551 research outputs found
Finding conserved gene order across multiple genomes
No full textThe ever increasing amount of annotated genomic sequences permits now to shed light on the molecular dynamics at the basis of evolution. Genome evolution involves both changes at the sequence level, but also rearrangements on the gene organization along the genome. Comparative analysis of gene order in multiple genomes may be thus of help in the investigation of general or lineage-specific genome plasticity, as well as in the inference of phylogenetic relationships. In particular, conserved gene contiguity in a chromosome, even if interrupted by intervening genes, may suggest potential functional couplings. This unit explains the usage of GeneSyn, a software tool for the automatic identification of conserved gene order across multiple annotated genomes
ORTHOGONAL POLYNOMIALS AND MIDDLE HANKEL-OPERATORS ON BERGMAN SPACES
No full textWe introduce a sequence of Hankel style operators H(k), k = 1, 2, 3,..., which act on the Bergman space of the unit disk. These operators are intermediate between the classical big and small Hankel operators. We study the boundedness and Schatten-von Neumann properties of the H(k) and show, among other things, that H(k) are cut-off at 1/k. Recall that the big Hankel operator is cut-off at 1 and the small Hankel operator at 0.MathematicsSCI(E)12ARTICLE157-7510
Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes
No full textSchmidt T, Stoye J. Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes. In: Bergman NH, ed. Comparative Genomics, Volume 2. Methods in Molecular Biology. Vol 396. Totowa, NJ: Humana Press Inc.; 2007: 165-182
Reaction kinetics and 3D architecture of a catalytic ribonucleic acid
No full textThesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 2001.Includes bibliographical references.The Class I ligase ribozyme was isolated previously from random sequences based on its ability to promote a reaction similar to a single step in RNA polymerization: attack of a primer 3'-hydroxyl on a 5'-triphosphate, with formation of a new 3'-5' bond and release of pyrophosphate. Derivatives have been shown to catalyze general primer extension reactions, making the ligase a useful paradigm for RNA self-replication and RNA polymerase biochemistry as well as RNA catalysis in general. In order to establish the ligase as a model system, we have characterized both the reaction and tertiary architecture of the ribozyme. The reaction kinetics of both multiple- and single-turnover ligation were examined, and from these data minimal kinetic frameworks were constructed. These frameworks provide a basis for the interpretation of future mechanistic work, and suggest strategies by which individual steps in the ligation reaction might be targeted for future improvement. In order to test whether the chemical step of Class I ligation could be further optimized, an in vitro selection was performed under conditions that specifically isolated chemistry. Selected variants had a slightly improved chemical step, and substantially improved Mg++-dependence, such that at 0.5 mM Mg++ a composite improved ligase was 50-fold faster than the parent ribozyme. The tertiary architecture of the ligase was examined using hydroxyl radical probing, which provided a measure of the solvent accessibility at each position in the RNA backbone. In collaboration with another group, these data were used to model the tertiary architecture of the ligase in three dimensions. Finally, the predictive value of the model was.tested and confirmed by photocrosslinking experiments.by Nicholas H. Bergman.Ph.D
Natural regeneration on staggered settings
No full textIn recent years much of the logging in the Douglas fir region has been by the staggered setting system. Consequently, the effects of this system upon natural coniferous regeneration have become increasingly important. This study was designed to analyze the effects of setting size and environmental factors upon natural regeneration of Douglas fir (Pseudotsuga taxifolia, Poir) and associated coniferous species. A number of settings in western Oregon were examined in 1953 and 1954. The following data were recorded for each mil-acre plot studied: number, age, and species of coniferous reproduction; distance from seed source; intensity of burn; intensity and type of plant cover; amount of slash; seedbed condition; and exposure. The effect of each of these factors was evaluated by statistical analysis of the field data. The results of the analysis indicated that: 1. There was no correlation between setting size and distance from seed source; there was little correlation between distance from seed source and occurrence of coniferous reproduction; therefore, no correlation exists between size of a staggered setting and speed of restocking. 