Relevant bibliographies by topics / Homology theory

Academic literature on the topic 'Homology theory'

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Published: 4 June 2021
Last updated: 31 July 2024

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Journal articles on the topic "Homology theory"

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Kauffman, Louis H. "Simplicial homotopy theory, link homology and Khovanov homology." Journal of Knot Theory and Its Ramifications 27, no. 07 (June 2018): 1841002. http://dx.doi.org/10.1142/s021821651841002x.

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This paper shows how, in principle, simplicial methods, including the well-known Dold–Kan construction can be applied to convert link homology theories into homotopy theories. The paper studies particularly the case of Khovanov homology and shows how simplicial structures are implicit in the construction of the Khovanov complex from a link diagram and how the homology of the Khovanov category, with coefficients in an appropriate Frobenius algebra, is related to Khovanov homology. This Khovanov category leads to simplicial groups satisfying the Kan condition that are relevant to a homotopy theory for Khovanov homology.
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Špakula, Ján. "Uniform K-homology theory." Journal of Functional Analysis 257, no. 1 (July 2009): 88–121. http://dx.doi.org/10.1016/j.jfa.2009.02.008.

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Talbi, Mohamed Elamine, and Djilali Benayat. "Homology Theory of Graphs." Mediterranean Journal of Mathematics 11, no. 2 (November 12, 2013): 813–28. http://dx.doi.org/10.1007/s00009-013-0358-x.

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Crabb, M. C. "LOOP HOMOLOGY AS FIBREWISE HOMOLOGY." Proceedings of the Edinburgh Mathematical Society 51, no. 1 (February 2008): 27–44. http://dx.doi.org/10.1017/s0013091505001483.

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AbstractThe loop homology ring of an oriented closed manifold, defined by Chas and Sullivan, is interpreted as a fibrewise homology Pontrjagin ring. The basic structure, particularly the commutativity of the loop multiplication and the homotopy invariance, is explained from the viewpoint of the fibrewise theory, and the definition is extended to arbitrary compact manifolds.
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Zastrow, Andreas. "On the (non)-coincidence of Milnor–Thurston homology theory with singular homology theory." Pacific Journal of Mathematics 186, no. 2 (December 1, 1998): 369–96. http://dx.doi.org/10.2140/pjm.1998.186.369.

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Anand, Swadha, Bhusan K. Kuntal, Anwesha Mohapatra, Vineet Bhatt, and Sharmila S. Mande. "FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information." Bioinformatics 36, no. 8 (December 27, 2019): 2575–77. http://dx.doi.org/10.1093/bioinformatics/btz957.

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Abstract Motivation Functional potential of genomes and metagenomes which are inferred using homology-based methods are often subjected to certain limitations, especially for proteins with homologs which function in multiple pathways. Augmenting the homology information with genomic location of the constituent genes can significantly improve the accuracy of estimated functions. This can help in distinguishing cognate homolog belonging to a candidate pathway from its other homologs functional in different pathways. Results In this article, we present a web-based analysis platform ‘FunGeCo’ to enable gene-context-based functional inference for microbial genomes and metagenomes. It is expected to be a valuable resource and complement the existing tools for understanding the functional potential of microbes which reside in an environment. Availability and implementation https://web.rniapps.net/fungeco [Freely available for academic use]. Supplementary information Supplementary data are available at Bioinformatics online.
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Agüero-Chapin, Guillermin, Deborah Galpert, Reinaldo Molina-Ruiz, Evys Ancede-Gallardo, Gisselle Pérez-Machado, Gustavo A. De la Riva, and Agostinho Antunes. "Graph Theory-Based Sequence Descriptors as Remote Homology Predictors." Biomolecules 10, no. 1 (December 23, 2019): 26. http://dx.doi.org/10.3390/biom10010026.

