (MMAA. This measurement was made while listeners were asked to turn their heads back and forth between ± 15° and the signals were stabilized in space. After this self-motion condition we measured MMAA in a second source-motion condition when listeners remained still and the virtual locations of the signals were moved using the trajectories from the first condition.For both normal and hearing impaired listeners, we found that the MMAA for signals moving relative to the head was ~1-2° smaller when the movement was the result of self motion than when it was the result of source motion, even though the motion with respect to the head was identical. These results as well as the results of past experiments suggest that spatial processing involves an ongoing and highly accurate comparison of spatial acoustic cues with self-motion cues.

  7. The SE sector of the Middle Weichselian Eurasian Ice Sheet was much smaller than assumed

    Science.gov (United States)

    Räsänen, Matti E.; Huitti, Janne V.; Bhattarai, Saroj; Harvey, Jerry; Huttunen, Sanna

    2015-08-01

    Quaternary climatic and glacial history must be known in order to understand future environments. Reconstructions of the last Weichselian glacial cycle 117,000-11,700 years (kyr) ago propose that S Finland, adjacent Russia and the Baltic countries in the SE sector of the Eurasian Ice Sheet (EIS), were glaciated during the Middle Weichselian time [marine isotope stage (MIS) 4, 71-57 kyr ago] and that this glaciation was preceded in S Finland by an Early Weichselian interstadial (MIS 5c, 105-93 kyr ago) with pine forest. We apply glacial sequence stratigraphy to isolated Late Pleistocene onshore outcrop sections and show, that these events did not take place. The one Late Weichselian glaciation (MIS 2, 29-11 kyr ago) was preceded in S Finland by a nearly 90 kyr non-glacial period, featuring tundra with permafrost and probably birch forest. Our new Middle Weichselian paleoenvironmental scenario revises the configuration and hydrology of the S part of EIS and gives new setting for the evolution of Scandinavian biota. If future development during the coming glacial cycle proves to be similar, the high-level nuclear waste stored in the bedrock of SW Finland should be located deeper than currently planned, i.e. below any possible future permafrost.

  8. Dispositional Mindfulness Co-Varies with Smaller Amygdala and Caudate Volumes in Community Adults

    Science.gov (United States)

    Taren, Adrienne A.; Creswell, J. David; Gianaros, Peter J.

    2013-01-01

    Mindfulness, a psychological process reflecting attention and awareness to what is happening in the present moment, has been associated with increased well-being and decreased depression and anxiety in both healthy and patient populations. However, little research has explored underlying neural pathways. Recent work suggests that mindfulness (and mindfulness training interventions) may foster neuroplastic changes in cortico-limbic circuits responsible for stress and emotion regulation. Building on this work, we hypothesized that higher levels of dispositional mindfulness would be associated with decreased grey matter volume in the amgydala. In the present study, a self-report measure of dispositional mindfulness and structural MRI images were obtained from 155 healthy community adults. Volumetric analyses showed that higher dispositional mindfulness is associated with decreased grey matter volume in the right amygdala, and exploratory analyses revealed that higher dispositional mindfulness is also associated with decreased grey matter volume in the left caudate. Moreover, secondary analyses indicate that these amygdala and caudate volume associations persist after controlling for relevant demographic and individual difference factors (i.e., age, total grey matter volume, neuroticism, depression). Such volumetric differences may help explain why mindful individuals have reduced stress reactivity, and suggest new candidate structural neurobiological pathways linking mindfulness with mental and physical health outcomes. PMID:23717632

  9. Dispositional mindfulness co-varies with smaller amygdala and caudate volumes in community adults.

    Directory of Open Access Journals (Sweden)

    Adrienne A Taren

    Full Text Available Mindfulness, a psychological process reflecting attention and awareness to what is happening in the present moment, has been associated with increased well-being and decreased depression and anxiety in both healthy and patient populations. However, little research has explored underlying neural pathways. Recent work suggests that mindfulness (and mindfulness training interventions may foster neuroplastic changes in cortico-limbic circuits responsible for stress and emotion regulation. Building on this work, we hypothesized that higher levels of dispositional mindfulness would be associated with decreased grey matter volume in the amgydala. In the present study, a self-report measure of dispositional mindfulness and structural MRI images were obtained from 155 healthy community adults. Volumetric analyses showed that higher dispositional mindfulness is associated with decreased grey matter volume in the right amygdala, and exploratory analyses revealed that higher dispositional mindfulness is also associated with decreased grey matter volume in the left caudate. Moreover, secondary analyses indicate that these amygdala and caudate volume associations persist after controlling for relevant demographic and individual difference factors (i.e., age, total grey matter volume, neuroticism, depression. Such volumetric differences may help explain why mindful individuals have reduced stress reactivity, and suggest new candidate structural neurobiological pathways linking mindfulness with mental and physical health outcomes.

  10. User perspectives on relevance criteria

    DEFF Research Database (Denmark)

    Maglaughlin, Kelly L.; Sonnenwald, Diane H.

    2002-01-01

    , partially relevant, or not relevant to their information need; and explained their decisions in an interview. Analysis revealed 29 criteria, discussed positively and negatively, that were used by the participants when selecting passages that contributed or detracted from a document's relevance......This study investigates the use of criteria to assess relevant, partially relevant, and not-relevant documents. Study participants identified passages within 20 document representations that they used to make relevance judgments; judged each document representation as a whole to be relevant...... matter, thought catalyst), full text (e.g., audience, novelty, type, possible content, utility), journal/publisher (e.g., novelty, main focus, perceived quality), and personal (e.g., competition, time requirements). Results further indicate that multiple criteria are used when making relevant, partially...

  11. Harvey, Mark S. (2003: Catalogue of the smaller arachnid orders of the world: Amblypygi, Uropygi, Schizomida, Palpigradi, Ricinulei and Solifugae

    Directory of Open Access Journals (Sweden)

    Blick, Theo

    2004-11-01

    Full Text Available book review: Harvey Mark S. (2003: Catalogue of the smaller arachnid orders of the world: Amblypygi, Uropygi, Schizomida, Palpigradi, Ricinulei and Solifugae. Includes checklists for Europe of: Amblypygi, Uropygi, Schizomida, Palpigradi, Solifugae.

  12. Framework for a sustainable development of neutron beam work in the smaller research reactors

    International Nuclear Information System (INIS)

    Carvalho, F.G.; Margaca, F.M.A.

    1995-01-01

    The authors analyze the present situation of research reactors for neutron beam work in the light of the changes that took place in the nuclear field during the last decades. Trends in supply and demand of neutron beam time in view of the specific requirements of the techniques and of the user's community are outlined. It is argued that resources, both human and material, should be considered in a global perspective, encompassing the national, regional and international levels, where national facilities, mostly low flux research reactors, should be looked upon as a valuable component of a commonwealth of resources to be usefully exploited for the benefit of the neutron user's community at large. The importance of international cooperation to develop a higher level of research reactor utilization is emphasized while suggestions concerning the role of IAEA are made, particularly, to promote the mobility of scientists and engineers directed from developed to less developed countries (LDC's) where research reactors are in operation. The potential of small research reactors in LDC's as an instrument of the country's general scientific and technological development is pointed out as well as difficulties commonly experienced and essential requirements of a successful performance with emphasis on the importance of establishing close links with the national scientific community and especially with university groups. The scientific and technological relevance of neutron scattering techniques is discussed. Reference is made to the techniques best suited to modest research reactor facilities as well as to the importance of developing a local competence in instrument design, optimization and construction. (author). 12 refs

  13. EOG feature relevance determination for microsleep detection

    Directory of Open Access Journals (Sweden)

    Golz Martin

    2017-09-01

    Full Text Available Automatic relevance determination (ARD was applied to two-channel EOG recordings for microsleep event (MSE recognition. 10 s immediately before MSE and also before counterexamples of fatigued, but attentive driving were analysed. Two type of signal features were extracted: the maximum cross correlation (MaxCC and logarithmic power spectral densities (PSD averaged in spectral bands of 0.5 Hz width ranging between 0 and 8 Hz. Generalised learn-ing vector quantisation (GRLVQ was used as ARD method to show the potential of feature reduction. This is compared to support-vector machines (SVM, in which the feature reduction plays a much smaller role. Cross validation yielded mean normalised relevancies of PSD features in the range of 1.6 – 4.9 % and 1.9 – 10.4 % for horizontal and vertical EOG, respectively. MaxCC relevancies were 0.002 – 0.006 % and 0.002 – 0.06 %, respectively. This shows that PSD features of vertical EOG are indispensable, whereas MaxCC can be neglected. Mean classification accuracies were estimated at 86.6±b 1.3 % and 92.3±b 0.2 % for GRLVQ and SVM, respectively. GRLVQ permits objective feature reduction by inclusion of all processing stages, but is not as accurate as SVM.

  14. EOG feature relevance determination for microsleep detection

    Directory of Open Access Journals (Sweden)

    Golz Martin

    2017-09-01

    Full Text Available Automatic relevance determination (ARD was applied to two-channel EOG recordings for microsleep event (MSE recognition. 10 s immediately before MSE and also before counterexamples of fatigued, but attentive driving were analysed. Two type of signal features were extracted: the maximum cross correlation (MaxCC and logarithmic power spectral densities (PSD averaged in spectral bands of 0.5 Hz width ranging between 0 and 8 Hz. Generalised learn-ing vector quantisation (GRLVQ was used as ARD method to show the potential of feature reduction. This is compared to support-vector machines (SVM, in which the feature reduction plays a much smaller role. Cross validation yielded mean normalised relevancies of PSD features in the range of 1.6 - 4.9 % and 1.9 - 10.4 % for horizontal and vertical EOG, respectively. MaxCC relevancies were 0.002 - 0.006 % and 0.002 - 0.06 %, respectively. This shows that PSD features of vertical EOG are indispensable, whereas MaxCC can be neglected. Mean classification accuracies were estimated at 86.6±b 1.3 % and 92.3±b 0.2 % for GRLVQ and SVM, respec-tively. GRLVQ permits objective feature reduction by inclu-sion of all processing stages, but is not as accurate as SVM.

  15. Comparison between smaller ruptured intracranial aneurysm and larger un-ruptured intracranial aneurysm: gene expression profile analysis.

    Science.gov (United States)

    Li, Hao; Li, Haowen; Yue, Haiyan; Wang, Wen; Yu, Lanbing; ShuoWang; Cao, Yong; Zhao, Jizong

    2017-07-01

    As it grows in size, an intracranial aneurysm (IA) is prone to rupture. In this study, we compared two extreme groups of IAs, ruptured IAs (RIAs) smaller than 10 mm and un-ruptured IAs (UIAs) larger than 10 mm, to investigate the genes involved in the facilitation and prevention of IA rupture. The aneurismal walls of 6 smaller saccular RIAs (size smaller than 10 mm), 6 larger saccular UIAs (size larger than 10 mm) and 12 paired control arteries were obtained during surgery. The transcription profiles of these samples were studied by microarray analysis. RT-qPCR was used to confirm the expression of the genes of interest. In addition, functional group analysis of the differentially expressed genes was performed. Between smaller RIAs and larger UIAs, 101 genes and 179 genes were significantly over-expressed, respectively. In addition, functional group analysis demonstrated that the up-regulated genes in smaller RIAs mainly participated in the cellular response to metal ions and inorganic substances, while most of the up-regulated genes in larger UIAs were involved in inflammation and extracellular matrix (ECM) organization. Moreover, compared with control arteries, inflammation was up-regulated and muscle-related biological processes were down-regulated in both smaller RIAs and larger UIAs. The genes involved in the cellular response to metal ions and inorganic substances may facilitate the rupture of IAs. In addition, the healing process, involving inflammation and ECM organization, may protect IAs from rupture.

  16. Smaller genitals at school age in boys whose mothers were exposed to non-persistent pesticides in early pregnancy

    DEFF Research Database (Denmark)

    Veje, Christine Wohlfahrt; Andersen, H R; Jensen, Tina Kold

    2012-01-01

    . The effects were associated with the maternal exposure levels, so that high-exposed boys had smaller genitals than medium-exposed boys, who had smaller genitals than those who were unexposed. Boys of mothers in the high exposure group (n = 23) had 24.7% smaller testes (95% CI: -62.2; -10.1) and 9.4% shorter...... penile length (95% CI: -16.8; -1.1) compared with the unexposed. The testicular volume and penile length at school age could be tracked to measures from the same boys made at 3 months, e.g. those that had small testes at school age also had small testes at 3 months. Pituitary and testicular hormone serum...

  17. Examining the Rule of Thumb of Not Using Multilevel Modeling: The "Design Effect Smaller than Two" Rule

    Science.gov (United States)

    Lai, Mark H. C.; Kwok, Oi-man

    2015-01-01

    Educational researchers commonly use the rule of thumb of "design effect smaller than 2" as the justification of not accounting for the multilevel or clustered structure in their data. The rule, however, has not yet been systematically studied in previous research. In the present study, we generated data from three different models…

  18. French Second Language Teacher Education and Continuing Professional Development in Canada: The Roles of Smaller Universities and Related Institutions.

    Science.gov (United States)

    Heffernan, Peter J.

    1991-01-01

    Discusses teacher shortages in French language instruction areas in Canada, both core and immersion; the rationalization of programs; staffing and financial support among Alberta's tertiary education; language teacher preparation; and continuing professional development. Suggestions are made as to how a smaller university can better fulfill its…

  19. Examining Behavioral, Relational, and Cognitive Engagement in Smaller Learning Communities: A Case Study of Reform in One Suburban District

    Science.gov (United States)

    Davis, Heather A.; Chang, Mei-Lin; Andrzejewski, Carey E.; Poirier, Ryan R.

    2010-01-01

    The purpose of this project was to examine the impact of Smaller Learning Community reform on students' behavioral, relational, and cognitive engagement in a suburban school district experiencing urbanization. We describe a project in which we evaluated the engagement of a cohort of 8th grade students as they transitioned to high school (n = 605).…

  20. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  1. The smaller windmill

    Energy Technology Data Exchange (ETDEWEB)

    Sanguinetti, P. [Trillium Windmills Inc., Orillia, ON (Canada)

    1997-06-01

    The importance of small windchargers, below a rating of 1000 watts, was discussed. These units can go wherever there is a need to charge a 12 volt or 24 volt battery and where there is no easily available conventional electricity source, such as a sailboat, farm, scientific site, or cottage. Trillium Windmills was set up to market the Rutland Windcharger which is a small windcharger rated at 75 watts in a 22 MPH wind. To give an indication of the size of the market, it was pointed out that two manufacturers, one in North America and one in England, have monthly production runs of more than 1000 small wind turbines of less than 500 watts.

  2. Making Microbiology Even Smaller!

    Science.gov (United States)

    Young, Linda Mull; Motz, Vicki Abrams

    2013-01-01

    We outline protocols for producing slant-minis (SLINIs) and mini-deeps (MEEPs) and examples of their use in simple microbiology experiments suitable for high school students. The principal benefits of these protocols are decreased cost associated with significantly reduced media use; easier, less expensive disposal of waste; and increased safety…

  3. Smaller than a gnat

    CERN Multimedia

    2006-01-01

    "CERN in Geneva is the largest research center for particle physics in the world; the Institute is a Mecca for scientists. Particle are projected into each other in gigantic ring accelerators to gain information from their reactions about the force and relations inside the elements. These experiments require high vacuum - Oerlikon Leybold Vacuum recently competed in a Eyropean call for bids for the Large Hadron Collider (LHC) and won the contract." (1,5 page)

  4. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  6. New tablet formulation of tacrolimus with smaller interindividual variability may become a better treatment option than the conventional capsule formulation in organ transplant patients

    Directory of Open Access Journals (Sweden)

    Kim YK

    2017-09-01

    Full Text Available Yu Kyong Kim,1 Anhye Kim,1,2 Shin Jung Park,3 Howard Lee1,4 1Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 2Clinical Trial Center, Ajou University Medical Center, Suwon, 3Research Institute, Chong Kun Dang Pharmaceutical Corp, Yongin, 4Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Republic of Korea Abstract: To evaluate the pharmacokinetic (PK and tolerability profiles of a new tablet formulation of tacrolimus and its interindividual variability (IIV in the systemic exposure, and to compare them with those of the conventional capsule formulation, a randomized, open-label, two-treatment, two-period, two-sequence, crossover study was performed in 47 healthy males. The capsule or tablet formulation of tacrolimus was orally administered, and serial blood samples were collected up to 96 hours after dosing. Whole-blood tacrolimus concentration was determined using liquid chromatography–tandem mass spectrometry. The maximum whole-blood tacrolimus concentration (Cmax and the area under the whole-blood tacrolimus concentration–time curve from 0 hour to the last quantifiable concentration (AUClast were compared between the two formulations. The similarity factor (f2 of the in vitro dissolution profiles was calculated. The geometric mean ratio (90% confidence interval of tablet to capsule was 0.9680 (0.8873–1.0560 and 1.0322 (0.9359–1.1385 for Cmax and AUClast, respectively. The IIV of Cmax and AUClast of the tablet was smaller than the capsule. The f2 values were >50 in all media. Both formulations were well tolerated. Thus, the tablet formulation of tacrolimus has smaller IIV in the systemic exposure than capsule, while having comparable PK and tolerability profiles, which may render it as a better treatment option for organ transplant patients. Keywords: new formulation, incrementally

  7. Profiles of Dialogue for Relevance

    Directory of Open Access Journals (Sweden)

    Douglas Walton

    2016-12-01

    Full Text Available This paper uses argument diagrams, argumentation schemes, and some tools from formal argumentation systems developed in artificial intelligence to build a graph-theoretic model of relevance shown to be applicable (with some extensions as a practical method for helping a third party judge issues of relevance or irrelevance of an argument in real examples. Examples used to illustrate how the method works are drawn from disputes about relevance in natural language discourse, including a criminal trial and a parliamentary debate.

  8. Detection of smaller J{sub c} region and damage in YBCO coated conductors by using permanent magnet method

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, K., E-mail: tey88221@st.yamagata-u.ac.jp [Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510 (Japan); Saito, A. [Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510 (Japan); Takano, Y.; Suzuki, T. [Tohoku Seiki Industries, Ltd., 3-1246, Tachiyagawa, Yamagata 990-2251 (Japan); Yamada, H.; Takayama, T.; Kamitani, A.; Ohshima, S. [Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510 (Japan)

    2011-11-15

    We developed a non-destructive method for measuring the critical current density (J{sub c}) in YBCO-coated conductors by using a permanent magnet (Sm{sub 2}Co{sub 17}). J{sub c} could be determined from the repulsive force (F{sub r}) generated between a permanent magnet and a coated conductor where shielding current flows. We also examined the influence of damage to the film on the J{sub c} distribution. The measured F{sub r} when the permanent magnet approached the cut part was smaller than that of the undamaged area. We developed a non-destructive method for measuring the critical current density (J{sub c}) in YBCO-coated conductors by using a permanent magnet (Sm{sub 2}Co{sub 17}). J{sub c} could be determined from the repulsive force (F{sub r}) generated between a permanent magnet and a coated conductor where shielding current flows. We tried to detect a smaller J{sub c} region in the coated conductor by using the system. The J{sub c} distribution could be determined without influence from the thick copper film on YBCO thin film. We also examined the influence of damage to the film on the J{sub c} distribution. The surface of the coated conductors was cut by using a knife. The measured F{sub r} when the permanent magnet approached the cut part was smaller than that of the undamaged area. This J{sub c} measurement technique will be useful for detecting smaller J{sub c} regions and defects in coated conductors.

  9. Increased expression and altered methylation of HERVWE1 in the human placentas of smaller fetuses from monozygotic, dichorionic, discordant twins.

    Directory of Open Access Journals (Sweden)

    Yu Gao

    Full Text Available BACKGROUND: The human endogenous retroviral family W, Env(C7, member 1 gene (HERVWE1 is thought to participate in trophoblast cell fusion, and its expression is diminished in the placentas of singleton intrauterine growth-retarded pregnancies. However, there is limited information about the role of HERVWE1 in discordant fetal growth in twins. This study was to compare HERVWE1 gene expression between the placentas of discordant monozygotic twins and to identify its regulation by methylation. METHODOLOGY/PRINCIPAL FINDINGS: Fetuses from twenty-one pairs of monozygotic, dichorionic, discordant twins were marked as "smaller" or "larger" according to birth weight. Placental HERVWE1 mRNA and protein expression profiles were analyzed using quantitative RT-PCR and immunohistochemistry (IHC staining. Methylation profiles of the HERVWE1 promoter region were analyzed using a pyrosequencing assay. DNA methyltransferase (DNMT transcript levels were analyzed by RT-PCR. 5-methyl cytosine (5-MC was stained using an immunohistochemical assay. There was a significant negative correlation between HERVWE1 mRNA levels and birth weight in twins (P0.05. The DNMT3b3 mRNA levels in the smaller group were significantly downregulated compared with the larger group in discordant twins(P<0.05, whereas the DNMT3b7 mRNA levels in the smaller group were significantly upregulated compared with the larger group in discordant twins(P<0.05. CONCLUSIONS/SIGNIFICANCE: In discordant, monozygotic, dichorionic twins, HERVWE1 expression was higher in smaller fetuses and lower in larger fetuses. Methylation of the HERVWE1 gene promoter region may participate in the regulation of HERVWE1 gene expression in discordant twin pregnancies.

  10. From “Smaller is Stronger” to “Size-Independent Strength Plateau”: Towards Measuring the Ideal Strength of Iron

    KAUST Repository

    Han, Wei-Zhong

    2015-04-17

    The trend from “smaller is stronger” to “size-independent strength plateau” is observed in the compression of spherical iron nanoparticles. When the diameter of iron nanospheres is less than a critical value, the maximum contact pressure saturates at 10.7 GPa, corresponding to a local shear stress of ≈9.4 GPa, which is comparable to the theoretical shear strength of iron.

  11. From “Smaller is Stronger” to “Size-Independent Strength Plateau”: Towards Measuring the Ideal Strength of Iron

    KAUST Repository

    Han, Wei-Zhong; Huang, Ling; Ogata, Shigenobu; Kimizuka, Hajime; Yang, Zhao-Chun; Weinberger, Christopher; Li, Qing-Jie; Liu, Bo-Yu; Zhang, Xixiang; Li, Ju; Ma, Evan; Shan, Zhi-Wei

    2015-01-01

    The trend from “smaller is stronger” to “size-independent strength plateau” is observed in the compression of spherical iron nanoparticles. When the diameter of iron nanospheres is less than a critical value, the maximum contact pressure saturates at 10.7 GPa, corresponding to a local shear stress of ≈9.4 GPa, which is comparable to the theoretical shear strength of iron.

  12. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  13. Application of a model for delivering occupational safety and health to smaller businesses: Case studies from the US.

    Science.gov (United States)

    Cunningham, Thomas R; Sinclair, Raymond

    2015-01-01

    Smaller firms are the majority in every industry in the US, and they endure a greater burden of occupational injuries, illnesses, and fatalities than larger firms. Smaller firms often lack the necessary resources for effective occupational safety and health activities, and many require external assistance with safety and health programming. Based on previous work by researchers in Europe and New Zealand, NIOSH researchers developed for occupational safety and health intervention in small businesses. This model was evaluated with several intermediary organizations. Four case studies which describe efforts to reach small businesses with occupational safety and health assistance include the following: trenching safety training for construction, basic compliance and hazard recognition for general industry, expanded safety and health training for restaurants, and fall prevention and respirator training for boat repair contractors. Successful efforts included participation by the initiator among the intermediaries' planning activities, alignment of small business needs with intermediary offerings, continued monitoring of intermediary activities by the initiator, and strong leadership for occupational safety and health among intermediaries. Common challenges were a lack of resources among intermediaries, lack of opportunities for in-person meetings between intermediaries and the initiator, and balancing the exchanges in the initiator-intermediary-small business relationships. The model offers some encouragement that initiator organizations can contribute to sustainable OSH assistance for small firms, but they must depend on intermediaries who have compatible interests in smaller businesses and they must work to understand the small business social system.

  14. Application of a model for delivering occupational safety and health to smaller businesses: Case studies from the US

    Science.gov (United States)

    Cunningham, Thomas R.; Sinclair, Raymond

    2015-01-01

    Smaller firms are the majority in every industry in the US, and they endure a greater burden of occupational injuries, illnesses, and fatalities than larger firms. Smaller firms often lack the necessary resources for effective occupational safety and health activities, and many require external assistance with safety and health programming. Based on previous work by researchers in Europe and New Zealand, NIOSH researchers developed for occupational safety and health intervention in small businesses. This model was evaluated with several intermediary organizations. Four case studies which describe efforts to reach small businesses with occupational safety and health assistance include the following: trenching safety training for construction, basic compliance and hazard recognition for general industry, expanded safety and health training for restaurants, and fall prevention and respirator training for boat repair contractors. Successful efforts included participation by the initiator among the intermediaries’ planning activities, alignment of small business needs with intermediary offerings, continued monitoring of intermediary activities by the initiator, and strong leadership for occupational safety and health among intermediaries. Common challenges were a lack of resources among intermediaries, lack of opportunities for in-person meetings between intermediaries and the initiator, and balancing the exchanges in the initiator–intermediary–small business relationships. The model offers some encouragement that initiator organizations can contribute to sustainable OSH assistance for small firms, but they must depend on intermediaries who have compatible interests in smaller businesses and they must work to understand the small business social system. PMID:26300585

  15. Relevance theory: pragmatics and cognition.

    Science.gov (United States)

    Wearing, Catherine J

    2015-01-01

    Relevance Theory is a cognitively oriented theory of pragmatics, i.e., a theory of language use. It builds on the seminal work of H.P. Grice(1) to develop a pragmatic theory which is at once philosophically sensitive and empirically plausible (in both psychological and evolutionary terms). This entry reviews the central commitments and chief contributions of Relevance Theory, including its Gricean commitment to the centrality of intention-reading and inference in communication; the cognitively grounded notion of relevance which provides the mechanism for explaining pragmatic interpretation as an intention-driven, inferential process; and several key applications of the theory (lexical pragmatics, metaphor and irony, procedural meaning). Relevance Theory is an important contribution to our understanding of the pragmatics of communication. © 2014 John Wiley & Sons, Ltd.

  16. Clinical relevance in anesthesia journals

    DEFF Research Database (Denmark)

    Lauritsen, Jakob; Møller, Ann M

    2006-01-01

    The purpose of this review is to present the latest knowledge and research on the definition and distribution of clinically relevant articles in anesthesia journals. It will also discuss the importance of the chosen methodology and outcome of articles.......The purpose of this review is to present the latest knowledge and research on the definition and distribution of clinically relevant articles in anesthesia journals. It will also discuss the importance of the chosen methodology and outcome of articles....

  17. Increased Expression and Altered Methylation of HERVWE1 in the Human Placentas of Smaller Fetuses from Monozygotic, Dichorionic, Discordant Twins

    Science.gov (United States)

    Wang, Zilian; Luo, Yanmin; Sun, Hongyu; Zhou, Yi; Huang, Linhuan; Li, Manchao; Fang, Qun; Jiang, Shiwen

    2012-01-01

    Background The human endogenous retroviral family W, Env(C7), member 1 gene (HERVWE1) is thought to participate in trophoblast cell fusion, and its expression is diminished in the placentas of singleton intrauterine growth-retarded pregnancies. However, there is limited information about the role of HERVWE1 in discordant fetal growth in twins. This study was to compare HERVWE1 gene expression between the placentas of discordant monozygotic twins and to identify its regulation by methylation. Methodology/Principal Findings Fetuses from twenty-one pairs of monozygotic, dichorionic, discordant twins were marked as “smaller” or “larger” according to birth weight. Placental HERVWE1 mRNA and protein expression profiles were analyzed using quantitative RT-PCR and immunohistochemistry (IHC) staining. Methylation profiles of the HERVWE1 promoter region were analyzed using a pyrosequencing assay. DNA methyltransferase (DNMT) transcript levels were analyzed by RT-PCR. 5-methyl cytosine (5-MC) was stained using an immunohistochemical assay. There was a significant negative correlation between HERVWE1 mRNA levels and birth weight in twins (P0.05). The DNMT3b3 mRNA levels in the smaller group were significantly downregulated compared with the larger group in discordant twins(P<0.05), whereas the DNMT3b7 mRNA levels in the smaller group were significantly upregulated compared with the larger group in discordant twins(P<0.05). Conclusions/Significance In discordant, monozygotic, dichorionic twins, HERVWE1 expression was higher in smaller fetuses and lower in larger fetuses. Methylation of the HERVWE1 gene promoter region may participate in the regulation of HERVWE1 gene expression in discordant twin pregnancies. PMID:22457770

  18. Smaller Anterior Cruciate Ligament Diameter Is a Predictor of Subjects Prone to Ligament Injuries: An Ultrasound Study

    Directory of Open Access Journals (Sweden)

    Parag Suresh Mahajan

    2015-01-01

    Full Text Available Purpose. To test if diameter of normal anterior cruciate ligament (ACL can be measured by ultrasound (US, to see if there is a relationship between smaller ACL diameter and ACL injury, and to assess agreement between radiologists in measuring ACL diameter in cases and matched controls. Materials and Methods. In this ethics committee-approved study, maximum diameter of ACL near tibial insertion site was measured by static and dynamic US study in 25 normal contralateral knees of subjects who suffered noncontact ACL injury and in 25 matched control subjects. Results. ACL was visualized as a thick linear hypoechoic band inserted approximately 11 mm caudal to the tibial plateau and the intercondylar eminence. Maximum diameter of contralateral ACL near tibial insertion site among injured subjects was significantly smaller than in noninjured subjects (0.62 ± 0.07 cm versus 0.81 ± 0.06 cm; P<0.0001. In the regression analysis, the diameter of ACL near tibial insertion site was found significantly proportional to body weight and not significantly associated to height, gender, and age. Conclusion. Diameter of normal ACL near tibial insertion site can be measured by US and the maximum diameter is significantly smaller among subjects with noncontact ACL injury. US is a promising modality that can be used as an excellent screening test to detect subjects especially aspiring athletes prone to ACL injury. Very strong agreement was observed between radiologists in measuring ACL diameter.

