Sample records for gaevi dragan djuri

  1. Evaluation of 3D-Jury on CASP7 models.

    PubMed

    Kaján, László; Rychlewski, Leszek

    2007-08-21

    3D-Jury, the structure prediction consensus method publicly available in the Meta Server http://meta.bioinfo.pl/, was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature http://meta.bioinfo.pl/compare_your_model_example.pl available in the Meta Server.

  2. Evaluation of 3D-Jury on CASP7 models

    PubMed Central

    Kaján, László; Rychlewski, Leszek

    2007-01-01

    Background 3D-Jury, the structure prediction consensus method publicly available in the Meta Server , was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. Results The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. Conclusion The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature available in the Meta Server. PMID:17711571

  3. [Lifetime achievements of Dragan M. Dugalić. 1934-1992].

    PubMed

    Stevović, Dragoslav M

    2002-09-01

    Dragan M. Dugalitsh was born on 2nd August 1934 in Stari Trg in Kosovo in a working family. He finished the elementary school in his birthplace and the secondary school in Kosovska Mitrovica. He entered the University School of Medicine in Belgrade in 1954 and finished the studies in 1961 as one of the best students in his generation (average mark 9.22). During the studies D. Dugalitsh was very active in the students' organization, especially in professional and sport activities. He was educator first at the Chair of Chemistry and later at the Chair of Physiology. He was member of the Yugoslav Communist Party since 1954. He participated in three federal work drives. After having done the internship and national service he began to work at the Institute of Physiology of the University School of Medicine in Belgrade. However, in 1963 he changed the Institute for the First Department of Surgery managed by professor Ljubomir Rashovitsh. In 1968 he passed the examination in general surgery with excellent mark and in 1969 he was elected assistant lecturer at the Department of Surgery. His doctor's thesis was entitled "Experimental transplantation of lungs in dogs". Then, he was elected senior lecturer in 1975, associate professor in 1980 and professor of surgery in 1985. At the Department of Surgery he passed through all professional grades, from clinical physician and head of a ward to director of the Department of Surgery (1988-1992). He was also secretary of the Chair of Surgery (1984-1987) and associate dean of the University School of Medicine in Belgrade. Several times he received advanced training abroad. D. Dugalitsh was the visiting lecturer and surgeon in many towns in former Yugoslavia. He was member of many national and international surgical associations (SIC/ICC, CICD) and member of editorial boards of domestic and foreign medical journals (ACI, SA, AGEH). He was very active in the Serbian Medical Society, especially in the Section of surgery where he was

  4. Fast Geometric Consensus Approach for Protein Model Quality Assessment

    PubMed Central

    Adamczak, Rafal; Pillardy, Jaroslaw; Vallat, Brinda K.

    2011-01-01

    Abstract Model quality assessment (MQA) is an integral part of protein structure prediction methods that typically generate multiple candidate models. The challenge lies in ranking and selecting the best models using a variety of physical, knowledge-based, and geometric consensus (GC)-based scoring functions. In particular, 3D-Jury and related GC methods assume that well-predicted (sub-)structures are more likely to occur frequently in a population of candidate models, compared to incorrectly folded fragments. While this approach is very successful in the context of diversified sets of models, identifying similar substructures is computationally expensive since all pairs of models need to be superimposed using MaxSub or related heuristics for structure-to-structure alignment. Here, we consider a fast alternative, in which structural similarity is assessed using 1D profiles, e.g., consisting of relative solvent accessibilities and secondary structures of equivalent amino acid residues in the respective models. We show that the new approach, dubbed 1D-Jury, allows to implicitly compare and rank N models in O(N) time, as opposed to quadratic complexity of 3D-Jury and related clustering-based methods. In addition, 1D-Jury avoids computationally expensive 3D superposition of pairs of models. At the same time, structural similarity scores based on 1D profiles are shown to correlate strongly with those obtained using MaxSub. In terms of the ability to select the best models as top candidates 1D-Jury performs on par with other GC methods. Other potential applications of the new approach, including fast clustering of large numbers of intermediate structures generated by folding simulations, are discussed as well. PMID:21244273

  5. Transgenic Rat Models for Breast Cancer Research

    DTIC Science & Technology

    1996-10-01

    colleagues, Dr. Henry Pitot , an expert in hepatocarcinogenesis, and Dr. Michael Gould, an expert in breast cancer. Through our initial attempts at...974-978. 29. Dragan, Y.P. and H.C. Pitot . 1992. The role of the stages of initiation and promotion in phenotypic diversity during hepatocarcinogenesis