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Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses. They have been especially useful to detect remote homologs within the twilight zone of highly diverse gene/protein families and superfamilies. The most popular alignment-free methodologies, as well as their applications to classification problems, have been described in previous reviews. Despite a new set of graph theory-derived sequence/structural descriptors that have been gaining relevance in the detection of remote homology, they have been omitted as AF predictors when the topic is addressed. Here, we first go over the most popular AF approaches used for detecting homology signals within the twilight zone and then bring out the state-of-the-art tools encoding graph theory-derived sequence/structure descriptors and their success for identifying remote homologs. We also highlight the tendency of integrating AF features/measures with the AB ones, either into the same prediction model or by assembling the predictions from different algorithms using voting/weighting strategies, for improving the detection of remote signals. Lastly, we briefly discuss the efforts made to scale up AB and AF features/measures for the comparison of multiple genomes and proteomes. Alongside the achieved experiences in remote homology detection by both the most popular AF tools and other less known ones, we provide our own using the graphical–numerical methodologies, MARCH-INSIDE, TI2BioP, and ProtDCal. We also present a new Python-based tool (SeqDivA) with a friendly graphical user interface (GUI) for delimiting the twilight zone by using several similar criteria.
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MIYATA, TAKAHISA. "Homology decompositions in shape theory." Publicationes Mathematicae Debrecen 78, no. 1 (January 1, 2011): 15–35. http://dx.doi.org/10.5486/pmd.2011.4325.

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Cortinas, Guillermo. "$L$-theory and dihedral homology." MATHEMATICA SCANDINAVICA 73 (December 1, 1993): 21. http://dx.doi.org/10.7146/math.scand.a-12453.

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Kotelskiy, Artem. "Bordered theory for pillowcase homology." Mathematical Research Letters 26, no. 5 (2019): 1467–516. http://dx.doi.org/10.4310/mrl.2019.v26.n5.a11.

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Dissertations / Theses on the topic "Homology theory"

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Jacobsson, Magnus. "Khovanov homology and link cobordisms /." Uppsala : Matematiska institutionen, Univ. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3765.

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McDougall, Adam Corey. "Relating Khovanov homology to a diagramless homology." Diss., University of Iowa, 2010. https://ir.uiowa.edu/etd/709.

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A homology theory is defined for equivalence classes of links under isotopy in the 3-sphere. Chain modules for a link L are generated by certain surfaces whose boundary is L, using surface signature as the homological grading. In the end, the diagramless homology of a link is found to be equal to some number of copies of the Khovanov homology of that link. There is also a discussion of how one would generalize the diagramless homology theory (hence the theory of Khovanov homology) to links in arbitrary closed oriented 3-manifolds.
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Brautaset, Olav. "Homology Theory from the Geometric Viewpoint." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for matematiske fag, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-15695.

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Given a multiplicative cohomology theory represented by a spectrum, E,we define its associated geometric homology theory by means of bordism. Restrictedto CW pairs, we show how the geometric homology theory is naturally equivalent to the homology theory associated E. This was done by M. Jakob in 2000, and we give an expositionfollowing his approach. We also consider a naturally occurring cap product.
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Yates, Stuart. "Discrete morse theory and L2 homology /." Title page, abstract and contents only, 1997. http://web4.library.adelaide.edu.au/theses/09SM/09smy34.pdf.

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Johnson, Christopher Aaron. "Applications of computational homology." Huntington, WV : [Marshall University Libraries], 2006. http://www.marshall.edu/etd/descript.asp?ref=621.

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Jia, Bei. "D-branes and K-homology." Thesis, Virginia Tech, 2013. http://hdl.handle.net/10919/32039.

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In this thesis the close relationship between the topological $K$-homology group of the spacetime manifold $X$ of string theory and D-branes in string theory is examined. An element of the $K$-homology group is given by an equivalence class of $K$-cycles $[M,E,\phi]$, where $M$ is a closed spin$^c$ manifold, $E$ is a complex vector bundle over $M$, and $\phi: M\rightarrow X$ is a continuous map. It is proposed that a $K$-cycle $[M,E,\phi]$ represents a D-brane configuration wrapping the subspace $\phi(M)$. As a consequence, the $K$-homology element defined by $[M,E,\phi]$ represents a class of D-brane configurations that have the same physical charge. Furthermore, the $K$-cycle representation of D-branes resembles the modern way of characterizing fundamental strings, in which the strings are represented as two-dimensional surfaces with maps into the spacetime manifold. This classification of D-branes also suggests the possibility of physically interpreting D-branes wrapping singular subspaces of spacetime, enlarging the known types of singularities that string theory can cope with.
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Song, Yongjin. "Hermitian algebraic K-theory and dihedral homology /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487681788252481.

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Levikov, Filipp. "L-theory, K-theory and involutions." Thesis, University of Aberdeen, 2013. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=201918.