  19. Global and regional associations of smaller cerebral gray and white matter volumes with gait in older people.

    Directory of Open Access Journals (Sweden)

    Michele L Callisaya

    Full Text Available BACKGROUND: Gait impairments increase with advancing age and can lead to falls and loss of independence. Brain atrophy also occurs in older age and may contribute to gait decline. We aimed to investigate global and regional relationships of cerebral gray and white matter volumes with gait speed, and its determinants step length and cadence, in older people. METHODS: In a population-based study, participants aged >60 years without Parkinson's disease or brain infarcts underwent magnetic resonance imaging and gait measurements using a computerized walkway. Linear regression was used to study associations of total gray and white matter volumes with gait, adjusting for each other, age, sex, height and white matter hyperintensity volume. Other covariates considered in analyses included weight and vascular disease history. Voxel-based morphometry was used to study regional relationships of gray and white matter with gait. RESULTS: There were 305 participants, mean age 71.4 (6.9 years, 54% male, mean gait speed 1.16 (0.22 m/s. Smaller total gray matter volume was independently associated with poorer gait speed (p = 0.001 and step length (p<0.001, but not cadence. Smaller volumes of cortical and subcortical gray matter in bilateral regions important for motor control, vision, perception and memory were independently associated with slower gait speed and shorter steps. No global or regional associations were observed between white matter volume and gait independent of gray matter volume, white matter hyperintensity volume and other covariates. CONCLUSION: Smaller gray matter volume in bilaterally distributed brain networks serving motor control was associated with slower gait speed and step length, but not cadence.

  20. "What time is my next meal?" delay-discounting individuals choose smaller portions under conditions of uncertainty.

    Science.gov (United States)

    Zimmerman, Annie R; Ferriday, Danielle; Davies, Sarah R; Martin, Ashley A; Rogers, Peter J; Mason, Alice; Brunstrom, Jeffrey M

    2017-09-01

    'Dietary' delay discounting is typically framed as a trade-off between immediate rewards and long-term health concerns. Our contention is that prospective thinking also occurs over shorter periods, and is engaged to select portion sizes based on the interval between meals (inter-meal interval; IMI). We sought to assess the extent to which the length of an IMI influences portion-size selection. We predicted that delay discounters would show 'IMI insensitivity' (relative lack of concern about hunger or fullness between meals). In particular, we were interested in participants' sensitivity to an uncertain IMI. We hypothesized that when meal times were uncertain, delay discounters would be less responsive and select smaller portion sizes. Participants (N = 90) selected portion sizes for lunch. In different trials, they were told to expect dinner at 5pm, 9pm, and either 5pm or 9pm (uncertain IMI). Individual differences in future-orientation were measured using a monetary delay-discounting task. Participants chose larger portions when the IMI was longer (p relationship between BMI and smaller portion selection in uncertainty (p < 0.05). This is the first study to report an association between delay discounting and IMI insensitivity. We reason that delay discounters selected smaller portions because they were less sensitive to the uncertain IMI, and overlooked concerns about potential future hunger. These findings are important because they illustrate that differences in discounting are expressed in short-term portion-size decisions and suggest that IMI insensitivity increases when meal timings are uncertain. Further research is needed to confirm whether these findings generalise to other populations. Copyright © 2017. Published by Elsevier Ltd.

  1. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  2. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  3. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  4. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  5. Shippingport: A relevant decommissioning project

    International Nuclear Information System (INIS)

    Crimi, F.P.

    1988-01-01

    Because of Shippingport's low electrical power rating (72 MWe), there has been some misunderstanding on the relevancy of the Shippingport Station Decommissioning Project (SSDP) to a modern 1175 MWe commercial pressurized water reactor (PWR) power station. This paper provides a comparison of the major components of the reactor plant of the 72 MWe Shippingport Atomic Power Station and an 1175 MWe nuclear plant and the relevancy of the Shippingport decommissioning as a demonstration project for the nuclear industry. For the purpose of this comparison, Portland General Electric Company's 1175 MWe Trojan Nuclear Plant at Rainier, Oregon, has been used as the reference nuclear power plant. 2 refs., 2 figs., 1 tab

  6. Sexually selected nest-building--Pomatoschistus minutus males build smaller nest-openings in the presence of sneaker males.

    Science.gov (United States)

    Svensson, O; Kvarnemo, C

    2003-09-01

    Both natural selection and sexual selection may act on nest-building. We tested experimentally how different regimes of egg-predation and male-male competition influence nest-building before mating, using the marine fish sand goby, Pomatoschistus minutus. Males with sneaker males present built the smallest nest-openings, smaller than males held alone or with Pomatoschistus microps males (which may predate eggs and compete over nest-sites but not compete over fertilizations). Males with visual access to other nest-building males tended also to build smaller openings than males held alone or with P. microps. Males with egg-predators present built nests with openings not differing significantly from any other treatment. Our results indicate that the small nest-openings found in the sneaker male treatment are sexually selected through protection against sneaking or by female choice. Across treatments, time span before a male started to build his nest also explained variation in nest-opening width; males starting late built larger nest-openings.

  7. Weekday AOD smaller than weekend AOD in eastern China on the basis of the MODIS AOD product

    Science.gov (United States)

    Song, Jingjing; Xia, Xiangao; Zhang, Xiaoling; Che, Huizheng; Li, Xiaojing

    2018-05-01

    A weekly cycle of surface particulate matter (PM) characterized by smaller values during weekends and larger values during weekdays was reported in eastern China. Whether column-integrated aerosol optical depth (AOD) showed similar weekly cycling as that of PM was debated. The weekly variation of AOD in eastern China was further studied by using the latest MODIS aerosol product (collection 6) with a fine spatial resolution (0.1°) from 2002 to 2015. We used three statistical methods to determine whether the weekly cycle of AOD was significant. AOD during weekdays (Wednesday to Friday) was lower than that during weekends. The maximum and minimum AOD was generally observed on Monday and Wednesday, respectively. This weekly pattern of AOD was in good agreement with previous results based on satellite aerosol products with a coarse spatial resolution, but it was in contrast to that of PM. Further analysis of the AOD weekly variability in 19 provincial cities suggested that AOD during weekdays was smaller than that during weekends in urban regions. Potential causes for the different weekly cycle of PM and AOD in eastern China were discussed.

  8. Stratification of mixtures in evaporating liquid films occurs only for a range of volume fractions of the smaller component

    Science.gov (United States)

    Sear, Richard P.

    2018-04-01

    I model the drying of a liquid film containing small and big colloid particles. Fortini et al. [Phys. Rev. Lett. 116, 118301 (2016)] studied these films with both computer simulation and experiment. They found that at the end of drying, the mixture had stratified with a layer of the smaller particles on top of the big particles. I develop a simple model for this process. The model has two ingredients: arrest of the diffusion of the particles at high density and diffusiophoretic motion of the big particles due to gradients in the volume fraction of the small particles. The model predicts that stratification only occurs over a range of initial volume fractions of the smaller colloidal species. Above and below this range, the downward diffusiophoretic motion of the big particles is too slow to remove the big particles from the top of the film, and so there is no stratification. In agreement with earlier work, the model also predicts that large Péclet numbers for drying are needed to see stratification.

  9. Comet 81p/Wild 2: The Updated Stardust Coma Dust Fluence Measurement for Smaller (Sub 10-Micrometre) Particles

    Science.gov (United States)

    Price, M. C.; Kearsley, A. T.; Burchell, M. J.; Horz, Friedrich; Cole, M. J.

    2009-01-01

    Micrometre and smaller scale dust within cometary comae can be observed by telescopic remote sensing spectroscopy [1] and the particle size and abundance can be measured by in situ spacecraft impact detectors [2]. Initial interpretation of the samples returned from comet 81P/Wild 2 by the Stardust spacecraft [3] appears to show that very fine dust contributes not only a small fraction of the solid mass, but is also relatively sparse [4], with a low negative power function describing grain size distribution, contrasting with an apparent abundance indicated by the on-board Dust Flux Monitor Instrument (DFMI) [5] operational during the encounter. For particles above 10 m diameter there is good correspondence between results from the DFMI and the particle size inferred from experimental calibration [6] of measured aerogel track and aluminium foil crater dimensions (as seen in Figure 4 of [4]). However, divergence between data-sets becomes apparent at smaller sizes, especially submicrometre, where the returned sample data are based upon location and measurement of tiny craters found by electron microscopy of Al foils. Here effects of detection efficiency tail-off at each search magnification can be seen in the down-scale flattening of each scale component, but are reliably compensated by sensible extrapolation between segments. There is also no evidence of malfunction in the operation of DFMI during passage through the coma (S. Green, personal comm.), so can the two data sets be reconciled?

  10. Smaller Dentate Gyrus and CA2 and CA3 Volumes Are Associated with Kynurenine Metabolites in Collegiate Football Athletes.

    Science.gov (United States)

    Meier, Timothy B; Savitz, Jonathan; Singh, Rashmi; Teague, T Kent; Bellgowan, Patrick S F

    2016-07-15

    An imbalance in kynurenine pathway metabolism is hypothesized to be associated with dysregulated glutamatergic neurotransmission, which has been proposed as a mechanism underlying the hippocampal volume loss observed in a variety of neurological disorders. Pre-clinical models suggest that the CA2-3 and dentate gyrus hippocampal subfields are particularly susceptible to excitotoxicity after experimental traumatic brain injury. We tested the hypothesis that smaller hippocampal volumes in collegiate football athletes with (n = 25) and without (n = 24) a concussion history would be most evident in the dentate gyrus and CA2-3 subfields relative to nonfootball healthy controls (n = 27). Further, we investigated whether the concentration of peripheral levels of kynurenine metabolites are altered in football athletes. Football athletes with and without a self-reported concussion history had smaller dentate gyrus (p Football athletes with and without a concussion history had a trend toward lower (p history had greater levels of quinolinic acid compared with athletes without a concussion history (p football athletes with a concussion history (p football athletes without a concussion history (p < 0.05). Our results raise the possibility that abnormalities of the kynurenine metabolic pathway constitute a mechanism for hippocampal volume differences in the context of sports-related brain injury.

  11. Improving CT detection sensitivity for nodal metastases in oesophageal cancer with combination of smaller size and lymph node axial ratio

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jianfang [Chinese Academy of Medical Sciences and Peking Union Medical College, National Cancer Center/Cancer Hospital, Beijing (China); Capital Medical University Electric Power Teaching Hospital, Beijing (China); Wang, Zhu; Qu, Dong; Yao, Libo [Chinese Academy of Medical Sciences and Peking Union Medical College, National Cancer Center/Cancer Hospital, Beijing (China); Shao, Huafei [Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai (China); Liu, Jian [Meitan General Hospital, Beijing (China)

    2018-01-15

    To investigate the value of CT with inclusion of smaller lymph node (LN) sizes and axial ratio to improve the sensitivity in diagnosis of regional lymph node metastases in oesophageal squamous cell carcinoma (OSCC). The contrast-enhanced multidetector row spiral CT (MDCT) multiplanar reconstruction images of 204 patients with OSCC were retrospectively analysed. The long-axis and short-axis diameters of the regional LNs were measured and axial ratios were calculated (short-axis/long-axis diameters). Nodes were considered round if the axial ratio exceeded the optimal LN axial ratio, which was determined by receiver operating characteristic analysis. A positive predictive value (PPV) exceeding 50% is needed. This was achieved only with LNs larger than 9 mm in short-axis diameter, but nodes of this size were rare (sensitivity 37.3%, specificity 96.4%, accuracy 85.8%). If those round nodes (axial ratio exceeding 0.66) between 7 mm and 9 mm in size were considered metastases as well, it might improve the sensitivity to 67.2% with a PPV of 63.9% (specificity 91.6%, accuracy 87.2%). Combination of a smaller size and axial ratio for LNs in MDCT as criteria improves the detection sensitivity for LN metastases in OSCC. (orig.)

  12. Smaller brain size likely in young adults (<40 years old) with depressive symptoms compared to healthy controls. A retrospective study

    International Nuclear Information System (INIS)

    Adachi, Michito; Sato, Takamichi; Kawaguchi, Etsuko; Shibata, Akiko

    2011-01-01

    The aim of this study was to determine whether the brain size of young patients with depressive symptoms is smaller than that of healthy controls using magnetic resonance imaging (MRI). We retrospectively evaluated brain size by calculating the ratio of the brain area to that of the skull (the brain-to-skull ratio) on routine MRI scans including the splenium of the corpus callosum obtained from 19 patients <40 years old with depressive symptoms in 2009. The controls were 12 healthy individuals <40 years old who underwent MRI for medical examinations. The mean brain-to-skull ratio of the control group was 0.850±0.022 (range 0.822-0.889), and that of the patient group was 0.819±0.041 (range 0.756-0.878). An unpaired t-test showed a significant difference in the brain-to-skull ratios between these groups (P=0.011). In particular, in 7 of the 19 patients with longer duration of illness and more severe symptoms, the brain-to-skull ratio was 89%-92% of the mean ratio of the control group. The brain size of young patients with depressive symptoms appears to be smaller than that of healthy controls. (author)

  13. Evaluating the scope for energy-efficiency improvements in the public sector: Benchmarking NHSScotland's smaller health buildings

    International Nuclear Information System (INIS)

    Murray, Joe; Pahl, O.; Burek, S.

    2008-01-01

    The National Health Service in Scotland (NHSScotland) has, in recent years, done much to reduce energy consumption in its major healthcare buildings (hospitals). On average, a reduction of 2% per year has been achieved since 2000, based on hospital buildings. However, there had been little or no attention paid to smaller premises such as health centres, clinics, dentists, etc. Such smaller healthcare buildings in Scotland constitute 29% of the total treated floor area of all NHSScotland buildings and, therefore, may contribute a similar percentage of carbon and other emissions to the environment. By concentrating on a sample of local health centres in Scotland, this paper outlines the creation of an energy benchmark target, which is part of a wider research project to investigate the environmental impacts of small healthcare buildings in Scotland and the scope for improvements. It was found that energy consumption varied widely between different centres but this variation could not be linked to building style, floor area or volume. Overall, it was found that a benchmark of 0.2 GJ/m 3 would be challenging, but realistic

  14. Organizational resilience: Sustained institutional effectiveness among smaller, private, non-profit US higher education institutions experiencing organizational decline.

    Science.gov (United States)

    Moran, Kenneth A

    2016-06-04

    Recent changes in the United States (US) economy have radically disrupted revenue generation among many institutions within higher education within the US. Chief among these disruptions has been fallout associated with the financial crisis of 2008-2009, which triggered a change in the US higher education environment from a period of relative munificence to a prolonged period of scarcity. The hardest hit by this disruption have been smaller, less wealthy institutions which tend to lack the necessary reserves to financially weather the economic storm. Interestingly, a review of institutional effectiveness among these institutions revealed that while many are struggling, some institutions have found ways to not only successfully cope with the impact of declining revenue, but have been able to capitalize on the disruption and thrive. Organizational response is an important factor in successfully coping with conditions of organizational decline. The study examined the impacts of organizational response on institutional effectiveness among higher education institutions experiencing organizational decline. The study's research question asked why some US higher educational institutions are more resilient at coping with organizational decline than other institutions operating within the same segment of the higher education sector. More specifically, what role does organizational resilience have in helping smaller, private non-profit institutions cope and remain effective during organizational decline? A total of 141 US smaller, private non-profit higher educational institutions participated in the study; specifically, the study included responses from participant institutions' key administrators. 60-item survey evaluated administrator responses corresponding to organizational response and institutional effectiveness. Factor analysis was used to specify the underlying structures of rigidity response, resilience response, and institutional effectiveness. Multiple regression

  15. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  16. Dramatic lives and relevant becomings

    DEFF Research Database (Denmark)

    Henriksen, Ann-Karina; Miller, Jody

    2012-01-01

    of marginality into positions of relevance. The analysis builds on empirical data from Copenhagen, Denmark, gained through ethnographic fieldwork with the participation of 20 female informants aged 13–22. The theoretical contribution proposes viewing conflicts as multi-linear, multi-causal and non...

  17. 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

  18. Percutaneous CT-guided biopsy for lung lesions 1 cm or smaller: the technique, results and complication

    International Nuclear Information System (INIS)

    Song, Chi Sung

    2006-01-01

    The author wanted to assess the diagnostic accuracy and safety of percutaneous biopsy for lung lesions 1 cm or smaller; the biopsies were performed on the basis of the modified coaxial technique under CT guidance. Thirty-five patients (22 men and 13 women) 23-76 years old (average age: 56.8 years) with lung lesions 1 cm or smaller underwent CT-guided percutaneous biopsy. Fifteen patients had underlying primary malignancies. After an 18 G guiding cannula was introduced to the border of the small lung lesion via the modified coaxial technique, fine-needle aspiration biopsy with 21 G needle and core tissue biopsies with 19.5 G or 20 G biopsy guns were performed through the lumen of the guiding cannula. The core tissue biopsies were finished after 6 macroscopic core tissue specimens were obtained. When the needle hit the eccentric portion of the small lung lesion, a 'fanning-out' technique with using the guiding cannula was applied to get multiple core tissue specimens from the small lung lesion. The diagnostic accuracy of this method was evaluated and the complications were reviewed. Both the cytopathologic and histopathologic specimens were obtained in all 35 cases. The fanning-out technique was necessary in 15 cases (43%) for obtaining six core tissue specimens from small lesions. The final diagnoses were 17 malignant lesions and 18 benign lesions. Sixteen lesions were true-positive, eighteen were true-negative, none was false-positive and one was false-negative. The overall diagnostic accuracy was 97%. The sensitivity for detecting malignancy and the specificity for benign lesion were 94% and 100%, respectively. The positive and negative predictive values were 100% and 95%, respectively. The diagnostic ability to characterize the specific cell type of the malignant lesion was 94% (16 of 17), that for the benign lesions was 83% (15 of 18), and overall diagnostic ability was 89% (31 of 35). Five patients (14%) developed a pneumopthorax, and one of them (3%) received

  19. Larger Subcortical Gray Matter Structures and Smaller Corpora Callosa at Age 5 Years in HIV Infected Children on Early ART

    Directory of Open Access Journals (Sweden)

    Steven R. Randall

    2017-11-01

    Full Text Available Sub-Saharan Africa is home to 90% of HIV infected (HIV+ children. Since the advent of antiretroviral therapy (ART, HIV/AIDS has transitioned to a chronic condition where central nervous system (CNS damage may be ongoing. Although, most guidelines recommend early ART to reduce CNS viral reservoirs, the brain may be more vulnerable to potential neurotoxic effects of ART during the rapid development phase in the first years of life. Here we investigate differences in subcortical volumes between 5-year-old HIV+ children who received early ART (before age 18 months and uninfected children using manual tracing of Magnetic Resonance Images. Participants included 61 Xhosa children (43 HIV+/18 uninfected, mean age = 5.4 ± 0.3 years, 25 male from the children with HIV early antiretroviral (CHER trial; 27 children initiated ART before 12 weeks of age (ART-Before12Wks and 16 after 12 weeks (ART-After12Wks. Structural images were acquired on a 3T Allegra MRI in Cape Town and manually traced using MultiTracer. Volumetric group differences (HIV+ vs. uninfected; ART-Before12Wks vs. ART-After12Wks were examined for the caudate, nucleus accumbens (NA, putamen (Pu, globus pallidus (GP, and corpus callosum (CC, as well as associations within infected children of structure volumes with age at ART initiation and CD4/CD8 as a proxy for immune health. HIV+ children had significantly larger NA and Pu volumes bilaterally and left GP volumes than controls, whilst CC was smaller. Bilateral Pu was larger in both treatment groups compared to controls, while left GP and bilateral NA were enlarged only in ART-After12Wks children. CC was smaller in both treatment groups compared to controls, and smaller in ART-After12Wks compared to ART-Before12Wks. Within infected children, delayed ART initiation was associated with larger Pu volumes, effects that remained significant when controlling for sex and duration of treatment interruption (left β = 0.447, p = 0.005; right β = 0

  20. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  1. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  2. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  3. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  4. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  5. Twentieth-century shifts in forest structure in California: Denser forests, smaller trees, and increased dominance of oaks.

    Science.gov (United States)

    McIntyre, Patrick J; Thorne, James H; Dolanc, Christopher R; Flint, Alan L; Flint, Lorraine E; Kelly, Maggi; Ackerly, David D

    2015-02-03

    We document changes in forest structure between historical (1930s) and contemporary (2000s) surveys of California vegetation through comparisons of tree abundance and size across the state and within several ecoregions. Across California, tree density in forested regions increased by 30% between the two time periods, whereas forest biomass in the same regions declined, as indicated by a 19% reduction in basal area. These changes reflect a demographic shift in forest structure: larger trees (>61 cm diameter at breast height) have declined, whereas smaller trees (Forest composition in California in the last century has also shifted toward increased dominance by oaks relative to pines, a pattern consistent with warming and increased water stress, and also with paleohistoric shifts in vegetation in California over the last 150,000 y.

  6. Smaller kidney size at birth in South Asians: findings from the Born in Bradford birth cohort study.

    Science.gov (United States)

    Roderick, Paul J; Jeffrey, Robin F; Yuen, Ho M; Godfrey, Keith M; West, Jane; Wright, John

    2016-03-01

    Rates of advanced chronic kidney disease and renal replacement therapy are higher in South Asian than in white British populations. Low birth weight is also more frequent in South Asian populations and has been associated with increased risks of kidney disease, perhaps due to a reduced nephron endowment. Using ultrasound scans at 34 weeks of gestation, we measured fetal kidney dimensions (transverse and anteroposterior diameters, length and circumference) and derived volume in a random sample of 872 white British and 715 South Asian participants in the Born in Bradford cohort study. Kidney measurements were compared between ethnic groups. Birth weight for gestational age at 40 weeks was 200 g less in South Asian babies compared with white British babies. The mean kidney volume for gestational age was 16% lower in South Asian than in white British babies [8.79 versus 10.45 cm(3), difference 1.66 cm(3) (95% confidence interval 1.40-1.93, P < 0.001)]. The difference was robust after adjustment for maternal age, socio-economic factors, marital status, body mass index, smoking and alcohol use in pregnancy, parity, baby's gender and birth weight for gestational age [adjusted difference 1.38 cm(3) (0.97-1.84), P < 0.001]. There were smaller reductions in other fetal measures. South Asian babies have smaller kidneys compared with white British babies, even after adjusting for potential confounders including birth weight. This finding may contribute to increased risks of adult kidney disease in South Asian populations. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

  7. Comparison of flexible ureterorenoscopy and mini-percutaneous nephrolithotomy in treatment of lower calyceal stones smaller than 2 cm.

    Science.gov (United States)

    Akbulut, Fatih; Kucuktopcu, Onur; Kandemir, Emre; Sonmezay, Erkan; Simsek, Abdulmuttalip; Ozgor, Faruk; Binbay, Murat; Muslumanoglu, Ahmet Yaser; Gurbuz, Gokhan

    2016-01-01

    To compare the outcomes of flexible ureterorenoscopy (F-URS) and mini-percutaneous nephrolithotomy (mini-PNL) in the treatment of lower calyceal stones smaller than 2 cm. Patients who underwent F-URS and mini-PNL for the treatment of lower calyceal stones smaller than 2 cm between March 2009 and December 2014 were retrospectively evaluated. Ninety-four patients were divided into two groups by treatment modality: F-URS (Group 1: 63 patients) and mini-PNL (Group 2: 31 patients). All patients were preoperatively diagnosed with intravenous pyelography or computed tomography. Success rates for F-URS and mini-PNL at postoperative first month were 85.7% and 90.3%, respectively. Operation time, fluoroscopy time, and hospitalization time for F-URS and mini-PNL patients were 44.40 min, 2.9 min, 22.4 h, and 91.9 min, 6.4 min, and 63.8 h, respectively. All three parameters were significantly shorter among the F-URS group (p PNL group (0.39 mg/dL vs. 1.15 mg/dL, p = 0.001). A comparison of complications according to the Clavien classification demonstrated significant differences between the groups (p = 0.001). More patients in the F-URS groups require antibiotics due to urinary tract infection, and more patients in the mini-PNL group required ureteral double J catheter insertion under general anesthesia. Although both F-URS and mini-PNL have similar success rates for the treatment of lower calyceal stones, F-URS appears to be more favorable due to shorter fluoroscopy and hospitalization times; and lower hemoglobin drops. Multicenter and studies using higher patient volumes are needed to confirm these findings.

  8. Dysfunctional lipoproteins from young smokers exacerbate cellular senescence and atherogenesis with smaller particle size and severe oxidation and glycation.

    Science.gov (United States)

    Park, Ki-Hoon; Shin, Dong-Gu; Cho, Kyung-Hyun

    2014-07-01

    Until now, there has been limited information on the effects of smoking on atherogenesis and senescence in the context of lipoprotein parameters, particularly in young smokers who have smoked fewer than 10 cigarettes per day for 3 years. In this study, lipoprotein profiles and functions were compared between smoker (n = 21) and control groups (n = 20). In the smoking group, ferric ion reduction abilities of serum and high-density lipoprotein (HDL) fractions were significantly reduced, and low-density lipoprotein (LDL) was severely oxidized. All lipoprotein particles from the smoker group showed higher advanced glycated end products with more triglyceride (TG) content compared with the control group. Lipoproteins from smokers showed faster agarose gel electromobility as well as greater smear band intensity in SDS-PAGE due to oxidation and glycation. LDL from smokers was more sensitive to oxidation and promoted foam cell forma-tion in macrophages. Gel filtration column chromatography revealed that the protein and cholesterol peaks of VLDL and LDL were elevated in the smoker group, whereas those of HDL were reduced. Human dermal fibroblast cells from the smoker group showed severe senescence following treatment with HDL2 and HDL3. Although HDL from young smokers showed impaired antioxidant ability, smaller particle size, and increased TG content, cholesteryl ester transfer protein activities were greatly enhanced in the serum and HDL fractions of the smoker group. In conclusion, smoking can cause production of dysfunctional lipoproteins having a smaller particle size that exacerbate senescence and atherogenic progress due to oxidation and glycation. © The Author 2014. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. The Improved Relevance Voxel Machine

    DEFF Research Database (Denmark)

    Ganz, Melanie; Sabuncu, Mert; Van Leemput, Koen

    The concept of sparse Bayesian learning has received much attention in the machine learning literature as a means of achieving parsimonious representations of features used in regression and classification. It is an important family of algorithms for sparse signal recovery and compressed sensing....... Hence in its current form it is reminiscent of a greedy forward feature selection algorithm. In this report, we aim to solve the problems of the original RVoxM algorithm in the spirit of [7] (FastRVM).We call the new algorithm Improved Relevance Voxel Machine (IRVoxM). Our contributions...... and enables basis selection from overcomplete dictionaries. One of the trailblazers of Bayesian learning is MacKay who already worked on the topic in his PhD thesis in 1992 [1]. Later on Tipping and Bishop developed the concept of sparse Bayesian learning [2, 3] and Tipping published the Relevance Vector...

  10. Relevant criteria for testing the quality of turbulence models

    DEFF Research Database (Denmark)

    Frandsen, Sten Tronæs; Ejsing Jørgensen, Hans; Sørensen, J.D.

    2007-01-01

    Seeking relevant criteria for testing the quality of turbulence models, the scale of turbulence and the gust factor have been estimated from data and compared with predictions from first-order models of these two quantities. It is found that the mean of the measured length scales is approx. 10......% smaller than the IEC model, for wind turbine hub height levels. The mean is only marginally dependent on trends in time series. It is also found that the coefficient of variation of the measured length scales is about 50%. 3sec and 10sec pre-averaging of wind speed data are relevant for MW-size wind...... turbines when seeking wind characteristics that correspond to one blade and the entire rotor, respectively. For heights exceeding 50-60m the gust factor increases with wind speed. For heights larger the 60-80m, present assumptions on the value of the gust factor are significantly conservative, both for 3...

  11. Functionally relevant microsatellites in sugarcane unigenes

    Directory of Open Access Journals (Sweden)

    Singh Nagendra K

    2010-11-01

    Full Text Available Abstract Background Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. Results The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. Conclusion Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6% of which functions were determined in silico. High level of

  12. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

    Science.gov (United States)

    Schirmer, Melanie; Ijaz, Umer Z; D'Amore, Rosalinda; Hall, Neil; Sloan, William T; Quince, Christopher

    2015-03-31

    With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Spectral entropy criteria for structural segmentation in genomic DNA sequences

    International Nuclear Information System (INIS)

    Chechetkin, V.R.; Lobzin, V.V.

    2004-01-01

    The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions

  14. Microdosing: Concept, application and relevance

    Directory of Open Access Journals (Sweden)

    Tushar Tewari

    2010-01-01

    Full Text Available The use of microdose pharmacokinetic studies as an essential tool in drug development is still to catch on. While this approach promises potential cost savings and a quantum leap in efficiencies of the drug development process, major hurdles still need to be overcome before the technique becomes commonplace and part of routine practice. Clear regulations in Europe and the USA have had an enabling effect. The lack of enabling provisions for microdosing studies in Indian regulation, despite low risk and manifest relevance for the local drug development industry, is inconsistent with the country′s aspirations to be among the leaders in pharmaceutical research.

  15. Smaller scars--what is the big deal: a survey of the perceived value of laparoscopic pyloromyotomy.

    Science.gov (United States)

    Haricharan, Ramanath N; Aprahamian, Charles J; Morgan, Traci L; Harmon, Carroll M; Georgeson, Keith E; Barnhart, Douglas C

    2008-01-01

    Laparoscopic and open pyloromyotomies are equally safe and effective, with the principal benefit of laparoscopy being better cosmesis. The goal of this study was to measure the perceived value of laparoscopic pyloromyotomy. Four hundred sixteen subjects (177 college freshmen, 126 first-year medical students, and 101 parents) were asked to complete a questionnaire after photographs of mature pyloromyotomy (open and laparoscopic) scars were shown to them. To measure the perceived value, subjects' willingness to pay hypothetical additional out-of-pocket expenses for their preferred operation was assessed. Data were analyzed using Cochran-Mantel-Haenszel test, t test and multivariable regression. Four hundred four surveys were complete. Overall, 74% preferred the appearance after laparoscopy. Eighty-eight percent would pay an additional out-of-pocket amount for their daughter and 85% for their son to have the cosmetic outcome after laparoscopy. Respondents were willing to pay more for their daughters (P < .0001) and sons (P < .0001) than themselves. As expected, income level (P < .0001) influenced the willingness to pay, whereas ethnicity, education, number of children, and sex did not. The cosmetic benefit of laparoscopic pyloromyotomy was valued by a wide demographic with 85% being willing to pay additional expenses for their children to have smaller scars.

  16. Waterborne cues from crabs induce thicker skeletons, smaller gonads and size-specific changes in growth rate in sea urchins.

    Science.gov (United States)

    Selden, Rebecca; Johnson, Amy S; Ellers, Olaf

    2009-01-01

    Indirect predator-induced effects on growth, morphology and reproduction have been extensively studied in marine invertebrates but usually without consideration of size-specific effects and not at all in post-metamorphic echinoids. Urchins are an unusually good system, in which, to study size effects because individuals of various ages within one species span four orders of magnitude in weight while retaining a nearly isometric morphology. We tracked growth of urchins, Strongylocentrotus droebachiensis (0.013-161.385 g), in the presence or absence of waterborne cues from predatory Jonah crabs, Cancer borealis. We ran experiments at ambient temperatures, once for 4 weeks during summer and again, with a second set of urchins, for 22 weeks over winter. We used a scaled, cube-root transformation of weight for measuring size more precisely and for equalizing variance across sizes. Growth rate of the smallest urchins (summer: scent by 7% in the winter. At the end of the 22-week experiment, additional gonadal and skeletal variables were measured. Cue-exposed urchins developed heavier, thicker skeletons and smaller gonads, but no differences in spine length or jaw size. The differences depended on urchin size, suggesting that there are size-specific shifts in gonadal and somatic investment in urchins.

