Готові списки джерел за темами / Clone search

Добірка наукової літератури з теми "Clone search"

Автор: Grafiati

Опубліковано: 8 червня 2024

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Статті в журналах з теми "Clone search":

Hammad, Muhammad, Onder Babur, Hamid Abdul Basit, and Mark Van Den Brand. "Clone-Seeker: Effective Code Clone Search Using Annotations." IEEE Access 10 (2022): 11696–713. http://dx.doi.org/10.1109/access.2022.3145686.

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Farhadi, Mohammad Reza, Benjamin C. M. Fung, Yin Bun Fung, Philippe Charland, Stere Preda, and Mourad Debbabi. "Scalable code clone search for malware analysis." Digital Investigation 15 (December 2015): 46–60. http://dx.doi.org/10.1016/j.diin.2015.06.001.

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ZHANG, YU, XUMING CHEN, LIHUA WU, ZIQIANG LUO, and XIAOJIE LIU. "MHC-INSPIRED ANTIBODY CLONE ALGORITHM." International Journal of Computational Methods 07, no. 02 (June 2010): 299–318. http://dx.doi.org/10.1142/s0219876210002179.

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For solving complex optimization problems in some engineering applications, intelligent optimization algorithms based on biological mechanisms have better performance than traditional optimization algorithms. Most of these intelligent algorithms, however, have disadvantages in population diversity and preservation of elitist antibody genes, which lead to the degenerative phenomenon, the zigzag phenomenon, poor global optimization, and low convergence speed. Drawing inspiration from the features of major histocompatibility complex (MHC) in the biological immune system, we propose a novel MHC-inspired antibody clone algorithm (ACAMHC) for solving the above problems. ACAMHC preserves elitist antibody genes through the MHC strings that emulate the MHC haplotype in order to improve its local search capability; it improves the antibody population diversity by gene mutation that mimick the MHC polymorphism to enhance its global search capability. To expand the antibody search space, ACAMHC will add some new random immigrant antibodies with a certain ratio. The convergence of ACAMHC is theoretically proven. The experiments of ACAMHC compared with the canonical clone selection algorithm (CLONALG) on 20 benchmark functions are carried out. The experimental results indicate that the performance of ACAMHC is better than that of CLONALG. The ACAMHC algorithm provides new opportunities for solving previously intractable optimization problems.

Zhang, Yu, Li Hua Wu, and Zi Qiang Luo. "Catastrophe-Based Antibody Clone Algorithm." Applied Mechanics and Materials 121-126 (October 2011): 4415–20. http://dx.doi.org/10.4028/www.scientific.net/amm.121-126.4415.

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In solving complex optimization problems, intelligent optimization algorithms such as immune algorithm show better advantages than traditional optimization algorithms. Most of these immune algorithms, however, have disadvantages in population diversity and preservation of elitist antibodies genes, which will lead to the degenerative phenomenon, the zigzag phenomenon, poor global optimization, and low convergence speed. By introducing the catastrophe factor into the ACAMHC algorithm, we propose a novel catastrophe-based antibody clone algorithm (CACA) to solve the above problems. CACA preserves elitist antibody genes through the vaccine library to improve its local search capability; it improves the antibody population diversity by gene mutation that mimics the catastrophe events to the natural world to enhance its global search capability. To expand the antibody search space, CACA will add some new random immigrant antibodies with a certain ratio. The convergence of CACA is theoretically proved. The experiments of CACA compared with the clone selection algorithm (ACAMHC) on some benchmark functions are carried out. The experimental results indicate that the performance of CACA is better than that of ACAMHC. The CACA algorithm provides new opportunities for solving previously intractable optimization problems.

Keivanloo, Iman, Chanchal K. Roy, and Juergen Rilling. "SeByte: Scalable clone and similarity search for bytecode." Science of Computer Programming 95 (December 2014): 426–44. http://dx.doi.org/10.1016/j.scico.2013.10.006.

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Tan, Yan Song. "An Improved Immune Clone Algorithm Logistics Delivery Strategy." Journal of Advanced Computational Intelligence and Intelligent Informatics 23, no. 2 (March 20, 2019): 309–12. http://dx.doi.org/10.20965/jaciii.2019.p0309.

