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  1. Reforestation Sites Show Similar and Nested AMF Communities to an Adjacent Pristine Forest in a Tropical Mountain Area of South Ecuador

    Science.gov (United States)

    Haug, Ingeborg; Setaro, Sabrina; Suárez, Juan Pablo

    2013-01-01

    Arbuscular mycorrhizae are important for growth and survival of tropical trees. We studied the community of arbuscular mycorrhizal fungi in a tropical mountain rain forest and in neighbouring reforestation plots in the area of Reserva Biológica San Francisco (South Ecuador). The arbuscular mycorrhizal fungi were analysed with molecular methods sequencing part of the 18 S rDNA. The sequences were classified as Operational Taxonomic Units (OTUs). We found high fungal species richness with OTUs belonging to Glomerales, Diversisporales and Archaeosporales. Despite intensive sampling, the rarefaction curves are still unsaturated for the pristine forest and the reforestation plots. The communities consisted of few frequent and many rare species. No specific interactions are recognizable. The plant individuals are associated with one to ten arbuscular mycorrhizal fungi and mostly with one to four. The fungal compositions associated with single plant individuals show a great variability and variety within one plant species. Planted and naturally occurring plants show high similarities in their fungal communities. Pristine forest and reforestation plots showed similar richness, similar diversity and a significantly nested structure of plant-AMF community. The results indicate that small-scale fragmentation presently found in this area has not destroyed the natural AMF community, at least yet. Thus, the regeneration potential of natural forest vegetation at the tested sites is not inhibited by a lack of appropriate mycobionts. PMID:23671682

  2. Face and body recognition show similar improvement during childhood.

    Science.gov (United States)

    Bank, Samantha; Rhodes, Gillian; Read, Ainsley; Jeffery, Linda

    2015-09-01

    Adults are proficient in extracting identity cues from faces. This proficiency develops slowly during childhood, with performance not reaching adult levels until adolescence. Bodies are similar to faces in that they convey identity cues and rely on specialized perceptual mechanisms. However, it is currently unclear whether body recognition mirrors the slow development of face recognition during childhood. Recent evidence suggests that body recognition develops faster than face recognition. Here we measured body and face recognition in 6- and 10-year-old children and adults to determine whether these two skills show different amounts of improvement during childhood. We found no evidence that they do. Face and body recognition showed similar improvement with age, and children, like adults, were better at recognizing faces than bodies. These results suggest that the mechanisms of face and body memory mature at a similar rate or that improvement of more general cognitive and perceptual skills underlies improvement of both face and body recognition. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis.

    Science.gov (United States)

    Cabrera, Javier; Fenoll, Carmen; Escobar, Carolina

    2015-01-01

    Plant endoparasitic nematodes, root-knot and cyst nematodes (RKNs and CNs) induce within the root vascular cylinder transfer cells used for nourishing, termed giant cells (GCs) and syncytia. Understanding the molecular mechanisms behind this process is essential to develop tools for nematode control. Based on the crucial role in gall development of LBD16, also a key component of the auxin pathway leading to the divisions in the xylem pole pericycle during lateral root (LR) formation, we investigated genes co-regulated with LBD16 in different transcriptomes and analyzed their similarities and differences with those of RKNs and CNs feeding sites (FS). This analysis confirmed LBD16 and its co-regulated genes, integrated in signaling cascades mediated by auxins during LR and callus formation, as a particular feature of RKN-FS distinct to CNs. However, LBD16, and its positively co-regulated genes, were repressed in syncytia, suggesting a selective down- regulation of the LBD16 auxin mediated pathways in CNs-FS. Interestingly, cytokinin-induced genes are enriched in syncytia and we encountered similarities between the transcriptome of shoot regeneration from callus, modulated by cytokinins, and that of syncytia. These findings establish differences in the regulatory networks leading to both FS formation, probably modulated by the auxin/cytokinin balance.

  4. Bipolar I disorder and major depressive disorder show similar brain activation during depression.

    Science.gov (United States)

    Cerullo, Michael A; Eliassen, James C; Smith, Christopher T; Fleck, David E; Nelson, Erik B; Strawn, Jeffrey R; Lamy, Martine; DelBello, Melissa P; Adler, Caleb M; Strakowski, Stephen M

    2014-11-01

    Despite different treatments and courses of illness, depressive symptoms appear similar in major depressive disorder (MDD) and bipolar I disorder (BP-I). This similarity of depressive symptoms suggests significant overlap in brain pathways underlying neurovegetative, mood, and cognitive symptoms of depression. These shared brain regions might be expected to exhibit similar activation in individuals with MDD and BP-I during functional magnetic resonance imaging (fMRI). fMRI was used to compare regional brain activation in participants with BP-I (n = 25) and MDD (n = 25) during a depressive episode as well as 25 healthy comparison (HC) participants. During the scans, participants performed an attentional task that incorporated emotional pictures. During the viewing of emotional images, subjects with BP-I showed decreased activation in the middle occipital gyrus, lingual gyrus, and middle temporal gyrus compared to both subjects with MDD and HC participants. During attentional processing, participants with MDD had increased activation in the parahippocampus, parietal lobe, and postcentral gyrus. However, among these regions, only the postcentral gyrus also showed differences between MDD and HC participants. No differences in cortico-limbic regions were found between participants with BP-I and MDD during depression. Instead, the major differences occurred in primary and secondary visual processing regions, with decreased activation in these regions in BP-I compared to major depression. These differences were driven by abnormal decreases in activation seen in the participants with BP-I. Posterior activation changes are a common finding in studies across mood states in participants with BP-I. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  6. Immature rats show ovulatory defects similar to those in adult rats lacking prostaglandin and progesterone actions

    Directory of Open Access Journals (Sweden)

    Sanchez-Criado Jose E

    2004-09-01

    Full Text Available Abstract Gonadotropin-primed immature rats (GPIR constitute a widely used model for the study of ovulation. Although the equivalence between the ovulatory process in immature and adult rats is generally assumed, the morphological and functional characteristics of ovulation in immature rats have been scarcely considered. We describe herein the morphological aspects of the ovulatory process in GPIR and their response to classical ovulation inhibitors, such as the inhibitor of prostaglandin (PG synthesis indomethacin (INDO and a progesterone (P receptor (PR antagonist (RU486. Immature Wistar rats were primed with equine chorionic gonadotropin (eCG at 21, 23 or 25 days of age, injected with human chorionic gonadotropin (hCG 48 h later, and sacrificed 16 h after hCG treatment, to assess follicle rupture and ovulation. Surprisingly, GPIR showed age-related ovulatory defects close similar to those in adult rats lacking P and PG actions. Rats primed with eCG at 21 or 23 days of age showed abnormally ruptured corpora lutea in which the cumulus-oocyte complex (COC was trapped or had been released to the ovarian interstitum, invading the ovarian stroma and blood and lymphatic vessels. Supplementation of immature rats with exogenous P and/or PG of the E series did not significantly inhibit abnormal follicle rupture. Otherwise, ovulatory defects were practically absent in rats primed with eCG at 25 days of age. GPIR treated with INDO showed the same ovulatory alterations than vehicle-treated ones, although affecting to a higher proportion of follicles. Blocking P actions with RU486 increased the number of COC trapped inside corpora lutea and decreased ovulation. The presence of ovulatory defects in GPIR, suggests that the capacity of the immature ovary to undergo the coordinate changes leading to effective ovulation is not fully established in Wistar rats primed with eCG before 25 days of age.

  7. Plant defenses against parasitic plants show similarities to those induced by herbivores and pathogens

    Science.gov (United States)

    Runyon, Justin B; Mescher, Mark C

    2010-01-01

    Herbivores and pathogens come quickly to mind when one thinks of the biotic challenges faced by plants. Important but less appreciated enemies are parasitic plants, which can have important consequences for the fitness and survival of their hosts. Our knowledge of plant perception, signaling and response to herbivores and pathogens has expanded rapidly in recent years, but information is generally lacking for parasitic species. In a recent paper we reported that some of the same defense responses induced by herbivores and pathogens—notably increases in jasmonic acid (JA), salicylic acid (SA), and a hypersensitive-like response (HLR)—also occur in tomato plants upon attack by the parasitic plant Cuscuta pentagona (field dodder). Parasitism induced a distinct pattern of JA and SA accumulation, and growth trials using genetically-altered tomato hosts suggested that both JA and SA govern effective defenses against the parasite, though the extent of the response varied with host plant age. Here we discuss similarities between the induced responses we observed in response to Cuscuta parasitism to those previously described for herbivores and pathogens and present new data showing that trichomes should be added to the list of plant defenses that act against multiple enemies and across kingdoms. PMID:20495380

  8. Two Genetically Similar H9N2 Influenza A Viruses Show Different Pathogenicity in Mice

    Directory of Open Access Journals (Sweden)

    Qingtao Liu

    2016-11-01

    Full Text Available H9N2 Avian influenza virus has repeatedly infected humans and other mammals, which highlights the need to determine the pathogenicity and the corresponding mechanism of this virus for mammals. In this study, we found two H9N2 viruses with similar genetic background but with different pathogenicity in mice. The A/duck/Nanjing/06/2003 (NJ06 virus was highly pathogenic for mice, with a 50% mouse lethal dose of 102.83 50% egg infectious dose, whereas the A/duck/Nanjing/01/1999 (NJ01 virus was low pathogenic for mice, with a 50% mouse lethal dose of >106.81 50% egg infectious dose. Further studies showed that the NJ06 virus grew faster and reached significantly higher titers than NJ01 in vivo and in vitro. Moreover, the NJ06 virus induced more severe lung lesions, and higher levels of inflammatory cellular infiltration and cytokine response in lungs than NJ01 did. However, only twelve different amino acid residues (HA-K157E, NA-A9T, NA-R435K, PB2-T149P, PB2-K627E, PB1-R187K, PA-L548M, PA-M550L, NP-G127E, NP-P277H, NP-D340N, NS1-D171N were found between the two viruses, and all these residues except for NA-R435K were located in the known functional regions involved in interaction of viral proteins or between the virus and host factors. Summary, our results suggest that multiple amino acid differences may be responsible for the higher pathogenicity of the NJ06 virus for mice, resulting in lethal infection, enhanced viral replication, severe lung lesions, and excessive inflammatory cellular infiltration and cytokine response in lungs. These observations will be helpful for better understanding the pathogenic potential and the corresponding molecular basis of H9N2 viruses that might pose threats to human health in the future.

  9. Methanol extract of grain dust shows complement fixing activity and other characteristics similar to tannic acid.

    Science.gov (United States)

    Skea, D; Broder, I

    1986-01-01

    We have found several similarities between tannic acid and grain dust extract prepared with methanol. Both formed a precipitate with IgG, and these interactions were inhibited by albumin. In addition, both preparations fixed complement; this activity was heat stable and was removed by prior adsorption of the preparations with hide powder. Adsorption with polyvinyl polypyrrolidone reduced the complement-fixing activity of tannic acid but not that of the methanol grain dust extract. The similarities between tannic acid and the methanol grain dust extract are consistent with the presence of a tannin or tanninlike material in grain dust. Images FIGURE 1. PMID:3709479

  10. Defining a similarity threshold for a functional proteinsequence pattern: The signal peptide cleavage site

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; von Heijne, Gunnar

    1996-01-01

    When preparing data sets of amino acid or nucleotide sequences it is necessary to exclude redundant or homologous sequences in order to avoid overestimating the predictive performance of an algorithm. For some time methods for doing this have been available in the area of protein structure...... prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary...

  11. Thyroid hyperfunctioning adenomas with and without Gsp/TSH receptor mutations show similar clinical features.

    Science.gov (United States)

    Arturi, F; Capula, C; Chiefari, E; Filetti, S; Russo, D

    1998-01-01

    Activating mutations of Gs alpha protein (gsp) and TSH receptor (TSH-R) identified in autonomously hyperfunctioning thyroid adenomas have been proposed as the primary event responsible for this disease. Since mutations have not been detected in 100% (ranging from less than 10% to 90%) of the patients, we evaluated whether the presence of gsp and TSH-R mutations cause differences in the clinical and biochemical parameters of the affected patients. Fifteen consecutive patients (11 women and 4 men) with autonomously hyperfunctioning thyroid adenomas who underwent thyroidectomy, previously examined for the presence of gsp or TSH-R mutations, were investigated. In all of the patients we examined plasma free T3, free T4, TSH levels and ultrasound volume of the nodules. The patients with mutations in gsp or TSH-R were similar to the patients without mutations for clinical presentation, sex distribution and mean age. Furthermore, basal serum FT3, TSH and tumor volume in the patients with mutations were not significantly different from the group without mutations. Our preliminary data demonstrate that no significant differences are present in the two groups of patients examined, suggesting that factors other than gsp or TSH-R mutations play a role in the clinical presentation of the disease.

  12. Mortality risk factors show similar trends in modern and historic populations exposed to plague.

    Science.gov (United States)

    Rubini, Mauro; Gualdi-Russo, Emanuela; Manzon, Vanessa S; Rinaldo, Natascia; Bianucci, Raffaella

    2016-05-31

    Plague has been responsible for two major historic pandemics (6th-8th century CE; 14th-19th century CE) and a modern one. The recent Malagasy plague outbreaks raised new concerns on the deadly potential of the plague-causing bacteria Yersinia pestis. Between September 2014 and April 2015, outbreaks of bubonic and pneumonic plague hit the Malagasy population. Two hundred and sixty-three cases, including 71 deaths, have been reported in 16 different districts with a case fatality rate of 27%. The scope of our study was to ascertain whether the risk factors for health in modern-day populations exposed to plague and in ancient populations that faced the two historic pandemics varied or remained substantially unaltered. The risk of mortality of the Malagasy population with those obtained from the reconstruction of three samples of European populations exposed to the historic pandemics was contrasted. The evidence shows that the risks of death are not uniform across age neither in modern nor in historic populations exposed to plague and shows precise concentrations in specific age groups (children between five and nine years of age and young adults). Although in the post-antibiotic era, the fatality rates have drastically reduced, both modern and historic populations were exposed to the same risk factors that are essentially represented by a low standard of environmental hygiene, poor nutrition, and weak health systems.

  13. Men and women show similar survival outcome in stage IV breast cancer.

    Science.gov (United States)

    Wu, San-Gang; Zhang, Wen-Wen; Liao, Xu-Lin; Sun, Jia-Yuan; Li, Feng-Yan; Su, Jing-Jun; He, Zhen-Yu

    2017-08-01

    To evaluate the clinicopathological features, patterns of distant metastases, and survival outcome between stage IV male breast cancer (MBC) and female breast cancer (FBC). Patients diagnosed with stage IV MBC and FBC between 2010 and 2013 were included using the Surveillance, Epidemiology, and End Results program. Univariate and multivariate Cox regression analyses were used to analyze risk factors for overall survival (OS). A total of 4997 patients were identified, including 60 MBC and 4937 FBC. Compared with FBC, patients with MBC were associated with a significantly higher rate of estrogen receptor-positive, progesterone receptor-positive, unmarried, lung metastases, and a lower frequency of liver metastases. Univariate and multivariate analyses showed no significant difference in OS between MBC and FBC. In the propensity score-matched population, there was also no difference in survival between MBC and FBC. Multivariate analysis of MBC showed that OS was longer for patients aged 50-69 years and with estrogen receptor-positive disease. There was no significant difference in survival outcome between stage IV MBC and FBC, but significant differences in clinicopathological features and patterns of metastases between the genders. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Experimental inoculation of calves with atypical Hobi-like pestivirus shows pattern similar to BVDV-1

    DEFF Research Database (Denmark)

    Larska, Magdalena; Polak, Mirosław P.; Uttenthal, Åse

    of experimental inoculation of European cattle with atypical pestivirus. The experiment included 4 groups of 5 calves each inoculated with: BVDV-1 (Ho916), Hobi-like pestivirus (Th/04_KhonKaen), a mixture of both viruses or EaglesMEM (control animals). Th/04_KhonKaen induced milder clinical signs than observed......, lymphocytes and granulocytes in blood on PID 2 correlated to the onset of viraemia. Animals started to seroconvert on PID 14, however the level of anti- Th/04_KhonKaen antibodies was significantly lower that the level of anti-BVDV-1 antibodies, probably due to the specificity of the test used. The experiment...... studies show that the viruses which were thought to be restricted to South America and Southeast Asia, may have reached other continents, including Europe. The pathogenesis of the infection with Hobi-like viruses has not yet been fully elucidated. The purpose of our study was to investigate the course...

  15. Post-cranial skeletons of hypothyroid cretins show a similar anatomical mosaic as Homo floresiensis.

    Science.gov (United States)

    Oxnard, Charles; Obendorf, Peter J; Kefford, Ben J

    2010-09-27

    Human remains, some as recent as 15 thousand years, from Liang Bua (LB) on the Indonesian island of Flores have been attributed to a new species, Homo floresiensis. The definition includes a mosaic of features, some like modern humans (hence derived: genus Homo), some like modern apes and australopithecines (hence primitive: not species sapiens), and some unique (hence new species: floresiensis). Conversely, because only modern humans (H. sapiens) are known in this region in the last 40 thousand years, these individuals have also been suggested to be genetic human dwarfs. Such dwarfs resemble small humans and do not show the mosaic combination of the most complete individuals, LB1 and LB6, so this idea has been largely dismissed. We have previously shown that some features of the cranium of hypothyroid cretins are like those of LB1. Here we examine cretin postcrania to see if they show anatomical mosaics like H. floresiensis. We find that hypothyroid cretins share at least 10 postcranial features with Homo floresiensis and unaffected humans not found in apes (or australopithecines when materials permit). They share with H. floresiensis, modern apes and australopithecines at least 11 postcranial features not found in unaffected humans. They share with H. floresiensis, at least 8 features not found in apes, australopithecines or unaffected humans. Sixteen features can be rendered metrically and multivariate analyses demonstrate that H. floresiensis co-locates with cretins, both being markedly separate from humans and chimpanzees (P0.999). We therefore conclude that LB1 and LB6, at least, are, most likely, endemic cretins from a population of unaffected Homo sapiens. This is consistent with recent hypothyroid endemic cretinism throughout Indonesia, including the nearby island of Bali.

  16. Post-cranial skeletons of hypothyroid cretins show a similar anatomical mosaic as Homo floresiensis.

    Directory of Open Access Journals (Sweden)

    Charles Oxnard

    Full Text Available Human remains, some as recent as 15 thousand years, from Liang Bua (LB on the Indonesian island of Flores have been attributed to a new species, Homo floresiensis. The definition includes a mosaic of features, some like modern humans (hence derived: genus Homo, some like modern apes and australopithecines (hence primitive: not species sapiens, and some unique (hence new species: floresiensis. Conversely, because only modern humans (H. sapiens are known in this region in the last 40 thousand years, these individuals have also been suggested to be genetic human dwarfs. Such dwarfs resemble small humans and do not show the mosaic combination of the most complete individuals, LB1 and LB6, so this idea has been largely dismissed. We have previously shown that some features of the cranium of hypothyroid cretins are like those of LB1. Here we examine cretin postcrania to see if they show anatomical mosaics like H. floresiensis. We find that hypothyroid cretins share at least 10 postcranial features with Homo floresiensis and unaffected humans not found in apes (or australopithecines when materials permit. They share with H. floresiensis, modern apes and australopithecines at least 11 postcranial features not found in unaffected humans. They share with H. floresiensis, at least 8 features not found in apes, australopithecines or unaffected humans. Sixteen features can be rendered metrically and multivariate analyses demonstrate that H. floresiensis co-locates with cretins, both being markedly separate from humans and chimpanzees (P0.999. We therefore conclude that LB1 and LB6, at least, are, most likely, endemic cretins from a population of unaffected Homo sapiens. This is consistent with recent hypothyroid endemic cretinism throughout Indonesia, including the nearby island of Bali.

  17. A mechanical wave system to show waveforms similar to quantum mechanical wavefunctions in a potential

    International Nuclear Information System (INIS)

    Faletič, Sergej

    2015-01-01

    Interviews with students suggest that even though they understand the formalism and the formal nature of quantum theory, they still often desire a mental picture of what the equations describe and some tangible experience with the wavefunctions. Here we discuss a mechanical wave system capable of reproducing correctly a mechanical equivalent of a quantum system in a potential, and the resulting waveforms in principle of any form. We have successfully reproduced the finite potential well, the potential barrier and the parabolic potential. We believe that these mechanical waveforms can provide a valuable experience base for introductory students to start from. We aim to show that mechanical systems that are described with the same mathematics as quantum mechanical, indeed behave in the same way. We believe that even if treated purely as a wave phenomenon, the system provides much insight into wave mechanics. This can be especially useful for physics teachers and others who often need to resort to concepts and experience rather than mathematics when explaining physical phenomena. (paper)

  18. iPads and LCDs show similar performance in the detection of pulmonary nodules

    Science.gov (United States)

    McEntee, Mark F.; Lowe, Joanna; Butler, Marie Louise; Pietrzyk, Mariusz; Evanoff, Michael G.; Ryan, John; Brennan, Patrick C.; Rainford, Louise A.

    2012-02-01

    In February 2011 the University of Chicago Medical School distributed iPads to its trainee doctors for use when reviewing clinical information and images on the ward or clinics. The use of tablet computing devices is becoming widespread in medicine with Apple™ heralding them as "revolutionary" in medicine. The question arises, just because it is technical achievable to use iPads for clinical evaluation of images, should we do so? The current work assesses the diagnostic efficacy of iPads when compared with LCD secondary display monitors for identifying lung nodules on chest x-rays. Eight examining radiologists of the American Board of Radiology were involved in the assessment, reading chest images on both the iPad and the an off-the-shelf LCD monitor. Thirty chest images were shown to each observer, of which 15 had one or more lung nodules. Radiologists were asked to locate the nodules and score how confident they were with their decision on a scale of 1-5. An ROC and JAFROC analysis was performed and modalities were compared using DBM MRMC. The results demonstrate no significant differences in performance between the iPad and the LCD for the ROC AUC (p<0.075) or JAFROC FOM (p<0.059) for random readers and random cases. Sample size estimation showed that this result is significant at a power of 0.8 and an effect size of 0.05 for ROC and 0.07 for JAFROC. This work demonstrates that for the task of identifying pulmonary nodules, the use of the iPad does not significantly change performance compared to an off-the-shelf LCD.

  19. Proposal for a Similar Question Search System on a Q&A Site

    Directory of Open Access Journals (Sweden)

    Katsutoshi Kanamori

    2014-06-01

    Full Text Available There is a service to help Internet users obtain answers to specific questions when they visit a Q&A site. A Q&A site is very useful for the Internet user, but posted questions are often not answered immediately. This delay in answering occurs because in most cases another site user is answering the question manually. In this study, we propose a system that can present a question that is similar to a question posted by a user. An advantage of this system is that a user can refer to an answer to a similar question. This research measures the similarity of a candidate question based on word and dependency parsing. In an experiment, we examined the effectiveness of the proposed system for questions actually posted on the Q&A site. The result indicates that the system can show the questioner the answer to a similar question. However, the system still has a number of aspects that should be improved.

  20. Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison

    Science.gov (United States)

    Sael, Lee; Kihara, Daisuke

    2012-01-01

    Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. PMID:22275074

  1. Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

    Science.gov (United States)

    Sael, Lee; Kihara, Daisuke

    2012-04-01

    Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. Copyright © 2011 Wiley Periodicals, Inc.

  2. Phylogeny, Traits, and Biodiversity of a Neotropical Bat Assemblage: Close Relatives Show Similar Responses to Local Deforestation.

    Science.gov (United States)

    Frank, Hannah K; Frishkoff, Luke O; Mendenhall, Chase D; Daily, Gretchen C; Hadly, Elizabeth A

    2017-08-01

    If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends. We analyzed a 5-year data set (5,011 captures) from 18 sites in a countryside landscape in southern Costa Rica using statistical models that account and correct for imperfect detection of species across sites, spatial autocorrelation, and consideration of spatial scale. Taxonomic and phylogenetic diversity decreased with deforestation, and assemblages became more phylogenetically clustered. Species' responses to deforestation were strongly phylogenetically correlated. Body mass and absolute wing loading explained a substantial portion of species variation in species' habitat preferences, likely related to these traits' influence on maneuverability in cluttered forest environments. Our findings highlight the role that evolutionary history plays in determining which species will survive human impacts and the need to consider diversity metrics, evolutionary history, and traits together when making predictions about species persistence for conservation or ecosystem functioning.

  3. Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

    Science.gov (United States)

    Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

    2013-06-01

    Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

  4. Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

    KAUST Repository

    Marcatili, P.

    2013-05-01

    Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated. Copyright © 2013 by The American Association of Immunologists, Inc.

  5. Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

    KAUST Repository

    Marcatili, P.; Ghiotto, F.; Tenca, C.; Chailyan, A.; Mazzarello, A. N.; Yan, X.-J.; Colombo, M.; Albesiano, E.; Bagnara, D.; Cutrona, G.; Morabito, F.; Bruno, S.; Ferrarini, M.; Chiorazzi, N.; Tramontano, A.; Fais, F.

    2013-01-01

    Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated. Copyright © 2013 by The American Association of Immunologists, Inc.

  6. BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server

    Directory of Open Access Journals (Sweden)

    Jiang Hualiang

    2010-01-01

    Full Text Available Abstract Background Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/structure-based methods have been devised with the aim of deciphering this delicate relationship, there still remain large gaps in this fundamental problem, which continuously drives researchers to develop novel methods to extract relevant information from sequences and structures and to infer the functions of newly identified genes by genomics technology. Results Here we present an ultrafast method, named BSSF(Binding Site Similarity & Function, which enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. After conducting the database searching, the hit list is further analyzed to provide basic statistical information about the occurrences of Gene Ontology terms and Enzyme Commission numbers, which may benefit researchers by helping them to design further experiments to study the query proteins. Conclusions This ultrafast web-based system will not only help researchers interested in drug design and structural genomics to identify similar binding sites, but also assist them by providing further analysis of hit list from database searching.

  7. Activity/inactivity circadian rhythm shows high similarities between young obesity-induced rats and old rats.

    Science.gov (United States)

    Bravo Santos, R; Delgado, J; Cubero, J; Franco, L; Ruiz-Moyano, S; Mesa, M; Rodríguez, A B; Uguz, C; Barriga, C

    2016-03-01

    The objective of the present study was to compare differences between elderly rats and young obesity-induced rats in their activity/inactivity circadian rhythm. The investigation was motivated by the differences reported previously for the circadian rhythms of both obese and elderly humans (and other animals), and those of healthy, young or mature individuals. Three groups of rats were formed: a young control group which was fed a standard chow for rodents; a young obesity-induced group which was fed a high-fat diet for four months; and an elderly control group with rats aged 2.5 years that was fed a standard chow for rodents. Activity/inactivity data were registered through actimetry using infrared actimeter systems in each cage to detect activity. Data were logged on a computer and chronobiological analysis were performed. The results showed diurnal activity (sleep time), nocturnal activity (awake time), amplitude, acrophase, and interdaily stability to be similar between the young obesity-induced group and the elderly control group, but different in the young control group. We have concluded that obesity leads to a chronodisruption status in the body similar to the circadian rhythm degradation observed in the elderly.

  8. Intrinsic atopic dermatitis shows similar TH2 and higher TH17 immune activation compared with extrinsic atopic dermatitis.

    Science.gov (United States)

    Suárez-Fariñas, Mayte; Dhingra, Nikhil; Gittler, Julia; Shemer, Avner; Cardinale, Irma; de Guzman Strong, Cristina; Krueger, James G; Guttman-Yassky, Emma

    2013-08-01

    Atopic dermatitis (AD) is classified as extrinsic and intrinsic, representing approximately 80% and 20% of patients with the disease, respectively. Although sharing a similar clinical phenotype, only extrinsic AD is characterized by high serum IgE levels. Because most patients with AD exhibit high IgE levels, an "allergic"/IgE-mediated disease pathogenesis was hypothesized. However, current models associate AD with T-cell activation, particularly TH2/TH22 polarization, and epidermal barrier defects. We sought to define whether both variants share a common pathogenesis. We stratified 51 patients with severe AD into extrinsic AD (n = 42) and intrinsic AD (n = 9) groups (with similar mean disease activity/SCORAD scores) and analyzed the molecular and cellular skin pathology of lesional and nonlesional intrinsic AD and extrinsic AD by using gene expression (real-time PCR) and immunohistochemistry. A significant correlation between IgE levels and SCORAD scores (r = 0.76, P extrinsic AD. Marked infiltrates of T cells and dendritic cells and corresponding epidermal alterations (keratin 16, Mki67, and S100A7/A8/A9) defined lesional skin of patients with both variants. However, higher activation of all inflammatory axes (including TH2) was detected in patients with intrinsic AD, particularly TH17 and TH22 cytokines. Positive correlations between TH17-related molecules and SCORAD scores were only found in patients with intrinsic AD, whereas only patients with extrinsic AD showed positive correlations between SCORAD scores and TH2 cytokine (IL-4 and IL-5) levels and negative correlations with differentiation products (loricrin and periplakin). Although differences in TH17 and TH22 activation exist between patients with intrinsic AD and those with extrinsic AD, we identified common disease-defining features of T-cell activation, production of polarized cytokines, and keratinocyte responses to immune products. Our data indicate that a TH2 bias is not the sole cause of high Ig

  9. Budesonide/formoterol and formoterol provide similar rapid relief in patients with acute asthma showing refractoriness to salbutamol

    Directory of Open Access Journals (Sweden)

    Lombardi DM

    2006-01-01

    Full Text Available Abstract Background To compare the efficacy and safety of budesonide/formoterol (Symbicort® with formoterol (Oxis® in the treatment of patients with acute asthma who showed evidence of refractoriness to short-acting β2-agonist therapy. Methods In a 3 hour, randomized, double-blind study, a total of 115 patients with acute asthma (mean FEV1 40% of predicted normal and a refractory response to salbutamol (mean reversibility 2% of predicted normal after inhalation of 400 μg, were randomized to receive either budesonide/formoterol (320/9 μg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 1280/36 μg] or formoterol (9 μg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 36 μg]. The primary efficacy variable was the average FEV1 from the first intake of study medication to the measurement at 90 minutes. Secondary endpoints included changes in FEV1 at other timepoints and change in respiratory rate at 180 minutes. Treatment success, treatment failure and patient assessment of the effectiveness of the study medication were also measured. Results FEV1 increased after administration of the study medication in both treatment groups. No statistically significant difference between the treatment groups was apparent for the primary outcome variable, or for any of the other efficacy endpoints. There were no statistically significant between-group differences for treatment success, treatment failure or patient assessment of medication effectiveness. Both treatments were well tolerated. Conclusion Budesonide/formoterol and formoterol provided similarly rapid relief of acute bronchoconstriction in patients with asthma who showed evidence of refractoriness to a short-acting β2-agonist.

  10. Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

    Science.gov (United States)

    May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

    2013-01-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

  11. Searching the protein structure database for ligand-binding site similarities using CPASS v.2

    Directory of Open Access Journals (Sweden)

    Caprez Adam

    2011-01-01

    Full Text Available Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2 database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores

  12. The nonenzymatic subunit of pseutarin C, a prothrombin activator from eastern brown snake (Pseudonaja textilis) venom, shows structural similarity to mammalian coagulation factor V.

    Science.gov (United States)

    Rao, Veena S; Swarup, Sanjay; Kini, R Manjunatha

    2003-08-15

    Pseutarin C is a group C prothrombin activator from the venom of the eastern brown snake Pseudonaja textilis. It is a multi-subunit protein complex consisting of catalytic and nonenzymatic subunits similar to coagulation factor Xa and factor Va, respectively. Here we describe the complete sequence of the nonenzymatic subunit. Based on the partial amino acid sequence of the nonenzymatic subunit, degenerate primers were designed. Using a "walking" strategy based on sequentially designed primers, we determined the complete cDNA sequence of the nonenzymatic subunit. The cDNA encodes a protein of 1461 amino acid residues, which includes a 30-residue signal peptide, a mature protein of 1430 amino acid residues, and a stop codon. cDNA blot analysis showed a single transcript of approximately 4.6 kb. The deduced amino acid sequence shows approximately 50% identity to mammalian factor V and by homology has a similar domain structure consisting of domains A1-A2-B-A3-C1-C2. Interestingly, the B domain of pseutarin C is shorter than that of mammalian factor V (FV). Although most of the proteolytic activation sites are conserved, 2 of 3 proteolytic sites cleaved by activated protein C are mutated, and thus activated protein C is not able to inactivate this procoagulant toxin. The predicted posttranslational modifications, including disulfide bonds, N-glycosylation, phosphorylation, and sulfation, in pseutarin C are significantly different compared with bovine factor V. Thus, our data demonstrate that the nonenzymatic subunit of group C prothrombin activators is structurally similar to mammalian FV.

  13. MRI of Mouse Models for Gliomas Shows Similarities to Humans and Can Be Used to Identify Mice for Preclinical Trials

    Directory of Open Access Journals (Sweden)

    Jason A. Koutcher

    2002-01-01

    Full Text Available Magnetic resonance imaging (MRI has been utilized for screening and detecting brain tumors in mice based upon their imaging characteristics appearance and their pattern of enhancement. Imaging of these tumors reveals many similarities to those observed in humans with identical pathology. Specifically, high-grade murine gliomas have histologic characteristics of glioblastoma multiforme (GBM with contrast enhancement after intravenous administration of gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA, implying disruption of the blood-brain barrier in these tumors. In contrast, low-grade murine oligodendrogliomas do not reveal contrast enhancement, similar to human tumors. MRI can be used to identify mice with brain neoplasms as inclusion criteria in preclinical trials.

  14. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.

    Directory of Open Access Journals (Sweden)

    Rick S Mitchell

    2004-08-01

    Full Text Available The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV, avian sarcoma-leukosis virus (ASLV, and murine leukemia virus (MLV. Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection.

  15. Intrinsic atopic dermatitis (AD) shows similar Th2 and higher Th17 immune activation compared to extrinsic AD

    Science.gov (United States)

    Suárez-Fariñas, M; Dhingra, N; Gittler, J; Shemer, A; Cardinale, I; de Guzman Strong, C; Krueger, JG; Guttman-Yassky, E

    2013-01-01

    Background Atopic dermatitis (AD) is classified as extrinsic (ADe) and intrinsic (ADi), representing approximately 80% and 20% of patients, respectively. While sharing a similar clinical phenotype, only ADe is characterized by high serum IgE. Since most AD patients exhibit high IgE, an “allergic”/IgE-mediated disease pathogenesis was hypothesized. However, current models associate AD with T-cell activation, particularly Th2/Th22 polarization, and epidermal barrier defects. Objective To define if both variants share a common pathogenesis. Methods We stratified 51 severe AD patients as ADe (42) and ADi (9) (with similar mean disease activity/SCORAD), and analyzed the molecular and cellular skin pathology of lesional and non-lesional ADi and ADe using gene-expression (RT-PCR) and immunohistochemistry. Results A significant correlation between IgE levels and SCORAD (r=0.76, pextrinsic and intrinsic AD variants might be treated with T-cell targeted therapeutics or agents that modify keratinocyte responses. PMID:23777851

  16. Meta-analysis shows similar re-bleeding rates among Western and Eastern populations after index video capsule endoscopy.

    Science.gov (United States)

    Tziatzios, Georgios; Gkolfakis, Paraskevas; Hassan, Cesare; Toth, Ervin; Zullo, Angelo; Koulaouzidis, Anastasios; Dimitriadis, George D; Triantafyllou, Konstantinos

    2018-03-01

    Video capsule endoscopy (VCE) is the first-line diagnostic procedure for investigating obscure gastrointestinal bleeding (OGIB). Different re-bleeding rates following index VCE have been reported among Western and Eastern studies. We conducted a comprehensive literature search to identify studies examining re-bleeding rates after VCE for OGIB. Meta-analysis assessed the pooled proportion of re-bleeding events after VCE for OGIB according to study's origin (Western vs. Eastern) and according to the length of follow-up (≥24 months vs. Western and 16 Eastern) studies with 5796 patients. Significant heterogeneity was detected among meta-analyzed studies. Overall, the pooled re-bleeding rate was similar between Western (29%; 95% CI: 23-34) and Eastern (21%; 95% CI: 15-27) populations, irrespective of the length of follow-up. The odds of re-bleeding was significantly higher after positive as compared to negative index VCE in Eastern studies (OR: 1.77; 95% CI: 1.07-2.94). Application of specific treatment after positive index VCE was associated with lower re-bleeding odds in both Western (OR: 0.37; 95% CI: 0.16-0.87) and Eastern (OR: 0.39; 95% CI: 0.21-0.72) populations. Patients undergoing VCE for OGIB have similar re-bleeding rates in the East and the West, regardless of the length of follow-up. However, increased re-bleeding odds after positive index VCE is observed in Eastern studies. Copyright © 2018 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  17. MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

    Science.gov (United States)

    Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

    2014-08-01

    We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

  18. Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design

    Science.gov (United States)

    Howard, Brittany L.; Thompson, Philip E.; Manallack, David T.

    2011-08-01

    The similarity between Plasmodium falciparum phosphodiesterase enzymes ( PfPDEs) and their human counterparts have been examined and human PDE9A was found to be a suitable template for the construction of homology models for each of the four PfPDE isoforms. In contrast, the architecture of the active sites of each model was most similar to human PDE1. Molecular docking was able to model cyclic guanosine monophosphate (cGMP) substrate binding in each case but a docking mode supporting cyclic adenosine monophosphate (cAMP) binding could not be found. Anticipating the potential of PfPDE inhibitors as anti-malarial drugs, a range of reported PDE inhibitors including zaprinast and sildenafil were docked into the model of PfPDEα. The results were consistent with their reported biological activities, and the potential of PDE1/9 inhibitor analogues was also supported by docking.

  19. Children with social anxiety and other anxiety disorders show similar deficits in habitual emotional regulation: evidence for a transdiagnostic phenomenon.

    Science.gov (United States)

    Keil, Verena; Asbrand, Julia; Tuschen-Caffier, Brunna; Schmitz, Julian

    2017-07-01

    Deficits in emotion regulation (ER) are an important factor in maintaining social anxiety disorder (SAD) in adults. As SAD and ER problems typically develop during childhood and adolescence, and are maintained dynamically within the parent-child dyad, research on families can help to reveal the role ER plays in the early development of SAD. The current study assessed self-reported habitual ER in dyads of children with SAD (n = 31), children with mixed anxiety disorders (MAD; n = 41) and healthy control children (HC; n = 36), and their parents. Results indicate a transdiagnostic quality of ER in that, children with SAD and children with MAD similarly reported less adaptive and more maladaptive ER strategies than HC children, whereas no group differences in parental ER strategies emerged. Furthermore, children's ER strategies aggressive action, withdrawal and self-devaluation and the parental ER strategy reappraisal were associated with social anxiety symptoms. These results suggest that there may be deficits in ER which generalize across childhood anxiety disorders. Our results are discussed in relation to current theories and their implications for treatment of childhood SAD.

  20. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish.

    Science.gov (United States)

    Symonová, Radka; Majtánová, Zuzana; Arias-Rodriguez, Lenin; Mořkovský, Libor; Kořínková, Tereza; Cavin, Lionel; Pokorná, Martina Johnson; Doležálková, Marie; Flajšhans, Martin; Normandeau, Eric; Ráb, Petr; Meyer, Axel; Bernatchez, Louis

    2017-11-01

    Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process. © 2016 Wiley Periodicals, Inc.

  1. 68Ga/177Lu-labeled DOTA-TATE shows similar imaging and biodistribution in neuroendocrine tumor model.

    Science.gov (United States)

    Liu, Fei; Zhu, Hua; Yu, Jiangyuan; Han, Xuedi; Xie, Qinghua; Liu, Teli; Xia, Chuanqin; Li, Nan; Yang, Zhi

    2017-06-01

    Somatostatin receptors are overexpressed in neuroendocrine tumors, whose endogenous ligands are somatostatin. DOTA-TATE is an analogue of somatostatin, which shows high binding affinity to somatostatin receptors. We aim to evaluate the 68 Ga/ 177 Lu-labeling DOTA-TATE kit in neuroendocrine tumor model for molecular imaging and to try human-positron emission tomography/computed tomography imaging of 68 Ga-DOTA-TATE in neuroendocrine tumor patients. DOTA-TATE kits were formulated and radiolabeled with 68 Ga/ 177 Lu for 68 Ga/ 177 Lu-DOTA-TATE (M-DOTA-TATE). In vitro and in vivo stability of 177 Lu-DOTA-TATE were performed. Nude mice bearing human tumors were injected with 68 Ga-DOTA-TATE or 177 Lu-DOTA-TATE for micro-positron emission tomography and micro-single-photon emission computed tomography/computed tomography imaging separately, and clinical positron emission tomography/computed tomography images of 68 Ga-DOTA-TATE were obtained at 1 h post-intravenous injection from patients with neuroendocrine tumors. Micro-positron emission tomography and micro-single-photon emission computed tomography/computed tomography imaging of 68 Ga-DOTA-TATE and 177 Lu-DOTA-TATE both showed clear tumor uptake which could be blocked by excess DOTA-TATE. In addition, 68 Ga-DOTA-TATE-positron emission tomography/computed tomography imaging in neuroendocrine tumor patients could show primary and metastatic lesions. 68 Ga-DOTA-TATE and 177 Lu-DOTA-TATE could accumulate in tumors in animal models, paving the way for better clinical peptide receptor radionuclide therapy for neuroendocrine tumor patients in Asian population.

  2. Biologic and Conventional Systemic Therapies Show Similar Safety and Efficacy in Elderly and Adult Patients With Moderate to Severe Psoriasis.

    Science.gov (United States)

    Garber, Caren; Plotnikova, Natalia; Au, Shiu-chung; Sorensen, Eric P; Gottlieb, Alice

    2015-08-01

    Despite the aging population, few studies have documented the treatment of geriatric psoriasis. The purpose of this study is to compare the efficacy, safety, and prescribing patterns of biologics and conventional systemic medications in elderly versus adult psoriasis. All patient visits coded for psoriasis or psoriatic arthritis (ICD-9 696.1 or 696.0) at the Tufts Medical Center General Dermatology Clinic from January 1, 2008, to March 1, 2015 were included in this retrospective cohort study. The outcome measure used was the validated simple-measure for assessing psoriasis activity (S-MAPA), the product of the physician's global assessment and the body surface area. 194 patients who underwent 278 treatment courses were included in the study. 48 patients were included in the elderly cohort (≥ 65 years old) and 146 in the adult cohort (18-64 years old). There was no significant difference in S-MAPA improvement at 12 weeks between the two cohorts when treated with biologics (42.92% improvement in adults, 48.77% in elderly; P=0.498) or conventional systemics (43.96% and 51.82%, respectively; P=0.448). Within the elderly cohort, there was no significant difference in efficacy of biologics versus conventional systemics at any time point. Topical prescription rates were significantly higher in the elderly cohort ( P=0.004) while biologic prescription rates were significantly lower ( P=0.014) despite the same baseline S-MAPA in both age groups. For both biologics and conventional systemics, there was no statistically significant intergroup difference in the rate of adverse events ( P=0.322 for biologics; P=0.581 for conventional systemics) or infection ( P=0.753 for biologics; P=0.828 for conventional systemics). Within the elderly cohort, there was a higher rate of adverse events with conventional systemic treatment than with biologic treatment ( P=0.033). This study provides preliminary evidence to suggest that biologic and conventional systemic therapies are similarly

  3. Prioritizing sites for conservation based on similarity to historical baselines and feasibility of protection.

    Science.gov (United States)

    Popejoy, Traci; Randklev, Charles R; Neeson, Thomas M; Vaughn, Caryn C

    2018-05-08

    The shifting baseline syndrome concept advocates for the use of historical knowledge to inform conservation baselines, but does not address the feasibility of restoring sites to those baselines. In many regions, conservation feasibility varies among sites due to differences in resource availability, statutory power, and land-owner participation. We use zooarchaeological records to identify a historical baseline of the freshwater mussel community's composition before Euro-American influence at a river-reach scale. We evaluate how the community reference position and the feasibility of conservation might enable identification of sites where conservation actions would preserve historically representative communities and be likely to succeed. We first present a conceptual model that incorporates community information and landscape factors to link the best conservation areas to potential cost and conservation benefits. Using fuzzy ordination, we identify modern mussel beds that are most like the historical baseline. We then quantify the housing density and land use near each reach to estimate feasibility of habitat restoration. Using our conceptual framework, we identify reaches that have high conservation value (i.e., reaches that contain the best mussel beds) and where restoration actions would be most likely to succeed. Reaches above Lake Belton in central Texas, U.S.A. were most similar in species composition and relative abundance to zooarchaeological sites. A subset of these mussel beds occurred in locations where conservation actions appear to be most feasible. This study demonstrates how to use zooarchaeological data (biodiversity data often readily available) and estimates of conservation feasibility to inform conservation priorities at a local spatial scale. This article is protected by copyright. All rights reserved.

  4. Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity to Historical Virulent Isolates from the 1940s

    Science.gov (United States)

    Dimitrov, Kiril M.; Lee, Dong-Hun; Williams-Coplin, Dawn; Olivier, Timothy L.; Miller, Patti J.

    2016-01-01

    Virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), a devastating disease of poultry and wild birds. Phylogenetic analyses clearly distinguish historical isolates (obtained prior to 1960) from currently circulating viruses of class II genotypes V, VI, VII, and XII through XVIII. Here, partial and complete genomic sequences of recent virulent isolates of genotypes II and IX from China, Egypt, and India were found to be nearly identical to those of historical viruses isolated in the 1940s. Phylogenetic analysis, nucleotide distances, and rates of change demonstrate that these recent isolates have not evolved significantly from the most closely related ancestors from the 1940s. The low rates of change for these virulent viruses (7.05 × 10−5 and 2.05 × 10−5 per year, respectively) and the minimal genetic distances existing between these and historical viruses (0.3 to 1.2%) of the same genotypes indicate an unnatural origin. As with any other RNA virus, Newcastle disease virus is expected to evolve naturally; thus, these findings suggest that some recent field isolates should be excluded from evolutionary studies. Furthermore, phylogenetic analyses show that these recent virulent isolates are more closely related to virulent strains isolated during the 1940s, which have been and continue to be used in laboratory and experimental challenge studies. Since the preservation of viable viruses in the environment for over 6 decades is highly unlikely, it is possible that the source of some of the recent virulent viruses isolated from poultry and wild birds might be laboratory viruses. PMID:26888902

  5. CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

    Directory of Open Access Journals (Sweden)

    Li Gong-Hua

    2010-08-01

    Full Text Available Abstract Background The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB, thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been developed to predict protein function, but these methods need to be improved further, such as, enhancing the accuracy, sensitivity, and the computational speed. Here, an accurate algorithm, the CMASA (Contact MAtrix based local Structural Alignment algorithm, has been developed to predict unknown functions of proteins based on the local protein structural similarity. This algorithm has been evaluated by building a test set including 164 enzyme families, and also been compared to other methods. Results The evaluation of CMASA shows that the CMASA is highly accurate (0.96, sensitive (0.86, and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function and SPASM (a local structure alignment method; and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods. The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA. Conclusions The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the

  6. Blood donor show behaviour after an invitation to donate : The influence of collection site factors

    NARCIS (Netherlands)

    Merz, E.-M.; Zijlstra, B.J.H.; de Kort, W.L.A.M.

    2017-01-01

    Background and Objectives Show behaviour after invitation to donate varies considerably across donors. More insight into this variation is important for blood banks in achieving stable stocks. This study examined individual factors determining intended show behaviour. Most importantly, however, this

  7. Blood donor show behavior after an invitation to donate: The influence of collection site factors

    NARCIS (Netherlands)

    Merz, E.M.; Zijlstra, Bonne; De Kort, Wim L.A.M.

    2017-01-01

    Background and Objectives Show behaviour after invitation to donate varies considerably across donors. More insight into this variation is important for blood banks in achieving stable stocks. This study examined individual factors determining intended show behaviour. Most importantly, however, this

  8. An Investigation of Equine Mesenchymal Stem Cell Characteristics from Different Harvest Sites: More Similar Than Not

    Directory of Open Access Journals (Sweden)

    Karla eLombana

    2015-12-01

    Full Text Available Diseases of the musculoskeletal system are a major cause of loss of use and retirement in sport horses. The use of bone marrow derived mesenchymal stem cells (BMDMSCs for healing of traumatized tissue has gained substantial favor in clinical settings and can assist healing and tissue regeneration in orthopaedic injuries. There are two common sites of harvest of BMDMSCs, the sternum and ilium. Our objective was to determine if any differences exist in BMDMSCs acquired from the sternum and the ilium. We compared the two harvest sites in their propensity to undergo multilineage differentiation, differences in cell surface markers or gene transduction efficiencies.BMDMSCs were isolated and culture-expanded from five mL aspirates of bone marrow from sternum and ilium. The cells were then plated and cultured with appropriate differentiation medium to result in multi-lineage differentiation and cell characteristics were compared between sternal and ilial samples. Cell surface antibody expression of CD11a/18, CD34, CD44 and CD90 were evaluated using flow cytometry and gene transduction efficiencies were evaluated using GFP scAAV. There were no statistically significant differences in cell characteristics between MSCs cultured from sternum and ilium under any circumstances.