  17. CONCEPTUAL DESIGN FOR A RADICALLY SMALLER, HIGHLY ADAPTIVE AND APPLICATION-FLEXIBLE MINING MACHINE FOR UTILITY AND DEVELOPMENT WORK

    Energy Technology Data Exchange (ETDEWEB)

    Andrew H. Stern

    2004-12-20

    The aim of this research project was to develop a preliminary ''conceptual design'' for a radically smaller, highly adaptive and application-flexible underground coal mining machine, for performing non-production utility work and/or also undertake limited production mining for the recovery of reserves that would otherwise be lost. Whereas historically, mining philosophies have reflected a shift to increasing larger mechanized systems [such as the continuous miner (CM)], specific mining operations that do not benefit from the economy of the large mining equipment are often ignored or addressed with significant inefficiencies. Developing this prototype concept will create a new class of equipment that can provide opportunities to re-think the very structure of the mining system across a broad range of possibilities, not able to be met by existing machinery. The approach involved pooling the collective input from mining professionals, using a structured listing of desired inputs in the form of a questionnaire, which was used to define the range of desired design specifications. From these inputs, a conceptual specification was blended, by the author, to embody the general concurrence of mission concepts for this machine.

  18. Bubbling bed catalytic hydropyrolysis process utilizing larger catalyst particles and smaller biomass particles featuring an anti-slugging reactor

    Science.gov (United States)

    Marker, Terry L; Felix, Larry G; Linck, Martin B; Roberts, Michael J

    2014-09-23

    This invention relates to a process for thermochemically transforming biomass or other oxygenated feedstocks into high quality liquid hydrocarbon fuels. In particular, a catalytic hydropyrolysis reactor, containing a deep bed of fluidized catalyst particles is utilized to accept particles of biomass or other oxygenated feedstocks that are significantly smaller than the particles of catalyst in the fluidized bed. The reactor features an insert or other structure disposed within the reactor vessel that inhibits slugging of the bed and thereby minimizes attrition of the catalyst. Within the bed, the biomass feedstock is converted into a vapor-phase product, containing hydrocarbon molecules and other process vapors, and an entrained solid char product, which is separated from the vapor stream after the vapor stream has been exhausted from the top of the reactor. When the product vapor stream is cooled to ambient temperatures, a significant proportion of the hydrocarbons in the product vapor stream can be recovered as a liquid stream of hydrophobic hydrocarbons, with properties consistent with those of gasoline, kerosene, and diesel fuel. Separate streams of gasoline, kerosene, and diesel fuel may also be obtained, either via selective condensation of each type of fuel, or via later distillation of the combined hydrocarbon liquid.

  19. Higher media multi-tasking activity is associated with smaller gray-matter density in the anterior cingulate cortex.

    Directory of Open Access Journals (Sweden)

    Kep Kee Loh

    Full Text Available Media multitasking, or the concurrent consumption of multiple media forms, is increasingly prevalent in today's society and has been associated with negative psychosocial and cognitive impacts. Individuals who engage in heavier media-multitasking are found to perform worse on cognitive control tasks and exhibit more socio-emotional difficulties. However, the neural processes associated with media multi-tasking remain unexplored. The present study investigated relationships between media multitasking activity and brain structure. Research has demonstrated that brain structure can be altered upon prolonged exposure to novel environments and experience. Thus, we expected differential engagements in media multitasking to correlate with brain structure variability. This was confirmed via Voxel-Based Morphometry (VBM analyses: Individuals with higher Media Multitasking Index (MMI scores had smaller gray matter density in the anterior cingulate cortex (ACC. Functional connectivity between this ACC region and the precuneus was negatively associated with MMI. Our findings suggest a possible structural correlate for the observed decreased cognitive control performance and socio-emotional regulation in heavy media-multitaskers. While the cross-sectional nature of our study does not allow us to specify the direction of causality, our results brought to light novel associations between individual media multitasking behaviors and ACC structure differences.

  20. A comparative economic assessment of hydrogen production from large central versus smaller distributed plant in a carbon constrained world

    International Nuclear Information System (INIS)

    Nguyen, Y.V.; Ngo, Y.A.; Tinkler, M.J.; Cowan, N.

    2003-01-01

    This paper compares the economics of producing hydrogen at large central plants versus smaller distributed plants at user sites. The economics of two types of central plant, each at 100 million standard cubic feet per day of hydrogen, based on electrolysis and natural gas steam reforming technologies, will be discussed. The additional cost of controlling CO 2 emissions from the natural gas steam reforming plant will be included in the analysis in order to satisfy the need to live in a future carbon constrained world. The cost of delivery of hydrogen from the large central plant to the user sites in a large metropolitan area will be highlighted, and the delivered cost will be compared to the cost from on-site distributed generation plants. Five types of distributed generation plants, based on proton exchange membrane, alkaline electrolysis and advanced steam reforming, will be analysed and discussed. Two criteria were used to rank various hydrogen production options, the cost of production and the price of hydrogen to achieve an acceptable return of investment. (author)

  1. Using a smaller dining plate does not suppress food intake from a buffet lunch meal in overweight, unrestrained women.

    Science.gov (United States)

    Yip, Wilson; Wiessing, Katy R; Budgett, Stephanie; Poppitt, Sally D

    2013-10-01

    The aim of the study was to determine whether plate size affects ad libitum energy intake (EI) at a buffet-style lunch in overweight, yet unrestrained women. Twenty overweight/obese (BMI=25-40 kg/m(2)) women attended two study visits, and were randomly assigned to small (19.5 cm) or large (26.5 cm) diameter plate size at a free choice lunch meal. At 9 am participants were given a small (0.5 MJ) breakfast, followed at 12 noon by the lunch meal from which they ate ad lib until comfortably full. Mean (SEM) EI at lunch was 3975 (239)kJ and 3901 (249) kJ respectively for small and large plate size. There was no detectable difference in EI between the two plate sizes (P>0.05). When in a raised state of hunger and offered a palatable buffet meal, altering the diameter of the dining plate onto which food was self-served did not significantly alter ad lib EI. We conclude there was no evidence that a smaller plate suppressed EI in a group of unrestrained, overweight women encouraged to eat to appetite from a wide choice of items. Whether plate size is a useful cue for portion size, and hence control of EI, in individuals actively restricting intake however remains possible, and requires investigation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Winnowing sequences from a database search.

    Science.gov (United States)

    Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

    2000-01-01

    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

  3. The relative age effect is larger in Italian soccer top-level youth categories and smaller in Serie A.

    Science.gov (United States)

    Brustio, Paolo Riccardo; Lupo, Corrado; Ungureanu, Alexandru Nicolae; Frati, Riccardo; Rainoldi, Alberto; Boccia, Gennaro

    2018-01-01

    The relative age effect (RAE; i.e., an asymmetry in the birth distribution) is a bias observed in sport competitions that may favour relatively older athletes in talent identification. Therefore, the aim of this study was to investigate the presence of RAE in elite soccer players competing in the Italian championships, even considering the discriminations of younger and older Serie A players (in relation to the median age of the sample), and different positional roles (i.e., goalkeeper, defender, midfielder, forward) for each observed category. A total of 2051 players competing into the 2017-2018 Italian under-15 (n = 265), under-16 (n = 362), under-17 (n = 403), Primavera (n = 421) and Serie A (n = 600) championships were analysed. The birth-date distributions, grouped in four quartiles (i.e., January-March, Q1; April-June, Q2; July-September, Q3; October-December, Q4), were compared to a uniform distribution using Chi-squared analysis. The week of birth was analysed using Poisson regression. The results showed a large over-representation of players born in Q1 in all soccer player categories. However, the effect size of this trend resulted smaller as age increased. Individuals born in Q1 have about two-folds more chances to become a Serie A player compared to those born in Q4. The Poisson regression analysis showed that RAE was greater for defenders than for forwards among all categories. Therefore, a strongly biased selection emerged among elite soccer players competing in Italian championships, highlighting how young individuals born in the first three months have many more chances to become elite players compared to the others.

  4. High temperatures result in smaller nurseries which lower reproduction of pollinators and parasites in a brood site pollination mutualism.

    Directory of Open Access Journals (Sweden)

    Anusha Krishnan

    Full Text Available In a nursery pollination mutualism, we asked whether environmental factors affected reproduction of mutualistic pollinators, non-mutualistic parasites and seed production via seasonal changes in plant traits such as inflorescence size and within-tree reproductive phenology. We examined seasonal variation in reproduction in Ficus racemosa community members that utilise enclosed inflorescences called syconia as nurseries. Temperature, relative humidity and rainfall defined four seasons: winter; hot days, cold nights; summer and wet seasons. Syconium volumes were highest in winter and lowest in summer, and affected syconium contents positively across all seasons. Greater transpiration from the nurseries was possibly responsible for smaller syconia in summer. The 3-5°C increase in mean temperatures between the cooler seasons and summer reduced fig wasp reproduction and increased seed production nearly two-fold. Yet, seed and pollinator progeny production were never negatively related in any season confirming the mutualistic fig-pollinator association across seasons. Non-pollinator parasites affected seed production negatively in some seasons, but had a surprisingly positive relationship with pollinators in most seasons. While within-tree reproductive phenology did not vary across seasons, its effect on syconium inhabitants varied with season. In all seasons, within-tree reproductive asynchrony affected parasite reproduction negatively, whereas it had a positive effect on pollinator reproduction in winter and a negative effect in summer. Seasonally variable syconium volumes probably caused the differential effect of within-tree reproductive phenology on pollinator reproduction. Within-tree reproductive asynchrony itself was positively affected by intra-tree variation in syconium contents and volume, creating a unique feedback loop which varied across seasons. Therefore, nursery size affected fig wasp reproduction, seed production and within

  5. High temperatures result in smaller nurseries which lower reproduction of pollinators and parasites in a brood site pollination mutualism.

    Science.gov (United States)

    Krishnan, Anusha; Pramanik, Gautam Kumar; Revadi, Santosh V; Venkateswaran, Vignesh; Borges, Renee M

    2014-01-01

    In a nursery pollination mutualism, we asked whether environmental factors affected reproduction of mutualistic pollinators, non-mutualistic parasites and seed production via seasonal changes in plant traits such as inflorescence size and within-tree reproductive phenology. We examined seasonal variation in reproduction in Ficus racemosa community members that utilise enclosed inflorescences called syconia as nurseries. Temperature, relative humidity and rainfall defined four seasons: winter; hot days, cold nights; summer and wet seasons. Syconium volumes were highest in winter and lowest in summer, and affected syconium contents positively across all seasons. Greater transpiration from the nurseries was possibly responsible for smaller syconia in summer. The 3-5°C increase in mean temperatures between the cooler seasons and summer reduced fig wasp reproduction and increased seed production nearly two-fold. Yet, seed and pollinator progeny production were never negatively related in any season confirming the mutualistic fig-pollinator association across seasons. Non-pollinator parasites affected seed production negatively in some seasons, but had a surprisingly positive relationship with pollinators in most seasons. While within-tree reproductive phenology did not vary across seasons, its effect on syconium inhabitants varied with season. In all seasons, within-tree reproductive asynchrony affected parasite reproduction negatively, whereas it had a positive effect on pollinator reproduction in winter and a negative effect in summer. Seasonally variable syconium volumes probably caused the differential effect of within-tree reproductive phenology on pollinator reproduction. Within-tree reproductive asynchrony itself was positively affected by intra-tree variation in syconium contents and volume, creating a unique feedback loop which varied across seasons. Therefore, nursery size affected fig wasp reproduction, seed production and within-tree reproductive phenology

  6. AMS measurement of samples smaller than 300 {mu}g at center for applied isotope studies, University of Georgia

    Energy Technology Data Exchange (ETDEWEB)

    Cherkinsky, Alexander, E-mail: acherkin@uga.edu [CENTER FOR APPLIED ISOTOPE STUDIES, University of Georgia, 120 Riverbend Road, Athens, GA 30602 (United States); Ravi Prasad, G.V.; Dvoracek, Doug [CENTER FOR APPLIED ISOTOPE STUDIES, University of Georgia, 120 Riverbend Road, Athens, GA 30602 (United States)

    2013-01-15

    The center for applied isotope studies has developed a protocol for the measurement of radiocarbon in the range 0.01-0.3 mg of carbon. We analyzed a series of radiocarbon-free and modern standards using the same sample preparation procedure as for unknown samples. We have studied the size dependency of {sup 12}C and {sup 13}C beam currents and {sup 14}C/{sup 13}C ratios from cathodes containing less than 1 mg of carbon. The iron catalyst used for graphite preparation contains some carbon with activity about 60 pMC and the level of contamination varies between batches from the same supplier. The cathodes in the range smaller than 50 {mu}g showed a very significant dependency between current and the sample size. In this range the current increased by about fifteen-fold; between 50 and 100 {mu}g the current increased two-fold. Samples larger than 300 {mu}g have shown negligible current variation. The {sup 14}C/{sup 13}C ratio was significantly affected only for the samples less than 50 {mu}g. Larger samples have shown very little variation in the {sup 14}C/{sup 13}C ratio. For the measurement of ultra-small unknown samples in the range of 10-50 {mu}g, we have found it to be important to use blanks and modern standards with exactly the same amount of carbon, which makes it possible to apply a mass-balanced correction.

  7. Two Inexpensive and Non-destructive Techniques to Correct for Smaller-Than-Gasket Leaf Area in Gas Exchange Measurements

    Directory of Open Access Journals (Sweden)

    Andreas M. Savvides

    2018-04-01

    Full Text Available The development of technology, like the widely-used off-the-shelf portable photosynthesis systems, for the quantification of leaf gas exchange rates and chlorophyll fluorescence offered photosynthesis research a massive boost. Gas exchange parameters in such photosynthesis systems are calculated as gas exchange rates per unit leaf area. In small chambers (<10 cm2, the leaf area used by the system for these calculations is actually the internal gasket area (AG, provided that the leaf covers the entire AG. In this study, we present two inexpensive and non-destructive techniques that can be used to easily quantify the enclosed leaf area (AL of plant species with leaves of surface area much smaller than the AG, such as that of cereal crops. The AL of the cereal crop species studied has been measured using a standard image-based approach (iAL and estimated using a leaf width-based approach (wAL. iAL and wAL did not show any significant differences between them in maize, barley, hard and soft wheat. Similar results were obtained when the wAL was tested in comparison with iAL in different positions along the leaf in all species studied. The quantification of AL and the subsequent correction of leaf gas exchange parameters for AL provided a precise quantification of net photosynthesis and stomatal conductance especially with decreasing AL. This study provides two practical, inexpensive and non-destructive solutions to researchers dealing with photosynthesis measurements on small-leaf plant species. The image-based technique can be widely used for quantifying AL in many plant species despite their leaf shape. The leaf width-based technique can be securely used for quantifying AL in cereal crop species such as maize, wheat and barley along the leaf. Both techniques can be used for a wide range of gasket shapes and sizes with minor technique-specific adjustments.

  8. Other relevant numerical modelling papers

    International Nuclear Information System (INIS)

    Chartier, M.

    1989-01-01

    The ocean modelling is a rapidly evolving science and a large number of results have been published. Several categories of papers are of particular interest for this review: the papers published by the international atomic institutions, such as the NEA (for the CRESP or Subseabed Programs), the IAEA (for example the Safety Series, the Technical Report Series or the TECDOC), and the ICRP, and the papers concerned by more fundamental research, which are published in specific scientific literature. This paper aims to list some of the most relevant publications for the CRESP purposes. It means by no way to be exhaustive, but informative on the incontestable progress recently achieved in that field. One should note that some of these papers are so recent that their final version has not yet been published

  9. Industrial relevance of thermophilic Archaea.

    Science.gov (United States)

    Egorova, Ksenia; Antranikian, Garabed

    2005-12-01

    The dramatic increase of newly isolated extremophilic microorganisms, analysis of their genomes and investigations of their enzymes by academic and industrial laboratories demonstrate the great potential of extremophiles in industrial (white) biotechnology. Enzymes derived from extremophiles (extremozymes) are superior to the traditional catalysts because they can perform industrial processes even under harsh conditions, under which conventional proteins are completely denatured. In particular, enzymes from thermophilic and hyperthermophilic Archaea have industrial relevance. Despite intensive investigations, our knowledge of the structure-function relationships of their enzymes is still limited. Information concerning the molecular properties of their enzymes and genes has to be obtained to be able to understand the mechanisms that are responsible for catalytic activity and stability at the boiling point of water.

  10. The Relevance of Hegel's Logic

    Directory of Open Access Journals (Sweden)

    John W Burbidge

    2007-12-01

    Full Text Available Hegel defines his Logic as the science that thinks about thinking.nbsp; But when we interpret that work as outlining what happens when we reason we are vulnerable to Fregersquo;s charge of psychologism.nbsp; I use Hegelrsquo;s tripartite distinction among understanding, dialectical and speculative reason as operations of pure thought to suggest how thinking can work with objective concepts.nbsp; In the last analysis, however, our ability to move from the subjective contingency of representations and ideas to the pure concepts we think develops from mechanical memory, which separates sign from sense so hat we can focus simply on the latter.nbsp; By becoming aware of the connections that underlie our thinking processes we may be able to both move beyond the abstractions of symbolic logic and clarify what informal logicians call relevance.

  11. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  12. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  13. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  14. Identification of a Flavivirus Sequence in a Marine Arthropod.

    Directory of Open Access Journals (Sweden)

    Michael J Conway

    Full Text Available Phylogenetic analysis has yet to uncover the early origins of flaviviruses. In this study, I mined a database of expressed sequence tags in order to discover novel flavivirus sequences. Flavivirus sequences were identified in a pool of mRNA extracted from the sea spider Endeis spinosa (Pycnogonida, Pantopoda. Reconstruction of the translated sequences and BLAST analysis matched the sequence to the flavivirus NS5 gene. Additional sequences corresponding to envelope and the NS5 MTase domain were also identified. Phylogenetic analysis of homologous NS5 sequences revealed that Endeis spinosa NS5 (ESNS5 is likely related to classical insect-specific flaviviruses. It is unclear if ESNS5 represents genetic material from an active viral infection or an integrated viral genome. These data raise the possibility that classical insect-specific flaviviruses and perhaps medically relevant flaviviruses, evolved from progenitors that infected marine arthropods.

  15. Colonies of Bumble Bees (Bombus impatiens Produce Fewer Workers, Less Bee Biomass, and Have Smaller Mother Queens Following Fungicide Exposure

    Directory of Open Access Journals (Sweden)

    Olivia M. Bernauer

    2015-06-01

    Full Text Available Bees provide vital pollination services to the majority of flowering plants in both natural and agricultural systems. Unfortunately, both native and managed bee populations are experiencing declines, threatening the persistence of these plants and crops. Agricultural chemicals are one possible culprit contributing to bee declines. Even fungicides, generally considered safe for bees, have been shown to disrupt honey bee development and impair bumble bee behavior. Little is known, however, how fungicides may affect bumble bee colony growth. We conducted a controlled cage study to determine the effects of fungicide exposure on colonies of a native bumble bee species (Bombus impatiens. Colonies of B. impatiens were exposed to flowers treated with field-relevant levels of the fungicide chlorothalonil over the course of one month. Colony success was assessed by the number and biomass of larvae, pupae, and adult bumble bees. Bumble bee colonies exposed to fungicide produced fewer workers, lower total bee biomass, and had lighter mother queens than control colonies. Our results suggest that fungicides negatively affect the colony success of a native bumble bee species and that the use of fungicides during bloom has the potential to severely impact the success of native bumble bee populations foraging in agroecosystems.

  16. Vygotsky's Crisis: Argument, context, relevance.

    Science.gov (United States)

    Hyman, Ludmila

    2012-06-01

    Vygotsky's The Historical Significance of the Crisis in Psychology (1926-1927) is an important text in the history and philosophy of psychology that has only become available to scholars in 1982 in Russian, and in 1997 in English. The goal of this paper is to introduce Vygotsky's conception of psychology to a wider audience. I argue that Vygotsky's argument about the "crisis" in psychology and its resolution can be fully understood only in the context of his social and political thinking. Vygotsky shared the enthusiasm, widespread among Russian leftist intelligentsia in the 1920s, that Soviet society had launched an unprecedented social experiment: The socialist revolution opened the way for establishing social conditions that would let the individual flourish. For Vygotsky, this meant that "a new man" of the future would become "the first and only species in biology that would create itself." He envisioned psychology as a science that would serve this humanist teleology. I propose that The Crisis is relevant today insofar as it helps us define a fundamental problem: How can we systematically account for the development of knowledge in psychology? I evaluate how Vygotsky addresses this problem as a historian of the crisis. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Relevance of equilibrium in multifragmentation

    International Nuclear Information System (INIS)

    Furuta, Takuya; Ono, Akira

    2009-01-01

    The relevance of equilibrium in a multifragmentation reaction of very central 40 Ca + 40 Ca collisions at 35 MeV/nucleon is investigated by using simulations of antisymmetrized molecular dynamics (AMD). Two types of ensembles are compared. One is the reaction ensemble of the states at each reaction time t in collision events simulated by AMD, and the other is the equilibrium ensemble prepared by solving the AMD equation of motion for a many-nucleon system confined in a container for a long time. The comparison of the ensembles is performed for the fragment charge distribution and the excitation energies. Our calculations show that there exists an equilibrium ensemble that well reproduces the reaction ensemble at each reaction time t for the investigated period 80≤t≤300 fm/c. However, there are some other observables that show discrepancies between the reaction and equilibrium ensembles. These may be interpreted as dynamical effects in the reaction. The usual static equilibrium at each instant is not realized since any equilibrium ensemble with the same volume as that of the reaction system cannot reproduce the fragment observables

  18. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  19. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  20. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  1. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  2. Statistical significance versus clinical relevance.

    Science.gov (United States)

    van Rijn, Marieke H C; Bech, Anneke; Bouyer, Jean; van den Brand, Jan A J G

    2017-04-01

    In March this year, the American Statistical Association (ASA) posted a statement on the correct use of P-values, in response to a growing concern that the P-value is commonly misused and misinterpreted. We aim to translate these warnings given by the ASA into a language more easily understood by clinicians and researchers without a deep background in statistics. Moreover, we intend to illustrate the limitations of P-values, even when used and interpreted correctly, and bring more attention to the clinical relevance of study findings using two recently reported studies as examples. We argue that P-values are often misinterpreted. A common mistake is saying that P < 0.05 means that the null hypothesis is false, and P ≥0.05 means that the null hypothesis is true. The correct interpretation of a P-value of 0.05 is that if the null hypothesis were indeed true, a similar or more extreme result would occur 5% of the times upon repeating the study in a similar sample. In other words, the P-value informs about the likelihood of the data given the null hypothesis and not the other way around. A possible alternative related to the P-value is the confidence interval (CI). It provides more information on the magnitude of an effect and the imprecision with which that effect was estimated. However, there is no magic bullet to replace P-values and stop erroneous interpretation of scientific results. Scientists and readers alike should make themselves familiar with the correct, nuanced interpretation of statistical tests, P-values and CIs. © The Author 2017. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

  3. Pattern recognition in complex activity travel patterns : comparison of Euclidean distance, signal-processing theoretical, and multidimensional sequence alignment methods

    NARCIS (Netherlands)

    Joh, C.H.; Arentze, T.A.; Timmermans, H.J.P.

    2001-01-01

    The application of a multidimensional sequence alignment method for classifying activity travel patterns is reported. The method was developed as an alternative to the existing classification methods suggested in the transportation literature. The relevance of the multidimensional sequence alignment

  4. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  5. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  6. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  7. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  8. Does relevance matter in academic policy research?

    DEFF Research Database (Denmark)

    Dredge, Dianne

    2015-01-01

    A reflection on whether relevance matters in tourism policy research. A debate among tourism scholars.......A reflection on whether relevance matters in tourism policy research. A debate among tourism scholars....

  9. Evaluating and Redesigning Teaching Learning Sequences at the Introductory Physics Level

    Science.gov (United States)

    Guisasola, Jenaro; Zuza, Kristina; Ametller, Jaume; Gutierrez-Berraondo, José

    2017-01-01

    In this paper we put forward a proposal for the design and evaluation of teaching and learning sequences in upper secondary school and university. We will connect our proposal with relevant contributions on the design of teaching sequences, ground it on the design-based research methodology, and discuss how teaching and learning sequences designed…

  10. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  11. Science and the struggle for relevance

    NARCIS (Netherlands)

    Hessels, L.K.|info:eu-repo/dai/nl/304832863

    2010-01-01

    This thesis deals with struggles for relevance of university researchers, their efforts to make their work correspond with ruling standards of relevance and to influence these standards. Its general research question is: How to understand changes in the struggle for relevance of Dutch academic

  12. The Personal Relevance of the Social Studies.

    Science.gov (United States)

    VanSickle, Ronald L.

    1990-01-01

    Conceptualizes a personal-relevance framework derived from Ronald L. VanSickle's five areas of life integrated with four general motivating goals from Abraham Maslow's hierarchy of needs and Richard and Patricia Schmuck's social motivation theory. Illustrates ways to apply the personal relevance framework to make social studies more relevant to…

  13. The Development of Relevance in Information Retrieval

    Directory of Open Access Journals (Sweden)

    Mu-hsuan Huang

    1997-12-01

    Full Text Available This article attempts to investigate the notion of relevance in information retrieval. It discusses various definitions for relevance from historical viewpoints and the characteristics of relevance judgments. Also, it introduces empirical results of important related researches.[Article content in Chinese

  14. Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts

    Science.gov (United States)

    Gorter de Vries, Arthur R.; Pronk, Jack T.

    2017-01-01

    ABSTRACT Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyces strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes. PMID:28341679

  15. Nostalgia's place among self-relevant emotions.

    Science.gov (United States)

    van Tilburg, Wijnand A P; Wildschut, Tim; Sedikides, Constantine

    2017-07-24

    How is nostalgia positioned among self-relevant emotions? We tested, in six studies, which self-relevant emotions are perceived as most similar versus least similar to nostalgia, and what underlies these similarities/differences. We used multidimensional scaling to chart the perceived similarities/differences among self-relevant emotions, resulting in two-dimensional models. The results were revealing. Nostalgia is positioned among self-relevant emotions characterised by positive valence, an approach orientation, and low arousal. Nostalgia most resembles pride and self-compassion, and least resembles embarrassment and shame. Our research pioneered the integration of nostalgia among self-relevant emotions.

  16. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  17. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  18. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  19. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  20. Functional and Immunological Relevance of Anaplasma marginale Major Surface Protein 1a Sequence and Structural Analysis

    Czech Academy of Sciences Publication Activity Database

    Cabezas Cruz, Alejandro; Passos, L.M.F.; Lis, K.; Kenneil, R.; Valdés, James J.; Ferrolho, J.; Tonk, Miray; Pohl, A.E.; Grubhoffer, Libor; Zweygarth, E.; Shkap, V.; Ribeiro, M.F.B.; Estrada-Pena, A.; Kocan, K.M.; de la Fuente, J.

    2013-01-01

    Roč. 8, č. 6 (2013), e65243 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) EE2.3.30.0032 EU Projects: European Commission(XE) 238511 - POSTICK Institutional support: RVO:60077344 Keywords : CD4(+) T-lymphocytes * B-cell epitopes * salivary glands Subject RIV: EC - Immunology Impact factor: 3.534, year: 2013

  1. The heterogeneous world of congruency sequence effects: An update.

    OpenAIRE

    Wout eDuthoo; Elger eAbrahamse; Senne eBraem; Senne eBraem; C. Nico Boehler; Wim eNotebaert

    2014-01-01

    Congruency sequence effects (CSEs) refer to the observation that congruency effects in conflict tasks are typically smaller following incongruent compared to following congruent trials. This measure has long been thought to provide a unique window into top-down attentional adjustments and their underlying brain mechanisms. According to the renowned conflict monitoring theory, CSEs reflect enhanced selective attention following conflict detection. Still, alternative accounts suggested that bot...

  2. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  3. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  4. The evolution of coronal activity in main sequence cool stars

    International Nuclear Information System (INIS)

    Stern, R.A.

    1984-01-01

    Stars spend most of their lifetime and show the least amount of nuclear evolution on the main sequence. However, the x-ray luminosities of cool star coronas change by orders of magnitude as a function of main sequence age. Such coronal evolution is discussed in relation to our knowledge of the solar corona, solar and stellar flares, stellar rotation and binarity. The relevance of X-ray observations to current speculations on stellar dynamos is also considered

  5. Intrauterine growth-restricted sheep fetuses exhibit smaller hindlimb muscle fibers and lower proportions of insulin-sensitive Type I fibers near term.

    Science.gov (United States)

    Yates, Dustin T; Cadaret, Caitlin N; Beede, Kristin A; Riley, Hannah E; Macko, Antoni R; Anderson, Miranda J; Camacho, Leticia E; Limesand, Sean W

    2016-06-01

    Intrauterine growth restriction (IUGR) reduces muscle mass and insulin sensitivity in offspring. Insulin sensitivity varies among muscle fiber types, with Type I fibers being most sensitive. Differences in fiber-type ratios are associated with insulin resistance in adults, and thus we hypothesized that near-term IUGR sheep fetuses exhibit reduced size and proportions of Type I fibers. Placental insufficiency-induced IUGR fetuses were ∼54% smaller (P fetal muscles develop smaller fibers and have proportionally fewer Type I fibers, which is indicative of developmental adaptations that may help explain the link between IUGR and adulthood insulin resistance. Copyright © 2016 the American Physiological Society.

  6. An Empirical Study on the Behavior of Monthly Stock Prices of Fortune 500 Firms and S&P Smaller Firms: Evidence and Implications

    OpenAIRE

    Young H. Kim; Edward L. Davis; Charles T. Moses

    2014-01-01

    This paper revisits a random walk hypothesis by investigating the behavior of monthly stock prices of 461 Fortune 500 firms over 45 years and 599 S&P smaller firms over 10 years. The Box-Jenkins ARIMA models are applied to time series analysis and stock market forecasting to find the monthly stock price behavior. The research findings show that 309 (67.03%) Fortune 500 firms and 449 (74.96%) S&P smaller firms follow a random walk. The monthly stock prices of Fortune 500 firms and S&P firms ...

  7. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  8. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  9. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  10. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  11. Relevance: An Interdisciplinary and Information Science Perspective

    Directory of Open Access Journals (Sweden)

    Howard Greisdorf

    2000-01-01

    Full Text Available Although relevance has represented a key concept in the field of information science for evaluating information retrieval effectiveness, the broader context established by interdisciplinary frameworks could provide greater depth and breadth to on-going research in the field. This work provides an overview of the nature of relevance in the field of information science with a cursory view of how cross-disciplinary approaches to relevance could represent avenues for further investigation into the evaluative characteristics of relevance as a means for enhanced understanding of human information behavior.