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Logistics routing problem is a typical NP hard problem, which is very difficult to solve accurately. On the basis of establishing logistics path optimization model, an immune clone algorithm is proposed. To improve the accuracy of search algorithms, the clonal selection and high frequency variations in the immune algorithm method are introduced. Then the antibody encoding virtual distribution point algorithm is designed to improve search efficiency. The benchmark problem of logistics delivery path optimization is simulated and analyzed. Experimental results show that the proposed immune cloning algorithm expands the range of population search and it have obvious advantages in solving large-scale complex physical distribution optimization problems. Also, the proposed algorithm can solve the optimal distribution of logistics effectively.

Park, Jin-woo, Mu-Woong Lee, Jong-Won Roh, Seung-won Hwang, and Sunghun Kim. "Surfacing code in the dark: an instant clone search approach." Knowledge and Information Systems 41, no. 3 (August 3, 2013): 727–59. http://dx.doi.org/10.1007/s10115-013-0677-z.

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Nishi, Manziba Akanda, and Kostadin Damevski. "Scalable code clone detection and search based on adaptive prefix filtering." Journal of Systems and Software 137 (March 2018): 130–42. http://dx.doi.org/10.1016/j.jss.2017.11.039.

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Ragkhitwetsagul, Chaiyong, and Jens Krinke. "Siamese: scalable and incremental code clone search via multiple code representations." Empirical Software Engineering 24, no. 4 (March 5, 2019): 2236–84. http://dx.doi.org/10.1007/s10664-019-09697-7.

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EL-MATBOULI, M., and H. SOLIMAN. "Construction and screening of a cDNA library from the triactinomyxon spores ofMyxobolus cerebralis, the causative agent of salmonid Whirling Diseases." Parasitology 132, no. 4 (January 3, 2006): 467–77. http://dx.doi.org/10.1017/s0031182005009522.

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The ZAP Express cDNA library was constructed using mRNA extracted from the triactinomyxon spores ofMyxobolus cerebralis. First-strand cDNA was synthesized using Moloney Murine leukaemia virus reverse transcriptase. Following second-strand cDNA synthesis, the double-stranded cDNA was digested withXhoI restriction enzyme, cDNA fragments less than 400 bp were removed and the remaining cDNA was ligated with the lambda ZAP Express vector. The recombinants were packagedin vitrousing Gigapack III gold packaging extract. The primary cDNA library titre contained 0·5×106clones, with 97% recombinant and only 3% non-recombinant clones. The cDNA library was then screened using the anti-triactinomyxon antibodies. Positive clones were selected and re-screened twice more to give a final selection of 526 clones. One clone (46-5) was selected randomly and subjected toin vivo excision of the pBK-CMV phagemid from the ZAP express vector. The sequence of the entire clone was obtained using rapid amplification of the cDNA ends. A search of the clone sequence against GenBank revealed that it related to ribosomal protein L23 and it had a high percentage similarity to this protein from different species. A conserved domain for ribosomal protein L23 was also identified in the clone sequence.

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Дисертації з теми "Clone search":

Ragkhitwetsagul, Chaiyong. "Code similarity and clone search in large-scale source code data." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10057538/.

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Software development is tremendously benefited from the Internet by having online code corpora that enable instant sharing of source code and online developer's guides and documentation. Nowadays, duplicated code (i.e., code clones) not only exists within or across software projects but also between online code repositories and websites. We call them "online code clones."' They can lead to license violations, bug propagation, and re-use of outdated code similar to classic code clones between software systems. Unfortunately, they are difficult to locate and fix since the search space in online code corpora is large and no longer confined to a local repository. This thesis presents a combined study of code similarity and online code clones. We empirically show that many code snippets on Stack Overflow are cloned from open source projects. Several of them become outdated or violate their original license and are possibly harmful to reuse. To develop a solution for finding online code clones, we study various code similarity techniques to gain insights into their strengths and weaknesses. A framework, called OCD, for evaluating code similarity and clone search tools is introduced and used to compare 34 state-of-the-art techniques on pervasively modified code and boiler-plate code. We also found that clone detection techniques can be enhanced by compilation and decompilation. Using the knowledge from the comparison of code similarity analysers, we create and evaluate Siamese, a scalable token-based clone search technique via multiple code representations. Our evaluation shows that Siamese scales to large-scale source code data of 365 million lines of code and offers high search precision and recall. Its clone search precision is comparable to seven state-of-the-art clone detection tools on the OCD framework. Finally, we demonstrate the usefulness of Siamese by applying the tool to find online code clones, automatically analyse clone licenses, and recommend tests for reuse.