  9. Avoiding competition? Site use, diet and foraging behaviours in two similarly sized geese wintering in China

    DEFF Research Database (Denmark)

    Zhao, Meijuan; Cao, Lei; Klaassen, Marcel

    2015-01-01

    at Shengjin Lake, China. To examine the potential for coexistence and possible avoidance strategies, we studied (1) their habitat use, (2) foraging behaviours and (3) diets of birds foraging in mixed- and single-species flocks. Both species extensively exploited sedge meadows, where they showed considerable...

  10. Carbon dioxide exchange in three tundra sites show a dissimilar response to environmental variables

    DEFF Research Database (Denmark)

    Mbufong, Herbert Njuabe; Lund, Magnus; Christensen, Torben Røjle

    2015-01-01

    variability. An improved understanding of the control of ancillary variables on net ecosystem exchange (NEE), gross primary production (GPP) and ecosystem respiration (Re) will improve the accuracy with which CO2 exchange seasonality in Arctic tundra ecosystems is modelled. Fluxes were measured with the eddy...... Lake. Growing season NEE correlated mainly to cumulative radiation and temperature-related variables at Zackenberg, while at Daring Lake the same variables showed significant correlations with the partitioned fluxes (GPP and Re). Stordalen was temperature dependent during the growing season. This study...

  11. Does cross-taxon analysis show similarity in diversity patterns between vascular plants and bryophytes? Some answers from a literature review.

    Science.gov (United States)

    Bagella, Simonetta

    2014-04-01

    The objective of this study was to clarify the taxon surrogacy hypothesis relative to vascular plants and bryophytes. A literature review was conducted to obtain papers that met the following criteria: (i) they examined species richness values; or (ii) they evaluated the species richness within the same study sites, or under the same spatial variation conditions. Twenty-seven papers were accessed. The richness of the two taxa, compared in 32 cases, positively co-varied in about half of the comparisons. The response to the spatial variation in environmental or human-induced factors of the two taxa in terms of species richness was rather variable. Based on current knowledge, the main documented findings regard forest habitats and nival gradients. In forest habitats, co-variation in species richness is likely when similar environments are analysed and seems to be strengthened for boreal forests. Along the nival gradient, a different response in terms of richness of the two taxa suggests that vascular plants cannot be considered good surrogates for bryophytes. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  12. Myalgic encephalomyelitis/chronic fatigue syndrome and encephalomyelitis disseminata/multiple sclerosis show remarkable levels of similarity in phenomenology and neuroimmune characteristics

    Science.gov (United States)

    2013-01-01

    Background ‘Encephalomyelitis disseminata’ (multiple sclerosis) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are both classified as diseases of the central nervous system by the World Health Organization. This review aims to compare the phenomenological and neuroimmune characteristics of MS with those of ME/CFS. Discussion There are remarkable phenomenological and neuroimmune overlaps between both disorders. Patients with ME/CFS and MS both experience severe levels of disabling fatigue and a worsening of symptoms following exercise and resort to energy conservation strategies in an attempt to meet the energy demands of day-to-day living. Debilitating autonomic symptoms, diminished cardiac responses to exercise, orthostatic intolerance and postural hypotension are experienced by patients with both illnesses. Both disorders show a relapsing-remitting or progressive course, while infections and psychosocial stress play a large part in worsening of fatigue symptoms. Activated immunoinflammatory, oxidative and nitrosative (O+NS) pathways and autoimmunity occur in both illnesses. The consequences of O+NS damage to self-epitopes is evidenced by the almost bewildering and almost identical array of autoantibodies formed against damaged epitopes seen in both illnesses. Mitochondrial dysfunctions, including lowered levels of ATP, decreased phosphocreatine synthesis and impaired oxidative phosphorylation, are heavily involved in the pathophysiology of both MS and ME/CFS. The findings produced by neuroimaging techniques are quite similar in both illnesses and show decreased cerebral blood flow, atrophy, gray matter reduction, white matter hyperintensities, increased cerebral lactate and choline signaling and lowered acetyl-aspartate levels. Summary This review shows that there are neuroimmune similarities between MS and ME/CFS. This further substantiates the view that ME/CFS is a neuroimmune illness and that patients with MS are immunologically primed to

  13. Phenobarbital and propiconazole toxicogenomic profiles in mice show major similarities consistent with the key role that constitutive androstane receptor (CAR) activation plays in their mode of action

    Science.gov (United States)

    Currie, Richard A.; Peffer, Richard C.; Goetz, Amber K.; Omiecinski, Curtis J.; Goodman, Jay I.

    2014-01-01

    Toxicogenomics (TGx) is employed frequently to investigate underlying molecular mechanisms of the compound of interest and, thus, has become an aid to mode of action determination. However, the results and interpretation of a TGx dataset are influenced by the experimental design and methods of analysis employed. This article describes an evaluation and reanalysis, by two independent laboratories, of previously published TGx mouse liver microarray data for a triazole fungicide, propiconazole (PPZ), and the anticonvulsant drug phenobarbital (PB). Propiconazole produced an increase incidence of liver tumors in male CD-1 mice only at a dose that exceeded the maximum tolerated dose (2500 ppm). Firstly, we illustrate how experimental design differences between two in vivo studies with PPZ and PB may impact the comparisons of TGx results. Secondly, we demonstrate that different researchers using different pathway analysis tools can come to different conclusions on specific mechanistic pathways, even when using the same datasets. Finally, despite these differences the results across three different analyses also show a striking degree of similarity observed for PPZ and PB treated livers when the expression data are viewed as major signaling pathways and cell processes affected. Additional studies described here show that the postulated key event of hepatocellular proliferation was observed in CD-1 mice for both PPZ and PB, and that PPZ is also a potent activator of the mouse CAR nuclear receptor. Thus, with regard to the events which are hallmarks of CAR-induced effects that are key events in the mode of action (MOA) of mouse liver carcinogenesis with PB, PPZ-induced tumors can be viewed as being promoted by a similar PB-like CAR-dependent MOA. PMID:24675475

  14. Phenobarbital and propiconazole toxicogenomic profiles in mice show major similarities consistent with the key role that constitutive androstane receptor (CAR) activation plays in their mode of action

    International Nuclear Information System (INIS)

    Currie, Richard A.; Peffer, Richard C.; Goetz, Amber K.; Omiecinski, Curtis J.; Goodman, Jay I.

    2014-01-01

    Toxicogenomics (TGx) is employed frequently to investigate underlying molecular mechanisms of the compound of interest and, thus, has become an aid to mode of action determination. However, the results and interpretation of a TGx dataset are influenced by the experimental design and methods of analysis employed. This article describes an evaluation and reanalysis, by two independent laboratories, of previously published TGx mouse liver microarray data for a triazole fungicide, propiconazole (PPZ), and the anticonvulsant drug phenobarbital (PB). Propiconazole produced an increase incidence of liver tumors in male CD-1 mice only at a dose that exceeded the maximum tolerated dose (2500 ppm). Firstly, we illustrate how experimental design differences between two in vivo studies with PPZ and PB may impact the comparisons of TGx results. Secondly, we demonstrate that different researchers using different pathway analysis tools can come to different conclusions on specific mechanistic pathways, even when using the same datasets. Finally, despite these differences the results across three different analyses also show a striking degree of similarity observed for PPZ and PB treated livers when the expression data are viewed as major signaling pathways and cell processes affected. Additional studies described here show that the postulated key event of hepatocellular proliferation was observed in CD-1 mice for both PPZ and PB, and that PPZ is also a potent activator of the mouse CAR nuclear receptor. Thus, with regard to the events which are hallmarks of CAR-induced effects that are key events in the mode of action (MOA) of mouse liver carcinogenesis with PB, PPZ-induced tumors can be viewed as being promoted by a similar PB-like CAR-dependent MOA

  15. ASD Is Not DLI: Individuals With Autism and Individuals With Syntactic DLI Show Similar Performance Level in Syntactic Tasks, but Different Error Patterns

    Directory of Open Access Journals (Sweden)

    Nufar Sukenik

    2018-04-01

    Full Text Available Do individuals with autism have a developmental syntactic impairment, DLI (formerly known as SLI? In this study we directly compared the performance of 18 individuals with Autism Spectrum Disorder (ASD aged 9;0–18;0 years with that of 93 individuals with Syntactic-Developmental Language Impairment (SyDLI aged 8;8–14;6 (and with 166 typically-developing children aged 5;2–18;1. We tested them using three syntactic tests assessing the comprehension and production of syntactic structures that are known to be sensitive to syntactic impairment: elicitation of subject and object relative clauses, reading and paraphrasing of object relatives, and repetition of complex syntactic structures including Wh questions, relative clauses, topicalized sentences, sentences with verb movement, sentences with A-movement, and embedded sentences. The results were consistent across the three tasks: the overall rate of correct performance on the syntactic tasks is similar for the children with ASD and those with SyDLI. However, once we look closer, they are very different. The types of errors of the ASD group differ from those of the SyDLI group—the children with ASD provide various types of pragmatically infelicitous responses that are not evinced in the SyDLI or in the age equivalent typically-developing groups. The two groups (ASD and SyDLI also differ in the pattern of performance—the children with SyDLI show a syntactically-principled pattern of impairment, with selective difficulty in specific sentence types (such as sentences derived by movement of the object across the subject, and normal performance on other structures (such as simple sentences. In contrast, the ASD participants showed generalized low performance on the various sentence structures. Syntactic performance was far from consistent within the ASD group. Whereas all ASD participants had errors that can originate in pragmatic/discourse difficulties, seven of them had completely normal syntax

  16. ASD Is Not DLI: Individuals With Autism and Individuals With Syntactic DLI Show Similar Performance Level in Syntactic Tasks, but Different Error Patterns.

    Science.gov (United States)

    Sukenik, Nufar; Friedmann, Naama

    2018-01-01

    Do individuals with autism have a developmental syntactic impairment, DLI (formerly known as SLI)? In this study we directly compared the performance of 18 individuals with Autism Spectrum Disorder (ASD) aged 9;0-18;0 years with that of 93 individuals with Syntactic-Developmental Language Impairment (SyDLI) aged 8;8-14;6 (and with 166 typically-developing children aged 5;2-18;1). We tested them using three syntactic tests assessing the comprehension and production of syntactic structures that are known to be sensitive to syntactic impairment: elicitation of subject and object relative clauses, reading and paraphrasing of object relatives, and repetition of complex syntactic structures including Wh questions, relative clauses, topicalized sentences, sentences with verb movement, sentences with A-movement, and embedded sentences. The results were consistent across the three tasks: the overall rate of correct performance on the syntactic tasks is similar for the children with ASD and those with SyDLI. However, once we look closer, they are very different. The types of errors of the ASD group differ from those of the SyDLI group-the children with ASD provide various types of pragmatically infelicitous responses that are not evinced in the SyDLI or in the age equivalent typically-developing groups. The two groups (ASD and SyDLI) also differ in the pattern of performance-the children with SyDLI show a syntactically-principled pattern of impairment, with selective difficulty in specific sentence types (such as sentences derived by movement of the object across the subject), and normal performance on other structures (such as simple sentences). In contrast, the ASD participants showed generalized low performance on the various sentence structures. Syntactic performance was far from consistent within the ASD group. Whereas all ASD participants had errors that can originate in pragmatic/discourse difficulties, seven of them had completely normal syntax in the structures we

  17. Feline bone marrow-derived mesenchymal stromal cells (MSCs) show similar phenotype and functions with regards to neuronal differentiation as human MSCs.

    Science.gov (United States)

    Munoz, Jessian L; Greco, Steven J; Patel, Shyam A; Sherman, Lauren S; Bhatt, Suresh; Bhatt, Rekha S; Shrensel, Jeffrey A; Guan, Yan-Zhong; Xie, Guiqin; Ye, Jiang-Hong; Rameshwar, Pranela; Siegel, Allan

    2012-09-01

    Mesenchymal stromal cells (MSCs) show promise for treatment of a variety of neurological and other disorders. Cat has a high degree of linkage with the human genome and has been used as a model for analysis of neurological disorders such as stroke, Alzheimer's disease and motor disorders. The present study was designed to characterize bone marrow-derived MSCs from cats and to investigate the capacity to generate functional peptidergic neurons. MSCs were expanded with cells from the femurs of cats and then characterized by phenotype and function. Phenotypically, feline and human MSCs shared surface markers, and lacked hematopoietic markers, with similar morphology. As compared to a subset of human MSCs, feline MSCs showed no evidence of the major histocompatibility class II. Since the literature suggested Stro-1 as an indicator of pluripotency, we compared early and late passages feline MSCs and found its expression in >90% of the cells. However, the early passage cells showed two distinct populations of Stro-1-expressing cells. At passage 5, the MSCs were more homogeneous with regards to Stro-1 expression. The passage 5 MSCs differentiated to osteogenic and adipogenic cells, and generated neurons with electrophysiological properties. This correlated with the expression of mature neuronal markers with concomitant decrease in stem cell-associated genes. At day 12 induction, the cells were positive for MAP2, Neuronal Nuclei, tubulin βIII, Tau and synaptophysin. This correlated with electrophysiological maturity as presented by excitatory postsynaptic potentials (EPSPs). The findings indicate that the cat may constitute a promising biomedical model for evaluation of novel therapies such as stem cell therapy in such neurological disorders as Alzheimer's disease and stroke. Copyright © 2012 International Society of Differentiation. Published by Elsevier B.V. All rights reserved.

  18. A duck hepatitis B virus strain with a knockout mutation in the putative X ORF shows similar infectivity and in vivo growth characteristics to wild-type virus

    International Nuclear Information System (INIS)

    Meier, P.; Scougall, C.A.; Will, H.; Burrell, C.J.; Jilbert, A.R.

    2003-01-01

    Hepadnaviruses including human hepatitis B virus (HBV) and duck hepatitis B virus (DHBV) express X proteins, HBx and DHBx, respectively. Both HBx and DHBx are transcriptional activators and modulate cellular signaling in in vitro assays. To test whether the DHBx protein plays a role in virus infection, we compared the in vivo infectivity and growth characteristics of a DHBV3 strain with a stop codon in the X-like ORF (DHBV3-X-K.O.) to those of the wild-type DHBV3 strain. Here we report that the two strains showed no significant difference in (i) their ability to induce infection that resulted in stable viraemia measured by serum surface antigen (DHBsAg) and DHBV DNA, and detection of viral proteins and replicative DNA intermediates in the liver; (ii) the rate of spread of infection in liver and extrahepatic sites after low-dose virus inoculation; and (iii) the ability to produce transient or persistent infection under balanced age/dose conditions designed to detect small differences between the strains. Thus, none of the infection parameters assayed were detectably affected by the X-ORF knockout mutation, raising the question whether DHBx expression plays a physiological role during in vivo infection with wild-type DHBV

  19. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.

    Science.gov (United States)

    Konc, Janez; Janezic, Dusanka

    2012-07-01

    The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.

  20. Highly similar prokaryotic communities of sunken wood at shallow and deep-sea sites across the oceans.

    Science.gov (United States)

    Palacios, Carmen; Zbinden, Magali; Pailleret, Marie; Gaill, Françoise; Lebaron, Philippe

    2009-11-01

    With an increased appreciation of the frequency of their occurrence, large organic falls such as sunken wood and whale carcasses have become important to consider in the ecology of the oceans. Organic-rich deep-sea falls may play a major role in the dispersal and evolution of chemoautotrophic communities at the ocean floor, and chemosynthetic symbiotic, free-living, and attached microorganisms may drive the primary production at these communities. However, little is known about the microbiota thriving in and around organic falls. Our aim was to investigate and compare free-living and attached communities of bacteria and archaea from artificially immersed and naturally sunken wood logs with varying characteristics at several sites in the deep sea and in shallow water to address basic questions on the microbial ecology of sunken wood. Multivariate indirect ordination analyses of capillary electrophoresis single-stranded conformation polymorphisms (CE-SSCP) fingerprinting profiles demonstrated high similarity of bacterial and archaeal assemblages present in timbers and logs situated at geographically distant sites and at different depths of immersion. This similarity implies that wood falls harbor a specialized microbiota as observed in other ecosystems when the same environmental conditions reoccur. Scanning and transmission electron microscopy observations combined with multivariate direct gradient analysis of Bacteria CE-SSCP profiles demonstrate that type of wood (hard vs. softwood), and time of immersion are important in structuring sunken wood bacterial communities. Archaeal populations were present only in samples with substantial signs of decay, which were also more similar in their bacterial assemblages, providing indirect evidence of temporal succession in the microbial communities that develop in and around wood falls.

  1. A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Tony Håndstad

    Full Text Available BACKGROUND: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS is key to inferring transcription factor regulatory networks. Several methods for predicting TFBS exist, but there are no standard genome-wide datasets on which to assess the performance of these prediction methods. Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial. RESULTS: Here we use published ChIP-seq data and an improved peak detection method to create comprehensive benchmark datasets for prediction methods which use known descriptors or binding motifs to detect TFBS in genomic sequences. We use this benchmark to assess the performance of five different prediction methods and find that the methods that use information about sequence conservation generally perform better than simpler motif-scanning methods. The difference is greater on high-affinity peaks and when using short and information-poor motifs. However, if the motifs are specific and information-rich, we find that simple motif-scanning methods can perform better than conservation-based methods. CONCLUSIONS: Our benchmark provides a comprehensive test that can be used to rank the relative performance of transcription factor binding site prediction methods. Moreover, our results show that, contrary to previous reports, sequence conservation is better suited for predicting strong than weak transcription factor binding sites.

  2. The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove

    DEFF Research Database (Denmark)

    Champion, Elise; Remaud-Simeon, Magali; Skov, Lars Kobberøe

    2009-01-01

    Glycoside hydrolase family 13 (GH-13) mainly contains starch-degrading or starch-modifying enzymes. Sucrose hydrolases utilize sucrose instead of amylose as the primary glucosyl donor. Here, the catalytic properties and X-ray structure of sucrose hydrolase from Xanthomonas campestris pv. campestris...... of GH-13. Comparisons with structures of the highly similar sucrose hydrolase from X. axonopodis pv. glycines most notably showed that residues Arg516 and Asp138, which form a salt bridge in the X. axonopodis sucrose complex and define part of the subsite -1 glucosyl-binding determinants...

  3. Tianeptine, olanzapine and fluoxetine show similar restoring effects on stress induced molecular changes in mice brain: An FT-IR study

    Science.gov (United States)

    Türker-Kaya, Sevgi; Mutlu, Oğuz; Çelikyurt, İpek K.; Akar, Furuzan; Ulak, Güner

    2016-05-01

    Chronic stress which can cause a variety of disorders and illness ranging from metabolic and cardiovascular to mental leads to alterations in content, structure and dynamics of biomolecules in brain. The determination of stress-induced changes along with the effects of antidepressant treatment on these parameters might bring about more effective therapeutic strategies. In the present study, we investigated unpredictable chronic mild stress (UCMS)-induced changes in biomolecules in mouse brain and the restoring effects of tianeptine (TIA), olanzapine (OLZ) and fluoxetine (FLX) on these variations, by Fourier transform infrared (FT-IR) spectroscopy. The results revealed that chronic stress causes different membrane packing and an increase in lipid peroxidation, membrane fluidity. A significant increment for lipid/protein, Cdbnd O/lipid, CH3/lipid, CH2/lipid, PO-2/lipid, COO-/lipid and RNA/protein ratios but a significant decrease for lipid/protein ratios were also obtained. Additionally, altered protein secondary structure components were estimated, such as increment in random coils and beta structures. The administration of TIA, OLZ and FLX drugs restored these stress-induced variations except for alterations in protein structure and RNA/protein ratio. This may suggest that these drugs have similar restoring effects on the consequences of stress activity in brain, in spite of the differences in their action mechanisms. All findings might have importance in understanding molecular mechanisms underlying chronic stress and contribute to studies aimed for drug development.

  4. Similarity of nutrient uptake and root dimensions of Engelmann spruce and subalpine fir at two contrasting sites in Colorado

    Energy Technology Data Exchange (ETDEWEB)

    Yanai, R; McFarlane, K; Lucash, M; Kulpa, S; Wood, D

    2009-10-09

    were indistinguishable in specific root length and diameter distribution, while most of the other ten species had statistically distinct diameter distributions across five diameter classes < 2 mm. Based on specific root length, subalpine fir and Engelmann spruce had significantly coarser roots than red pine (Pinus resinosa Soland), yellow birch (Betula allegheniensis Britt.), sugar maple (Acer saccharum Marsh.), chestnut oak (Quercus prinus L.), black cherry (Prunus serotina Ehrh.), and red spruce (Picea rubens Sarg.). White oak (Quercus alba L.), balsam fir (Abies balsamea (L.) Mill.), American beech (Fagus grandifolia Ehrh.) and loblolly pine (Pinus taeda L.) were intermediate in SRL (indistinguishable from Engelmann spruce and subalpine fir by ANOVA). Species that differ more in physiology and morphology than the two species we compared would likely show dissimilar uptake characteristics even at the same site.

  5. Candida tropicalis from veterinary and human sources shows similar in vitro hemolytic activity, antifungal biofilm susceptibility and pathogenesis against Caenorhabditis elegans.

    Science.gov (United States)

    Brilhante, Raimunda Sâmia Nogueira; Oliveira, Jonathas Sales de; Evangelista, Antônio José de Jesus; Serpa, Rosana; Silva, Aline Lobão da; Aguiar, Felipe Rodrigues Magalhães de; Pereira, Vandbergue Santos; Castelo-Branco, Débora de Souza Collares Maia; Pereira-Neto, Waldemiro Aquino; Cordeiro, Rossana de Aguiar; Sidrim, José Júlio Costa; Rocha, Marcos Fábio Gadelha

    2016-08-30

    The aim of this study was to evaluate the in vitro hemolytic activity and biofilm antifungal susceptibility of veterinary and human Candida tropicalis strains, as well as their pathogenesis against Caenorhabditis elegans. Twenty veterinary isolates and 20 human clinical isolates of C. tropicalis were used. The strains were evaluated for their hemolytic activity and biofilm production. Biofilm susceptibility to itraconazole, fluconazole, voriconazole, amphotericin B and caspofungin was assessed using broth microdilution assay. The in vivo evaluation of strain pathogenicity was investigated using the nematode C. elegans. Hemolytic factor was observed in 95% of the strains and 97.5% of the isolates showed ability to form biofilm. Caspofungin and amphotericin B showed better results than azole antifungals against mature biofilms. Paradoxical effect on mature biofilm metabolic activity was observed at elevated concentrations of caspofungin (8-64μg/mL). Azole antifungals were not able to inhibit mature C. tropicalis biofilms, even at the higher tested concentrations. High mortality rates of C. elegans were observed when the worms were exposed to with C. tropicalis strains, reaching up to 96%, 96h after exposure of the worms to C. tropicalis strains. These results reinforce the high pathogenicity of C. tropicalis from veterinary and human sources and show the effectiveness of caspofungin and amphotericin B against mature biofilms of this species. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Enriching consumer health vocabulary through mining a social Q&A site: A similarity-based approach.

    Science.gov (United States)

    He, Zhe; Chen, Zhiwei; Oh, Sanghee; Hou, Jinghui; Bian, Jiang

    2017-05-01

    The widely known vocabulary gap between health consumers and healthcare professionals hinders information seeking and health dialogue of consumers on end-user health applications. The Open Access and Collaborative Consumer Health Vocabulary (OAC CHV), which contains health-related terms used by lay consumers, has been created to bridge such a gap. Specifically, the OAC CHV facilitates consumers' health information retrieval by enabling consumer-facing health applications to translate between professional language and consumer friendly language. To keep up with the constantly evolving medical knowledge and language use, new terms need to be identified and added to the OAC CHV. User-generated content on social media, including social question and answer (social Q&A) sites, afford us an enormous opportunity in mining consumer health terms. Existing methods of identifying new consumer terms from text typically use ad-hoc lexical syntactic patterns and human review. Our study extends an existing method by extracting n-grams from a social Q&A textual corpus and representing them with a rich set of contextual and syntactic features. Using K-means clustering, our method, simiTerm, was able to identify terms that are both contextually and syntactically similar to the existing OAC CHV terms. We tested our method on social Q&A corpora on two disease domains: diabetes and cancer. Our method outperformed three baseline ranking methods. A post-hoc qualitative evaluation by human experts further validated that our method can effectively identify meaningful new consumer terms on social Q&A. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. 3ircular dichroism simulation shows a site-II-to-site-I displacement of human serum albumin-bound diclofenac by ibuprofen

    OpenAIRE

    Yamasaki, Keishi; Rahman, Mohammed Hablbur; Tsutsumi, Yasuhiro; Maruyama, Toru; Ahmed, Shamim; Kragh-Hansen; Otagiri, Masaki

    2000-01-01

    Purpose: The purpose of this study was to confirm the hypothesis that a site-II-to-site-I displacement takes place when some nonsteroidal anti-inflammatory drugs are displaced by another drug from their high-affinity binding site to a site of lower affinity on human serum albumin (HSA).Methods: Diclofenac, sodium salt, was used as a representative example because of its prominent reversal of the Cotton effect. Effects of site-specific drugs on the free fraction of diclofenac were determined b...

  8. Bioavailability of particulate metal to zebra mussels: biodynamic modelling shows that assimilation efficiencies are site-specific.

    Science.gov (United States)

    Bourgeault, Adeline; Gourlay-Francé, Catherine; Priadi, Cindy; Ayrault, Sophie; Tusseau-Vuillemin, Marie-Hélène

    2011-12-01

    This study investigates the ability of the biodynamic model to predict the trophic bioaccumulation of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni) and zinc (Zn) in a freshwater bivalve. Zebra mussels were transplanted to three sites along the Seine River (France) and collected monthly for 11 months. Measurements of the metal body burdens in mussels were compared with the predictions from the biodynamic model. The exchangeable fraction of metal particles did not account for the bioavailability of particulate metals, since it did not capture the differences between sites. The assimilation efficiency (AE) parameter is necessary to take into account biotic factors influencing particulate metal bioavailability. The biodynamic model, applied with AEs from the literature, overestimated the measured concentrations in zebra mussels, the extent of overestimation being site-specific. Therefore, an original methodology was proposed for in situ AE measurements for each site and metal. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Bioavailability of particulate metal to zebra mussels: Biodynamic modelling shows that assimilation efficiencies are site-specific

    Energy Technology Data Exchange (ETDEWEB)

    Bourgeault, Adeline, E-mail: bourgeault@ensil.unilim.fr [Cemagref, Unite de Recherche Hydrosystemes et Bioprocedes, 1 rue Pierre-Gilles de Gennes, 92761 Antony (France); FIRE, FR-3020, 4 place Jussieu, 75005 Paris (France); Gourlay-France, Catherine, E-mail: catherine.gourlay@cemagref.fr [Cemagref, Unite de Recherche Hydrosystemes et Bioprocedes, 1 rue Pierre-Gilles de Gennes, 92761 Antony (France); FIRE, FR-3020, 4 place Jussieu, 75005 Paris (France); Priadi, Cindy, E-mail: cindy.priadi@eng.ui.ac.id [LSCE/IPSL CEA-CNRS-UVSQ, Avenue de la Terrasse, 91198 Gif-sur-Yvette (France); Ayrault, Sophie, E-mail: Sophie.Ayrault@lsce.ipsl.fr [LSCE/IPSL CEA-CNRS-UVSQ, Avenue de la Terrasse, 91198 Gif-sur-Yvette (France); Tusseau-Vuillemin, Marie-Helene, E-mail: Marie-helene.tusseau@ifremer.fr [IFREMER Technopolis 40, 155 rue Jean-Jacques Rousseau, 92138 Issy-Les-Moulineaux (France)

    2011-12-15

    This study investigates the ability of the biodynamic model to predict the trophic bioaccumulation of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni) and zinc (Zn) in a freshwater bivalve. Zebra mussels were transplanted to three sites along the Seine River (France) and collected monthly for 11 months. Measurements of the metal body burdens in mussels were compared with the predictions from the biodynamic model. The exchangeable fraction of metal particles did not account for the bioavailability of particulate metals, since it did not capture the differences between sites. The assimilation efficiency (AE) parameter is necessary to take into account biotic factors influencing particulate metal bioavailability. The biodynamic model, applied with AEs from the literature, overestimated the measured concentrations in zebra mussels, the extent of overestimation being site-specific. Therefore, an original methodology was proposed for in situ AE measurements for each site and metal. - Highlights: > Exchangeable fraction of metal particles did not account for the bioavailability of particulate metals. > Need for site-specific biodynamic parameters. > Field-determined AE provide a good fit between the biodynamic model predictions and bioaccumulation measurements. - The interpretation of metal bioaccumulation in transplanted zebra mussels with biodynamic modelling highlights the need for site-specific assimilation efficiencies of particulate metals.

  10. Non-native western tubenose gobies Proterorhinus semilunaris show distinct site, sex and age-related differences in diet

    Czech Academy of Sciences Publication Activity Database

    Všetičková, Lucie; Janáč, Michal; Vašek, Mojmír; Roche, Kevin Francis; Jurajda, Pavel

    2014-01-01

    Roč. 414, č. 10 (2014), s. 1-19 ISSN 1961-9502 R&D Projects: GA ČR(CZ) GAP505/11/1768 Institutional support: RVO:68081766 Keywords : invasive species * Gobiidae * Proterorhinus semilunaris * diet * site-effect * sex-differences Subject RIV: EG - Zoology Impact factor: 0.928, year: 2014

  11. Similar distributions of repaired sites in chromatin of normal and xeroderma pigmentosum variant cells damaged by ultraviolet light

    International Nuclear Information System (INIS)

    Cleaver, J.E.

    1979-01-01

    Excision repair of damage from ultraviolet light in both normal and xeroderma pigmentosum variant fibroblasts at early times after irradiation occurred preferentially in regions of DNA accessible to micrococcal nuclease digestion. These regions are predominantly the linker regions between nucleosomes in chromatin. The alterations reported at polymerization and ligation steps of excision repair in the variant are therefore not associated with changes in the relative distributions of repair sites in linker and core particle regions of DNA. (Auth.)

  12. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Directory of Open Access Journals (Sweden)

    R. E. Schwartz

    2010-06-01

    Full Text Available Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR and X-ray fluorescence (XRF techniques for organic functional groups (OFG and elemental composition. Organic mass (OM concentrations ranged from less than 0.5 to 3.1 μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC, including isoprene and monoterpenes from biogenic VOC (BVOC emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR, were made using co-located proton transfer reaction mass spectrometry (PTR-MS. We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups was similar to that of secondary organic aerosol (SOA reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional

  13. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Science.gov (United States)

    Schwartz, R. E.; Russell, L. M.; Sjostedt, S. J.; Vlasenko, A.; Slowik, J. G.; Abbatt, J. P. D.; MacDonald, A. M.; Li, S. M.; Liggio, J.; Toom-Sauntry, D.; Leaitch, W. R.

    2010-06-01

    Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR) and X-ray fluorescence (XRF) techniques for organic functional groups (OFG) and elemental composition. Organic mass (OM) concentrations ranged from less than 0.5 to 3.1 μg m-3, with a project mean and standard deviation of 1.3±1.0 μg m-3 and 0.21±0.16 μg m-3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and volatile organic compounds (VOC), including isoprene and monoterpenes from biogenic VOC (BVOC) emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR), were made using co-located proton transfer reaction mass spectrometry (PTR-MS). We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF) analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups) was similar to that of secondary organic aerosol (SOA) reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional group composition and morphology of single particles, which were analyzed by scanning transmission X-ray microscopy near edge X

  14. The capsule biosynthesis locus of Haemophilus influenzae show conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer

    DEFF Research Database (Denmark)

    Nielsen, Signe Maria; de Gier, Camilla; Dimopoulou, Chrysoula

    2015-01-01

    in export and processing of the capsular material, show high similarity to the corresponding genes in capsulate lineages of the pathogenic species Haemophilus influenzae; indeed, standard bexA and bexB PCRs for detection of capsulated strains of H. influenzae give positive results with strains of H....... sputorum was only distantly related to H. influenzae. In contrast to H. influenzae, the capsule locus in H. sputorum is not associated with transposases or other transposable elements. Our data suggest that the capsule locus of capsulate lineages of H. influenzae may relatively recently have been recruited...

  15. Macrophage inflammatory protein-1α shows predictive value as a risk marker for subjects and sites vulnerable to bone loss in a longitudinal model of aggressive periodontitis.

    Science.gov (United States)

    Fine, Daniel H; Markowitz, Kenneth; Fairlie, Karen; Tischio-Bereski, Debbie; Ferrandiz, Javier; Godboley, Dipti; Furgang, David; Gunsolley, John; Best, Al

    2014-01-01

    Improved diagnostics remains a fundamental goal of biomedical research. This study was designed to assess cytokine biomarkers that could predict bone loss (BL) in localized aggressive periodontitis. 2,058 adolescents were screened. Two groups of 50 periodontally healthy adolescents were enrolled in the longitudinal study. One group had Aggregatibacter actinomycetemcomitans (Aa), the putative pathogen, while the matched cohort did not. Cytokine levels were assessed in saliva and gingival crevicular fluid (GCF). Participants were sampled, examined, and radiographed every 6 months for 2-3 years. Disease was defined as radiographic evidence of BL. Saliva and GCF was collected at each visit, frozen, and then tested retrospectively after detection of BL. Sixteen subjects with Aa developed BL. Saliva from Aa-positive and Aa-negative healthy subjects was compared to subjects who developed BL. GCF was collected from 16 subjects with BL and from another 38 subjects who remained healthy. GCF from BL sites in the 16 subjects was compared to healthy sites in these same subjects and to healthy sites in subjects who remained healthy. Results showed that cytokines in saliva associated with acute inflammation were elevated in subjects who developed BL (i.e., MIP-1α MIP-1β IL-α, IL-1β and IL-8; p<0.01). MIP-1α was elevated 13-fold, 6 months prior to BL. When MIP-1α levels were set at 40 pg/ml, 98% of healthy sites were below that level (Specificity); whereas, 93% of sites with BL were higher (Sensitivity), with comparable Predictive Values of 98%; p<0.0001; 95% C.I. = 42.5-52.7). MIP-1α consistently showed elevated levels as a biomarker for BL in both saliva and GCF, 6 months prior to BL. MIP-1α continues to demonstrate its strong candidacy as a diagnostic biomarker for both subject and site vulnerability to BL.

  16. Macrophage inflammatory protein-1α shows predictive value as a risk marker for subjects and sites vulnerable to bone loss in a longitudinal model of aggressive periodontitis.

    Directory of Open Access Journals (Sweden)

    Daniel H Fine

    Full Text Available Improved diagnostics remains a fundamental goal of biomedical research. This study was designed to assess cytokine biomarkers that could predict bone loss (BL in localized aggressive periodontitis. 2,058 adolescents were screened. Two groups of 50 periodontally healthy adolescents were enrolled in the longitudinal study. One group had Aggregatibacter actinomycetemcomitans (Aa, the putative pathogen, while the matched cohort did not. Cytokine levels were assessed in saliva and gingival crevicular fluid (GCF. Participants were sampled, examined, and radiographed every 6 months for 2-3 years. Disease was defined as radiographic evidence of BL. Saliva and GCF was collected at each visit, frozen, and then tested retrospectively after detection of BL. Sixteen subjects with Aa developed BL. Saliva from Aa-positive and Aa-negative healthy subjects was compared to subjects who developed BL. GCF was collected from 16 subjects with BL and from another 38 subjects who remained healthy. GCF from BL sites in the 16 subjects was compared to healthy sites in these same subjects and to healthy sites in subjects who remained healthy. Results showed that cytokines in saliva associated with acute inflammation were elevated in subjects who developed BL (i.e., MIP-1α MIP-1β IL-α, IL-1β and IL-8; p<0.01. MIP-1α was elevated 13-fold, 6 months prior to BL. When MIP-1α levels were set at 40 pg/ml, 98% of healthy sites were below that level (Specificity; whereas, 93% of sites with BL were higher (Sensitivity, with comparable Predictive Values of 98%; p<0.0001; 95% C.I. = 42.5-52.7. MIP-1α consistently showed elevated levels as a biomarker for BL in both saliva and GCF, 6 months prior to BL. MIP-1α continues to demonstrate its strong candidacy as a diagnostic biomarker for both subject and site vulnerability to BL.

  17. The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions.

    Science.gov (United States)

    Bartho, Joseph D; Bellini, Dom; Wuerges, Jochen; Demitri, Nicola; Toccafondi, Mirco; Schmitt, Armin O; Zhao, Youfu; Walsh, Martin A; Benini, Stefano

    2017-01-01

    AmyR is a stress and virulence associated protein from the plant pathogenic Enterobacteriaceae species Erwinia amylovora, and is a functionally conserved ortholog of YbjN from Escherichia coli. The crystal structure of E. amylovora AmyR reveals a class I type III secretion chaperone-like fold, despite the lack of sequence similarity between these two classes of protein and lacking any evidence of a secretion-associated role. The results indicate that AmyR, and YbjN proteins in general, function through protein-protein interactions without any enzymatic action. The YbjN proteins of Enterobacteriaceae show remarkably low sequence similarity with other members of the YbjN protein family in Eubacteria, yet a high level of structural conservation is observed. Across the YbjN protein family sequence conservation is limited to residues stabilising the protein core and dimerization interface, while interacting regions are only conserved between closely related species. This study presents the first structure of a YbjN protein from Enterobacteriaceae, the most highly divergent and well-studied subgroup of YbjN proteins, and an in-depth sequence and structural analysis of this important but poorly understood protein family.

  18. Inflammatory myofibroblastic tumor of maxilla showing sarcomatous change in an edentulous site with a history of tooth extraction following periodontitis: A case report with discussion.

    Science.gov (United States)

    Biniraj, K R; Janardhanan, Mahija

    2014-05-01

    Inflammatory myofibroblastic tumor (IMT) is a rare tumor of uncertain origin with variable biological behavior ranging from reactive lesions to highly aggressive malignancy. Oral IMTs are extremely rare and only 25 cases had been reported so far. A case of IMT with sarcomatous transformation in an extraction site with a history of tooth extraction following tooth mobility of an upper left molar tooth is presented here. The tooth was extracted following a complaint of gingival swelling and mobility of tooth. Though malignant transformation in IMTs had been documented in the extra oral sites, wide search of associated literature suggests, this is the first case of oral IMT showing malignant change associated with gingiva. The case report attempts to highlight the variant possibilities of tooth mobility other than periodontitis and the importance of assessing the primary cause of such conditions.

  19. Species B adenovirus serotypes 3, 7, 11 and 35 share similar binding sites on the membrane cofactor protein CD46 receptor.

    Science.gov (United States)

    Fleischli, Christoph; Sirena, Dominique; Lesage, Guillaume; Havenga, Menzo J E; Cattaneo, Roberto; Greber, Urs F; Hemmi, Silvio

    2007-11-01

    We recently characterized the domains of the human cofactor protein CD46 involved in binding species B2 adenovirus (Ad) serotype 35. Here, the CD46 binding determinants are mapped for the species B1 Ad serotypes 3 and 7 and for the species B2 Ad11. Ad3, 7 and 11 bound and transduced CD46-positive rodent BHK cells at levels similar to Ad35. By using antibody-blocking experiments, hybrid CD46-CD4 receptor constructs and CD46 single point mutants, it is shown that Ad3, 7 and 11 share many of the Ad35-binding features on CD46. Both CD46 short consensus repeat domains SCR I and SCR II were necessary and sufficient for optimal binding and transgene expression, provided that they were positioned at an appropriate distance from the cell membrane. Similar to Ad35, most of the putative binding residues of Ad3, 7 and 11 were located on the same glycan-free, solvent-exposed face of the SCR I or SCR II domains, largely overlapping with the binding surface of the recently solved fiber knob Ad11-SCR I-II three-dimensional structure. Differences between species B1 and B2 Ads were documented with competition experiments based on anti-CD46 antibodies directed against epitopes flanking the putative Ad-binding sites, and with competition experiments based on soluble CD46 protein. It is concluded that the B1 and B2 species of Ad engage CD46 through similar binding surfaces.

  20. Adapted J6/JFH1-based Hepatitis C virus recombinants with genotype-specific NS4A show similar efficacies against lead protease inhibitors, alpha interferon, and a putative NS4A inhibitor

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Sanne B; Serre, Stéphanie B N

    2013-01-01

    To facilitate studies of hepatitis C virus (HCV) NS4A, we aimed at developing J6/JFH1-based recombinants with genotype 1- to 7-specific NS4A proteins. We developed efficient culture systems expressing NS4A proteins of genotypes (isolates) 1a (H77 and TN), 1b (J4), 2a (J6), 4a (ED43), 5a (SA13), 6a...... (HK6a), and 7a (QC69), with peak infectivity titers of ∼3.5 to 4.5 log10 focus-forming units per ml. Except for genotype 2a (J6), growth depended on adaptive mutations identified in long-term culture. Genotype 1a, 1b, and 4a recombinants were adapted by amino acid substitutions F772S (p7) and V1663A...... (NS4A), while 5a, 6a, and 7a recombinants required additional substitutions in the NS3 protease and/or NS4A. We demonstrated applicability of the developed recombinants for study of antivirals. Genotype 1 to 7 NS4A recombinants showed similar responses to the protease inhibitors telaprevir (VX-950...

  1. Site-directed mutagenesis and molecular modelling studies show the role of Asp82 and cysteines in rat acylase 1, a member of the M20 family

    International Nuclear Information System (INIS)

    Herga, Sameh; Brutus, Alexandre; Vitale, Rosa Maria; Miche, Helene; Perrier, Josette; Puigserver, Antoine; Scaloni, Andrea; Giardina, Thierry

    2005-01-01

    Acylase 1 from rat kidney catalyzes the hydrolysis of acyl-amino acids. Sequence alignment has shown that this enzyme belongs to the metalloprotein family M20. Site-directed mutagenesis experiments led to the identification of one functionally important amino acid residue located near one of the zinc coordinating residues, which play a critical role in the enzymatic activity. The D82N- and D82E-substituted forms showed no significant activity and very low activity, respectively, along with a loss of zinc coordination. Molecular modelling investigations indicated a putative role of D82 in ensuring a proper protonation of catalytic histidine. In addition, none of the five cysteine residues present in the rat kidney acylase 1 sequence seemed involved in the catalytic process: the loss of activity induced by the C294A substitution was probably due to a conformational change in the 3D structure

  2. Nonintrusive field experiments show different plant responses to warming and drought among sites, seasons, and species in a north-south European gradient

    DEFF Research Database (Denmark)

    Penuelas, J.; Gordon, C.; Llorens, L.

    2004-01-01

    -limited. In the water-stressed southern site, there was no increase in total aboveground plant biomass growth as expected since warming increases water loss, and temperatures in those ecosystems are already close to the optimum for photosynthesis. The southern site presented instead the most negative response...... a 15% increase in total aboveground plant biomass growth in the UK site. Both direct and indirect effects of warming, such as longer growth season and increased nutrient availability, are likely to be particularly important in this and the other northern sites which tend to be temperature...... to the drought treatment consisting of a soil moisture reduction at the peak of the growing season ranging from 33% in the Spanish site to 82% in The Netherlands site. In the Spanish site there was a 14% decrease in total aboveground plant biomass growth relative to control. Flowering was decreased by drought...

  3. Somatostatin receptor 2 knockout/lacZ knockin mice show impaired motor coordination and reveal sites of somatostatin action within the striatum.

    Science.gov (United States)

    Allen, Jeremy P; Hathway, Gareth J; Clarke, Neil J; Jowett, Mike I; Topps, Stephanie; Kendrick, Keith M; Humphrey, Patrick P A; Wilkinson, Lawrence S; Emson, Piers C

    2003-05-01

    The peptide somatostatin can modulate the functional output of the basal ganglia. The exact sites and mechanisms of this action, however, are poorly understood, and the physiological context in which somatostatin acts is unknown. Somatostatin acts as a neuromodulator via a family of five 7-transmembrane G protein-coupled receptors, SSTR1-5, one of which, SSTR2, is known to be functional in the striatum. We have investigated the role of SSTR2 in basal ganglia function using mice in which Sstr2 has been inactivated and replaced by the lacZ reporter gene. Analysis of Sstr2lacZ expression in the brain by beta-galactosidase histochemistry demonstrated a widespread pattern of expression. By comparison to previously published in situ hybridization and immunohistochemical data, Sstr2lacZ expression was shown to accurately recapitulate that of Sstr2 and thus provided a highly sensitive model to investigate cell-type-specific expression of Sstr2. In the striatum, Sstr2 expression was identified in medium spiny projection neurons restricted to the matrix compartment and in cholinergic interneurons. Sstr2 expression was not detected in any other nuclei of the basal ganglia except for a sparse number of nondopaminergic neurons in the substantia nigra. Microdialysis in the striatum showed Sstr2-null mice were selectively refractory to somatostatin-induced dopamine and glutamate release. In behavioural tests, Sstr2-null mice showed normal levels of locomotor activity and normal coordination in undemanding tasks. However, in beam-walking, a test of fine motor control, Sstr2-null mice were severely impaired. Together these data implicate an important neuromodulatory role for SSTR2 in the striatum.

  4. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes: a randomised educational trial

    Science.gov (United States)

    Sørensen, Jette Led; van der Vleuten, Cees; Rosthøj, Susanne; Østergaard, Doris; LeBlanc, Vicki; Johansen, Marianne; Ekelund, Kim; Starkopf, Liis; Lindschou, Jane; Gluud, Christian; Weikop, Pia; Ottesen, Bent

    2015-01-01

    Objective To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. Design Investigator-initiated single-centre randomised superiority educational trial. Setting Obstetrics and anaesthesiology departments, Rigshospitalet, University of Copenhagen, Denmark. Participants 100 participants in teams of 10, comprising midwives, specialised midwives, auxiliary nurses, nurse anaesthetists, operating theatre nurses, and consultant doctors and trainees in obstetrics and anaesthesiology. Interventions Two multiprofessional simulations (clinical management of an emergency caesarean section and a postpartum haemorrhage scenario) were conducted in teams of 10 in the ISS versus the OSS setting. Primary outcome Knowledge assessed by a multiple choice question test. Exploratory outcomes Individual outcomes: scores on the Safety Attitudes Questionnaire, stress measurements (State-Trait Anxiety Inventory, cognitive appraisal and salivary cortisol), Intrinsic Motivation Inventory and perceptions of simulations. Team outcome: video assessment of team performance. Organisational impact: suggestions for organisational changes. Results The trial was conducted from April to June 2013. No differences between the two groups were found for the multiple choice question test, patient safety attitude, stress measurements, motivation or the evaluation of the simulations. The participants in the ISS group scored the authenticity of the simulation significantly higher than did the participants in the OSS group. Expert video assessment of team performance showed no differences between the ISS versus the OSS group. The ISS group provided more ideas and suggestions for changes at the organisational level. Conclusions In this randomised trial, no significant differences were found regarding knowledge, patient safety attitude, motivation or stress

  5. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes: a randomised educational trial

    NARCIS (Netherlands)

    Sorensen, J.L.; Vleuten, C. van der; Rosthoj, S.; Ostergaard, D.; Leblanc, V.; Johansen, M.; Ekelund, K.; Starkopf, L.; Lindschou, J.; Gluud, C.; Weikop, P.; Ottesen, B.

    2015-01-01

    OBJECTIVE: To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. DESIGN: Investigator-initiated single-centre randomised superiority

  6. Species composition and similarities among anuran assemblages of forest sites in southeastern Brazil Composição de espécies e similaridades entre taxocenoses de anuros de áreas florestais do sudeste do Brasil

    Directory of Open Access Journals (Sweden)

    Jaime Bertoluci

    2007-08-01

    Full Text Available Neotropical forests show high anuran species richness, but some Brazilian forest formations, like cerradão, semideciduous forests and restingas, remain poorly known. The composition of anuran species were determined for four forest sites belonging to different biomes in southeastern Brazil, based on two complementary techniques (visual encounter survey and survey on breeding sites, both applied simultaneously. A total of 60 anuran species belonging to eight families was recorded. Species richness and levels of endemism were higher in the Atlantic rainforest site. Sites located in the Cerrado domain were more alike than those located in the Atlantic Forest Domain. Similarity in anuran species composition was negatively correlated to the geographical distance among sites, which explains part of similarities in species composition. Factors affecting these occurrence patterns are discussed. One species (if its identity is confirmed is considered Data Deficient by IUCN (The World Conservation Union, though it is not included in the Brazilian list of threatened amphibians. The presence of certain species with special habitats and microclimate requirements (bioindicators suggests well-preserved ecosystems.As florestas neotropicais apresentam altas riquezas de espécies de anuros, mas algumas formações florestais brasileiras, como o cerradão, as florestas semidecíduas e as restingas, permanecem pouco conhecidas. A composição de espécies de anuros de quatro áreas florestais pertencentes a diferentes biomas do sudeste do Brasil foi determinada com base em duas técnicas complementares (procura visual e investigação nos sítios reprodutivos, aplicadas de forma simultânea. Registramos um total de 60 espécies de anuros, incluídas em oito famílias. A riqueza de espécies e o nível de endemismo foram maiores na área coberta por floresta pluvial atlântica. As áreas localizadas no domínio do Cerrado foram mais similares entre si do que as

  7. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets....... Our results show that the proposed functions work better than other methods proposed in the literature....