  12. Macroscale hydrologic modeling of ecologically relevant flow metrics

    Science.gov (United States)

    Wenger, Seth J.; Luce, Charles H.; Hamlet, Alan F.; Isaak, Daniel J.; Neville, Helen M.

    2010-09-01

    Stream hydrology strongly affects the structure of aquatic communities. Changes to air temperature and precipitation driven by increased greenhouse gas concentrations are shifting timing and volume of streamflows potentially affecting these communities. The variable infiltration capacity (VIC) macroscale hydrologic model has been employed at regional scales to describe and forecast hydrologic changes but has been calibrated and applied mainly to large rivers. An important question is how well VIC runoff simulations serve to answer questions about hydrologic changes in smaller streams, which are important habitat for many fish species. To answer this question, we aggregated gridded VIC outputs within the drainage basins of 55 streamflow gages in the Pacific Northwest United States and compared modeled hydrographs and summary metrics to observations. For most streams, several ecologically relevant aspects of the hydrologic regime were accurately modeled, including center of flow timing, mean annual and summer flows and frequency of winter floods. Frequencies of high and low flows in the summer were not well predicted, however. Predictions were worse for sites with strong groundwater influence, and some sites showed errors that may result from limitations in the forcing climate data. Higher resolution (1/16th degree) modeling provided small improvements over lower resolution (1/8th degree). Despite some limitations, the VIC model appears capable of representing several ecologically relevant hydrologic characteristics in streams, making it a useful tool for understanding the effects of hydrology in delimiting species distributions and predicting the potential effects of climate shifts on aquatic organisms.

  13. Deliberate practice theory: relevance, effort, and inherent enjoyment of music practice.

    Science.gov (United States)

    Hyllegard, Randy; Bories, Tamara L

    2008-10-01

    This study examined three assumptions of the theory of deliberate practice for practice playing music on an electronic keyboard. 40 undergraduate students, divided into two separate groups, practiced one of two music sequences and rated the relevance of practice for improving performance on the sequences, the amount of effort needed to learn the sequences, and the inherent enjoyment of practice sessions. Findings for each assumption were consistent with those suggested by theory but also showed that perceptions are affected by the amount of practice completed and performance of the skill.

  14. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  15. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  16. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  17. Dynamic Effects of Self-Relevance and Task on the Neural Processing of Emotional Words in Context.

    Science.gov (United States)

    Fields, Eric C; Kuperberg, Gina R

    2015-01-01

    We used event-related potentials (ERPs) to examine the interactions between task, emotion, and contextual self-relevance on processing words in social vignettes. Participants read scenarios that were in either third person (other-relevant) or second person (self-relevant) and we recorded ERPs to a neutral, pleasant, or unpleasant critical word. In a previously reported study (Fields and Kuperberg, 2012) with these stimuli, participants were tasked with producing a third sentence continuing the scenario. We observed a larger LPC to emotional words than neutral words in both the self-relevant and other-relevant scenarios, but this effect was smaller in the self-relevant scenarios because the LPC was larger on the neutral words (i.e., a larger LPC to self-relevant than other-relevant neutral words). In the present work, participants simply answered comprehension questions that did not refer to the emotional aspects of the scenario. Here we observed quite a different pattern of interaction between self-relevance and emotion: the LPC was larger to emotional vs. neutral words in the self-relevant scenarios only, and there was no effect of self-relevance on neutral words. Taken together, these findings suggest that the LPC reflects a dynamic interaction between specific task demands, the emotional properties of a stimulus, and contextual self-relevance. We conclude by discussing implications and future directions for a functional theory of the emotional LPC.

  18. Dynamic effects of self-relevance and task on the neural processing of emotional words in context

    Directory of Open Access Journals (Sweden)

    Eric C. Fields

    2016-01-01

    Full Text Available We used event-related potentials (ERPs to examine the interactions between task, emotion, and contextual self-relevance on processing words in social vignettes. Participants read scenarios that were in either third person (other-relevant or second person (self-relevant and we recorded ERPs to a neutral, pleasant, or unpleasant critical word. In a previously reported study (Fields & Kuperberg, 2012 with these stimuli, participants were tasked with producing a third sentence continuing the scenario. We observed a larger LPC to emotional words than neutral words in both the self-relevant and other-relevant scenarios, but this effect was smaller in the self-relevant scenarios because the LPC was larger on the neutral words (i.e., a larger LPC to self-relevant than other-relevant neutral words. In the present work, participants simply answered comprehension questions that did not refer to the emotional aspects of the scenario. Here we observed quite a different pattern of interaction between self-relevance and emotion: the LPC was larger to emotional versus neutral words in the self-relevant scenarios only, and there was no effect of self-relevance on neutral words. Taken together, these findings suggest that the LPC reflects a dynamic interaction between specific task demands, the emotional properties of a stimulus, and contextual self-relevance. We conclude by discussing implications and future directions for a functional theory of the emotional LPC.

  19. Smaller Hippocampal Volume in Posttraumatic Stress Disorder : A Multisite ENIGMA-PGC Study: Subcortical Volumetry Results From Posttraumatic Stress Disorder Consortia

    NARCIS (Netherlands)

    Logue, Mark W.; van Rooij, Sanne J H; Dennis, Emily L.; Davis, Sarah L.; Hayes, Jasmeet P.; Stevens, Jennifer S.; Densmore, Maria; Haswell, Courtney C.; Ipser, Jonathan; Koch, Saskia B.J.; Korgaonkar, Mayuresh; Lebois, Lauren A.M.; Peverill, Matthew; Baker, Justin T.; Boedhoe, Premika S W; Frijling, Jessie L.; Gruber, Staci A.; Harpaz-Rotem, Ilan; Jahanshad, Neda; Koopowitz, Sheri; Levy, Ifat; Nawijn, Laura; O'Connor, Lauren; Olff, Miranda; Salat, David H.; Sheridan, Margaret A.; Spielberg, Jeffrey M.; van Zuiden, Mirjam; Winternitz, Sherry R.; Wolff, Jonathan D.; Wolf, Erika J.; Wang, Xin; Wrocklage, Kristen; Abdallah, Chadi G.; Bryant, Richard A.; Geuze, Elbert; Jovanovic, Tanja; Kaufman, Milissa L.; King, Anthony P.; Krystal, John H.; Lagopoulos, Jim; Bennett, Maxwell; Lanius, Ruth; Liberzon, Israel; McGlinchey, Regina E.; McLaughlin, Katie A.; Milberg, William P.; Miller, Mark W.; Ressler, Kerry J; Veltman, Dick J.; Stein, Dan J; Thomaes, Kathleen; Thompson, Paul M.; Morey, Rajendra A.

    2018-01-01

    Background Many studies report smaller hippocampal and amygdala volumes in posttraumatic stress disorder (PTSD), but findings have not always been consistent. Here, we present the results of a large-scale neuroimaging consortium study on PTSD conducted by the Psychiatric Genomics Consortium

  20. Gelada vocal sequences follow Menzerath’s linguistic law

    Science.gov (United States)

    Gustison, Morgan L.; Semple, Stuart; Ferrer-i-Cancho, Ramon; Bergman, Thore J.

    2016-01-01

    Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are found in nonhuman animals. Menzerath’s law is a linguistic law that states that, the larger the construct, the smaller the size of its constituents. Here, to our knowledge, we present the first evidence that Menzerath’s law holds in the vocal communication of a nonhuman species. We show that, in vocal sequences of wild male geladas (Theropithecus gelada), construct size (sequence size in number of calls) is negatively correlated with constituent size (duration of calls). Call duration does not vary significantly with position in the sequence, but call sequence composition does change with sequence size and most call types are abbreviated in larger sequences. We also find that intercall intervals follow the same relationship with sequence size as do calls. Finally, we provide formal mathematical support for the idea that Menzerath’s law reflects compression—the principle of minimizing the expected length of a code. Our findings suggest that a common principle underpins human and gelada vocal communication, highlighting the value of exploring the applicability of linguistic laws in vocal systems outside the realm of language. PMID:27091968

  1. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  2. Application of high-throughput DNA sequencing in phytopathology.

    Science.gov (United States)

    Studholme, David J; Glover, Rachel H; Boonham, Neil

    2011-01-01

    The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses. Copyright © 2011 by Annual Reviews. All rights reserved.

  3. Does relevance matter in academic policy research

    DEFF Research Database (Denmark)

    Dredge, Dianne

    2015-01-01

    A reflection on whether relevance matters in tourism policy research, and if so, to whom/what should it matter......A reflection on whether relevance matters in tourism policy research, and if so, to whom/what should it matter...

  4. Inoculating Relevance Feedback Against Poison Pills

    NARCIS (Netherlands)

    Dehghani, Mostafa; Azarbonyad, Hosein; Kamps, Jaap; Hiemstra, Djoerd; Marx, Maarten

    2016-01-01

    Relevance Feedback is a common approach for enriching queries, given a set of explicitly or implicitly judged documents to improve the performance of the retrieval. Although it has been shown that on average, the overall performance of retrieval will be improved after relevance feedback, for some

  5. Relevant cost information for order acceptance decisions

    NARCIS (Netherlands)

    Wouters, M.J.F.

    1997-01-01

    Some economic considerations for order acceptance decisions are discussed. The relevant economic considerations for order acceptance are widely discussed in the literature: only those costs are relevant which would be avoidable by not accepting the order incremental costs plus opportunity costs .

  6. Android Smartphone Relevance to Military Weather Applications

    Science.gov (United States)

    2011-10-01

    lithium -ion battery that may be replaced by the user (unlike Apple iPod Touch devices), thus spare batteries can be carried. If there is only sporadic...Android Smartphone Relevance to Military Weather Applications by David Sauter ARL-TR-5793 October 2011...Android Smartphone Relevance to Military Weather Applications David Sauter Computational and Information Sciences Directorate, ARL

  7. Using small XML elements to support relevance

    NARCIS (Netherlands)

    G. Ramirez Camps (Georgina); T.H.W. Westerveld (Thijs); A.P. de Vries (Arjen)

    2006-01-01

    htmlabstractSmall XML elements are often estimated relevant by the retrieval model but they are not desirable retrieval units. This paper presents a generic model that exploits the information obtained from small elements. We identify relationships between small and relevant elements and use this

  8. Translation as secondary communication. The relevance theory ...

    African Journals Online (AJOL)

    Ernst-August Gutt started one of the greatest translation debates of the past ten years when he suggested that relevance theory holds the key to providing a unified account of translation. The bulk of the debate has been between practitioners of functional equivalence and advocates of a relevance theoretic approach to ...

  9. Irreducible Tests for Space Mission Sequencing Software

    Science.gov (United States)

    Ferguson, Lisa

    2012-01-01

    As missions extend further into space, the modeling and simulation of their every action and instruction becomes critical. The greater the distance between Earth and the spacecraft, the smaller the window for communication becomes. Therefore, through modeling and simulating the planned operations, the most efficient sequence of commands can be sent to the spacecraft. The Space Mission Sequencing Software is being developed as the next generation of sequencing software to ensure the most efficient communication to interplanetary and deep space mission spacecraft. Aside from efficiency, the software also checks to make sure that communication during a specified time is even possible, meaning that there is not a planet or moon preventing reception of a signal from Earth or that two opposing commands are being given simultaneously. In this way, the software not only models the proposed instructions to the spacecraft, but also validates the commands as well.To ensure that all spacecraft communications are sequenced properly, a timeline is used to structure the data. The created timelines are immutable and once data is as-signed to a timeline, it shall never be deleted nor renamed. This is to prevent the need for storing and filing the timelines for use by other programs. Several types of timelines can be created to accommodate different types of communications (activities, measurements, commands, states, events). Each of these timeline types requires specific parameters and all have options for additional parameters if needed. With so many combinations of parameters available, the robustness and stability of the software is a necessity. Therefore a baseline must be established to ensure the full functionality of the software and it is here where the irreducible tests come into use.

  10. Sequence Matching Analysis for Curriculum Development

    Directory of Open Access Journals (Sweden)

    Liem Yenny Bendatu

    2015-06-01

    Full Text Available Many organizations apply information technologies to support their business processes. Using the information technologies, the actual events are recorded and utilized to conform with predefined model. Conformance checking is an approach to measure the fitness and appropriateness between process model and actual events. However, when there are multiple events with the same timestamp, the traditional approach unfit to result such measures. This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain. A case study in the field of educational process has been conducted. This study also proposes a curriculum analysis framework to test the proposed approach. By considering the learning sequence of students, it results some measurements for curriculum development. Finally, the result of the proposed approach has been verified by relevant instructors for further development.

  11. Geoseq: a tool for dissecting deep-sequencing datasets

    Directory of Open Access Journals (Sweden)

    Homann Robert

    2010-10-01

    Full Text Available Abstract Background Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO, Sequence Read Archive (SRA hosted by the NCBI, or the DNA Data Bank of Japan (ddbj. Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Results Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Conclusions Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a identify differential isoform expression in mRNA-seq datasets, b identify miRNAs (microRNAs in libraries, and identify mature and star sequences in miRNAS and c to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

  12. Evolutionary relevance facilitates visual information processing.

    Science.gov (United States)

    Jackson, Russell E; Calvillo, Dusti P

    2013-11-03

    Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  13. Evolutionary Relevance Facilitates Visual Information Processing

    Directory of Open Access Journals (Sweden)

    Russell E. Jackson

    2013-07-01

    Full Text Available Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  14. Experience of targeted Usher exome sequencing as a clinical test

    Science.gov (United States)

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  15. Smaller plates, less food waste

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Schmidt, Karsten; Skov, Laurits Rhoden

    With roughly one-third of food produced for human consumption lost or wasted globally (about 1.3 billion tons per year), the impact on the environment cannot be anymore neglected. Actions at all points in the production chain are now urgent, including reductions in food waste at home, by retailer...... the hypothesis that dishware size plays an important role in the amount of food wasted among Danish adults in a self-service eating setting. This finding has PHN implications: slight changes in the foodscape can contribute to sustainable food consumption goals.......With roughly one-third of food produced for human consumption lost or wasted globally (about 1.3 billion tons per year), the impact on the environment cannot be anymore neglected. Actions at all points in the production chain are now urgent, including reductions in food waste at home, by retailers...... and producers. Northern European consumers are among the most environmentally concerned consumers, however, their concerns do not always translate in more sustainable food-related behaviours. Furthermore, food choices are not always rational and could be non-reflective. Hence, the objective of this pilot study...

  16. Smaller plates, less food waste

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Schmidt, Karsten; Skov, Laurits Rhoden

    With roughly one-third of food produced for human consumption lost or wasted globally (about 1.3 billion tons per year), the impact on the environment cannot be anymore neglected. Actions at all points in the production chain are now urgent, including reductions in food waste at home, by retailers...... the hypothesis that dishware size plays an important role in the amount of food wasted among Danish adults in a self-service eating setting. This finding has PHN implications: slight changes in the foodscape can contribute to sustainable food consumption goals....

  17. Smaller plates, less food waste

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Schmidt, Karsten; Skov, Laurits Rhoden

    and producers. Northern European consumers are among the most environmentally concerned consumers, however, their concerns do not always translate in more sustainable food-related behaviours. Furthermore, food choices are not always rational and could be non-reflective. Hence, the objective of this pilot study......With roughly one-third of food produced for human consumption lost or wasted globally (about 1.3 billion tons per year), the impact on the environment cannot be anymore neglected. Actions at all points in the production chain are now urgent, including reductions in food waste at home, by retailers...... was to investigate whether the size of the dishware would non-reflectively influence the amount of foods taken from an “ad-libitum” buffet and the resulting amount of waste. Sample consisted of Danish business leaders that took part in a congress in Copenhagen, Denmark. Two buffet tables were set up on two separate...

  18. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  19. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  20. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  1. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  2. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  3. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis

    In this thesis we describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon codes with non-uniform profile. With this scheme decoding with good performance...... is possible as low as Eb/No=0.6 dB, which is about 1.7 dB below the signal-to-noise ratio that marks the cut-off rate for the convolutional code. This is possible since the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability...... of computational overflow. Analytical results for the probability that the first Reed-Solomon word is decoded after C computations are presented. This is supported by simulation results that are also extended to other parameters....

  4. Simple procedure for evaluating earthquake response spectra of large-event motions based on site amplification factors derived from smaller-event records

    International Nuclear Information System (INIS)

    Dan, Kazuo; Miyakoshi, Jun-ichi; Yashiro, Kazuhiko.

    1996-01-01

    A primitive procedure was proposed for evaluating earthquake response spectra of large-event motions to make use of records from smaller events. The result of the regression analysis of the response spectra was utilized to obtain the site amplification factors in the proposed procedure, and the formulation of the seismic-source term in the regression analysis was examined. A linear form of the moment magnitude, Mw, is good for scaling the source term of moderate earthquakes with Mw of 5.5 to 7.0, while a quadratic form of Mw and the ω-square source-spectrum model is appropriate for scaling the source term of smaller and greater earthquakes, respectively. (author). 52 refs

  5. Influence of irradiation (Co60) in pre-implant rabbits embryos: effect on blastocyst diameters and embryos smaller than 2 mm

    International Nuclear Information System (INIS)

    Approbato, Mario S.; Oliveira Moura, Katia K.V. de; Souza Florencio, Rodopiano de; Cunha Junior, Carlos; Garcia, Ricardo; Faria, Renato S.; Benedetti, Leonardo N.; Goulart, Flamarion B.

    1995-01-01

    We studied the effect of ionizing irradiation on 12 New Zealand rabbits (65 embryos), in three different times: at match time (zero hour), two days after and four days after, with two different irradiation doses, 5 c Gy and 10 c Gy. Six rabbits (36 blastocysts) were used as controls. The matching instant was the zero hour. Exactly six days after (± 60 minutes) the embryos of each rabbit was picked up by flushing the uterus with culture media. The embryos were fixed in methanol for 48 hours, and colored with acid Mayer hematoxylin. The following embryos parameters were studied: diameter growth; percentage of embryos smaller than 2 mm. We observed that only the irradiation time influenced the blastocysts diameter (no irradiation dose). There was no relation between percentage of embryos smaller than 2 mm and the irradiation. (author)

  6. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  7. Ballooning mode second stability region for sequences of tokamak equilibria

    International Nuclear Information System (INIS)

    Sugiyama, L.; Mark, J.W.K.

    A numerical study of several sequences of tokamak equilibria derived from two flux conserving sequences confirms the tendency of high n ideal MHD ballooning modes to stabilize for values of the plasma beta greater than a second critical beta, for sufficiently favorable equilibria. The major stabilizing effect of increasing the inverse rotational transform profile q(Psi) for equilibria with the same flux surface geometry is shown. The unstable region shifts toward larger shear d ln q/d ln γ and the width of the region measured in terms of the poloidal beta or a pressure gradient parameter, for fixed shear, decreases. The smaller aspect ratio sequences are more sensitive to changes in q and have less stringent limits on the attainable value of the plasma beta in the high beta stable region. Finally, the disconnected mode approximation is shown to provide a reasonable description of the second high beta stability boundary

  8. Astrophysical relevance of γ transition energies

    International Nuclear Information System (INIS)

    Rauscher, Thomas

    2008-01-01

    The relevant γ energy range is explicitly identified where additional γ strength must be located to have an impact on astrophysically relevant reactions. It is shown that folding the energy dependences of the transmission coefficients and the level density leads to maximal contributions for γ energies of 2≤E γ ≤4 unless quantum selection rules allow isolated states to contribute. Under this condition, electric dipole transitions dominate. These findings allow us to more accurately judge the relevance of modifications of the γ strength for astrophysics

  9. Neutrophil programming dynamics and its disease relevance.

    Science.gov (United States)

    Ran, Taojing; Geng, Shuo; Li, Liwu

    2017-11-01

    Neutrophils are traditionally considered as first responders to infection and provide antimicrobial host defense. However, recent advances indicate that neutrophils are also critically involved in the modulation of host immune environments by dynamically adopting distinct functional states. Functionally diverse neutrophil subsets are increasingly recognized as critical components mediating host pathophysiology. Despite its emerging significance, molecular mechanisms as well as functional relevance of dynamically programmed neutrophils remain to be better defined. The increasing complexity of neutrophil functions may require integrative studies that address programming dynamics of neutrophils and their pathophysiological relevance. This review aims to provide an update on the emerging topics of neutrophil programming dynamics as well as their functional relevance in diseases.

  10. New conducted electrical weapons: Electrical safety relative to relevant standards.

    Science.gov (United States)

    Panescu, Dorin; Nerheim, Max; Kroll, Mark W; Brave, Michael A

    2017-07-01

    We have previously published about TASER ® conducted electrical weapons (CEW) compliance with international standards. CEWs deliver electrical pulses that can inhibit a person's neuromuscular control or temporarily incapacitate. An eXperimental Rotating-Field (XRF) waveform CEW and the X2 CEW are new 2-shot electrical weapon models designed to target a precise amount of delivered charge per pulse. They both can deploy 1 or 2 dart pairs, delivered by 2 separate cartridges. Additionally, the XRF controls delivery of incapacitating pulses over 4 field vectors, in a rotating sequence. As in our previous study, we were motivated by the need to understand the cardiac safety profile of these new CEWs. The goal of this paper is to analyze the nominal electrical outputs of TASER XRF and X2 CEWs in reference to provisions of all relevant international standards that specify safety requirements for electrical medical devices and electrical fences. Although these standards do not specifically mention CEWs, they are the closest electrical safety standards and hence give very relevant guidance. The outputs of several TASER XRF and X2 CEWs were measured under normal operating conditions. The measurements were compared against manufacturer specifications. CEWs electrical output parameters were reviewed against relevant safety requirements of UL 69, IEC 60335-2-76 Ed 2.1, IEC 60479-1, IEC 60479-2, AS/NZS 60479.1, AS/NZS 60479.2, IEC 60601-1 and BS EN 60601-1. Our study confirmed that the nominal electrical outputs of TASER XRF and X2 CEWs lie within safety bounds specified by relevant standards.

  11. Comparison of retrograde intrarenal surgery and mini-percutaneous nephrolithotomy in management of lower-pole renal stones with a diameter of smaller than 15 mm.

    Science.gov (United States)

    Kirac, Mustafa; Bozkurt, Ömer Faruk; Tunc, Lutfi; Guneri, Cagri; Unsal, Ali; Biri, Hasan

    2013-06-01

    The aim of this study was to compare the outcomes of retrograde intrarenal surgery (RIRS) and miniaturized percutaneous nephrolithotomy (mini-PNL) in management of lower-pole renal stones with a diameter smaller than 15 mm. Between December 2009 and July 2012, the patients with the diagnosis of lower-pole stones were evaluated by ultrasonography, intravenous pyelography and computed tomography. The records of 73 evaluable patients who underwent mini-PNL (n = 37) or RIRS (n = 36) for lower-pole (LP) stones with diameter smaller than 15 mm were reviewed retrospectively. Of the 73 patients, 37 underwent mini-PNL and 36 underwent RIRS. The stone-free rates were 89.1 and 88.8 % for mini-PNL and RIRS groups, respectively. The mean operation time was 53.7 ± 14.5 in the mini-PNL group but 66.4 ± 15.8 in the RIRS group (P = 0.01). The mean fluoroscopy times and hospitalization times were significantly higher in the mini-PNL group. There was no major complication in any patient. RIRS and mini-PNL are safe and effective methods for treatment of LP calculi with a diameter smaller than 15 mm. RIRS is a non-invasive and feasible treatment option, and has also short hospitalization time, low morbidity and complication rate. It may be an alternative of mini-PNL in the treatment LP calculi with smaller than 15 mm.

  12. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  13. Smaller Hippocampal Volume in Posttraumatic Stress Disorder: A Multisite ENIGMA-PGC Study: Subcortical Volumetry Results From Posttraumatic Stress Disorder Consortia

    Science.gov (United States)

    Logue, Mark W.; van Rooij, Sanne J.H.; Dennis, Emily L.; Davis, Sarah L.; Hayes, Jasmeet P.; Stevens, Jennifer S.; Densmore, Maria; Haswell, Courtney C.; Ipser, Jonathan; Koch, Saskia B.J.; Korgaonkar, Mayuresh; Lebois, Lauren A.M.; Peverill, Matthew; Baker, Justin T.; Boedhoe, Premika S.W.; Frijling, Jessie L.; Gruber, Staci A.; Harpaz-Rotem, Ilan; Jahanshad, Neda; Koopowitz, Sheri; Levy, Ifat; Nawijn, Laura; O’Connor, Lauren; Olff, Miranda; Salat, David H.; Sheridan, Margaret A.; Spielberg, Jeffrey M.; van Zuiden, Mirjam; Winternitz, Sherry R.; Wolff, Jonathan D.; Wolf, Erika J.; Wang, Xin; Wrocklage, Kristen; Abdallah, Chadi G.; Bryant, Richard A.; Geuze, Elbert; Jovanovic, Tanja; Kaufman, Milissa L.; King, Anthony P.; Krystal, John H.; Lagopoulos, Jim; Bennett, Maxwell; Lanius, Ruth; Liberzon, Israel; McGlinchey, Regina E.; McLaughlin, Katie A.; Milberg, William P.; Miller, Mark W.; Ressler, Kerry J.; Veltman, Dick J.; Stein, Dan J.; Thomaes, Kathleen; Thompson, Paul M.; Morey, Rajendra A.

    2018-01-01

    BACKGROUND Many studies report smaller hippocampal and amygdala volumes in posttraumatic stress disorder (PTSD), but findings have not always been consistent. Here, we present the results of a large-scale neuroimaging consortium study on PTSD conducted by the Psychiatric Genomics Consortium (PGC)–Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) PTSD Working Group. METHODS We analyzed neuroimaging and clinical data from 1868 subjects (794 PTSD patients) contributed by 16 cohorts, representing the largest neuroimaging study of PTSD to date. We assessed the volumes of eight subcortical structures (nucleus accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus, and lateral ventricle). We used a standardized image-analysis and quality-control pipeline established by the ENIGMA consortium. RESULTS In a meta-analysis of all samples, we found significantly smaller hippocampi in subjects with current PTSD compared with trauma-exposed control subjects (Cohen’s d = −0.17, p = .00054), and smaller amygdalae (d = −0.11, p = .025), although the amygdala finding did not survive a significance level that was Bonferroni corrected for multiple subcortical region comparisons (p < .0063). CONCLUSIONS Our study is not subject to the biases of meta-analyses of published data, and it represents an important milestone in an ongoing collaborative effort to examine the neurobiological underpinnings of PTSD and the brain’s response to trauma. PMID:29217296

  14. Overexpression of Jatropha Gibberellin 2-oxidase 6 (JcGA2ox6 Induces Dwarfism and Smaller Leaves, Flowers and Fruits in Arabidopsis and Jatropha

    Directory of Open Access Journals (Sweden)

    Ying-Xiong Hu

    2017-12-01

    Full Text Available Gibberellins (GAs are plant hormones that play fundamental roles in plant growth and development. Gibberellin 2-oxidase (GA2ox plays a direct role in determining the levels of bioactive GAs by catalyzing bioactive GAs or their immediate precursors to inactive forms. In this study, a GA2ox gene, designated JcGA2ox6, was isolated from Jatropha curcas. JcGA2ox6 is expressed in all tissues of adult Jatropha, with the highest expression level in male flowers and the lowest expression level in young leaves. Overexpression of JcGA2ox6 in Arabidopsis resulted in a typical dwarf phenotype, along with late flowering, smaller leaves and flowers, shorter siliques and smaller seeds. Similarly, when JcGA2ox6 was overexpressed in Jatropha, the transgenic plants exhibited a dwarf phenotype with dark-green leaves and smaller inflorescences, flowers, fruits and seeds. However, the flowering time of Jatropha was not affected by overexpression of JcGA2ox6, unlike that in the transgenic Arabidopsis. Moreover, the number of flowers per inflorescence, the weight of 10 seeds and the seed oil content were significantly decreased in transgenic Jatropha. The results indicated that overexpression of JcGA2ox6 had a great impact on the vegetative and reproductive growth of transgenic Jatropha. Furthermore, we found that the dwarf phenotype of transgenic Jatropha was caused by a decrease in endogenous bioactive GA4, which was correlated with the degree of dwarfism.

  15. Dietary Differences in Male Workers among Smaller Occupational Groups within Large Occupational Categories: Findings from the Japan Environment and Children's Study (JECS).

    Science.gov (United States)

    Tanaka, Rie; Tsuji, Mayumi; Senju, Ayako; Kusuhara, Koichi; Kawamoto, Toshihiro

    2018-05-11

    Studies examining workers' diet according to smaller occupational groups within "large occupational categories" are sparse. The aim of this study was to examine the potential differences in workers' diets based on the classification of workers into smaller occupational groups that comprise "large occupational categories". The subjects of this study were working fathers who had participated in the Japan Environment and Children's Study (N = 38,656). Energy and nutrient intake were calculated based on data collected from the Food Frequency Questionnaire. Occupations were classified according to the Japanese Standard Occupational Classification. Logistic regression analyses were performed to examine the adherence to current dietary recommendations within smaller occupational groups. In particular, significant differences were observed among the categorical groups of "professional and engineering workers", "service workers", and "agricultural, forestry, and fishery workers". In "professional and engineering workers", teachers showed higher odds of adherence to calcium intake recommendations compared with nurses (OR, 2.54; 95% CI, 2.02⁻3.14; p < 0.001). In "agricultural, forestry, and fishery workers", agriculture workers showed higher odds of adherence to calcium (OR, 2.15; 95% CI, 1.46⁻3.15; p < 0.001) and vitamin C (OR 1.90, 95% CI 1.31⁻2.74, p = 0.001) intake recommendations compared with forestry and fishery workers. These findings may be beneficial from a research perspective as well as in the development of more effective techniques to improve workers' diet and health.

  16. Combined value of Virtual Touch tissue quantification and conventional sonographic features for differentiating benign and malignant thyroid nodules smaller than 10 mm.

    Science.gov (United States)

    Zhang, Huiping; Shi, Qiusheng; Gu, Jiying; Jiang, Luying; Bai, Min; Liu, Long; Wu, Ying; Du, Lianfang

    2014-02-01

    This study aimed to investigate the value of sonographic features including Virtual Touch tissue quantification (VTQ; Siemens Medical Solutions, Mountain View, CA) for differentiating benign and malignant thyroid nodules smaller than 10 mm. Seventy-one thyroid nodules smaller than 10 mm with pathologic diagnoses were included in this study. The conventional sonographic features and quantitative elasticity features (VTQ) were observed and compared between benign and malignant nodules. There were 39 benign and 32 malignant nodules according to histopathologic examination. When compared with benign nodules, malignant nodules were more frequently taller than wide, poorly defined, and markedly hypoechoic (P benign and malignant nodules. The VTQ value for malignant nodules (mean ± SD 3.260 ± 0.725 m/s) was significantly higher than that of benign ones (2.108 ± 0.455 m/s; P benign and malignant thyroid nodules smaller than 10 mm. When VTQ was combined with B-mode sonographic features, the sensitivity was improved significantly.