  6. Scientific and Organizational Awards | NREL

    Science.gov Websites

    Rehman, Fan Zhang, Michael Evzelman, Regan Zane, Kandler Smith, and Dragan Maksimovic 2015 Best Paper organizations. American Association of Blacks in Energy (AABE) 2005 Chairman's Cup Syl Morgan-Smith American Metropolitan Denver 2006 Outstanding Community Service Award Syl Morgan-Smith World Renewable Energy Congress

  7. JPRS Report, East Europe

    DTIC Science & Technology

    1991-06-13

    Belgrade NIN in Serbo-Croatian 17 May 91 pp 20-21 [Article by Dragan Belie: "Troubles With Parish Priests"] [Text] The lucid Dr. Slaven Letica , now...fact that the intellectual group of "Croats from the coast" ( Letica , Nobilo...) represent a sizable portion of his team of advisers, but that

  8. Solids and Surfaces: A Chemist’s View of Bonding in Extended Structures

    DTIC Science & Technology

    1988-07-20

    Zonnevylle, Susan Jansen, Wolfgang Tremel, Dragan Vuckovic and Jing Li. In the early stages of this work, very important to me was a renewed...work of Norskov et a1 8 7 come from the initial dominance of "kinetic-energy repulsion". This is the Pauli effect at work, and I would like to draw a

  9. Spatial entanglement of nonvacuum Gaussian states

    NASA Astrophysics Data System (ADS)

    Kiałka, Filip; Ahmadi, Mehdi; Dragan, Andrzej

    2016-06-01

    The vacuum state of a relativistic quantum field contains entanglement between regions separated by spacelike intervals. Such spatial entanglement can be revealed using an operational method introduced in [M. Rodriguez-Vazquez, M. del Rey, H. Westman, and J. Leon, Ann. Phys. (N.Y.) 351, 112 (2014), E. G. Brown, M. del Rey, H. Westman, J. Leon, and A. Dragan, Phys. Rev. D 91, 016005 (2015)]. In this approach, a cavity is instantaneously divided into halves by an introduction of an extra perfect mirror. Causal separation of the two regions of the cavity reveals nonlocal spatial correlations present in the field, which can be quantified by measuring particles generated in the process. We use this method to study spatial entanglement properties of nonvacuum Gaussian field states. In particular, we show how to enhance the amount of harvested spatial entanglement by an appropriate choice of the initial state of the field in the cavity. We find a counterintuitive influence of the initial entanglement between cavity modes on the spatial entanglement which is revealed by dividing the cavity in half.

  10. High Energy Theory Workshops and Visitors at the Michigan Center for Theoretical Physics FY14

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pierce, Aaron T.

    The workshop was held from September 23-25, 2013 on the University of Michigan campus. Local organizers were Dragan Huterer, Katherine Freese, and Heidi Wu (University of Michigan). Marilena Lo Verde (University of Chicago) also served as an external organizer. This workshop sought to gather experimentalists and theorists to discuss and define directions in cosmology research after the 1st year release of Planck data. The workshop included 35 invited (non-U-M) cosmologists, most of them relatively junior. The workshop was notable for spirited discussion of various theoretical ideas and experimental developments, and particularly on how one could test theory with ongoing andmore » future experiments. In our follow-up poll, 95% of participants reported that interactions with other participants at the workshop may lead to further collaboration. Most participants (again about 95%) reported that they are very satisfied with the quality of the program, information they received, and the logistical support. Slides are available on line at: http://www.umich.edu/~mctp/SciPrgPgs/events/2013/CAP13/program.html. The YHET visitor program invited weekly young visitors to the University of Michigan campus to present their work. This year 23 participants came under the program. Slides are available on line for talks when applicable: http://mctp.physics.lsa.umich.edu/brown-bag-seminar-history/winter 2014 and http://mctp.physics.lsa.umich.edu/brown-bag-seminar-history/fall-2013.« less

  11. Detailed mechanism of squalene epoxidase inhibition by terbinafine.

    PubMed

    Nowosielski, Marcin; Hoffmann, Marcin; Wyrwicz, Lucjan S; Stepniak, Piotr; Plewczynski, Dariusz M; Lazniewski, Michal; Ginalski, Krzysztof; Rychlewski, Leszek