2. For a given mil-acre plot the following environmental factors are favorable to the establishment of coniferous reproduction: no burri, northerly exposures, light slash cover, light herbaceous cover. 3. For a given mil-acre plot the following environmental factors .are not favorable to the establishment of coniferous reproduction: any degree of burn, southerly exposures, medium or heavy slash, and heavy herbaceous cover or woody plant cover.Abstract -- Introduction -- Examination of study areas -- Selection of areas -- Sampling methods -- Data recorded for each Mil-Acre plot -- Cover class -- Slash class -- Burn class -- Seed bed conditions -- Coniferous reproduction -- Distance from seed source -- Automatic machine compilation -- Results -- Composition of coniferous reproduction by species -- Stocking at various distances from seed source -- Stocking on various cover classes -- Stocking on various exposures -- Stocking on various slash classes -- Stocking on various burn classes -- Separate effects of individual factors -- Summary and conclusions -- Discussion -- Statistical analysis -- Plants commonly found on areas examined -- Bibliography.by Denis P. Lavender, Morris H. Bergman [and] Lyle D. Calvin."December, 1956."This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Includes bibliographical references (page 36).Mode of access: Internet from the Oregon Government Publications Collection.Text in English
The quality in qualitative methods
No full textQuality concerns play a central role throughout all steps of the research process in qualitative methods, from the inception of a research question and data collection, to the analysis and interpretation of research findings. For instance, the type of instrument or procedure to collect data may be evaluated in relation to quality criteria, and these may be different from those which are used to judge the data obtained from such instruments or procedures. All these may yet again be different from quality criteria that may apply to the qualitative analyses of data. A national resource center for qualitative methods can contribute to the establishment and maintenance of certain quality standards. In this article, we will explore some of these quality criteria and how they can be established and maintained by a national resource center for qualitative methods.
URN: urn:nbn:de:0114-fqs050234
On boundedness and compactness of Toeplitz operators in weighted H-infinity-spaces
No full text[EN] We characterize the boundedness and compactness of Toeplitz operators T-a with radial symbols a in weighted H-infinity-spaces H(v)(infinity)on the open unit disc of the complex plane. The weights v are also assumed radial and to satisfy the condition (B) introduced by the second named author. The main technique uses Taylor coefficient multipliers, and the results are first proved for them. We formulate a related sufficient condition for the boundedness and compactness of Toeplitz operators in reflexive weighted Bergman spaces on the disc. We also construct a bounded harmonic symbol f such that T-f is not bounded in H-v(infinity) for any v satisfying mild assumptions. As a corollary, the Bergman projection is never bounded with respect to the corresponding weighted sup-norms. However, we also show that, for normal weights v, all Toeplitz operators with a trigonometric polynomial as the symbol are bounded on H-v(infinity) . (C) 2020 Elsevier Inc. All rights reserved.The research of Bonet was partially supported by the projects MTM2016-76647-P and GV Prometeo/2017/102 (Spain). The research of Taskinen was partially supported by a research grant from the Faculty of Science of the University of Helsinki.Bonet Solves, JA.; Lusky, W.; Taskinen, J. (2020). On boundedness and compactness of Toeplitz operators in weighted H-infinity-spaces. Journal of Functional Analysis. 