  8. Making Benefit Transfers Work: Deriving and Testing Principles for Value Transfers for Similar and Dissimilar Sites Using a Case Study of the Non-Market Benefits of Water Quality Improvements Across Europe

    DEFF Research Database (Denmark)

    Bateman, Ian; Brouwer, Roy; Ferreri, Silvia

    2011-01-01

    We implement a controlled, multi-site experiment to develop and test guidance principles for benefits transfers. These argue that when transferring across relatively similar sites, simple mean value transfers are to be preferred but that when sites are relatively dissimilar then value function...... transfers will yield lower errors. The paper also provides guidance on the appropriate specification of transferable value functions arguing that these should be developed from theoretical rather than ad-hoc statistical approaches. These principles are tested via a common format valuation study of water...... quality improvements across five countries. While this provides an idealised tested, results support the above principles and suggest directions for future transfer studies....

  9. Free Recall Shows Similar Reactivation Behavior as Recognition & Cued Recall

    OpenAIRE

    Tarnow, Eugen

    2016-01-01

    I find that the total retrieval time in word free recall increases linearly with the total number of items recalled. Measured slopes, the time to retrieve an additional item, vary from 1.4-4.5 seconds per item depending upon presentation rate, subject age and whether there is a delay after list presentation or not. These times to retrieve an additional item obey a second linear relationship as a function of the recall probability averaged over the experiment, explicitly independent of subject...

  10. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes

    DEFF Research Database (Denmark)

    Sørensen, Jette Led; van der Vleuten, Cees; Rosthøj, Susanne

    2015-01-01

    choice question test. EXPLORATORY OUTCOMES: Individual outcomes: scores on the Safety Attitudes Questionnaire, stress measurements (State-Trait Anxiety Inventory, cognitive appraisal and salivary cortisol), Intrinsic Motivation Inventory and perceptions of simulations. Team outcome: video assessment......OBJECTIVE: To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. DESIGN: Investigator-initiated single-centre randomised superiority...... educational trial. SETTING: Obstetrics and anaesthesiology departments, Rigshospitalet, University of Copenhagen, Denmark. PARTICIPANTS: 100 participants in teams of 10, comprising midwives, specialised midwives, auxiliary nurses, nurse anaesthetists, operating theatre nurses, and consultant doctors...

  11. Incorporating C60 as Nucleation Sites Optimizing PbI2 Films To Achieve Perovskite Solar Cells Showing Excellent Efficiency and Stability via Vapor-Assisted Deposition Method.

    Science.gov (United States)

    Chen, Hai-Bin; Ding, Xi-Hong; Pan, Xu; Hayat, Tasawar; Alsaedi, Ahmed; Ding, Yong; Dai, Song-Yuan

    2018-01-24

    To achieve high-quality perovskite solar cells (PSCs), the morphology and carrier transportation of perovskite films need to be optimized. Herein, C 60 is employed as nucleation sites in PbI 2 precursor solution to optimize the morphology of perovskite films via vapor-assisted deposition process. Accompanying the homogeneous nucleation of PbI 2 , the incorporation of C 60 as heterogeneous nucleation sites can lower the nucleation free energy of PbI 2 , which facilitates the diffusion and reaction between PbI 2 and organic source. Meanwhile, C 60 could enhance carrier transportation and reduce charge recombination in the perovskite layer due to its high electron mobility and conductivity. In addition, the grain sizes of perovskite get larger with C 60 optimizing, which can reduce the grain boundaries and voids in perovskite and prevent the corrosion because of moisture. As a result, we obtain PSCs with a power conversion efficiency (PCE) of 18.33% and excellent stability. The PCEs of unsealed devices drop less than 10% in a dehumidification cabinet after 100 days and remain at 75% of the initial PCE during exposure to ambient air (humidity > 60% RH, temperature > 30 °C) for 30 days.

  12. Phylogenetic diversity and similarity of active sites of Shiga toxin (stx) in Shiga toxin-producing Escherichia coli (STEC) isolates from humans and animals.

    Science.gov (United States)

    Asakura, H; Makino, S; Kobori, H; Watarai, M; Shirahata, T; Ikeda, T; Takeshi, K

    2001-08-01

    Nucleotide sequences of Shiga toxin (Stx) genes in STEC from various origins were determined and characterized by phylogenetic analysis based on Shiga toxin (Stx) with those deposited in GenBank. The phylogenetic trees placed Stx1 and Stx2 into two and five groups respectively, and indicated that Stx1 in sheep-origin STEC were placed into a different group from those in other STEC, and that Stx2 of deer-origin STEC also belonged to the unique group and appeared to be distantly related to human-origin STEC. On the other hand, Stx of STEC isolated from cattle, seagulls and flies were closely related to those of human-origin STEC. Such a diversity of Stx suggested that STEC might be widely disseminated in many animal species, and be dependent on their host species or their habitat. In addition, the active sites in both toxins were compared; the active sites in both subunits of Stx in all the animal-origin STEC were identical to those in human-origin STEC, suggesting that all the toxin of STEC from animals might be also cytotoxic, and therefore, such animal-origin STEC might have potential pathogenicity for humans.

  13. Fusion proteins of HIV-1 envelope glycoprotein gp120 with CD4-induced antibodies showed enhanced binding to CD4 and CD4 binding site antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Weizao, E-mail: chenw3@mail.nih.gov [Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States); Feng, Yang [Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States); Wang, Yanping [Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States); The Basic Research Program, Science Applications International Corporation-Frederick, Inc., National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States); Zhu, Zhongyu; Dimitrov, Dimiter S. [Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States)

    2012-09-07

    Highlights: Black-Right-Pointing-Pointer Some recombinant HIV-1 gp120s do not preserve their conformations on gp140s. Black-Right-Pointing-Pointer We hypothesize that CD4i antibodies could induce conformational changes in gp120. Black-Right-Pointing-Pointer CD4i antibodies enhance binding of CD4 and CD4bs antibodies to gp120. Black-Right-Pointing-Pointer CD4i antibody-gp120 fusion proteins could have potential as vaccine immunogens. -- Abstract: Development of successful AIDS vaccine immunogens continues to be a major challenge. One of the mechanisms by which HIV-1 evades antibody-mediated neutralizing responses is the remarkable conformational flexibility of its envelope glycoprotein (Env) gp120. Some recombinant gp120s do not preserve their conformations on gp140s and functional viral spikes, and exhibit decreased recognition by CD4 and neutralizing antibodies. CD4 binding induces conformational changes in gp120 leading to exposure of the coreceptor-binding site (CoRbs). In this study, we test our hypothesis that CD4-induced (CD4i) antibodies, which target the CoRbs, could also induce conformational changes in gp120 leading to better exposed conserved neutralizing antibody epitopes including the CD4-binding site (CD4bs). We found that a mixture of CD4i antibodies with gp120 only weakly enhanced CD4 binding. However, such interactions in single-chain fusion proteins resulted in gp120 conformations which bound to CD4 and CD4bs antibodies better than the original or mutagenically stabilized gp120s. Moreover, the two molecules in the fusion proteins synergized with each other in neutralizing HIV-1. Therefore, fusion proteins of gp120 with CD4i antibodies could have potential as components of HIV-1 vaccines and inhibitors of HIV-1 entry, and could be used as reagents to explore the conformational flexibility of gp120 and mechanisms of entry and immune evasion.

  14. Cells deficient in PARP-1 show an accelerated accumulation of DNA single strand breaks, but not AP sites, over the PARP-1-proficient cells exposed to MMS

    Energy Technology Data Exchange (ETDEWEB)

    Pachkowski, Brian F. [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC (United States); Tano, Keizo [Research Reactor Institute, Kyoto University, Kumatori (Japan); Afonin, Valeriy [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC (United States); Elder, Rhoderick H. [School of Environment and Life Sciences, University of Salford, Greater Manchester (United Kingdom); Takeda, Shunichi [Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto (Japan); Watanabe, Masami [Research Reactor Institute, Kyoto University, Kumatori (Japan); Swenberg, James A. [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC (United States); Nakamura, Jun, E-mail: ynakamur@email.unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC (United States)

    2009-12-01

    Poly(ADP-ribose) polymerase-1 (PARP-1) is a base excision repair (BER) protein that binds to DNA single strand breaks (SSBs) and subsequently synthesizes and transfers poly(ADP-ribose) polymers to various nuclear proteins. Numerous biochemical studies have implicated PARP-1 as a modulator of BER; however, the role of PARP-1 in BER in living cells remains unclear partly due to lack of accurate quantitation of BER intermediates existing in cells. Since DT40 cells, chicken B lymphocytes, naturally lack PARP-2, DT40 cells allow for the investigation of the PARP-1 null phenotype without confounding by PARP-2. To test the hypothesis that PARP-1 is necessary for efficient BER during methylmethane sulfonate (MMS) exposure in vertebrate cells, intact DT40 cells and their isogenic PARP-1 null counterparts were challenged with different exposure scenarios for phenotypic characterization. With chronic exposure, PARP-1 null cells exhibited sensitivity to MMS but with an acute exposure did not accumulate base lesions or AP sites to a greater extent than wild-type cells. However, an increase in SSB content in PARP-1 null cell DNA, as indicated by glyoxal gel electrophoresis under neutral conditions, suggested the presence of BER intermediates. These data suggest that during exposure, PARP-1 impacts the stage of BER after excision of the deoxyribosephosphate moiety from the 5' end of DNA strand breaks by polymerase {beta}.

  15. Cells deficient in PARP-1 show an accelerated accumulation of DNA single strand breaks, but not AP sites, over the PARP-1-proficient cells exposed to MMS.

    Science.gov (United States)

    Pachkowski, Brian F; Tano, Keizo; Afonin, Valeriy; Elder, Rhoderick H; Takeda, Shunichi; Watanabe, Masami; Swenberg, James A; Nakamura, Jun

    2009-12-01

    Poly(ADP-ribose) polymerase-1 (PARP-1) is a base excision repair (BER) protein that binds to DNA single strand breaks (SSBs) and subsequently synthesizes and transfers poly(ADP-ribose) polymers to various nuclear proteins. Numerous biochemical studies have implicated PARP-1 as a modulator of BER; however, the role of PARP-1 in BER in living cells remains unclear partly due to lack of accurate quantitation of BER intermediates existing in cells. Since DT40 cells, chicken B lymphocytes, naturally lack PARP-2, DT40 cells allow for the investigation of the PARP-1 null phenotype without confounding by PARP-2. To test the hypothesis that PARP-1 is necessary for efficient BER during methylmethane sulfonate (MMS) exposure in vertebrate cells, intact DT40 cells and their isogenic PARP-1 null counterparts were challenged with different exposure scenarios for phenotypic characterization. With chronic exposure, PARP-1 null cells exhibited sensitivity to MMS but with an acute exposure did not accumulate base lesions or AP sites to a greater extent than wild-type cells. However, an increase in SSB content in PARP-1 null cell DNA, as indicated by glyoxal gel electrophoresis under neutral conditions, suggested the presence of BER intermediates. These data suggest that during exposure, PARP-1 impacts the stage of BER after excision of the deoxyribosephosphate moiety from the 5' end of DNA strand breaks by polymerase beta.

  16. IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities [v2; ref status: indexed, http://f1000r.es/13y

    Directory of Open Access Journals (Sweden)

    Natalja Kurbatova

    2013-05-01

    Full Text Available IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder.

  17. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  18. Use of multiple attributes decision-making Technique for Order Preference by Similarity to Ideal Solution (TOPSIS for Ghare-Gheshlagh calcite in determination of optimum geochemical sampling sites

    Directory of Open Access Journals (Sweden)

    Mansour Rezaei Azizi

    2015-04-01

    for green, white and pink calcites were varied 0.087, 0.247 and 0.997 respectively. The low amounts of Eu anomaly for green and white calcites attributed to low rock/fluid ratio (Nesbitt et al., 1990 and relatively more pH value (Cheng et al., 2013, however, increasing the Eu anomaly may be due to high rock/fluid ratio and less pH value. Ce anomalies are 0.0241, 0.0113 and 0.0131 in pink, white and green calcites respectively. The most negative Ce anomaly values show that calcite have precipitated under reduction conditions (Nesbitt et al., 1990. Discussion Recently, multiple attributes decision-making techniques help scientist to solve decision-making problems related to various controlling factors (Zhijun et al., 2013. One of these techniques is a Technique for Order Preference by Similarity to Ideal Solution (TOPSIS which is a quantitative weighted method (Momenei 2006. The identified criteria are CaO abundant in solution (C1, Eu anomaly (C2, Ce anomaly (C3, Sr abundant (C4 and volume (C5. The Index-Rock matrix also includes A1, A2 and A3 alternatives; as pink, green and white calcite respectively. The weighted normalized decision matrix can be calculated by multiplying the normalized evaluation matrix with its associated weight to obtain the result. The result show that Eu anomaly, volume, Sr abundant and Ce anomaly in order have higher role to investigate the geochemical study of area. Calculation of the relative closeness to the ideal solution (Cl * for pink, green and white calcites are 0.837, 0.445 and 0.157 respectively. It can be deduced that the most preferable calcite to be sampled for investigating geochemically are pink and green calcites. References Cheng, D.L., Jiang-haob, L., Shou-pengc, Z., Lianga, L., Zhao-bina, Y., Guo-lina, G. and Tinga, L., 2013. Geochemical characteristics of calcite and dolomite in sandstone of Dongying Sinking, Shandong Province, China. Procedia Earth and Planetary Science, 7(4: 504 – 507. Eftekharnezhad, J., 1973

  19. The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

    Science.gov (United States)

    Humbert, Olivier; Salama, Nina R.

    2008-01-01

    The naturally competent organism Helicobacter pylori encodes a large number of restriction–modification (R–M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R–M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R–M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R–M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel ‘half pipe’ structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model. PMID:18978016

  20. Phoneme Similarity and Confusability

    Science.gov (United States)

    Bailey, T.M.; Hahn, U.

    2005-01-01

    Similarity between component speech sounds influences language processing in numerous ways. Explanation and detailed prediction of linguistic performance consequently requires an understanding of these basic similarities. The research reported in this paper contrasts two broad classes of approach to the issue of phoneme similarity-theoretically…

  1. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

    Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support experien...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level....... experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners. The results also indicated that the only form of support in which the students expressed more matched support than mismatched support was informational support. Further investigation showed that the Danish students reported a high level of mismatch in emotional support than their Finnish...

  2. Molecular similarity measures.

    Science.gov (United States)

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2011-01-01

    Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

  3. Processes of Similarity Judgment

    Science.gov (United States)

    Larkey, Levi B.; Markman, Arthur B.

    2005-01-01

    Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

  4. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  5. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  6. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...... not perform well, even for data that satisfies all its assumptions....

  7. Personalized recommendation with corrected similarity

    International Nuclear Information System (INIS)

    Zhu, Xuzhen; Tian, Hui; Cai, Shimin

    2014-01-01

    Personalized recommendation has attracted a surge of interdisciplinary research. Especially, similarity-based methods in applications of real recommendation systems have achieved great success. However, the computations of similarities are overestimated or underestimated, in particular because of the defective strategy of unidirectional similarity estimation. In this paper, we solve this drawback by leveraging mutual correction of forward and backward similarity estimations, and propose a new personalized recommendation index, i.e., corrected similarity based inference (CSI). Through extensive experiments on four benchmark datasets, the results show a greater improvement of CSI in comparison with these mainstream baselines. And a detailed analysis is presented to unveil and understand the origin of such difference between CSI and mainstream indices. (paper)

  8. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  9. Self-similar factor approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  10. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  11. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  12. Patterns of turnover and floristic similarity show a non-random distribution of naturalized flora in Chile, South America Patrones de recambio y similitud florística muestran una distribución no aleatoria de la flora naturalizada en Chile, Sudamérica

    Directory of Open Access Journals (Sweden)

    SERGIO A CASTRO

    2008-03-01

    Full Text Available The current geographical distribution of alien species could be informative of processes involved in the biological invasions facilitated by humans. Because environmental and anthropic factors affect the geographic distribution of alien plants, we hypothesize that naturalized plants have a non-random distribution along extensive geographical ranges. On the basis of a complete and updated database of naturalized plants in Chile, we analyzed their turnover and floristic similarities among regions that encompass a wide latitudinal gradient in South America. Using Moran's index and Mantel's test we characterized the spatial auto-correlation (regional aggregation and the effect of geographical distance on the index values. Additionally, we used clustering methods and resampling procedures to detect plant assemblages at regional level. Whittaker's index displayed a positive tilt, increasing according to geographical distance and reaching a plateau; conversely, Jaccard's index was negatively associated with geographical distance. Removing the effect of distance, both Whittaker's and Jaccard's values showed no significant trends. Multivariate analysis combined with resampling procedures revealed the existence of three distinctive plant clusters: Northernmost Chile, Central-southern Chile, and Southernmost Chile. These clusters are characterized by naturalized plants that are not present in the others. Based on this evidence, we conclude that the set of naturalized plants in Chile exhibits a non-random geographical distribution, displaying an ordered geographical pattern across regions (latitude. We discuss the role of the environmental variables (climate, latitude and land use post-European colonization as factors in the distributional patterns here documentedLa distribución geográfica actual de especies exóticas puede ser informativa de los procesos involucrados en las invasiones biológicas facilitadas por humanos. Debido a que los factores

  13. Show-Bix &

    DEFF Research Database (Denmark)

    2014-01-01

    The anti-reenactment 'Show-Bix &' consists of 5 dias projectors, a dial phone, quintophonic sound, and interactive elements. A responsive interface will enable the Dias projectors to show copies of original dias slides from the Show-Bix piece ”March på Stedet”, 265 images in total. The copies are...

  14. Three-dimensional structure of the large cytoplasmic H-4-H-5 loop of Na(+)/K(+)-ATPase deduced by restraint-based comparative modeling shows only one ATP binding site

    Czech Academy of Sciences Publication Activity Database

    Ettrich, Rüdiger; Melicherčík, M.; Teisinger, Jan; Ettrichová, Olga; Krumscheid, R.; Hofbauerová, Kateřina; Kvasnička, P.; Schoner, W.; Amler, Evžen

    2001-01-01

    Roč. 7, č. 6 (2001), s. 184-192 ISSN 0948-5023 R&D Projects: GA MŠk VS961410; GA ČR GA204/98/0468; GA AV ČR IAA7011801; GA ČR GA204/98/0416 Grant - others:IWTZ(DE) TSR-088-97; Volkswagen Foundation(DE) I/74679 Institutional research plan: CEZ:AV0Z5011922 Keywords : Sodium potassium adenosine triphosphate * tertiary structure * adenosine triphosphate binding site Subject RIV: BO - Biophysics Impact factor: 1.011, year: 2001

  15. How acquainting shows verbally

    DEFF Research Database (Denmark)

    Hermann, Jesper

    2004-01-01

    A central tenet of the integrational view of language and communication is an anchoring in the acting and integrating behaviour of the communicants themselves. In this way the integrational approach has a certain phenomenological slant. What happens when this approach is combined with a ¿psycholo...... to some of William James' classical psychological observations. 16...... of linguistic exertion¿ based upon the descriptions of the  stream of thought, and of conception (>acquainting) by William James? Text-examples taken from an internet site for dieters illustrate the combined James'ian & integrational approach in practice. Some of the examples are also specifically related......A central tenet of the integrational view of language and communication is an anchoring in the acting and integrating behaviour of the communicants themselves. In this way the integrational approach has a certain phenomenological slant. What happens when this approach is combined with a ¿psychology...

  16. Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1).

    Science.gov (United States)

    Yung, Yuk-Lin; Cheung, Ming-Yan; Miao, Rui; Fong, Yu-Hang; Li, Kwan-Pok; Yu, Mei-Hui; Chye, Mee-Len; Wong, Kam-Bo; Lam, Hon-Ming

    2015-09-25

    The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that a member of this group, OsGAP1, is able to alleviate salt stress and stimulate defense responses, and bind to both phospholipids and an unconventional G-protein, OsYchF1. Here we solved the crystal structure of OsGAP1 to a resolution of 1.63 Å. Using site-directed mutagenesis, we successfully differentiated between the clusters of surface residues that are required for binding to phospholipids versus OsYchF1, which, in turn, is critical for its role in stimulating defense responses. On the other hand, the ability to alleviate salt stress by OsGAP1 is dependent only on its ability to bind OsYchF1 and is independent of its phospholipid-binding activity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Talking with TV shows

    DEFF Research Database (Denmark)

    Sandvik, Kjetil; Laursen, Ditte

    2014-01-01

    User interaction with radio and television programmes is not a new thing. However, with new cross-media production concepts such as X Factor and Voice, this is changing dramatically. The second-screen logic of these productions encourages viewers, along with TV’s traditional one-way communication...... mode, to communicate on interactive (dialogue-enabling) devices such as laptops, smartphones and tablets. Using the TV show Voice as our example, this article shows how the technological and situational set-up of the production invites viewers to engage in new ways of interaction and communication...

  18. Domain similarity based orthology detection.

    Science.gov (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  19. Talk Show Science.

    Science.gov (United States)

    Moore, Mitzi Ruth

    1992-01-01

    Proposes having students perform skits in which they play the roles of the science concepts they are trying to understand. Provides the dialog for a skit in which hot and cold gas molecules are interviewed on a talk show to study how these properties affect wind, rain, and other weather phenomena. (MDH)

  20. Obesity in show cats.

    Science.gov (United States)

    Corbee, R J

    2014-12-01

    Obesity is an important disease with a high prevalence in cats. Because obesity is related to several other diseases, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain cat breeds has been suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, 268 cats of 22 different breeds investigated by determining their body condition score (BCS) on a nine-point scale by inspection and palpation, at two different cat shows. Overall, 45.5% of the show cats had a BCS > 5, and 4.5% of the show cats had a BCS > 7. There were significant differences between breeds, which could be related to the breed standards. Most overweight and obese cats were in the neutered group. It warrants firm discussions with breeders and cat show judges to come to different interpretations of the standards in order to prevent overweight conditions in certain breeds from being the standard of beauty. Neutering predisposes for obesity and requires early nutritional intervention to prevent obese conditions. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

  1. Honored Teacher Shows Commitment.

    Science.gov (United States)

    Ratte, Kathy

    1987-01-01

    Part of the acceptance speech of the 1985 National Council for the Social Studies Teacher of the Year, this article describes the censorship experience of this honored social studies teacher. The incident involved the showing of a videotape version of the feature film entitled "The Seduction of Joe Tynan." (JDH)

  2. CERN on show

    CERN Multimedia

    2012-01-01

    Last week I was in Ankara to discuss Turkish accession to CERN, and to take part in the opening of CERN’s main travelling exhibition at the Middle East Technical University. I was astonished at the crowds of people the exhibition drew in, and I’m told that it’s a similar story wherever it goes. Our smaller exhibition stands are also much in demand across our Member States.   You don’t have to travel to Ankara, however, to experience the same phenomenon – just go to Building 33 any time from Monday to Saturday and you’ll get the idea. But although we’ve worked hard over recent years to increase our capacity for visits to a level approaching 80,000 per year, there’s still a long waiting list. And that’s a problem. The success of the Visits Service rests on the goodwill of all the CERNois who volunteer to be guides, as well as those who graciously allow increasing numbers of visitors into their workplaces...

  3. Similarity-based Fisherfaces

    DEFF Research Database (Denmark)

    Delgado-Gomez, David; Fagertun, Jens; Ersbøll, Bjarne Kjær

    2009-01-01

    databases (XM2VTS, AR and Equinox) show consistently good results. The proposed algorithm achieves Equal Error Rate (EER) and Half-Total Error Rate (HTER) values in the ranges of 0.41-1.67% and 0.1-1.95%, respectively. Our approach yields results comparable to the top two winners in recent contests reported...

  4. The energy show

    International Nuclear Information System (INIS)

    1988-01-01

    The Energy Show is a new look at the problems of world energy, where our supplies come from, now and in the future. The programme looks at how we need energy to maintain our standards of living. Energy supply is shown as the complicated set of problems it is - that Fossil Fuels are both raw materials and energy sources, that some 'alternatives' so readily suggested as practical options are in reality a long way from being effective. (author)

  5. Emergent self-similarity of cluster coagulation

    Science.gov (United States)

    Pushkin, Dmtiri O.

    A wide variety of nonequilibrium processes, such as coagulation of colloidal particles, aggregation of bacteria into colonies, coalescence of rain drops, bond formation between polymerization sites, and formation of planetesimals, fall under the rubric of cluster coagulation. We predict emergence of self-similar behavior in such systems when they are 'forced' by an external source of the smallest particles. The corresponding self-similar coagulation spectra prove to be power laws. Starting from the classical Smoluchowski coagulation equation, we identify the conditions required for emergence of self-similarity and show that the power-law exponent value for a particular coagulation mechanism depends on the homogeneity index of the corresponding coagulation kernel only. Next, we consider the current wave of mergers of large American banks as an 'unorthodox' application of coagulation theory. We predict that the bank size distribution has propensity to become a power law, and verify our prediction in a statistical study of the available economical data. We conclude this chapter by discussing economically significant phenomenon of capital condensation and predicting emergence of power-law distributions in other economical and social data. Finally, we turn to apparent semblance between cluster coagulation and turbulence and conclude that it is not accidental: both of these processes are instances of nonlinear cascades. This class of processes also includes river network formation models, certain force-chain models in granular mechanics, fragmentation due to collisional cascades, percolation, and growing random networks. We characterize a particular cascade by three indicies and show that the resulting power-law spectrum exponent depends on the indicies values only. The ensuing algebraic formula is remarkable for its simplicity.

  6. Modeling of similar economies

    Directory of Open Access Journals (Sweden)

    Sergey B. Kuznetsov

    2017-06-01

    Full Text Available Objective to obtain dimensionless criteria ndash economic indices characterizing the national economy and not depending on its size. Methods mathematical modeling theory of dimensions processing statistical data. Results basing on differential equations describing the national economy with the account of economical environment resistance two dimensionless criteria are obtained which allow to compare economies regardless of their sizes. With the theory of dimensions we show that the obtained indices are not accidental. We demonstrate the implementation of the obtained dimensionless criteria for the analysis of behavior of certain countriesrsquo economies. Scientific novelty the dimensionless criteria are obtained ndash economic indices which allow to compare economies regardless of their sizes and to analyze the dynamic changes in the economies with time. nbsp Practical significance the obtained results can be used for dynamic and comparative analysis of different countriesrsquo economies regardless of their sizes.

  7. Showing Value (Editorial

    Directory of Open Access Journals (Sweden)

    Denise Koufogiannakis

    2009-06-01

    Full Text Available When Su Cleyle and I first decided to start Evidence Based Library and Information Practice, one of the things we agreed upon immediately was that the journal be open access. We knew that a major obstacle to librarians using the research literature was that they did not have access to the research literature. Although Su and I are both academic librarians who can access a wide variety of library and information literature from our institutions, we belong to a profession where not everyone has equal access to the research in our field. Without such access to our own body of literature, how can we ever hope for practitioners to use research evidence in their decision making? It would have been contradictory to the principles of evidence based library and information practice to do otherwise.One of the specific groups we thought could use such an open access venue for discovering research literature was school librarians. School librarians are often isolated and lacking access to the research literature that may help them prove to stakeholders the importance of their libraries and their role within schools. Certainly, school libraries have been in decline and the use of evidence to show value is needed. As Ken Haycock noted in his 2003 report, The Crisis in Canada’s School Libraries: The Case for Reform and Reinvestment, “Across the country, teacher-librarians are losing their jobs or being reassigned. Collections are becoming depleted owing to budget cuts. Some principals believe that in the age of the Internet and the classroom workstation, the school library is an artifact” (9. Within this context, school librarians are looking to our research literature for evidence of the impact that school library programs have on learning outcomes and student success. They are integrating that evidence into their practice, and reflecting upon what can be improved locally. They are focusing on students and showing the impact of school libraries and

  8. Similarity analysis between quantum images

    Science.gov (United States)

    Zhou, Ri-Gui; Liu, XingAo; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

    2018-06-01

    Similarity analyses between quantum images are so essential in quantum image processing that it provides fundamental research for the other fields, such as quantum image matching, quantum pattern recognition. In this paper, a quantum scheme based on a novel quantum image representation and quantum amplitude amplification algorithm is proposed. At the end of the paper, three examples and simulation experiments show that the measurement result must be 0 when two images are same, and the measurement result has high probability of being 1 when two images are different.

  9. Microbial Communities Show Parallels at Sites with Distinct

    Czech Academy of Sciences Publication Activity Database

    Ságová-Marečková, M.; Omelka, M.; Čermák, L.; Kameník, Zdeněk; Olšovská, J.; Hackl, E.; Kopecký, J.; Hadacek, F.

    2011-01-01

    Roč. 77, č. 21 (2011), s. 7560-7567 ISSN 0099-2240 Institutional research plan: CEZ:AV0Z50200510 Keywords : 16S RIBOSOMAL-RNA * LENGTH-POLYMORPHISM ANALYSIS * MULTIPLE SEQUENCE ALIGNMENT Subject RIV: EE - Microbiology, Virology Impact factor: 3.829, year: 2011

  10. Personality similarity and life satisfaction in couples

    OpenAIRE

    Furler Katrin; Gomez Veronica; Grob Alexander

    2013-01-01

    The present study examined the association between personality similarity and life satisfaction in a large nationally representative sample of 1608 romantic couples. Similarity effects were computed for the Big Five personality traits as well as for personality profiles with global and differentiated indices of similarity. Results showed substantial actor and partner effects indicating that both partners' personality traits were related to both partners' life satisfaction. Personality similar...

  11. Plant defenses against parasitic plants show similarities to those induced by herbivores and pathogens

    Science.gov (United States)

    Justin B. Runyon; Mark C. Mescher; Consuelo M. De Moraes

    2010-01-01

    Herbivores and pathogens come quickly to mind when one thinks of the biotic challenges faced by plants. Important but less appreciated enemies are parasitic plants, which can have important consequences for the fitness and survival of their hosts. Our knowledge of plant perception, signaling and response to herbivores and pathogens has expanded rapidly in recent years...

  12. Self-similar gravitational clustering

    International Nuclear Information System (INIS)

    Efstathiou, G.; Fall, S.M.; Hogan, C.

    1979-01-01

    The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

  13. Similarity increases altruistic punishment in humans.

    Science.gov (United States)

    Mussweiler, Thomas; Ockenfels, Axel

    2013-11-26

    Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics--a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others' uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions.

  14. Surf similarity and solitary wave runup

    DEFF Research Database (Denmark)

    Fuhrman, David R.; Madsen, Per A.

    2008-01-01

    The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative to a previ...... functional dependence on their respective surf similarity parameters. Important equivalencies in the runup of sinusoidal and solitary waves are thus revealed.......The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative...... to a previous parameterization, which was not given in an explicit form. Good coherency with experimental (breaking) runup data is preserved with this simpler parameter. A recasting of analytical (nonbreaking) runup expressions for sinusoidal and solitary waves additionally shows that they contain identical...

  15. Site development

    International Nuclear Information System (INIS)

    Gaynor, R.K.

    1989-01-01

    Development of a low-level radioactive waste land disposal facility is little different than any industrial development of similar scope. Consideration must be made for normal business and operations management, security, facility maintenance, traffic control and necessary amenities for personnel. The item specific to the low-level waste site is the handling of radioactive waste materials and the regulatory and environmental protection procedures that must be planned for and accomodated in the site design and development. Each of these elements and the facility as a whole must be designed to be compatible with local land use plans, available transportation and support services, and the social and economic goals of the local community. Plans should also be made for quality control and orderly construction. This chapter deals with those aspects of the facility, its design and construction which are integral parts to the overall performance of the site

  16. Similar speaker recognition using nonlinear analysis

    International Nuclear Information System (INIS)

    Seo, J.P.; Kim, M.S.; Baek, I.C.; Kwon, Y.H.; Lee, K.S.; Chang, S.W.; Yang, S.I.

    2004-01-01

    Speech features of the conventional speaker identification system, are usually obtained by linear methods in spectral space. However, these methods have the drawback that speakers with similar voices cannot be distinguished, because the characteristics of their voices are also similar in spectral space. To overcome the difficulty in linear methods, we propose to use the correlation exponent in the nonlinear space as a new feature vector for speaker identification among persons with similar voices. We show that our proposed method surprisingly reduces the error rate of speaker identification system to speakers with similar voices

  17. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  18. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  19. Self-similar cosmological models

    Energy Technology Data Exchange (ETDEWEB)

    Chao, W Z [Cambridge Univ. (UK). Dept. of Applied Mathematics and Theoretical Physics

    1981-07-01

    The kinematics and dynamics of self-similar cosmological models are discussed. The degrees of freedom of the solutions of Einstein's equations for different types of models are listed. The relation between kinematic quantities and the classifications of the self-similarity group is examined. All dust local rotational symmetry models have been found.

  20. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  1. Towards Personalized Medicine: Leveraging Patient Similarity and Drug Similarity Analytics

    Science.gov (United States)

    Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

    2014-01-01

    The rapid adoption of electronic health records (EHR) provides a comprehensive source for exploratory and predictive analytic to support clinical decision-making. In this paper, we investigate how to utilize EHR to tailor treatments to individual patients based on their likelihood to respond to a therapy. We construct a heterogeneous graph which includes two domains (patients and drugs) and encodes three relationships (patient similarity, drug similarity, and patient-drug prior associations). We describe a novel approach for performing a label propagation procedure to spread the label information representing the effectiveness of different drugs for different patients over this heterogeneous graph. The proposed method has been applied on a real-world EHR dataset to help identify personalized treatments for hypercholesterolemia. The experimental results demonstrate the effectiveness of the approach and suggest that the combination of appropriate patient similarity and drug similarity analytics could lead to actionable insights for personalized medicine. Particularly, by leveraging drug similarity in combination with patient similarity, our method could perform well even on new or rarely used drugs for which there are few records of known past performance. PMID:25717413

  2. Correlation between social proximity and mobility similarity.

    Science.gov (United States)

    Fan, Chao; Liu, Yiding; Huang, Junming; Rong, Zhihai; Zhou, Tao

    2017-09-20

    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  3. Scalar Similarity for Relaxed Eddy Accumulation Methods

    Science.gov (United States)

    Ruppert, Johannes; Thomas, Christoph; Foken, Thomas

    2006-07-01

    The relaxed eddy accumulation (REA) method allows the measurement of trace gas fluxes when no fast sensors are available for eddy covariance measurements. The flux parameterisation used in REA is based on the assumption of scalar similarity, i.e., similarity of the turbulent exchange of two scalar quantities. In this study changes in scalar similarity between carbon dioxide, sonic temperature and water vapour were assessed using scalar correlation coefficients and spectral analysis. The influence on REA measurements was assessed by simulation. The evaluation is based on observations over grassland, irrigated cotton plantation and spruce forest. Scalar similarity between carbon dioxide, sonic temperature and water vapour showed a distinct diurnal pattern and change within the day. Poor scalar similarity was found to be linked to dissimilarities in the energy contained in the low frequency part of the turbulent spectra ( definition.

  4. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    Yoshifumi Fukunishi

    2009-01-01

    Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

  5. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  6. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  7. Fast business process similarity search

    NARCIS (Netherlands)

    Yan, Z.; Dijkman, R.M.; Grefen, P.W.P.J.

    2012-01-01

    Nowadays, it is common for organizations to maintain collections of hundreds or even thousands of business processes. Techniques exist to search through such a collection, for business process models that are similar to a given query model. However, those techniques compare the query model to each

  8. Glove boxes and similar containments

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    According to the present invention a glove box or similar containment is provided with an exhaust system including a vortex amplifier venting into the system, the vortex amplifier also having its main inlet in fluid flow connection with the containment and a control inlet in fluid flow connection with the atmosphere outside the containment. (U.S.)

  9. The baryonic self similarity of dark matter

    International Nuclear Information System (INIS)

    Alard, C.

    2014-01-01

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M 1/4 . These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  10. An Alfven eigenmode similarity experiment

    International Nuclear Information System (INIS)

    Heidbrink, W W; Fredrickson, E; Gorelenkov, N N; Hyatt, A W; Kramer, G; Luo, Y

    2003-01-01

    The major radius dependence of Alfven mode stability is studied by creating plasmas with similar minor radius, shape, magnetic field (0.5 T), density (n e ≅3x10 19 m -3 ), electron temperature (1.0 keV) and beam ion population (near-tangential 80 keV deuterium injection) on both NSTX and DIII-D. The major radius of NSTX is half the major radius of DIII-D. The super-Alfvenic beam ions that drive the modes have overlapping values of v f /v A in the two devices. Observed beam-driven instabilities include toroidicity-induced Alfven eigenmodes (TAE). The stability threshold for the TAE is similar in the two devices. As expected theoretically, the most unstable toroidal mode number n is larger in DIII-D

  11. Compressional Alfven Eigenmode Similarity Study

    Science.gov (United States)

    Heidbrink, W. W.; Fredrickson, E. D.; Gorelenkov, N. N.; Rhodes, T. L.

    2004-11-01

    NSTX and DIII-D are nearly ideal for Alfven eigenmode (AE) similarity experiments, having similar neutral beams, fast-ion to Alfven speed v_f/v_A, fast-ion pressure, and shape of the plasma, but with a factor of 2 difference in the major radius. Toroidicity-induced AE with ˜100 kHz frequencies were compared in an earlier study [1]; this paper focuses on higher frequency AE with f ˜ 1 MHz. Compressional AE (CAE) on NSTX have a polarization, dependence on the fast-ion distribution function, frequency scaling, and low-frequency limit that are qualitatively consistent with CAE theory [2]. Global AE (GAE) are also observed. On DIII-D, coherent modes in this frequency range are observed during low-field (0.6 T) similarity experiments. Experiments will compare the CAE stability limits on DIII-D with the NSTX stability limits, with the aim of determining if CAE will be excited by alphas in a reactor. Predicted differences in the frequency splitting Δ f between excited modes will also be used. \\vspace0.25em [1] W.W. Heidbrink, et al., Plasmas Phys. Control. Fusion 45, 983 (2003). [2] E.D. Fredrickson, et al., Princeton Plasma Physics Laboratory Report PPPL-3955 (2004).

  12. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  13. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  14. Similarity flows in relativistic hydrodynamics

    International Nuclear Information System (INIS)

    Blaizot, J.P.; Ollitrault, J.Y.

    1986-01-01

    In ultra-relativistic heavy ion collisions, one expects in particular to observe a deconfinement transition leading to a formation of quark gluon plasma. In the framework of the hydrodynamic model, experimental signatures of such a plasma may be looked for as observable consequences of a first order transition on the evolution of the system. In most of the possible scenario, the phase transition is accompanied with discontinuities in the hydrodynamic flow, such as shock waves. The method presented in this paper has been developed to treat without too much numerical effort such discontinuous flow. It relies heavily on the use of similarity solutions of the hydrodynamic equations

  15. Are calanco landforms similar to river basins?

    Science.gov (United States)

    Caraballo-Arias, N A; Ferro, V

    2017-12-15

    In the past badlands have been often considered as ideal field laboratories for studying landscape evolution because of their geometrical similarity to larger fluvial systems. For a given hydrological process, no scientific proof exists that badlands can be considered a model of river basin prototypes. In this paper the measurements carried out on 45 Sicilian calanchi, a type of badlands that appears as a small-scale hydrographic unit, are used to establish their morphological similarity with river systems whose data are available in the literature. At first the geomorphological similarity is studied by identifying the dimensionless groups, which can assume the same value or a scaled one in a fixed ratio, representing drainage basin shape, stream network and relief properties. Then, for each property, the dimensionless groups are calculated for the investigated calanchi and the river basins and their corresponding scale ratio is evaluated. The applicability of Hack's, Horton's and Melton's laws for establishing similarity criteria is also tested. The developed analysis allows to conclude that a quantitative morphological similarity between calanco landforms and river basins can be established using commonly applied dimensionless groups. In particular, the analysis showed that i) calanchi and river basins have a geometrically similar shape respect to the parameters Rf and Re with a scale factor close to 1, ii) calanchi and river basins are similar respect to the bifurcation and length ratios (λ=1), iii) for the investigated calanchi the Melton number assumes values less than that (0.694) corresponding to the river case and a scale ratio ranging from 0.52 and 0.78 can be used, iv) calanchi and river basins have similar mean relief ratio values (λ=1.13) and v) calanchi present active geomorphic processes and therefore fall in a more juvenile stage with respect to river basins. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Risk Aversion in Game Shows

    DEFF Research Database (Denmark)

    Andersen, Steffen; Harrison, Glenn W.; Lau, Morten I.

    2008-01-01

    We review the use of behavior from television game shows to infer risk attitudes. These shows provide evidence when contestants are making decisions over very large stakes, and in a replicated, structured way. Inferences are generally confounded by the subjective assessment of skill in some games......, and the dynamic nature of the task in most games. We consider the game shows Card Sharks, Jeopardy!, Lingo, and finally Deal Or No Deal. We provide a detailed case study of the analyses of Deal Or No Deal, since it is suitable for inference about risk attitudes and has attracted considerable attention....

  17. Measuring performance at trade shows

    DEFF Research Database (Denmark)

    Hansen, Kåre

    2004-01-01

    Trade shows is an increasingly important marketing activity to many companies, but current measures of trade show performance do not adequately capture dimensions important to exhibitors. Based on the marketing literature's outcome and behavior-based control system taxonomy, a model is built...... that captures a outcome-based sales dimension and four behavior-based dimensions (i.e. information-gathering, relationship building, image building, and motivation activities). A 16-item instrument is developed for assessing exhibitors perceptions of their trade show performance. The paper presents evidence...

  18. Cultural similarity and adjustment of expatriate academics

    DEFF Research Database (Denmark)

    Selmer, Jan; Lauring, Jakob

    2009-01-01

    The findings of a number of recent empirical studies of business expatriates, using different samples and methodologies, seem to support the counter-intuitive proposition that cultural similarity may be as difficult to adjust to as cultural dissimilarity. However, it is not obvious...... and non-EU countries. Results showed that although the perceived cultural similarity between host and home country for the two groups of investigated respondents was different, there was neither any difference in their adjustment nor in the time it took for them to become proficient. Implications...

  19. Measuring structural similarity in large online networks.

    Science.gov (United States)

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. A Novel Hybrid Similarity Calculation Model

    Directory of Open Access Journals (Sweden)

    Xiaoping Fan

    2017-01-01

    Full Text Available This paper addresses the problems of similarity calculation in the traditional recommendation algorithms of nearest neighbor collaborative filtering, especially the failure in describing dynamic user preference. Proceeding from the perspective of solving the problem of user interest drift, a new hybrid similarity calculation model is proposed in this paper. This model consists of two parts, on the one hand the model uses the function fitting to describe users’ rating behaviors and their rating preferences, and on the other hand it employs the Random Forest algorithm to take user attribute features into account. Furthermore, the paper combines the two parts to build a new hybrid similarity calculation model for user recommendation. Experimental results show that, for data sets of different size, the model’s prediction precision is higher than the traditional recommendation algorithms.

  1. Phonological similarity in working memory span tasks.

    Science.gov (United States)

    Chow, Michael; Macnamara, Brooke N; Conway, Andrew R A

    2016-08-01

    In a series of four experiments, we explored what conditions are sufficient to produce a phonological similarity facilitation effect in working memory span tasks. By using the same set of memoranda, but differing the secondary-task requirements across experiments, we showed that a phonological similarity facilitation effect is dependent upon the semantic relationship between the memoranda and the secondary-task stimuli, and is robust to changes in the representation, ordering, and pool size of the secondary-task stimuli. These findings are consistent with interference accounts of memory (Brown, Neath, & Chater, Psychological Review, 114, 539-576, 2007; Oberauer, Lewandowsky, Farrell, Jarrold, & Greaves, Psychonomic Bulletin & Review, 19, 779-819, 2012), whereby rhyming stimuli provide a form of categorical similarity that allows distractors to be excluded from retrieval at recall.

  2. Seniority bosons from similarity transformations

    International Nuclear Information System (INIS)

    Geyer, H.B.

    1986-01-01

    The requirement of associating in the boson space seniority with twice the number of non-s bosons defines a similarity transformation which re-expresses the Dyson pair boson images in terms of seniority bosons. In particular the fermion S-pair creation operator is mapped onto an operator which, unlike the pair boson image, does not change the number of non-s bosons. The original results of Otsuka, Arima and Iachello are recovered by this procedure while at the same time they are generalized to include g-bosons or even bosons with J>4 as well as any higher order boson terms. Furthermore the seniority boson images are valid for an arbitrary number of d- or g-bosons - a result which is not readily obtainable within the framework of the usual Marumori- or OAI-method

  3. Tokyo Motor Show 2003; Tokyo Motor Show 2003

    Energy Technology Data Exchange (ETDEWEB)

    Joly, E.

    2004-01-01

    The text which follows present the different techniques exposed during the 37. Tokyo Motor Show. The report points out the great tendencies of developments of the Japanese automobile industry. The hybrid electric-powered vehicles or those equipped with fuel cells have been highlighted by the Japanese manufacturers which allow considerable budgets in the research of less polluting vehicles. The exposed models, although being all different according to the manufacturer, use always a hybrid system: fuel cell/battery. The manufacturers have stressed too on the intelligent systems for navigation and safety as well as on the design and comfort. (O.M.)

  4. Alaska, Gulf spills share similarities

    International Nuclear Information System (INIS)

    Usher, D.

    1991-01-01

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide

  5. Reality show: um paradoxo nietzschiano

    Directory of Open Access Journals (Sweden)

    Ilana Feldman

    2011-01-01

    Full Text Available

    O fenômeno dos reality shows - e a subseqüente relação entre imagem e verdade - assenta-se sobre uma série de paradoxos. Tais paradoxos podem ser compreendidos à luz do pensamento do filósofo alemão Friedrich Nietzsche, que, através dos usos de formulações paradoxais, concebia a realidade como um mundo de pura aparência e a verdade como um acréscimo ficcional, como um efeito. A ficção é então tomada, na filosofia de Nietzsche, não em seu aspecto falsificante e desrealizador - como sempre pleiteou nossa tradição metafísica -, mas como condição necessária para que certa espécie de invenção possa operar como verdade. Sendo assim, a própria expressão reality show, através de sua formulação paradoxal, engendra explicitamente um mundo de pura aparência, em que a verdade, a parte reality da proposição, é da ordem do suplemento, daquilo que se acrescenta ficcionalmente - como um adjetivo - a show. O ornamento, nesse caso, passa a ocupar o lugar central, apontando para o efeito produzido: o efeito-de-verdade. Seguindo, então, o pensamento nietzschiano e sua atualização na contemporaneidade, investigaremos de que forma os televisivos “shows de realidade” operam paradoxalmente, em consonância com nossas paradoxais práticas culturais.

  6. Cancer mortality around nuclear sites

    International Nuclear Information System (INIS)

    Hill, C.; LaPlanche, A.

    1991-01-01

    Studies (including that of Gardner) of cancer mortality around individual nuclear sites in Britain show an excess of childhood leukemia near such sites. These have been attributed to radioactive discharges, increased radiation doses and radiation doses to the fathers of affected children. However, no such excess has been found in studies in other countries including France, Canada and the USA where similar radiation doses could have been received. Several explanations of this discrepancy are reviewed. It is possible that results from the small UK samples may be due to chance. A difference in external and internal doses for reprocessing plant workers may also be a factor. The possibility of a viral infection for leukemia spreading in new town populations is also mentioned. Whilst the studies in other countries are reassuring, the childhood leukemia excesses found in Britain round nuclear sites are still unexplained. (UK)

  7. Similarity-based Polymorphic Shellcode Detection

    Directory of Open Access Journals (Sweden)

    Denis Yurievich Gamayunov

    2013-02-01

    Full Text Available In the work the method for polymorphic shellcode dedection based on the set of known shellcodes is proposed. The method’s main idea is in sequential applying of deobfuscating transformations to a data analyzed and then recognizing similarity with malware samples. The method has been tested on the sets of shellcodes generated using Metasploit Framework v.4.1.0 and PELock Obfuscator and shows 87 % precision with zero false positives rate.

  8. Hanford Site environmental management specification

    International Nuclear Information System (INIS)

    Grygiel, M.L.