    2011-02-28

    Squalene epoxidase (SE) is a key flavin adenine dinucleotide (FAD)-dependent enzyme of ergosterol and cholesterol biosynthetic pathways and an attractive potential target for drugs used to inhibit the growth of pathogenic fungi or to lower cholesterol level. Although many studies on allylamine drugs activity have been published during the last 30 years, up until now no detailed mechanism of the squalene epoxidase inhibition has been presented. Our study brings such a model at atomic resolution in the case of yeast Saccharomyces cerevisiae . Presented data resulting from modeling studies are in excellent agreement with experimental findings. A fully atomic three-dimensional (3D) model of squalene epoxidase (EC 1.14.99.7) from S. cerevisiae was built with the help of 3D-Jury approach and further screened based on data known from mutation experiments leading to terbinafine resistance. Docking studies followed by molecular dynamics simulations and quantum interaction energy calculations [MP2/6-31G(d)] resulted in the identification of the terbinafine-squalene epoxidase mode of interaction. In the energetically most likely orientation of terbinafine its interaction energy with the protein is ca. 120 kJ/mol. In the favorable position the terbinafine lipophilic moiety is located vertically inside the squalene epoxidase binding pocket with the tert-butyl group oriented toward its center. Such a position results in the SE conformational changes and prevents the natural substrate from being able to bind to the enzyme's active site. That would explain the noncompetitive manner of SE inhibition. We found that the strongest interaction between terbinafine and SE stems from hydrogen bonding between hydrogen-bond donors, hydroxyl group of Tyr90 and amine nitrogen atom of terbinafine. Moreover, strong attractive interactions were recorded for amino acids whose mutations resulted in terbinafine resistance. Our results, elucidating at a molecular level the mode of terbinafine

  12. Continuing Professional Development via Social Media or Conference Attendance: A Cost Analysis.

    PubMed

    Maloney, Stephen; Tunnecliff, Jacqueline; Morgan, Prue; Gaida, James; Keating, Jennifer; Clearihan, Lyn; Sadasivan, Sivalal; Ganesh, Shankar; Mohanty, Patitapaban; Weiner, John; Rivers, George; Ilic, Dragan

    2017-03-30

    Professional development is essential in the health disciplines. Knowing the cost and value of educational approaches informs decisions and choices about learning and teaching practices. The primary aim of this study was to conduct a cost analysis of participation in continuing professional development via social media compared with live conference attendance. Clinicians interested in musculoskeletal care were invited to participate in the study activities. Quantitative data were obtained from an anonymous electronic questionnaire. Of the 272 individuals invited to contribute data to this study, 150 clinicians predominantly from Australia, United States, United Kingdom, India, and Malaysia completed the outcome measures. Half of the respondents (78/150, 52.0%) believed that they would learn more with the live conference format. The median perceived participation costs for the live conference format was Aus $1596 (interquartile range, IQR 172.50-2852.00). The perceived cost of participation for equivalent content delivered via social media was Aus $15 (IQR 0.00-58.50). The majority of the clinicians (114/146, 78.1%, missing data n=4) indicated that they would pay for a subscription-based service, delivered by social media, to the median value of Aus $59.50. Social media platforms are evolving into an acceptable and financially sustainable medium for the continued professional development of health professionals. When factoring in the reduced costs of participation and the reduced loss of employable hours from the perspective of the health service, professional development via social media has unique strengths that challenge the traditional live conference delivery format. ©Stephen Maloney, Jacqueline Tunnecliff, Prue Morgan, James Gaida, Jennifer Keating, Lyn Clearihan, Sivalal Sadasivan, Shankar Ganesh, Patitapaban Mohanty, John Weiner, George Rivers, Dragan Ilic. Originally published in JMIR Medical Education (http://mededu.jmir.org), 30.03.2017.