  17. Smaller Hippocampal Volume in Posttraumatic Stress Disorder: A Multisite ENIGMA-PGC Study: Subcortical Volumetry Results From Posttraumatic Stress Disorder Consortia.

    Science.gov (United States)

    Logue, Mark W; van Rooij, Sanne J H; Dennis, Emily L; Davis, Sarah L; Hayes, Jasmeet P; Stevens, Jennifer S; Densmore, Maria; Haswell, Courtney C; Ipser, Jonathan; Koch, Saskia B J; Korgaonkar, Mayuresh; Lebois, Lauren A M; Peverill, Matthew; Baker, Justin T; Boedhoe, Premika S W; Frijling, Jessie L; Gruber, Staci A; Harpaz-Rotem, Ilan; Jahanshad, Neda; Koopowitz, Sheri; Levy, Ifat; Nawijn, Laura; O'Connor, Lauren; Olff, Miranda; Salat, David H; Sheridan, Margaret A; Spielberg, Jeffrey M; van Zuiden, Mirjam; Winternitz, Sherry R; Wolff, Jonathan D; Wolf, Erika J; Wang, Xin; Wrocklage, Kristen; Abdallah, Chadi G; Bryant, Richard A; Geuze, Elbert; Jovanovic, Tanja; Kaufman, Milissa L; King, Anthony P; Krystal, John H; Lagopoulos, Jim; Bennett, Maxwell; Lanius, Ruth; Liberzon, Israel; McGlinchey, Regina E; McLaughlin, Katie A; Milberg, William P; Miller, Mark W; Ressler, Kerry J; Veltman, Dick J; Stein, Dan J; Thomaes, Kathleen; Thompson, Paul M; Morey, Rajendra A

    2018-02-01

    Many studies report smaller hippocampal and amygdala volumes in posttraumatic stress disorder (PTSD), but findings have not always been consistent. Here, we present the results of a large-scale neuroimaging consortium study on PTSD conducted by the Psychiatric Genomics Consortium (PGC)-Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) PTSD Working Group. We analyzed neuroimaging and clinical data from 1868 subjects (794 PTSD patients) contributed by 16 cohorts, representing the largest neuroimaging study of PTSD to date. We assessed the volumes of eight subcortical structures (nucleus accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus, and lateral ventricle). We used a standardized image-analysis and quality-control pipeline established by the ENIGMA consortium. In a meta-analysis of all samples, we found significantly smaller hippocampi in subjects with current PTSD compared with trauma-exposed control subjects (Cohen's d = -0.17, p = .00054), and smaller amygdalae (d = -0.11, p = .025), although the amygdala finding did not survive a significance level that was Bonferroni corrected for multiple subcortical region comparisons (p < .0063). Our study is not subject to the biases of meta-analyses of published data, and it represents an important milestone in an ongoing collaborative effort to examine the neurobiological underpinnings of PTSD and the brain's response to trauma. Published by Elsevier Inc.

  18. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  19. The foundation of the concept of relevance

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2010-01-01

    that what was regarded as the most fundamental view by Saracevic in 1975 has not since been considered (with very few exceptions). Other views, which are based on less fruitful assumptions, have dominated the discourse on relevance in information retrieval and information science. Many authors have...... reexamined the concept of relevance in information science, but have neglected the subject knowledge view, hence basic theoretical assumptions seem not to have been properly addressed. It is as urgent now as it was in 1975 seriously to consider “the subject knowledge view” of relevance (which may also...... be termed “the epistemological view”). The concept of relevance, like other basic concepts, is influenced by overall approaches to information science, such as the cognitive view and the domain-analytic view. There is today a trend toward a social paradigm for information science. This paper offers...

  20. Exploring Educational Quality and Relevance through Integrating ...

    African Journals Online (AJOL)

    Exploring Educational Quality and Relevance through Integrating Environmental and Social Issues in Science Education. ... However, the new contextualised concept of learning and teaching was applied only to one of them. A post-test was ...

  1. Has Financial Statement Information become Less Relevant?

    DEFF Research Database (Denmark)

    Thinggaard, Frank; Damkier, Jesper

    This paper presents insights into the question of whether accounting information based on the EU’s Accounting Directives has become less value-relevant to investors over time. The study is based on a research design first used by Francis and Schipper (1999), where value-relevance is measured......? The sample is based on non-financial companies listed on the Copenhagen Stock Exchange in the period 1984-2002. Our analyses show that all the applied accounting measures are value-relevant as investment strategies based on the information earn positive market-adjusted returns in our sample period....... The results provide some indication of a decline in the value-relevance of earnings information in the 1984-2001 period, and mixed, but not statistically reliable, evidence for accounting measures where book value information and asset values are also extracted from financial statements. The results seem...

  2. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  3. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  4. Clinical relevance is associated with allergen-specific wheal size in skin prick testing

    DEFF Research Database (Denmark)

    Haahtela, T.; Burbach, G. J.; Bachert, C.

    2014-01-01

    , asthma, atopic dermatitis, food allergy). The effects of age, gender, and geographical area on SPT results were assessed. For each allergen, the wheal size in mm with an 80% positive predictive value (PPV) for being clinically relevant was calculated. ResultsDepending on the allergen, from 40% (blatella...... by providing quantitative decision points. MethodsThe GA(2)LEN SPT study with 3068 valid data sets was used to investigate the relationship between SPT results and patient-reported clinical relevance for each of the 18 inhalant allergens as well as SPT wheal size and physician-diagnosed allergy (rhinitis...... SPT reactions had a smaller risk of sensitizations being clinically relevant compared with adults. The 80% PPV varied from 3 to 10mm depending on the allergen. ConclusionThese reading keys' for 18 inhalant allergens can help interpret SPT results with respect to their clinical significance. A SPT form...

  5. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  6. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  7. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  8. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  9. The effect of ISM absorption on stellar activity measurements and its relevance for exoplanet studies

    Science.gov (United States)

    Fossati, L.; Marcelja, S. E.; Staab, D.; Cubillos, P. E.; France, K.; Haswell, C. A.; Ingrassia, S.; Jenkins, J. S.; Koskinen, T.; Lanza, A. F.; Redfield, S.; Youngblood, A.; Pelzmann, G.

    2017-05-01

    Past ultraviolet and optical observations of stars hosting close-in Jupiter-mass planets have shown that some of these stars present an anomalously low chromospheric activity, significantly below the basal level. For the hot Jupiter planet host WASP-13, observations have shown that the apparent lack of activity is possibly caused by absorption from the intervening interstellar medium (ISM). Inspired by this result, we study the effect of ISM absorption on activity measurements (S and log R 'HK indices) for main-sequence late-type stars. To this end, we employ synthetic stellar photospheric spectra combined with varying amounts of chromospheric emission and ISM absorption. We present the effect of ISM absorption on activity measurements by varying several instrumental (spectral resolution), stellar (projected rotational velocity, effective temperature, and chromospheric emission flux), and ISM parameters (relative velocity between stellar and ISM Ca II lines, broadening b-parameter, and Ca II column density). We find that for relative velocities between the stellar and ISM lines smaller than 30-40 km s-1 and for ISM Ca II column densities log NCaII ⪆ 12, the ISM absorption has a significant influence on activity measurements. Direct measurements and three dimensional maps of the Galactic ISM absorption indicate that an ISM Ca II column density of log NCaII = 12 is typically reached by a distance of about 100 pc along most sight lines. In particular, for a Sun-like star lying at a distance greater than 100 pc, we expect a depression (bias) in the log R'HK value larger than 0.05-0.1 dex, about the same size as the typical measurement and calibration uncertainties on this parameter. This work shows that the bias introduced by ISM absorption must always be considered when measuring activity for stars lying beyond 100 pc. We also consider the effect of multiple ISM absorption components. We discuss the relevance of this result for exoplanet studies and revise the

  10. Learning predictive statistics from temporal sequences: Dynamics and strategies.

    Science.gov (United States)

    Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

    2017-10-01

    Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

  11. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis; Paaske, Erik

    1998-01-01

    We describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon (RS) codes with nonuniform profile. With this scheme decoding with good performance is possible as low...... as Eb/N0=0.6 dB, which is about 1.25 dB below the signal-to-noise ratio (SNR) that marks the cutoff rate for the full system. Accounting for about 0.45 dB due to the outer codes, sequential decoding takes place at about 1.7 dB below the SNR cutoff rate for the convolutional code. This is possible since...... the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability of computational overflow. Analytical results for the probability that the first RS word is decoded after C computations are presented. These results are supported...

  12. Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities.

    Science.gov (United States)

    Drury, Suzanne; Williams, Hywel; Trump, Natalie; Boustred, Christopher; Lench, Nicholas; Scott, Richard H; Chitty, Lyn S

    2015-10-01

    In the absence of aneuploidy or other pathogenic cytogenetic abnormality, fetuses with increased nuchal translucency (NT ≥ 3.5 mm) and/or other sonographic abnormalities have a greater incidence of genetic syndromes, but defining the underlying pathology can be challenging. Here, we investigate the value of whole exome sequencing in fetuses with sonographic abnormalities but normal microarray analysis. Whole exome sequencing was performed on DNA extracted from chorionic villi or amniocytes in 24 fetuses with unexplained ultrasound findings. In the first 14 cases sequencing was initially performed on fetal DNA only. For the remaining 10, the trio of fetus, mother and father was sequenced simultaneously. In 21% (5/24) cases, exome sequencing provided definitive diagnoses (Milroy disease, hypophosphatasia, achondrogenesis type 2, Freeman-Sheldon syndrome and Baraitser-Winter Syndrome). In a further case, a plausible diagnosis of orofaciodigital syndrome type 6 was made. In two others, a single mutation in an autosomal recessive gene was identified, but incomplete sequencing coverage precluded exclusion of the presence of a second mutation. Whole exome sequencing improves prenatal diagnosis in euploid fetuses with abnormal ultrasound scans. In order to expedite interpretation of results, trio sequencing should be employed, but interpretation can still be compromised by incomplete coverage of relevant genes. © 2015 John Wiley & Sons, Ltd.

  13. A microfabricated hybrid device for DNA sequencing.

    Science.gov (United States)

    Liu, Shaorong

    2003-11-01

    We have created a hybrid device of a microfabricated round-channel twin-T injector incorporated with a separation capillary in order to extend the straight separation distance for high speed and long readlength DNA sequencing. Semicircular grooves on glass wafers are obtained using a photomask with a narrow line-width and a standard isotropic photolithographic etching process. Round channels are made when two etched wafers are face-to-face aligned and bonded. A two-mask fabrication process has been developed to make channels of two different diameters. The twin-T injector is formed by the smaller channels whose diameter matches the bore of the separation capillary, and the "usual" separation channel, now called the connection channel, is formed by the larger ones whose diameter matches the outer diameter of the separation capillary. The separation capillary is inserted through the connection channel all the way to the twin-T injector to allow the capillary bore flush with the twin-T injector channels. The total dead-volume of the connection is estimated to be approximately 5 pL. To demonstrate the efficiency of this hybrid device, we have performed four-color DNA sequencing on it. Using a 200 microm twin-T injector coupled with a separation capillary of 20 cm effective separation distance, we have obtained readlengths of 800 plus bases at an accuracy of 98.5% in 56 min, compared to about 650 bases in 100 min on a conventional 40 cm long capillary sequencing machine under similar conditions. At an increased separation field strength and using a diluted sieving matrix, the separation time has been reduced to 20 min with a readlength of 700 bases at 98.5% base-calling accuracy.

  14. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  15. Sequence analysis of the its-2 region: a tool to identify strains of Scenedesmus (Chlorophyceae)

    NARCIS (Netherlands)

    Van Hannen, E.J.; Lürling, M.; Van Donk, E.

    2000-01-01

    The genetic distances between several strains of Senedesmus obliquus (Turp,) Kutz,, S, acutus Hortobagyi, and S, naegelii Chod. calculated from ITS-2 sequences were found to be smaller than the genetic distances within other strains of Scenedesmus-that is, in S, acuminatus (Lagerh,) Chod, and S,

  16. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  17. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    Jansson Jesper

    2011-01-01

    Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

  18. Inferring relevance in a changing world

    Directory of Open Access Journals (Sweden)

    Robert C Wilson

    2012-01-01

    Full Text Available Reinforcement learning models of human and animal learning usually concentrate on how we learn the relationship between different stimuli or actions and rewards. However, in real world situations stimuli are ill-defined. On the one hand, our immediate environment is extremely multi-dimensional. On the other hand, in every decision-making scenario only a few aspects of the environment are relevant for obtaining reward, while most are irrelevant. Thus a key question is how do we learn these relevant dimensions, that is, how do we learn what to learn about? We investigated this process of representation learning experimentally, using a task in which one stimulus dimension was relevant for determining reward at each point in time. As in real life situations, in our task the relevant dimension can change without warning, adding ever-present uncertainty engendered by a constantly changing environment. We show that human performance on this task is better described by a suboptimal strategy based on selective attention and serial hypothesis testing rather than a normative strategy based on probabilistic inference. From this, we conjecture that the problem of inferring relevance in general scenarios is too computationally demanding for the brain to solve optimally. As a result the brain utilizes approximations, employing these even in simplified scenarios in which optimal representation learning is tractable, such as the one in our experiment.

  19. Level and Contamination Assessment of Environmentally Sensitive Elements in Smaller than 100 μm Street Dust Particles from Xining, China

    Directory of Open Access Journals (Sweden)

    Ni Zhao

    2014-02-01

    Full Text Available Concentrations of the environmentally sensitive elements (ESEs As, Co, Cu, Mn, Ni, Pb, V and Zn in smaller than 100 μm street dust particles from Xining were measured using X-ray fluorescence spectrometry and their contamination levels were assessed based on enrichment factor (EF, geoaccumulation index (Igeo and pollution load index (PLI. The concentrations of As, Co, Cu, Mn, Ni, Pb, V and Zn in smaller than 100 μm street dust particles from Xining are 0.1–0.8, 2.7–10.9, 0.7–5.2, 0.3–1.1, 0.6–2.5, 1.2–11.1, 0.7–1.3 and 0.4–2.9 times the background values of Qinghai soil, respectively. The calculated EF and Igeo values reveal the order Co > Pb > Cu > Zn > V > Ni > Mn > As. The EF and Igeo values of Co, Cu, Pb and Zn are higher indicating that there is considerable pollution by these elements in smaller than 100 μm street dust particles, especially for Co. The EF and Igeo of Mn, Ni and V are lower and the assessment results indicate an absence of distinct Mn, Ni and V pollution in the studied samples. The mean value of PLIsite is 1.14, indicating a slightly pollution in the whole city of Xining. The order of PLIarea for the five tested districts is Center District (CD > East District (ED > West District (WD > North District (ND > South District (SD, showing that ESEs pollution in the South District is the lightest while it is the highest in the Central District.

  20. Effects of a lighter, smaller football on acute match injuries in adolescent female football: a pilot cluster-randomized controlled trial.

    Science.gov (United States)

    Zebis, Mette K; Thorborg, Kristian; Andersen, Lars L; Møller, Merete; Christensen, Karl B; Clausen, Mikkel B; Hölmich, Per; Wedderkopp, Niels; Andersen, Thomas B; Krustrup, Peter

    2018-05-01

    The high injury incidence during match-play in female adolescent football is a major concern. In football, males and females play matches with the same football size. No studies have investigated the effect of football size on injury incidence in female adolescent football. Thus, the aim of the present study was to investigate the effects of introducing a lighter, smaller football on the injury pattern in female adolescent football. We conducted a pilot cluster randomized controlled trial including 26 football teams representing 346 adolescent female football players (age 15-18 years). The teams were randomized to a new lighter, smaller football (INT, N.=12 teams) or a traditional FIFA size 5 football (CON, N.=14 teams) during a full match-season. Acute time-loss injuries and football-exposure during match-play were reported weekly by text-message questions and verified subsequently by telephone interview. In total, 46 acute time-loss injuries were registered (5 severe injuries), yielding an incidence rate of 15.2 injuries per 1000 hours of match-play (95% CI: 8.5-27.2) in INT and 18.6 injuries per 1000 hours of match-play (95% CI: 14.0-24.8) in CON. The estimated 22% greater injury incidence rate risk (IRR: 1.22 [95% CI: 0.64-2.35]) in the CON group was not significant. With an IRR of 1.22, a future RCT main study would need to observe 793 acute time-loss injuries during match-play, in order to have a power of 80%. A large-scaled RCT is required to definitively test for beneficial or harmful effects of a lighter, smaller football in adolescent female football.

  1. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  2. Laboratory exercises to teach clinically relevant chemistry of antibiotics.

    Science.gov (United States)

    El Sayed, Khalid A; Chelette, Candace T

    2014-03-12

    To design, implement, and evaluate student performance on clinically relevant chemical and spectral laboratory exercises on antibiotics. In the first of 2 exercises, second-year pharmacy students enrolled in an integrated laboratory sequence course studied the aqueous stability of ß-lactam antibiotics using a spectral visual approach. In a second exercise, students studied the tendency of tetracycline, rifamycins, and fluoroquinolones to form insoluble chelate complexes (turbidity) with polyvalent metals. On a survey to assess achievement of class learning objectives, students agreed the laboratory activities helped them better retain important information concerning antibiotic stability and interactions. A significant improvement was observed in performance on examination questions related to the laboratory topics for 2012 and 2013 students compared to 2011 students who did not complete the laboratory. A 1-year follow-up examination question administered in a separate course showed >75% of the students were able to identify rifamycins-food interactions compared with laboratory exercises. The use of spectral visual approaches allowed students to investigate antibiotic stability and interactions, thus reinforcing the clinical relevance of medicinal chemistry. Students' performance on questions at the 1-year follow-up suggested increased retention of the concepts learned as a result of completing the exercises.

  3. The complexity of DNA damage: relevance to biological consequences

    International Nuclear Information System (INIS)

    Ward, J.F.

    1994-01-01

    Ionizing radiation causes both singly and multiply damaged sites in DNA when the range of radical migration is limited by the presence of hydroxyl radical scavengers (e.g. within cells). Multiply damaged sites are considered to be more biologically relevant because of the challenges they present to cellular repair mechanisms. These sites occur in the form of DNA double-strand breaks (dsb) but also as other multiple damages that can be converted to dsb during attempted repair. The presence of a dsb can lead to loss of base sequence information and/or can permit the two ends of a break to separate and rejoin with the wrong partner. (Multiply damaged sites may also be the biologically relevant type of damage caused by other agents, such as UVA, B and/or C light, and some antitumour antibiotics). The quantitative data available from radiation studies of DNA are shown to support the proposed mechanisms for the production of complex damage in cellular DNA, i.e. via scavengable and non-scavengable mechanisms. The yields of complex damages can in turn be used to support the conclusion that cellular mutations are a consequence of the presence of these damages within a gene. (Author)

  4. Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts.

    Science.gov (United States)

    Gorter de Vries, Arthur R; Pronk, Jack T; Daran, Jean-Marc G

    2017-06-01

    Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyce s strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes. Copyright © 2017 Gorter de Vries et al.

  5. Passage relevance models for genomics search

    Directory of Open Access Journals (Sweden)

    Frieder Ophir

    2009-03-01

    Full Text Available Abstract We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and document are represented as potential functions within a Markov Random Field. The probability of a passage being relevant to a biologist's information need is represented as the joint distribution across all potential functions. Relevance model feedback of top ranked passages is used to improve distributional estimates of query concepts and topics in context, and a dimensional indexing strategy is used for efficient aggregation of concept and term statistics. By integrating multiple sources of evidence including dependencies between topics, concepts, and terms, we seek to improve genomics literature passage retrieval precision. Using this model, we are able to demonstrate statistically significant improvements in retrieval precision using a large genomics literature corpus.

  6. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  7. MODELING THE RED SEQUENCE: HIERARCHICAL GROWTH YET SLOW LUMINOSITY EVOLUTION

    International Nuclear Information System (INIS)

    Skelton, Rosalind E.; Bell, Eric F.; Somerville, Rachel S.

    2012-01-01

    We explore the effects of mergers on the evolution of massive early-type galaxies by modeling the evolution of their stellar populations in a hierarchical context. We investigate how a realistic red sequence population set up by z ∼ 1 evolves under different assumptions for the merger and star formation histories, comparing changes in color, luminosity, and mass. The purely passive fading of existing red sequence galaxies, with no further mergers or star formation, results in dramatic changes at the bright end of the luminosity function and color-magnitude relation. Without mergers there is too much evolution in luminosity at a fixed space density compared to observations. The change in color and magnitude at a fixed mass resembles that of a passively evolving population that formed relatively recently, at z ∼ 2. Mergers among the red sequence population ('dry mergers') occurring after z = 1 build up mass, counteracting the fading of the existing stellar populations to give smaller changes in both color and luminosity for massive galaxies. By allowing some galaxies to migrate from the blue cloud onto the red sequence after z = 1 through gas-rich mergers, younger stellar populations are added to the red sequence. This manifestation of the progenitor bias increases the scatter in age and results in even smaller changes in color and luminosity between z = 1 and z = 0 at a fixed mass. The resultant evolution appears much slower, resembling the passive evolution of a population that formed at high redshift (z ∼ 3-5), and is in closer agreement with observations. We conclude that measurements of the luminosity and color evolution alone are not sufficient to distinguish between the purely passive evolution of an old population and cosmologically motivated hierarchical growth, although these scenarios have very different implications for the mass growth of early-type galaxies over the last half of cosmic history.

  8. Identity theory and personality theory: mutual relevance.

    Science.gov (United States)

    Stryker, Sheldon

    2007-12-01

    Some personality psychologists have found a structural symbolic interactionist frame and identity theory relevant to their work. This frame and theory, developed in sociology, are first reviewed. Emphasized in the review are a multiple identity conception of self, identities as internalized expectations derived from roles embedded in organized networks of social interaction, and a view of social structures as facilitators in bringing people into networks or constraints in keeping them out, subsequently, attention turns to a discussion of the mutual relevance of structural symbolic interactionism/identity theory and personality theory, looking to extensions of the current literature on these topics.

  9. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  10. Insertional mutagenesis in Populus: relevance and feasibility

    Science.gov (United States)

    Victor Busov; Matthias Fladung; Andrew Groover; Steven Strauss

    2005-01-01

    The recent sequencing of the first tree genome, that of the black cottonwood (Populus trichocarpa), opens a new chapter in tree functional genomics. While the completion of the genome is a milestone, mobilizing this significant resource for better understanding the growth and development of woody perennials will be an even greater undertaking in the...

  11. Modularization--A Road to Relevance?

    Science.gov (United States)

    Palow, William P.

    This paper describes a modular program at a community college for instructing non-science majors in college algebra. The two-course sequence is comprised of four modules each and successful completion of a module is required before a student proceeds to the next. Placement, grading policies, and scheduling are all discussed. A formative evaluation…

  12. Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.

    Science.gov (United States)

    Panja, Anindya Sundar; Bandopadhyay, Bidyut; Maiti, Smarajit

    2015-01-01

    Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, psalt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (psalt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.

  13. A neuro-data envelopment analysis approach for optimization of uncorrelated multiple response problems with smaller the better type controllable factors

    Science.gov (United States)

    Bashiri, Mahdi; Farshbaf-Geranmayeh, Amir; Mogouie, Hamed

    2013-11-01

    In this paper, a new method is proposed to optimize a multi-response optimization problem based on the Taguchi method for the processes where controllable factors are the smaller-the-better (STB)-type variables and the analyzer desires to find an optimal solution with smaller amount of controllable factors. In such processes, the overall output quality of the product should be maximized while the usage of the process inputs, the controllable factors, should be minimized. Since all possible combinations of factors' levels, are not considered in the Taguchi method, the response values of the possible unpracticed treatments are estimated using the artificial neural network (ANN). The neural network is tuned by the central composite design (CCD) and the genetic algorithm (GA). Then data envelopment analysis (DEA) is applied for determining the efficiency of each treatment. Although the important issue for implementation of DEA is its philosophy, which is maximization of outputs versus minimization of inputs, this important issue has been neglected in previous similar studies in multi-response problems. Finally, the most efficient treatment is determined using the maximin weight model approach. The performance of the proposed method is verified in a plastic molding process. Moreover a sensitivity analysis has been done by an efficiency estimator neural network. The results show efficiency of the proposed approach.

  14. Two phosphoenolpyruvate carboxykinases coexist in the Crassulacean Acid Metabolism plant Ananas comosus. Isolation and characterization of the smaller 65 kDa form.

    Science.gov (United States)

    Martín, Mariana; Rius, Sebastián Pablo; Podestá, Florencio Esteban

    2011-06-01

    Two phosphoenolpyruvate carboxykinase (PEPCK, EC 4.1.1.49) isoforms of 74 and 65 kDa were found to coexist in vivo in pineapple leaves, a constitutive Crassulacean Acid Metabolism plant. The 65 kDa form was not the result of proteolytic cleavage of the larger form since extraction methods reported to prevent PEPCK proteolysis in other plant tissues failed to yield a single immunoreactive PEPCK polypeptide in leaf extracts. In this work, the smaller form of 65 kDa was purified to homogeneity and physically and kinetically characterized and showed parameters compatible with a fully active enzyme. The specific activity was nearly twice higher for decarboxylation of oxaloacetate when compared to carboxylation of phosphoenolpyruvate. Kinetic parameters fell within the range of those estimated for other plant PEPCKs. Its activity was affected by several metabolites, as shown by inhibition by 3-phosphoglycerate, citrate, malate, fructose-1,6-bisphosphate, l-asparagine and activation of the decarboxylating activity by succinate. A break in the Arrhenius plot at about 30°C indicates that PEPCK structure is responsive to changes in temperature. The results indicate that pineapple leaves contain two PEPCK forms. The biochemical characterization of the smaller isoform performed in this work suggests that it could participate in both carbon and nitrogen metabolism in vivo by acting as a decarboxylase. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  15. Design and control of integrated chromatography column sequences.

    Science.gov (United States)

    Andersson, Niklas; Löfgren, Anton; Olofsson, Marianne; Sellberg, Anton; Nilsson, Bernt; Tiainen, Peter

    2017-07-01

    To increase the productivity in biopharmaceutical production, a natural step is to introduce integrated continuous biomanufacturing which leads to fewer buffer and storage tanks, smaller sizes of integrated unit operations, and full automation of the operation. The main contribution of this work is to illustrate a methodology for design and control of a downstream process based on integrated column sequences. For small scale production, for example, pre-clinical studies, integrated column sequences can be implemented on a single chromatography system. This makes for a very efficient drug development platform. The proposed methodology is composed of four steps and is governed by a set of tools, that is presented, that makes the transition from batch separations to a complete integrated separation sequence as easy as possible. This methodology, its associated tools and the physical implementation is presented and illustrated on a case study where the target protein is separated from impurities through an integrated four column sequence. This article shows that the design and control of an integrated column sequence was successfully implemented for a tertiary protein separation problem. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:923-930, 2017. © 2017 American Institute of Chemical Engineers.

  16. Bible Translation And Relevance Theory | Deist | Stellenbosch ...

    African Journals Online (AJOL)

    Stellenbosch Papers in Linguistics Plus. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 22 (1992) >. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register. Bible Translation And Relevance Theory. F Deist ...

  17. Relevant Scatterers Characterization in SAR Images

    Science.gov (United States)

    Chaabouni, Houda; Datcu, Mihai

    2006-11-01

    Recognizing scenes in a single look meter resolution Synthetic Aperture Radar (SAR) images, requires the capability to identify relevant signal signatures in condition of variable image acquisition geometry, arbitrary objects poses and configurations. Among the methods to detect relevant scatterers in SAR images, we can mention the internal coherence. The SAR spectrum splitted in azimuth generates a series of images which preserve high coherence only for particular object scattering. The detection of relevant scatterers can be done by correlation study or Independent Component Analysis (ICA) methods. The present article deals with the state of the art for SAR internal correlation analysis and proposes further extensions using elements of inference based on information theory applied to complex valued signals. The set of azimuth looks images is analyzed using mutual information measures and an equivalent channel capacity is derived. The localization of the "target" requires analysis in a small image window, thus resulting in imprecise estimation of the second order statistics of the signal. For a better precision, a Hausdorff measure is introduced. The method is applied to detect and characterize relevant objects in urban areas.

  18. Seeking Relevance: American Political Science and America

    Science.gov (United States)

    Maranto, Robert; Woessner, Matthew C.

    2012-01-01

    In this article, the authors talk about the relevance of American political science and America. Political science has enormous strengths in its highly talented practitioners and sophisticated methods. However, its disconnection from its host society, while not so severe as for fields like English and sociology, nonetheless poses an existential…

  19. Is Enterprise Education Relevant to Social Enterprise?

    Science.gov (United States)

    Bridge, Simon

    2015-01-01

    Purpose: Both enterprise education and social enterprise have become fashionable but what, if any, should be the connections between them? The purpose of this paper is to explore those connections and to reflect on what relevance the two concepts might have for each other. Design/methodology/approach: Both enterprise education and social…

  20. The Relevant Physical Trace in Criminal Investigation

    Directory of Open Access Journals (Sweden)

    Durdica Hazard

    2016-01-01

    Full Text Available A criminal investigation requires the forensic scientist to search and to interpret vestiges of a criminal act that happened in the past. The forensic scientist is one of the many stakeholders who take part in the information quest within the criminal justice system. She reads the investigation scene in search of physical traces that should enable her to tell the story of the offense/crime that allegedly occurred. The challenge for any investigator is to detect and recognize relevant physical traces in order to provide clues for investigation and intelligence purposes, and that will constitute sound and relevant evidence for the court. This article shows how important it is to consider the relevancy of physical traces from the beginning of the investigation and what might influence the evaluation process. The exchange and management of information between the investigation stakeholders are important. Relevancy is a dimension that needs to be understood from the standpoints of law enforcement personnel and forensic scientists with the aim of strengthening investigation and ultimately the overall judicial process.

  1. Interpersonal communication: It's relevance to nursing practice ...

    African Journals Online (AJOL)

    This paper is aimed at highlighting how essential interpersonal communication is necessary for establishing rapport, understanding the needs of the patients and planning effective intervention for meeting holistic health care. To be continually relevant, Nurses have to improve on their communication skills to meet the ...

  2. Inferring feature relevances from metric learning

    DEFF Research Database (Denmark)

    Schulz, Alexander; Mokbel, Bassam; Biehl, Michael

    2015-01-01

    Powerful metric learning algorithms have been proposed in the last years which do not only greatly enhance the accuracy of distance-based classifiers and nearest neighbor database retrieval, but which also enable the interpretability of these operations by assigning explicit relevance weights...