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In Part 1, we consider two descriptions of L-homology of a (polyhedron of a) simplicial complex X. The classical approach of Ranicki via (Z,X)-modules (cf. [Ran92]) iswell established and is used in Ranicki’s definition of the total surgery obstruction and his formulation of the algebraic surgery exact sequence (cf. [Ran79], [Ran92],[KMM]). This connection between algebraic surgery and geometric surgery has numerous applications in the theory of (highdimensional) manifolds. The approach described in [RW10] uses a category of homotopy complexes of cosheaves to construct for a manifold M a (rational) orientation class [M]L• in symmetric L-homology which is topologically invariant per construction. This is used to reprove the topological invariance of rational Pontryagin classes. The L-theory of the category of homotopy complexes of sheaves over an ENR X can be naturally identified with L-homology of X. If X is a simplicial complex, both definitions give L-homology, there is no direct comparison however. We close this gap by constructing a functor from the category of (Z,X)-modules to the category of homotopy cosheaves of chain complexes of Ranicki-Weiss inducing an equivalence on L-theory. The work undertaken in Part 1 may be considered as an addendum to [RW10] and suggests some translation of ideas of [Ran92] into the language of [RW10]. Without significant alterations, this work may be generalised to the case of X being a △-set. The L-theory of △-sets is considered in [RW12]. Let A be a unital ring and I a category with objects given by natural numbers and two kinds of morphisms mn → n satisfying certain relations (see Ch.3.4). There is an I-diagram, given by n 7→ ˜K (A[x]/xn) where the tilde indicates the homotopy fiber of the projection induced map on algebraic K-theory (of free modules) K(A[x]/xn) → K(A). In Part 2 we consider the following result by Betley and Schlichtkrull [BS05]. After completion there is an equivalence of spectra TC(A)∧ ≃ holim I ˜K(A[x]/xn)∧ where TC(A) is the topological cyclic homology of A. This is a very important invariant of K-theory (cf. [BHM93], [DGM12]) and comes with the cyclotomic trace map tr : K(A) → TC(A). In [BS05], the authors prove that under the above identification the trace map corresponds to a “multiplication” with an element u∞ ∈ holim I ˜K (Z[x]/xn). In this work we are interested in a generalisation of this result. We construct an element u∞ ∈ holim I ˜K(Cn). where Cn can be viewed as the category of freemodules over the nilpotent extension S[x]/xn of the sphere spectrum S. Let G be a discrete group and S[G] its spherical group ring. Using our lift of u∞ we construct a map trBS : K(S[G]) → holim I ˜K (CG n ) where CG n should be interpreted as the category of free modules over the extension S[G][x]/xn. After linearisation this map coincides with the trace map constructed by Betley and Schlichtkrull. We conjecture but do not prove, that after completion the domain coincides with the topological cyclic homology of S[G]. Some indication is given at the end of the final chapter. To construct the element u∞ we rely on a generalisation of a result of Grayson on the K-theory of endomorphisms (cf. [Gra77]). Denote by EndC the category of endomorphisms of finite CW-spectra and by RC the Waldhausen category of free CW-spectra with an action of N, which are finite in the equivariant sense. Cofibrations are given by cellular inclusions and weak equivalences are given bymaps inducing an equivalence of (reduced) cellular chain complexes of Z[x]-modules, after inverting the set {1 + xZ[x]}. In Chapter 5 we prove (5.8) that there is a homotopy equivalence of spectra ˜K (EndC) ≃ ˜K (RC). where tildes indicate that homotopy fibres of the respective projections are considered. Furthermore, we pursue the goal of constructing an involutive tracemap for themodel of [BS05]. We employ the framework ofWaldhausen categories with duality (cf. [WW98]) to introduce for any G involutions on holim I ˜K (CG n ). We give enough indication for our trace map being involutive, in particular in the last three sections of Chapter 5, we sketch how the generalisation of the theoremof Grayson (5.8) can be improved to an involutive version. In the final chapter, we develop this further. Assuming that the element u∞ ∈ holim I ˜K (Cn) is a homotopy fixed point of the introduced involution, we construct a map from quadratic L-theory of S[G] to the Tate homology spectrum of Z/2 acting on the fibre of trBS (see 6.9) : L•(S[G]) → (hofib(trBS))thZ/2 and discuss the connection of this to a conjecture of Rognes andWeiss. The two parts of the thesis are preluded with their own introduction andmay be read independently. The fewcross references are completely neglectible.
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Kaygun, Atabey. "Bialgebra cyclic homology with coefficients." Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1107564231.