278(10):1-26. https://doi.org/10.1016/j.jfa.2019.108456S12627810Bonet, J., Lusky, W., & Taskinen, J. (2018). Solid hulls and cores of weighted H ∞ -spaces. Revista Matemática Complutense, 31(3), 781-804. doi:10.1007/s13163-018-0265-6Bonet, J., Lusky, W., & Taskinen, J. (2019). Solid cores and solid hulls of weighted Bergman spaces. Banach Journal of Mathematical Analysis, 13(2), 468-485. doi:10.1215/17358787-2018-0049Constantin, O., & Peláez, J. Á. (2015). Boundedness of the Bergman projection on Lp-spaces with exponential weights. Bulletin des Sciences Mathématiques, 139(3), 245-268. doi:10.1016/j.bulsci.2014.08.012Dostanić, M. R. (2004). UNBOUNDEDNESS OF THE BERGMAN PROJECTIONS ON SPACES WITH EXPONENTIAL WEIGHTS. Proceedings of the Edinburgh Mathematical Society, 47(1), 111-117. doi:10.1017/s0013091501000190Engliš, M. (2008). Toeplitz operators and weighted Bergman kernels. Journal of Functional Analysis, 255(6), 1419-1457. doi:10.1016/j.jfa.2008.06.026Grudsky, S., & Vasilevski, N. (2001). Bergman-Toeplitz operators: Radial component influence. Integral Equations and Operator Theory, 40(1), 16-33. doi:10.1007/bf01202952Harutyunyan, A., & Lusky, W. (2010). On L1-subspaces of holomorphic functions. Studia Mathematica, 198(2), 157-175. doi:10.4064/sm198-2-4Luecking, D. H. (1987). Trace ideal criteria for Toeplitz operators. Journal of Functional Analysis, 73(2), 345-368. doi:10.1016/0022-1236(87)90072-3Luecking, D. H. (2007). Finite rank Toeplitz operators on the Bergman space. Proceedings of the American Mathematical Society, 136(05), 1717-1724. doi:10.1090/s0002-9939-07-09119-8Lusky, W. (1995). On Weighted Spaces of Harmonic and Holomorphic Functions. Journal of the London Mathematical Society, 51(2), 309-320. doi:10.1112/jlms/51.2.309Lusky, W. (2006). On the isomorphism classes of weighted spaces of harmonic and holomorphic functions. Studia Mathematica, 175(1), 19-45. doi:10.4064/sm175-1-2Lusky, W., & Taskinen, J. (2008). Bounded holomorphic projections for exponentially decreasing weights. Journal of Function Spaces and Applications, 6(1), 59-70. doi:10.1155/2008/217160Lusky, W., & Taskinen, J. (2011). Toeplitz operators on Bergman spaces and Hardy multipliers. Studia Mathematica, 204(2), 137-154. doi:10.4064/sm204-2-3Mannersalo, P. (2016). Toeplitz operators with locally integrable symbols on Bergman spaces of bounded simply connected domains. Complex Variables and Elliptic Equations, 61(6), 854-874. doi:10.1080/17476933.2015.1120293STROETHOFF, K. (1998). Compact Toeplitz operators on Bergman spaces. Mathematical Proceedings of the Cambridge Philosophical Society, 124(1), 151-160. doi:10.1017/s0305004197002375Taskinen, J., & Virtanen, J. (2010). Toeplitz operators on Bergman spaces with locally integrable symbols. Revista Matemática Iberoamericana, 693-706. doi:10.4171/rmi/614Zorboska, N. (2003). Toeplitz operators with BMO symbols and the Berezin transform. International Journal of Mathematics and Mathematical Sciences, 2003(46), 2929-2945. doi:10.1155/s016117120321203
Position-based scanning for comparative genomics and identification of genetic islands in Haemophilus influenzae type b
No full textBacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered in the genome of the type b serotype of Haemophilus influenzae, a human pathogen able to cause meningitis, pneumonia, and septicemia. Here we report application of a PCR-based scanning procedure to compare the genome of a virulent type b (Hib) strain with that of the laboratory-passaged Rd KW20 strain for which a complete genome sequence is available. We have identified seven DNA segments or H. influenzae genetic islands (HiGIs) present in the type b genome and absent from the Rd genome. These segments vary in size and content and show signs of horizontal gene transfer in that their percent G+C content differs from that of the rest of the H. influenzae genome, they contain genes similar to those found on phages or other mobile elements, or they are flanked by DNA repeats. Several of these loci represent potential pathogenicity islands, because they contain genes likely to mediate interactions with the host. These newly identified genetic islands provide areas of investigation into both the evolution and pathogenesis of H. influenzae. In addition, the genome scanning approach developed to identify these islands provides a rapid means to compare the genomes of phenotypically diverse bacterial strains once the genome sequence of one representative strain has been determined