  3. The Relevance of Causal Social Construction

    Directory of Open Access Journals (Sweden)

    Marques Teresa

    2017-02-01

    Full Text Available Social constructionist claims are surprising and interesting when they entail that presumably natural kinds are in fact socially constructed. The claims are interesting because of their theoretical and political importance. Authors like Díaz-León argue that constitutive social construction is more relevant for achieving social justice than causal social construction. This paper challenges this claim. Assuming there are socially salient groups that are discriminated against, the paper presents a dilemma: if there were no constitutively constructed social kinds, the causes of the discrimination of existing social groups would have to be addressed, and understanding causal social construction would be relevant to achieve social justice. On the other hand, not all possible constitutively socially constructed kinds are actual social kinds. If an existing social group is constitutively constructed as a social kind K, the fact that it actually exists as a K has social causes. Again, causal social construction is relevant. The paper argues that (i for any actual social kind X, if X is constitutively socially constructed as K, then it is also causally socially constructed; and (ii causal social construction is at least as relevant as constitutive social construction for concerns of social justice. For illustration, I draw upon two phenomena that are presumed to contribute towards the discrimination of women: (i the poor performance effects of stereotype threat, and (ii the silencing effects of gendered language use.

  4. The economic lot size and relevant costs

    NARCIS (Netherlands)

    Corbeij, M.H.; Jansen, R.A.; Grübström, R.W.; Hinterhuber, H.H.; Lundquist, J.

    1993-01-01

    In many accounting textbooks it is strongly argued that decisions should always be evaluated on relevant costs; that is variable costs and opportunity costs. Surprisingly, when it comes to Economic Order Quantities or Lot Sizes, some textbooks appear to be less straightforward. The question whether

  5. Bootstrapping Visual Categorization with Relevant Negatives

    NARCIS (Netherlands)

    Li, X.; Snoek, C.G.M.; Worring, M.; Koelma, D.; Smeulders, A.W.M.

    Learning classifiers for many visual concepts are important for image categorization and retrieval. As a classifier tends to misclassify negative examples which are visually similar to positive ones, inclusion of such misclassified and thus relevant negatives should be stressed during learning.

  6. Why ritual plant use has ethnopharmacological relevance

    NARCIS (Netherlands)

    Quiroz, Diana; Sosef, Marc; Andel, Van Tinde

    2016-01-01

    Ethnopharmacological relevance Although ritual plant use is now recognised both for its socio-cultural importance and for its contribution to nature conservation, its potential pharmacological effects remain overlooked. Aim of the study Our objective was to see whether ritual plant use could have

  7. Bradford's Law and Its Relevance to Researchers

    Science.gov (United States)

    Shenton, Andrew K.; Hay-Gibson, Naomi V.

    2009-01-01

    Bradford's Law has been the subject of much discussion and analysis in library and information science since its formulation in the 1930s and remains frequently debated to this day. It has been applied to various practices within the discipline, especially with regard to collection development, but its relevance to researchers and the potential it…

  8. The relevance of cosmopolitanism for moral education

    NARCIS (Netherlands)

    Merry, M.S.; de Ruyter, D.J.

    2011-01-01

    In this article we defend a moral conception of cosmopolitanism and its relevance for moral education. Our moral conception of cosmopolitanism presumes that persons possess an inherent dignity in the Kantian sense and therefore they should be recognised as ends-in-themselves. We argue that

  9. Ranking Music Data by Relevance and Importance

    DEFF Research Database (Denmark)

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

    2008-01-01

    Due to the rapidly increasing availability of audio files on the Web, it is relevant to augment search engines with advanced audio search functionality. In this context, the ranking of the retrieved music is an important issue. This paper proposes a music ranking method capable of flexibly fusing...

  10. Fast multi-output relevance vector regression

    OpenAIRE

    Ha, Youngmin

    2017-01-01

    This paper aims to decrease the time complexity of multi-output relevance vector regression from O(VM^3) to O(V^3+M^3), where V is the number of output dimensions, M is the number of basis functions, and V

  11. Pragmatic inferences and self-relevant judgments

    DEFF Research Database (Denmark)

    Puente-Diaz, Rogelio; Cavazos Arroyo, Judith; Brem, Alexander

    2016-01-01

    Three studies examined the influence of type of scale on self-relevant judgments and the moderating role of age, prevention, focus, and need for cogni- tion. Participants were randomly assigned to a bipolar or a unipolar scale condition in all three studies. Results from study 1 with a representa...

  12. Making Chemistry Relevant to the Engineering Major

    Science.gov (United States)

    Basu-Dutt, Sharmistha; Slappey, Charles; Bartley, Julie K.

    2010-01-01

    As part of a campus-wide, externally funded project to increase performance in, enthusiasm for, and retention within STEM disciplines, we developed an interdisciplinary, team-taught first-year seminar course. The construction and delivery of this course was designed to show the relevance of selected general chemistry topics such as matter and…

  13. Contingent Attentional Capture by Conceptually Relevant Images

    Science.gov (United States)

    Wyble, Brad; Folk, Charles; Potter, Mary C.

    2013-01-01

    Attentional capture is an unintentional shift of visuospatial attention to the location of a distractor that is either highly salient, or relevant to the current task set. The latter situation is referred to as contingent capture, in that the effect is contingent on a match between characteristics of the stimuli and the task-defined…

  14. The Relevance Aura of Bibliographic Records.

    Science.gov (United States)

    Brooks, Terrence A.

    1997-01-01

    Analyzes relevance assessments of topical descriptors for bibliographic records for two dimensions: (1) a vertical conceptual hierarchy of broad to narrow descriptors, and (2) a horizontal linkage of related terms. The data were analyzed for a semantic distance and semantic direction effect as postulated by the Semantic Distance Model. (Author/LRW)

  15. The Relevance of Cosmopolitanism for Moral Education

    Science.gov (United States)

    Merry, Michael S.; de Ruyter, Doret J.

    2011-01-01

    In this article we defend a moral conception of cosmopolitanism and its relevance for moral education. Our moral conception of cosmopolitanism presumes that persons possess an inherent dignity in the Kantian sense and therefore they should be recognised as ends-in-themselves. We argue that cosmopolitan ideals can inspire moral educators to awaken…

  16. Directed PCR-free engineering of highly repetitive DNA sequences

    Directory of Open Access Journals (Sweden)

    Preissler Steffen

    2011-09-01

    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  17. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  18. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  19. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  20. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  1. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  2. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  3. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

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

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

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

  5. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

    Directory of Open Access Journals (Sweden)

    Alexander M Sevy

    2015-07-01

    Full Text Available Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD paradigm. Multi-specificity design (MSD, on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON. The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

  6. Organizational and social-psychological issues relevant to fallout-shelter evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Wernette, D.R.

    1983-01-01

    This paper presents the results of a preliminary review of the literature on organizational and social-psychological issues relevant to fallout-shelter evaluation. Fallout-shelter options are evaluated along two dimensions: shelter size, and extent of shelteree participation in the shelter construction. Four functional criteria are used in the evaluation: decision-making, member coordination, social control, and maintaining morale. Smaller shelters requiring shelteree participation in construction appear preferable as measured in most of these criteria. Additional factors mentioned include demographic characteristics of the shelter population, degree and type of ventilation system, and availability of medical equipment and personnel. 10 references.

  7. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  8. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  9. Permeability of public and private spaces in reproductive healthcare seeking: barriers to uptake of services among low income African American women in a smaller urban setting.

    Science.gov (United States)

    Golden, Annis G

    2014-05-01

    This study was undertaken in partnership with a publicly funded reproductive healthcare organization to better understand barriers to utilization of its services as perceived by low income African American women in its community and how those barriers might be managed. The study uses a place-based, ecological perspective to theorize privacy challenges across different levels of the communication ecology. Analysis of participant observation, interviews, and focus group data identified three key public-private problematics in African American women's experience of reproductive healthcare seeking in a smaller urban setting: a public-private problematic of organizational identity, of organizational regions, and of organizational members. Potential strategies are identified for managing these problematics by the organization and community members. Copyright © 2014. Published by Elsevier Ltd.

  10. Foxtail Millet [Setaria italica (L. Beauv.] Grown under Low Nitrogen Shows a Smaller Root System, Enhanced Biomass Accumulation, and Nitrate Transporter Expression

    Directory of Open Access Journals (Sweden)

    Faisal Nadeem

    2018-02-01

    Full Text Available Foxtail millet (FM [Setaria italica (L. Beauv.] is a grain and forage crop well adapted to nutrient-poor soils. To date little is known how FM adapts to low nitrogen (LN at the morphological, physiological, and molecular levels. Using the FM variety Yugu1, we found that LN led to lower chlorophyll contents and N concentrations, and higher root/shoot and C/N ratios and N utilization efficiencies under hydroponic culture. Importantly, enhanced biomass accumulation in the root under LN was in contrast to a smaller root system, as indicated by significant decreases in total root length; crown root number and length; and lateral root number, length, and density. Enhanced carbon allocation toward the root was rather for significant increases in average diameter of the LN root, potentially favorable for wider xylem vessels or other anatomical alterations facilitating nutrient transport. Lower levels of IAA and CKs were consistent with a smaller root system and higher levels of GA may promote root thickening under LN. Further, up-regulation of SiNRT1.1, SiNRT2.1, and SiNAR2.1 expression and nitrate influx in the root and that of SiNRT1.11 and SiNRT1.12 expression in the shoot probably favored nitrate uptake and remobilization as a whole. Lastly, more soluble proteins accumulated in the N-deficient root likely as a result of increases of N utilization efficiencies. Such “excessive” protein-N was possibly available for shoot delivery. Thus, FM may preferentially transport carbon toward the root facilitating root thickening/nutrient transport and allocate N toward the shoot maximizing photosynthesis/carbon fixation as a primary adaptive strategy to N limitation.

  11. Foxtail Millet [Setaria italica (L.) Beauv.] Grown under Low Nitrogen Shows a Smaller Root System, Enhanced Biomass Accumulation, and Nitrate Transporter Expression.

    Science.gov (United States)

    Nadeem, Faisal; Ahmad, Zeeshan; Wang, Ruifeng; Han, Jienan; Shen, Qi; Chang, Feiran; Diao, Xianmin; Zhang, Fusuo; Li, Xuexian

    2018-01-01

    Foxtail millet (FM) [ Setaria italica (L.) Beauv.] is a grain and forage crop well adapted to nutrient-poor soils. To date little is known how FM adapts to low nitrogen (LN) at the morphological, physiological, and molecular levels. Using the FM variety Yugu1, we found that LN led to lower chlorophyll contents and N concentrations, and higher root/shoot and C/N ratios and N utilization efficiencies under hydroponic culture. Importantly, enhanced biomass accumulation in the root under LN was in contrast to a smaller root system, as indicated by significant decreases in total root length; crown root number and length; and lateral root number, length, and density. Enhanced carbon allocation toward the root was rather for significant increases in average diameter of the LN root, potentially favorable for wider xylem vessels or other anatomical alterations facilitating nutrient transport. Lower levels of IAA and CKs were consistent with a smaller root system and higher levels of GA may promote root thickening under LN. Further, up-regulation of SiNRT1.1, SiNRT2.1, and SiNAR2.1 expression and nitrate influx in the root and that of SiNRT1.11 and SiNRT1.12 expression in the shoot probably favored nitrate uptake and remobilization as a whole. Lastly, more soluble proteins accumulated in the N-deficient root likely as a result of increases of N utilization efficiencies. Such "excessive" protein-N was possibly available for shoot delivery. Thus, FM may preferentially transport carbon toward the root facilitating root thickening/nutrient transport and allocate N toward the shoot maximizing photosynthesis/carbon fixation as a primary adaptive strategy to N limitation.

  12. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

    DEFF Research Database (Denmark)

    Zakrzewski, Martha; Goesmann, Alexander; Jaenicke, Sebastian

    2012-01-01

    of the community by classification of 16S ribosomal sequence tags revealed that members of the Euryarchaeota and Firmicutes account for the dominant phyla. Only smaller fractions of the 16S ribosomal sequence tags were assigned to the phyla Bacteroidetes, Actinobacteria and Synergistetes. Among the m...

  13. CRISPR-Cas: biology, mechanisms and relevance

    Science.gov (United States)

    Hille, Frank

    2016-01-01

    Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’. PMID:27672148

  14. Environmental radiation studies relevant to thermoluminescence dating

    International Nuclear Information System (INIS)

    Murray, A.S.; Bowman, S.G.E.; Aitken, M.J.

    1980-01-01

    To determine the age of a potsherd by the thermoluminescence (TL) technique, one must have an accurate knowledge of the cosmic and environmental gamma dose rate in quartz. This is obtained by leaving a sensitive TL dosimeter buried as near as possible to the position from which the sherd was removed. The ratios of the response of a quartz-like dosimeter to those of CaF 2 and LiF have been measured. This experiment used a 1-m cube of concrete containing 3000 ppM of uranium and its daughters. Smaller, less active matrixes of 40 K and thorium and its daughters have also been constructed. A means of making direct dose-rate determinations when the site context remains but burial of a dosimeter is impractical was developed using a NaI(Tl) system. The equipment was field tested on approx. 40 Peruvian archaeological sites, and results are compared with CaF 2 measurements

  15. MRI investigation of normal fetal lung maturation using signal intensities on different imaging sequences

    International Nuclear Information System (INIS)

    Balassy, Csilla; Kasprian, Gregor; Weber, Michael; Hoermann, Marcus; Prayer, Daniela; Brugger, Peter C.; Csapo, Bence; Mittermayer, Christoph

    2007-01-01

    To purpose of this paper is to study the relation between normal lung maturation signal and changes in intensity ratios (SIR) and to determine which magnetic resonance imaging sequence provides the strongest correlation of normal lung SIs with gestational age. 126 normal singleton pregnancies (20-37 weeks) were examined with a 1.5 Tesla unit. Mean SIs for lungs, liver, and gastric fluid were assessed on six different sequences, and SIRs of lung/liver (LLSIR) and lung/gastric fluid (LGSIR) were correlated with gestational age for each sequence. To evaluate the feasibility of SIRs in the prediction of the state of the lung maturity, accuracy of the predicted SIRs (D*) was measured by calculating relative residuals (D*-D)/D for each sequence. LLSIRs showed significant changes in every sequence (p<0.05), while LGSIRs only on two sequences. Significant differences were shown for the mean of absolute residuals for both LLSIRs (p<0.001) and for LGSIRs (p=0.003). Relative residuals of LLSIRs were significantly smaller on T1-weighted sequence, whereas they were significantly higher for LGSIRs on FLAIR sequence. Fetal liver seems to be adequate reference for the investigation of lung maturation. T1-weighted sequence was the most accurate for the measurement of the lung SIs; thus, we propose to determine LLSIR on T1-weighted sequence when evaluating lung development. (orig.)

  16. MRI investigation of normal fetal lung maturation using signal intensities on different imaging sequences

    Energy Technology Data Exchange (ETDEWEB)

    Balassy, Csilla; Kasprian, Gregor; Weber, Michael; Hoermann, Marcus; Prayer, Daniela [Medical University of Vienna, Department of Radiology, Vienna (Austria); Brugger, Peter C. [Medical University of Vienna, Center of Anatomy and Cell Biology, Vienna (Austria); Csapo, Bence [Medical University of Vienna, Department of Obstetrics and Gyneocology, Vienna (Austria); Mittermayer, Christoph [Medical University of Vienna, Department of Pediatrics, Vienna (Austria)

    2007-03-15

    To purpose of this paper is to study the relation between normal lung maturation signal and changes in intensity ratios (SIR) and to determine which magnetic resonance imaging sequence provides the strongest correlation of normal lung SIs with gestational age. 126 normal singleton pregnancies (20-37 weeks) were examined with a 1.5 Tesla unit. Mean SIs for lungs, liver, and gastric fluid were assessed on six different sequences, and SIRs of lung/liver (LLSIR) and lung/gastric fluid (LGSIR) were correlated with gestational age for each sequence. To evaluate the feasibility of SIRs in the prediction of the state of the lung maturity, accuracy of the predicted SIRs (D*) was measured by calculating relative residuals (D*-D)/D for each sequence. LLSIRs showed significant changes in every sequence (p<0.05), while LGSIRs only on two sequences. Significant differences were shown for the mean of absolute residuals for both LLSIRs (p<0.001) and for LGSIRs (p=0.003). Relative residuals of LLSIRs were significantly smaller on T1-weighted sequence, whereas they were significantly higher for LGSIRs on FLAIR sequence. Fetal liver seems to be adequate reference for the investigation of lung maturation. T1-weighted sequence was the most accurate for the measurement of the lung SIs; thus, we propose to determine LLSIR on T1-weighted sequence when evaluating lung development. (orig.)

  17. Tomographic diagnosis and relevant aspects of otosclerosis

    International Nuclear Information System (INIS)

    Gaiotti, Juliana Oggioni; Gomes, Natalia Delage; Costa, Ana Maria Doffemond; Villela, Caroline Laurita Batista Couto; Moreira, Wanderval; Diniz, Renata Lopes Furletti Caldeira

    2013-01-01

    A literature review and pictorial essay were developed to discuss the importance of knowing the main findings and locations of otosclerosis at multidetector computed tomography (MDCT). The authors performed a retrospective review of cases of otosclerosis diagnosed in their institution by means of high resolution multidetector computed tomography. Otosclerosis corresponds to otic capsule dysplasia characterized by metabolic derangement of its endochondral layer. Such condition constitutes a relevant cause of sensorineural hearing loss, affecting about 7% to 10% of the general population. The diagnosis is usually clinical, but imaging methods play a significant role in the anatomical detailing, differential diagnosis, surgical planning and evaluation of postoperative complications. Among such methods, the relevance of MDCT is highlighted. Radiologists should be familiar with the MDCT findings of otosclerosis, as well as with the temporal bone anatomy to assist in the appropriate clinical management of this disease. (author)

  18. Tomographic diagnosis and relevant aspects of otosclerosis

    Energy Technology Data Exchange (ETDEWEB)

    Gaiotti, Juliana Oggioni; Gomes, Natalia Delage; Costa, Ana Maria Doffemond; Villela, Caroline Laurita Batista Couto; Moreira, Wanderval; Diniz, Renata Lopes Furletti Caldeira, E-mail: jugaiotti@gmail.com [Hospital Mater Dei-Mater Imagem, Belo Horizonte, MG (Brazil)

    2013-09-15

    A literature review and pictorial essay were developed to discuss the importance of knowing the main findings and locations of otosclerosis at multidetector computed tomography (MDCT). The authors performed a retrospective review of cases of otosclerosis diagnosed in their institution by means of high resolution multidetector computed tomography. Otosclerosis corresponds to otic capsule dysplasia characterized by metabolic derangement of its endochondral layer. Such condition constitutes a relevant cause of sensorineural hearing loss, affecting about 7% to 10% of the general population. The diagnosis is usually clinical, but imaging methods play a significant role in the anatomical detailing, differential diagnosis, surgical planning and evaluation of postoperative complications. Among such methods, the relevance of MDCT is highlighted. Radiologists should be familiar with the MDCT findings of otosclerosis, as well as with the temporal bone anatomy to assist in the appropriate clinical management of this disease. (author)

  19. Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast

    Science.gov (United States)

    Oud, Bart; Maris, Antonius J A; Daran, Jean-Marc; Pronk, Jack T

    2012-01-01

    Successful reverse engineering of mutants that have been obtained by nontargeted strain improvement has long presented a major challenge in yeast biotechnology. This paper reviews the use of genome-wide approaches for analysis of Saccharomyces cerevisiae strains originating from evolutionary engineering or random mutagenesis. On the basis of an evaluation of the strengths and weaknesses of different methods, we conclude that for the initial identification of relevant genetic changes, whole genome sequencing is superior to other analytical techniques, such as transcriptome, metabolome, proteome, or array-based genome analysis. Key advantages of this technique over gene expression analysis include the independency of genome sequences on experimental context and the possibility to directly and precisely reproduce the identified changes in naive strains. The predictive value of genome-wide analysis of strains with industrially relevant characteristics can be further improved by classical genetics or simultaneous analysis of strains derived from parallel, independent strain improvement lineages. PMID:22152095

  20. EOG feature relevance determination for microsleep detection

    OpenAIRE

    Golz Martin; Wollner Sebastian; Sommer David; Schnieder Sebastian

    2017-01-01

    Automatic relevance determination (ARD) was applied to two-channel EOG recordings for microsleep event (MSE) recognition. 10 s immediately before MSE and also before counterexamples of fatigued, but attentive driving were analysed. Two type of signal features were extracted: the maximum cross correlation (MaxCC) and logarithmic power spectral densities (PSD) averaged in spectral bands of 0.5 Hz width ranging between 0 and 8 Hz. Generalised learn-ing vector quantisation (GRLVQ) was used as ARD...

  1. Is QCD relevant to nuclear physics

    International Nuclear Information System (INIS)

    Thomas, A.W.

    1985-01-01

    A review is given of recent work on baryon structure in a number of QCD-motivated models. After establishing a prima facie case that the quark model should be relevant in a consistent description of the nucleus over a wide range of momentum transfer, the author looks for experimental confirmation. The discussion includes the search for exotic states, for a six quark component of the deuteron, and an up to date report on the interpretation of the EMC effect. (Auth.)

  2. Trade Off Relevance Dan Reliability: Isu Ifrs

    OpenAIRE

    Mahmudah, Hadi

    2013-01-01

    Financial reports containing qualitative characteristic that are useful for usernya.For a long time believed to be the existence of trade off between characteristic of qualitative relevance and reliability. Trade off due to the fact that the use of the method of measurement historical cost and fair value. Trade off occur because of the interests of for the purpose of the preparation of reports on finance. Accountability for the purpose of the measurement of the cost of historical still reliab...

  3. Hydrogen interaction with fusion-relevant materials

    International Nuclear Information System (INIS)

    Caorlin, M.

    1990-01-01

    This paper is an outline of the work carried out at JRC Ispra in the Tritium-materials Interaction Laboratory, on the interaction of gaseous hydrogen with several materials of interest in the field of fusion technology. Experimental work is reported and a concise review of relevant theoretical and numerical supporting activity is given as well. A period of about seven years is covered since 1982. Current work and possible future extensions are also briefly mentioned. 11 figs., 18 refs

  4. Nanostructure symmetry: Relevance for physics and computing

    International Nuclear Information System (INIS)

    Dupertuis, Marc-André; Oberli, D. Y.; Karlsson, K. F.; Dalessi, S.; Gallinet, B.; Svendsen, G.

    2014-01-01

    We review the research done in recent years in our group on the effects of nanostructure symmetry, and outline its relevance both for nanostructure physics and for computations of their electronic and optical properties. The exemples of C3v and C2v quantum dots are used. A number of surprises and non-trivial aspects are outlined, and a few symmetry-based tools for computing and analysis are shortly presented

  5. Nanostructure symmetry: Relevance for physics and computing

    Energy Technology Data Exchange (ETDEWEB)

    Dupertuis, Marc-André; Oberli, D. Y. [Laboratory for Physics of Nanostructure, EPF Lausanne (Switzerland); Karlsson, K. F. [Department of Physics, Chemistry, and Biology (IFM), Linköping University (Sweden); Dalessi, S. [Computational Biology Group, Department of Medical Genetics, University of Lausanne (Switzerland); Gallinet, B. [Nanophotonics and Metrology Laboratory, EPF Lausanne (Switzerland); Svendsen, G. [Dept. of Electronics and Telecom., Norwegian University of Science and Technology, Trondheim (Norway)

    2014-03-31

    We review the research done in recent years in our group on the effects of nanostructure symmetry, and outline its relevance both for nanostructure physics and for computations of their electronic and optical properties. The exemples of C3v and C2v quantum dots are used. A number of surprises and non-trivial aspects are outlined, and a few symmetry-based tools for computing and analysis are shortly presented.

  6. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  7. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  8. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  10. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  11. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  12. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  13. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  14. Monochloramine Cometabolism by Nitrifying Biofilm Relevant ...

    Science.gov (United States)

    Recently, biological monochloramine removal (i.e., cometabolism) by a pure culture ammonia–oxidizing bacteria, Nitrosomonas europaea, and a nitrifying mixed–culture have been shown to increase monochloramine demand. Although important, these previous suspended culture batch kinetic experiments were not representative of drinking water distribution systems where bacteria grow predominantly as biofilm attached to pipe walls or sediments and physiological differences may exist between suspension and biofilm growth. Therefore, the current research was an important next step in extending the previous results to investigate monochloramine cometabolism by biofilm grown in annular reactors under drinking water relevant conditions. Estimated monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (25–40% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in drinking water relevant nitrifying biofilm; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in distribution systems. Investigate whether or not nitrifying biofilm can biologically transform monochloramine under drinking water relevant conditions.

  15. Selection of relevant dietary indicators for health.

    Science.gov (United States)

    Steingrímsdóttir, L; Ovesen, L; Moreiras, O; Jacob, S

    2002-05-01

    To define a set of dietary components that are relevant determinants for health in Europe. The selected components are intended to serve as nutrition indicators for health in the European Health Monitoring Programme and, as such, must be limited in number, relevant to health in Europe and practical for all involved countries with respect to data gathering and comparability of data. Major nutrition factors were determined by reviewing relevant epidemiological and clinical literature in nutrition and health as well as referring to reports from international expert groups, including the report from the project Nutrition and Diet for Healthy Lifestyles in Europe. The selection of factors was also based on the relative ease and cost involved for participating countries to obtain comparable and valid data. The selected factors include foods or food groups as well as individual nutrients. Biomarkers are suggested for selected nutrients that pose the greatest difficulty in obtaining valid and comparable data from dietary studies. The following list of diet indicators for health monitoring in Europe was agreed upon by the EFCOSUM group in 2001, in order of priority: vegetables, fruit, bread, fish, saturated fatty acids as percentage of energy (%E), total fat as %E, and ethanol in grams per day. Biomarkers were suggested for the following nutrients: folate, vitamin D, iron, iodine and sodium. Energy has to be assessed in order to calculate %E from total fat and saturated fatty acids.

  16. The value relevance of environmental emissions

    Directory of Open Access Journals (Sweden)

    Melinda Lydia Nelwan

    2016-07-01

    Full Text Available This study examines whether environmental performance has value relevance by investigating the relations between environmental emissions and stock prices for the U.S. public companies. The previous studies argued that the conjectured relations between accounting performance measures and environmental performance do not have a strong theoretical basis, and the modeling of relations between market per-formance measures and environmental performance do not adequately consider the relevance of accounting performance to market value. Therefore, this study examines whether publicly reported environmental emissions provide incremental information to accounting earnings in pricing companies stocks. It is done among the complete set of industries covered by Toxics Release Inventory (TRI reporting for the period 2007 to 2010. Using Ohlson model but modified to include different types of emis-sions, it is found that ground emissions (underground injection and land emissions are value relevant but other emission types (air and water and transferred-out emis-sions appear to not provide incremental information in the valuation model. The result in this study raise concerns that different types of emissions are assessed differently by the market, confirming that studies should not aggregate such measures.

  17. Valerian: No Evidence for Clinically Relevant Interactions

    Directory of Open Access Journals (Sweden)

    Olaf Kelber

    2014-01-01

    Full Text Available In recent popular publications as well as in widely used information websites directed to cancer patients, valerian is claimed to have a potential of adverse interactions with anticancer drugs. This questions its use as a safe replacement for, for example, benzodiazepines. A review on the interaction potential of preparations from valerian root (Valeriana officinalis L. root was therefore conducted. A data base search and search in a clinical drug interaction data base were conducted. Thereafter, a systematic assessment of publications was performed. Seven in vitro studies on six CYP 450 isoenzymes, on p-glycoprotein, and on two UGT isoenzymes were identified. However, the methodological assessment of these studies did not support their suitability for the prediction of clinically relevant interactions. In addition, clinical studies on various valerian preparations did not reveal any relevant interaction potential concerning CYP 1A2, 2D6, 2E1, and 3A4. Available animal and human pharmacodynamic studies did not verify any interaction potential. The interaction potential of valerian preparations therefore seems to be low and thereby without clinical relevance. We conclude that there is no specific evidence questioning their safety, also in cancer patients.

  18. Functional dyspepsia: Are psychosocial factors of relevance?

    Institute of Scientific and Technical Information of China (English)

    Sandra Barry; Timothy G Dinan

    2006-01-01

    The pathogenesis of Functional Dyspepsia (FD) remains unclear, appears diverse and is thus inadequately understood. Akin to other functional gastrointestinal disorders, research has demonstrated an association between this common diagnosis and psychosocial factors and psychiatric morbidity. Conceptualising the relevance of these factors within the syndrome of FD requires application of the biopsychosocial model of disease.Using this paradigm, dysregulation of the reciprocal communication between the brain and the gut is central to symptom generation, interpretation and exacerbation.Appreciation and understanding of the neurobiological correlates of various psychological states is also relevant.The view that psychosocial factors exert their influence in FD predominantly through motivation of health care seeking also persists. This appears too one-dimensional an assertion in light of the evidence available supporting a more intrinsic aetiological link. Evolving understanding of pathogenic mechanisms and the heterogeneous nature of the syndrome will facilitate effective management.Co-morbid psychiatric illness warrants treatment with conventional therapies. Acknowledging the relevance of psychosocial variables in FD, the degree of which is subject to variation, has implications for assessment and management. Available evidence suggests psychological therapies may benefit FD patients particularly those with chronic symptoms. The rationale for use of psychotropic medications in FD is apparent but the evidence base to support the use of antidepressant pharmacotherapy is to date limited.

  19. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  20. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  1. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  2. 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)

  3. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  4. Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

    Science.gov (United States)

    Neuwald, Andrew F; Altschul, Stephen F

    2016-12-01

    Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

  5. Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

    Directory of Open Access Journals (Sweden)

    Andrew F Neuwald

    2016-12-01

    Full Text Available Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs, which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu.

  6. Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367

    KAUST Repository

    Abdallah, A. M.; Rashid, M.; Adroub, S. A.; Elabdalaoui, H.; Ali, Shahjahan; van Soolingen, D.; Bitter, W.; Pain, Arnab

    2012-01-01

    Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species. Like other nontuberculous mycobacteria, M. xenopi more commonly infects humans with altered immune function, such as chronic obstructive pulmonary disease patients. It is considered clinically relevant in a significant proportion of the patients from whom it is isolated. We report here the whole genome sequence of M. xenopi type strain RIVM700367.

  7. Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367

    KAUST Repository

    Abdallah, A. M.

    2012-05-24

    Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species. Like other nontuberculous mycobacteria, M. xenopi more commonly infects humans with altered immune function, such as chronic obstructive pulmonary disease patients. It is considered clinically relevant in a significant proportion of the patients from whom it is isolated. We report here the whole genome sequence of M. xenopi type strain RIVM700367.