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Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains vii, 77 p.; also includes graphics Includes bibliographical references (p. 76-77). Available online via OhioLINK's ETD Center
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Frøyshov, Kim A. "On Floer homology and four-manifolds with boundary." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282194.

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Books on the topic "Homology theory"

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Vick, James W. Homology Theory. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4612-0881-5.

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Loday, Jean-Louis. Cyclic Homology. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998.

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Loday, Jean-Louis. Cyclic homology. 2nd ed. Berlin: Springer, 1998.

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Loday, Jean-Louis. Cyclic homology. Berlin: Springer-Verlag, 1992.

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Matthias, Schwarz. Morse homology. Basel: Birkhäuser Verlag, 1993.

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1957-, Lyubeznik Gennady, ed. Local cohomology and its applications. New York: Marcel Dekker, 2002.

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Michael, Mischaikow Konstantin, and Mrozek Marian, eds. Computational homology. New York: Springer, 2010.

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Baues, Hans J. Homotopy type and homology. Oxford: Clarendon Press, 1996.

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Audin, Michèle, and Mihai Damian. Morse Theory and Floer Homology. London: Springer London, 2014. http://dx.doi.org/10.1007/978-1-4471-5496-9.

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Kirwan, Frances. An introductionto intersection homology theory. Harlow: Longman Scientific & Technical, 1988.

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Book chapters on the topic "Homology theory"

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Crabb, Michael Charles, and Ioan Mackenzie James. "Homology Theory." In Springer Monographs in Mathematics, 309–29. London: Springer London, 1998. http://dx.doi.org/10.1007/978-1-4471-1265-5_7.

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Bredon, Glen E. "Homology Theory." In Graduate Texts in Mathematics, 168–259. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4757-6848-0_4.

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Golovin, V. D. "Homology Theory." In Homology of Analytic Sheaves and Duality Theorems, 63–86. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1677-0_2.

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Borisovich, Yuri G., Nikolai M. Bliznyakov, Tatyana N. Fomenko, and Yakov A. Izrailevich. "Homology Theory." In Kluwer Texts in the Mathematical Sciences, 387–476. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-017-1959-9_5.

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Schwarz, Matthias. "Morse Homology Theory." In Morse Homology, 133–98. Basel: Birkhäuser Basel, 1993. http://dx.doi.org/10.1007/978-3-0348-8577-5_4.

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Prasolov, V. "Simplicial homology." In Elements of Homology Theory, 1–58. Providence, Rhode Island: American Mathematical Society, 2007. http://dx.doi.org/10.1090/gsm/081/01.

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Prasolov, V. "Singular homology." In Elements of Homology Theory, 195–262. Providence, Rhode Island: American Mathematical Society, 2007. http://dx.doi.org/10.1090/gsm/081/04.

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Bredon, Glen E. "Borel-Moore Homology." In Sheaf Theory, 279–416. New York, NY: Springer New York, 1997. http://dx.doi.org/10.1007/978-1-4612-0647-7_5.

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Switzer, Robert M. "Ordinary Homology Theory." In Algebraic Topology — Homotopy and Homology, 167–89. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-61923-6_11.

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Lang, Serge. "General Homology Theory." In Algebra, 761–834. New York, NY: Springer New York, 2002. http://dx.doi.org/10.1007/978-1-4613-0041-0_20.

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Conference papers on the topic "Homology theory"

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Ranicki, Andrew, and Masayuki Yamasaki. "Controlled L–theory." In Workshop on Exotic Homology Manifolds. Mathematical Sciences Publishers, 2006. http://dx.doi.org/10.2140/gtm.2006.9.105.

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Pedersen, Erik Kjær, and Masayuki Yamasaki. "Stability in controlled L–theory." In Workshop on Exotic Homology Manifolds. Mathematical Sciences Publishers, 2006. http://dx.doi.org/10.2140/gtm.2006.9.67.

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Witten, Edward. "Khovanov homology and gauge theory." In Low-dimensional manifolds and high-dimensional categories -- A conference in honor of Michael Hartley Freedman. Mathematical Sciences Publishers, 2012. http://dx.doi.org/10.2140/gtm.2012.18.291.

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Tamaki, Dai. "Twisting Segal's K-Homology Theory." In Proceedings of the Noncommutative Geometry and Physics 2008, on K-Theory and D-Branes & Proceedings of the RIMS Thematic Year 2010 on Perspectives in Deformation Quantization and Noncommutative Geometry. WORLD SCIENTIFIC, 2013. http://dx.doi.org/10.1142/9789814425018_0007.