Review of UK microgeneration. Part 1 : policy and behavioural aspects
No full textA critical review of the literature relating to government policy and behavioural aspects relevant to the uptake and application of microgeneration in the UK is presented. Given the current policy context aspiring to zero-carbon new homes by 2016 and a variety of minimum standards and financial policy instruments supporting microgeneration in existing dwellings, it appears that this class of technologies could make a significant contribution to UK energy supply and low-carbon buildings in the future. Indeed, achievement of a reduction in greenhouse gas emissions by 80% (the UK government's 2050 target) for the residential sector may entail substantial deployment of microgeneration. Realisation of the large potential market for microgeneration relies on a variety of inter-related factors such as microeconomics, behavioural aspects, the structure of supporting policy instruments and well-informed technology development. This article explores these issues in terms of current and proposed policy instruments in the UK. Behavioural aspects associated with both initial uptake of the technology and after purchase are also considered
3.17 Verdere ontwikkeling benthos module (BENBOX): T.b.v. integraal model effectketen Noordzee Fase 2
No full textHet doel van dit deelproject om de effecten van de aanleg van Flyland (veranderingen gesuspendeerd inert particulair materiaal in de waterkolom, fytoplanktonconcentraties en sedimentatie) op lager trofisch niveau (macrobenthos) beter door te vertalen naar hogere trofische niveaus zoals b.v. garnalen en vissen. Het gaat om een kwantitatieve schatting van grootschalige veranderingen van voedselstromen en productieprocessen ten gevolge van het luchthaven-in-zee-project. Het model is opgebouwd uit een aantal functionele groepen met kenmerkende eigenschappen wat betreft voedselopname en voedselbronnen. Het basisidee is dat bepaalde groepen van benthische organismen verschillend reageren wat betreft voedselopname en groei op de aansturende factoren (gedifferentieerde, functionele respons). De directe respons van bepaalde benthosgroepen werkt indirect door tot hoger trofische niveaus. Een functionele groep wordt in het model gerepresenteerd door een serie grootte- klassen die het groottespectrum vormen zoals waargenomen in het veld (het Nederlandse Continentale Plat). Behalve de biomassa (mg C) van een functionele groep worden de aantallen (dichtheid) en de grootteverdeling bijgehouden. Er wordt gebruik gemaakt van al bestaande groei modellen (Von Bertalanffy en DEB model), die rekening houden met allometrische relaties en een software techniek om op een redelijk eenvoudige wijze grootte- klassen te kunnen modelleren. Bovendien wordt de dN15 indicatie bijgehouden, die een aanwijzing geeft over het trofische niveau van de functionele groepen (positie in het voedselweb) en gebruikt kan worden voor vergelijkingen met veldmetingen van deze grootheid. De indeling van trofische niveaus in het BENBOX-model wordt bepaald door voedselrelaties tussen de verschillende functionele groepen. Een belangrijk kenmerk is het aansturen van de functionele groepen vanuit verschillende voedselbronnen (multichannel omnivory). In het BENBOX-model wordt vereenvoudigd rekening gehouden met de zeer complexe rekruteringsproces en mortaliteit van bodemdieren door visserij. De biomassaverdeling over verschillende functionele groepen geeft aanwijzingen op welke manier gebruik gemaakt wordt van de basale voedselbronnen (pelagische en benthische bronnen) en hoe het voedselweb wordt aangestuurd. Een modelschatting van biomassaontwikkelingen en productie wordt geacht als een geschikte methode om de grootteorde van de effecten op natuurwaarden en gebruiksfuncties door dit soort ingrepen te schatten of de effecten van mitigerende maatregelen te analyseren. Er zijn geschikte datasets en voldoende literatuurgegevens om het BENBOX-model te parametersereen en te valideren. De technische ontwikkeling is binnen afzienbare tijd voor gebruik te verwezenlijken. De modeluitkomsten zijn vergelijkbaar met referentiesituatie. De variatie van parameters zal nog getoetst moeten worden. Het grootste voordeel van een modelmatige (generieke) aanpak is de brede inzetbaarheid ook bij verandering van randvoorwaarden of soortgelijke problemen.Luchthaven in Ze
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