Simões, Manuel Areias Sobrinho. "In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib." Doctoral thesis, Faculdade de Medicina da Universidade do Porto, 2010. http://hdl.handle.net/10216/56734.

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Simões, Manuel Areias Sobrinho. "In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib." Tese, Faculdade de Medicina da Universidade do Porto, 2010. http://hdl.handle.net/10216/56734.

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Saffer, R. A., and J. Liebert. "Search for Close Binary Evolved Stars." Steward Observatory, The University of Arizona (Tucson, Arizona), 1988. http://hdl.handle.net/10150/623897.

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We report on a search for short -period binary systems composed of pairs of evolved stars. The search is being carried out concurrently with a program to characterize the kinematical properties of two different samples of stars. Each sample has produced one close binary candidate for which further spectroscopic observations are planned. We also recapitulate the discovery of a close detached binary system composed of two cool DA white dwarfs, and we discuss the null results of Ha observations of the suspected white dwarf /brown dwarf system G 29-38.

Benoit, Tristan. "Cartographie des programmes et de leurs interrelations." Electronic Thesis or Diss., Université de Lorraine, 2023. http://www.theses.fr/2023LORR0320.

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Dans le domaine du génie logiciel, assurer la qualité et la sûreté des logiciels est complexe. Ce contexte est dû à un ensemble de facteurs, notamment l'utilisation croissante de bibliothèques et le recours à des pratiques comme la copie de codes à partir de services en ligne. Une réponse courante à cette problématique est l'application de méthodes formelles de validation des programmes avant leur diffusion. Cette approche, cependant, requiert une compréhension précise des enjeux à vérifier et un haut degré d'expertise. Cette thèse introduit des méthodes innovantes de rétro-ingénierie pour collecter automatiquement des informations sur l'origine d'un programme et pour identifier des clones de programmes au sein de larges jeux de données. Notre première contribution est le nouveau modèle de réseau de neurones Site Neural Network (SNN) qui prédit la chaîne de compilation utilisée pour produire un programme entier. SNN offre une grande rapidité ainsi qu'une bonne précision. Sa modularité grâce à l'utilisation de hiérarchies de classificateurs permet de considérer facilement des chaînes de compilation supplémentaires. Notre seconde contribution est Program Spectral Similarity (PSS), un outil qui fournit un moyen rapide et efficace de détecter des clones de programmes, même quand leur architecture matérielle visée diffère ou en cas d'offuscation. Contrairement aux méthodes basées sur les fonctions binaires ou sur la distance d'édition des graphes, qui sont chronophages et peu robustes, PSS s'appuie sur l'analyse spectrale de graphes pour mesurer la similarité entre programmes. Cette thèse participe ainsi à renforcer la sécurité des systèmes en mettant à disposition des outils pour identifier rapidement les clones de programmes malveillants. En outre, elle apporte un soutien à l'investigation numérique en donnant des informations pertinentes sur la chaîne de compilation. Ce travail ouvre la voie à de nouveaux réseaux de neurones spécialisés pour les programmes, ainsi qu'au développement de méthodes d'analyse spectrale pour l'étude de la similarité des codes binaires
In the field of software engineering, ensuring the quality and security of software is complex. This context is due to a set of factors, notably the increasing use of libraries and the use of practices such as copying codes from online services. The usual solution to this problem is the application of formal methods for program validation before their release. However, this approach requires a precise specification and a high degree of expertise. This thesis introduces new reverse engineering methods to automatically collect information about a program toolchain provenance and identify program clones within large data repositories. Our first contribution is the innovative neural network model Site Neural Network (SNN), which predicts the compilation toolchain used to produce an entire program. SNN offers excellent speed as well as good accuracy. Its modularity due to the use of hierarchies of classifiers allows for easy consideration of additional toolchains. Our second contribution is the Program Spectral Similarity (PSS), a tool that provides a quick and efficient way to detect program clones, even when their target hardware architecture differs or in the case of obfuscation. Unlike binary function-based methods or graph edit distance methods, which are time-consuming and low resilient, PSS relies on the spectral analysis of graphs to measure the similarity between programs. This thesis thus contributes to cyber security by providing tools to identify malware clones quickly. In addition, it supports computer forensics by providing relevant information on the compilation chain. This work paves the way for new neural networks for programs, as well as the development of spectral graph analysis methods for studying binary code similarity

Cowperthwaite, P. S., E. Berger, M. Soares-Santos, J. Annis, D. Brout, D. A. Brown, E. Buckley-Geer, et al. "A DECAM SEARCH FOR AN OPTICAL COUNTERPART TO THE LIGO GRAVITATIONAL-WAVE EVENT GW151226." IOP PUBLISHING LTD, 2016. http://hdl.handle.net/10150/621399.