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Bao, Jinri, Zicong Wang, Junli Wang, and Chungang Yan. "Persistent Homology Based Generative Adversarial Network." In 18th International Conference on Computer Vision Theory and Applications. SCITEPRESS - Science and Technology Publications, 2023. http://dx.doi.org/10.5220/0011648200003417.

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Fel'shtyn, Alexander. "Nielsen fixed point theory and symplectic Floer homology." In Fixed Point Theory and its Applications. Warsaw: Institute of Mathematics Polish Academy of Sciences, 2007. http://dx.doi.org/10.4064/bc77-0-7.

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EKHOLM, TOBIAS. "KNOT CONTACT HOMOLOGY AND OPEN GROMOV–WITTEN THEORY." In International Congress of Mathematicians 2018. WORLD SCIENTIFIC, 2019. http://dx.doi.org/10.1142/9789813272880_0088.

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Bouchaffra, Djamel, Assia Baouta, Faycal Ykhlef, Meriem Khelladi, and Jun Tan. "Land Cover Change Detection based on Homology Theory." In 2019 6th International Conference on Image and Signal Processing and their Applications (ISPA). IEEE, 2019. http://dx.doi.org/10.1109/ispa48434.2019.8966911.

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Kashiwa, Kouji, Takenori Hirakida, and Hiroaki Kouno. "Persistent homology analysis for QCD effective models." In The 38th International Symposium on Lattice Field Theory. Trieste, Italy: Sissa Medialab, 2022. http://dx.doi.org/10.22323/1.396.0346.

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Goerss, Paul G. "Realizing families of Landweber exact homology theories." In New topological contexts for Galois theory and algebraic geometry. Mathematical Sciences Publishers, 2009. http://dx.doi.org/10.2140/gtm.2009.16.49.

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Reports on the topic "Homology theory"

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Hengartner, Michael O. Identification and Characterization of Novel Nematode Cell Death Genes and Their Mammalian Homologs. Fort Belvoir, VA: Defense Technical Information Center, August 2000. http://dx.doi.org/10.21236/ada398562.

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Hengartner, Michael. Identification and Characterization of Novel Nematode Cell Death Genes and Their Mammalian Homologs. Fort Belvoir, VA: Defense Technical Information Center, July 1998. http://dx.doi.org/10.21236/ada360212.

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Applebaum, Shalom W., Lawrence I. Gilbert, and Daniel Segal. Biochemical and Molecular Analysis of Juvenile Hormone Synthesis and its Regulation in the Mediterranean Fruit Fly (Ceratitis capitata). United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7570564.bard.