    1998-01-01

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL's application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents

  9. Hanford Site environmental management specification

    Energy Technology Data Exchange (ETDEWEB)

    Grygiel, M.L.

    1998-06-10

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL`s application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents.

  10. Popularity versus similarity in growing networks

    Science.gov (United States)

    Krioukov, Dmitri; Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, Mariangeles; Boguna, Marian

    2012-02-01

    Preferential attachment is a powerful mechanism explaining the emergence of scaling in growing networks. If new connections are established preferentially to more popular nodes in a network, then the network is scale-free. Here we show that not only popularity but also similarity is a strong force shaping the network structure and dynamics. We develop a framework where new connections, instead of preferring popular nodes, optimize certain trade-offs between popularity and similarity. The framework admits a geometric interpretation, in which preferential attachment emerges from local optimization processes. As opposed to preferential attachment, the optimization framework accurately describes large-scale evolution of technological (Internet), social (web of trust), and biological (E.coli metabolic) networks, predicting the probability of new links in them with a remarkable precision. The developed framework can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

  11. Similar on the Inside (pre-grinding)

    Science.gov (United States)

    2004-01-01

    This approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity show the rock called 'Pilbara' located in the small crater dubbed 'Fram.' The rock appears to be dotted with the same 'blueberries,' or spherules, found at 'Eagle Crater.' Spirit drilled into this rock with its rock abrasion tool. After analyzing the hole with the rover's scientific instruments, scientists concluded that Pilbara has a similar chemical make-up, and thus watery past, to rocks studied at Eagle Crater. This image was taken with the panoramic camera's 480-, 530- and 600-nanometer filters.

  12. Similar on the Inside (post-grinding)

    Science.gov (United States)

    2004-01-01

    This approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity show the hole drilled into the rock called 'Pilbara,' which is located in the small crater dubbed 'Fram.' Spirit drilled into this rock with its rock abrasion tool. The rock appears to be dotted with the same 'blueberries,' or spherules, found at 'Eagle Crater.' After analyzing the hole with the rover's scientific instruments, scientists concluded that Pilbara has a similar chemical make-up, and thus watery past, to rocks studied at Eagle Crater. This image was taken with the panoramic camera's 480-, 530- and 600-nanometer filters.

  13. Diversity patterns and freshwater molluscs similarities in small water reservoirs

    Directory of Open Access Journals (Sweden)

    Tomáš Čejka

    2011-02-01

    Full Text Available The survey presents the molluscan fauna from six impoundment systems of two sides (NW and SE of the Small Carpathians. Altogether 25 species (15 gastropod and 10 bivalve species were identified in reservoirs and their subsystems (inflows and outlets. The number of species per site ranged from 2 to 12, the mean number of species per site was 7. The mean number of individuals per site ranged from 15 to 905 (mean 174 ind/m2. Radix auricularia, R. ovata, Gyraulus albus, Gyraulus parvus/laevis, Hippeutis complanatus and Pisidium casertanum were present in more than 50% of reservoirs. The most abundant and frequent species in the entire area and all subsystems were Pisidium casertanum, Pisidium subtruncatum and Gyraulus parvus/laevis. Faunistic similarity indices indicate moderate degree of beta diversity i.e., differentiation among the sites; good separation of sites by cluster analysis indicates a different composition among inflows/outlets and littoral molluscan faunas of reservoirs.

  14. Development of similarity theory for control systems

    Science.gov (United States)

    Myshlyaev, L. P.; Evtushenko, V. F.; Ivushkin, K. A.; Makarov, G. V.

    2018-05-01

    The area of effective application of the traditional similarity theory and the need necessity of its development for systems are discussed. The main statements underlying the similarity theory of control systems are given. The conditions for the similarity of control systems and the need for similarity control control are formulated. Methods and algorithms for estimating and similarity control of control systems and the results of research of control systems based on their similarity are presented. The similarity control of systems includes the current evaluation of the degree of similarity of control systems and the development of actions controlling similarity, and the corresponding targeted change in the state of any element of control systems.

  15. Recombinant human melatonin receptor MT1 isolated in mixed detergents shows pharmacology similar to that in mammalian cell membranes.

    Directory of Open Access Journals (Sweden)

    Christel Logez

    Full Text Available The human melatonin MT1 receptor-belonging to the large family of G protein-coupled receptors (GPCRs-plays a key role in circadian rhythm regulation and is notably involved in sleep disorders and depression. Structural and functional information at the molecular level are highly desired for fine characterization of this receptor; however, adequate techniques for isolating soluble MT1 material suitable for biochemical and biophysical studies remain lacking. Here we describe the evaluation of a panel of constructs and host systems for the production of recombinant human MT1 receptors, and the screening of different conditions for their solubilization and purification. Our findings resulted in the establishment of an original strategy using a mixture of Fos14 and CHAPS detergents to extract and purify a recombinant human MT1 from Pichia pastoris membranes. This procedure enabled the recovery of relatively pure, monomeric and ligand-binding active MT1 receptor in the near-milligram range. A comparative study based on extensive ligand-binding characterization highlighted a very close correlation between the pharmacological profiles of MT1 purified from yeast and the same receptor present in mammalian cell membranes. The high quality of the purified MT1 was further confirmed by its ability to activate its cognate Gαi protein partner when reconstituted in lipid discs, thus opening novel paths to investigate this receptor by biochemical and biophysical approaches.

  16. Vinorelbine/carboplatin vs gemcitabine/carboplatin in advanced NSCLC shows similar efficacy, but different impact of toxicity

    DEFF Research Database (Denmark)

    Helbekkmo, N; Sundstrøm, S H; Aasebø, U

    2007-01-01

    This randomised phase III study in advanced non-small cell lung cancer (NSCLC) patients was conducted to compare vinorelbine/carboplatin (VC) and gemcitabine/carboplatin (GC) regarding efficacy, health-related quality of life (HRQOL) and toxicity. Chemonaive patients with NSCLC stage IIIB....../IV and WHO performance status 0-2 were eligible. No upper age limit was defined. Patients received vinorelbine 25 mg m(-2) or gemcitabine 1000 mg m(-2) on days 1 and 8 and carboplatin AUC4 on day 1 and three courses with 3-week cycles. HRQOL questionnaires were completed at baseline, before chemotherapy...... and every 8 weeks until 49 weeks. During 14 months, 432 patients were included (VC, n=218; GC, n=214). Median survival was 7.3 vs 6.4 months, 1-year survival 28 vs 30% and 2-year survival 7 vs 7% in the VC and GC arm, respectively (P=0.89). HRQOL, represented by global QOL, nausea/vomiting, dyspnoea...

  17. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish

    Czech Academy of Sciences Publication Activity Database

    Symonová, Radka; Majtánová, Zuzana; Arias-Rodriquez, L.; Mořkovský, L.; Kořínková, Tereza; Cavin, L.; Johnson Pokorná, Martina; Doležálková, Marie; Flajšhans, M.; Normandeau, E.; Ráb, Petr; Meyer, A.; Bernatchez, L.

    2017-01-01

    Roč. 328, č. 7 (2017), s. 607-619 ISSN 1552-5007 R&D Projects: GA ČR(CZ) GPP506/11/P596; GA ČR GA14-02940S Institutional support: RVO:67985904 Keywords : biased gene conversion * cold-blooded vertebrates * density gradient centrifugation Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.387, year: 2016

  18. Atxn2 Knockout and CAG42-Knock-in Cerebellum Shows Similarly Dysregulated Expression in Calcium Homeostasis Pathway.

    Science.gov (United States)

    Halbach, Melanie Vanessa; Gispert, Suzana; Stehning, Tanja; Damrath, Ewa; Walter, Michael; Auburger, Georg

    2017-02-01

    Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominantly inherited neurodegenerative disorder with preferential affection of Purkinje neurons, which are known as integrators of calcium currents. The expansion of a polyglutamine (polyQ) domain in the RNA-binding protein ataxin-2 (ATXN2) is responsible for this disease, but the causal roles of deficient ATXN2 functions versus aggregation toxicity are still under debate. Here, we studied mouse mutants with Atxn2 knockout (KO) regarding their cerebellar global transcriptome by microarray and RT-qPCR, in comparison with data from Atxn2-CAG42-knock-in (KIN) mouse cerebellum. Global expression downregulations involved lipid and growth signaling pathways in good agreement with previous data. As a novel effect, downregulations of key factors in calcium homeostasis pathways (the transcription factor Rora, transporters Itpr1 and Atp2a2, as well as regulator Inpp5a) were observed in the KO cerebellum, and some of them also occurred subtly early in KIN cerebellum. The ITPR1 protein levels were depleted from soluble fractions of cerebellum in both mutants, but accumulated in its membrane-associated form only in the SCA2 model. Coimmunoprecipitation demonstrated no association of ITPR1 with Q42-expanded or with wild-type ATXN2. These findings provide evidence that the physiological functions and protein interactions of ATXN2 are relevant for calcium-mediated excitation of Purkinje cells as well as for ATXN2-triggered neurotoxicity. These insights may help to understand pathogenesis and tissue specificity in SCA2 and other polyQ ataxias like SCA1, where inositol regulation of calcium flux and RORalpha play a role.

  19. Recombinant human melatonin receptor MT1 isolated in mixed detergents shows pharmacology similar to that in mammalian cell membranes.

    Science.gov (United States)

    Logez, Christel; Berger, Sylvie; Legros, Céline; Banères, Jean-Louis; Cohen, William; Delagrange, Philippe; Nosjean, Olivier; Boutin, Jean A; Ferry, Gilles; Simonin, Frédéric; Wagner, Renaud

    2014-01-01

    The human melatonin MT1 receptor-belonging to the large family of G protein-coupled receptors (GPCRs)-plays a key role in circadian rhythm regulation and is notably involved in sleep disorders and depression. Structural and functional information at the molecular level are highly desired for fine characterization of this receptor; however, adequate techniques for isolating soluble MT1 material suitable for biochemical and biophysical studies remain lacking. Here we describe the evaluation of a panel of constructs and host systems for the production of recombinant human MT1 receptors, and the screening of different conditions for their solubilization and purification. Our findings resulted in the establishment of an original strategy using a mixture of Fos14 and CHAPS detergents to extract and purify a recombinant human MT1 from Pichia pastoris membranes. This procedure enabled the recovery of relatively pure, monomeric and ligand-binding active MT1 receptor in the near-milligram range. A comparative study based on extensive ligand-binding characterization highlighted a very close correlation between the pharmacological profiles of MT1 purified from yeast and the same receptor present in mammalian cell membranes. The high quality of the purified MT1 was further confirmed by its ability to activate its cognate Gαi protein partner when reconstituted in lipid discs, thus opening novel paths to investigate this receptor by biochemical and biophysical approaches.

  20. Stochastic self-similar and fractal universe

    International Nuclear Information System (INIS)

    Iovane, G.; Laserra, E.; Tortoriello, F.S.

    2004-01-01

    The structures formation of the Universe appears as if it were a classically self-similar random process at all astrophysical scales. An agreement is demonstrated for the present hypotheses of segregation with a size of astrophysical structures by using a comparison between quantum quantities and astrophysical ones. We present the observed segregated Universe as the result of a fundamental self-similar law, which generalizes the Compton wavelength relation. It appears that the Universe has a memory of its quantum origin as suggested by R. Penrose with respect to quasi-crystal. A more accurate analysis shows that the present theory can be extended from the astrophysical to the nuclear scale by using generalized (stochastically) self-similar random process. This transition is connected to the relevant presence of the electromagnetic and nuclear interactions inside the matter. In this sense, the presented rule is correct from a subatomic scale to an astrophysical one. We discuss the near full agreement at organic cell scale and human scale too. Consequently the Universe, with its structures at all scales (atomic nucleus, organic cell, human, planet, solar system, galaxy, clusters of galaxy, super clusters of galaxy), could have a fundamental quantum reason. In conclusion, we analyze the spatial dimensions of the objects in the Universe as well as space-time dimensions. The result is that it seems we live in an El Naschie's E-infinity Cantorian space-time; so we must seriously start considering fractal geometry as the geometry of nature, a type of arena where the laws of physics appear at each scale in a self-similar way as advocated long ago by the Swedish school of astrophysics

  1. Marriage Matters: Spousal Similarity in Life Satisfaction

    OpenAIRE

    Ulrich Schimmack; Richard Lucas

    2006-01-01

    Examined the concurrent and cross-lagged spousal similarity in life satisfaction over a 21-year period. Analyses were based on married couples (N = 847) in the German Socio-Economic Panel (SOEP). Concurrent spousal similarity was considerably higher than one-year retest similarity, revealing spousal similarity in the variable component of life satisfac-tion. Spousal similarity systematically decreased with length of retest interval, revealing simi-larity in the changing component of life sati...

  2. A Minimum Spanning Tree Representation of Anime Similarities

    OpenAIRE

    Wibowo, Canggih Puspo

    2016-01-01

    In this work, a new way to represent Japanese animation (anime) is presented. We applied a minimum spanning tree to show the relation between anime. The distance between anime is calculated through three similarity measurements, namely crew, score histogram, and topic similarities. Finally, the centralities are also computed to reveal the most significance anime. The result shows that the minimum spanning tree can be used to determine the similarity anime. Furthermore, by using centralities c...

  3. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures

    OpenAIRE

    Someswara Rao, Chinta; Viswanadha Raju, S.

    2016-01-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship b...

  4. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  5. Preferential occupation of pyroxene sites by iron in diogenite meteorites

    International Nuclear Information System (INIS)

    Verma, H. C.; Tewari, V. C.; Paliwal, B. S.; Tripathi, R. P.

    2008-01-01

    Three diogenite meteorites ALHA77256-121, Tatahounie and Bilanga are studied using Moessbauer spectroscopy to look at the iron occupancy in the two inequivalent pyroxene sites. Though the three meteorites belong to three different conditions, one is an Antarctica find, one is 75 years old fall and one is a recent fall, the iron occupancy in pyroxene sites is very similar. Fe 2+ occupies only the less distorted site and hence a single sharp doublet is observed in the Moessbauer spectra of all these samples. In contrast eucrites show a distribution of iron ions in the two sites of pyroxenes.

  6. Self-similar pattern formation and continuous mechanics of self-similar systems

    Directory of Open Access Journals (Sweden)

    A. V. Dyskin

    2007-01-01

    Full Text Available In many cases, the critical state of systems that reached the threshold is characterised by self-similar pattern formation. We produce an example of pattern formation of this kind – formation of self-similar distribution of interacting fractures. Their formation starts with the crack growth due to the action of stress fluctuations. It is shown that even when the fluctuations have zero average the cracks generated by them could grow far beyond the scale of stress fluctuations. Further development of the fracture system is controlled by crack interaction leading to the emergence of self-similar crack distributions. As a result, the medium with fractures becomes discontinuous at any scale. We develop a continuum fractal mechanics to model its physical behaviour. We introduce a continuous sequence of continua of increasing scales covering this range of scales. The continuum of each scale is specified by the representative averaging volume elements of the corresponding size. These elements determine the resolution of the continuum. Each continuum hides the cracks of scales smaller than the volume element size while larger fractures are modelled explicitly. Using the developed formalism we investigate the stability of self-similar crack distributions with respect to crack growth and show that while the self-similar distribution of isotropically oriented cracks is stable, the distribution of parallel cracks is not. For the isotropically oriented cracks scaling of permeability is determined. For permeable materials (rocks with self-similar crack distributions permeability scales as cube of crack radius. This property could be used for detecting this specific mechanism of formation of self-similar crack distributions.

  7. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

    Among the several DOE sites that have been radiologically decontaminated under the auspices of the Nevada Operations Office are three whose physical characteristics are unique. These are the Tatum Dome Test Site (TDTS) near Hattiesburg, Mississippi; a location of mountainous terrain (Pahute Mesa) on the Nevada Test Site; and the GNOME site near Carlsbad, New Mexico. In each case the contamination, the terrain, and the climate conditions were different. This presentation includes a brief description of each site, the methods used to perform radiological surveys, the logistics required to support the decontamination (including health physics and sample analysis), and the specific techniques used to reduce or remove the contamination

  8. Hilar cholangiocarcinoma is pathologically similar to pancreatic duct adenocarcinoma: suggestions of similar background and development.

    Science.gov (United States)

    Nakanuma, Yasuni; Sato, Yasunori

    2014-07-01

    Routine experiences suggest that cholangiocarcinomas (CCAs) show different clinicopathological behaviors along the biliary tree, and hilar CCA apparently resembles pancreatic duct adenocarcinoma (PDAC). Herein, the backgrounds for these similarities were reviewed. While all cases of PDAC, hilar CCA, intrahepatic CCA (ICCA) and CCA components of combined hepatocellular-cholangiocarcinoma (cHC-CCA) were adenocarcinomas, micropapillary patterns and columnar carcinoma cells were common in PDAC and hilar CCA, and trabecular components and cuboidal carcinoma cells were common in ICCA and CCA components of cHC-CCA. Anterior gradient protein-2 and S100P were frequently expressed in perihilar CCA and PDAC, while neural cell adhesion molecule and luminal epithelial membrane antigen were common in CCA components of c-HC-CCA. Pdx1 and Hes1 were frequently and markedly expressed aberrantly in PDAC and perihilar CCA, although their expression was rare and mild in CCA components in cHC-CCA and ICCA. Hilar CCA showed a similar postoperative prognosis to PDAC but differed from ICCA and cHC-CCA. Taken together, hilar CCA may differ from ICCA and CCA components of cHC-CCA but have a similar development to PDAC. These similarities may be explained by the unique anatomical, embryological and reactive nature of the pancreatobiliary tract. Further studies of these intractable malignancies are warranted. © 2014 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

  9. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  10. On different forms of self similarity

    International Nuclear Information System (INIS)

    Aswathy, R.K.; Mathew, Sunil

    2016-01-01

    Fractal geometry is mainly based on the idea of self-similar forms. To be self-similar, a shape must able to be divided into parts that are smaller copies, which are more or less similar to the whole. There are different forms of self similarity in nature and mathematics. In this paper, some of the topological properties of super self similar sets are discussed. It is proved that in a complete metric space with two or more elements, the set of all non super self similar sets are dense in the set of all non-empty compact sub sets. It is also proved that the product of self similar sets are super self similar in product metric spaces and that the super self similarity is preserved under isometry. A characterization of super self similar sets using contracting sub self similarity is also presented. Some relevant counterexamples are provided. The concepts of exact super and sub self similarity are introduced and a necessary and sufficient condition for a set to be exact super self similar in terms of condensation iterated function systems (Condensation IFS’s) is obtained. A method to generate exact sub self similar sets using condensation IFS’s and the denseness of exact super self similar sets are also discussed.

  11. Popularity versus similarity in growing networks.

    Science.gov (United States)

    Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, M Ángeles; Boguñá, Marián; Krioukov, Dmitri

    2012-09-27

    The principle that 'popularity is attractive' underlies preferential attachment, which is a common explanation for the emergence of scaling in growing networks. If new connections are made preferentially to more popular nodes, then the resulting distribution of the number of connections possessed by nodes follows power laws, as observed in many real networks. Preferential attachment has been directly validated for some real networks (including the Internet), and can be a consequence of different underlying processes based on node fitness, ranking, optimization, random walks or duplication. Here we show that popularity is just one dimension of attractiveness; another dimension is similarity. We develop a framework in which new connections optimize certain trade-offs between popularity and similarity, instead of simply preferring popular nodes. The framework has a geometric interpretation in which popularity preference emerges from local optimization. As opposed to preferential attachment, our optimization framework accurately describes the large-scale evolution of technological (the Internet), social (trust relationships between people) and biological (Escherichia coli metabolic) networks, predicting the probability of new links with high precision. The framework that we have developed can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

  12. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

    The present paper deals with criteria for the choice of a production unit or power plant site, the organization and development of a site in terms of its particular characteristics and takes into account personnel considerations in site organizations as well as the problem of integrating the architecture into the environment. (RW) [de

  13. Humans and mice express similar olfactory preferences.

    Directory of Open Access Journals (Sweden)

    Nathalie Mandairon

    Full Text Available In humans, the pleasantness of odors is a major contributor to social relationships and food intake. Smells evoke attraction and repulsion responses, reflecting the hedonic value of the odorant. While olfactory preferences are known to be strongly modulated by experience and learning, it has been recently suggested that, in humans, the pleasantness of odors may be partly explained by the physicochemical properties of the odorant molecules themselves. If odor hedonic value is indeed predetermined by odorant structure, then it could be hypothesized that other species will show similar odor preferences to humans. Combining behavioral and psychophysical approaches, we here show that odorants rated as pleasant by humans were also those which, behaviorally, mice investigated longer and human subjects sniffed longer, thereby revealing for the first time a component of olfactory hedonic perception conserved across species. Consistent with this, we further show that odor pleasantness rating in humans and investigation time in mice were both correlated with the physicochemical properties of the molecules, suggesting that olfactory preferences are indeed partly engraved in the physicochemical structure of the odorant. That odor preferences are shared between mammal species and are guided by physicochemical features of odorant stimuli strengthens the view that odor preference is partially predetermined. These findings open up new perspectives for the study of the neural mechanisms of hedonic perception.

  14. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.

    Science.gov (United States)

    Someswara Rao, Chinta; Viswanadha Raju, S

    2016-03-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship between the H. sapiens and monkey. This similarity will be helpful at theft identification, maternity identification, disease identification, etc.

  15. Being similar while judging right and wrong: The effects of personal and situational similarity on moral judgements.

    Science.gov (United States)

    Pascal, Emilia

    2017-07-20

    This study investigated the effects of similarity with the transgressor and the victim on the perceived immorality of the transgression. Participants read two stories describing a person that cheated on their partner and a police officer that mistreated somebody. In the first story we manipulated participants' personal similarity to the transgressor and in the second their personal similarity to the victim. In each story, participants' past situational similarity to the target character was assessed according to their previous experiences of being in the same position. Results show that both personal and past situational similarity to the transgressor determine less severe moral judgements, while personal and past situational similarity with the victim have the opposite effect. We also tested several potential mediators of these effects, derived from competing theoretical accounts of the influence of similarity on perceived responsibility. Empathy emerged as mediating most of the effects of similarity on moral judgements, except those induced by past situational similarity with the victim. The foreseen probability of being in a similar situation mediated only the effects of similarity to the transgressor, and not those of similarity to the victim. Overall, results highlight the complex mechanisms of the influences of similarity on moral judgements. © 2017 International Union of Psychological Science.

  16. Site operations

    International Nuclear Information System (INIS)

    House, W.B.; Ebenhack, D.G.

    1989-01-01

    This chapter is a discussion of the management and operations practices used at the Barnwell Waste Management Facility in Barnwell, SC. The following topics are discussed: (1) Waste receiving and inspection, including manifest and certificates of compliance, radiological surveys, disposition of nonconforming items, and decontamination and disposition of secondary waste streams; (2) Waste disposal, including Title 10 CFR 61 requirements, disposal area evaluations, shipment offloading, container emplacement, and radiation protection; (3) Trench closure, including trench backfilling, trench capping, and permanent markers; (4) Site maintenance and stabilization, including trench maintenance, surface water management, and site closure activities; (5) Site monitoring programs, including operational monitoring, and environmental monitoring program; (6) Personnel training and qualifications, including basic training program, safety training program, special skills training, and physical qualifications; (7) Records management, including waste records, personnel training records, personnel dosimetry records, site monitoring records, trench qualification and construction records, and site drawings and stabilization records; (8) Site security; (9) Emergency response plans; and (10) Quality assurance

  17. Hanford Site Environmental Management Specification

    International Nuclear Information System (INIS)

    DAILY, J.L.

    2001-01-01

    The US Department of Energy, Richland Operations Office (RL) has established a document hierarchy as part of its integrated management system. The Strategic Plan defines the vision, values, missions, strategic goals, high-level outcomes, and the basic strategies in achieving those outcomes. As shown in Figure 1-1, the Site Specification derives requirements from the Strategic Plan and documents the top-level mission technical requirements for the work involved in the RL Hanford Site cleanup and infrastructure activities under the responsibility of the U.S. Department of Energy, Office of Environmental Management (EM). It also provides the basis for all contract technical requirements. Since this is limited to the EM work, neither the Fast Flux Test Facility (FFTF) nor the Pacific Northwest National Laboratory (PNNL) non-EM science activities are included. Figure 1-1 also shows the relationship between this Site Specification and the other Site management and planning documents. Similarly, the documents, orders, and laws referenced in this document represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents

  18. Determination of subjective similarity for pairs of masses and pairs of clustered microcalcifications on mammograms: Comparison of similarity ranking scores and absolute similarity ratings

    International Nuclear Information System (INIS)

    Muramatsu, Chisako; Li Qiang; Schmidt, Robert A.; Shiraishi, Junji; Suzuki, Kenji; Newstead, Gillian M.; Doi, Kunio

    2007-01-01

    The presentation of images that are similar to that of an unknown lesion seen on a mammogram may be helpful for radiologists to correctly diagnose that lesion. For similar images to be useful, they must be quite similar from the radiologists' point of view. We have been trying to quantify the radiologists' impression of similarity for pairs of lesions and to establish a ''gold standard'' for development and evaluation of a computerized scheme for selecting such similar images. However, it is considered difficult to reliably and accurately determine similarity ratings, because they are subjective. In this study, we compared the subjective similarities obtained by two different methods, an absolute rating method and a 2-alternative forced-choice (2AFC) method, to demonstrate that reliable similarity ratings can be determined by the responses of a group of radiologists. The absolute similarity ratings were previously obtained for pairs of masses and pairs of microcalcifications from five and nine radiologists, respectively. In this study, similarity ranking scores for eight pairs of masses and eight pairs of microcalcifications were determined by use of the 2AFC method. In the first session, the eight pairs of masses and eight pairs of microcalcifications were grouped and compared separately for determining the similarity ranking scores. In the second session, another similarity ranking score was determined by use of mixed pairs, i.e., by comparison of the similarity of a mass pair with that of a calcification pair. Four pairs of masses and four pairs of microcalcifications were grouped together to create two sets of eight pairs. The average absolute similarity ratings and the average similarity ranking scores showed very good correlations in the first study (Pearson's correlation coefficients: 0.94 and 0.98 for masses and microcalcifications, respectively). Moreover, in the second study, the correlations between the absolute ratings and the ranking scores were also

  19. Perceptions of Ideal and Former Partners’ Personality and Similarity

    Directory of Open Access Journals (Sweden)

    Pieternel Dijkstra

    2010-12-01

    Full Text Available The present study aimed to test predictions based on both the ‗similarity-attraction‘ hypothesis and the ‗attraction-similarity‘ hypothesis, by studying perceptions of ideal and former partners. Based on the ‗similarity-attraction‘ hypothesis, we expected individuals to desire ideal partners who are similar to the self in personality. In addition, based on the ‗attraction-similarity hypothesis‘, we expected individuals to perceive former partners as dissimilar to them in terms of personality. Findings showed that, whereas the ideal partner was seen as similar to and more positive than the self, the former partner was seen as dissimilar to and more negative than the self. In addition, our study showed that individuals did not rate similarity in personality as very important when seeking a mate. Our findings may help understand why so many relationships end in divorce due to mismatches in personality.

  20. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim; Cisse, Moustapha; Gao, Xin; Zhang, Xiangliang

    2016-01-01

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer

  1. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji; Genton, Marc G.; Jun, Mikyoung

    2016-01-01

    extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi

  2. Similarity queries for temporal toxicogenomic expression profiles.

    Directory of Open Access Journals (Sweden)

    Adam A Smith

    2008-07-01

    Full Text Available We present an approach for answering similarity queries about gene expression time series that is motivated by the task of characterizing the potential toxicity of various chemicals. Our approach involves two key aspects. First, our method employs a novel alignment algorithm based on time warping. Our time warping algorithm has several advantages over previous approaches. It allows the user to impose fairly strong biases on the form that the alignments can take, and it permits a type of local alignment in which the entirety of only one series has to be aligned. Second, our method employs a relaxed spline interpolation to predict expression responses for unmeasured time points, such that the spline does not necessarily exactly fit every observed point. We evaluate our approach using expression time series from the Edge toxicology database. Our experiments show the value of using spline representations for sparse time series. More significantly, they show that our time warping method provides more accurate alignments and classifications than previous standard alignment methods for time series.

  3. NASA GIBS Use in Live Planetarium Shows

    Science.gov (United States)

    Emmart, C. B.

    2015-12-01

    The American Museum of Natural History's Hayden Planetarium was rebuilt in year 2000 as an immersive theater for scientific data visualization to show the universe in context to our planet. Specific astrophysical movie productions provide the main daily programming, but interactive control software, developed at AMNH allows immersive presentation within a data aggregation of astronomical catalogs called the Digital Universe 3D Atlas. Since 2006, WMS globe browsing capabilities have been built into a software development collaboration with Sweden's Linkoping University (LiU). The resulting Uniview software, now a product of the company SCISS, is operated by about fifty planetariums around that world with ability to network amongst the sites for global presentations. Public presentation of NASA GIBS has allowed authoritative narratives to be presented within the range of data available in context to other sources such as Science on a Sphere, NASA Earth Observatory and Google Earth KML resources. Specifically, the NOAA supported World Views Network conducted a series of presentations across the US that focused on local ecological issues that could then be expanded in the course of presentation to national and global scales of examination. NASA support of for GIBS resources in an easy access multi scale streaming format like WMS has tremendously enabled particularly facile presentations of global monitoring like never before. Global networking of theaters for distributed presentations broadens out the potential for impact of this medium. Archiving and refinement of these presentations has already begun to inform new types of documentary productions that examine pertinent, global interdependency topics.

  4. Optimal neighborhood indexing for protein similarity search.

    Science.gov (United States)

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-12-16

    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  5. Optimal neighborhood indexing for protein similarity search

    Directory of Open Access Journals (Sweden)

    Nguyen Van

    2008-12-01

    Full Text Available Abstract Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. Results The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. Conclusion We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  6. Interpersonal Similarity and Knowledge Sharing within Multinational Organizations

    DEFF Research Database (Denmark)

    Mäkelä, Kristiina; Andersson, Ulf; Seppälä, Tomi

    2012-01-01

    Previous research has established that interpersonal similarity can influence knowledge sharing in such a way that similar people are more likely to share knowledge than those who are dissimilar. We contribute to the literature by showing that in the MNC context, cultural and functional similarit....... These microfoundations of inter-unit knowledge exchange point to important theoretical and practical implications for international management....

  7. Engaging narratives evoke similar neural activity and lead to similar time perception.

    Science.gov (United States)

    Cohen, Samantha S; Henin, Simon; Parra, Lucas C

    2017-07-04

    It is said that we lose track of time - that "time flies" - when we are engrossed in a story. How does engagement with the story cause this distorted perception of time, and what are its neural correlates? People commit both time and attentional resources to an engaging stimulus. For narrative videos, attentional engagement can be represented as the level of similarity between the electroencephalographic responses of different viewers. Here we show that this measure of neural engagement predicted the duration of time that viewers were willing to commit to narrative videos. Contrary to popular wisdom, engagement did not distort the average perception of time duration. Rather, more similar brain responses resulted in a more uniform perception of time across viewers. These findings suggest that by capturing the attention of an audience, narrative videos bring both neural processing and the subjective perception of time into synchrony.

  8. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  9. Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.

    Science.gov (United States)

    Osipiuk, J; Górnicki, P; Maj, L; Dementieva, I; Laskowski, R; Joachimiak, A

    2001-11-01

    The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 A. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 A from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer alpha/beta sandwich with the overall shape of a cylinder and shows no structural homology to proteins of known structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the alpha-beta plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.

  10. Similarity of eigenstates in generalized labyrinth tilings

    International Nuclear Information System (INIS)

    Thiem, Stefanie; Schreiber, Michael

    2010-01-01

    The eigenstates of d-dimensional quasicrystalline models with a separable Hamiltonian are studied within the tight-binding model. The approach is based on mathematical sequences, constructed by an inflation rule P = {w → s,s → sws b-1 } describing the weak/strong couplings of atoms in a quasiperiodic chain. Higher-dimensional quasiperiodic tilings are constructed as a direct product of these chains and their eigenstates can be directly calculated by multiplying the energies E or wave functions ψ of the chain, respectively. Applying this construction rule, the grid in d dimensions splits into 2 d-1 different tilings, for which we investigated the characteristics of the wave functions. For the standard two-dimensional labyrinth tiling constructed from the octonacci sequence (b = 2) the lattice breaks up into two identical lattices, which consequently yield the same eigenstates. While this is not the case for b ≠ 2, our numerical results show that the wave functions of the different grids become increasingly similar for large system sizes. This can be explained by the fact that the structure of the 2 d-1 grids mainly differs at the boundaries and thus for large systems the eigenstates approach each other. This property allows us to analytically derive properties of the higher-dimensional generalized labyrinth tilings from the one-dimensional results. In particular participation numbers and corresponding scaling exponents have been determined.

  11. Genetic and 'cultural' similarity in wild chimpanzees.

    Science.gov (United States)

    Langergraber, Kevin E; Boesch, Christophe; Inoue, Eiji; Inoue-Murayama, Miho; Mitani, John C; Nishida, Toshisada; Pusey, Anne; Reynolds, Vernon; Schubert, Grit; Wrangham, Richard W; Wroblewski, Emily; Vigilant, Linda

    2011-02-07

    The question of whether animals possess 'cultures' or 'traditions' continues to generate widespread theoretical and empirical interest. Studies of wild chimpanzees have featured prominently in this discussion, as the dominant approach used to identify culture in wild animals was first applied to them. This procedure, the 'method of exclusion,' begins by documenting behavioural differences between groups and then infers the existence of culture by eliminating ecological explanations for their occurrence. The validity of this approach has been questioned because genetic differences between groups have not explicitly been ruled out as a factor contributing to between-group differences in behaviour. Here we investigate this issue directly by analysing genetic and behavioural data from nine groups of wild chimpanzees. We find that the overall levels of genetic and behavioural dissimilarity between groups are highly and statistically significantly correlated. Additional analyses show that only a very small number of behaviours vary between genetically similar groups, and that there is no obvious pattern as to which classes of behaviours (e.g. tool-use versus communicative) have a distribution that matches patterns of between-group genetic dissimilarity. These results indicate that genetic dissimilarity cannot be eliminated as playing a major role in generating group differences in chimpanzee behaviour.

  12. Phonological similarity and orthographic similarity affect probed serial recall of Chinese characters.

    Science.gov (United States)

    Lin, Yi-Chen; Chen, Hsiang-Yu; Lai, Yvonne C; Wu, Denise H

    2015-04-01

    The previous literature on working memory (WM) has indicated that verbal materials are dominantly retained in phonological representations, whereas other linguistic information (e.g., orthography, semantics) only contributes to verbal WM minimally, if not negligibly. Although accumulating evidence has suggested that multiple linguistic components jointly support verbal WM, the visual/orthographic contribution has rarely been addressed in alphabetic languages, possibly due to the difficulty of dissociating the effects of word forms from the effects of their pronunciations in relatively shallow orthography. In the present study, we examined whether the orthographic representations of Chinese characters support the retention of verbal materials in this language of deep orthography. In Experiments 1a and 2, we independently manipulated the phonological and orthographic similarity of horizontal and vertical characters, respectively, and found that participants' accuracy of probed serial recall was reduced by both similar pronunciations and shared phonetic radicals in the to-be-remembered stimuli. Moreover, Experiment 1b showed that only the effect of phonological, but not that of orthographic, similarity was affected by concurrent articulatory suppression. Taken together, the present results indicate the indispensable contribution of orthographic representations to verbal WM of Chinese characters, and suggest that the linguistic characteristics of a specific language not only determine long-term linguistic-processing mechanisms, but also delineate the organization of verbal WM for that language.

  13. Similar or different? The role of the ventrolateral prefrontal cortex in similarity detection.

    Directory of Open Access Journals (Sweden)

    Béatrice Garcin

    Full Text Available Patients with frontal lobe syndrome can exhibit two types of abnormal behaviour when asked to place a banana and an orange in a single category: some patients categorize them at a concrete level (e.g., "both have peel", while others continue to look for differences between these objects (e.g., "one is yellow, the other is orange". These observations raise the question of whether abstraction and similarity detection are distinct processes involved in abstract categorization, and that depend on separate areas of the prefrontal cortex (PFC. We designed an original experimental paradigm for a functional magnetic resonance imaging (fMRI study involving healthy subjects, confirming the existence of two distinct processes relying on different prefrontal areas, and thus explaining the behavioural dissociation in frontal lesion patients. We showed that: 1 Similarity detection involves the anterior ventrolateral PFC bilaterally with a right-left asymmetry: the right anterior ventrolateral PFC is only engaged in detecting physical similarities; 2 Abstraction per se activates the left dorsolateral PFC.

  14. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  15. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  16. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

    The subject of this paper is a general view over all necessary considerations to develop the site after it has been chosen and before starting with the construction of a nuclear power plant. (orig./RW) [de

  17. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO 2 content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate

  18. Detection of secondary binding sites in proteins using fragment screening.

    Science.gov (United States)

    Ludlow, R Frederick; Verdonk, Marcel L; Saini, Harpreet K; Tickle, Ian J; Jhoti, Harren

    2015-12-29

    Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

  19. Dynamical similarity of geomagnetic field reversals.

    Science.gov (United States)

    Valet, Jean-Pierre; Fournier, Alexandre; Courtillot, Vincent; Herrero-Bervera, Emilio

    2012-10-04

    No consensus has been reached so far on the properties of the geomagnetic field during reversals or on the main features that might reveal its dynamics. A main characteristic of the reversing field is a large decrease in the axial dipole and the dominant role of non-dipole components. Other features strongly depend on whether they are derived from sedimentary or volcanic records. Only thermal remanent magnetization of lava flows can capture faithful records of a rapidly varying non-dipole field, but, because of episodic volcanic activity, sequences of overlying flows yield incomplete records. Here we show that the ten most detailed volcanic records of reversals can be matched in a very satisfactory way, under the assumption of a common duration, revealing common dynamical characteristics. We infer that the reversal process has remained unchanged, with the same time constants and durations, at least since 180 million years ago. We propose that the reversing field is characterized by three successive phases: a precursory event, a 180° polarity switch and a rebound. The first and third phases reflect the emergence of the non-dipole field with large-amplitude secular variation. They are rarely both recorded at the same site owing to the rapidly changing field geometry and last for less than 2,500 years. The actual transit between the two polarities does not last longer than 1,000 years and might therefore result from mechanisms other than those governing normal secular variation. Such changes are too brief to be accurately recorded by most sediments.

  20. On self-similar Tolman models

    International Nuclear Information System (INIS)

    Maharaj, S.D.

    1988-01-01

    The self-similar spherically symmetric solutions of the Einstein field equation for the case of dust are identified. These form a subclass of the Tolman models. These self-similar models contain the solution recently presented by Chi [J. Math. Phys. 28, 1539 (1987)], thereby refuting the claim of having found a new solution to the Einstein field equations

  1. Mining Diagnostic Assessment Data for Concept Similarity

    Science.gov (United States)

    Madhyastha, Tara; Hunt, Earl

    2009-01-01

    This paper introduces a method for mining multiple-choice assessment data for similarity of the concepts represented by the multiple choice responses. The resulting similarity matrix can be used to visualize the distance between concepts in a lower-dimensional space. This gives an instructor a visualization of the relative difficulty of concepts…

  2. Similarity indices I: what do they measure

    International Nuclear Information System (INIS)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities

  3. Measuring transferring similarity via local information

    Science.gov (United States)

    Yin, Likang; Deng, Yong

    2018-05-01

    Recommender systems have developed along with the web science, and how to measure the similarity between users is crucial for processing collaborative filtering recommendation. Many efficient models have been proposed (i.g., the Pearson coefficient) to measure the direct correlation. However, the direct correlation measures are greatly affected by the sparsity of dataset. In other words, the direct correlation measures would present an inauthentic similarity if two users have a very few commonly selected objects. Transferring similarity overcomes this drawback by considering their common neighbors (i.e., the intermediates). Yet, the transferring similarity also has its drawback since it can only provide the interval of similarity. To break the limitations, we propose the Belief Transferring Similarity (BTS) model. The contributions of BTS model are: (1) BTS model addresses the issue of the sparsity of dataset by considering the high-order similarity. (2) BTS model transforms uncertain interval to a certain state based on fuzzy systems theory. (3) BTS model is able to combine the transferring similarity of different intermediates using information fusion method. Finally, we compare BTS models with nine different link prediction methods in nine different networks, and we also illustrate the convergence property and efficiency of the BTS model.

  4. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco

    2008-01-01

    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes th...

  5. Self-Similar Traffic In Wireless Networks

    OpenAIRE

    Jerjomins, R.; Petersons, E.

    2005-01-01

    Many studies have shown that traffic in Ethernet and other wired networks is self-similar. This paper reveals that wireless network traffic is also self-similar and long-range dependant by analyzing big amount of data captured from the wireless router.

  6. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth

    1985-01-01

    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  7. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities.

  8. Information filtering based on transferring similarity.

    Science.gov (United States)

    Sun, Duo; Zhou, Tao; Liu, Jian-Guo; Liu, Run-Ran; Jia, Chun-Xiao; Wang, Bing-Hong

    2009-07-01

    In this Brief Report, we propose an index of user similarity, namely, the transferring similarity, which involves all high-order similarities between users. Accordingly, we design a modified collaborative filtering algorithm, which provides remarkably higher accurate predictions than the standard collaborative filtering. More interestingly, we find that the algorithmic performance will approach its optimal value when the parameter, contained in the definition of transferring similarity, gets close to its critical value, before which the series expansion of transferring similarity is convergent and after which it is divergent. Our study is complementary to the one reported in [E. A. Leicht, P. Holme, and M. E. J. Newman, Phys. Rev. E 73, 026120 (2006)], and is relevant to the missing link prediction problem.

  9. Self-similar continued root approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.

    2012-01-01

    A novel method of summing asymptotic series is advanced. Such series repeatedly arise when employing perturbation theory in powers of a small parameter for complicated problems of condensed matter physics, statistical physics, and various applied problems. The method is based on the self-similar approximation theory involving self-similar root approximants. The constructed self-similar continued roots extrapolate asymptotic series to finite values of the expansion parameter. The self-similar continued roots contain, as a particular case, continued fractions and Padé approximants. A theorem on the convergence of the self-similar continued roots is proved. The method is illustrated by several examples from condensed-matter physics.

  10. Similarity in Bilateral Isolated Internal Orbital Fractures.

    Science.gov (United States)

    Chen, Hung-Chang; Cox, Jacob T; Sanyal, Abanti; Mahoney, Nicholas R

    2018-04-13

    In evaluating patients sustaining bilateral isolated internal orbital fractures, the authors have observed both similar fracture locations and also similar expansion of orbital volumes. In this study, we aim to investigate if there is a propensity for the 2 orbits to fracture in symmetrically similar patterns when sustaining similar trauma. A retrospective chart review was performed studying all cases at our institution of bilateral isolated internal orbital fractures involving the medial wall and/or the floor at the time of presentation. The similarity of the bilateral fracture locations was evaluated using the Fisher's exact test. The bilateral expanded orbital volumes were analyzed using the Wilcoxon signed-rank test to assess for orbital volume similarity. Twenty-four patients with bilateral internal orbital fractures were analyzed for fracture location similarity. Seventeen patients (70.8%) had 100% concordance in the orbital subregion fractured, and the association between the right and the left orbital fracture subregion locations was statistically significant (P < 0.0001). Fifteen patients were analyzed for orbital volume similarity. The average orbital cavity volume was 31.2 ± 3.8 cm on the right and 32.0 ± 3.7 cm on the left. There was a statistically significant difference between right and left orbital cavity volumes (P = 0.0026). The data from this study suggest that an individual who suffers isolated bilateral internal orbital fractures has a statistically significant similarity in the location of their orbital fractures. However, there does not appear to be statistically significant similarity in the expansion of the orbital volumes in these patients.

  11. Opioid binding site in EL-4 thymoma cell line

    International Nuclear Information System (INIS)

    Fiorica, E.; Spector, S.

    1988-01-01

    Using EL-4 thymoma cell-line we found a binding site similar to the k opioid receptor of the nervous system. The Scatchard analysis of the binding of [ 3 H] bremazocine indicated a single site with a K/sub D/ = 60 +/- 17 nM and Bmax = 2.7 +/- 0.8 pmols/10 6 cells. To characterize this binding site, competition studies were performed using selective compounds for the various opioid receptors. The k agonist U-50,488H was the most potent displacer of [ 3 H] bremazocine with an IC 50 value = 0.57μM. The two steroisomers levorphanol and dextrorphan showed the same affinity for this site. While morphine, [D-Pen 2 , D-Pen 5 ] enkephalin and β-endorphin failed to displace, except at very high concentrations, codeine demonstrated a IC 50 = 60μM, that was similar to naloxone. 32 references, 3 figures, 2 tables

  12. Hybrid pine for tough sites

    International Nuclear Information System (INIS)

    Davidson, W.H.

    1994-01-01

    A test planting of 30 first- and second-generation pitch x loblolly pine (pinus rigida x P. taeda) hybrids was established on a West Virginia minesoil in 1985. The site was considered orphaned because earlier attempts at revegetation were unsuccessful. The soil was acid (pH 4.6), lacking in nutrients, and compacted. Vegetation present at the time of planting consisted of a sparse cover of tall fescue (Festuca arundinacea) and poverty grass (Danthonia spicata) and a few sourwood (Oxydendrum arboreum) and mountain laurel (Kalmia latifolia) seedlings. In the planting trial, 30 different hybrids were set out in 4 tree linear plots replicated 5 times. The seedlings had been grown in containers for 1 yr before outplanting. Evaluations made after 6 growing seasons showed overall plantation survival was 93%; six hybrids and one open-pollinated cross survived 100%. Individual tree heights ranged from 50 to 425 cm with a plantation average of 235 cm (7.7 ft). Eleven of the hybrids had average heights that exceeded the plantation average. Another test planting of tree and shrub species on this site has very poor survival. Therefore, pitch x loblolly hybrid pine can be recommended for reclaiming this and similar sites

  13. Common neighbour structure and similarity intensity in complex networks

    Science.gov (United States)

    Hou, Lei; Liu, Kecheng

    2017-10-01

    Complex systems as networks always exhibit strong regularities, implying underlying mechanisms governing their evolution. In addition to the degree preference, the similarity has been argued to be another driver for networks. Assuming a network is randomly organised without similarity preference, the present paper studies the expected number of common neighbours between vertices. A symmetrical similarity index is accordingly developed by removing such expected number from the observed common neighbours. The developed index can not only describe the similarities between vertices, but also the dissimilarities. We further apply the proposed index to measure of the influence of similarity on the wring patterns of networks. Fifteen empirical networks as well as artificial networks are examined in terms of similarity intensity and degree heterogeneity. Results on real networks indicate that, social networks are strongly governed by the similarity as well as the degree preference, while the biological networks and infrastructure networks show no apparent similarity governance. Particularly, classical network models, such as the Barabási-Albert model, the Erdös-Rényi model and the Ring Lattice, cannot well describe the social networks in terms of the degree heterogeneity and similarity intensity. The findings may shed some light on the modelling and link prediction of different classes of networks.

  14. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

    Full Text Available The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

  15. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar

    2016-03-21

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  16. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo

    2017-09-07

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  17. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar; Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knuepfer, Christian; Liebermeister, Wolfram

    2016-01-01

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users' intuition about model similarity, and to support complex model searches in databases.

  18. Similarity-based pattern analysis and recognition

    CERN Document Server

    Pelillo, Marcello

    2013-01-01

    This accessible text/reference presents a coherent overview of the emerging field of non-Euclidean similarity learning. The book presents a broad range of perspectives on similarity-based pattern analysis and recognition methods, from purely theoretical challenges to practical, real-world applications. The coverage includes both supervised and unsupervised learning paradigms, as well as generative and discriminative models. Topics and features: explores the origination and causes of non-Euclidean (dis)similarity measures, and how they influence the performance of traditional classification alg

  19. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed...... that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...

  20. Quantitative mass spectrometry analysis reveals similar substrate consensus motif for human Mps1 kinase and Plk1.

    Directory of Open Access Journals (Sweden)

    Zhen Dou

    Full Text Available BACKGROUND: Members of the Mps1 kinase family play an essential and evolutionarily conserved role in the spindle assembly checkpoint (SAC, a surveillance mechanism that ensures accurate chromosome segregation during mitosis. Human Mps1 (hMps1 is highly phosphorylated during mitosis and many phosphorylation sites have been identified. However, the upstream kinases responsible for these phosphorylations are not presently known. METHODOLOGY/PRINCIPAL FINDINGS: Here, we identify 29 in vivo phosphorylation sites in hMps1. While in vivo analyses indicate that Aurora B and hMps1 activity are required for mitotic hyper-phosphorylation of hMps1, in vitro kinase assays show that Cdk1, MAPK, Plk1 and hMps1 itself can directly phosphorylate hMps1. Although Aurora B poorly phosphorylates hMps1 in vitro, it positively regulates the localization of Mps1 to kinetochores in vivo. Most importantly, quantitative mass spectrometry analysis demonstrates that at least 12 sites within hMps1 can be attributed to autophosphorylation. Remarkably, these hMps1 autophosphorylation sites closely resemble the consensus motif of Plk1, demonstrating that these two mitotic kinases share a similar substrate consensus. CONCLUSIONS/SIGNIFICANCE: hMps1 kinase is regulated by Aurora B kinase and its autophosphorylation. Analysis on hMps1 autophosphorylation sites demonstrates that hMps1 has a substrate preference similar to Plk1 kinase.