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We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg(2) of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2-24 days after the GW detection. We achieve 5 sigma point-source limiting magnitudes of i approximate to 21.7 and z approximate to 21.5, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with greater than or similar to 3 sigma significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of i - z approximate to 0.3 mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.

Soares-Santos, M., R. Kessler, E. Berger, J. Annis, D. Brout, E. Buckley-Geer, H. Chen, et al. "A DARK ENERGY CAMERA SEARCH FOR AN OPTICAL COUNTERPART TO THE FIRST ADVANCED LIGO GRAVITATIONAL WAVE EVENT GW150914." IOP PUBLISHING LTD, 2016. http://hdl.handle.net/10150/621228.

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We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg(2) area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4-5, 7, and 24 days after the trigger. The median 5 sigma point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg(2), corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4-5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i - z) = 1, 0, - 1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

Alsahafy, Maram Saad M. "Efficient Algorithms for Speeding Up Graph Data Analytics." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/26166.

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Graph model has been playing an important role in analyzing the data from real applications such as social networks, communication networks, and information networks. It models entities of the applications as vertices/nodes in the graph, and models relationships among the entities as edges between vertices in the graph. In recent years there has been an increasing number of studies of complex graph analysis coinciding with the rapid development of information technologies, such as online social networks and (mobile/email) communication networks. Due to the growing sizes of these graph data, traditional algorithms and tools are not capable of carrying out the desired operations on the growing amount of data. Motivated by this, we in this thesis investigate three representation problems in graph data analytics, and propose efficient algorithms for these problems. Firstly, we study the problem of community detection in undirected graphs. Community, as one important characteristic of real-world graphs, is relevant to a variety of problems, e.g., community detection, clustering and community search. How can communities of real networks be extracted within reasonable execution time and with high accuracy? Unlike existing community detection algorithms, which suffer from resolution limits or long execution times, the recently proposed interaction model based on distance dynamics has a logic view that simulates the interaction among vertices over time and leads to the discovery of qualified communities. However, the state-of-the-art algorithm Attractor for distance dynamics does not scale to large graphs, especially those with large maximum vertex degrees. In this thesis, we aim to scale distance dynamics to large graphs. To achieve that, we propose a fast distance dynamics algorithm FDD. We show that FDD has a worst-case time complexity of O(T · γ · m), where T is the number of iterations until convergence, γ is a small constant, and m is the number of edges in the input graph. Thus, the time complexity of FDD does not depend on the maximum vertex degree. Moreover, we also propose three optimization techniques to alleviate the dependency on T: active-edge queue, transitivity, and distance computation. Extensive empirical studies on large real graphs demonstrated the efficiency and effectiveness of FDD. Secondly, we study the problem of community search over directed graphs. We aim to identify a directed community such that it contains a set Q of query vertices and its members are frequently interacting with each other. The existing models for community search over directed graphs have some drawbacks. For example, the D-core-based model returns a sparse graph and requires end-users to provide two sensitive input parameters that are hard to specify in practice. We formulate a novel measure of cohesiveness for directed graph, called minimum interaction degree (ID), based on which we then define the notion of ID-core. Using the ID-core model, we formulate an ID-core-based community search problem and ID-core-based closest community search problem for directed graphs. We also design three algorithms namely, index-free algorithm, index-based algorithm and closest community search algorithm to solve the problems efficiently. While index-free algorithm incur reasonable time costs in answering a query, our index-based algorithm can answer a query efficiently in optimal time complexity with regard to the community size. On the other hand, the closest community search algorithm guarantees the best quality in an efficient time. Extensive empirical studies on large real directed graphs demonstrated the efficiency and the effectiveness of our models and our algorithms. Lastly, we study the problem of computing a maximum independent set on a large graph which is a key topic in the field of graph analytics and algorithms. Kernelization is a technique for developing exact and approximate maximum independent set algorithms by applying reduction rules on the graph until a smaller graph (kernel) is obtained to which no rule can be applied. While exact algorithms produce a small kernel by slow kernelization, heuristic algorithms yield a large kernel by fast kernelization. To achieve a small kernel using fast kernelization, we propose a novel method that produces a small kernel with high quality independent sets by partitioning the graph and applying simple and advanced reduction rules incrementally, using four techniques that accelerate the kernelization process. We then apply an efficient maximum clique computation algorithm on the complementary kernel to collect the remaining independent set. Empirical studies verify that, in real datasets, our two-step method can generate a maximum, or near-maximum, independent set. Our method, compared with the existing algorithms for the best-known produced kernels (VCSolver (Akiba and Iwata 2016) and ParFastKer (Hespe et al. 2018)), can achieve smaller kernels than ParFastKer with a similar kernelization processing speed, and achieve faster kernelization than VCSolver with a similar kernels.