  8. The impact of positive, negative and topical relevance feedback

    NARCIS (Netherlands)

    Kaptein, Rianne; Kamps, Jaap; Hiemstra, Djoerd

    2008-01-01

    This document contains a description of experiments for the 2008 Relevance Feedback track. We experiment with different amounts of feedback, including negative relevance feedback. Feedback is implemented using massive weighted query expansion. Parsimonious query expansion using only relevant

  9. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  10. Technologies relevant for gasification and methanation in Denmark

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, Niels Bjarne

    2012-09-15

    This report is a Milestone report for Task 3.1 of the project ''Detailed analysis of bio-SNG technologies and other RE-gases'', Forsk-NG 10689. It is a report on inventory of relevant bio-SNG technologies. In this report a list of technologies relevant for production of bio-SNG from gasification of biomass is presented. During a long period of time a range of gasification technologies has been developed in Denmark. All Danish gasification technologies are characterised by the fact that the producer gases - immediately after gasification - are used in a boiler or an engine. This use is initially the most effective because after purification and without modification the gases can be used directly in a boiler or an engine. However, a gasifier plant is rather expensive, which means that in order to be cost-effective the gasifier must operate as base load. In the future, an expected larger production of producer gases will, therefore, cause a need for storage of the energy - because there won't be correspondence between production and utilisation. This storage is possible by producing bio-SNG by methanation and then adding it to the natural gas grid and storages. There are two ways of making gasification plants more cost effective: ''Saving by size'' and ''Saving by number''. Large plants of course have the advantage of smaller specific price for the installation. On the other hand a great number of equal plants scattered across the country would also reduce the specific cost of installations and the expenses for transport would reduce as well. Even a third possibility is to install at a plant several parallel units for gasification technologies that have maximum unit size and attaching one common methanation unit. This increases the operational reliability of the plant and save installation costs where possible. In Denmark, as an example, a plant of 60 MW (output) might be considered, corresponding to

  11. NEW COOLING SEQUENCES FOR OLD WHITE DWARFS

    International Nuclear Information System (INIS)

    Renedo, I.; Althaus, L. G.; GarcIa-Berro, E.; Miller Bertolami, M. M.; Romero, A. D.; Corsico, A. H.; Rohrmann, R. D.

    2010-01-01

    We present full evolutionary calculations appropriate for the study of hydrogen-rich DA white dwarfs. This is done by evolving white dwarf progenitors from the zero-age main sequence, through the core hydrogen-burning phase, the helium-burning phase, and the thermally pulsing asymptotic giant branch phase to the white dwarf stage. Complete evolutionary sequences are computed for a wide range of stellar masses and for two different metallicities, Z = 0.01, which is representative of the solar neighborhood, and Z = 0.001, which is appropriate for the study of old stellar systems, like globular clusters. During the white dwarf cooling stage, we self-consistently compute the phase in which nuclear reactions are still important, the diffusive evolution of the elements in the outer layers and, finally, we also take into account all the relevant energy sources in the deep interior of the white dwarf, such as the release of latent heat and the release of gravitational energy due to carbon-oxygen phase separation upon crystallization. We also provide colors and magnitudes for these sequences, based on a new set of improved non-gray white dwarf model atmospheres, which include the most up-to-date physical inputs like the Lyα quasi-molecular opacity. The calculations are extended down to an effective temperature of 2500 K. Our calculations provide a homogeneous set of evolutionary cooling tracks appropriate for mass and age determinations of old DA white dwarfs and for white dwarf cosmochronology of the different Galactic populations.

  12. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  13. Identifying Relevant Studies in Software Engineering

    DEFF Research Database (Denmark)

    Zhang, He; Ali Babar, Muhammad; Tell, Paolo

    2011-01-01

    Context: Systematic literature review (SLR) has become an important research methodology in software engineering since the introduction of evidence-based software engineering (EBSE) in 2004. One critical step in applying this methodology is to design and execute appropriate and effective search....... Objective: The main objective of the research reported in this paper is to improve the search step of undertaking SLRs in software engineering (SE) by devising and evaluating systematic and practical approaches to identifying relevant studies in SE. Method: We have systematically selected and analytically...

  14. Happiness: origins, forms, and technical relevance.

    Science.gov (United States)

    Akhtar, Salman

    2010-09-01

    By critically reviewing Freud's views on happiness, and also those of Helene Deutsch, Bertram Lewin, Melanie Klein, and Heinz Kohut, the author evolves a complex and multilayered perspective on the phenomenon. He categorizes happiness into four related and occasionally overlapping varieties: pleasure-based happiness (elation), assertion-based happiness (joy), merger-based happiness (ecstasy), and fulfillment-based happiness (contentment). After entering some caveats and drawing from his clinical experience, the author then demonstrates the relevance of these ideas to the conduct of psychotherapy and psychoanalysis.

  15. Relevance of physics to the pharmacy major.

    Science.gov (United States)

    McCall, Richard P

    2007-08-15

    To offer a physics course that is relevant to pharmacy students, yet still contains many of the fundamental principles of physics. The course was modified over a period of several years to include activities and examples that were related to other courses in the curriculum. Course evaluations were given to assess student attitudes about the importance of physics in the pharmacy curriculum. Students' attitudes have changed over time to appreciate the role that physics plays in their studies. Students gained confidence in their ability to learn in other courses.

  16. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  17. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  18. Mohs micrographic surgery in dermatofibrosarcoma protuberans allows tumour clearance with smaller margins and greater preservation of healthy tissue compared with conventional surgery: a study of 74 primary cases.

    Science.gov (United States)

    Serra-Guillén, C; Llombart, B; Nagore, E; Guillén, C; Requena, C; Traves, V; Kindem, S; Alcalá, R; Rivas, N; Sanmartín, O

    2015-01-01

    Dermatofibrosarcoma protuberans (DFSP) is an uncommon skin tumour with aggressive local growth. Whether DFSP should be treated with conventional surgery (CS) or Mohs micrographic surgery (MMS) has long been a topic of debate. To calculate, in a large series of DFSP treated by MMS, the minimum margin that would have been needed to achieve complete clearance by CS. Secondly, to calculate the percentage of healthy tissue that was preserved by MMS rather than CS with 2- and 3-cm margins. The minimum margin was calculated by measuring the largest distance from the visible edge of the tumour to the edge of the definitive surgical defect. Tumour and surgical defect areas for hypothetical CS with 2- and 3-cm margins were calculated using AutoCAD for Windows. A mean minimum margin of 1·34 cm was required to achieve complete clearance for the 74 tumours analysed. The mean percentages of skin spared using MMS rather than CS with 2- and 3-cm margins were 49·4% and 67·9%, respectively. MMS can achieve tumour clearance with smaller margins and greater preservation of healthy tissue than CS. © 2014 British Association of Dermatologists.

  19. Gamma knife radiosurgery for acoustic schwannomas. An analysis of the method of low dose and conformal multiple shots with smaller collimator

    International Nuclear Information System (INIS)

    Fukuoka, Seiji; Takanashi, Masami; Hojo, Atsufumi; Konishi, Masanori; Nakamura, Hirohiko

    2003-01-01

    The purpose of this study was to analyze tumor control and possible complications of gamma knife radiosurgery (GKRS) in patients with acoustic schwannomas treated using low marginal dose and conformal multiple shots with smaller collimators to fit irregular tumor shapes. The authors evaluated 183 patients with follow-up periods ranging from 3 to 11 years. Marginal doses were 9 to 15 Gy (median 12 Gy), with corresponding treatment volumes being between 0.1 and 18.7 ml (median 1.8 ml). The number of isocenter varied from 2 to 24 shots (median 9 shots). The actuarial tumor control rate (resection-free survival) was 96.5%. Useful hearing, trigeminal and facial functions were preserved at 75%, 97.4%, and 100%, respectively. Hydrocephalus was recognized in 5.7% of all patients, and seems to occur in cases with medium sized tumors where mild ventricular enlargement is evident prior to treatment. GKRS proves to be a safe and effective therapy for small to medium sized tumors. However, the indication for larger sized tumors (diameter 3+ cm) should be carefully considered, larger tumors being less easy to control and liable to cause ataxia due to transient expansion. (author)

  20. The Smaller Alignment Index (SALI) applied in a study of stellar orbits in barred galaxies potential models using the LP-VIcode

    Science.gov (United States)

    Caritá, Lucas Antonio; Rodrigues, Irapuan; Puerari, Ivânio; Schiavo, Luiz Eduardo Camargo Aranha

    2018-04-01

    The Smaller Alignment Index (SALI) is a mathematical tool, not yet conventional, for chaos detection in the phase space of Hamiltonian Dynamical Systems. The SALI values has temporal behaviors very specific to ordered or chaotic motions, what makes the distinction between order and chaos easily observable in these systems. In this paper, this method will be applied to the stability study of stellar orbits immersed in gravitational potential of barred galaxies, since the motion of a test particle in a rotating barred galaxy model is given by a Hamiltonian function. Extracting four parameter sets from the Manos and Athanassoula (2011) work and elaborating a different initial conditions set for each case, we were able to introduce another point of view of their stability study for two degrees of freedom. We have also introduced two new extreme models that corroborates with the conclusions that more axisymmetric bars create an environment with less chaos and that more massive bars create an environment with more chaos. Separate studies were carried out for prograde and retrograde orbits that showed that the retrograde orbits seem more conducive to chaos. To perform all the orbits integrations we used the LP-VIcode program.

  1. Expression profiling and comparative sequence derived insights into lipid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Callow, Matthew J.; Rubin, Edward M.

    2001-12-19

    Expression profiling and genomic DNA sequence comparisons are increasingly being applied to the identification and analysis of the genes involved in lipid metabolism. Not only has genome-wide expression profiling aided in the identification of novel genes involved in important processes in lipid metabolism such as sterol efflux, but the utilization of information from these studies has added to our understanding of the regulation of pathways participating in the process. Coupled with these gene expression studies, cross species comparison, searching for sequences conserved through evolution, has proven to be a powerful tool to identify important non-coding regulatory sequences as well as the discovery of novel genes relevant to lipid biology. An example of the value of this approach was the recent chance discovery of a new apolipoprotein gene (apo AV) that has dramatic effects upon triglyceride metabolism in mice and humans.

  2. Other relevant papers in physical oceanography

    International Nuclear Information System (INIS)

    Nyffeler, F.

    1989-01-01

    During the past few years, significant progress has occurred in the field of physical oceanography partly as a consequence of developing cooperation and international participation in well-coordinated ocean research programmes. Although these programs were not designed specifically to address CRESP problems, many have proved to be directly relevant to CRESP objectives. For example, MODE, POLYMODE, and Tourbillon were intensive site-specific experiments that included studies of dispersion processes throughout the water column. NOAMP and GME were also site specific, involved the entire water column, and even stressed near-bottom and suspended-sediment processes. Others, (e.g., WOCE) are larger in scope and include extensive observations of the general circulation of entire ocean basins. As a whole, they contribute immensely to improving the data base for exchange and transport processes and thereby for the verification and validation of both regional-scale and general-circulation ocean models. That, in turn, is directly relevant to radiological assessments. Selected papers deriving from experiments such as these are discussed and referenced below

  3. [Terbinafine : Relevant drug interactions and their management].

    Science.gov (United States)

    Dürrbeck, A; Nenoff, P

    2016-09-01

    The allylamine terbinafine is the probably most frequently prescribed systemic antifungal agent in Germany for the treatment of dermatomycoses and onychomycoses. According to the German drug law, terbinafine is approved for patients who are 18 years and older; however, this antifungal agent is increasingly used off-label for treatment of onychomycoses and tinea capitis in children. Terbinafine is associated with only a few interactions with other drugs, which is why terbinafine can generally be used without problems in older and multimorbid patients. Nevertheless, some potential interactions of terbinafine with certain drug substances are known, including substances of the group of antidepressants/antipsychotics and some cardiovascular drugs. Decisive for the relevance of interactions is-along with the therapeutic index of the substrate and the possible alternative degradation pathways-the genetically determined type of metabolism. When combining terbinafine with tricyclic antidepressants or selective serotonin reuptake inhibitors and serotonin/noradrenalin reuptake inhibitors, the clinical response and potential side effects must be monitored. Problematic is the use of terbinafine with simultaneous treatment with tamoxifen. The administration of potent CYP2D6 inhibitors leads to a diminished efficacy of tamoxifen because one of its most important active metabolites-endoxifen-is not sufficiently available. Therefore, combination of tamoxifen and terbinafine should be avoided. In conclusion, the number of substances which are able to cause clinically relevant interactions in case of simultaneously administration with terbinafine is clear and should be manageable in the dermatological office with adequate monitoring.

  4. Relevance of randomised controlled trials in oncology.

    Science.gov (United States)

    Tannock, Ian F; Amir, Eitan; Booth, Christopher M; Niraula, Saroj; Ocana, Alberto; Seruga, Bostjan; Templeton, Arnoud J; Vera-Badillo, Francisco

    2016-12-01

    Well-designed randomised controlled trials (RCTs) can prevent bias in the comparison of treatments and provide a sound basis for changes in clinical practice. However, the design and reporting of many RCTs can render their results of little relevance to clinical practice. In this Personal View, we discuss the limitations of RCT data and suggest some ways to improve the clinical relevance of RCTs in the everyday management of patients with cancer. RCTs should ask questions of clinical rather than commercial interest, avoid non-validated surrogate endpoints in registration trials, and have entry criteria that allow inclusion of all patients who are fit to receive treatment. Furthermore, RCTs should be reported with complete accounting of frequency and management of toxicities, and with strict guidelines to ensure freedom from bias. Premature reporting of results should be avoided. The bar for clinical benefit should be raised for drug registration, which should require publication and review of mature data from RCTs, post-marketing health outcome studies, and value-based pricing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  6. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  7. Identification of clinically relevant viridans streptococci by an oligonucleotide array.

    Science.gov (United States)

    Chen, Chao Chien; Teng, Lee Jene; Kaiung, Seng; Chang, Tsung Chain

    2005-04-01

    Viridans streptococci (VS) are common etiologic agents of subacute infective endocarditis and are capable of causing a variety of pyogenic infections. Many species of VS are difficult to differentiate by phenotypic traits. An oligonucleotide array based on 16S-23S rRNA gene intergenic spacer (ITS) sequences was developed to identify 11 clinically relevant VS. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The method consisted of PCR amplification of the ITS regions by using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species-specific oligonucleotides immobilized on a nylon membrane. After 120 strains of the 11 species of VG and 91 strains of other bacteria were tested, the sensitivity and specificity of the oligonucleotide array were found to be 100% (120 of 120 strains) and 95.6% (87 of 91 strains), respectively. S. pneumoniae cross-hybridized to the probes used for the identification of S. mitis, and simple biochemical tests such as optochin susceptibility or bile solubility should be used to differentiate S. pneumoniae from S. mitis. In conclusion, identification of species of VS by use of the present oligonucleotide array is accurate and could be used as an alternative reliable method for species identification of strains of VS.

  8. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  9. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  10. Are babies conceived during Ramadan born smaller and sooner than babies conceived at other times of the year? A Born in Bradford Cohort Study.

    Science.gov (United States)

    Daley, Amanda; Pallan, Miranda; Clifford, Sue; Jolly, Kate; Bryant, Maria; Adab, Peymane; Cheng, K K; Roalfe, Andrea

    2017-07-01

    It is not known whether infants exposed to intermittent maternal fasting at conception are born smaller or have a higher risk of premature birth than those who are not. Doctors are therefore unsure about what advice to give women about the safety of Ramadan fasting. This cohort study aimed to investigate these questions in Muslim mother-infant pairs to inform prenatal care. Routinely collected data accessed from maternity records were the source for information. Mothers were considered exposed if they were Muslim and Ramadan overlapped with their infant conception date, estimated to be 14 days after the last menstrual period. Infants were included as exposed if their estimated conception date was in the first 21 days of Ramadan or 7 days prior to Ramadan. After adjusting for gestational age, maternal age, infant gender, maternal body mass index at booking, smoking status, gestational diabetes, parity and year of birth, there was no significant difference in birth weight between infants born to Muslim mothers who were conceived during Ramadan (n=479) and those who were not (n=4677) (adjusted mean difference =24.3 g, 95% CI -16.4 to 64.9). There was no difference in rates of premature births in exposed and unexposed women (5.2% vs 4.9%; OR=1.08, 95% CI 0.71 to 1.65). Healthy Muslim women considering becoming pregnant prior to, or during Ramadan, can be advised that fasting does not seem to have a detrimental effect on the size (weight) of their baby and it appears not to increase the likelihood of giving birth prematurely. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  11. Carriers of loss-of-function mutations in EXT display impaired pancreatic beta-cell reserve due to smaller pancreas volume.

    Directory of Open Access Journals (Sweden)

    Sophie J Bernelot Moens

    Full Text Available Exotosin (EXT proteins are involved in the chain elongation step of heparan sulfate (HS biosynthesis, which is intricately involved in organ development. Loss of function mutations (LOF in EXT1 and EXT2 result in hereditary exostoses (HME. Interestingly, HS plays a role in pancreas development and beta-cell function, and genetic variations in EXT2 are associated with an increased risk for type 2 diabetes mellitus. We hypothesized that loss of function of EXT1 or EXT2 in subjects with hereditary multiple exostoses (HME affects pancreatic insulin secretion capacity and development. We performed an oral glucose tolerance test (OGTT followed by hyperglycemic clamps to investigate first-phase glucose-stimulated insulin secretion (GSIS in HME patients and age and gender matched non-affected relatives. Pancreas volume was assessed with magnetic resonance imaging (MRI. OGTT did not reveal significant differences in glucose disposal, but there was a markedly lower GSIS in HME subjects during hyperglycemic clamp (iAUC HME: 0.72 [0.46-1.16] vs. controls 1.53 [0.69-3.36] nmol·l-1·min-1, p<0.05. Maximal insulin response following arginine challenge was also significantly attenuated (iAUC HME: 7.14 [4.22-10.5] vs. controls 10.2 [7.91-12.70] nmol·l-1·min-1 p<0.05, indicative of an impaired beta-cell reserve. MRI revealed a significantly smaller pancreatic volume in HME subjects (HME: 72.0±15.8 vs. controls 96.5±26.0 cm3 p = 0.04. In conclusion, loss of function of EXT proteins may affect beta-cell mass and insulin secretion capacity in humans, and render subjects at a higher risk of developing type 2 diabetes when exposed to environmental risk factors.

  12. Tracking "apolar" NMe4+ ions within two polyoxothiomolybdates that have the same pores: smaller clathrate and larger highly porous clusters in action.

    Science.gov (United States)

    Korenev, Vladimir S; Boulay, Antoine G; Haouas, Mohamed; Bannani, Fatma; Fedin, Vladimir P; Sokolov, Maxim N; Terazzi, Emmanuel; Garai, Somenath; Müller, Achim; Taulelle, Francis; Marrot, Jérôme; Leclerc, Nathalie; Floquet, Sébastien; Cadot, Emmanuel

    2014-03-10

    Two nanosized polyoxothiometalates were synthesized based on linking oxomolybdate building blocks with {Mo2O2S2}(2+) groups. Remarkably, both compounds are formed selectively primarily upon changing the related concentrations in a logical way; they exhibit common structural features based on the same {Mo9O6S3}-type pores, which result in connections between {Mo6O21} pentagons and {Mo2O2S2}(2+) linkers. Whereas the much larger spherical Mo132-type Keplerate contains twenty pores, the smaller Mo63 -type cluster remarkably contains only two. The two compounds and a similar Keplerate exhibit interesting supramolecular properties related to interactions with the unusual predominantly apolar NMe4(+) cations. Structural characterization of the Mo63 -type compound reveals in the solid state a clathrate-like species that contains four NMe4(+) cations embedded in two types of structurally well-adapted pockets. Related NMR spectroscopic investigations in solution using NMe4(+) as the NMR spectroscopic probe are in agreement with the solid-state description. (1)H NMR spectroscopic experiments (1D variable-temperature, 2D total correlation spectroscopy (TOCSY), exchange spectroscopy (EXSY), and diffusion-ordered spectroscopy (DOSY)) feature firmly immobilized and mobile NMe4(+) ions in relationship with the type of host-guest arrangements. The use of the (1)H NMR DOSY spectroscopic methodology has been successfully applied to track the interactions of the NMe4(+) cations with the {Mo9O6S3} pores of a sulfurated Keplerate, thereby allowing the first quantitative analysis of this type of plugging process. The stability constant K=(210±20) mol(-1)  L is discussed related to the character of the process. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. When men appear smaller or larger than they really are: preliminary evidence that women are fooled by size illusions in attractiveness judgment tasks

    Directory of Open Access Journals (Sweden)

    Ludwig Yannick S.

    2014-12-01

    Full Text Available In humans, studies have shown that contrast illusions can affect perceptions of facial attractiveness and dominance. In non-human animals, recent research found that contrast illusions of size positively affected male mate value. In humans, male height is a potentially important indicator of mate value, with women preferring men taller than themselves. We tested in two studies whether height contrast illusions could affect women’s perceptions of male height and mate value, particularly attractiveness, dominance, and muscularity. Using computer-generated images of men of different heights standing in groups of three, 104 female participants rated targets either surrounded by shorter, same height, or taller distractors in a within-subject design. The second experiment (N=80 replicated and extended the first by making the images more realistic and adding natural backgrounds, suggesting that when participants are given a visual anchor, in order to get a better sense of the absolute height of the targets, the effects remain. In both studies, results showed that, compared with same height distractors, male targets were rated as taller when surrounded by shorter distractors, and as shorter when surrounded by taller distractors. Additionally, attractiveness, dominance, and muscularity perceptions were affected in a similar manner, with most of the differences in these appraisals being mediated by the perceived height differences. Therefore, differently sized distractors affected the perceived height and mate value of the targets, which were in effect all of the same constant size. These findings indicate that context dependent effects could potentially influence attractiveness judgments. The same man might thus be perceived as more attractive when surrounded by men of similar or smaller height, as opposed to when surrounded by men who are taller.

  14. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  15. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  16. Constitutional relevance of atomic energy law

    International Nuclear Information System (INIS)

    Lettow, S.

    1980-01-01

    In a decision publicized on December 20, 1979 the German Federal Constitutional Court rejected a claim of unconstitutionality in connection with the licensing procedure of the Muelheim-Kaerlich Nuclear Power Station currently under construction. This constitutes confirmation, by the 1st Department of the Court, of a decision in 1978 by the 2nd Department about the Kalkar fast breeder power plant, in which the peaceful utilization of nuclear energy had been found to be constitutional. However, the new decision by the Federal Constitutional Court particularly emphasizes the constitutional relevance of the rules of procedure under the Atomic Energy Act and their function with respect to the protection of civil rights. (orig.) [de

  17. Mirror neurons and their clinical relevance.

    Science.gov (United States)

    Rizzolatti, Giacomo; Fabbri-Destro, Maddalena; Cattaneo, Luigi

    2009-01-01

    One of the most exciting events in neurosciences over the past few years has been the discovery of a mechanism that unifies action perception and action execution. The essence of this 'mirror' mechanism is as follows: whenever individuals observe an action being done by someone else, a set of neurons that code for that action is activated in the observers' motor system. Since the observers are aware of the outcome of their motor acts, they also understand what the other individual is doing without the need for intermediate cognitive mediation. In this Review, after discussing the most pertinent data concerning the mirror mechanism, we examine the clinical relevance of this mechanism. We first discuss the relationship between mirror mechanism impairment and some core symptoms of autism. We then outline the theoretical principles of neurorehabilitation strategies based on the mirror mechanism. We conclude by examining the relationship between the mirror mechanism and some features of the environmental dependency syndromes.

  18. The Integrin Receptor in Biologically Relevant Bilayers

    DEFF Research Database (Denmark)

    Kalli, Antreas C.; Róg, Tomasz; Vattulainen, Ilpo

    2017-01-01

    /talin complex was inserted in biologically relevant bilayers that resemble the cell plasma membrane containing zwitterionic and charged phospholipids, cholesterol and sphingolipids to study the dynamics of the integrin receptor and its effect on bilayer structure and dynamics. The results of this study...... demonstrate the dynamic nature of the integrin receptor and suggest that the presence of the integrin receptor alters the lipid organization between the two leaflets of the bilayer. In particular, our results suggest elevated density of cholesterol and of phosphatidylserine lipids around the integrin....../talin complex and a slowing down of lipids in an annulus of ~30 Å around the protein due to interactions between the lipids and the integrin/talin F2–F3 complex. This may in part regulate the interactions of integrins with other related proteins or integrin clustering thus facilitating signal transduction...

  19. PREDICTING RELEVANT EMPTY SPOTS IN SOCIAL INTERACTION

    Institute of Scientific and Technical Information of China (English)

    Yoshiharu MAENO; Yukio OHSAWA

    2008-01-01

    An empty spot refers to an empty hard-to-fill space which can be found in the records of the social interaction, and is the clue to the persons in the underlying social network who do not appear in the records. This contribution addresses a problem to predict relevant empty spots in social interaction. Homogeneous and inhomogeneous networks are studied as a model underlying the social interaction. A heuristic predictor function method is presented as a new method to address the problem. Simulation experiment is demonstrated over a homogeneous network. A test data set in the form of market baskets is generated from the simulated communication. Precision to predict the empty spots is calculated to demonstrate the performance of the presented method.

  20. Mathematical Properties Relevant to Geomagnetic Field Modeling

    DEFF Research Database (Denmark)

    Sabaka, Terence J.; Hulot, Gauthier; Olsen, Nils

    2010-01-01

    be directly measured. In this chapter, the mathematical foundation of global (as opposed to regional) geomagnetic field modeling is reviewed, and the spatial modeling of the field in spherical coordinates is focussed. Time can be dealt with as an independent variable and is not explicitly considered......Geomagnetic field modeling consists in converting large numbers of magnetic observations into a linear combination of elementary mathematical functions that best describes those observations.The set of numerical coefficients defining this linear combination is then what one refers.......The relevant elementary mathematical functions are introduced, their properties are reviewed, and how they can be used to describe the magnetic field in a source-free (such as the Earth’s neutral atmosphere) or source-dense (such as the ionosphere) environment is explained. Completeness and uniqueness...

  1. Mathematical Properties Relevant to Geomagnetic Field Modeling

    DEFF Research Database (Denmark)

    Sabaka, Terence J.; Hulot, Gauthier; Olsen, Nils

    2014-01-01

    be directly measured. In this chapter, the mathematical foundation of global (as opposed to regional) geomagnetic field modeling is reviewed, and the spatial modeling of the field in spherical coordinates is focused. Time can be dealt with as an independent variable and is not explicitly considered......Geomagnetic field modeling consists in converting large numbers of magnetic observations into a linear combination of elementary mathematical functions that best describes those observations. The set of numerical coefficients defining this linear combination is then what one refers....... The relevant elementary mathematical functions are introduced, their properties are reviewed, and how they can be used to describe the magnetic field in a source-free (such as the Earth’s neutral atmosphere) or source-dense (such as the ionosphere) environment is explained. Completeness and uniqueness...

  2. Towards increased policy relevance in energy modeling

    Energy Technology Data Exchange (ETDEWEB)

    Worrell, Ernst; Ramesohl, Stephan; Boyd, Gale

    2003-07-29

    Historically, most energy models were reasonably equipped to assess the impact of a subsidy or change in taxation, but are often insufficient to assess the impact of more innovative policy instruments. We evaluate the models used to assess future energy use, focusing on industrial energy use. We explore approaches to engineering-economic analysis that could help improve the realism and policy relevance of engineering-economic modeling frameworks. We also explore solutions to strengthen the policy usefulness of engineering-economic analysis that can be built from a framework of multi-disciplinary cooperation. We focus on the so-called ''engineering-economic'' (or ''bottom-up'') models, as they include the amount of detail that is commonly needed to model policy scenarios. We identify research priorities for the modeling framework, technology representation in models, policy evaluation and modeling of decision-making behavior.

  3. Climate-relevant monitorings in Germany

    International Nuclear Information System (INIS)

    Metternich, P.

    1993-01-01

    This catalogue contains so-called meta-data; i.e. information on data. For each measuring programme or set of data, users find the address (postal address, telephone, fax-number) of the respective contact person at the beginning of the entry. The catalogue has three parts: Part A is a compilation of monitoring programmes using conventional methods adopted on the ground. Part B contains research programmes or sets of data from the field of remote sensing. In part C, data sets from time series of climate-relevant parameters are described. Section A was additionally structured according so the compartments of the climate system: Atmosphere, hydrosphere, cryosphere, biosphere. (orig./KW) [de

  4. Bacteriophage lambda: early pioneer and still relevant

    Science.gov (United States)

    Casjens, Sherwood R.; Hendrix, Roger W.

    2015-01-01

    Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives have continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle. PMID:25742714

  5. Reach and Relevance of Prison Research

    Directory of Open Access Journals (Sweden)

    Hilde Tubex

    2015-04-01

    Full Text Available In this contribution I reflect on the changes in the penal landscape and how they impact on prison research. I do this from my experiences as a prison researcher in a variety of roles, in both Europe and Australia. The growing dominance of managerialism has impacted on both corrective services and universities, in ways that have changed the relationship between current prison practices and academically oriented research. Therefore, academics have to question how their contemporary prison research can bridge the emerging gap: how they can not only produce research that adheres to the roots of criminology and provides a base for a rational penal policy, but also how they can develop strategies to get recognition of and funding for this broader contextual work which, although it might not produce results that are immediately identifiable, can be of relevance in indirect ways and in the longer term.

  6. Relevance of protection quantities in medical exposures

    International Nuclear Information System (INIS)

    Pradhan, A.S.

    2008-01-01

    International Commission on Radiological Protection (ICRP) continues to classify the exposures to radiation in three categories; namely 1- occupational exposure, 2- public exposure, and 3- medical exposure. Protection quantities are primarily meant for the regulatory purpose in radiological protection for controlling and limiting stochastic risks in occupational and public exposures. These are based on two basic assumptions of 1- linear no-threshold dose-effect relationship (LNT) at low doses and 2- long-term additivity of low doses. Medical exposure are predominantly delivered to individuals (patients) undergoing diagnostic examinations, interventional procedures and radiation therapy but also include individual caring for or comforting patients incurring exposure and the volunteers of biomedical medical research programmes. Radiation protection is as relevant to occupational and public exposure as to medical exposures except that the dose limits set for the formers are not applicable to medical exposure but reference levels and dose constrains are recommended for diagnostic and interventional medical procedures. In medical institutions, both the occupational and medical exposure takes place. Since the doses in diagnostic examinations are low, it has been observed that not only the protection quantities are often used in such cases but these are extended to estimate the number of cancer deaths due to such practices. One of the striking features of the new ICRP recommendations has been to elaborate the concepts of the dosimetric quantities. The limitation of protection quantities ((Effective dose, E=Σ RT D TR .W T .W R and Equivalent Dose H T =Σ RT D TR .W R ) have been brought out and this has raised a great concern and initiated debates on the use of these quantities in medical exposures. Consequently, ICRP has set a task group to provide more details and the recommendations. It has, therefore, became important to draw the attention of medical physics community

  7. Ecological principles relevant to nuclear war

    International Nuclear Information System (INIS)

    Hutchinson, T.C.; Cropper, W.P. Jr.; Grover, H.D.