  1. Improved collaborative filtering recommendation algorithm of similarity measure

    Science.gov (United States)

    Zhang, Baofu; Yuan, Baoping

    2017-05-01

    The Collaborative filtering recommendation algorithm is one of the most widely used recommendation algorithm in personalized recommender systems. The key is to find the nearest neighbor set of the active user by using similarity measure. However, the methods of traditional similarity measure mainly focus on the similarity of user common rating items, but ignore the relationship between the user common rating items and all items the user rates. And because rating matrix is very sparse, traditional collaborative filtering recommendation algorithm is not high efficiency. In order to obtain better accuracy, based on the consideration of common preference between users, the difference of rating scale and score of common items, this paper presents an improved similarity measure method, and based on this method, a collaborative filtering recommendation algorithm based on similarity improvement is proposed. Experimental results show that the algorithm can effectively improve the quality of recommendation, thus alleviate the impact of data sparseness.

  2. Similar words analysis based on POS-CBOW language model

    Directory of Open Access Journals (Sweden)

    Dongru RUAN

    2015-10-01

    Full Text Available Similar words analysis is one of the important aspects in the field of natural language processing, and it has important research and application values in text classification, machine translation and information recommendation. Focusing on the features of Sina Weibo's short text, this paper presents a language model named as POS-CBOW, which is a kind of continuous bag-of-words language model with the filtering layer and part-of-speech tagging layer. The proposed approach can adjust the word vectors' similarity according to the cosine similarity and the word vectors' part-of-speech metrics. It can also filter those similar words set on the base of the statistical analysis model. The experimental result shows that the similar words analysis algorithm based on the proposed POS-CBOW language model is better than that based on the traditional CBOW language model.

  3. Average is Boring: How Similarity Kills a Meme's Success

    Science.gov (United States)

    Coscia, Michele

    2014-09-01

    Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success.

  4. HYPOTHESIS TESTING WITH THE SIMILARITY INDEX

    Science.gov (United States)

    Mulltilocus DNA fingerprinting methods have been used extensively to address genetic issues in wildlife populations. Hypotheses concerning population subdivision and differing levels of diversity can be addressed through the use of the similarity index (S), a band-sharing coeffic...

  5. On self-similarity of crack layer

    Science.gov (United States)

    Botsis, J.; Kunin, B.

    1987-01-01

    The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

  6. Bilateral Trade Flows and Income Distribution Similarity

    Science.gov (United States)

    2016-01-01

    Current models of bilateral trade neglect the effects of income distribution. This paper addresses the issue by accounting for non-homothetic consumer preferences and hence investigating the role of income distribution in the context of the gravity model of trade. A theoretically justified gravity model is estimated for disaggregated trade data (Dollar volume is used as dependent variable) using a sample of 104 exporters and 108 importers for 1980–2003 to achieve two main goals. We define and calculate new measures of income distribution similarity and empirically confirm that greater similarity of income distribution between countries implies more trade. Using distribution-based measures as a proxy for demand similarities in gravity models, we find consistent and robust support for the hypothesis that countries with more similar income-distributions trade more with each other. The hypothesis is also confirmed at disaggregated level for differentiated product categories. PMID:27137462

  7. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation.......Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...

  8. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  9. Lagrangian-similarity diffusion-deposition model

    International Nuclear Information System (INIS)

    Horst, T.W.

    1979-01-01

    A Lagrangian-similarity diffusion model has been incorporated into the surface-depletion deposition model. This model predicts vertical concentration profiles far downwind of the source that agree with those of a one-dimensional gradient-transfer model

  10. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  11. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung

    2012-02-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  12. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  13. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  14. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo

    2018-04-04

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  15. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

    2018-01-01

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  16. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

    To help resolve the problem of site selection for the proposed 300 GeV machine, the Council selected "three wise men" (left to right, J H Bannier of the Netherlands, A Chavanne of Switzerland and L K Boggild of Denmark).

  17. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  18. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2001-01-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations

  19. Word Similarity from Dictionaries: Inferring Fuzzy Measures from Fuzzy Graphs

    Directory of Open Access Journals (Sweden)

    Vicenc Torra

    2008-01-01

    Full Text Available WORD SIMILARITY FROM DICTIONARIES: INFERRING FUZZY MEASURES FROM FUZZY GRAPHS The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.

  20. Estimating correlation and covariance matrices by weighting of market similarity

    OpenAIRE

    Michael C. M\\"unnix; Rudi Sch\\"afer; Oliver Grothe

    2010-01-01

    We discuss a weighted estimation of correlation and covariance matrices from historical financial data. To this end, we introduce a weighting scheme that accounts for similarity of previous market conditions to the present one. The resulting estimators are less biased and show lower variance than either unweighted or exponentially weighted estimators. The weighting scheme is based on a similarity measure which compares the current correlation structure of the market to the structures at past ...

  1. New similarity of triangular fuzzy number and its application.

    Science.gov (United States)

    Zhang, Xixiang; Ma, Weimin; Chen, Liping

    2014-01-01

    The similarity of triangular fuzzy numbers is an important metric for application of it. There exist several approaches to measure similarity of triangular fuzzy numbers. However, some of them are opt to be large. To make the similarity well distributed, a new method SIAM (Shape's Indifferent Area and Midpoint) to measure triangular fuzzy number is put forward, which takes the shape's indifferent area and midpoint of two triangular fuzzy numbers into consideration. Comparison with other similarity measurements shows the effectiveness of the proposed method. Then, it is applied to collaborative filtering recommendation to measure users' similarity. A collaborative filtering case is used to illustrate users' similarity based on cloud model and triangular fuzzy number; the result indicates that users' similarity based on triangular fuzzy number can obtain better discrimination. Finally, a simulated collaborative filtering recommendation system is developed which uses cloud model and triangular fuzzy number to express users' comprehensive evaluation on items, and result shows that the accuracy of collaborative filtering recommendation based on triangular fuzzy number is higher.

  2. 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.

  3. A Progress Evaluation of Four Bilingual Children's Television Shows.

    Science.gov (United States)

    Klein, Stephen P.; And Others

    An evaluation of a bilingual education TV series was conducted involving 6-year-old English speaking, Spanish speaking, and bilingual children at four sites. Children were assigned to control and experimental groups with the latter group seeing four 30 minute shows. A pretest-posttest design was employed with the pretest serving as the covariate…

  4. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    GPCR binding site-directed techniques are rapidly evolving into powerful tools for modern drug discovery. Many of these approaches bridge chemistry and biology, which are inseparable concepts in nature but are often treated as separate worlds in drug discovery and science in general. This review ...

  5. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    The weight of links in a network is often related to the similarity of thenodes. Here, we introduce a simple tunable measure for analysing the similarityof nodes across different link weights. In particular, we use the measure toanalyze homophily in a group of 659 freshman students at a large...... university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data...... might bepresent in one layer of the multilayer network and simultaneously be absent inthe other layers. For a variable such as gender, our measure reveals atransition from similarity between nodes connected with links of relatively lowweight to dis-similarity for the nodes connected by the strongest...

  6. Universal self-similarity of propagating populations.

    Science.gov (United States)

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

    This paper explores the universal self-similarity of propagating populations. The following general propagation model is considered: particles are randomly emitted from the origin of a d-dimensional Euclidean space and propagate randomly and independently of each other in space; all particles share a statistically common--yet arbitrary--motion pattern; each particle has its own random propagation parameters--emission epoch, motion frequency, and motion amplitude. The universally self-similar statistics of the particles' displacements and first passage times (FPTs) are analyzed: statistics which are invariant with respect to the details of the displacement and FPT measurements and with respect to the particles' underlying motion pattern. Analysis concludes that the universally self-similar statistics are governed by Poisson processes with power-law intensities and by the Fréchet and Weibull extreme-value laws.

  7. Universal self-similarity of propagating populations

    Science.gov (United States)

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

    This paper explores the universal self-similarity of propagating populations. The following general propagation model is considered: particles are randomly emitted from the origin of a d -dimensional Euclidean space and propagate randomly and independently of each other in space; all particles share a statistically common—yet arbitrary—motion pattern; each particle has its own random propagation parameters—emission epoch, motion frequency, and motion amplitude. The universally self-similar statistics of the particles’ displacements and first passage times (FPTs) are analyzed: statistics which are invariant with respect to the details of the displacement and FPT measurements and with respect to the particles’ underlying motion pattern. Analysis concludes that the universally self-similar statistics are governed by Poisson processes with power-law intensities and by the Fréchet and Weibull extreme-value laws.

  8. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

    2017-01-01

    With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm's per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  9. Unveiling Music Structure Via PLSA Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Meng, Anders; Petersen, Kaare Brandt

    2007-01-01

    Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious. In this p......Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious...... observed similarities can be satisfactorily explained using the latent semantics. Additionally, this approach significantly simplifies the song retrieval phase, leading to a more practical system implementation. The suitability of the PLSA model for representing music structure is studied in a simplified...

  10. Finding Similarities in Ancient Ceramics by EDXRF and Multivariate Methods

    International Nuclear Information System (INIS)

    Civici, N.; Stamati, F.

    1999-01-01

    We have studied 39 samples of fragments from ceramic roof tiles with different stamps(Diamalas and Heraion), dated between 330 to 170 BC and found at the archaeological site of Dimales, some 30 km from the Adriatic coast. The data from these samples were compared with those obtained from 7 samples of similar objects and period with the stamp H eraion , found at the archaeological site of APOLLONIA. The samples were analyzed by energy-dispersive X -ray fluorescence(EDXRF), using of the x-ray lines of the elements to the intensity of the Compton peak. The results have been treated with diverse multivariate methods. The application of hierarchical cluster analysis and factor analysis permitted the identification of two main clusters. The first cluster is composed from the ''Heraion'' samples discovered in Apollonia, while the second comprises all the samples discovered in Dimale independent of their stamp. (authors)

  11. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim

    2016-01-07

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer condition is not satisfied, or the Mercer condition is difficult to verify. Examples of such indefinite similarities in machine learning applications are ample including, for instance, the BLAST similarity score between protein sequences, human-judged similarities between concepts and words, and the tangent distance or the shape matching distance in computer vision. Nevertheless, previous works on classification with indefinite similarities are not fully satisfactory. They have either introduced sources of inconsistency in handling past and future examples using kernel approximation, settled for local-minimum solutions using non-convex optimization, or produced non-sparse solutions by learning in Krein spaces. Despite the large volume of research devoted to this subject lately, we demonstrate in this paper how an old idea, namely the 1-norm support vector machine (SVM) proposed more than 15 years ago, has several advantages over more recent work. In particular, the 1-norm SVM method is conceptually simpler, which makes it easier to implement and maintain. It is competitive, if not superior to, all other methods in terms of predictive accuracy. Moreover, it produces solutions that are often sparser than more recent methods by several orders of magnitude. In addition, we provide various theoretical justifications by relating 1-norm SVM to well-established learning algorithms such as neural networks, SVM, and nearest neighbor classifiers. Finally, we conduct a thorough experimental evaluation, which reveals that the evidence in favor of 1-norm SVM is statistically significant.

  12. Similarity joins in relational database systems

    CERN Document Server

    Augsten, Nikolaus

    2013-01-01

    State-of-the-art database systems manage and process a variety of complex objects, including strings and trees. For such objects equality comparisons are often not meaningful and must be replaced by similarity comparisons. This book describes the concepts and techniques to incorporate similarity into database systems. We start out by discussing the properties of strings and trees, and identify the edit distance as the de facto standard for comparing complex objects. Since the edit distance is computationally expensive, token-based distances have been introduced to speed up edit distance comput

  13. Outsourced Similarity Search on Metric Data Assets

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Assent, Ira; Jensen, Christian S.

    2012-01-01

    . Outsourcing offers the data owner scalability and a low initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying......This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example...

  14. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data...... might bepresent in one layer of the multilayer network and simultaneously be absent inthe other layers. For a variable such as gender, our measure reveals atransition from similarity between nodes connected with links of relatively lowweight to dis-similarity for the nodes connected by the strongest...

  15. The similarity of river evolution at the initial stage of channel erosion

    Science.gov (United States)

    Lin, Jiun-Chuan

    2014-05-01

    The study deals with a comparison study of two types of rocks at the initial stage of channel erosion in Taiwan. It is interesting that channel erosion at different types of rocks shows some similarity. There are two types of rocks: sandstone at Ta-an River, central Taiwan where river channel erosion from the nick point because of earthquake uplifting and mud rock at Tainan, southern Taiwan where rill erosion on a flat surface after artificial engineering. These two situations are both at the beginning stage of channel erosion, there are some similar landform appeared on channels. However the rate of erosion and magnitude of erosion are different. According to the using of photogrammetry method to reconstruct archive imageries and field surveying by total station and 3D scanner at different stages. The incision rate is high both at the Ta-an River and the bank erosion and it is even more obvious at mud rock area because of erodibility of mud rock. The results show that bank erosion and incision both are obvious processes. Bank erosion made channel into meander. The bank erosion cause slope in a asymmetric channel profile. The incision process will start at the site where land is relatively uplifted. This paper demonstrates such similarity and landform characters.

  16. Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

    Science.gov (United States)

    Kassam, Daud; Seki, Shingo; Horic, Michio; Yamaoka, Kosaku

    2006-08-01

    The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

  17. Clustering biomolecular complexes by residue contacts similarity

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions.

  18. Similarity principles for equipment qualification by experience

    International Nuclear Information System (INIS)

    Kana, D.D.; Pomerening, D.J.

    1988-07-01

    A methodology is developed for seismic qualification of nuclear plant equipment by applying similarity principles to existing experience data. Experience data are available from previous qualifications by analysis or testing, or from actual earthquake events. Similarity principles are defined in terms of excitation, equipment physical characteristics, and equipment response. Physical similarity is further defined in terms of a critical transfer function for response at a location on a primary structure, whose response can be assumed directly related to ultimate fragility of the item under elevated levels of excitation. Procedures are developed for combining experience data into composite specifications for qualification of equipment that can be shown to be physically similar to the reference equipment. Other procedures are developed for extending qualifications beyond the original specifications under certain conditions. Some examples for application of the procedures and verification of them are given for certain cases that can be approximated by a two degree of freedom simple primary/secondary system. Other examples are based on use of actual test data available from previous qualifications. Relationships of the developments with other previously-published methods are discussed. The developments are intended to elaborate on the rather broad revised guidelines developed by the IEEE 344 Standards Committee for equipment qualification in new nuclear plants. However, the results also contribute to filling a gap that exists between the IEEE 344 methodology and that previously developed by the Seismic Qualification Utilities Group. The relationship of the results to safety margin methodology is also discussed. (author)

  19. 7 CFR 51.1997 - Similar type.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar type. 51.1997 Section 51.1997 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946...

  20. Efficient Similarity Retrieval in Music Databases

    DEFF Research Database (Denmark)

    Ruxanda, Maria Magdalena; Jensen, Christian Søndergaard

    2006-01-01

    Audio music is increasingly becoming available in digital form, and the digital music collections of individuals continue to grow. Addressing the need for effective means of retrieving music from such collections, this paper proposes new techniques for content-based similarity search. Each music...

  1. Similarity search of business process models

    NARCIS (Netherlands)

    Dumas, M.; García-Bañuelos, L.; Dijkman, R.M.

    2009-01-01

    Similarity search is a general class of problems in which a given object, called a query object, is compared against a collection of objects in order to retrieve those that most closely resemble the query object. This paper reviews recent work on an instance of this class of problems, where the

  2. Evaluating gender similarities and differences using metasynthesis.

    Science.gov (United States)

    Zell, Ethan; Krizan, Zlatan; Teeter, Sabrina R

    2015-01-01

    Despite the common lay assumption that males and females are profoundly different, Hyde (2005) used data from 46 meta-analyses to demonstrate that males and females are highly similar. Nonetheless, the gender similarities hypothesis has remained controversial. Since Hyde's provocative report, there has been an explosion of meta-analytic interest in psychological gender differences. We utilized this enormous collection of 106 meta-analyses and 386 individual meta-analytic effects to reevaluate the gender similarities hypothesis. Furthermore, we employed a novel data-analytic approach called metasynthesis (Zell & Krizan, 2014) to estimate the average difference between males and females and to explore moderators of gender differences. The average, absolute difference between males and females across domains was relatively small (d = 0.21, SD = 0.14), with the majority of effects being either small (46%) or very small (39%). Magnitude of differences fluctuated somewhat as a function of the psychological domain (e.g., cognitive variables, social and personality variables, well-being), but remained largely constant across age, culture, and generations. These findings provide compelling support for the gender similarities hypothesis, but also underscore conditions under which gender differences are most pronounced. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  3. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds

  4. Phonological Similarity in American Sign Language.

    Science.gov (United States)

    Hildebrandt, Ursula; Corina, David

    2002-01-01

    Investigates deaf and hearing subjects' ratings of American Sign Language (ASL) signs to assess whether linguistic experience shapes judgments of sign similarity. Findings are consistent with linguistic theories that posit movement and location as core structural elements of syllable structure in ASL. (Author/VWL)

  5. Structural similarity and category-specificity

    DEFF Research Database (Denmark)

    Gerlach, Christian; Law, Ian; Paulson, Olaf B

    2004-01-01

    It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationshi...

  6. Music Retrieval based on Melodic Similarity

    NARCIS (Netherlands)

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how

  7. Measurement of Similarity in Academic Contexts

    Directory of Open Access Journals (Sweden)

    Omid Mahian

    2017-06-01

    Full Text Available We propose some reflections, comments and suggestions about the measurement of similar and matched content in scientific papers and documents, and the need to develop appropriate tools and standards for an ethically fair and equitable treatment of authors.

  8. Appropriate Similarity Measures for Author Cocitation Analysis

    NARCIS (Netherlands)

    N.J.P. van Eck (Nees Jan); L. Waltman (Ludo)

    2007-01-01

    textabstractWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of

  9. Similarity of Experience and Empathy in Preschoolers.

    Science.gov (United States)

    Barnett, Mark A.

    The present study examined the role of similarity of experience in young children's affective reactions to others. Some preschoolers played one of two games (Puzzle Board or Buckets) and were informed that they had either failed or succeeded; others merely observed the games being played and were given no evaluative feedback. Subsequently, each…

  10. Cultural Similarities and Differences on Idiom Translation

    Institute of Scientific and Technical Information of China (English)

    黄频频; 陈于全

    2010-01-01

    Both English and Chinese are abound with idioms. Idioms are an important part of the hnguage and culture of a society. English and Chinese idioms carved with cultural characteristics account for a great part in the tramlation. This paper studies the translation of idioms concerning their cultural similarities, cultural differences and transhtion principles.

  11. Learning by similarity in coordination problems

    Czech Academy of Sciences Publication Activity Database

    Steiner, Jakub; Stewart, C.

    -, č. 324 (2007), s. 1-40 ISSN 1211-3298 R&D Projects: GA MŠk LC542 Institutional research plan: CEZ:AV0Z70850503 Keywords : similarity * learning * case-based reasoning Subject RIV: AH - Economics http://www.cerge-ei.cz/pdf/wp/Wp324.pdf

  12. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Sø ndergaard; Kalnis, Panos

    2012-01-01

    for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise

  13. 99mTc-HM-PAO SPECT of epileptic patients showing focal paroxysm on electroencephalography

    International Nuclear Information System (INIS)

    Takaishi, Yasuko; Hashimoto, Kiyoshi; Fujino, Osamu; Kamayachi, Satoshi; Fujita, Takehisa; Enokido, Hisashi; Komatsuzaki, Hideki; Kawakami, Yasuhiko; Hirayama, Tsunenori

    1995-01-01

    The usefulness of 99m Tc-HM-PAO SPECT in diagnosing epilepsy was studied. The subjects were 33 epileptic patients, ranging in age from 5 years and 5 months to 28 years and 3 months, who showed focal paroxysm on electroencephalograms. Lowered accumulation site was found on SPECT in 19 patients. Four patients with abnormal findings on X-ray CT or MRI showed lowered accumulation and focal paroxysm at the same site. Of 29 patients with normal X-ray CT or MRI findings, 15 (52%) showed lowered accumulation. Five patients showed a focal paroxysm at the site of lowered accumulation. In 8 patients the focal paroxysm site was partly coincided with the accumulation site. In some patients the focal site predicted by the findings of clinical symptoms and the lowered accumulation site coincided. SPECT is therefore a useful method in diagnosing a focal site in epilepsy and considered to reflect the severity of disease. (Y.S.)

  14. Experimental site and design

    Energy Technology Data Exchange (ETDEWEB)

    Guenette, C. C. [SINTEF Applied Cemistry, Trondheim (Norway)

    1999-08-01

    Design and site selection criteria for the Svalbard oil spill experiments are described. All three experimental sites have coarse and mixed sediment beaches of sand and pebble; within each site wave exposure is very similar; along-shore and across-shore sediment characteristics are also relatively homogeneous. Tidal range is in the order of 0.6 m at neaps, and 1.8 m at springs. All three sites are open to wave action and are ice-free during the experimental period of mid-July to mid-October. Study plots at each site were selected for different treatments from within the continuous stretch of oiled shoreline, with oiled buffer zones between plots and at either end of the oiled zone. Treatments included mixing (tilling), sediment relocation (surf washing) and bioremediation (nutrient enrichment). Measurements and observations were carried out during the summers of 1997 and 1998. The characteristics measured were: wave and wind conditions; beach topography and elevation; sediment grain size distribution; mineral fines size distribution and mineral composition; background hydrocarbons; concentration of oil within experimental plots and the rate of oil loss over time; depth of oil penetration and thickness of the oiled sediment layer; oil concentration and toxicity of near-shore benthic sediments; mineral composition of suspended particulate material captured in sub-tidal sediment traps; and oil-fines interaction in near-shore water samples. 1 fig.

  15. Experimental site and design

    Energy Technology Data Exchange (ETDEWEB)

    Guenette, C. C. [SINTEF Applied Cemistry, Trondheim (Norway)

    1999-07-01

    Design and site selection criteria for the Svalbard oil spill experiments are described. All three experimental sites have coarse and mixed sediment beaches of sand and pebble; within each site waveexposure is very similar; along-shore and across-shore sediment characteristics are also relatively homogeneous. Tidal range is in the order of 0.6 m at neaps, and 1.8 m at springs. All three sites are open to wave action and are ice-free during the experimental period of mid-July to mid-October. Study plots at each site were selected for different treatments from within the continuous stretch of oiled shoreline, with oiled buffer zones between plots and at either end of the oiled zone. Treatments included mixing (tilling), sediment relocation (surf washing) and bioremediation (nutrient enrichment). Measurements and observations were carried out during the summers of 1997 and 1998. The characteristics measured were: wave and wind conditions; beach topography and elevation; sediment grain size distribution; mineral fines size distribution and mineral composition; background hydrocarbons; concentration of oil within experimental plots and the rate of oil loss over time; depth of oil penetration and thickness of the oiled sediment layer; oil concentration and toxicity of near-shore benthic sediments; mineral composition of suspended particulate material captured in sub-tidal sediment traps; and oil-fines interaction in near-shore water samples. 1 fig.

  16. Criteria of site assessment

    International Nuclear Information System (INIS)

    Gibbs, P.; Fuchs, H.

    1975-01-01

    The criteria which lead to the choice of a particular site for a nuclear power station are in general very similar to those which would apply to any other type of power station. The principal differences derive from the simpler transport problems for the fuel compared with, say, solid fuel and the special safety considerations which attach to nuclear reactors. The search for a suitable site obviously starts by considering where the power is needed, i.e. where the load centers are and also the existing transmission network which may help to bring the power from a more remote site to the load centers. This economic incentive to put the plant close to loads conflicts directly with the nuclear safety argument which favours more remote siting, and part of the problem of site selection is to reconcile these two matters. In addition, there are many other important matters which will be considered later concerning the adequacy of cooling water supplies, foundation conditions, etc., all of which must be examined in considerable detail. (orig./TK) [de

  17. Extending the Similarity-Attraction Effect : The effects of When-Similarity in mediated communication

    NARCIS (Netherlands)

    Kaptein, M.C.; Castaneda, D.; Fernandez, N.; Nass, C.

    2014-01-01

    The feeling of connectedness experienced in computer-mediated relationships can be explained by the similarity-attraction effect (SAE). Though SAE is well established in psychology, the effects of some types of similarity have not yet been explored. In 2 studies, we demonstrate similarity-attraction

  18. Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

    Science.gov (United States)

    Ikram, Najmul; Qadir, Muhammad Abdul; Afzal, Muhammad Tanvir

    2018-01-01

    Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic similarity methods, and in protein function prediction. In this research, we investigate the relationship between the two similarity methods. The results suggest absence of a strong correlation between sequence and semantic similarities. There is a large number of proteins with low sequence similarity and high semantic similarity. We observe that Pearson's correlation coefficient is not sufficient to explain the nature of this relationship. Interestingly, the term semantic similarity values above 0 and below 1 do not seem to play a role in improving the correlation. That is, the correlation coefficient depends only on the number of common GO terms in proteins under comparison, and the semantic similarity measurement method does not influence it. Semantic similarity and sequence similarity have a distinct behavior. These findings are of significant effect for future works on protein comparison, and will help understand the semantic similarity between proteins in a better way.

  19. Interbehavioral psychology and radical behaviorism: Some similarities and differences

    Science.gov (United States)

    Morris, Edward K.

    1984-01-01

    Both J. R. Kantor's interbehavioral psychology and B. F. Skinner's radical behaviorism represent wellarticulated approaches to a natural science of behavior. As such, they share a number of similar features, yet they also differ on a number of dimensions. Some of these similarities and differences are examined by describing their emergence in the professional literature and by comparing the respective units of analysis of the two approaches—the interbehavioral field and the three-term contingency. An evaluation of the similarities and differences shows the similarities to be largely fundamental, and the differences largely ones of emphasis. Nonetheless, the two approaches do make unique contributions to a natural science of behavior, the integration of which can facilitate the development of that science and its acceptance among other sciences and within society at large. PMID:22478612

  20. On finding similar items in a stream of transactions

    DEFF Research Database (Denmark)

    Campagna, Andrea; Pagh, Rasmus

    2010-01-01

    While there has been a lot of work on finding frequent itemsets in transaction data streams, none of these solve the problem of finding similar pairs according to standard similarity measures. This paper is a first attempt at dealing with this, arguably more important, problem. We start out with ...... in random order, and show that surprisingly, not only is small-space similarity mining possible for the most common similarity measures, but the mining accuracy {\\em improves\\/} with the length of the stream for any fixed support threshold....... with a negative result that also explains the lack of theoretical upper bounds on the space usage of data mining algorithms for finding frequent itemsets: Any algorithm that (even only approximately and with a chance of error) finds the most frequent $k$-itemset must use space $\\Omega...

  1. Coal mine site reclamation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-02-15

    Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

  2. The X chromosome shows less genetic variation at restriction sites than the autosomes

    NARCIS (Netherlands)

    Hofker, M. H.; Skraastad, M. I.; Bergen, A. A.; Wapenaar, M. C.; Bakker, E.; Millington-Ward, A.; van Ommen, G. J.; Pearson, P. L.

    1986-01-01

    Using a standard technique, 122 single-copy probes were screened for their ability to detect restriction fragment length polymorphisms (RFLPs) in the human genome. The use of a standardized RFLP screening enables the introduction of statistical methods in the analysis of differences in RFLP content

  3. Ants show a leftward turning bias when exploring unknown nest sites.

    Science.gov (United States)

    Hunt, Edmund R; O'Shea-Wheller, Thomas; Albery, Gregory F; Bridger, Tamsyn H; Gumn, Mike; Franks, Nigel R

    2014-12-01

    Behavioural lateralization in invertebrates is an important field of study because it may provide insights into the early origins of lateralization seen in a diversity of organisms. Here, we present evidence for a leftward turning bias in Temnothorax albipennis ants exploring nest cavities and in branching mazes, where the bias is initially obscured by thigmotaxis (wall-following) behaviour. Forward travel with a consistent turning bias in either direction is an effective nest exploration method, and a simple decision-making heuristic to employ when faced with multiple directional choices. Replication of the same bias at the colony level would also reduce individual predation risk through aggregation effects, and may lead to a faster attainment of a quorum threshold for nest migration. We suggest the turning bias may be the result of an evolutionary interplay between vision, exploration and migration factors, promoted by the ants' eusociality.

  4. Roadside soils show low plant available zinc and copper concentrations.

    Science.gov (United States)

    Morse, Natalie; Walter, M Todd; Osmond, Deanna; Hunt, William

    2016-02-01

    Vehicle combustion and component wear are a major source of metal contamination in the environment, which could be especially concerning where road ditches are actively farmed. The objective of this study was to assess how site variables, namely age, traffic (vehicles day(-1)), and percent carbon (%C) affect metal accumulation in roadside soils. A soil chronosequence was established with sites ranging from 3 to 37 years old and bioavailable, or mobile, concentrations of Zinc (Zn) and Copper (Cu) were measured along major highways in North Carolina using a Mehlich III extraction. Mobile Zn and Cu concentrations were low overall, and when results were scaled via literature values to "total metal", the results were still generally lower than previous roadside studies. This could indicate farming on lands near roads would pose a low plant toxicity risk. Zinc and Cu were not correlated with annual average traffic count, but were positively correlated with lifetime traffic load (the product of site age and traffic count). This study shows an often overlooked variable, site age, should be included when considering roadside pollution accumulation. Zinc and Cu were more strongly associated with %C, than traffic load. Because vehicle combustion is also a carbon source, it is not obvious whether the metals and carbon are simply co-accumulating or whether the soil carbon in roadside soils may facilitate previously overlooked roles in sequestering metals on-site. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Integral fast reactor shows its mettle

    International Nuclear Information System (INIS)

    Chang, Ya.; Lajnberri, M.; Barris, L.; Uoters, L.

    1988-01-01

    The main aspects of the problem of developing a closed fuel cycle at a NPP built in the so-called integrated version when a fast reactor and the plant for spent fuel regeneration and fuel element production are located in the same site (IFR project), are considered. The technologies of U-Pu-Zr alloy fuel reprocessing and production based on high-temperature metallurgical process and the method of casting under pressure are described. The demonstration of practical feasibility of the fuel cycle on the basis of the IFR reactor is planned for 1990

  6. Similarity, trust in institutions, affect, and populism

    DEFF Research Database (Denmark)

    Scholderer, Joachim; Finucane, Melissa L.

    -based evaluations are fundamental to human information processing, they can contribute significantly to other judgments (such as the risk, cost-effectiveness, trustworthiness) of the same stimulus object. Although deliberation and analysis are certainly important in some decision-making circumstances, reliance...... on affect is a quicker, easier, and a more efficient way of navigating in a complex and uncertain world. Hence, many theorists give affect a direct and primary role in motivating behavior. Taken together, the results provide uncannily strong support for the value-similarity hypothesis, strengthening...... types of information about gene technology. The materials were attributed to different institutions. The results indicated that participants' trust in an institution was a function of the similarity between the position advocated in the materials and participants' own attitudes towards gene technology...

  7. Contingency and similarity in response selection.

    Science.gov (United States)

    Prinz, Wolfgang

    2018-05-09

    This paper explores issues of task representation in choice reaction time tasks. How is it possible, and what does it take, to represent such a task in a way that enables a performer to do the task in line with the prescriptions entailed in the instructions? First, a framework for task representation is outlined which combines the implementation of task sets and their use for performance with different kinds of representational operations (pertaining to feature compounds for event codes and code assemblies for task sets, respectively). Then, in a second step, the framework is itself embedded in the bigger picture of the classical debate on the roles of contingency and similarity for the formation of associations. The final conclusion is that both principles are needed and that the operation of similarity at the level of task sets requires and presupposes the operation of contingency at the level of event codes. Copyright © 2018 The Author. Published by Elsevier Inc. All rights reserved.

  8. Similarity and Modeling in Science and Engineering

    CERN Document Server

    Kuneš, Josef

    2012-01-01

    The present text sets itself in relief to other titles on the subject in that it addresses the means and methodologies versus a narrow specific-task oriented approach. Concepts and their developments which evolved to meet the changing needs of applications are addressed. This approach provides the reader with a general tool-box to apply to their specific needs. Two important tools are presented: dimensional analysis and the similarity analysis methods. The fundamental point of view, enabling one to sort all models, is that of information flux between a model and an original expressed by the similarity and abstraction. Each chapter includes original examples and ap-plications. In this respect, the models can be divided into several groups. The following models are dealt with separately by chapter; mathematical and physical models, physical analogues, deterministic, stochastic, and cybernetic computer models. The mathematical models are divided into asymptotic and phenomenological models. The phenomenological m...

  9. Similarity solutions for phase-change problems

    Science.gov (United States)

    Canright, D.; Davis, S. H.

    1989-01-01

    A modification of Ivantsov's (1947) similarity solutions is proposed which can describe phase-change processes which are limited by diffusion. The method has application to systems that have n-components and possess cross-diffusion and Soret and Dufour effects, along with convection driven by density discontinuities at the two-phase interface. Local thermal equilibrium is assumed at the interface. It is shown that analytic solutions are possible when the material properties are constant.

  10. Quasi-Similarity Model of Synthetic Jets

    Czech Academy of Sciences Publication Activity Database

    Tesař, Václav; Kordík, Jozef

    2009-01-01

    Roč. 149, č. 2 (2009), s. 255-265 ISSN 0924-4247 R&D Projects: GA AV ČR IAA200760705; GA ČR GA101/07/1499 Institutional research plan: CEZ:AV0Z20760514 Keywords : jets * synthetic jets * similarity solution Subject RIV: BK - Fluid Dynamics Impact factor: 1.674, year: 2009 http://www.sciencedirect.com

  11. Multidimensional Scaling Visualization using Parametric Similarity Indices

    OpenAIRE

    Machado, J. A. Tenreiro; Lopes, António M.; Galhano, A.M.

    2015-01-01

    In this paper, we apply multidimensional scaling (MDS) and parametric similarity indices (PSI) in the analysis of complex systems (CS). Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, an...

  12. The fluid similarity of the boiling crisis

    International Nuclear Information System (INIS)

    Katsaounis, A.

    1986-01-01

    Most of the measurements related to the boiling crisis have, until now, been undertaken for a wide parameter variation in the water, and were mainly related to the water-cooled reactor. This article investigates, whether or how the measuring results can be transferred to other fluids. Derived dimensionless similarity figures and those taken from literature are verified by measurements from complex geometries in water and freon 12. (orig.) [de

  13. The fluid similarity of the boiling crisis

    International Nuclear Information System (INIS)

    Katsaounis, A.

    1987-01-01

    Most of the measurements related to the boiling crisis have, until now, been undertaken for a wide parameter variation in the water, and were mainly related to the water-cooled reactor. This article investigates, whether or how the measuring results can be transferred to other fluids. Derived dimensionless similarity figures and those taken from literature are verified by measurements from complex geometries in water and freon 12. (orig./GL) [de

  14. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-06-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  15. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  16. Similarity Theory and Dimensionless Numbers in Heat Transfer

    Science.gov (United States)

    Marin, E.; Calderon, A.; Delgado-Vasallo, O.

    2009-01-01

    We present basic concepts underlying the so-called similarity theory that in our opinion should be explained in basic undergraduate general physics courses when dealing with heat transport problems, in particular with those involving natural or free convection. A simple example is described that can be useful in showing a criterion for neglecting…

  17. Facilitating Navigation in Quality Manuals by Providing Bookmarks or Similar

    International Nuclear Information System (INIS)

    Shaharum bin Ramli

    2012-01-01

    Nuclear Malaysia level quality manuals need to be shared with all divisions. A manual is usually distributed in the form of an electronic document that contains all procedures. Navigation from one heading or procedure to another should be facilitated by providing bookmarks or similar. This paper shows how to do it for Microsoft Word and PDF documents. (author)

  18. Assessment of Vegetation Structural Diversity and Similarity Index of ...

    African Journals Online (AJOL)

    Data were analysed using descriptive statistics, relative density, diversity and similarity indices. The result showed that the forest reserve has one hundred and ninety species of plants belonging to sixty three families. The dominant plant families recorded in the forest are Leguminosae (12.63%), Rubiaceae (8.42%), ...

  19. Brazilian N2 laser similar to imported models

    International Nuclear Information System (INIS)

    Santos, P.A.M. dos; Tavares Junior, A.D.; Silva Reis, H. da; Tagliaferri, A.A.; Massone, C.A.

    1981-09-01

    The development of a high power N 2 Laser, similar to imported models but built enterely with Brazilian materials is described. The prototype shows pulse repetitivity that varies from 1 to 50 per second and has a peak power of 500 kW. (Author) [pt

  20. Young Children's Analogical Reasoning across Cultures: Similarities and Differences

    Science.gov (United States)

    Richland, Lindsey Engle; Chan, Tsz-Kit; Morrison, Robert G.; Au, Terry Kit-Fong

    2010-01-01

    A cross-cultural comparison between U.S. and Hong Kong preschoolers examined factors responsible for young children's analogical reasoning errors. On a scene analogy task, both groups had adequate prerequisite knowledge of the key relations, were the same age, and showed similar baseline performance, yet Chinese children outperformed U.S. children…

  1. US nuclear cleanup shows signs of progress

    International Nuclear Information System (INIS)

    Renner, R.

    1997-01-01

    The U.S. Department of Energy's program for dealing with the radioactive and hazardous wastes at its former nuclear weapons production sites and at the national laboratories has been criticized for its expense and slow pace of cleanup. The largest environmental restoration and waste management program in the world faces formidable technical and scientific problems and these, according to numerous investigative committees and commissions, have been compounded by poor management, misuse of technology, and failure to appreciate the need for new basic scientific knowledge to solve many of the cleanup problems. In the past three years, DOE's Office of Environmental Management (EM), often spurred by congressional action, has begun to trim costs and accomplish more. New measures have been introduced to improve contract efficiency, better utilize existing remediation technologies, renegotiate compliance agreements, and begin basic research. Environmental Management Assistant Undersecretary Alvin Alm, appointed in May 1996, is seeking to solidify these changes into an ambitious plan to clean up most of DOE's 130 sites by 2006. But there are widespread doubts that EM has the money, skill, and will to turn itself around. There are also concerns that, in the name of efficiency and economy, EM may be negotiating lower cleanup standards and postponing some difficult cleanup tasks. This article discusses these issues. 7 refs

  2. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  3. How similar are recognition memory and inductive reasoning?

    Science.gov (United States)

    Hayes, Brett K; Heit, Evan

    2013-07-01

    Conventionally, memory and reasoning are seen as different types of cognitive activities driven by different processes. In two experiments, we challenged this view by examining the relationship between recognition memory and inductive reasoning involving multiple forms of similarity. A common study set (members of a conjunctive category) was followed by a test set containing old and new category members, as well as items that matched the study set on only one dimension. The study and test sets were presented under recognition or induction instructions. In Experiments 1 and 2, the inductive property being generalized was varied in order to direct attention to different dimensions of similarity. When there was no time pressure on decisions, patterns of positive responding were strongly affected by property type, indicating that different types of similarity were driving recognition and induction. By comparison, speeded judgments showed weaker property effects and could be explained by generalization based on overall similarity. An exemplar model, GEN-EX (GENeralization from EXamples), could account for both the induction and recognition data. These findings show that induction and recognition share core component processes, even when the tasks involve flexible forms of similarity.

  4. Distributional Similarity for Chinese: Exploiting Characters and Radicals

    Directory of Open Access Journals (Sweden)

    Peng Jin

    2012-01-01

    Full Text Available Distributional Similarity has attracted considerable attention in the field of natural language processing as an automatic means of countering the ubiquitous problem of sparse data. As a logographic language, Chinese words consist of characters and each of them is composed of one or more radicals. The meanings of characters are usually highly related to the words which contain them. Likewise, radicals often make a predictable contribution to the meaning of a character: characters that have the same components tend to have similar or related meanings. In this paper, we utilize these properties of the Chinese language to improve Chinese word similarity computation. Given a content word, we first extract similar words based on a large corpus and a similarity score for ranking. This rank is then adjusted according to the characters and components shared between the similar word and the target word. Experiments on two gold standard datasets show that the adjusted rank is superior and closer to human judgments than the original rank. In addition to quantitative evaluation, we examine the reasons behind errors drawing on linguistic phenomena for our explanations.

  5. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

    In Mochovce site the construction of four units of WWER 440 NPP with V-213 type of reactor is being carried out. The financing of Mochovce units completion was resolved in April 1996. The completion work commenced at the construction site under leadership of SKODA Prague, the general supplier. The completion work on building part and tests of constructional electric distributions and lightning constructors started. The revisions in technological part were finished, and final protocols from revisions are the basis for starting of completion work. The assembly of transport container anchorage,ventilation system in hermetic areas and hermetic coverage of pools for stored spent nuclear fuel is being carried out. The pre-completion tests of instrumentation and control of ventilation systems, individual dosimetric control in medical station, and tests of nuclear programme according to commissioning and assembling work schedule at the equipment for physical protection of the NPP area started. Inspection activities at Mochovce were performed in accordance with inspection plan for 1996. Evaluation of routine inspections was performed by means of quarterly protocols. Main findings from the inspections performed in Mochovce were in the following areas: (a) deficiencies in the knowledge of the respective regulation and conditions from the Resolution of the state regulatory body, concerning selected employees; (b) training of the selected employees; (c) aim of the measures imposes by inspectors is to eliminate deficiencies in preparation of programmes for pre-completion and completion testing. NRA SR assessment activities at Mochovce NPP were focused mainly on approving and inspecting of design modification to approving programmes for pre-completion and completion testing of system s and equipment and on approving quality assurance programmes. The suggestions of international missions, which reviewed Mochovce safety in the years, were taken into consideration in the programme

  6. Spherically symmetric self-similar universe

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, C C [Toronto Univ., Ontario (Canada)

    1979-10-01

    A spherically symmetric self-similar dust-filled universe is considered as a simple model of a hierarchical universe. Observable differences between the model in parabolic expansion and the corresponding homogeneous Einstein-de Sitter model are considered in detail. It is found that an observer at the centre of the distribution has a maximum observable redshift and can in principle see arbitrarily large blueshifts. It is found to yield an observed density-distance law different from that suggested by the observations of de Vaucouleurs. The use of these solutions as central objects for Swiss-cheese vacuoles is discussed.

  7. Image magnification based on similarity analogy

    International Nuclear Information System (INIS)

    Chen Zuoping; Ye Zhenglin; Wang Shuxun; Peng Guohua

    2009-01-01

    Aiming at the high time complexity of the decoding phase in the traditional image enlargement methods based on fractal coding, a novel image magnification algorithm is proposed in this paper, which has the advantage of iteration-free decoding, by using the similarity analogy between an image and its zoom-out and zoom-in. A new pixel selection technique is also presented to further improve the performance of the proposed method. Furthermore, by combining some existing fractal zooming techniques, an efficient image magnification algorithm is obtained, which can provides the image quality as good as the state of the art while greatly decrease the time complexity of the decoding phase.

  8. Modeling Timbre Similarity of Short Music Clips.

    Science.gov (United States)

    Siedenburg, Kai; Müllensiefen, Daniel

    2017-01-01

    There is evidence from a number of recent studies that most listeners are able to extract information related to song identity, emotion, or genre from music excerpts with durations in the range of tenths of seconds. Because of these very short durations, timbre as a multifaceted auditory attribute appears as a plausible candidate for the type of features that listeners make use of when processing short music excerpts. However, the importance of timbre in listening tasks that involve short excerpts has not yet been demonstrated empirically. Hence, the goal of this study was to develop a method that allows to explore to what degree similarity judgments of short music clips can be modeled with low-level acoustic features related to timbre. We utilized the similarity data from two large samples of participants: Sample I was obtained via an online survey, used 16 clips of 400 ms length, and contained responses of 137,339 participants. Sample II was collected in a lab environment, used 16 clips of 800 ms length, and contained responses from 648 participants. Our model used two sets of audio features which included commonly used timbre descriptors and the well-known Mel-frequency cepstral coefficients as well as their temporal derivates. In order to predict pairwise similarities, the resulting distances between clips in terms of their audio features were used as predictor variables with partial least-squares regression. We found that a sparse selection of three to seven features from both descriptor sets-mainly encoding the coarse shape of the spectrum as well as spectrotemporal variability-best predicted similarities across the two sets of sounds. Notably, the inclusion of non-acoustic predictors of musical genre and record release date allowed much better generalization performance and explained up to 50% of shared variance ( R 2 ) between observations and model predictions. Overall, the results of this study empirically demonstrate that both acoustic features related

  9. Self-similar magnetohydrodynamic boundary layers

    Energy Technology Data Exchange (ETDEWEB)

    Nunez, Manuel; Lastra, Alberto, E-mail: mnjmhd@am.uva.e [Departamento de Analisis Matematico, Universidad de Valladolid, 47005 Valladolid (Spain)

    2010-10-15

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  10. Self-similar magnetohydrodynamic boundary layers

    International Nuclear Information System (INIS)

    Nunez, Manuel; Lastra, Alberto

    2010-01-01

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  11. [Similarity system theory to evaluate similarity of chromatographic fingerprints of traditional Chinese medicine].

    Science.gov (United States)

    Liu, Yongsuo; Meng, Qinghua; Jiang, Shumin; Hu, Yuzhu

    2005-03-01

    The similarity evaluation of the fingerprints is one of the most important problems in the quality control of the traditional Chinese medicine (TCM). Similarity measures used to evaluate the similarity of the common peaks in the chromatogram of TCM have been discussed. Comparative studies were carried out among correlation coefficient, cosine of the angle and an improved extent similarity method using simulated data and experimental data. Correlation coefficient and cosine of the angle are not sensitive to the differences of the data set. They are still not sensitive to the differences of the data even after normalization. According to the similarity system theory, an improved extent similarity method was proposed. The improved extent similarity is more sensitive to the differences of the data sets than correlation coefficient and cosine of the angle. And the character of the data sets needs not to be changed compared with log-transformation. The improved extent similarity can be used to evaluate the similarity of the chromatographic fingerprints of TCM.

  12. Similarity Analysis of Cable Insulations by Chemical Test

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Seog [Central Research Institute of Korea Hydro and Nuclear Power Co., Daejeon (Korea, Republic of)

    2013-10-15

    As result of this experiment, it was found that FT-IR test for material composition, TGA test for aging trend are applicable for similarity analysis of cable materials. OIT is recommended as option if TGA doesn't show good trend. Qualification of new insulation by EQ report of old insulation should be based on higher activation energy of new insulation than that of old one in the consideration of conservatism. In old nuclear power plant, it is easy to find black cable which has no marking of cable information such as manufacturer, material name and voltage. If a type test is required for qualification of these cables, how could I select representative cable? How could I determine the similarity of these cables? If manufacturer has qualified a cable for nuclear power plant more than a decade ago and composition of cable material is changed with similar one, is it acceptable to use the old EQ report for recently manufactured cable? It is well known to use FT-IR method to determine the similarity of cable materials. Infrared ray is easy tool to compare compositions of each material. But, it is not proper to compare aging trend of these materials. Study for similarity analysis of cable insulation by chemical test is described herein. To study a similarity evaluation method for polymer materials, FT-IR, TGA and OIT tests were performed for two cable insulation(old and new) which were supplied from same manufacturer. FT-IR shows good result to compare material compositions while TGA and OIT show good result to compare aging character of materials.