Holland, David Charles. "The behaviour of resin bonded rock bolts and other anchorages subjected to close proximity blasting." Thesis, University of Aberdeen, 1993. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU603184.

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The provision of a safe and economic rock support system is of primary importance for any excavation programme. If the excavation is to be developed by explosives, then the effect of blast forces on the performance of the rock support system must be considered. A review of current literature has highlighted a general lack of information regarding rock anchorage performance under blast loading. With this in mind, a full scale field test programme was undertaken to study the effect of close proximity blasting on resin bonded rock bolts, during the construction of the Pen y Clip Tunnel in North Wales together with a re-analysis of data from a previous study at the nearby Penmaenbach Tunnel. In both cases, accelerometers were used to monitor vibration and hydraulic load cells recorded the changes in rock bolt load during production face blasting. For the Pen y Clip trials, an additional monitoring system was developed which incorporated load cells positioned along the length of specially made experimental rock bolts. Further trials were conducted at an Edinburgh City Centre site to assess the likelihood of damage to temporary, cement grouted rock anchorages whose fixed anchors were positioned as close as 5m from nearby tunnel blasting. These trials involved the measurement of vibrations, both on the anchor head and down specially constructed boreholes, together with lift off load testing. Analysis consisted of the time and frequency domain examination of the signals, recorded on FM magnetic tape, from the three sets of field trials. Resin bonded rock bolts installed in microdiorite and rhyolite were found to be highly resilient to blasting, even those positioned down to lm from full face tunnel blasting. Temporary anchorages in mudstone were more susceptible to blasting but damage could be limited by monitoring of vibrations and careful control of blast parameters. The frequency response of the anchor head was found to be dependent on the characteristics of the anchorage and the nature of the environment in which it was installed. This raises the possibility that the analysis of spectral responses could form the basis of a technique for the non destructive testing of rock anchorages.

Stock, Stephan Amir [Verfasser], and Sabine [Akademischer Betreuer] Reffert. "Analysis of High-Precision Spectroscopic Data in Search of Exoplanet Signals Close to the Stellar Noise Limit / Stephan Amir Stock ; Betreuer: Sabine Reffert." Heidelberg : Universitätsbibliothek Heidelberg, 2021. http://d-nb.info/123415210X/34.

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Книги з теми "Clone search":

Thibodeau, Beverly Anne. The search for relationships between respiration and growth in hybrid Populus clones. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Long, David. Pirates magnified: See history up close on this search-and-find adventure. New York, NY: Wide Eyed Editions, 2017.

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Fernandes, Sujatha. Close to the edge: In search of the global hip hop generation. London: Verso, 2011.

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Bolen, Jean Shinoda. Close to the bone: Life-threatening illness and the search for meaning. New York: Scribner, 1996.

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Stankiewicz, W. J. In search of a political philosophy: Ideologies at the close of the twentieth century. London: Routledge, 1993.

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Waern, Annika, and Anders Sundnes Løvlie. Hybrid Museum Experiences. Nieuwe Prinsengracht 89 1018 VR Amsterdam Nederland: Amsterdam University Press, 2022. http://dx.doi.org/10.5117/9789463726443.