    1985-01-01

    The ecological principles outlined are very basic ones; the authors anticipate a readership trained in a broad range of disciplines, including those unfamiliar with the academic discipline of ecology. The authors include substantial discussion on ecophysiology (i.e., the responses of organisms to their environment) because this is relevant to the new understanding of the potential climatic consequences of nuclear war. In particular, the physiological sensitivity of organisms to reduced levels of light and temperature are a key part of the analysis of the potential ecological effects and agricultural effects of nuclear war. Much of the ecological analysis has been organized around major biological units called biomes. The authors describe the biome concept and discuss some of the environmental-climatic factors that are believed to control biome distribution. Emphasis is given to plants because of their controlling influence on ecosystem functions through their role as primary producers. Future reports are needed to address more fully the potential effects on animals. Much more research needs to be done on both plant and animal responses to the types of perturbations possible for the aftermath of a nuclear war. Another important element for analysis of the potential ecological consequences of nuclear war concerns recovery processes. As the post-nuclear war environmental extremes ameliorate, ecological communities in devastated regions would begin to reorganize. It is not possible to predict the course of such a succession precisely, but some principles concerning post-perturbation replacement (such as seed banks and germination), relevant successional patterns, and organism strategies are discussed

  8. Thermochemical data for environmentally-relevant elements

    International Nuclear Information System (INIS)

    Markich, S.J.; Brown, P.L.

    1999-01-01

    This study provides an extensive stability constant (log K) database suitable for calculating the speciation of selected environmentally-relevant elements (H, Na, K, Ca, Mg, Fe, Mn, U, Al Pb, Zn, Cu and cd) in an aqueous system, where a model fulvic acid (comprising aspartic, citric, malonic, salicylic and tricarballylic acids) is used to simulate metal binding by dissolved organic material Stability constants for inorganic metal complexes and minerals were selected primarily from critical literature complications and/or reviews. In contrast, few critically evaluated data were available for metal complexes with aspartic, citric, malonic, salicylic and tricarballylic acids. Consequently, data from original research articles were carefully evaluated and compiled as part of the study, following defined selection criteria. to meet the objective of compiling a comprehensive and reliable database of stability constants, all relevant equilibria and species, ranging from simple binary metal complexes to more complex ternary and even quaternary, metal complexes were included where possible in addition to the selection of stability constants from empirical sources, estimates of stability constants were performed when this could be done reliably, based on the unified theory of metal ion complexation and/or linear tree energy relationships The stability constants are given as common logarithms (logo) in the form required by the HARPHRQ geochemical code and refer to the standard state, i.e 298.15 K (25 deg C), 10 5 Pa (1 atm) and, for all species, infinite dilution (ionic strength = 0 mol L -1 ). In addition to the compilation of stability constant data, an overview is given of geochemical speciation modelling in aqueous systems and available conceptual models of metal binding by humic substances. (authors)

  9. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  10. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  11. Single molecule sequencing-guided scaffolding and correction of draft assemblies.

    Science.gov (United States)

    Zhu, Shenglong; Chen, Danny Z; Emrich, Scott J

    2017-12-06

    Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies. We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm. Our experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.

  12. The minimally important difference for the health assessment questionnaire in rheumatoid arthritis clinical practice is smaller than in randomized controlled trials.

    Science.gov (United States)

    Pope, Janet E; Khanna, Dinesh; Norrie, Deborah; Ouimet, Janine M

    2009-02-01

    Patient-reported outcomes are used in clinical practice and trials. We studied a large clinical practice to determine the minimally important difference (MID) estimates for (1) the Health Assessment Questionnaire-Damage Index (HAQ-DI): improvement and worsening using patient global assessment anchor; and (2) pain using a patient-reported pain anchor. Patients with rheumatoid arthritis (RA; N = 225) had clinic visits at 2 timepoints within 1 year, completed the HAQ-DI and pain visual analog scale (VAS; 0-100 mm), and answered the question, "How would you describe your overall status/overall pain since the last visit?", as much worsened, somewhat worsened, the same, somewhat improved, or much improved. If rated as somewhat improved or worsened, they were defined as the minimally changed subgroups. Eighty-three percent were women, mean age 60 years, with disease duration 11.7 +/- 10.7 years. The baseline HAQ-DI was 0.97 +/- SD 0.76, and at followup 1.0 +/- 0.77 (mean change +0.03 +/- 0.40). The baseline pain VAS was 42.3 +/- 28.8, and at followup 38.5 +/- 27.9 (mean change -2.8 +/- 25.9). The mean (SD) HAQ-DI change score was -0.09 (0.42) for somewhat improved and 0.15 (0.33) for somewhat worsened. The HAQ-DI change for somewhat/much better was -0.20 +/- 0.52, and for somewhat/much worse +0.21 +/- 0.33. For pain, somewhat improved changed by -11.9 mm on the VAS, and somewhat worsened by 6.8 mm. Estimates for HAQ-DI and pain were larger than the for no-change group, 0.03 (0.32) and -3.2 (20.9). The MID for HAQ-DI in clinical practice is smaller than it is in trials. This may have implications for observational studies and clinical care.

  13. Renal tissue alterations were size-dependent with smaller ones induced more effects and related with time exposure of gold nanoparticles

    Directory of Open Access Journals (Sweden)

    Jarrar Bashir M

    2011-09-01

    interfering with the antioxidant defense mechanism and leading to reactive oxygen species (ROS generation which in turn may induce stress in the renal cells to undergo atrophy and necrosis. The produced alterations were size-dependent with smaller ones induced more affects and related with time exposure of GNPs.

  14. Misonidazole cytotoxicity in vivo: a comparison of large single doses with smaller doses and extended contact of the drug with tumor cells

    International Nuclear Information System (INIS)

    Conroy, P.J.; Sutherland, R.M.; Passalacqua, W.

    1980-01-01

    Experiments were performed to determine the kinetics and magnitude of misonidazole cytotoxicity in EMT6/Ro tumors using an in vivo-in vitro clonogenicity assay. A comparison was made between the cytotoxic effects of large single doses with smaller doses of misonidazole administered ip and those produced on extended contact of the drug with tumor cells using a continuous iv drug infusion system. After a single ip dose of 1 mg/g, cytotoxicity was maximum at 18 to 24 h; by 72 h the clonogenic cells per tumor had returned to control levels. The maximum cytotoxicity was greater (a decrease of 10 times) if the animals were kept at 37 0 C compared with ambient conditions (a decrease of 4.5 times) where the body temperature would decrease due to the drug. A dose-response curve performed with the animals at 37 0 C showed no significant cytotoxicity at 18 h after single ip doses of 0.5 mg/g or less. Other experiments were carried out at 37 0 C using a drug continuous infusion system. Two profiles were studied: (a) continuous constant rate infusion over 3 days of constant serum and tumor levels of both 100 and 200 μg/ml and (b) continuous variable rate infusion where the maximum serum levels reached 80 or 200 μg/ml after 2 to 4 h and decayed with a half-life of 12 h as in humans. Significant cytotoxicity was obtained under both of these conditions. Maximum cytotoxicity occurred at about 24 h in both types of experiments and amounted to decreases of clonogenic tumor cells of 4.5 and 7 times for 100 and 200 μg/ml, respectively, after constant rate infusion and 2 to 4 times for 80 and 200 μg/ml, respectively, after variable rate infusion. Because of the relatively rapid recovery in the number of clonogenic tumor cells by 72 h, the cytotoxic effects were not reflected as changes in tumor size even when the animals were maintained at 37 0 C

  15. Can you sequence ecology? Metagenomics of adaptive diversification.

    Science.gov (United States)

    Marx, Christopher J

    2013-01-01

    Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the evolutionary and ecological processes that are occurring? For example, can we determine if a species is adapting to one niche, or if it is diversifying into multiple specialists that inhabit distinct niches? Fortunately, adaptation of populations in the laboratory can serve as a model to test our ability to make such inferences about evolution and ecology from sequencing. Even adaptation to a single niche can give rise to complex temporal dynamics due to the transient presence of multiple competing lineages. If there are multiple niches, this complexity is augmented by segmentation of the population into multiple specialists that can each continue to evolve within their own niche. For a known example of parallel diversification that occurred in the laboratory, sequencing data gave surprisingly few obvious, unambiguous signs of the ecological complexity present. Whereas experimental systems are open to direct experimentation to test hypotheses of selection or ecological interaction, the difficulty in "seeing ecology" from sequencing for even such a simple system suggests translation to communities like the human microbiome will be quite challenging. This will require both improved empirical methods to enhance the depth and time resolution for the relevant polymorphisms and novel statistical approaches to rigorously examine time-series data for signs of various evolutionary and ecological phenomena within and between species.

  16. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes

    Directory of Open Access Journals (Sweden)

    Paul Dunn

    2018-02-01

    Full Text Available Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS techniques such as targeted gene panels, whole exome sequencing (WES and whole genome sequencing (WGS. For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.

  17. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  18. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  19. Reconstruction of peak water levels, peak discharges and long-term occurrence of extreme- as well as smaller pre-instrumental flood events of river Aare, Limmat, Reuss, Rhine and Saane in Switzerland. Part I

    Science.gov (United States)

    Wetter, Oliver; Tuttenuj, Daniel

    2016-04-01

    Part I: Dr. Oliver Wetter. (Oeschger Centre for Climate Change Research, University of Bern, Switzerland) Part II: PhD student Daniel Tuttenuj (Oeschger Centre of Climate Change Research, University of Bern, Switzerland) The methodology developed by Wetter et al. (2011) combines different documentary and instrumental sources, retaining relevant information for the reconstruction of extreme pre-instrumental flood events. These include hydrological measurements (gauges), historic river profiles (cross and longitudinal profiles), flood marks, historic city maps, documentary flood evidence (reports in chronicles and newspapers) as well as paintings and drawings. It has been shown that extreme river Rhine flood events of the pre-instrumental period can be reconstructed in terms of peak discharges for the last 750 years by applying this methodology to the site of Basel. Pfister & Wetter (2011) furthermore demonstrated that this methodology is also principally transferable to other locations and rivers. Institutional documentary evidence has not been systematically analysed in the context of historical hydrology in Switzerland so far. The term institutional documentary evidence generally outlines sources that were produced by governments or other (public) bodies including the church, hospitals, and the office of the bridge master. Institutional bodies were typically not directly interested in describing climate or hydrological events but they were obliged to document their activities, especially if they generated financial costs (bookkeeping), and in doing so they often indirectly recorded climatologic or hydrological events. The books of weekly expenditures of Basel ("Wochenausgabenbücher der Stadt Basel") were first analysed by Fouquet (1999). He found recurring records of wage expenditures for a squad of craftsmen that was called up onto the bridge with the task of preventing the bridge from being damaged by fishing out drifting logs from the flood waters. Fouquet

  20. Reconstruction of peak water levels, peak discharges and long-term occurrence of extreme- as well as smaller pre-instrumental flood events of river Aare, Limmat, Reuss, Rhine and Saane in Switzerland. Part II.

    Science.gov (United States)

    Tuttenuj, Daniel; Wetter, Oliver

    2016-04-01

    The methodology developed by Wetter et al. (2011) combines different documentary and instrumental sources, retaining relevant information for the reconstruction of extreme pre-instrumental flood events. These include hydrological measurements (gauges), historic river profiles (cross and longitudinal profiles), flood marks, historic city maps, documentary flood evidence (reports in chronicles and newspapers) as well as paintings and drawings. It has been shown that extreme river Rhine flood events of the pre-instrumental period can be reconstructed in terms of peak discharges for the last 750 years by applying this methodology to the site of Basel. Pfister & Wetter (2011) furthermore demonstrated that this methodology is also principally transferable to other locations and rivers in Switzerland. Institutional documentary evidence has not been systematically analysed in the context of historical hydrology in Switzerland so far. The term institutional documentary evidence generally outlines sources that were produced by governments or other (public) bodies including the church, hospitals, and the office of the bridge master. Institutional bodies were typically not directly interested in describing climate or hydrological events but they were obliged to document their activities, especially if they generated financial costs (bookkeeping), and in doing so they often indirectly recorded climatologic or hydrological events. The books of weekly expenditures of Basel ("Wochenausgabenbücher der Stadt Basel") were first analysed by Fouquet (1999). He found recurring records of wage expenditures for a squad of craftsmen that was called up onto the bridge with the task of preventing the bridge from being damaged by fishing out drifting logs from the flood waters. Fouquet systematically analysed the period from 1446-1542 and could prove a large number of pre-instrumental flood events of river Rhine, Birs, Birsig and Wiese in Basel. All in all the weekly led account books

  1. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  2. Recognition of depositional sequences and stacking patterns, Late Devonian (Frasnian) carbonate platforms, Alberta basin

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, J.H.; Reeckmann, S.A.; Sarg, J.F.; Greenlee, S.M.

    1987-05-01

    Six depositional sequences bounded by regional unconformities or their correlative equivalents (sequence boundaries) have been recognized in Late Devonian (Frasnian) carbonate platforms in the Alberta basin. These sequences consist of a predictable vertical succession of smaller scale shoaling-upward cycles (parasequences). Parasequences are arranged in retrogradational, aggradational, and progradational stacking patterns that can be modeled as a sediment response to relative changes in sea level. Sequence boundaries are recognized by onlap onto underlying shelf or shelf margin strata. This onlap includes shelf margin wedges and deep marine onlap. In outcrop sections shelf margin wedges exhibit an abrupt juxtaposition of shallow water facies over deeper water deposits with no gradational facies changes at the boundaries. High on the platform, subaerial exposure fabrics may be present. The shelf margin wedges are interpreted to have formed during lowstands in sea level and typically exhibit an aggradational stacking pattern. On the platform, two types of sequences are recognized. A type 1 cycle occurs where the sequence boundary is overlain by a flooding surface and subsequent parasequences exhibit retrogradational stacking. In a type 2 cycle the sequence boundary is overlain by an aggradational package of shallow water parasequences, followed by a retrogradational package. These two types of sequences can be modeled using a sinusoidal eustatic sea level curve superimposed on thermo-tectonic subsidence.

  3. Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

    Energy Technology Data Exchange (ETDEWEB)

    McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

    2005-08-26

    Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

  4. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  5. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  6. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

    DEFF Research Database (Denmark)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo

    2012-01-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp...... these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species....

  7. Early onset depression: the relevance of anxiety.

    Science.gov (United States)

    Parker, G; Wilhelm, K; Asghari, A

    1997-01-01

    The aim of this study was to determine risk factors that may differentiate early onset from late onset depression. A non-clinical cohort that had been assessed from 1978 to 1993 at 5 yearly intervals and that had a high prevalence rate of lifetime depression took part in the study. We established an appropriate age cut-off to distinguish early onset (i.e. before 26 years) of major and of minor depression, and examined the relevance of a number of possible determinants of early onset depression assessed over the life of the study. Despite several dimensional measures of depression, self-esteem and personality being considered, they generally failed (when assessed early in the study) to discriminate subsequent early onset depression, with the exception of low masculinity scores being a weak predictor of major and/or minor depression. Early onset depression was strongly predicted, however, by a lifetime episode of a major anxiety disorder, with generalised anxiety being a somewhat stronger and more consistent predictor than panic disorder, agoraphobia and minor anxiety disorders (ie social phobia, simple phobia). The possibility that anxiety may act as a key predispositional factor to early onset depression and to a greater number of depressive episodes is important in that clinical assessment and treatment of any existing anxiety disorder may be a more efficient and useful strategy than focussing primarily on the depressive disorder.

  8. Top studies relevant to primary care practice.

    Science.gov (United States)

    Perry, Danielle; Kolber, Michael R; Korownyk, Christina; Lindblad, Adrienne J; Ramji, Jamil; Ton, Joey; Allan, G Michael

    2018-04-01

    To summarize 10 high-quality studies from 2017 that have strong relevance to primary care practice. Study selection involved routine literature surveillance by a group of primary care health professionals. This included screening abstracts of important journals and Evidence Alerts, as well as searching the American College of Physicians Journal Club. Topics of the 2017 articles include whether treating subclinical hypothyroidism improves outcomes or symptoms; whether evolocumab reduces cardiovascular disease as well as low-density lipoprotein levels; whether lifestyle interventions reduce medication use in patients with diabetes; whether vitamin D prevents cardiovascular disease, cancer, or upper respiratory tract infections; whether canagliflozin reduces clinical events in patients with diabetes; how corticosteroid injections affect knee osteoarthritis; whether drained abscesses benefit from antibiotic treatment; whether patients with diabetes benefit from bariatric surgery; whether exenatide reduces clinical events in patients with diabetes; and whether tympanostomy tubes affect outcomes in recurrent acute otitis media or chronic otitis media. We provide brief summaries, context where needed, and final recommendations for 10 studies with potential effects on primary care. We also briefly review 5 "runner-up" studies. Research from 2017 produced several high-quality studies in diabetes management. These have demonstrated benefit for alternative therapies and offered evidence not previously available. This year's selection of studies also provided information on a variety of conditions and therapies that are, or might become, more common in primary care settings. Copyright© the College of Family Physicians of Canada.

  9. Clinically Relevant Anticancer Polymer Paclitaxel Therapeutics

    Directory of Open Access Journals (Sweden)

    Danbo Yang

    2010-12-01

    Full Text Available The concept of utilizing polymers in drug delivery has been extensively explored for improving the therapeutic index of small molecule drugs. In general, polymers can be used as polymer-drug conjugates or polymeric micelles. Each unique application mandates its own chemistry and controlled release of active drugs. Each polymer exhibits its own intrinsic issues providing the advantage of flexibility. However, none have as yet been approved by the U.S. Food and Drug Administration. General aspects of polymer and nano-particle therapeutics have been reviewed. Here we focus this review on specific clinically relevant anticancer polymer paclitaxel therapeutics. We emphasize their chemistry and formulation, in vitro activity on some human cancer cell lines, plasma pharmacokinetics and tumor accumulation, in vivo efficacy, and clinical outcomes. Furthermore, we include a short review of our recent developments of a novel poly(L-g-glutamylglutamine-paclitaxel nano-conjugate (PGG-PTX. PGG-PTX has its own unique property of forming nano-particles. It has also been shown to possess a favorable profile of pharmacokinetics and to exhibit efficacious potency. This review might shed light on designing new and better polymer paclitaxel therapeutics for potential anticancer applications in the clinic.

  10. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)

    2014-07-15

    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  11. Relevance of extracellular DNA in rhizosphere

    Science.gov (United States)

    Pietramellara, Giacomo; Ascher, Judith; Baraniya, Divyashri; Arfaioli, Paola; Ceccherini, Maria Teresa; Hawes, Martha

    2013-04-01

    One of the most promising areas for future development is the manipulation of the rhizosphere to produce sustainable and efficient agriculture production systems. Using Omics approaches, to define the distinctive features of eDNA systems and structures, will facilitate progress in rhizo-enforcement and biocontrol studies. The relevance of these studies results clear when we consider the plethora of ecological functions in which eDNA is involved. This fraction can be actively extruded by living cells or discharged during cellular lysis and may exert a key role in the stability and variability of the soil bacterial genome, resulting also a source of nitrogen and phosphorus for plants due to the root's capacity to directly uptake short DNA fragments. The adhesive properties of the DNA molecule confer to eDNA the capacity to inhibit or kill pathogenic bacteria by cation limitation induction, and to facilitate formation of biofilm and extracellular traps (ETs), that may protect microorganisms inhabiting biofilm and plant roots against pathogens and allelopathic substances. The ETs are actively extruded by root border cells when they are dispersed in the rhizosphere, conferring to plants the capacity to extend an endogenous pathogen defence system outside the organism. Moreover, eDNA could be involved in rhizoremediation in heavy metal polluted soil acting as a bioflotation reagent.

  12. Relevance of tidal heating on large TNOs

    Science.gov (United States)

    Saxena, Prabal; Renaud, Joe P.; Henning, Wade G.; Jutzi, Martin; Hurford, Terry

    2018-03-01

    We examine the relevance of tidal heating for large Trans-Neptunian Objects, with a focus on its potential to melt and maintain layers of subsurface liquid water. Depending on their past orbital evolution, tidal heating may be an important part of the heat budget for a number of discovered and hypothetical TNO systems and may enable formation of, and increased access to, subsurface liquid water. Tidal heating induced by the process of despinning is found to be particularly able to compete with heating due to radionuclide decay in a number of different scenarios. In cases where radiogenic heating alone may establish subsurface conditions for liquid water, we focus on the extent by which tidal activity lifts the depth of such conditions closer to the surface. While it is common for strong tidal heating and long lived tides to be mutually exclusive, we find this is not always the case, and highlight when these two traits occur together. We find cases where TNO systems experience tidal heating that is a significant proportion of, or greater than radiogenic heating for periods ranging from100‧s of millions to a billion years. For subsurface oceans that contain a small antifreeze component, tidal heating due to very high initial spin states may enable liquid water to be preserved right up to the present day. Of particular interest is the Eris-Dysnomia system, which in those cases may exhibit extant cryovolcanism.

  13. Extracellular vesicles: fundamentals and clinical relevance

    Directory of Open Access Journals (Sweden)

    Wael Nassar

    2015-01-01

    Full Text Available All types of cells of eukaryotic organisms produce and release small nanovesicles into their extracellular environment. Early studies have described these vesicles as ′garbage bags′ only to remove obsolete cellular molecules. Valadi and colleagues, in 2007, were the first to discover the capability of circulating extracellular vesicles (EVs to horizontally transfer functioning gene information between cells. These extracellular vesicles express components responsible for angiogenesis promotion, stromal remodeling, chemoresistance, genetic exchange, and signaling pathway activation through growth factor/receptor transfer. EVs represent an important mode of intercellular communication by serving as vehicles for transfer between cells of membrane and cytosolic proteins, lipids, signaling proteins, and RNAs. They contribute to physiology and pathology, and they have a myriad of potential clinical applications in health and disease. Moreover, vesicles can pass the blood-brain barrier and may perhaps even be considered as naturally occurring liposomes. These cell-derived EVs not only represent a central mediator of the disease microenvironment, but their presence in the peripheral circulation may serve as a surrogate for disease biopsies, enabling real-time diagnosis and disease monitoring. In this review, we′ll be addressing the characteristics of different types of extracellular EVs, as well as their clinical relevance and potential as diagnostic markers, and also define therapeutic options.

  14. Human error theory: relevance to nurse management.

    Science.gov (United States)

    Armitage, Gerry

    2009-03-01

    Describe, discuss and critically appraise human error theory and consider its relevance for nurse managers. Healthcare errors are a persistent threat to patient safety. Effective risk management and clinical governance depends on understanding the nature of error. This paper draws upon a wide literature from published works, largely from the field of cognitive psychology and human factors. Although the content of this paper is pertinent to any healthcare professional; it is written primarily for nurse managers. Error is inevitable. Causation is often attributed to individuals, yet causation in complex environments such as healthcare is predominantly multi-factorial. Individual performance is affected by the tendency to develop prepacked solutions and attention deficits, which can in turn be related to local conditions and systems or latent failures. Blame is often inappropriate. Defences should be constructed in the light of these considerations and to promote error wisdom and organizational resilience. Managing and learning from error is seen as a priority in the British National Health Service (NHS), this can be better achieved with an understanding of the roots, nature and consequences of error. Such an understanding can provide a helpful framework for a range of risk management activities.

  15. Clinically Relevant Anticancer Polymer Paclitaxel Therapeutics

    International Nuclear Information System (INIS)

    Yang, Danbo; Yu, Lei; Van, Sang

    2010-01-01

    The concept of utilizing polymers in drug delivery has been extensively explored for improving the therapeutic index of small molecule drugs. In general, polymers can be used as polymer-drug conjugates or polymeric micelles. Each unique application mandates its own chemistry and controlled release of active drugs. Each polymer exhibits its own intrinsic issues providing the advantage of flexibility. However, none have as yet been approved by the U.S. Food and Drug Administration. General aspects of polymer and nano-particle therapeutics have been reviewed. Here we focus this review on specific clinically relevant anticancer polymer paclitaxel therapeutics. We emphasize their chemistry and formulation, in vitro activity on some human cancer cell lines, plasma pharmacokinetics and tumor accumulation, in vivo efficacy, and clinical outcomes. Furthermore, we include a short review of our recent developments of a novel poly(l-γ-glutamylglutamine)-paclitaxel nano-conjugate (PGG-PTX). PGG-PTX has its own unique property of forming nano-particles. It has also been shown to possess a favorable profile of pharmacokinetics and to exhibit efficacious potency. This review might shed light on designing new and better polymer paclitaxel therapeutics for potential anticancer applications in the clinic

  16. Accreditation - Its relevance for laboratories measuring radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Palsson, S E [Icelandic Radiation Protection Inst. (Iceland)

    2001-11-01

    Accreditation is an internationally recognised way for laboratories to demonstrate their competence. Obtaining and maintaining accreditation is, however, a costly and time-consuming procedure. The benefits of accreditation also depend on the role of the laboratory. Accreditation may be of limited relevance for a research laboratory, but essential for a laboratory associated with a national authority and e.g. issuing certificates. This report describes work done within the NKSBOK-1.1 sub-project on introducing accreditation to Nordic laboratories measuring radionuclides. Initially the focus was on the new standard ISO/IEC 17025, which was just in a draft form at the time, but which provides now a new framework for accreditation of laboratories. Later the focus was widened to include a general introduction to accreditation and providing through seminars a forum for exchanging views on the experience laboratories have had in this field. Copies of overheads from the last such seminar are included in the appendix to this report. (au)

  17. Perspective: Organizational professionalism: relevant competencies and behaviors.

    Science.gov (United States)

    Egener, Barry; McDonald, Walter; Rosof, Bernard; Gullen, David

    2012-05-01

    The professionalism behaviors of physicians have been extensively discussed and defined; however, the professionalism behaviors of health care organizations have not been systemically categorized or described. Defining organizational professionalism is important because the behaviors of a health care organization may substantially impact the behaviors of physicians and others within the organization as well as other institutions and the larger community. In this article, the authors discuss the following competencies of organizational professionalism, derived from ethical values: service, respect, fairness, integrity, accountability, mindfulness, and self-motivation. How nonprofit health care organizations can translate these competencies into behaviors is described. For example, incorporating metrics of population health into assessments of corporate success may increase collaboration among regional health care organizations while also benefiting the community. The unique responsibilities of leadership to model these competencies, promote them in the community, and develop relevant organizational strategies are clarified. These obligations elevate the importance of the executive leadership's capacity for self-reflection and the governing boards' responsibility for mapping operational activities to organizational mission. Lastly, the authors consider how medical organizations are currently addressing professionalism challenges. In an environment made turbulent by regulatory change and financial constraints, achieving proficiency in professionalism competencies can assist nonprofit health care organizations to promote population health and the well-being of their workforces.

  18. Media and mental illness: Relevance to India

    Directory of Open Access Journals (Sweden)

    S K Padhy

    2014-01-01

    Full Text Available Media has a complex interrelationship with mental illnesses. This narrative review takes a look at the various ways in which media and mental illnesses interact. Relevant scientific literature and electronic databases were searched, including Pubmed and GoogleScholar, to identify studies, viewpoints and recommendations using keywords related to media and mental illnesses. This review discusses both the positive and the negative portrayals of mental illnesses through the media. The portrayal of mental health professionals and psychiatric treatment is also discussed. The theories explaining the relationship of how media influences the attitudes and behavior are discussed. Media has also been suggested to be a risk factor for the genesis or exacerbation of mental illnesses like eating disorders and substance use disorders. The potential use of media to understand the psychopathology and plight of those with psychiatric disorders is referred to. The manner in which media can be used as a tool for change to reduce the stigma surrounding mental illnesses is explored.

  19. EXTRACELLULAR VESICLES: CLASSIFICATION, FUNCTIONS AND CLINICAL RELEVANCE

    Directory of Open Access Journals (Sweden)

    A. V. Oberemko

    2014-12-01

    Full Text Available This review presents a generalized definition of vesicles as bilayer extracellular organelles of all celular forms of life: not only eu-, but also prokaryotic. The structure and composition of extracellular vesicles, history of research, nomenclature, their impact on life processes in health and disease are discussed. Moreover, vesicles may be useful as clinical instruments for biomarkers, and they are promising as biotechnological drug. However, many questions in this area are still unresolved and need to be addressed in the future. The most interesting from the point of view of practical health care represents a direction to study the effect of exosomes and microvesicles in the development and progression of a particular disease, the possibility of adjusting the pathological process by means of extracellular vesicles of a particular type, acting as an active ingredient. Relevant is the further elucidation of the role and importance of exosomes to the surrounding cells, tissues and organs at the molecular level, the prospects for the use of non-cellular vesicles as biomarkers of disease.

  20. Clinically Relevant Anticancer Polymer Paclitaxel Therapeutics

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Danbo [Biomedical Engineering and Technology Institute, Institutes for Advanced Interdisciplinary Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062 (China); Yu, Lei, E-mail: yu-lei@gg.nitto.co.jp [Biomedical Engineering and Technology Institute, Institutes for Advanced Interdisciplinary Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062 (China); Biomedical Group, Nitto Denko Technical Corporation, 501 Via Del Monte, Oceanside, CA 92058 (United States); Van, Sang [Biomedical Group, Nitto Denko Technical Corporation, 501 Via Del Monte, Oceanside, CA 92058 (United States)

    2010-12-23

    The concept of utilizing polymers in drug delivery has been extensively explored for improving the therapeutic index of small molecule drugs. In general, polymers can be used as polymer-drug conjugates or polymeric micelles. Each unique application mandates its own chemistry and controlled release of active drugs. Each polymer exhibits its own intrinsic issues providing the advantage of flexibility. However, none have as yet been approved by the U.S. Food and Drug Administration. General aspects of polymer and nano-particle therapeutics have been reviewed. Here we focus this review on specific clinically relevant anticancer polymer paclitaxel therapeutics. We emphasize their chemistry and formulation, in vitro activity on some human cancer cell lines, plasma pharmacokinetics and tumor accumulation, in vivo efficacy, and clinical outcomes. Furthermore, we include a short review of our recent developments of a novel poly(l-γ-glutamylglutamine)-paclitaxel nano-conjugate (PGG-PTX). PGG-PTX has its own unique property of forming nano-particles. It has also been shown to possess a favorable profile of pharmacokinetics and to exhibit efficacious potency. This review might shed light on designing new and better polymer paclitaxel therapeutics for potential anticancer applications in the clinic.