  13. Similarity Analysis of Cable Insulations by Chemical Test

    International Nuclear Information System (INIS)

    Kim, Jong Seog

    2013-01-01

    As result of this experiment, it was found that FT-IR test for material composition, TGA test for aging trend are applicable for similarity analysis of cable materials. OIT is recommended as option if TGA doesn't show good trend. Qualification of new insulation by EQ report of old insulation should be based on higher activation energy of new insulation than that of old one in the consideration of conservatism. In old nuclear power plant, it is easy to find black cable which has no marking of cable information such as manufacturer, material name and voltage. If a type test is required for qualification of these cables, how could I select representative cable? How could I determine the similarity of these cables? If manufacturer has qualified a cable for nuclear power plant more than a decade ago and composition of cable material is changed with similar one, is it acceptable to use the old EQ report for recently manufactured cable? It is well known to use FT-IR method to determine the similarity of cable materials. Infrared ray is easy tool to compare compositions of each material. But, it is not proper to compare aging trend of these materials. Study for similarity analysis of cable insulation by chemical test is described herein. To study a similarity evaluation method for polymer materials, FT-IR, TGA and OIT tests were performed for two cable insulation(old and new) which were supplied from same manufacturer. FT-IR shows good result to compare material compositions while TGA and OIT show good result to compare aging character of materials

  14. Savannah River Site's Site Specific Plan

    International Nuclear Information System (INIS)

    1991-01-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering

  15. Roadside soils show low plant available zinc and copper concentrations

    International Nuclear Information System (INIS)

    Morse, Natalie; Walter, M. Todd; Osmond, Deanna; Hunt, William

    2016-01-01

    Vehicle combustion and component wear are a major source of metal contamination in the environment, which could be especially concerning where road ditches are actively farmed. The objective of this study was to assess how site variables, namely age, traffic (vehicles day"−"1), and percent carbon (%C) affect metal accumulation in roadside soils. A soil chronosequence was established with sites ranging from 3 to 37 years old and bioavailable, or mobile, concentrations of Zinc (Zn) and Copper (Cu) were measured along major highways in North Carolina using a Mehlich III extraction. Mobile Zn and Cu concentrations were low overall, and when results were scaled via literature values to “total metal”, the results were still generally lower than previous roadside studies. This could indicate farming on lands near roads would pose a low plant toxicity risk. Zinc and Cu were not correlated with annual average traffic count, but were positively correlated with lifetime traffic load (the product of site age and traffic count). This study shows an often overlooked variable, site age, should be included when considering roadside pollution accumulation. Zinc and Cu were more strongly associated with %C, than traffic load. Because vehicle combustion is also a carbon source, it is not obvious whether the metals and carbon are simply co-accumulating or whether the soil carbon in roadside soils may facilitate previously overlooked roles in sequestering metals on-site. - Highlights: • Low plant available zinc and copper concentrations in roadside soils of the southeast U.S. • Metals from vehicular traffic may not be adversely affecting plants in roadside environment. • Traffic volume and site age better predictor of metal pollution than traffic volume alone. - Mobile concentrations of Zn and Cu in roadside soils were below toxic levels. Zn and Cu concentrations were better correlated with lifetime vehicle load, as opposed to traffic volume.

  16. Implementing ‘Site BIM’

    DEFF Research Database (Denmark)

    Davies, Richard; Harty, Chris

    2013-01-01

    Numerous Building Information Modelling (BIM) tools are well established and potentially beneficial in certain uses. However, issues of adoption and implementation persist, particularly for on-site use of BIM tools in the construction phase. We describe an empirical case-study of the implementation...... of an innovative ‘Site BIM’ system on a major hospital construction project. The main contractor on the project developed BIM-enabled tools to allow site workers using mobile tablet personal computers to access design information and to capture work quality and progress data on-site. Accounts show that ‘Site BIM...

  17. Gait Recognition Using Image Self-Similarity

    Directory of Open Access Journals (Sweden)

    Chiraz BenAbdelkader

    2004-04-01

    Full Text Available Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have sufficient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of difficulty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98% is achieved for a data set of 6 people, and 70% for a data set of 54 people.

  18. Self-similarity in applied superconductivity

    International Nuclear Information System (INIS)

    Dresner, Lawrence

    1981-09-01

    Self-similarity is a descriptive term applying to a family of curves. It means that the family is invariant to a one-parameter group of affine (stretching) transformations. The property of self-similarity has been exploited in a wide variety of problems in applied superconductivity, namely, (i) transient distribution of the current among the filaments of a superconductor during charge-up, (ii) steady distribution of current among the filaments of a superconductor near the current leads, (iii) transient heat transfer in superfluid helium, (iv) transient diffusion in cylindrical geometry (important in studying the growth rate of the reacted layer in A15 materials), (v) thermal expulsion of helium from quenching cable-in-conduit conductors, (vi) eddy current heating of irregular plates by slow, ramped fields, and (vii) the specific heat of type-II superconductors. Most, but not all, of the applications involve differential equations, both ordinary and partial. The novel methods explained in this report should prove of great value in other fields, just as they already have done in applied superconductivity. (author)

  19. Phonological similarity effect in complex span task.

    Science.gov (United States)

    Camos, Valérie; Mora, Gérôme; Barrouillet, Pierre

    2013-01-01

    The aim of our study was to test the hypothesis that two systems are involved in verbal working memory; one is specifically dedicated to the maintenance of phonological representations through verbal rehearsal while the other would maintain multimodal representations through attentional refreshing. This theoretical framework predicts that phonologically related phenomena such as the phonological similarity effect (PSE) should occur when the domain-specific system is involved in maintenance, but should disappear when concurrent articulation hinders its use. Impeding maintenance in the domain-general system by a concurrent attentional demand should impair recall performance without affecting PSE. In three experiments, we manipulated the concurrent articulation and the attentional demand induced by the processing component of complex span tasks in which participants had to maintain lists of either similar or dissimilar words. Confirming our predictions, PSE affected recall performance in complex span tasks. Although both the attentional demand and the articulatory requirement of the concurrent task impaired recall, only the induction of an articulatory suppression during maintenance made the PSE disappear. These results suggest a duality in the systems devoted to verbal maintenance in the short term, constraining models of working memory.

  20. Predicting the performance of fingerprint similarity searching.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2011-01-01

    Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

  1. Morphological similarities between DBM and a microeconomic model of sprawl

    Science.gov (United States)

    Caruso, Geoffrey; Vuidel, Gilles; Cavailhès, Jean; Frankhauser, Pierre; Peeters, Dominique; Thomas, Isabelle

    2011-03-01

    We present a model that simulates the growth of a metropolitan area on a 2D lattice. The model is dynamic and based on microeconomics. Households show preferences for nearby open spaces and neighbourhood density. They compete on the land market. They travel along a road network to access the CBD. A planner ensures the connectedness and maintenance of the road network. The spatial pattern of houses, green spaces and road network self-organises, emerging from agents individualistic decisions. We perform several simulations and vary residential preferences. Our results show morphologies and transition phases that are similar to Dieletric Breakdown Models (DBM). Such similarities were observed earlier by other authors, but we show here that it can be deducted from the functioning of the land market and thus explicitly connected to urban economic theory.

  2. UV Photography Shows Hidden Sun Damage

    Science.gov (United States)

    ... mcat1=de12", ]; for (var c = 0; c UV photography shows hidden sun damage A UV photograph gives ... developing skin cancer and prematurely aged skin. Normal photography UV photography 18 months of age: This boy's ...

  3. Similar or different?: the importance of similarities and differences for support between siblings

    NARCIS (Netherlands)

    Voorpostel, M.; van der Lippe, T.; Dykstra, P.A.; Flap, H.

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  4. Similar or Different? The Importance of Similarities and Differences for Support Between Siblings

    NARCIS (Netherlands)

    Voorpostel, Marieke; Lippe, Tanja van der; Dykstra, Pearl A.; Flap, Henk

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  5. Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.

    Science.gov (United States)

    Núñez-Vivanco, Gabriel; Valdés-Jiménez, Alejandro; Besoaín, Felipe; Reyes-Parada, Miguel

    2016-01-01

    Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, protein clustering, drug discovery and the establishment of evolutionary relationships. Thus, several computational applications to identify, describe and compare 3D patterns (or motifs) have been developed. Often, these tools consider a 3D pattern as that described by the residues surrounding co-crystallized/docked ligands available from X-ray crystal structures or homology models. Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc. This makes necessary the development of new ligand-independent methods to search and compare 3D patterns in all available protein structures. Here we introduce Geomfinder, an intuitive, flexible, alignment-free and ligand-independent web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. We used around 1100 protein structures to form pairs of proteins which were assessed with Geomfinder. In these analyses each protein was considered in only one pair (e.g. in a subset of 100 different proteins, 50 pairs of proteins can be defined). Thus: (a) Geomfinder detected identical pairs of 3D patterns in a series of monoamine oxidase-B structures, which corresponded to the effectively similar ligand binding sites at these proteins; (b) we identified structural similarities among pairs of protein structures which are targets of compounds such as acarbose, benzamidine, adenosine triphosphate and pyridoxal phosphate; these similar 3D patterns are not detected using sequence-based methods; (c) the detailed evaluation of three specific cases showed the versatility

  6. Similar net ecosystem exchange of beech stands located in France and Denmark

    DEFF Research Database (Denmark)

    Granier, A.; Pilegaard, K.; Jensen, N.O.

    2002-01-01

    Net ecosystem exchange (NEE), as measured with eddy covariance was compared for two European beech stands for the years 1996-1999: a young beech forest (32 year-old) growing in east France, and a mature beech stand (80 year-old) located in Denmark. Those sites are included in the Carboeuroflux....../Carbodata European networks. Except for some short-term differences (1-5 days), the temporal variation of NEE followed similar patterns in both sites. This similarity followed from similar values of. (i) dates of bud break and of leaf fall; (ii) ecosystem respiration rates during winter; (iii) diurnal NEE during...

  7. Self-similar potential in the near wake

    International Nuclear Information System (INIS)

    Diebold, D.; Hershkowitz, N.; Intrator, T.; Bailey, A.

    1987-01-01

    The plasma potential is measured near the edge of an electrically floating obstacle placed in a steady-state, supersonic, unmagnetized, neutral plasma flow. Equipotential contours show the sheath of the upstream side of the obstacle wrapping around the edge of the obstacle and fanning out into the near wake. Both fluid theory and the data find the near-wake plasma potential to be self-similar when ionization, charge exchange, and magnetic field can be neglected. The theory also finds that fluid velocity is self-similar, the near wake is nonneutral, and plasma density is not self-similar. Strong electric fields are found near the obstacle and equipotential contours are found to conform to all boundaries

  8. Similarity problems and completely bounded maps

    CERN Document Server

    Pisier, Gilles

    2001-01-01

    These notes revolve around three similarity problems, appearing in three different contexts, but all dealing with the space B(H) of all bounded operators on a complex Hilbert space H. The first one deals with group representations, the second one with C* -algebras and the third one with the disc algebra. We describe them in detail in the introduction which follows. This volume is devoted to the background necessary to understand these three problems, to the solutions that are known in some special cases and to numerous related concepts, results, counterexamples or extensions which their investigation has generated. While the three problems seem different, it is possible to place them in a common framework using the key concept of "complete boundedness", which we present in detail. Using this notion, the three problems can all be formulated as asking whether "boundedness" implies "complete boundedness" for linear maps satisfying certain additional algebraic identities. Two chapters have been added on the HALMO...

  9. Social values as arguments: similar is convincing

    Science.gov (United States)

    Maio, Gregory R.; Hahn, Ulrike; Frost, John-Mark; Kuppens, Toon; Rehman, Nadia; Kamble, Shanmukh

    2014-01-01

    Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., “equality leads to freedom”). Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness. PMID:25147529

  10. Image Steganalysis with Binary Similarity Measures

    Directory of Open Access Journals (Sweden)

    Kharrazi Mehdi

    2005-01-01

    Full Text Available We present a novel technique for steganalysis of images that have been subjected to embedding by steganographic algorithms. The seventh and eighth bit planes in an image are used for the computation of several binary similarity measures. The basic idea is that the correlation between the bit planes as well as the binary texture characteristics within the bit planes will differ between a stego image and a cover image. These telltale marks are used to construct a classifier that can distinguish between stego and cover images. We also provide experimental results using some of the latest steganographic algorithms. The proposed scheme is found to have complementary performance vis-à-vis Farid's scheme in that they outperform each other in alternate embedding techniques.

  11. A Lithium Vapor Box Divertor Similarity Experiment

    Science.gov (United States)

    Cohen, Robert A.; Emdee, Eric D.; Goldston, Robert J.; Jaworski, Michael A.; Schwartz, Jacob A.

    2017-10-01

    A lithium vapor box divertor offers an alternate means of managing the extreme power density of divertor plasmas by leveraging gaseous lithium to volumetrically extract power. The vapor box divertor is a baffled slot with liquid lithium coated walls held at temperatures which increase toward the divertor floor. The resulting vapor pressure differential drives gaseous lithium from hotter chambers into cooler ones, where the lithium condenses and returns. A similarity experiment was devised to investigate the advantages offered by a vapor box divertor design. We discuss the design, construction, and early findings of the vapor box divertor experiment including vapor can construction, power transfer calculations, joint integrity tests, and thermocouple data logging. Heat redistribution of an incident plasma-based heat flux from a typical linear plasma device is also presented. This work supported by DOE Contract No. DE-AC02-09CH11466 and The Princeton Environmental Institute.

  12. Correct Bayesian and frequentist intervals are similar

    International Nuclear Information System (INIS)

    Atwood, C.L.

    1986-01-01

    This paper argues that Bayesians and frequentists will normally reach numerically similar conclusions, when dealing with vague data or sparse data. It is shown that both statistical methodologies can deal reasonably with vague data. With sparse data, in many important practical cases Bayesian interval estimates and frequentist confidence intervals are approximately equal, although with discrete data the frequentist intervals are somewhat longer. This is not to say that the two methodologies are equally easy to use: The construction of a frequentist confidence interval may require new theoretical development. Bayesians methods typically require numerical integration, perhaps over many variables. Also, Bayesian can easily fall into the trap of over-optimism about their amount of prior knowledge. But in cases where both intervals are found correctly, the two intervals are usually not very different. (orig.)

  13. Soldier motivation – different or similar?

    DEFF Research Database (Denmark)

    Brænder, Morten; Andersen, Lotte Bøgh

    Recent research in military sociology has shown that in addition to their strong peer motivation modern soldiers are oriented toward contributing to society. It has not, however, been tested how soldier motivation differs from the motivation of other citizens in this respect. In this paper......, by means of public service motivation, a concept developed within the public administration literature, we compare soldier and civilian motivation. The contribution of this paper is an analysis of whether and how Danish combat soldiers differs from other Danes in regard to public service motivation? Using...... surveys with similar questions, we find that soldiers are more normatively motivated to contribute to society than other citizens (higher commitment to the public interest), while their affectively based motivation is lower (lower compassion). This points towards a potential problem in regard...

  14. Social Values as Arguments: Similar is Convincing

    Directory of Open Access Journals (Sweden)

    Gregory R Maio

    2014-08-01

    Full Text Available Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., equality leads to freedom. Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness.

  15. Formulation of similarity porous media systems

    International Nuclear Information System (INIS)

    Anderson, R.M.; Ford, W.T.; Ruttan, A.; Strauss, M.J.

    1982-01-01

    The mathematical formulation of the Porous Media System (PMS) describing two-phase, immiscible, compressible fluid flow in linear, homogeneous porous media is reviewed and expanded. It is shown that families of common vertex, coaxial parabolas and families of parallel lines are the only families of curves on which solutions of the PMS may be constant. A coordinate transformation is used to change the partial differential equations of the PMS to a system of ordinary differential equations, referred to as a similarity Porous Media System (SPMS), in which the independent variable denotes movement from curve to curve in a selected family of curves. Properties of solutions of the first boundary value problem are developed for the SPMS

  16. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine

    2010-01-01

    -seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts......, given an example expert. Our approach combines expertise-seeking and retrieval research. First, we conduct a user study to identify contextual factors that may play a role in the studied task and environment. Then, we design expert retrieval models to capture these factors. We combine these with content......-based retrieval models and evaluate them in a retrieval experiment. Our main finding is that while content-based features are the most important, human participants also take contextual factors into account, such as media experience and organizational structure. We develop two principled ways of modeling...

  17. Educational Outreach: The Space Science Road Show

    Science.gov (United States)

    Cox, N. L. J.

    2002-01-01

    The poster presented will give an overview of a study towards a "Space Road Show". The topic of this show is space science. The target group is adolescents, aged 12 to 15, at Dutch high schools. The show and its accompanying experiments would be supported with suitable educational material. Science teachers at schools can decide for themselves if they want to use this material in advance, afterwards or not at all. The aims of this outreach effort are: to motivate students for space science and engineering, to help them understand the importance of (space) research, to give them a positive feeling about the possibilities offered by space and in the process give them useful knowledge on space basics. The show revolves around three main themes: applications, science and society. First the students will get some historical background on the importance of space/astronomy to civilization. Secondly they will learn more about novel uses of space. On the one hand they will learn of "Views on Earth" involving technologies like Remote Sensing (or Spying), Communication, Broadcasting, GPS and Telemedicine. On the other hand they will experience "Views on Space" illustrated by past, present and future space research missions, like the space exploration missions (Cassini/Huygens, Mars Express and Rosetta) and the astronomy missions (Soho and XMM). Meanwhile, the students will learn more about the technology of launchers and satellites needed to accomplish these space missions. Throughout the show and especially towards the end attention will be paid to the third theme "Why go to space"? Other reasons for people to get into space will be explored. An important question in this is the commercial (manned) exploration of space. Thus, the questions of benefit of space to society are integrated in the entire show. It raises some fundamental questions about the effects of space travel on our environment, poverty and other moral issues. The show attempts to connect scientific with

  18. Characterization of a Smad motif similar to Drosophila mad in the mouse Msx 1 promoter.

    Science.gov (United States)

    Alvarez Martinez, Cristina E; Binato, Renata; Gonzalez, Sayonara; Pereira, Monica; Robert, Benoit; Abdelhay, Eliana

    2002-03-01

    Mouse Msx 1 gene, orthologous of the Drosophila msh, is involved in several developmental processes. BMP family members are major proteins in the regulation of Msx 1 expression. BMP signaling activates Smad 1/5/8 proteins, which associate to Smad 4 before translocating to the nucleus. Analysis of Msx 1 promoter revealed the presence of three elements similar to the consensus established for Mad, the Smad 1 Drosophila counterpart. Notably, such an element was identified in an enhancer important for Msx 1 regulation. Gel shift analysis demonstrated that proteins from 13.5 dpc embryo associate to this enhancer. Remarkably, supershift assays showed that Smad proteins are present in the complex. Purified Smad 1 and 4 also bind to this fragment. We demonstrate that functional binding sites in this enhancer are confined to the Mad motif and flanking region. Our data suggest that this Mad motif may be functional in response to BMP signaling. ©2002 Elsevier Science (USA).

  19. Archaea Signal Recognition Particle Shows the Way

    Directory of Open Access Journals (Sweden)

    Christian Zwieb

    2010-01-01

    Full Text Available Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY. Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY are strikingly diverse or absent even among the members of a taxonomic subgroup.

  20. 2008 LHC Open Days Physics: the show

    CERN Multimedia

    2008-01-01

    A host of events and activities await visitors to the LHC Open Days on 5 and 6 April. A highlight will be the physics shows funded by the European Physical Society (EPS), which are set to surprise and challenge children and adults alike! School children use their experience of riding a bicycle to understand how planets move around the sun (Copyright : Circus Naturally) Participating in the Circus Naturally show could leave a strange taste in your mouth! (Copyright : Circus Naturally) The Rino Foundation’s experiments with liquid nitrogen can be pretty exciting! (Copyright: The Rino Foundation)What does a bicycle have in common with the solar system? Have you ever tried to weigh air or visualise sound? Ever heard of a vacuum bazooka? If you want to discover the answers to these questions and more then come to the Physics Shows taking place at the CERN O...

  1. Online Italian fandoms of American TV shows

    Directory of Open Access Journals (Sweden)

    Eleonora Benecchi

    2015-06-01

    Full Text Available The Internet has changed media fandom in two main ways: it helps fans connect with each other despite physical distance, leading to the formation of international fan communities; and it helps fans connect with the creators of the TV show, deepening the relationship between TV producers and international fandoms. To assess whether Italian fan communities active online are indeed part of transnational online communities and whether the Internet has actually altered their relationship with the creators of the original text they are devoted to, qualitative analysis and narrative interviews of 26 Italian fans of American TV shows were conducted to explore the fan-producer relationship. Results indicated that the online Italian fans surveyed preferred to stay local, rather than using geography-leveling online tools. Further, the sampled Italian fans' relationships with the show runners were mediated or even absent.

  2. Single-provenance mature conifers show higher non-structural carbohydrate storage and reduced growth in a drier location.

    Science.gov (United States)

    Piper, Frida I; Fajardo, Alex; Hoch, Günter

    2017-08-01

    Since growth is more sensitive to drought than photosynthesis, trees inhabiting dry regions are expected to exhibit higher carbohydrate storage and less growth than their conspecifics from more humid regions. However, the same pattern can be the result of different genotypes inhabiting contrasting humidity conditions. To test if reduced growth and high carbohydrate storage are environmentally driven by drought, we examined the growth and non-structural carbohydrate (NSC) concentrations in single-provenance stands of mature trees of Pinus contorta Douglas and Pinus ponderosa Douglas ex C. Lawson planted at contrasting humidity conditions (900 versus 300 mm of annual precipitation) in Patagonia, Chile. Individual tree growth was measured for each species and at each location as mean basal area increment of the last 10 years (BAI10), annual shoot elongation for the period 2011-14, and needle length for 2013 and 2014 cohorts. Additionally, needle, branch, stem sapwood and roots were collected from each sampled tree to determine soluble sugars, starch and total NSC concentrations. The two species showed lower mean BAI10 and 2013 needle length in the dry site; P. ponderosa also had lower annual shoot extension for 2011 and 2014, and lower 2014 needle length, in the dry than in the mesic site. By contrast, NSC concentrations of all woody tissues for both species were either similar or higher in the dry site when compared with the mesic site. Patterns of starch and sugars were substantially different: starch concentrations were similar between sites except for roots of P. ponderosa, which were higher in the dry site, while sugar concentrations of all woody tissues in both species were higher in the dry site. Overall, our study provides evidence that reduced growth along with carbon (C) accumulation is an environmentally driven response to drought. Furthermore, the significant accumulation of low-molecular weight sugars in the dry site is compatible with a prioritized C

  3. A similarity measure method combining location feature for mammogram retrieval.

    Science.gov (United States)

    Wang, Zhiqiong; Xin, Junchang; Huang, Yukun; Li, Chen; Xu, Ling; Li, Yang; Zhang, Hao; Gu, Huizi; Qian, Wei

    2018-05-28

    Breast cancer, the most common malignancy among women, has a high mortality rate in clinical practice. Early detection, diagnosis and treatment can reduce the mortalities of breast cancer greatly. The method of mammogram retrieval can help doctors to find the early breast lesions effectively and determine a reasonable feature set for image similarity measure. This will improve the accuracy effectively for mammogram retrieval. This paper proposes a similarity measure method combining location feature for mammogram retrieval. Firstly, the images are pre-processed, the regions of interest are detected and the lesions are segmented in order to get the center point and radius of the lesions. Then, the method, namely Coherent Point Drift, is used for image registration with the pre-defined standard image. The center point and radius of the lesions after registration are obtained and the standard location feature of the image is constructed. This standard location feature can help figure out the location similarity between the image pair from the query image to each dataset image in the database. Next, the content feature of the image is extracted, including the Histogram of Oriented Gradients, the Edge Direction Histogram, the Local Binary Pattern and the Gray Level Histogram, and the image pair content similarity can be calculated using the Earth Mover's Distance. Finally, the location similarity and content similarity are fused to form the image fusion similarity, and the specified number of the most similar images can be returned according to it. In the experiment, 440 mammograms, which are from Chinese women in Northeast China, are used as the database. When fusing 40% lesion location feature similarity and 60% content feature similarity, the results have obvious advantages. At this time, precision is 0.83, recall is 0.76, comprehensive indicator is 0.79, satisfaction is 96.0%, mean is 4.2 and variance is 17.7. The results show that the precision and recall of this

  4. Link-Based Similarity Measures Using Reachability Vectors

    Directory of Open Access Journals (Sweden)

    Seok-Ho Yoon

    2014-01-01

    Full Text Available We present a novel approach for computing link-based similarities among objects accurately by utilizing the link information pertaining to the objects involved. We discuss the problems with previous link-based similarity measures and propose a novel approach for computing link based similarities that does not suffer from these problems. In the proposed approach each target object is represented by a vector. Each element of the vector corresponds to all the objects in the given data, and the value of each element denotes the weight for the corresponding object. As for this weight value, we propose to utilize the probability of reaching from the target object to the specific object, computed using the “Random Walk with Restart” strategy. Then, we define the similarity between two objects as the cosine similarity of the two vectors. In this paper, we provide examples to show that our approach does not suffer from the aforementioned problems. We also evaluate the performance of the proposed methods in comparison with existing link-based measures, qualitatively and quantitatively, with respect to two kinds of data sets, scientific papers and Web documents. Our experimental results indicate that the proposed methods significantly outperform the existing measures.

  5. Genetic similarity of soybean genotypes revealed by seed protein

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2005-01-01

    Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

  6. A Measure of Similarity Between Trajectories of Vessels

    Directory of Open Access Journals (Sweden)

    Le QI

    2016-03-01

    Full Text Available The measurement of similarity between trajectories of vessels is one of the kernel problems that must be addressed to promote the development of maritime intelligent traffic system (ITS. In this study, a new model of trajectory similarity measurement was established to improve the data processing efficiency in dynamic application and to reflect actual sailing behaviors of vessels. In this model, a feature point detection algorithm was proposed to extract feature points, reduce data storage space and save computational resources. A new synthesized distance algorithm was also created to measure the similarity between trajectories by using the extracted feature points. An experiment was conducted to measure the similarity between the real trajectories of vessels. The growth of these trajectories required measurements to be conducted under different voyages. The results show that the similarity measurement between the vessel trajectories is efficient and correct. Comparison of the synthesized distance with the sailing behaviors of vessels proves that results are consistent with actual situations. The experiment results demonstrate the promising application of the proposed model in studying vessel traffic and in supplying reliable data for the development of maritime ITS.

  7. AREAL FEATURE MATCHING BASED ON SIMILARITY USING CRITIC METHOD

    Directory of Open Access Journals (Sweden)

    J. Kim

    2015-10-01

    Full Text Available In this paper, we propose an areal feature matching method that can be applied for many-to-many matching, which involves matching a simple entity with an aggregate of several polygons or two aggregates of several polygons with fewer user intervention. To this end, an affine transformation is applied to two datasets by using polygon pairs for which the building name is the same. Then, two datasets are overlaid with intersected polygon pairs that are selected as candidate matching pairs. If many polygons intersect at this time, we calculate the inclusion function between such polygons. When the value is more than 0.4, many of the polygons are aggregated as single polygons by using a convex hull. Finally, the shape similarity is calculated between the candidate pairs according to the linear sum of the weights computed in CRITIC method and the position similarity, shape ratio similarity, and overlap similarity. The candidate pairs for which the value of the shape similarity is more than 0.7 are determined as matching pairs. We applied the method to two geospatial datasets: the digital topographic map and the KAIS map in South Korea. As a result, the visual evaluation showed two polygons that had been well detected by using the proposed method. The statistical evaluation indicates that the proposed method is accurate when using our test dataset with a high F-measure of 0.91.

  8. Areal Feature Matching Based on Similarity Using Critic Method

    Science.gov (United States)

    Kim, J.; Yu, K.

    2015-10-01

    In this paper, we propose an areal feature matching method that can be applied for many-to-many matching, which involves matching a simple entity with an aggregate of several polygons or two aggregates of several polygons with fewer user intervention. To this end, an affine transformation is applied to two datasets by using polygon pairs for which the building name is the same. Then, two datasets are overlaid with intersected polygon pairs that are selected as candidate matching pairs. If many polygons intersect at this time, we calculate the inclusion function between such polygons. When the value is more than 0.4, many of the polygons are aggregated as single polygons by using a convex hull. Finally, the shape similarity is calculated between the candidate pairs according to the linear sum of the weights computed in CRITIC method and the position similarity, shape ratio similarity, and overlap similarity. The candidate pairs for which the value of the shape similarity is more than 0.7 are determined as matching pairs. We applied the method to two geospatial datasets: the digital topographic map and the KAIS map in South Korea. As a result, the visual evaluation showed two polygons that had been well detected by using the proposed method. The statistical evaluation indicates that the proposed method is accurate when using our test dataset with a high F-measure of 0.91.

  9. Measuring site occupancy

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, Adelina; Wojdyla, Katarzyna; Williamson, James

    2014-01-01

    occupancy of the modification site. We show that, on one hand, heavily modified cysteines are not necessarily involved in the response to oxidative stress. On the other hand residues with low modification level can be dramatically affected by mild oxidative imbalance. We make use of high resolution mass...... peptides corresponding to 90 proteins. Only 6 modified peptides changed significantly under mild oxidative stress. Quantitative information allowed us to determine relative modification site occupancy of each identified modified residue and pin point heavily modified ones. The method proved to be precise...... and sensitive enough to detect and quantify endogenous levels of oxidative stress on proteome-wide scale and brings a new perspective on the role of the modification site occupancy in cellular redox response....

  10. Duchenne muscular dystrophy models show their age

    OpenAIRE

    Chamberlain, Jeffrey S.

    2010-01-01

    The lack of appropriate animal models has hampered efforts to develop therapies for Duchenne muscular dystrophy (DMD). A new mouse model lacking both dystrophin and telomerase (Sacco et al., 2010) closely mimics the pathological progression of human DMD and shows that muscle stem cell activity is a key determinant of disease severity.

  11. Show Them You Really Want the Job

    Science.gov (United States)

    Perlmutter, David D.

    2012-01-01

    Showing that one really "wants" the job entails more than just really wanting the job. An interview is part Broadway casting call, part intellectual dating game, part personality test, and part, well, job interview. When there are 300 applicants for a position, many of them will "fit" the required (and even the preferred) skills listed in the job…

  12. A Talk Show from the Past.

    Science.gov (United States)

    Gallagher, Arlene F.

    1991-01-01

    Describes a two-day activity in which elementary students examine voting rights, the right to assemble, and women's suffrage. Explains the game, "Assemble, Reassemble," and a student-produced talk show with five students playing the roles of leaders of the women's suffrage movement. Profiles Elizabeth Cady Stanton, Lucretia Mott, Susan…

  13. Laser entertainment and light shows in education

    Science.gov (United States)

    Sabaratnam, Andrew T.; Symons, Charles

    2002-05-01

    Laser shows and beam effects have been a source of entertainment since its first public performance May 9, 1969, at Mills College in Oakland, California. Since 1997, the Photonics Center, NgeeAnn Polytechnic, Singapore, has been using laser shows as a teaching tool. Students are able to exhibit their creative skills and learn at the same time how lasers are used in the entertainment industry. Students will acquire a number of skills including handling three- phase power supply, operation of cooling system, and laser alignment. Students also acquire an appreciation of the arts, learning about shapes and contours as they develop graphics for the shows. After holography, laser show animation provides a combination of the arts and technology. This paper aims to briefly describe how a krypton-argon laser, galvanometer scanners, a polychromatic acousto-optic modulator and related electronics are put together to develop a laser projector. The paper also describes how students are trained to make their own laser animation and beam effects with music, and at the same time have an appreciation of the operation of a Class IV laser and the handling of optical components.

  14. The Last Great American Picture Show

    NARCIS (Netherlands)

    Elsaesser, Thomas; King, Noel; Horwath, Alexander

    2004-01-01

    The Last Great American Picture Show brings together essays by scholars and writers who chart the changing evaluations of the American cinema of the 1970s, sometimes referred to as the decade of the lost generation, but now more and more recognized as the first New Hollywood, without which the

  15. Spousal similarity in life satisfaction before and after divorce.

    Science.gov (United States)

    Wortman, Jessica; Lucas, Richard E

    2016-04-01

    Previous research has explored possible origins of individual differences in subjective well-being, focusing largely on stable, internal characteristics of traits as predictors of life satisfaction (Diener & Lucas, 1999). Although past work has demonstrated that life satisfaction is largely stable over the life span, other evidence has also demonstrated the lasting impact of life events. In this study, we use married couples as a test of the impact of life circumstances on life satisfaction, focusing on similarity in life satisfaction before and after divorce. If life satisfaction is impacted by shared life circumstances, married couples (who share life circumstances) should show greater similarity in life satisfaction before divorce than after. We tested this possibility using a dyadic latent-state-trait model that examined cross-spouse similarity in the stable and changing components of life satisfaction. Using a nationally representative panel study from Germany (Wagner, Frick & Schupp, 2007), we showed that similarity declined substantially following divorce. This suggests that life satisfaction is related to shared life circumstances. (c) 2016 APA, all rights reserved).

  16. Enteric neurons show a primary cilium.

    Science.gov (United States)

    Luesma, Ma José; Cantarero, Irene; Castiella, Tomás; Soriano, Mario; Garcia-Verdugo, José Manuel; Junquera, Concepción

    2013-01-01

    The primary cilium is a non-motile cilium whose structure is 9+0. It is involved in co-ordinating cellular signal transduction pathways, developmental processes and tissue homeostasis. Defects in the structure or function of the primary cilium underlie numerous human diseases, collectively termed ciliopathies. The presence of single cilia in the central nervous system (CNS) is well documented, including some choroid plexus cells, neural stem cells, neurons and astrocytes, but the presence of primary cilia in differentiated neurons of the enteric nervous system (ENS) has not yet been described in mammals to the best of our knowledge. The enteric nervous system closely resembles the central nervous system. In fact, the ultrastructure of the ENS is more similar to the CNS ultrastructure than to the rest of the peripheral nervous system. This research work describes for the first time the ultrastructural characteristics of the single cilium in neurons of rat duodenum myenteric plexus, and reviews the cilium function in the CNS to propose the possible role of cilia in the ENS cells. © 2012 The Authors. Published by Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  17. Similarity, Data Compression and a dead composer

    NARCIS (Netherlands)

    Koopmans, J.M.A.; van den Berg, D.; Zaytsev, V.

    2015-01-01

    Domenico Scarlatti (1685-1759) is well-known for his 555 keyboard sonatas. Although his work is greatly revered by many professional musicians, some claim that it does not show any compository development. In this paper, his sonatas are clustered by normalized compression distance (NCD), an

  18. Different-but-Similar Judgments by Bumblebees

    Directory of Open Access Journals (Sweden)

    Vicki Xu

    2016-08-01

    Full Text Available This study examines picture perception in an invertebrate. Two questions regarding possible picture-object correspondence are addressed for bumblebees (Bombus impatiens: (1 Do bees perceive the difference between an object and its corresponding picture even when they have not been trained to do so? (2 Do they also perceive the similarity? Twenty bees from each of four colonies underwent discrimination training of stimuli placed in a radial maze. Bees were trained to discriminate between two objects (artificial flowers in one group and between photos of those objects in another. Subsequent testing on unrewarding stimuli revealed, for both groups, a significant discrimination between the object and its photo: discrimination training was not necessary for bees to detect a difference between corresponding objects and pictures. We obtained not only object-to-picture transfer, as in previous research, but also the reverse: picture-to-object transfer. In the absence of the rewarding object, its photo, though never seen before by the bees, was accepted as a substitute. The reverse was also true. Bumblebees treated pictures as “different-but-similar” without having been trained to do so, which is in turn useful in floral categorization.

  19. Block generators for the similarity renormalization group

    Energy Technology Data Exchange (ETDEWEB)

    Huether, Thomas; Roth, Robert [TU Darmstadt (Germany)

    2016-07-01

    The Similarity Renormalization Group (SRG) is a powerful tool to improve convergence behavior of many-body calculations using NN and 3N interactions from chiral effective field theory. The SRG method decouples high and low-energy physics, through a continuous unitary transformation implemented via a flow equation approach. The flow is determined by a generator of choice. This generator governs the decoupling pattern and, thus, the improvement of convergence, but it also induces many-body interactions. Through the design of the generator we can optimize the balance between convergence and induced forces. We explore a new class of block generators that restrict the decoupling to the high-energy sector and leave the diagonalization in the low-energy sector to the many-body method. In this way one expects a suppression of induced forces. We analyze the induced many-body forces and the convergence behavior in light and medium-mass nuclei in No-Core Shell Model and In-Medium SRG calculations.

  20. State and Mafia, Differences and Similarities

    Directory of Open Access Journals (Sweden)

    Alfano Vincenzo

    2015-02-01

    Full Text Available The purpose of this article is to investigate about the differences and, if any, the similarities among the modern State and the mafia criminal organizations. In particular, starting from their definitions, I will try to find the differences between State and mafia, to then focus on the operational aspects of the functioning of these two organizations, with specific reference to the effect/impact that both these human constructs have on citizens’ existences, and especially on citizen’s economic lives. All this in order to understand whether it is possible to identify an objective difference – beside morals – between taxation by the modern State and extortion by criminal organizations. With this of course I do not want to argue that the mafia is in any way justifiable or absolvable, nor that it is better than the State. However, I want to investigate whether there is a real, logical reason why the State should be considered by the citizens more desirable than the criminal organizations oppressing Southern Italy, from a strictly logical point of view and not from the point of view of ethics and morality.

  1. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2015-03-01

    Full Text Available In this paper, we apply multidimensional scaling (MDS and parametric similarity indices (PSI in the analysis of complex systems (CS. Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, and we generate the corresponding MDS maps of ‘points’. Third, we use Procrustes analysis to linearly transform the MDS charts for maximum superposition and to build a globalMDS map of “shapes”. This final plot captures the time evolution of the phenomena and is sensitive to the PSI adopted. The generalized correlation, theMinkowski distance and four entropy-based indices are tested. The proposed approach is applied to the Dow Jones Industrial Average stock market index and the Europe Brent Spot Price FOB time-series.

  2. Exploring similarities among many species distributions

    Science.gov (United States)

    Simmerman, Scott; Wang, Jingyuan; Osborne, James; Shook, Kimberly; Huang, Jian; Godsoe, William; Simons, Theodore R.

    2012-01-01

    Collecting species presence data and then building models to predict species distribution has been long practiced in the field of ecology for the purpose of improving our understanding of species relationships with each other and with the environment. Due to limitations of computing power as well as limited means of using modeling software on HPC facilities, past species distribution studies have been unable to fully explore diverse data sets. We build a system that can, for the first time to our knowledge, leverage HPC to support effective exploration of species similarities in distribution as well as their dependencies on common environmental conditions. Our system can also compute and reveal uncertainties in the modeling results enabling domain experts to make informed judgments about the data. Our work was motivated by and centered around data collection efforts within the Great Smoky Mountains National Park that date back to the 1940s. Our findings present new research opportunities in ecology and produce actionable field-work items for biodiversity management personnel to include in their planning of daily management activities.

  3. Similarities and differences in vapor explosion criteria

    International Nuclear Information System (INIS)

    Cronenberg, A.W.

    1978-01-01

    An overview of recent ideas pertaining to vapor explosion criteria indicates that in general sense, a consensus of opinion is emerging on the conditions applicable to explosive vaporization. Experimental and theoretical work has lead a number of investigators to the formulation of such conditions which are quite similar in many respects, although the quantitative details of the model formulation of such conditions are somewhat different. All model concepts are consistent in that an initial period of stable film boiling, separating molten fuel from coolant, is considered necessary (at least for large-scale interactions and efficient intermixing), with subsequent breakdown of film boiling due to pressure and/or thermal effects, followed by intimate fuel-coolant contact and a rapid vaporization process which is sufficient to cause shock pressurization. Although differences arise as to the conditions for and the energetics associated with film boiling destabilization and the mode and energetics of fragmentation and intermixing. However, the principal area of difference seems to be the question of what constitutes the requisite condition(s) for rapid vapor production to cause shock pressurization

  4. A vertex similarity index for better personalized recommendation

    Science.gov (United States)

    Chen, Ling-Jiao; Zhang, Zi-Ke; Liu, Jin-Hu; Gao, Jian; Zhou, Tao

    2017-01-01

    Recommender systems benefit us in tackling the problem of information overload by predicting our potential choices among diverse niche objects. So far, a variety of personalized recommendation algorithms have been proposed and most of them are based on similarities, such as collaborative filtering and mass diffusion. Here, we propose a novel vertex similarity index named CosRA, which combines advantages of both the cosine index and the resource-allocation (RA) index. By applying the CosRA index to real recommender systems including MovieLens, Netflix and RYM, we show that the CosRA-based method has better performance in accuracy, diversity and novelty than some benchmark methods. Moreover, the CosRA index is free of parameters, which is a significant advantage in real applications. Further experiments show that the introduction of two turnable parameters cannot remarkably improve the overall performance of the CosRA index.

  5. Branch length similarity entropy-based descriptors for shape representation

    Science.gov (United States)

    Kwon, Ohsung; Lee, Sang-Hee

    2017-11-01

    In previous studies, we showed that the branch length similarity (BLS) entropy profile could be successfully used for the shape recognition such as battle tanks, facial expressions, and butterflies. In the present study, we proposed new descriptors, roundness, symmetry, and surface roughness, for the recognition, which are more accurate and fast in the computation than the previous descriptors. The roundness represents how closely a shape resembles to a circle, the symmetry characterizes how much one shape is similar with another when the shape is moved in flip, and the surface roughness quantifies the degree of vertical deviations of a shape boundary. To evaluate the performance of the descriptors, we used the database of leaf images with 12 species. Each species consisted of 10 - 20 leaf images and the total number of images were 160. The evaluation showed that the new descriptors successfully discriminated the leaf species. We believe that the descriptors can be a useful tool in the field of pattern recognition.

  6. Privacy in social networking sites

    OpenAIRE

    Λεονάρδος, Γεώργιος; Leonardos, Giorgos

    2016-01-01

    The purpose of this study is to explore the aspects of privacy over the use of social networks web sites. More specific, we will show the types of social networks, their privacy mechanisms that are different in each social network site, their privacy options that are offered to users. We will report some serious privacy violations incidents of the most popular social networks sites such as Facebook, Twitter, LinkedIn. Also, we will report some important surveys about social networks and pr...

  7. Reality, ficción o show

    Directory of Open Access Journals (Sweden)

    Sandra Ruíz Moreno

    2002-01-01

    Full Text Available Para tener un punto de vista claro y objetivo frente a la polémica establecida en torno al programa “Protagonistas de novela” y la tendiente proliferación de los reality show en las parrillas de programación de la televisión colombiana, se realizó un análisis de texto y contenido de dicho programa, intentando definirlo desde sus posibilidades de realidad, ficción y show. Las unidades de análisis y el estudio de su tratamiento arrojaron un alto contenido que gira en torno a las emociones del ser humano relacionadas con la convivencia, tratadas a manera de show y con algunos aportes textuales de ficción, pero sin su elemento mediador básico, el actor, quitándole toda la posibilidad de tener un tratamiento con la profundidad, distancia y ética que requieren los temas de esta índole. El resultado es un formato que sólo busca altos índices de sintonía y que pertenece más a la denominada televisión “trash”, que a una búsqueda de realidad del hombre y mucho menos de sociedad.

  8. Similarly shaped letters evoke similar colors in grapheme-color synesthesia.

    Science.gov (United States)

    Brang, David; Rouw, Romke; Ramachandran, V S; Coulson, Seana

    2011-04-01

    Grapheme-color synesthesia is a neurological condition in which viewing numbers or letters (graphemes) results in the concurrent sensation of color. While the anatomical substrates underlying this experience are well understood, little research to date has investigated factors influencing the particular colors associated with particular graphemes or how synesthesia occurs developmentally. A recent suggestion of such an interaction has been proposed in the cascaded cross-tuning (CCT) model of synesthesia, which posits that in synesthetes connections between grapheme regions and color area V4 participate in a competitive activation process, with synesthetic colors arising during the component-stage of grapheme processing. This model more directly suggests that graphemes sharing similar component features (lines, curves, etc.) should accordingly activate more similar synesthetic colors. To test this proposal, we created and regressed synesthetic color-similarity matrices for each of 52 synesthetes against a letter-confusability matrix, an unbiased measure of visual similarity among graphemes. Results of synesthetes' grapheme-color correspondences indeed revealed that more similarly shaped graphemes corresponded with more similar synesthetic colors, with stronger effects observed in individuals with more intense synesthetic experiences (projector synesthetes). These results support the CCT model of synesthesia, implicate early perceptual mechanisms as driving factors in the elicitation of synesthetic hues, and further highlight the relationship between conceptual and perceptual factors in this phenomenon. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. A Quantum Approach to Subset-Sum and Similar Problems

    OpenAIRE

    Daskin, Ammar

    2017-01-01

    In this paper, we study the subset-sum problem by using a quantum heuristic approach similar to the verification circuit of quantum Arthur-Merlin games. Under described certain assumptions, we show that the exact solution of the subset sum problem my be obtained in polynomial time and the exponential speed-up over the classical algorithms may be possible. We give a numerical example and discuss the complexity of the approach and its further application to the knapsack problem.

  10. Similarity flows between a rotating and a stationary disk

    International Nuclear Information System (INIS)

    Buchmann, J.H.; Qassim, R.Y.

    1981-07-01

    The radial distribution of fluid pressure on a stationary disk coaxial with a rotating disk is determined experimentally for various inter-disc spacings. The results show that similarity flows are only possible for both small and large values of this distance. In the former case, the flow faraway from the stationary disk appears to be that suggested by Batchelor, while in the latter case, the flow turns out to be in accordance with the assumption of Stewartson. (Author) [pt

  11. Self-similar oscillations of a Z pinch

    International Nuclear Information System (INIS)

    Felber, F.S.

    1982-01-01

    A new analytic, self-similar solution of the equations of ideal magnetohydrodynamics describes cylindrically symmetric plasmas conducting constant current. The solution indicates that an adiabatic Z pinch oscillates radially with a period typically of the order of a few acoustic transit times. A stability analysis, which shows the growth rate of the sausage instability to be a saturating function of wavenumber, suggests that the oscillations are observable

  12. Word Similarity From Dictionaries: Inferring Fuzzy Measures From Fuzzy Graphs

    Directory of Open Access Journals (Sweden)

    Torra

    2008-01-01

    Full Text Available The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.

  13. Naked singularities in self-similar spherical gravitational collapse

    International Nuclear Information System (INIS)

    Ori, A.; Piran, T.

    1987-01-01

    We present general-relativistic solutions of self-similar spherical collapse of an adiabatic perfect fluid. We show that if the equation of state is soft enough (Γ-1<<1), a naked singularity forms. The singularity resembles the shell-focusing naked singularities that arise in dust collapse. This solution increases significantly the range of matter fields that should be ruled out in order that the cosmic-censorship hypothesis will hold

  14. Exploiting Data Similarity to Reduce Memory Footprints

    Science.gov (United States)

    2011-01-01

    ure 1 illustrates. We expect the budget for an exascale system to be approximately $200M and memory costs will account for about half of that budget [21...Figure 2 shows that monetary considerations will lead to significantly less main memory relative to compute capability in exascale systems even if...J. Davenport, T. Schlagel, F. John- son, and P. Messina. A Decadal DOE Plan for Providing Exascale Applications and Technologies for DOE Mission

  15. Asteroid clusters similar to asteroid pairs

    Science.gov (United States)

    Pravec, P.; Fatka, P.; Vokrouhlický, D.; Scheeres, D. J.; Kušnirák, P.; Hornoch, K.; Galád, A.; Vraštil, J.; Pray, D. P.; Krugly, Yu. N.; Gaftonyuk, N. M.; Inasaridze, R. Ya.; Ayvazian, V. R.; Kvaratskhelia, O. I.; Zhuzhunadze, V. T.; Husárik, M.; Cooney, W. R.; Gross, J.; Terrell, D.; Világi, J.; Kornoš, L.; Gajdoš, Š.; Burkhonov, O.; Ehgamberdiev, Sh. A.; Donchev, Z.; Borisov, G.; Bonev, T.; Rumyantsev, V. V.; Molotov, I. E.

    2018-04-01

    We studied the membership, size ratio and rotational properties of 13 asteroid clusters consisting of between 3 and 19 known members that are on similar heliocentric orbits. By backward integrations of their orbits, we confirmed their cluster membership and estimated times elapsed since separation of the secondaries (the smaller cluster members) from the primary (i.e., cluster age) that are between 105 and a few 106 years. We ran photometric observations for all the cluster primaries and a sample of secondaries and we derived their accurate absolute magnitudes and rotation periods. We found that 11 of the 13 clusters follow the same trend of primary rotation period vs mass ratio as asteroid pairs that was revealed by Pravec et al. (2010). We generalized the model of the post-fission system for asteroid pairs by Pravec et al. (2010) to a system of N components formed by rotational fission and we found excellent agreement between the data for the 11 asteroid clusters and the prediction from the theory of their formation by rotational fission. The two exceptions are the high-mass ratio (q > 0.7) clusters of (18777) Hobson and (22280) Mandragora for which a different formation mechanism is needed. Two candidate mechanisms for formation of more than one secondary by rotational fission were published: the secondary fission process proposed by Jacobson and Scheeres (2011) and a cratering collision event onto a nearly critically rotating primary proposed by Vokrouhlický et al. (2017). It will have to be revealed from future studies which of the clusters were formed by one or the other process. To that point, we found certain further interesting properties and features of the asteroid clusters that place constraints on the theories of their formation, among them the most intriguing being the possibility of a cascade disruption for some of the clusters.