  13. How the mainstream limits the spreading of alternative hypotheses

    NASA Astrophysics Data System (ADS)

    Kalenda, Pavel

    2014-05-01

    that prof. Djuric had tried for more than 10 years to publish this article in various peer-reviewed journals. So, prof. Djuric got into the official book (list) of "scientific dissidents" among hundreds of other professors and doctors of science (De Climont 2012). These "scientific dissidents" do not have access to established journals and may possibly publish privately or at best on the web in marginal journals whose list was published by De Climont (2012). Such a marginal journal in the field of geophysics and geology is New Concepts in Global Tectonics. This journal has been established because the current hypothesis about the movement of the continents due to convection currents in the mantle becomes under the weight of new observation quite untenable. 4) Scientific consensus History has known many hypotheses that were accepted as proven truth but later, in the light of new knowledge, they completely failed. - No one has the right to decide which scientific hypotheses will be accepted and which will not get into print. Perhaps the worst situation is in climatology (due to global effects and impacts), when the plenary session of IPCC consensually stated that the current global warming was mainly due to the human activity. References De Climont, J. (2012): The worldwide list of dissident scientists. http://astrojan.hostei.com/droa.htm. Djurič, J. (2006): Unification Of Gravitation And Electromagnetism. http://jovandjuric.tripod.com/ David H. Douglass, John R. Christy, Benjamin D. Pearson and S. Fred Singer (2007): A comparison of tropical temperature trends with model predictions. International Journal of Climatology, Volume 28, Issue 13, 15 November 2008, Pages: 1693-1701. http://onlinelibrary.wiley.com/doi/10.1002/joc.1651/pdf. Einstein, A. : List of scientific publications by Albert Einstein. /wiki/List_of_scientific_publications_by_Albert_Einstein. Kolínský, P., Valenta, J. and Gaždová, R. (2012): Seismicity, groundwater level variations and earth tides in

  14. EDITORIAL Solar harvest Solar harvest

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2010-12-01

    investigating organic solar cell technology. In spring 2011, Nanotechnology launches a new section wholly dedicated to the coverage of new and stimulating research into energy sources based on nanoscale science and technology. There is at present considerable concern over how to fuel the planet in a sustainable manner with the increasingly energy-thirsty human population. Yet the Earth receives more solar energy in one hour than the world population consumes in one year [8]. No wonder research into photovoltaics and ways of increasing the efficiency with which this energy can be harnessed continues to hold so much fascination. References [1] Levin I and White C E 1949 J. Chem. Phys. 18 417 [2] Chirvase D, Parisi J, Hummelen J C and Dyakonov V 2004 Nanotechnology 15 1317 [3] Kwong C Y, Choy W C H, Djurišić A B, Chui P C, Cheng K W and Chan W K 2004 Nanotechnology 15 1156 [4] Krebs F C, Thomann Y, Thomann R and Andreasen J W 2008 Nanotechnology 19 424013 [5] Zeng T-W, Lin Y-Y, Lo H-H, Chen C-W, Chen C-H, Liou S-C, Huang H-Y and Su W-F 2006 Nanotechnology 17 5387 [6] Dissanayake D M N M, Hatton R A, Lutz T, Curry R J and Silva S R P 2009 Nanotechnology 20 245202 [7] Nicholson P G and Castro F A 2010 Nanotechnology 21 492001 [8] http://www.solarenergyworld.org/solar-energy-facts/

  15. PREFACE: XXVIth International Conference on Photonic, Electronic and Atomic Collisions

    NASA Astrophysics Data System (ADS)

    Orel, Ann; Starace, Anthony F.; Nikolić, Dragan; Berrah, Nora; Gorczyca, Thomas W.; Kamber, Emanuel Y.; Tanis, John A.

    2009-12-01

    developing/disadvantaged countries. All in all, the XXVIth ICPEAC in Kalamazoo was very successful. The plenary lectures and the progress and special reports bridged the gap between the different fields of collision physics, making it possible for non-experts in a given area to gain insight into new areas. Also, included among the speakers were several young scientists, namely, postdocs and students, who brought new perspectives to their fields. The next ICPEAC will take place in Belfast in 2011, and the ones after that will be in Lanzhou in 2013 and Madrid in 2015. Given the rapidity with which science is advancing in all of the areas covered by ICPEAC, we expect that these future ICPEAC conferences will be as stimulating as this most recent one was, as indicated by the contributions presented in this proceedings volume. Ann Orel, University of California-Davis Anthony F Starace, University of Nebraska-Lincoln Dragan Nikolić, Western Michigan University Nora Berrah, Western Michigan University Thomas W Gorczyca, Western Michigan University Emanuel Y Kamber, Western Michigan University John A Tanis, Western Michigan University The PDF file contains details of the Sponsors and Exhibitors, Committees and Previous Proceedings. Conference photograph

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