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Original Objectives and revisions: (1) "To determine the biosynthetic pathway of JHB3 in the adult C. capitata CA in order to establish parameters for the future choice and synthesis of suitable inhibitors". Modified: to determine the pattern of FR-7 biosynthesis during normal reproductive maturation, and identify enzymes potentially involved in its synthesis. (2) "To correlate allatal epoxidase activity to the biosynthesis of JHB3 at different stages of reproductive maturation/vitellogenesis and evaluate the hypothesis that a specific JH-epoxidase may be rate limiting". Modified: to study the effects of epoxidase inhibitors on the pattern of allatal JH biosynthesis in vitro and on female reproduction in vive. (3) "To probe and clone the gene homologous to ap from C. capitata, determine its exon-intron organization, sequence it and demonstrate its spatial and temporal expression in larvae, pupae and adults." The "Medfly" (Ceratitis capitata) is a serious polyphagous fruit pest, widely distributed in subtropical regions. Damage is caused by oviposition and subsequent development of larvae. JH's are dominant gonadotropic factors in insects. In the higher Diptera, to which the Medfly belongs, JHB3 is a major homolog. It comprises 95% of the total JH produced in vitro in D. melanogaster, with JH-III found as a minor component. The biosynthesis of both JH-III and JHB3 is dependent on epoxidation of double bonds in the JH molecule. The specificity of such epoxidases is unknown. The male accessory gland D. melanogaster produces a Sex Peptide, transferred to the female during copulation. SP reduces female receptivity while activating specific JH biosynthesis in vitro and inducing oviposition in vive. It also reduces pheromone production and activates CA of the moth Helicoverpa armigera. In a previous study, mutants of the apterous (ap) gene of D. melanogaster were analyzed. This gene induces previteilogenic arrest which can be rescued by external application of JH. Considerable progress has been made in recombinant DNA technology of the Medfly. When fully operative, it might be possible to effectively transfer D. melanogaster endocrine gene-lesions into the Medfly as a strategy for their genetic control. A marked heterogeneity in the pattern of JH homologs produced by Medfly CA was observed. Contrary to the anticipated biosynthesis of JHB;, significant amounts of an unknown JH-like compound, of unknown structure and provisionally termed FR-7, were produced, in addition to significant amounts of JH-III and JHB3. Inhibitors of monooxygenases, devised for their effects on ecdysteroid biosynthesis, affect Medfly JH biosynthesis but do not reduce egg deposition. FR-7 was isolated from incubation media of Medfly CA and examined by various MS procedures, but its structure is not yet resolved. MS analysis is being done in collaboration with Professor R.R.W. Rickards of the Australian National University in Canberra, Australia. A homologue of the ap gene of D. melanogaster exists in the Medfly. LIM domains and the homeo-domain, important for the function of the D. melanogaster ap gene, are conserved here too. Attempts to clone the complete gene were unsuccessful. Due to the complexity of JH homologs, presence of related FR-7 in the biosynthetic products of Medfly CA and lack of reduction in eggs deposited in the presence of monooxygenase inhibitors, inhibition of epoxidases is not a feasible alternative to control Medfly reproduction, and raises questions which cannot be resolved within the current dogma of hormonal control of reproduction in Diptera. The Medfly ap gene has similar domains to the D. melanogaster ap gene. Although mutant ap genes are involved in JH deficiency, ap is a questionable candidate for an endocrine lesion, especially since the D. melanogoster gene functions is a transcription factor.
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Nechushtai, Rachel, and Parag Chitnis. Role of the HSP70 Homologue from Chloroplasts in the Assembly of the Photosynthetic Apparatus. United States Department of Agriculture, July 1993. http://dx.doi.org/10.32747/1993.7568743.bard.

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The major goal of the proposed research was to study the role of a 70-kDa heat shock cognate protein from chloroplasts (ct-HSP70) in the assembly of chlorophyll-protein complexes. The latters are mostly important in allowing photosynthesis to occur. Photosynthesis is at the heart of crop productivity and the knowledge of the biogenesis of the photosynthetic apparatus is essential to manipulate the efficiency of photosynthesis. The characterization of the function of the ct-HSP70 was planned to be studied in vitro by assaying its capability to physically interact with the thylakoid proteins and to assist their assembly into thylakoid membranes. We planned to identify regions in the light-harvesting complex protein (LHCP) that interact with the ct-HSP70 and characterize the interaction between them. We also intended to isolate cDNA clones encoding ct-HSP70, sequence them, express one of them in E. coli and use the purified protein for functional assays. The research in this BARD proposal aimed at providing insights and aid in understanding the mechanism by which plants may respond to the heat stress. Since plants often experience increased temperatures.
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5

Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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Arazi, Tzahi, Vivian Irish, and Asaph Aharoni. Micro RNA Targeted Transcription Factors for Fruit Quality Improvement. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7592651.bard.