  16. Expanding the boundaries of local similarity analysis.

    Science.gov (United States)

    Durno, W Evan; Hanson, Niels W; Konwar, Kishori M; Hallam, Steven J

    2013-01-01

    Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets. To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm²n) to O(m²n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software. The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.

  17. UNSOLVED AND LATENT CRIME: DIFFERENCES AND SIMILARITIES

    Directory of Open Access Journals (Sweden)

    Mikhail Kleymenov

    2017-01-01

    Full Text Available УДК 343Purpose of the article is to study the specific legal and informational nature of the unsolved crime in comparison with the phenomenon of delinquency, special study and analysis to improve the efficiency of law enforcement.Methods of research are abstract-logical, systematic, statistical, study of documents. The main results of research. Unsolved crime has specific legal, statistical and informational na-ture as the crime phenomenon, which is expressed in cumulative statistical population of unsolved crimes. An array of unsolved crimes is the sum of the number of acts, things of which is suspended and not terminated. The fault of the perpetrator in these cases is not proven, they are not considered by the court, it is not a conviction. Unsolved crime must be registered. Latent crime has a different informational nature. The main symptom of latent crimes is the uncertainty for the subjects of law enforcement, which delegated functions of identification, registration and accounting. Latent crime is not recorded. At the same time, there is a "border" area between the latent and unsolved crimes, which includes covered from the account of the crime. In modern Russia the majority of crimes covered from accounting by passing the decision about refusal in excitation of criminal case. Unsolved crime on their criminogenic consequences represents a significant danger to the public is higher compared to latent crime.It is conducted in the article a special analysis of the differences and similarities in the unsolved latent crime for the first time in criminological literature.The analysis proves the need for radical changes in the current Russian assessment of the state of crime and law enforcement to solve crimes. The article argues that an unsolved crime is a separate and, in contrast to latent crime, poorly understood phenomenon. However unsolved latent crime and have common features and areas of interaction.

  18. DAST in Flight Showing Diverging Wingtip Oscillations

    Science.gov (United States)

    1980-01-01

    Two BQM-34 Firebee II drones were modified with supercritical airfoils, called the Aeroelastic Research Wing (ARW), for the Drones for Aerodynamic and Structural Testing (DAST) program, which ran from 1977 to 1983. In this view of DAST-1 (Serial # 72-1557), taken on June 12, 1980, severe wingtip flutter is visible. Moments later, the right wing failed catastrophically and the vehicle crashed near Cuddeback Dry Lake. Before the drone was lost, it had made two captive and two free flights. Its first free flight, on October 2, 1979, was cut short by an uplink receiver failure. The drone was caught in midair by an HH-3 helicopter. The second free flight, on March 12, 1980, was successful, ending in a midair recovery. The third free flight, made on June 12, was to expand the flutter envelope. All of these missions launched from the NASA B-52. From 1977 to 1983, the Dryden Flight Research Center, Edwards, California, (under two different names) conducted the DAST Program as a high-risk flight experiment using a ground-controlled, pilotless aircraft. Described by NASA engineers as a 'wind tunnel in the sky,' the DAST was a specially modified Teledyne-Ryan BQM-34E/F Firebee II supersonic target drone that was flown to validate theoretical predictions under actual flight conditions in a joint project with the Langley Research Center, Hampton, Virginia. The DAST Program merged advances in electronic remote control systems with advances in airplane design. Drones (remotely controlled, missile-like vehicles initially developed to serve as gunnery targets) had been deployed successfully during the Vietnamese conflict as reconnaissance aircraft. After the war, the energy crisis of the 1970s led NASA to seek new ways to cut fuel use and improve airplane efficiency. The DAST Program's drones provided an economical, fuel-conscious method for conducting in-flight experiments from a remote ground site. DAST explored the technology required to build wing structures with less than

  19. Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects

    Science.gov (United States)

    Zhang, Yinan; Samee, Md. Abul Hassan; Halfon, Marc S.; Sinha, Saurabh

    2014-01-01

    Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like “long germband” development is highly derived and confined to a subset of insect families. Whether or not these similarities extend to the regulatory level is unknown. Identification of regulatory regions beyond the well-studied Drosophila has been challenging as even within the Diptera (flies, including mosquitoes) regulatory sequences have diverged past the point of recognition by standard alignment methods. Here, we demonstrate that methods we previously developed for computational cis-regulatory module (CRM) discovery in Drosophila can be used effectively in highly diverged (250–350 Myr) insect species including Anopheles gambiae, Tribolium castaneum, Apis mellifera, and Nasonia vitripennis. In Drosophila, we have successfully used small sets of known CRMs as “training data” to guide the search for other CRMs with related function. We show here that although species-specific CRM training data do not exist, training sets from Drosophila can facilitate CRM discovery in diverged insects. We validate in vivo over a dozen new CRMs, roughly doubling the number of known CRMs in the four non-Drosophila species. Given the growing wealth of Drosophila CRM annotation, these results suggest that extensive regulatory sequence annotation will be possible in newly sequenced insects without recourse to costly and labor-intensive genome-scale experiments. We develop a new method, Regulus, which computes a probabilistic score of similarity based on binding site composition (despite the absence of nucleotide-level sequence alignment), and demonstrate similarity between functionally related CRMs from orthologous loci. Our work represents an important step toward being able to trace the evolutionary

  20. Glyceraldehyde-3-phosphate dehydrogenase from Chironomidae showed differential activity towards metals.

    Science.gov (United States)

    Chong, Isaac K W; Ho, Wing S

    2013-09-01

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known to interact with different biomolecules and was implicated in many novel cellular activities including programmed cell death, nuclear RNA transport unrelated to the commonly known carbohydrate metabolism. We reported here the purification of GAPDH from Chironomidae larvae (Insecta, Diptera) that showed different biologic activity towards heavy metals. It was inhibited by copper, cobalt nickel, iron and lead but was activated by zinc. The GAPDH was purified by ammonium sulphate fractionation and Chelating Sepharose CL-6B chromatography followed by Blue Sepharose CL-6B chromatography. The 150-kDa tetrameric GAPDH showed optimal activity at pH 8.5 and 37°C. The multiple alignment of sequence of the Chironomidae GAPDH with other known species showed 78 - 88% identity to the conserved regions of the GADPH. Bioinformatic analysis unveils substantial N-terminal sequence similarity of GAPDH of Chironomidae larvae to mammalian GADPHs. However, the GADPH of Chironomidae larvae showed different biologic activities and cytotoxicity towards heavy metals. The GAPDH enzyme would undergo adaptive molecular changes through binding at the active site leading to higher tolerance to heavy metals.

  1. Recognition of functional sites in protein structures.

    Science.gov (United States)

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2004-06-04

    Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

  2. A similarity-based data warehousing environment for medical images.

    Science.gov (United States)

    Teixeira, Jefferson William; Annibal, Luana Peixoto; Felipe, Joaquim Cezar; Ciferri, Ricardo Rodrigues; Ciferri, Cristina Dutra de Aguiar

    2015-11-01

    A core issue of the decision-making process in the medical field is to support the execution of analytical (OLAP) similarity queries over images in data warehousing environments. In this paper, we focus on this issue. We propose imageDWE, a non-conventional data warehousing environment that enables the storage of intrinsic features taken from medical images in a data warehouse and supports OLAP similarity queries over them. To comply with this goal, we introduce the concept of perceptual layer, which is an abstraction used to represent an image dataset according to a given feature descriptor in order to enable similarity search. Based on this concept, we propose the imageDW, an extended data warehouse with dimension tables specifically designed to support one or more perceptual layers. We also detail how to build an imageDW and how to load image data into it. Furthermore, we show how to process OLAP similarity queries composed of a conventional predicate and a similarity search predicate that encompasses the specification of one or more perceptual layers. Moreover, we introduce an index technique to improve the OLAP query processing over images. We carried out performance tests over a data warehouse environment that consolidated medical images from exams of several modalities. The results demonstrated the feasibility and efficiency of our proposed imageDWE to manage images and to process OLAP similarity queries. The results also demonstrated that the use of the proposed index technique guaranteed a great improvement in query processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Classifying Multi-Model Wheat Yield Impact Response Surfaces Showing Sensitivity to Temperature and Precipitation Change

    Science.gov (United States)

    Fronzek, Stefan; Pirttioja, Nina; Carter, Timothy R.; Bindi, Marco; Hoffmann, Holger; Palosuo, Taru; Ruiz-Ramos, Margarita; Tao, Fulu; Trnka, Miroslav; Acutis, Marco; hide

    2017-01-01

    Crop growth simulation models can differ greatly in their treatment of key processes and hence in their response to environmental conditions. Here, we used an ensemble of 26 process-based wheat models applied at sites across a European transect to compare their sensitivity to changes in temperature (minus 2 to plus 9 degrees Centigrade) and precipitation (minus 50 to plus 50 percent). Model results were analysed by plotting them as impact response surfaces (IRSs), classifying the IRS patterns of individual model simulations, describing these classes and analysing factors that may explain the major differences in model responses. The model ensemble was used to simulate yields of winter and spring wheat at four sites in Finland, Germany and Spain. Results were plotted as IRSs that show changes in yields relative to the baseline with respect to temperature and precipitation. IRSs of 30-year means and selected extreme years were classified using two approaches describing their pattern. The expert diagnostic approach (EDA) combines two aspects of IRS patterns: location of the maximum yield (nine classes) and strength of the yield response with respect to climate (four classes), resulting in a total of 36 combined classes defined using criteria pre-specified by experts. The statistical diagnostic approach (SDA) groups IRSs by comparing their pattern and magnitude, without attempting to interpret these features. It applies a hierarchical clustering method, grouping response patterns using a distance metric that combines the spatial correlation and Euclidian distance between IRS pairs. The two approaches were used to investigate whether different patterns of yield response could be related to different properties of the crop models, specifically their genealogy, calibration and process description. Although no single model property across a large model ensemble was found to explain the integrated yield response to temperature and precipitation perturbations, the

  4. Myopes show increased susceptibility to nearwork aftereffects.

    Science.gov (United States)

    Ciuffreda, K J; Wallis, D M

    1998-09-01

    Some aspects of accommodation may be slightly abnormal (or different) in myopes, compared with accommodation in emmetropes and hyperopes. For example, the initial magnitude of accommodative adaptation in the dark after nearwork is greatest in myopes. However, the critical test is to assess this initial accommodative aftereffect and its subsequent decay in the light under more natural viewing conditions with blur-related visual feedback present, if a possible link between this phenomenon and clinical myopia is to be considered. Subjects consisted of adult late- (n = 11) and early-onset (n = 13) myopes, emmetropes (n = 11), and hyperopes (n = 9). The distance-refractive state was assessed objectively using an autorefractor immediately before and after a 10-minute binocular near task at 20 cm (5 diopters [D]). Group results showed that myopes were most susceptible to the nearwork aftereffect. It averaged 0.35 D in initial magnitude, with considerably faster posttask decay to baseline in the early-onset (35 seconds) versus late-onset (63 seconds) myopes. There was no myopic aftereffect in the remaining two refractive groups. The myopes showed particularly striking accommodatively related nearwork aftereffect susceptibility. As has been speculated and found by many others, transient pseudomyopia may cause or be a precursor to permanent myopia or myopic progression. Time-integrated increased retinal defocus causing axial elongation is proposed as a possible mechanism.

  5. Ancient bacteria show evidence of DNA repair

    DEFF Research Database (Denmark)

    Johnson, Sarah Stewart; Hebsgaard, Martin B; Christensen, Torben R

    2007-01-01

    -term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence...... geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long...... that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability....

  6. Microbiological and environmental issues in show caves.

    Science.gov (United States)

    Saiz-Jimenez, Cesareo

    2012-07-01

    Cultural tourism expanded in the last half of the twentieth century, and the interest of visitors has come to include caves containing archaeological remains. Some show caves attracted mass tourism, and economical interests prevailed over conservation, which led to a deterioration of the subterranean environment and the rock art. The presence and the role of microorganisms in caves is a topic that is often ignored in cave management. Knowledge of the colonisation patterns, the dispersion mechanisms, and the effect on human health and, when present, over rock art paintings of these microorganisms is of the utmost importance. In this review the most recent advances in the study of microorganisms in caves are presented, together with the environmental implications of the findings.

  7. SFR site investigation. Bedrock Hydrogeochemistry

    International Nuclear Information System (INIS)

    Nilsson, Ann-Chatrin; Tullborg, Eva-Lena; Smellie, John; Gimeno, Maria J.; Gomez, Javier B.; Auque, Luis F.; Sandstroem, Bjoern; Pedersen, Karsten

    2011-11-01

    -SMOW) similar to that reported from the Forsmark site investigations (Laaksoharju et al. 2008). At the SFR, marine indicators such as Mg/Cl, K/Cl and Br/Cl also show relatively large variations considering the limited salinity range. This information together with palaeoclimatic considerations were used to differentiate the groundwaters into four major types; 1) local Baltic Seawater type, 2) Littorina type water with a glacial component, 3) brackish-glacial water type, and 4) mixed brackish water (transition type). Based on these types, explorative analyses using traditional geochemical approaches have been performed initially to describe groundwater conditions (origin and evolution) followed by further detailed evaluation using different modelling approaches such as mixing modelling, geochemical equilibrium modelling and redox modelling. From measured Eh values, and in accordance with the chemistry of Fe, Mn, S and U, it is concluded that mildly reduced conditions (-140 to -190 mV) generally prevail in the investigated groundwaters and, importantly, also for the youngest Baltic Sea type groundwaters. In terms of redox buffer capacity, the most important fracture minerals available are the Fe(II)-bearing minerals coating the water conductive fractures, which at SFR comprise mainly chlorite, clay minerals and pyrite. Calcite coatings are also frequent, which results in a rapid response to changes in pH by dissolution or precipitation and thereby provides an important buffering capacity against acidification. The division into different groundwater types has facilitated interaction and integration with the geological and hydrogeological models making it possible to construct a hydrogeochemical site descriptive model for the SFR site. The distribution of the different groundwater types shows that the major deformation zones have served as important groundwater flow pathways over long periods of geological time while single discrete fractures in rock volumes between zones

  8. SFR site investigation. Bedrock Hydrogeochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Ann-Chatrin [Geosigma AB, Uppsala (Sweden); Tullborg, Eva-Lena [Terralogica AB, Graabo (Sweden); Smellie, John [Conterra AB, Uppsala (Sweden); Gimeno, Maria J.; Gomez, Javier B.; Auque, Luis F. [Univ. of Zaragoza, Zaragoza (Spain); Sandstroem, Bjoern [WSP Sverige AB, Goeteborg (Sweden); Pedersen, Karsten [Micans AB, Moelnlycke (Sweden)

    2011-11-15

    -SMOW) similar to that reported from the Forsmark site investigations (Laaksoharju et al. 2008). At the SFR, marine indicators such as Mg/Cl, K/Cl and Br/Cl also show relatively large variations considering the limited salinity range. This information together with palaeoclimatic considerations were used to differentiate the groundwaters into four major types; 1) local Baltic Seawater type, 2) Littorina type water with a glacial component, 3) brackish-glacial water type, and 4) mixed brackish water (transition type). Based on these types, explorative analyses using traditional geochemical approaches have been performed initially to describe groundwater conditions (origin and evolution) followed by further detailed evaluation using different modelling approaches such as mixing modelling, geochemical equilibrium modelling and redox modelling. From measured Eh values, and in accordance with the chemistry of Fe, Mn, S and U, it is concluded that mildly reduced conditions (-140 to -190 mV) generally prevail in the investigated groundwaters and, importantly, also for the youngest Baltic Sea type groundwaters. In terms of redox buffer capacity, the most important fracture minerals available are the Fe(II)-bearing minerals coating the water conductive fractures, which at SFR comprise mainly chlorite, clay minerals and pyrite. Calcite coatings are also frequent, which results in a rapid response to changes in pH by dissolution or precipitation and thereby provides an important buffering capacity against acidification. The division into different groundwater types has facilitated interaction and integration with the geological and hydrogeological models making it possible to construct a hydrogeochemical site descriptive model for the SFR site. The distribution of the different groundwater types shows that the major deformation zones have served as important groundwater flow pathways over long periods of geological time while single discrete fractures in rock volumes between zones

  9. Clustering and visualizing similarity networks of membrane proteins.

    Science.gov (United States)

    Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

    2015-08-01

    We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

  10. Ultra-accurate collaborative information filtering via directed user similarity

    Science.gov (United States)

    Guo, Q.; Song, W.-J.; Liu, J.-G.

    2014-07-01

    A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones in opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random walks proposed by Liu et al. (Int. J. Mod. Phys. C, 20 (2009) 285) the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3% and 19.1% for MovieLens and Netflix, respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.

  11. Personality traits across countries: Support for similarities rather than differences.

    Science.gov (United States)

    Kajonius, Petri; Mac Giolla, Erik

    2017-01-01

    In the current climate of migration and globalization, personality characteristics of individuals from different countries have received a growing interest. Previous research has established reliable differences in personality traits across countries. The present study extends this research by examining 30 personality traits in 22 countries, based on an online survey in English with large national samples (NTotal = 130,602). The instrument used was a comprehensive, open-source measure of the Five Factor Model (FFM) (IPIP-NEO-120). We postulated that differences in personality traits between countries would be small, labeling this a Similarities Hypothesis. We found support for this in three stages. First, similarities across countries were observed for model fits for each of the five personality trait structures. Second, within-country sex differences for the five personality traits showed similar patterns across countries. Finally, the overall the contribution to personality traits from countries was less than 2%. In other words, the relationship between a country and an individual's personality traits, however interesting, are small. We conclude that the most parsimonious explanation for the current and past findings is a cross-country personality Similarities Hypothesis.

  12. Similarity of Ferrosilicon Submerged Arc Furnaces With Different Geometrical Parameters

    Directory of Open Access Journals (Sweden)

    Machulec B.

    2017-12-01

    Full Text Available In order to determine reasons of unsatisfactory production output regarding one of the 12 MVA furnaces, a comparative analysis with a furnace of higher power that showed a markedly better production output was performed. For comparison of ferrosilicon furnaces with different geometrical parameters and transformer powers, the theory of physical similarity was applied. Geometrical, electrical and thermal parameters of the reaction zones are included in the comparative analysis. For furnaces with different geometrical parameters, it is important to ensure the same temperature conditions of the reaction zones. Due to diverse mechanisms of heat generation, different criteria for determination of thermal and electrical similarity for the upper and lower reaction zones were assumed contrary to other publications. The parameter c3 (Westly was assumed the similarity criterion for the upper furnace zones where heat is generated as a result of resistive heating while the parameter J1 (Jaccard was assumed the similarity criterion for the lower furnace zones where heat is generated due to arc radiation.

  13. Similar Symmetries: The Role of Wallpaper Groups in Perceptual Texture Similarity

    Directory of Open Access Journals (Sweden)

    Fraser Halley

    2011-05-01

    Full Text Available Periodic patterns and symmetries are striking visual properties that have been used decoratively around the world throughout human history. Periodic patterns can be mathematically classified into one of 17 different Wallpaper groups, and while computational models have been developed which can extract an image's symmetry group, very little work has been done on how humans perceive these patterns. This study presents the results from a grouping experiment using stimuli from the different wallpaper groups. We find that while different images from the same wallpaper group are perceived as similar to one another, not all groups have the same degree of self-similarity. The similarity relationships between wallpaper groups appear to be dominated by rotations.

  14. Structure and floristic similarities of upper montane forests in Serra Fina mountain range, southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Leonardo Dias Meireles

    2015-03-01

    Full Text Available The upper montane forests in the southern and southeastern regions of Brazil have an unusual and discontinuous geographic distribution at the top of the Atlantic coastal mountain ranges. To describe the floristic composition and structure of the Atlantic Forest near its upper altitudinal limit in southeastern Brazil, 30 plots with 10 × 10 m were installed in three forest sites between 2,200 and 2,300 m.a.s.l. at Serra Fina. The floristic composition and phytosociological structure of this forest were compared with other montane and upper montane forests. In total, 704 individuals were included, belonging to 24 species, 15 families, and 19 genera. Myrsinaceae, Myrtaceae, Symplocaceae, and Cunoniaceae were the most important families, and Myrsine gardneriana, Myrceugenia alpigena, Weinmannia humilis, and Symplocos corymboclados were the most important species. The three forest sites revealed differences in the abundance of species, density, canopy height, and number of stems per individual. The upper montane forests showed structural similarities, such as lower richness, diversity, and effective number of species, and they tended to have higher total densities and total dominance per hectare to montane forests. The most important species in these upper montane forests belong to Austral-Antartic genera or neotropical and pantropical genera that are typical of montane areas. The high number of species shared by these forests suggests past connections between the vegetation in southern Brazilian high-altitude areas.

  15. Age-related changes in vertebral and iliac crest 3D bone microstructure--differences and similarities.

    Science.gov (United States)

    Thomsen, J S; Jensen, M V; Niklassen, A S; Ebbesen, E N; Brüel, A

    2015-01-01

    Age-related changes of vertebra and iliac crest 3D microstructure were investigated, and we showed that they were in general similar. The 95th percentile of vertebral trabecular thickness distribution increased with age for women. Surprisingly, vertebral and iliac crest bone microstructure was only weakly correlated (r = 0.38 to 0.75), despite the overall similar age-related changes. The purposes of the study were to determine the age-related changes in iliac and vertebral bone microstructure for women and men over a large age range and to investigate the relationship between the bone microstructure at these skeletal sites. Matched sets of transiliac crest bone biopsies and lumbar vertebral body (L2) specimens from 41 women (19-96 years) and 39 men (23-95 years) were micro-computed tomography (μCT) scanned, and the 3D microstructure was quantified. For both women and men, bone volume per total volume (BV/TV), connectivity density (CD), and trabecular number (Tb.N) decreased significantly, while structure model index (SMI) and trabecular separation (Tb.Sp) increased significantly with age at either skeletal site. Vertebral trabecular thickness (Tb.Th) was independent of age for both women and men, while iliac Tb.Th decreased significantly with age for men, but not for women. In general, the vertebral and iliac age-related changes were similar. The 95th percentile of the Tb.Th distribution increased significantly with age for women but was independent of age for men at the vertebral body, while it was independent of age for either sex at the iliac crest. The Tb.Th probability density functions at the two skeletal sites became significantly more similar with age for women, but not for men. The microstructural parameters at the iliac crest and the vertebral bodies were only moderately correlated from r = 0.38 for SMI in women to r = 0.75 for Tb.Sp in men. Age-related changes in vertebral and iliac bone microstructure were in general similar. The iliac

  16. Similarity and self-similarity in high energy density physics: application to laboratory astrophysics

    International Nuclear Information System (INIS)

    Falize, E.

    2008-10-01

    The spectacular recent development of powerful facilities allows the astrophysical community to explore, in laboratory, astrophysical phenomena where radiation and matter are strongly coupled. The titles of the nine chapters of the thesis are: from high energy density physics to laboratory astrophysics; Lie groups, invariance and self-similarity; scaling laws and similarity properties in High-Energy-Density physics; the Burgan-Feix-Munier transformation; dynamics of polytropic gases; stationary radiating shocks and the POLAR project; structure, dynamics and stability of optically thin fluids; from young star jets to laboratory jets; modelling and experiences for laboratory jets

  17. PHOG analysis of self-similarity in aesthetic images

    Science.gov (United States)

    Amirshahi, Seyed Ali; Koch, Michael; Denzler, Joachim; Redies, Christoph

    2012-03-01

    non-aesthetic categories of monochrome images. The aesthetic image datasets comprise a large variety of artworks of Western provenance. Other man-made aesthetically pleasing images, such as comics, cartoons and mangas, were also studied. For comparison, a database of natural scene photographs is used, as well as datasets of photographs of plants, simple objects and faces that are in general of low aesthetic value. As expected, natural scenes exhibit the highest degree of PHOG self-similarity. Images of artworks also show high selfsimilarity values, followed by cartoons, comics and mangas. On average, other (non-aesthetic) image categories are less self-similar in the PHOG analysis. A measure of scale-invariant self-similarity (PHOG) allows a good separation of the different aesthetic and non-aesthetic image categories. Our results provide further support for the notion that, like complex natural scenes, images of artworks display a higher degree of self-similarity across different scales of resolution than other image categories. Whether the high degree of self-similarity is the basis for the perception of beauty in both complex natural scenery and artworks remains to be investigated.

  18. Potential sites for a spent unreprocessed fuel facility (SURFF), southwesten part of the Nevada Test Site

    International Nuclear Information System (INIS)

    Hoover, D.L.; Eckel, E.B.; Ohl, J.P.

    1978-01-01

    In the absence of specific criteria, the topography, geomorphology, and geology of Jackass Flats and vicinity in the southwestern part of the Nevada Test Site are evaluated by arbitrary guidelines for a Spent Unreprocessed Fuel Facility. The guidelines include requirements for surface slopes of less than 5%, 61 m of alluvium beneath the site, an area free of active erosion or deposition, lack of faults, a minimum area of 5 km 2 , no potential for flooding, and as many logistical support facilities as possible. The geology of the Jackass Flats area is similar to the rest of the Nevada Test Site in topographic relief (305-1,200 m), stratigraphy (complexly folded and faulted Paleozoic sediments overlain by Tertiary ash-flow tuffs and lavas overlain in turn by younger alluvium), and structure (Paleozoic thrust faults and folds, strike-slip faults, proximity to volcanic centers, and Basin and Range normal faults). Of the stratigraphic units at the potential Spent Unreprocessed Fuel Facility site in Jackass Flats, only the thickness and stability of the alluvium are of immediate importance. Basin and Range faults and a possible extension of the Mine Mountain fault need further investigation. The combination of a slope map and a simplified geologic and physiographic map into one map shows several potential sites for a Spent Unreprocessed Fuel Facility in Jackass Flats. The potential areas have slopes of less than 5% and contain only desert pavement or segmented pavement--the two physiographic categories having the greatest geomorphic and hydraulic stability. Before further work can be done, specific criteria for a Spent Unreprocessed Fuel Facility site must be defined. Following criteria definition, potential sites will require detailed topographic and geologic studies, subsurface investigations (including geophysical methods, trenching, and perhaps shallow drilling for faults in alluvium), detailed surface hydrologic studies, and possibly subsurface hydrologic studies

  19. Does computer-synthesized speech manifest personality? Experimental tests of recognition, similarity-attraction, and consistency-attraction.

    Science.gov (United States)

    Nass, C; Lee, K M

    2001-09-01

    Would people exhibit similarity-attraction and consistency-attraction toward unambiguously computer-generated speech even when personality is clearly not relevant? In Experiment 1, participants (extrovert or introvert) heard a synthesized voice (extrovert or introvert) on a book-buying Web site. Participants accurately recognized personality cues in text to speech and showed similarity-attraction in their evaluation of the computer voice, the book reviews, and the reviewer. Experiment 2, in a Web auction context, added personality of the text to the previous design. The results replicated Experiment 1 and demonstrated consistency (voice and text personality)-attraction. To maximize liking and trust, designers should set parameters, for example, words per minute or frequency range, that create a personality that is consistent with the user and the content being presented.

  20. Age-related changes in vertebral and iliac crest 3D bone microstructure-differences and similarities

    DEFF Research Database (Denmark)

    Thomsen, Jesper Skovhus; Jensen, Michael Vinkel; Niklassen, Andreas Steenholt

    2015-01-01

    Summary Age-related changes of vertebra and iliac crest 3D microstructure were investigated, and we showed that they were in general similar. The 95th percentile of vertebral trabecular thickness distribution increased with age for women. Surprisingly, vertebral and iliac crest bone microstructure...... was only weakly correlated (r = 0.38 to 0.75), despite the overall similar age-related changes.Introduction The purposes of the study were to determine the age-related changes in iliac and vertebral bone microstructure for women and men over a large age range and to investigate the relationship between...... the bone microstructure at these skeletal sites.Methods Matched sets of transiliac crest bone biopsies and lumbar vertebral body (L2) specimens from 41 women (19–96 years) and 39 men (23–95 years) were micro-computed tomography (μCT) scanned, and the 3D microstructure was quantified.Results For both women...

  1. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  2. Similarity of Symbol Frequency Distributions with Heavy Tails

    Directory of Open Access Journals (Sweden)

    Martin Gerlach

    2016-04-01

    Full Text Available Quantifying the similarity between symbolic sequences is a traditional problem in information theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to texts, the distribution of symbol frequencies is characterized by heavy-tailed distributions (e.g., Zipf’s law. The large number of low-frequency symbols in these distributions poses major difficulties to the estimation of the similarity between sequences; e.g., they hinder an accurate finite-size estimation of entropies. Here, we show analytically how the systematic (bias and statistical (fluctuations errors in these estimations depend on the sample size N and on the exponent γ of the heavy-tailed distribution. Our results are valid for the Shannon entropy (α=1, its corresponding similarity measures (e.g., the Jensen-Shanon divergence, and also for measures based on the generalized entropy of order α. For small α’s, including α=1, the errors decay slower than the 1/N decay observed in short-tailed distributions. For α larger than a critical value α^{*}=1+1/γ≤2, the 1/N decay is recovered. We show the practical significance of our results by quantifying the evolution of the English language over the last two centuries using a complete α spectrum of measures. We find that frequent words change more slowly than less frequent words and that α=2 provides the most robust measure to quantify language change.

  3. Using a Similarity Matrix Approach to Evaluate the Accuracy of Rescaled Maps

    Directory of Open Access Journals (Sweden)

    Peijun Sun

    2018-03-01

    Full Text Available Rescaled maps have been extensively utilized to provide data at the appropriate spatial resolution for use in various Earth science models. However, a simple and easy way to evaluate these rescaled maps has not been developed. We propose a similarity matrix approach using a contingency table to compute three measures: overall similarity (OS, omission error (OE, and commission error (CE to evaluate the rescaled maps. The Majority Rule Based aggregation (MRB method was employed to produce the upscaled maps to demonstrate this approach. In addition, previously created, coarser resolution land cover maps from other research projects were also available for comparison. The question of which is better, a map initially produced at coarse resolution or a fine resolution map rescaled to a coarse resolution, has not been quantitatively investigated. To address these issues, we selected study sites at three different extent levels. First, we selected twelve regions covering the continental USA, then we selected nine states (from the whole continental USA, and finally we selected nine Agriculture Statistical Districts (ASDs (from within the nine selected states as study sites. Crop/non-crop maps derived from the USDA Crop Data Layer (CDL at 30 m as base maps were used for the upscaling and existing maps at 250 m and 1 km were utilized for the comparison. The results showed that a similarity matrix can effectively provide the map user with the information needed to assess the rescaling. Additionally, the upscaled maps can provide higher accuracy and better represent landscape pattern compared to the existing coarser maps. Therefore, we strongly recommend that an evaluation of the upscaled map and the existing coarser resolution map using a similarity matrix should be conducted before deciding which dataset to use for the modelling. Overall, extending our understanding on how to perform an evaluation of the rescaled map and investigation of the applicability

  4. Allegheny County Summer Food Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This data set shows the Summer Food Sites located within Allegheny County for children (18 years and younger) for breakfast and lunch during summer recess. OPEN...

  5. [Genome similarity of Baikal omul and sig].

    Science.gov (United States)

    Bychenko, O S; Sukhanova, L V; Ukolova, S S; Skvortsov, T A; Potapov, V K; Azhikina, T L; Sverdlov, E D

    2009-01-01

    Two members of the Baikal sig family, a lake sig (Coregonus lavaretus baicalensis Dybovsky) and omul (C. autumnalis migratorius Georgi), are close relatives that diverged from the same ancestor 10-20 thousand years ago. In this work, we studied genomic polymorphism of these two fish species. The method of subtraction hybridization (SH) did not reveal the presence of extended sequences in the sig genome and their absence in the omul genome. All the fragments found by SH corresponded to polymorphous noncoding genome regions varying in mononucleotide substitutions and short deletions. Many of them are mapped close to genes of the immune system and have regions identical to the Tc-1-like transposons abundant among fish, whose transcription activity may affect the expression of adjacent genes. Thus, we showed for the first time that genetic differences between Baikal sig family members are extremely small and cannot be revealed by the SH method. This is another endorsement of the hypothesis on the close relationship between Baikal sig and omul and their evolutionarily recent divergence from a common ancestor.

  6. Geoscience is Important? Show Me Why

    Science.gov (United States)

    Boland, M. A.

    2017-12-01

    "The public" is not homogenous and no single message or form of messaging will connect the entire public with the geosciences. One approach to promoting trust in, and engagement with, the geosciences is to identify specific sectors of the public and then develop interactions and communication products that are immediately relevant to that sector's interests. If the content and delivery are appropriate, this approach empowers people to connect with the geosciences on their own terms and to understand the relevance of the geosciences to their own situation. Federal policy makers are a distinct and influential subgroup of the general public. In preparation for the 2016 presidential election, the American Geosciences Institute (AGI) in collaboration with its 51 member societies prepared Geoscience for America's Critical Needs: Invitation to a National Dialogue, a document that identified major geoscience policy issues that should be addressed in a national policy platform. Following the election, AGI worked with eight other geoscience societies to develop Geoscience Policy Recommendations for the New Administration and the 115th Congress, which outlines specific policy actions to address national issues. State and local decision makers are another important subgroup of the public. AGI has developed online content, factsheets, and case studies with different levels of technical complexity so people can explore societally-relevant geoscience topics at their level of technical proficiency. A related webinar series is attracting a growing worldwide audience from many employment sectors. Partnering with government agencies and other scientific and professional societies has increased the visibility and credibility of these information products with our target audience. Surveys and other feedback show that these products are raising awareness of the geosciences and helping to build reciprocal relationships between geoscientists and decision makers. The core message of all

  7. Bacteriophages show promise as antimicrobial agents.

    Science.gov (United States)

    Alisky, J; Iczkowski, K; Rapoport, A; Troitsky, N

    1998-01-01

    The emergence of antibiotic-resistant bacteria has prompted interest in alternatives to conventional drugs. One possible option is to use bacteriophages (phage) as antimicrobial agents. We have conducted a literature review of all Medline citations from 1966-1996 that dealt with the therapeutic use of phage. There were 27 papers from Poland, the Soviet Union, Britain and the U.S.A. The Polish and Soviets administered phage orally, topically or systemically to treat a wide variety of antibiotic-resistant pathogens in both adults and children. Infections included suppurative wound infections, gastroenteritis, sepsis, osteomyelitis, dermatitis, empyemas and pneumonia; pathogens included Staphylococcus, Streptococcus, Klebsiella, Escherichia, Proteus, Pseudomonas, Shigella and Salmonella spp. Overall, the Polish and Soviets reported success rates of 80-95% for phage therapy, with rare, reversible gastrointestinal or allergic side effects. However, efficacy of phage was determined almost exclusively by qualitative clinical assessment of patients, and details of dosages and clinical criteria were very sketchy. There were also six British reports describing controlled trials of phage in animal models (mice, guinea pigs and livestock), measuring survival rates and other objective criteria. All of the British studies raised phage against specific pathogens then used to create experimental infections. Demonstrable efficacy against Escherichia, Acinetobacter, Pseudomonas and Staphylococcus spp. was noted in these model systems. Two U.S. papers dealt with improving the bioavailability of phage. Phage is sequestered in the spleen and removed from circulation. This can be overcome by serial passage of phage through mice to isolate mutants that resist sequestration. In conclusion, bacteriophages may show promise for treating antibiotic resistant pathogens. To facilitate further progress, directions for future research are discussed and a directory of authors from the reviewed

  8. Improved cosine similarity measures of simplified neutrosophic setsfor medical diagnoses

    OpenAIRE

    Jun Ye

    2014-01-01

    In pattern recognition and medical diagnosis, similarity measure is an important mathematicaltool. To overcome some disadvantages of existing cosine similarity measures of simplified neutrosophicsets (SNSs) in vector space, this paper proposed improved cosine similarity measures of SNSs based oncosine function, including single valued neutrosophic cosine similarity measures and interval neutro-sophic cosine similarity measures. Then, weighted cosine similarity measures of SNSs were introduced...

  9. When high similarity copycats lose and moderate similarity copycats gain: The impact of comparative evaluation

    NARCIS (Netherlands)

    Van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  10. When high similarity copycats lose and moderate similarity copycats gain : The impact of comparative evaluation

    NARCIS (Netherlands)

    van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  11. LHRH-pituitary plasma membrane binding: the presence of specific binding sites in other tissues.

    Science.gov (United States)

    Marshall, J C; Shakespear, R A; Odell, W D

    1976-11-01

    Two specific binding sites for LHRH are present on plasma membranes prepared from rat and bovine anterior pituitary glands. One site is of high affinity (K = 2X108 1/MOL) and the second is of lower affinity (8-5X105 1/mol) and much greater capacity. Studies on membrane fractions prepared from other tissues showed the presence of a single specific site for LHRH. The kinetics and specificity of this site were similar to those of the lower affinity pituitary receptor. These results indicate that only pituitary membranes possess the higher affinity binding site and suggest that the low affinity site is not of physiological importance in the regulation of gonadotrophin secretion. After dissociation from membranes of non-pituitary tissues 125I-LHRH rebound to pituitary membrane preparations. Thus receptor binding per se does not result in degradation of LHRH and the function of these peripheral receptors remains obscure.

  12. Similar local and landscape processes affect both a common and a rare newt species.

    Science.gov (United States)

    Denoël, Mathieu; Perez, Amélie; Cornet, Yves; Ficetola, Gentile Francesco

    2013-01-01

    Although rare species are often the focus of conservation measures, more common species may experience similar decline and suffer from the same threatening processes. We tested this hypothesis by examining, through an information-theoretic approach, the importance of ecological processes at multiple scales in the great crested newt Triturus cristatus, regionally endangered and protected in Europe, and the more common smooth newt, Lissotriton vulgaris. Both species were similarly affected by the same processes, i.e. suitability of aquatic and terrestrial components of their habitat at different scales, connectivity among breeding sites, and the presence of introduced fish. T. cristatus depended more on water depth and aquatic vegetation than L. vulgaris. The results show that environmental pressures threaten both common and rare species, and therefore the more widespread species should not be neglected in conservation programs. Because environmental trends are leading to a deterioration of aquatic and terrestrial habitat features required by newt populations, populations of the common species may follow the fate of the rarest species. This could have substantial conservation implications because of the numerical importance of common species in ecosystems and because commonness could be a transient state moving towards rarity. On the other hand, in agreement with the umbrella species concept, targeting conservation efforts on the most demanding species would also protect part of the populations of the most common species.

  13. Easier operation and similar power of 10 g monofilament test for screening diabetic peripheral neuropathy.

    Science.gov (United States)

    Zhang, Qi; Yi, Na; Liu, Siying; Zheng, Hangping; Qiao, Xiaona; Xiong, Qian; Liu, Xiaoxia; Zhang, Shuo; Wen, Jie; Ye, Hongying; Zhou, Linuo; Li, Yiming; Hu, Renming; Lu, Bin

    2018-01-01

    Objective The 10 g Semmes-Weinstein monofilament evaluation (SWME) of 4 sites on each foot is recommended for distal symmetric polyneuropathy screening and diagnosis. A similar method has been proposed to diagnose 'high-risk' (for ulceration) feet, using 3 sites per foot. This study compared the effectiveness of SWME for testing 3, 4 and 10 sites per foot to identify patients with diabetic neuropathy. Methods We included 3497 subjects in a SWME of 10 sites; records from the 10-site SWME were used for a SWME of 3 and 4 sites. Neuropathy symptom scores and neuropathy deficit scores were evaluated to identify patients with diabetic peripheral neuropathy. Results The sensitivities of the 10 g SWME for 3, 4 and 10 sites were 17.8%, 19.0% and 22.4%, respectively. The Kappa coefficients for the SWME tests of 3, 4 and 10 sites were high (range: 0.78-0.93). Conclusions There were no significant differences in the effectiveness of 3-, 4- and 10-site SWME testing for diabetic peripheral neuropathy screening. SWME testing of 3 sites on each foot may be sufficient to screen for diabetic neuropathy.

  14. The application of similar image retrieval in electronic commerce.

    Science.gov (United States)

    Hu, YuPing; Yin, Hua; Han, Dezhi; Yu, Fei

    2014-01-01

    Traditional online shopping platform (OSP), which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers' experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system.

  15. An Energy-Based Similarity Measure for Time Series

    Directory of Open Access Journals (Sweden)

    Pierre Brunagel

    2007-11-01

    Full Text Available A new similarity measure, called SimilB, for time series analysis, based on the cross-ΨB-energy operator (2004, is introduced. ΨB is a nonlinear measure which quantifies the interaction between two time series. Compared to Euclidean distance (ED or the Pearson correlation coefficient (CC, SimilB includes the temporal information and relative changes of the time series using the first and second derivatives of the time series. SimilB is well suited for both nonstationary and stationary time series and particularly those presenting discontinuities. Some new properties of ΨB are presented. Particularly, we show that ΨB as similarity measure is robust to both scale and time shift. SimilB is illustrated with synthetic time series and an artificial dataset and compared to the CC and the ED measures.

  16. Density-based similarity measures for content based search

    Energy Technology Data Exchange (ETDEWEB)

    Hush, Don R [Los Alamos National Laboratory; Porter, Reid B [Los Alamos National Laboratory; Ruggiero, Christy E [Los Alamos National Laboratory

    2009-01-01

    We consider the query by multiple example problem where the goal is to identify database samples whose content is similar to a coUection of query samples. To assess the similarity we use a relative content density which quantifies the relative concentration of the query distribution to the database distribution. If the database distribution is a mixture of the query distribution and a background distribution then it can be shown that database samples whose relative content density is greater than a particular threshold {rho} are more likely to have been generated by the query distribution than the background distribution. We describe an algorithm for predicting samples with relative content density greater than {rho} that is computationally efficient and possesses strong performance guarantees. We also show empirical results for applications in computer network monitoring and image segmentation.

  17. Diffusion-like recommendation with enhanced similarity of objects

    Science.gov (United States)

    An, Ya-Hui; Dong, Qiang; Sun, Chong-Jing; Nie, Da-Cheng; Fu, Yan

    2016-11-01

    In the last decade, diversity and accuracy have been regarded as two important measures in evaluating a recommendation model. However, a clear concern is that a model focusing excessively on one measure will put the other one at risk, thus it is not easy to greatly improve diversity and accuracy simultaneously. In this paper, we propose to enhance the Resource-Allocation (RA) similarity in resource transfer equations of diffusion-like models, by giving a tunable exponent to the RA similarity, and traversing the value of this exponent to achieve the optimal recommendation results. In this way, we can increase the recommendation scores (allocated resource) of many unpopular objects. Experiments on three benchmark data sets, MovieLens, Netflix and RateYourMusic show that the modified models can yield remarkable performance improvement compared with the original ones.

  18. Self-similar radiation from numerical Rosenau-Hyman compactons

    International Nuclear Information System (INIS)

    Rus, Francisco; Villatoro, Francisco R.

    2007-01-01

    The numerical simulation of compactons, solitary waves with compact support, is characterized by the presence of spurious phenomena, as numerically induced radiation, which is illustrated here using four numerical methods applied to the Rosenau-Hyman K(p, p) equation. Both forward and backward radiations are emitted from the compacton presenting a self-similar shape which has been illustrated graphically by the proper scaling. A grid refinement study shows that the amplitude of the radiations decreases as the grid size does, confirming its numerical origin. The front velocity and the amplitude of both radiations have been studied as a function of both the compacton and the numerical parameters. The amplitude of the radiations decreases exponentially in time, being characterized by a nearly constant scaling exponent. An ansatz for both the backward and forward radiations corresponding to a self-similar function characterized by the scaling exponent is suggested by the present numerical results

  19. Class Origin and Sibling Similarities in Long-run Income

    DEFF Research Database (Denmark)

    Andrade, Stefan Bastholm

    2016-01-01

    Sibling correlations have gained increasing prominence in inequality studies as a Measurement of the total impact of family background on individual outcomes. Whilst previous studies have tended to use traditional socio-economic measures such as parent’s income or education, this paper introduces......’ education and income – include modifications of the Erikson–Goldthorpe–Portocarero schemes ranging from 3 to 15 classes and Grusky’s microclass scheme of 72 classes. The results show that although class adds to explanations of the family influence on children’s income, most of the sibling similarities...... are not explained by parental education, income or class. Depending on gender, the class schemes explain between 8 and 13 per cent of the sibling similarities and 15 to 20 per cent when parents’ income and educations are also included. Models with different class schemes demonstrate that elaborated versions...

  20. The Application of Similar Image Retrieval in Electronic Commerce

    Directory of Open Access Journals (Sweden)

    YuPing Hu

    2014-01-01

    Full Text Available Traditional online shopping platform (OSP, which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers’ experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system.

  1. The Application of Similar Image Retrieval in Electronic Commerce

    Science.gov (United States)

    Hu, YuPing; Yin, Hua; Han, Dezhi; Yu, Fei

    2014-01-01

    Traditional online shopping platform (OSP), which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers' experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system. PMID:24883411

  2. Buffer mass test - Site documentation

    International Nuclear Information System (INIS)

    Pusch, R.

    1983-10-01

    The purpose of this report is to compile test site data that are assumed to be of importance for the interpretation of the Buffer Mass Test. Since this test mainly concerns water uptake and migration processes in the integrated rock/backfill system and the development of temperature fields in this system, the work has been focused on the constitution and hydrology of the rock. The major constitutional rock feature of interest for the BMT is the frequency and distribution of joints and fractures. The development of models for water uptake into the highly compacted bentonite in the heater holes requires a very detailed fracture survey. The present investigation shows that two of the holes (no. 1 and 2) are located in richly fractured rock, while the others are located in fracture-poor to moderately fractured rock. The hydrological conditions of the rock in the BMT area are characterized by water pressures of as much as 100 m water head at a few meters distance from the test site. The average hydraulic conductivity of the rock that confines the BMT tunnel has been estimated at about 10 -10 m/s by Lawrence Laboratory. The actual distribution of the water that enters the tunnel has been estimated by observing the successive moistening after having switched off the ventilation, and this has offered basis of predicting the rate and uniformity of the water uptake in the tunnel backfill. As to the heater holes the detailed fracture patterns and various inflow measurements have yielded a similar basis. The report also gives major data on the rock temperature, gas conditions, mineralogy, rock mechanics, and groundwater chemistry for BMT purposes. (author)

  3. The Effect of Script Similarity on Executive Control in Bilinguals

    Directory of Open Access Journals (Sweden)

    Emily L Coderre

    2014-09-01

    Full Text Available The need for executive control (EC during bilingual language processing is thought to enhance these abilities, conferring a ‘bilingual advantage’ on EC tasks. Recently, the reliability and robustness of the bilingual advantage has been questioned, with many variables reportedly affecting the size and presence of the bilingual advantage. This study investigates one further variable that may affect bilingual EC abilities: the similarity of a bilingual’s two languages. We hypothesize that bilinguals whose two languages have a larger degree of orthographic overlap will require greater EC to manage their languages compared to bilinguals who use two languages with less overlap. We tested three groups of bilinguals with language pairs ranging from high- to low-similarity (German-English (GE, Polish-English (PE, and Arabic-English (AE, respectively and a group of English monolinguals on a Stroop and Simon task. Two components of the bilingual advantage were investigated: an interference advantage, such that bilinguals have smaller interference effects than monolinguals; and a global RT advantage, such that bilinguals are faster overall than monolinguals. Between bilingual groups, these effects were expected to be modulated by script similarity. AE bilinguals showed the smallest Stroop interference effects, but the longest overall RTs in both tasks. These seemingly contradictory results are explained by the presence of cross-linguistic interference in the Stroop task. We conclude that similar-script bilinguals demonstrated more effective domain-general EC than different-script bilinguals, since high orthographic overlap creates more cross-linguistic activation and increases the daily demands on cognitive control. The role of individual variation is also discussed. These results suggest that script similarity is an important variable to consider in investigations of bilingual executive control abilities.

  4. Similarity of the ruminal bacteria across individual lactating cows.

    Science.gov (United States)

    Jami, Elie; Mizrahi, Itzhak

    2012-06-01

    Dairy cattle hold enormous significance for man as a source of milk and meat. Their remarkable ability to convert indigestible plant mass into these digestible food products resides in the rumen - an anaerobic chambered compartment - in the bovine digestive system. The rumen houses a complex microbiota which is responsible for the degradation of plant material, consequently enabling the conversion of plant fibers into milk and meat and determining their quality and quantity. Hence, an understanding of this complex ecosystem has major economic implications. One important question that is yet to be addressed is the degree of conservation of rumen microbial composition across individual animals. Here we quantified the degree of similarity between rumen bacterial populations of 16 individual cows. We used real-time PCR to determine the variance of specific ruminal bacterial species with different metabolic functions, revealing that while some bacterial strains vary greatly across animals, others show only very low variability. This variance could not be linked to the metabolic traits of these bacteria. We examined the degree of similarity in the dominant bacterial populations across all animals using automated ribosomal intergenic spacer analysis (ARISA), and identified a bacterial community consisting of 32% operational taxonomic units (OTUs) shared by at least 90% of the animals and 19% OTUs shared by 100% of the animals. Looking only at the presence or absence of each OTU gave an average similarity of 75% between each cow pair. When abundance of each OTU was added to the analysis, this similarity decreased to an average of less than 60%. Thus, as suggested in similar recent studies of the human gut, a bovine rumen core microbiome does exist, but taxa abundance may vary greatly across animals. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. CT findings of rectosigmoid carcinoma showing exophytic growth

    International Nuclear Information System (INIS)

    Ohgi, Kazuyuki; Kohno, Atsushi; Higuchi, Mutsumi

    1987-01-01

    CT findings of 7 rectosigmoid carcinomas showing exophytic growth were evaluated. All cases had bulky masses, ranging from 6.0 to 11.5 cm in maximum diameter. All masses were difficult to differentiate from the other pelvic masses on CT, presumably due to their exophytic growth and/or invasion to the surrounding organs. However, 3 out of 7 cases showed diffuse rectosigmoidal wall thickening adjacent to the primary tumor, and it is considered to be valuable in the determination of primary site. All female cases had gynecological symptom such as genital bleeding, due to uterine and/or vaginal invasion. When indeterminate pelvic mass is revealed by CT, rectosigmoid carcinoma should be considered into differential diagnosis. (author)

  6. Similarity analyses of chromatographic herbal fingerprints: A review

    International Nuclear Information System (INIS)

    Goodarzi, Mohammad; Russell, Paul J.; Vander Heyden, Yvan

    2013-01-01

    Graphical abstract: -- Highlights: •Similarity analyses of herbal fingerprints are reviewed. •Different (dis)similarity approaches are discussed. •(Dis)similarity-metrics and exploratory-analysis approaches are illustrated. •Correlation and distance-based measures are overviewed. •Similarity analyses illustrated by several case studies. -- Abstract: Herbal medicines are becoming again more popular in the developed countries because being “natural” and people thus often assume that they are inherently safe. Herbs have also been used worldwide for many centuries in the traditional medicines. The concern of their safety and efficacy has grown since increasing western interest. Herbal materials and their extracts are very complex, often including hundreds of compounds. A thorough understanding of their chemical composition is essential for conducting a safety risk assessment. However, herbal material can show considerable variability. The chemical constituents and their amounts in a herb can be different, due to growing conditions, such as climate and soil, the drying process, the harvest season, etc. Among the analytical methods, chromatographic fingerprinting has been recommended as a potential and reliable methodology for the identification and quality control of herbal medicines. Identification is needed to avoid fraud and adulteration. Currently, analyzing chromatographic herbal fingerprint data sets has become one of the most applied tools in quality assessment of herbal materials. Mostly, the entire chromatographic profiles are used to identify or to evaluate the quality of the herbs investigated. Occasionally only a limited number of compounds are considered. One approach to the safety risk assessment is to determine whether the herbal material is substantially equivalent to that which is either readily consumed in the diet, has a history of application or has earlier been commercialized i.e. to what is considered as reference material. In order

  7. Similarity analyses of chromatographic herbal fingerprints: A review

    Energy Technology Data Exchange (ETDEWEB)

    Goodarzi, Mohammad [Department of Analytical Chemistry and Pharmaceutical Technology, Center for Pharmaceutical Research, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels (Belgium); Russell, Paul J. [Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ (United Kingdom); Vander Heyden, Yvan, E-mail: yvanvdh@vub.ac.be [Department of Analytical Chemistry and Pharmaceutical Technology, Center for Pharmaceutical Research, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels (Belgium)

    2013-12-04

    Graphical abstract: -- Highlights: •Similarity analyses of herbal fingerprints are reviewed. •Different (dis)similarity approaches are discussed. •(Dis)similarity-metrics and exploratory-analysis approaches are illustrated. •Correlation and distance-based measures are overviewed. •Similarity analyses illustrated by several case studies. -- Abstract: Herbal medicines are becoming again more popular in the developed countries because being “natural” and people thus often assume that they are inherently safe. Herbs have also been used worldwide for many centuries in the traditional medicines. The concern of their safety and efficacy has grown since increasing western interest. Herbal materials and their extracts are very complex, often including hundreds of compounds. A thorough understanding of their chemical composition is essential for conducting a safety risk assessment. However, herbal material can show considerable variability. The chemical constituents and their amounts in a herb can be different, due to growing conditions, such as climate and soil, the drying process, the harvest season, etc. Among the analytical methods, chromatographic fingerprinting has been recommended as a potential and reliable methodology for the identification and quality control of herbal medicines. Identification is needed to avoid fraud and adulteration. Currently, analyzing chromatographic herbal fingerprint data sets has become one of the most applied tools in quality assessment of herbal materials. Mostly, the entire chromatographic profiles are used to identify or to evaluate the quality of the herbs investigated. Occasionally only a limited number of compounds are considered. One approach to the safety risk assessment is to determine whether the herbal material is substantially equivalent to that which is either readily consumed in the diet, has a history of application or has earlier been commercialized i.e. to what is considered as reference material. In order

  8. Ecosystem monitoring two Department of Energy sites

    International Nuclear Information System (INIS)

    Gray, R.

    1995-01-01

    The US Department of Energy's Hanford Site was established in southeastern Washington to produce plutonium during World War II. The Pantex Plant in the Texas Panhandle, originally used for loading conventional ammunition shells and bombs, was rehabilitated and enhanced in the 1950s to assemble nuclear weapons. Environmental monitoring has been ongoing at both locations for several decades. Monitoring objectives are to detect and assess potential impacts of facility operations on air, surface and ground waters, foodstuffs, fish, wildlife, soils, and vegetation. Currently, measured concentrations of airborne radionuclides around the perimeters of both sites are below applicable guidelines. Concentrations of radionuclides and nonradiological water quality in the Columbia River at Hanford, and radiological and nonradiological water quality in the Ogallala Aquifer beneath the Pantex Plant are in compliance with applicable standards. Foodstuffs irrigated with river water downstream from the Hanford Site show levels of radionuclides that are similar to those found in foodstuffs from control areas. The low levels of 137 Cs and 9O Sr in some onsite Hanford wildlife samples and concentrations of radionuclides in soils and vegetation from onsite and offsite at both locations are typical of those attributable to naturally occurring radioactivity and to worldwide fallout. The calculated dose potentially received by a maximally exposed individual (i.e., based on hypothetical, worst-case assumptions for all routes of exposure) at both sites in 1993 was ≤ 0.03 mrem. Ironically, by virtue of its size (1450 km 2 [560 mi 2 ]), restricted public access, and conservative use of undeveloped land, the Hanford Site has provided a sanctuary for plant and animal populations that have been eliminated from, or greatly reduced on, surrounding agricultural and range lands. Ongoing studies will determine if this is also true at Pantex Plant

  9. Similarity between neonatal profile and socioeconomic index: a spatial approach

    Directory of Open Access Journals (Sweden)

    d'Orsi Eleonora

    2005-01-01

    Full Text Available This study aims to compare neonatal characteristics and socioeconomic conditions in Rio de Janeiro city neighborhoods in order to identify priority areas for intervention. The study design was ecological. Two databases were used: the Brazilian Population Census and the Live Birth Information System, aggregated by neighborhoods. Spatial analysis, multivariate cluster classification, and Moran's I statistics for detection of spatial clustering were used. A similarity index was created to compare socioeconomic clusters with the neonatal profile in each neighborhood. The proportions of Apgar score above 8 and cesarean sections showed positive spatial correlation and high similarity with the socioeconomic index. The proportion of low birth weight infants showed a random spatial distribution, indicating that at this scale of analysis, birth weight is not sufficiently sensitive to discriminate subtler differences among population groups. The observed relationship between the neighborhoods' neonatal profile (particularly Apgar score and mode of delivery and socioeconomic conditions shows evidence of a change in infant health profile, where the possibility for intervention shifts to medical services and the Apgar score assumes growing significance as a risk indicator.

  10. Similarity and Equality in Greek Mathematics: Semiotics, History of Mathematics, and Mathematics Education

    Science.gov (United States)

    Fried, Michael N.

    2009-01-01

    The first goal of this article to show the profound difference between how equality and similarity are understood in Greek geometry and how they are presented in modern mathematics classes. It highlights that the formula "equal-and-similar" reflects the distinct character of "equal" and "similar" as signs in Greek…

  11. Geohydrology of industrial waste disposal site

    International Nuclear Information System (INIS)

    Gaynor, R.K.

    1984-01-01

    An existing desert site for hazardous chemical and low-level radioactive waste disposal is evaluated for suitability. This site is characterized using geologic, geohydrologic, geochemical, and other considerations. Design and operation of the disposal facility is considered. Site characteristics are also evaluated with respect to new and proposed regulatory requirements under the Resource Conservation and Recovery Act (1976) regulations, 40 CFR Part 264, and the ''Licensing Requirements for Landfill Disposal of Radioactive Waste,'' 10 CRF Part 61. The advantages and disadvantages of siting new disposal facilities in similar desert areas are reviewed and contrasted to siting in humid locations

  12. The use of computerized tomography in patients showing tardive dyskinesia

    International Nuclear Information System (INIS)

    Themelis, I.

    1983-01-01

    29 patients showing moderate to markedly pronounced tardive dyskinesia (TD) and a further 29 control patients (C) under a similar long-term medication with neuroleptics that had been so chosen as to match the age and sex distributions of the former group were subjected to computered tomography, neurological examination and psychological testing. The results did not point to any correlations between the structural changes and duration of treatment and the clinical signs or symptoms of extrapyramidal disorder. This was taken as further evidence in support of the theory that the initial damage in tardive dyskinesia mainly is at the level of the basal ganglia. (orig./MG) [de

  13. A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks

    Directory of Open Access Journals (Sweden)

    Alejandra García-Hernández

    2017-11-01

    Full Text Available Human Activity Recognition (HAR is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  14. [-25]A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks.

    Science.gov (United States)

    García-Hernández, Alejandra; Galván-Tejada, Carlos E; Galván-Tejada, Jorge I; Celaya-Padilla, José M; Gamboa-Rosales, Hamurabi; Velasco-Elizondo, Perla; Cárdenas-Vargas, Rogelio

    2017-11-21

    Human Activity Recognition (HAR) is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  15. Recurrent and multiple bladder tumors show conserved expression profiles

    International Nuclear Information System (INIS)

    Lindgren, David; Fioretos, Thoas; Månsson, Wiking; Höglund, Mattias; Gudjonsson, Sigurdur; Jee, Kowan Ja; Liedberg, Fredrik; Aits, Sonja; Andersson, Anna; Chebil, Gunilla; Borg, Åke; Knuutila, Sakari

    2008-01-01

    Urothelial carcinomas originate from the epithelial cells of the inner lining of the bladder and may appear as single or as multiple synchronous tumors. Patients with urothelial carcinomas frequently show recurrences after treatment making follow-up necessary. The leading hypothesis explaining the origin of meta- and synchronous tumors assumes a monoclonal origin. However, the genetic relationship among consecutive tumors has been shown to be complex in as much as the genetic evolution does not adhere to the chronological appearance of the metachronous tumors. Consequently, genetically less evolved tumors may appear chronologically later than genetically related but more evolved tumors. Forty-nine meta- or synchronous urothelial tumors from 22 patients were analyzed using expression profiling, conventional CGH, LOH, and mutation analyses. We show by CGH that partial chromosomal losses in the initial tumors may not be present in the recurring tumors, by LOH that different haplotypes may be lost and that detected regions of LOH may be smaller in recurring tumors, and that mutations present in the initial tumor may not be present in the recurring ones. In contrast we show that despite apparent genomic differences, the recurrent and multiple bladder tumors from the same patients display remarkably similar expression profiles. Our findings show that even though the vast majority of the analyzed meta- and synchronous tumors from the same patients are not likely to have originated directly from the preceding tumor they still show remarkably similar expressions profiles. The presented data suggests that an expression profile is established early in tumor development and that this profile is stable and maintained in recurring tumors

  16. On the Complexity of Inner Product Similarity Join

    DEFF Research Database (Denmark)

    Ahle, Thomas Dybdahl; Pagh, Rasmus; Razenshteyn, Ilya

    2016-01-01

    A number of tasks in classification, information retrieval, recommendation systems, and record linkage reduce to the core problem of inner product similarity join (IPS join): identifying pairs of vectors in a collection that have a sufficiently large inner product. IPS join is well understood when...... bounds for (A)LSH-based algorithms. In particular, we show that asymmetry can be avoided by relaxing the LSH definition to only consider the collision probability of distinct elements. A new indexing method for IPS based on linear sketches, implying that our hardness results are not far from being tight...

  17. On similarity and scaling of the radiative transfer equation

    International Nuclear Information System (INIS)

    Mitrescu, C.; Stephens, G.L.

    2004-01-01

    The present paper shows how the well-known similarity and scaling concepts are properties of the radiative transfer equation and not specifically of the degree of anisotropy of the phase function. It is shown that the key assumption regarding the angular dependence of the radiative field is essential in determining both the value for the parameter used to scale the radiative transfer, as well as the number of streams used in calculating the radiances for various atmospheric problems. Simulations performed on realistic type of cirrus clouds, characterized by strongly anisotropic functions, demonstrates the superior computational advantage for accurately simulating radiances. A new approach for determining the scaling parameter is introduced

  18. Mechanical similarity as a generalization of scale symmetry

    International Nuclear Information System (INIS)

    Gozzi, E; Mauro, D

    2006-01-01

    In this paper, we study the symmetry known (Landau and Lifshits 1976 Course of Theoretical Physics vol 1: Mechanics (Oxford: Pergamon)) as mechanical similarity (LMS) and present for any monomial potential. We analyse it in the framework of the Koopman-von Neumann formulation of classical mechanics and prove that in this framework the LMS can be given a canonical implementation. We also show that the LMS is a generalization of the scale symmetry which is present only for the inverse square and a few other potentials. Finally, we study the main obstructions which one encounters in implementing the LMS at the quantum-mechanical level

  19. Similar tests and the standardized log likelihood ratio statistic

    DEFF Research Database (Denmark)

    Jensen, Jens Ledet

    1986-01-01

    When testing an affine hypothesis in an exponential family the 'ideal' procedure is to calculate the exact similar test, or an approximation to this, based on the conditional distribution given the minimal sufficient statistic under the null hypothesis. By contrast to this there is a 'primitive......' approach in which the marginal distribution of a test statistic considered and any nuisance parameter appearing in the test statistic is replaced by an estimate. We show here that when using standardized likelihood ratio statistics the 'primitive' procedure is in fact an 'ideal' procedure to order O(n -3...

  20. Accelerating Neuroimage Registration through Parallel Computation of Similarity Metric.

    Directory of Open Access Journals (Sweden)

    Yun-Gang Luo

    Full Text Available Neuroimage registration is crucial for brain morphometric analysis and treatment efficacy evaluation. However, existing advanced registration algorithms such as FLIRT and ANTs are not efficient enough for clinical use. In this paper, a GPU implementation of FLIRT with the correlation ratio (CR as the similarity metric and a GPU accelerated correlation coefficient (CC calculation for the symmetric diffeomorphic registration of ANTs have been developed. The comparison with their corresponding original tools shows that our accelerated algorithms can greatly outperform the original algorithm in terms of computational efficiency. This paper demonstrates the great potential of applying these registration tools in clinical applications.

  1. Protontherapy versus carbon ion therapy advantages, disadvantages and similarities

    CERN Document Server

    d’Ávila Nunes, Marcos

    2015-01-01

    This book presents a comparison analysis of two cancer treatment therapies: carbon ion therapy and protontherapy. It is divided in 5 sections. The first ones gives the reader a brief history of Radiotherapy and types of radiation. In the second section, the techniques and equipments, including new ones in development such as Cyclinac , Laser and DWA, are described. The third section describes biophysical (such as stopping power and LET) and biological (such as RBE and OER) properties, the fundamental experiments and clinical area. The fourth section presents models and the fifth section compares both techniques, showing advantages and disadvantages of each, and their similarities.

  2. Self-similarity and flow characteristics of vertical-axis wind turbine wakes: an LES study

    Science.gov (United States)

    Abkar, Mahdi; Dabiri, John O.

    2017-04-01

    Large eddy simulation (LES) is coupled with a turbine model to study the structure of the wake behind a vertical-axis wind turbine (VAWT). In the simulations, a tuning-free anisotropic minimum dissipation model is used to parameterise the subfilter stress tensor, while the turbine-induced forces are modelled with an actuator line technique. The LES framework is first validated in the simulation of the wake behind a model straight-bladed VAWT placed in the water channel and then used to study the wake structure downwind of a full-scale VAWT sited in the atmospheric boundary layer. In particular, the self-similarity of the wake is examined, and it is found that the wake velocity deficit can be well characterised by a two-dimensional multivariate Gaussian distribution. By assuming a self-similar Gaussian distribution of the velocity deficit, and applying mass and momentum conservation, an analytical model is developed and tested to predict the maximum velocity deficit downwind of the turbine. Also, a simple parameterisation of VAWTs for LES with very coarse grid resolutions is proposed, in which the turbine is modelled as a rectangular porous plate with the same thrust coefficient. The simulation results show that, after some downwind distance (x/D ≈ 6), both actuator line and rectangular porous plate models have similar predictions for the mean velocity deficit. These results are of particular importance in simulations of large wind farms where, due to the coarse spatial resolution, the flow around individual VAWTs is not resolved.

  3. Detecting groups of similar components in complex networks

    International Nuclear Information System (INIS)

    Wang Jiao; Lai, C-H

    2008-01-01

    We study how to detect groups in a complex network each of which consists of component nodes sharing a similar connection pattern. Based on the mixture models and the exploratory analysis set up by Newman and Leicht (2007 Proc. Natl. Acad. Sci. USA 104 9564), we develop an algorithm that is applicable to a network with any degree distribution. The partition of a network suggested by this algorithm also applies to its complementary network. In general, groups of similar components are not necessarily identical with the communities in a community network; thus partitioning a network into groups of similar components provides additional information of the network structure. The proposed algorithm can also be used for community detection when the groups and the communities overlap. By introducing a tunable parameter that controls the involved effects of the heterogeneity, we can also investigate conveniently how the group structure can be coupled with the heterogeneity characteristics. In particular, an interesting example shows a group partition can evolve into a community partition in some situations when the involved heterogeneity effects are tuned. The extension of this algorithm to weighted networks is discussed as well.

  4. A similarity based agglomerative clustering algorithm in networks

    Science.gov (United States)

    Liu, Zhiyuan; Wang, Xiujuan; Ma, Yinghong

    2018-04-01

    The detection of clusters is benefit for understanding the organizations and functions of networks. Clusters, or communities, are usually groups of nodes densely interconnected but sparsely linked with any other clusters. To identify communities, an efficient and effective community agglomerative algorithm based on node similarity is proposed. The proposed method initially calculates similarities between each pair of nodes, and form pre-partitions according to the principle that each node is in the same community as its most similar neighbor. After that, check each partition whether it satisfies community criterion. For the pre-partitions who do not satisfy, incorporate them with others that having the biggest attraction until there are no changes. To measure the attraction ability of a partition, we propose an attraction index that based on the linked node's importance in networks. Therefore, our proposed method can better exploit the nodes' properties and network's structure. To test the performance of our algorithm, both synthetic and empirical networks ranging in different scales are tested. Simulation results show that the proposed algorithm can obtain superior clustering results compared with six other widely used community detection algorithms.

  5. Graphemes Sharing Phonetic Features Tend to Induce Similar Synesthetic Colors.

    Science.gov (United States)

    Kang, Mi-Jeong; Kim, Yeseul; Shin, Ji-Young; Kim, Chai-Youn

    2017-01-01

    Individuals with grapheme-color synesthesia experience idiosyncratic colors when viewing achromatic letters or digits. Despite large individual differences in grapheme-color association, synesthetes tend to associate graphemes sharing a perceptual feature with similar synesthetic colors. Sound has been suggested as one such feature. In the present study, we investigated whether graphemes of which representative phonemes have similar phonetic features tend to be associated with analogous synesthetic colors. We tested five Korean multilingual synesthetes on a color-matching task using graphemes from Korean, English, and Japanese orthography. We then compared the similarity of synesthetic colors induced by those characters sharing a phonetic feature. Results showed that graphemes associated with the same phonetic feature tend to induce synesthetic color in both within- and cross-script analyses. Moreover, this tendency was consistent for graphemes that are not transliterable into each other as well as graphemes that are. These results suggest that it is the perceptual-i.e., phonetic-properties associated with graphemes, not just conceptual associations such as transliteration, that determine synesthetic color.

  6. Graphemes Sharing Phonetic Features Tend to Induce Similar Synesthetic Colors

    Science.gov (United States)

    Kang, Mi-Jeong; Kim, Yeseul; Shin, Ji-Young; Kim, Chai-Youn

    2017-01-01

    Individuals with grapheme-color synesthesia experience idiosyncratic colors when viewing achromatic letters or digits. Despite large individual differences in grapheme-color association, synesthetes tend to associate graphemes sharing a perceptual feature with similar synesthetic colors. Sound has been suggested as one such feature. In the present study, we investigated whether graphemes of which representative phonemes have similar phonetic features tend to be associated with analogous synesthetic colors. We tested five Korean multilingual synesthetes on a color-matching task using graphemes from Korean, English, and Japanese orthography. We then compared the similarity of synesthetic colors induced by those characters sharing a phonetic feature. Results showed that graphemes associated with the same phonetic feature tend to induce synesthetic color in both within- and cross-script analyses. Moreover, this tendency was consistent for graphemes that are not transliterable into each other as well as graphemes that are. These results suggest that it is the perceptual—i.e., phonetic—properties associated with graphemes, not just conceptual associations such as transliteration, that determine synesthetic color. PMID:28348537

  7. Similarity of trajectories taking into account geographic context

    Directory of Open Access Journals (Sweden)

    Maike Buchin

    2014-12-01

    Full Text Available The movements of animals, people, and vehicles are embedded in a geographic context. This context influences the movement and may cause the formation of certain behavioral responses. Thus, it is essential to include context parameters in the study of movement and the development of movement pattern analytics. Advances in sensor technologies and positioning devices provide valuable data not only of moving agents but also of the circumstances embedding the movement in space and time. Developing knowledge discovery methods to investigate the relation between movement and its surrounding context is a major challenge in movement analysis today. In this paper we show how to integrate geographic context into the similarity analysis of movement data. For this, we discuss models for geographic context of movement data. Based on this we develop simple but efficient context-aware similarity measures for movement trajectories, which combine a spatial and a contextual distance. These are based on well-known similarity measures for trajectories, such as the Hausdorff, Fréchet, or equal time distance. We validate our approach by applying these measures to movement data of hurricanes and albatross.

  8. Walking on a user similarity network towards personalized recommendations.

    Directory of Open Access Journals (Sweden)

    Mingxin Gan

    Full Text Available Personalized recommender systems have been receiving more and more attention in addressing the serious problem of information overload accompanying the rapid evolution of the world-wide-web. Although traditional collaborative filtering approaches based on similarities between users have achieved remarkable success, it has been shown that the existence of popular objects may adversely influence the correct scoring of candidate objects, which lead to unreasonable recommendation results. Meanwhile, recent advances have demonstrated that approaches based on diffusion and random walk processes exhibit superior performance over collaborative filtering methods in both the recommendation accuracy and diversity. Building on these results, we adopt three strategies (power-law adjustment, nearest neighbor, and threshold filtration to adjust a user similarity network from user similarity scores calculated on historical data, and then propose a random walk with restart model on the constructed network to achieve personalized recommendations. We perform cross-validation experiments on two real data sets (MovieLens and Netflix and compare the performance of our method against the existing state-of-the-art methods. Results show that our method outperforms existing methods in not only recommendation accuracy and diversity, but also retrieval performance.

  9. Walking on a user similarity network towards personalized recommendations.

    Science.gov (United States)

    Gan, Mingxin

    2014-01-01

    Personalized recommender systems have been receiving more and more attention in addressing the serious problem of information overload accompanying the rapid evolution of the world-wide-web. Although traditional collaborative filtering approaches based on similarities between users have achieved remarkable success, it has been shown that the existence of popular objects may adversely influence the correct scoring of candidate objects, which lead to unreasonable recommendation results. Meanwhile, recent advances have demonstrated that approaches based on diffusion and random walk processes exhibit superior performance over collaborative filtering methods in both the recommendation accuracy and diversity. Building on these results, we adopt three strategies (power-law adjustment, nearest neighbor, and threshold filtration) to adjust a user similarity network from user similarity scores calculated on historical data, and then propose a random walk with restart model on the constructed network to achieve personalized recommendations. We perform cross-validation experiments on two real data sets (MovieLens and Netflix) and compare the performance of our method against the existing state-of-the-art methods. Results show that our method outperforms existing methods in not only recommendation accuracy and diversity, but also retrieval performance.

  10. Social cognition in schizophrenia and healthy aging: differences and similarities.

    Science.gov (United States)

    Silver, Henry; Bilker, Warren B

    2014-12-01

    Social cognition is impaired in schizophrenia but it is not clear whether this is specific for the illness and whether emotion perception is selectively affected. To study this we examined the perception of emotional and non-emotional clues in facial expressions, a key social cognitive skill, in schizophrenia patients and old healthy individuals using young healthy individuals as reference. Tests of object recognition, visual orientation, psychomotor speed, and working memory were included to allow multivariate analysis taking into account other cognitive functions Schizophrenia patients showed impairments in recognition of identity and emotional facial clues compared to young and old healthy groups. Severity was similar to that for object recognition and visuospatial processing. Older and younger healthy groups did not differ from each other on these tests. Schizophrenia patients and old healthy individuals were similarly impaired in the ability to automatically learn new faces during the testing procedure (measured by the CSTFAC index) compared to young healthy individuals. Social cognition is distinctly impaired in schizophrenia compared to healthy aging. Further study is needed to identify the mechanisms of automatic social cognitive learning impairment in schizophrenia patients and healthy aging individuals and determine whether similar neural systems are affected. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Improved personalized recommendation based on a similarity network

    Science.gov (United States)

    Wang, Ximeng; Liu, Yun; Xiong, Fei

    2016-08-01

    A recommender system helps individual users find the preferred items rapidly and has attracted extensive attention in recent years. Many successful recommendation algorithms are designed on bipartite networks, such as network-based inference or heat conduction. However, most of these algorithms define the resource-allocation methods for an average allocation. That is not reasonable because average allocation cannot indicate the user choice preference and the influence between users which leads to a series of non-personalized recommendation results. We propose a personalized recommendation approach that combines the similarity function and bipartite network to generate a similarity network that improves the resource-allocation process. Our model introduces user influence into the recommender system and states that the user influence can make the resource-allocation process more reasonable. We use four different metrics to evaluate our algorithms for three benchmark data sets. Experimental results show that the improved recommendation on a similarity network can obtain better accuracy and diversity than some competing approaches.

  12. Multicriteria Similarity-Based Anomaly Detection Using Pareto Depth Analysis.

    Science.gov (United States)

    Hsiao, Ko-Jen; Xu, Kevin S; Calder, Jeff; Hero, Alfred O

    2016-06-01

    We consider the problem of identifying patterns in a data set that exhibits anomalous behavior, often referred to as anomaly detection. Similarity-based anomaly detection algorithms detect abnormally large amounts of similarity or dissimilarity, e.g., as measured by the nearest neighbor Euclidean distances between a test sample and the training samples. In many application domains, there may not exist a single dissimilarity measure that captures all possible anomalous patterns. In such cases, multiple dissimilarity measures can be defined, including nonmetric measures, and one can test for anomalies by scalarizing using a nonnegative linear combination of them. If the relative importance of the different dissimilarity measures are not known in advance, as in many anomaly detection applications, the anomaly detection algorithm may need to be executed multiple times with different choices of weights in the linear combination. In this paper, we propose a method for similarity-based anomaly detection using a novel multicriteria dissimilarity measure, the Pareto depth. The proposed Pareto depth analysis (PDA) anomaly detection algorithm uses the concept of Pareto optimality to detect anomalies under multiple criteria without having to run an algorithm multiple times with different choices of weights. The proposed PDA approach is provably better than using linear combinations of the criteria, and shows superior performance on experiments with synthetic and real data sets.

  13. The Similar Structures and Control Problems of Complex Systems

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In this paper, the naturally evolving complex systems, such as biotic and social ones, are considered. Focusing on their structures, a feature is noteworthy, i.e., the similarity in structures. The relations between the functions and behaviors of these systems and their similar structures will be studied. Owing to the management of social systems and the course of evolution of biotic systems may be regarded as control processes, the researches will be within the scope of control problems. Moreover, since it is difficult to model for biotic and social systems, it will start with the control problems of complex systems, possessing similar structures, in engineering.The obtained results show that for either linear or nonlinear systems and for a lot of control problemssimilar structures lead to a series of simplifications. In general, the original system may be decomposed into reduced amount of subsystems with lower dimensions and simpler structures. By virtue of such subsystems, the control problems of original system can be solved more simply.At last, it turns round to observe the biotic and social systems and some analyses are given.

  14. Autoradiographic localization of peptide YY and neuropeptide Y binding sites in the medulla oblongata

    International Nuclear Information System (INIS)

    Leslie, R.A.; McDonald, T.J.; Robertson, H.A.

    1988-01-01

    Peptide YY is a highly potent emetic when given intravenously in dogs. We hypothesized that the area postrema, a small brain stem nucleus that acts as a chemoreceptive trigger zone for vomiting and lies outside the blood-brain barrier, might have receptors that PYY would bind to, in order to mediate the emetic response. We prepared [ 125 I]PYY and used autoradiography to show that high affinity binding sites for this ligand were highly localized in the area postrema and related nuclei of the dog medulla oblongata. Furthermore, the distribution of [ 125 I]PYY binding sites in the rat medulla oblongata was very similar to that in the dog; the distribution of [ 125 I]PYY binding sites throughout the rat brain was seen to be similar to the distribution of [ 125 I]NPY binding sites

  15. Siting Conflicts in Renewable Energy Projects in Sweden: Experiences From the Siting of a Biogas Plant

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Jamil

    2001-05-01

    This paper seeks to contribute to an increased understanding of what characterises conflicts regarding the siting of renewable energy facilities. The paper starts out with a brief introduction to different types of renewable energy and the conflicts they might generate as well as a discussion about the differences and similarities in comparison with conflicts over more controversial issues, such as nuclear plants, chemical factories and the construction of roads. The main part of the paper discusses the results from a case study on a failed attempt to site a biogas plant in southern Sweden. The results show that there was a lack of public participation in the early stages of planning, and that peoples negative perceptions of the possibilities to influence the decision-making and of the attitude of the developer, contributed to the development of a public opposition and a polarisation of the conflict. There is also a discussion about the reasons for a shift in the political support for the project and about the role of the legislation in shaping planning processes that either handle conflicts or make them worse. The paper concludes with the observation that the biogas case, in many ways, resembled traditional siting conflicts and that further research is needed to explore the nature of different renewable energy siting conflicts.

  16. Warping similarity space in category learning by human subjects: the role of task difficulty

    OpenAIRE

    Pevtzow, Rachel; Harnad, Stevan

    1997-01-01

    In innate Categorical Perception (CP) (e.g., colour perception), similarity space is "warped," with regions of increased within-category similarity (compression) and regions of reduced between-category similarity (separation) enh ancing the category boundaries and making categorisation reliable and all-or-none rather than graded. We show that category learning can likewise warp similarity space, resolving uncertainty near category boundaries. Two Hard and two Easy texture learning tasks were ...

  17. Narcissists of a Feather Flock Together: Narcissism and the Similarity of Friends.

    Science.gov (United States)

    Maaß, Ulrike; Lämmle, Lena; Bensch, Doreen; Ziegler, Matthias

    2016-03-01

    Who is willing to expose himself or herself to narcissists on a long-term basis? Studies that address the interactions of narcissists focus mainly on their interactions with strangers. Hence, the aim of the present study was to investigate the extent to which two best friends' similarity in narcissism would influence their similarities in other personality profiles. A total of 290 best friends' dyads filled out measurements of the whole Dark Triad as well as the Big Five. For each personality domain, profile similarity and its dependence on the similarity in the Dark Triad were determined. Results showed that the friends' similarity in narcissism significantly predicted similarity in all Big Five domains. For the general Big Five similarity as well as extraversion, the effect of narcissism similarity was stronger for male than female or mixed friends. Similarity in psychopathy and Machiavellianism significantly predicted all domains except for openness and extraversion, respectively. © 2016 by the Society for Personality and Social Psychology, Inc.

  18. New Genome Similarity Measures based on Conserved Gene Adjacencies.

    Science.gov (United States)

    Doerr, Daniel; Kowada, Luis Antonio B; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M E; Stoye, Jens

    2017-06-01

    Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome. The simplest models impose the strong restriction that each genome under study must contain the same genes, each in exactly one copy. More realistic models allow several copies of a gene in a genome. One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based. The most powerful-but also most complex-models avoid this preprocessing of the input data and instead integrate the family assignment within the comparative analysis. Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures. Introducing this simpler model, called gene connections, we focus on the combinatorial aspects of gene family-free genome comparison. While in most cases, the computational costs to the general family-free case are the same, we also find an instance where the gene connections model has lower complexity. Within the gene connections model, we define three variants of genomic similarity measures that have different expression powers. We give polynomial-time algorithms for two of them, while we show NP-hardness for the third, most powerful one. We also generalize the measures and algorithms to make them more robust against recent local disruptions in gene order. Our theoretical findings are supported by experimental results, proving the applicability and performance of our newly defined similarity measures.

  19. Nuclear installations sites safety

    International Nuclear Information System (INIS)

    Barber, P.; Candes, P.; Duclos, P.; Doumenc, A.; Faure, J.; Hugon, J.; Mohammadioun, B.

    1988-11-01

    This report is divided into ten parts bearing: 1 Safety analysis procedures for Basis Nuclear Installations sites (BNI) in France 2 Site safety for BNI in France 3 Industrial and transport activities risks for BNI in France 4 Demographic characteristics near BNI sites in France 5 Meteorologic characteristics of BNI sites in France 6 Geological aspects near the BNI sites in France 7 Seismic studies for BNI sites in France 8 Hydrogeological aspects near BNI sites in France 9 Hydrological aspects near BNI sites in France 10 Ecological and radioecological studies of BNI sites in France [fr

  20. Use of DOE site selection criteria for screening low-level waste disposal sites on the Oak Ridge Reservation

    International Nuclear Information System (INIS)

    Lee, D.W.; Ketelle, R.H.; Stinton, L.H.

    1983-09-01

    The proposed Department of Energy (DOE) site selection criteria were applied to the Oak Ridge Reservation, and the application was evaluated to determine the criteria's usefulness in the selection of a low-level waste disposal site. The application of the criteria required the development of a methodology to provide a framework for evaluation. The methodology is composed of site screening and site characterization stages. The site screening stage relies on reconnaissance data to identify a preferred site capable of satisfying the site selection criteria. The site characterization stage relies on a detailed site investigation to determine site acceptability. The site selection criteria were applied to the DOE Oak Ridge Reservation through the site screening stage. Results of this application were similar to those of a previous siting study on the Oak Ridge Reservation. The DOE site selection criteria when coupled with the methodology that was developed were easily applied and would be adaptable to any region of interest

  1. SITE INDEX CURVES AND HYPSOMETRIC RELATIONSHIP FOR Eucalyptus grandis PLANTATIONS FOR THE CAMPOS GERAIS REGION, PARANA STATE

    Directory of Open Access Journals (Sweden)

    Fabiane Aparecida de Souza Retslaff

    2015-06-01

    Full Text Available The study aimed to fit mathematical models for the construction of Site Index curves and to estimate heights at different ages for Eucalyptus grandis in the Campos Gerais region, Parana State. The data used to fit the models came from permanent, temporary plots and pre-harvesting inventory, covering ages from 2.5 to 26.5 years. Several models were tested to represent the sites and the hypsometric relationship. The Site Index curves were constructed by the guide-curve method. For the Site Index, the Chapman-Richards model showed the best fit and precision statistics, generating 5 Site Index curves (range of 5 m with the Chapman-Richards model. The four hypsometric models tested showed satisfactory performance and similar statistics and the inclusion of the variables dominant height or site index did not substantially improve the goodness of fit statistics, but the residues were more homogeneous and closer to zero.

  2. Social Media Sites

    Science.gov (United States)

    Media Sites Site Registration Contact Us Search AF.mil: Home > AF Sites > Social Media Sites Social Media Welcome to the Air Force social media directory! The directory is a one-stop shop of official Air Force social media pages across various social media sites. Social media is all about

  3. Learning, memory and exploratory similarities in genetically identical cloned dogs.

    Science.gov (United States)

    Shin, Chi Won; Kim, Geon A; Park, Won Jun; Park, Kwan Yong; Jeon, Jeong Min; Oh, Hyun Ju; Kim, Min Jung; Lee, Byeong Chun

    2016-12-30

    Somatic cell nuclear transfer allows generation of genetically identical animals using donor cells derived from animals with particular traits. To date, few studies have investigated whether or not these cloned dogs will show identical behavior patterns. To address this question, learning, memory and exploratory patterns were examined using six cloned dogs with identical nuclear genomes. The variance of total incorrect choice number in the Y-maze test among cloned dogs was significantly lower than that of the control dogs. There was also a significant decrease in variance in the level of exploratory activity in the open fields test compared to age-matched control dogs. These results indicate that cloned dogs show similar cognitive and exploratory patterns, suggesting that these behavioral phenotypes are related to the genotypes of the individuals.

  4. Pythoscape: A framework for generation of large protein similarity networks

    OpenAIRE

    Babbitt, Patricia; Barber, AE; Babbitt, PC

    2012-01-01

    Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among pr

  5. Neural pattern similarity underlies the mnemonic advantages for living words.

    Science.gov (United States)

    Xiao, Xiaoqian; Dong, Qi; Chen, Chuansheng; Xue, Gui

    2016-06-01

    It has been consistently shown that words representing living things are better remembered than words representing nonliving things, yet the underlying cognitive and neural mechanisms have not been clearly elucidated. The present study used both univariate and multivariate pattern analyses to examine the hypotheses that living words are better remembered because (1) they draw more attention and/or (2) they share more overlapping semantic features. Subjects were asked to study a list of living and nonliving words during a semantic judgment task. An unexpected recognition test was administered 30 min later. We found that subjects recognized significantly more living words than nonliving words. Results supported the overlapping semantic feature hypothesis by showing that (a) semantic ratings showed greater semantic similarity for living words than for nonliving words, (b) there was also significantly greater neural global pattern similarity (nGPS) for living words than for nonliving words in the posterior portion of left parahippocampus (LpPHG), (c) the nGPS in the LpPHG reflected the rated semantic similarity, and also mediated the memory differences between two semantic categories, and (d) greater univariate activation was found for living words than for nonliving words in the left hippocampus (LHIP), which mediated the better memory performance for living words and might reflect greater semantic context binding. In contrast, although living words were processed faster and elicited a stronger activity in the dorsal attention network, these differences did not mediate the animacy effect in memory. Taken together, our results provide strong support to the overlapping semantic features hypothesis, and emphasize the important role of semantic organization in episodic memory encoding. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Self-similarity and scaling theory of complex networks

    Science.gov (United States)

    Song, Chaoming

    Scale-free networks have been studied extensively due to their relevance to many real systems as diverse as the World Wide Web (WWW), the Internet, biological and social networks. We present a novel approach to the analysis of scale-free networks, revealing that their structure is self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a self-similar exponent, which classifies fractal and non-fractal networks. By using the concept of renormalization as a mechanism for the growth of fractal and non-fractal modular networks, we show that the key principle that gives rise to the fractal architecture of networks is a strong effective "repulsion" between the most connected nodes (hubs) on all length scales, rendering them very dispersed. We show that a robust network comprised of functional modules, such as a cellular network, necessitates a fractal topology, suggestive of a evolutionary drive for their existence. These fundamental properties help to understand the emergence of the scale-free property in complex networks.

  7. Dimensional analysis, similarity, analogy, and the simulation theory

    International Nuclear Information System (INIS)

    Davis, A.A.

    1978-01-01

    Dimensional analysis, similarity, analogy, and cybernetics are shown to be four consecutive steps in application of the simulation theory. This paper introduces the classes of phenomena which follow the same formal mathematical equations as models of the natural laws and the interior sphere of restraints groups of phenomena in which one can introduce simplfied nondimensional mathematical equations. The simulation by similarity in a specific field of physics, by analogy in two or more different fields of physics, and by cybernetics in nature in two or more fields of mathematics, physics, biology, economics, politics, sociology, etc., appears as a unique theory which permits one to transport the results of experiments from the models, convenably selected to meet the conditions of researches, constructions, and measurements in the laboratories to the originals which are the primary objectives of the researches. Some interesting conclusions which cannot be avoided in the use of simplified nondimensional mathematical equations as models of natural laws are presented. Interesting limitations on the use of simulation theory based on assumed simplifications are recognized. This paper shows as necessary, in scientific research, that one write mathematical models of general laws which will be applied to nature in its entirety. The paper proposes the extent of the second law of thermodynamics as the generalized law of entropy to model life and its activities. This paper shows that the physical studies and philosophical interpretations of phenomena and natural laws cannot be separated in scientific work; they are interconnected and one cannot be put above the others

  8. A self-similar hierarchy of the Korean stock market

    Science.gov (United States)

    Lim, Gyuchang; Min, Seungsik; Yoo, Kun-Woo

    2013-01-01

    A scaling analysis is performed on market values of stocks listed on Korean stock exchanges such as the KOSPI and the KOSDAQ. Different from previous studies on price fluctuations, market capitalizations are dealt with in this work. First, we show that the sum of the two stock exchanges shows a clear rank-size distribution, i.e., the Zipf's law, just as each separate one does. Second, by abstracting Zipf's law as a γ-sequence, we define a self-similar hierarchy consisting of many levels, with the numbers of firms at each level forming a geometric sequence. We also use two exponential functions to describe the hierarchy and derive a scaling law from them. Lastly, we propose a self-similar hierarchical process and perform an empirical analysis on our data set. Based on our findings, we argue that all money invested in the stock market is distributed in a hierarchical way and that a slight difference exists between the two exchanges.

  9. Prioritization of candidate disease genes by combining topological similarity and semantic similarity.

    Science.gov (United States)

    Liu, Bin; Jin, Min; Zeng, Pan

    2015-10-01

    The identification of gene-phenotype relationships is very important for the treatment of human diseases. Studies have shown that genes causing the same or similar phenotypes tend to interact with each other in a protein-protein interaction (PPI) network. Thus, many identification methods based on the PPI network model have achieved good results. However, in the PPI network, some interactions between the proteins encoded by candidate gene and the proteins encoded by known disease genes are very weak. Therefore, some studies have combined the PPI network with other genomic information and reported good predictive performances. However, we believe that the results could be further improved. In this paper, we propose a new method that uses the semantic similarity between the candidate gene and known disease genes to set the initial probability vector of a random walk with a restart algorithm in a human PPI network. The effectiveness of our method was demonstrated by leave-one-out cross-validation, and the experimental results indicated that our method outperformed other methods. Additionally, our method can predict new causative genes of multifactor diseases, including Parkinson's disease, breast cancer and obesity. The top predictions were good and consistent with the findings in the literature, which further illustrates the effectiveness of our method. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Firework displays as sources of particles similar to gunshot residue.

    Science.gov (United States)

    Grima, Matthew; Butler, Mark; Hanson, Robert; Mohameden, Ahmed

    2012-03-01

    In light of past research being targeted to find specific particles which may be similar to gunshot residue (GSR), this project was formulated to detect any possible particulate by random particle fallout onto substrates at firework displays and to assess the impact this may have on GSR evidence. Firework residue was collected at a display site, from amongst spectators as well as from the author's hair 90min after the display. SEM-EDX analysis has detected such particulate in all three scenarios, with the firework particle population at large providing a solid ground for discrimination from GSR. Wind dispersal was found to decrease the particle population and subsequently, the latter's discriminatory power. Some particles, if treated individually were found to be indistinguishable from GSR. Findings also include residues which may mimic strontium based GSR as well as GSR which may be mixed with that from previous firings. The continuous changes made to primer and propellant compositions by manufacturers also call for greater consideration when classifying particles as originating from pyrotechnic devices. Furthermore, authorities such as police forces should be made more aware about the incidence of such particle transfer in firework related periods. Copyright © 2011 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  11. QSAR models based on quantum topological molecular similarity.

    Science.gov (United States)

    Popelier, P L A; Smith, P J

    2006-07-01

    A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

  12. Human Splice-Site Prediction with Deep Neural Networks.

    Science.gov (United States)

    Naito, Tatsuhiko

    2018-04-18

    Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site. The length of input is 140 nucleotides, with the consensus sequence (i.e., "GT" and "AG" for the donor and acceptor sites, respectively) in the middle. Each input sequence model is applied to the pretrained DNN model that determines the probability that an input is a splice site. The model consists of convolutional layers and bidirectional long short-term memory network layers. The pretraining and validation were conducted using the data set tested in previously reported methods. The performance evaluation results showed that the proposed method can outperform the previous methods. In addition, the pattern learned by the DNNs was visualized as position frequency matrices (PFMs). Some of PFMs were very similar to the consensus sequence. The trained DNN model and the brief source code for the prediction system are uploaded. Further improvement will be achieved following the further development of DNNs.

  13. Similar effects of substance P on learning and memory function between hippocampus and striatal marginal division

    Science.gov (United States)

    Yu, Yan; Zeng, Changchun; Shu, Siyun; Liu, Xuemei; Li, Chuhua

    2014-01-01

    Substance P is an endogenous neurokinin that is present in the central and peripheral nervous systems. The neuropeptide substance P and its high-affinity receptor neurokinin 1 receptor are known to play an important role in the central nervous system in inflammation, blood pressure, motor behavior and anxiety. The effects of substance P in the hippocampus and the marginal division of the striatum on memory remain poorly understood. Compared with the hippocampus as a control, immunofluorescence showed high expression of the substance P receptor, neurokinin 1, in the marginal division of the striatum of normal rats. Unilateral or bilateral injection of an antisense oligonucleotide against neurokinin 1 receptor mRNA in the rat hippocampus or marginal division of the striatum effectively reduced neurokinin 1 receptor expression. Independent of injection site, rats that received this antisense oligonucleotide showed obviously increased footshock times in a Y-maze test. These results indicate that the marginal division of the striatum plays a similar function in learning and memory to the hippocampus, which is a valuable addition to our mechanistic understanding of the learning and memory functions of the marginal division of the striatum. PMID:25206901

  14. Site specific plan

    International Nuclear Information System (INIS)

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. 8 refs., 46 figs., 23 tabs

  15. Distance decay of tree species similarity in protected areas on terra firme forests in Colombian Amazonia

    NARCIS (Netherlands)

    Duque, Á.; Phillips, J.F.; von Hildebrand, P.; Posada, C.A.; Prieto, A.; Rudas, A.; Suescún, M.; Stevenson, P.

    2009-01-01

    In this study, we investigated the pattern of floristic similarity as a function of geographical distances and environmental variability in well-drained uplands (terra firme) in Colombian Amazonia. The study site comprised three National Natural Parks, Tinigua, Chiribiquete, and Amacayacu, located

  16. The effects of familiarity and similarity on compliance in social networks

    NARCIS (Netherlands)

    Kaptein, M.C.; Nass, C.; Markopoulos, P.

    2014-01-01

    Advertisers on social network sites often use recommendations by others in a user's networks to endorse products. While these familiar others are hypothesised to be more effective in influencing users than unfamiliar others, there is a catch: familiarity does not necessarily ensure similarity to the

  17. Ethnic Similarity, Therapist Adherence, and Long-Term Multisystemic Therapy Outcomes

    Science.gov (United States)

    Chapman, Jason E.; Schoenwald, Sonja K.

    2011-01-01

    The current study investigated relations among ethnic similarity in caregiver-therapist pairs of youth participating in Multisystemic Therapy, therapist adherence, and youth long-term behavioral and criminal outcomes. Participants were 1,979 youth and families treated by 429 therapists across provider organizations in 45 sites. Relations were…

  18. Cross-National Similarities and Differences in Employee Perceptions of Issues in the Work Environment

    Science.gov (United States)

    Ripley, David; Hudson, Irene; Turner, Robin; Osman-Gani, AAhad

    2006-01-01

    This exploratory study examines cross-national similarities and differences in employee perceptions of issues in the work environment in 17 organizational work settings in seven Asia-Pacific countries; Australia, Malaysia, New Zealand, Singapore, South Korea, Taiwan, and the United States. Employees at these 17 sites indicated their degree of…

  19. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

    Directory of Open Access Journals (Sweden)

    Lee Rita SF

    2010-03-01

    Full Text Available Abstract Background Cloning of cattle by somatic cell nuclear transfer (SCNT is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI. Results Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1 showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. Conclusion These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a

  20. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.