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Fruits are unique to flowering plants and represent an important component of human and animal diets. Development and maturation of tomato fruit is a well-programmed process, and yet, only a limited number of factors involved in its regulation have been characterized. Micro-RNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in animals and plants. Plant miRNAs have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators, especially transcription factors. Recently, we and others have demonstrated that miRNAs and other type of small RNAs are expressed in tomato fruit, and target putative transcription factors during its development and maturation. The original objectives of the approved proposal were: 1. To identify fruit miRNA transcription factor target genes through a bioinformatic approach. 2. To identify fruit miRNA transcription factor target genes up-regulated in tomato Dicer-like 1 silenced fruit. 3. To establish the biological functions of selected transcription factors and examine their utility for improving fleshy fruit quality trait. This project was approved by BARD as a feasibility study to allow initial experiments to peruse objective 2 as described above in order to provide initial evidence that miRNAs do play a role in fruit development. The approach planned to achieve objective 2, namely to identify miRNA transcription factor targets was to clone and silence the expression of a tomato DCL1 homolog in different stages of fruit development and examine alterations to gene expression in such a fruit in order to identify pathways and target genes that are regulated by miRNA via DCL1. In parallel, we characterized two transcription factors that are regulated by miRNAs in the fruit. We report here on the cloning of tomato DCL1 homolog, characterization of its expression in fruit flesh and peel of wild type and ripening mutants and generation of transgenic plants that silence SlDCL1 specifically in the fruit. Our results suggest that the tomato homolog of DCL1, which is the major plant enzyme involved in miRNA biogenesis, is present in fruit flesh and peel and differentially expressed during various stages of fruit development. In addition, its expression is altered in ripening mutants. We also report on the cloning and expression analysis of Sl_SBP and Sl_ARF transcription factors, which serve as targets of miR157 and miR160, respectively. Our data suggest that Sl_SBP levels are highest during fruit ripening supporting a role for this gene in that process. On the other hand Sl_ARF is strongly expressed in green fruit up to breaker indicating a role for that gene at preripening stage which is consistent with preliminary in_situ analyses that suggest expression in ovules of immature green fruit. The results of this feasibility study together with our previous results that miRNAs are expressed in the fruit indeed provide initial evidence that these regulators and their targets play roles in fruit development and ripening. These genes are expected to provide novel means for genetic improvement of tomato fleshy fruit.
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7

Lee, Richard, Moshe Bar-Joseph, K. S. Derrick, Aliza Vardi, Roland Brlansky, Yuval Eshdat, and Charles Powell. Production of Antibodies to Citrus Tristeza Virus in Transgenic Citrus. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7613018.bard.

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Citrus tristeza virus (CTV) is the most important virus disease of citrus in the world. CTV causes death of trees on sour orange rootstock and/or stem pitting of scions regardless of rootstock which results in trees of low vigor, reduced yield with reduction in size and quality of fruit. The purpose of this project was to produce monoclonal antibodies (MABs) to CTV coat protein (CP), develop single domain antibodies (dAbs) or Fab fragments which neutralize the infection by binding to the virus, and to produce transformed plants which express the dAbs. The objectives of this research have been met and putative transgenic tobacco and citrus plants have been developed. These putative transgenic plants are presently undergoing evaluation to determine the level of dAbs expression and to determine their resistance to CTV. Additionally, the CTV genome has been sequenced and the CP gene of several biologically characterized CTV strains molecular characterized. This has indicated a correlation between CP sequence homology and biological activity, and the finding of DI RNAs associated with some CTV strains. Several MABs have been produced which enable broad spectrum identification of CTV strains while other MABs enable differentiation between mild and severe strains. The use of selected MAbs and determination of the CP gene sequence has enabled predictions of biological activities of unknown CTV isolates. The epitopes of two MABs, one reacting selectively with severe CTV strains and the other reacting with all strains, have been characterized at the molecular level.
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8

Sadot, Einat, Christopher Staiger, and Zvi Kam Weizmann. functional genomic screen for new plant cytoskeletal proteins and the determination of their role in actin mediated functions and guard cells regulation. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7587725.bard.

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The original objectives of the approved proposal were: 1. To construct a YFP fused Arabidopsis cDNA library in a mammalian expression vector. 2. To infect the library into a host fibroblast cell line and to screen for new cytoskeletal associated proteins using an automated microscope. 3. Isolate the new genes. 4. Characterize their role in plants. The project was approved as a feasibility study to allow proof of concept that would entail building the YFP library and picking up a couple of positive clones using the fluorescent screen. We report here on the construction of the YFP library, the development of the automatic microscope, the establishment of the screen and the isolation of positive clones that are plant cDNAs encoding cytoskeleton associated proteins. The rational underling a screen of plant library in fibroblasts is based on the high conservation of the cytoskeleton building blocks, actin and tubulin, between the two kingdoms (80-90% homology at the level of amino acids sequence). In addition, several publications demonstrated the recognition of mammalian cytoskeleton by plant cytoskeletal binding proteins and vice versa. The major achievements described here are: 1. The development of an automated microscope equipped with fast laser auto-focusing for high magnification and a software controlling 6 dimensions; X, Y position, auto focus, time, color, and the distribution and density of the fields acquired. This system is essential for the high throughput screen. 2. The construction of an extremely competent YFP library efficiently cloned (tens of thousands of clones collected, no empty vectors detected) with all inserts oriented 5't03'. These parameters render it well representative of the whole transcriptome and efficient in "in-frame" fusion to YFP. 3. The strategy developed for the screen allowing the isolation of individual positive cDNA clones following three rounds of microscopic scans. The major conclusion accomplished from the work described here is that the concept of using mammalian host cells for fishing new plant cytoskeletal proteins is feasible and that screening system developed is complete for addressing one of the major bottlenecks of the plant cytoskeleton field: the need for high throughput identification of functionally active cytoskeletal proteins. The new identified plant cytoskeletal proteins isolated in the pilot screen and additional new proteins which will be isolated in a comprehensive screen will shed light on cytoskeletal mediated processes playing a major role in cellular activities such as cell division, morphogenesis, and functioning such as chloroplast positioning, pollen tube and root hair elongation and the movement of guard cells. Therefore, in the long run the screen described here has clear agricultural implications.
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9

Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.

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Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
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10

Coplin, David, Isaac Barash, and Shulamit Manulis. Role of Proteins Secreted by the Hrp-Pathways of Erwinia stewartii and E. herbicola pv. gypsophilae in Eliciting Water-Soaking Symptoms and Initiating Galls. United States Department of Agriculture, June 2001. http://dx.doi.org/10.32747/2001.7580675.bard.

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Many bacterial pathogens of plants can inject pathogenicity proteins into host cells using a specialized type III secretion system encoded by hrpgenes. This system deliver effector proteins, into plant cells that function in both susceptible and resistant interactions. We have found that the virulence of Erwinia stewartii(Es; syn. Pantoea stewartii) and Erwinia herbicola pv. gypsophilae (Ehg, syn. Pantoea agglomerans), which cause Stewart's wilt of corn and galls on Gypsophila, respectively, depends on hrpgenes. The major objectives of this project were: To increase expression of hrpgenes in order to identify secreted proteins; to identify genes for proteins secreted by the type-III systems and determine if they are required for pathogenicity; and to determine if the secreted proteins can function within eukaryotic cells. We found that transcription of the hrp and effector genes in Es and Ehg is controlled by at least four genes that constitute a regulatory cascade. Environmental and/or physiological signaling appears to be mediated by the HrpX/HrpY two component system, with HrpX functioning as a sensor-kinase and HrpY as a response regulator. HrpYupregulateshrpS, which encodes a transcriptional enhancer. HrpS then activates hrpL, which encodes an alternate sigma factor that recognizes "hrp boxes". All of the regulatory genes are essential for pathogenicity, except HrpX, which appears only to be required for induction of the HR in tobacco by Es. In elucidating this regulatory pathway in both species, we made a number of significant new discoveries. HrpX is unusual for a sensor-kinase because it is cytoplasmic and contains PAS domains, which may sense the redox state of the bacterium. In Es, a novel methyl-accepting protein may function upstream of hrpY and repress hrp gene expression in planta. The esaIR quorum sensing system in Es represses hrp gene expression in Es in response to cell-density. We have discovered six new type III effector proteins in these species, one of which (DspE in Ehg and WtsE in Es) is common to both pathogens. In addition, Es wtsG, which is a homolog of an avrPpiB from P. syringae pv. pisi, and an Ehg ORF, which is a homolog of P. syringae pv. phaseolicola AvrPphD, were both demonstrated to encode virulence proteins. Two plasmidborne, Ehg Hop proteins, HsvG and PthG, are required for infection of gypsophilia, but interestingly, PthG also acts as an Avr elicitor in beets. Using a calmodulin-dependent adenylate cyclase (cyaA) reporter gene, we were successful in demonstrating that an HsvG-CyaA fusion protein can be transferred into human HeLa cells by the type-III system of enteropathogenic E. coli. This is a highly significant accomplishment because it is the first direct demonstration that an effector protein from a plant pathogenic bacterium is capable of being translocated into a eukaryotic cell by a type-III secretion system. Ehg is considered a limiting factor in Gypsophila production in Israel and Stewart’s Wilt is a serious disease in the Eastern and North Central USA, especially on sweet corn in epidemic years. We believe that our basic research on the characterization of type III virulence effectors should enable future identification of their receptors in plant cells. This may lead to novel approaches for genetically engineering resistant plants by modifying their receptors or inactivating effectors and thus blocking the induction of the susceptible response. Alternatively, hrp gene regulation might also provide a target for plant produced compounds that interfere with recognition of the host by the pathogen. Such strategies would be broadly applicable to a wide range of serious bacterial diseases on many crops throughout the USA and Israel.
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