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"So you're the one getting this gift? Lucky you! Someone who knows you has visited the museum. They searched out things they thought you would care about, and they took photos and left messages for you." This is the welcoming message for the Gift app, designed to create a very personal museum visit. Hybrid Museum Experiences use new technologies to augment, expand or alter the physical experience of visiting the museum. They are designed to be experienced in close relation to the physical space and exhibit. In this book we discuss three forms of hybridity in museum experiences: Incorporating the digital and the physical, creating social, yet personal and intimate experiences, and exploring ways to balance visitor participation and museum curation. This book reports on a 3-year cross-disciplinary research project in which artists, design researchers and museum professionals have collaborated to create technology-mediated experiences that merge with the museum environment.

Bolen, Jean Shinoda. Close to the Bone: Life Threatening Illness and the Search for Meaning. Scribner, 1998.

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Close to the Bone: Life-Threatening Illness and the Search for Meaning. Audio Literature, 1998.

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Manasse, Mark S. On the Efficient Determination of Most near Neighbors: Horseshoes, Hand Grenades, Web Search and Other Situations When Close Is Close Enough. Morgan & Claypool Publishers, 2012.

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Stankiewicz, W. J. In Search of a Political Philosophy: Ideologies at the Close of the Twentieth Century. Taylor & Francis Group, 2002.

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Частини книг з теми "Clone search":

Keivanloo, Iman, and Juergen Rilling. "Source Code Clone Search." In Code Clone Analysis, 121–34. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-1927-4_9.

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Ragkhitwetsagul, Chaiyong, Matheus Paixao, Manal Adham, Saheed Busari, Jens Krinke, and John H. Drake. "Searching for Configurations in Clone Evaluation – A Replication Study." In Search Based Software Engineering, 250–56. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-47106-8_20.

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Martens, Koen, Hugh D. Loxdale, and Isa Schön. "The Elusive Clone – In Search of Its True Nature and Identity." In Lost Sex, 187–200. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-90-481-2770-2_9.

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Mazeh, Tsevi, David W. Latham, Robert P. Stefanik, Guillermo Torres, and Eti Wasserman. "A Radial-Velocity Search for Brown Dwarfs and the Low-Mass Companion of HD114762." In Active Close Binaries, 267–76. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-0679-2_22.

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Consoli, Sergio, Domenico Perrotta, and Marco Turchi. "Reduced Variable Neighbourhood Search for the Generation of Controlled Circular Data." In Variable Neighborhood Search, 83–98. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69625-2_7.

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AbstractA number of artificial intelligence and machine learning problems need to be formulated within a directional space, where classical Euclidean geometry does not apply or needs to be readjusted into the circle. This is typical, for example, in computational linguistics and natural language processing, where language models based on Bag-of-Words, Vector Space, or Word Embedding, are largely used for tasks like document classification, information retrieval and recommendation systems, among others. In these contexts, for assessing document clustering and outliers detection applications, it is often necessary to generate data with directional properties and units that follow some model assumptions and possibly form close groups. In the following we propose a Reduced Variable Neighbourhood Search heuristic which is used to generate high-dimensional data controlled by the desired properties aimed at representing several real-world contexts. The whole problem is formulated as a non-linear continuous optimization problem, and it is shown that the proposed Reduced Variable Neighbourhood Search is able to generate high-dimensional solutions to the problem in short computational time. A comparison with the state-of-the-art local search routine used to address this problem shows the greater efficiency of the approach presented here.

Sun, Gao-Ji. "Knowledge-Guided Neighborhood Search Algorithm for Close-Open Vehicle Routing Problem." In Uncertainty and Operations Research, 157–63. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-5720-0_18.

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Mkrtichian, D., S. L. Kim, A. V. Kusakin, E. Rovithis-Livaniou, P. Rovithis, P. Lampens, P. van Cauteren, et al. "A Search for Pulsating, Mass-Accreting Components in Algol-Type Eclipsing Binaries." In Close Binaries in the 21st Century: New Opportunities and Challenges, 167–69. Dordrecht: Springer Netherlands, 2006. http://dx.doi.org/10.1007/978-1-4020-5027-5_41.

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Lantican, Gaudencia A. "Field Screening of Gamma-Irradiated Cavendish Bananas." In Efficient Screening Techniques to Identify Mutants with TR4 Resistance in Banana, 97–109. Berlin, Heidelberg: Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-64915-2_7.

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AbstractIn our search for Cavendish bananas to withstand Fusarium oxysporum f. sp. cubense (Foc TR4) and other diseases, field screening of tissue-cultured Grand Nain banana seedlings derived from gamma-irradiated shoot tips was explored. Six months after irradiation and multiplication in the laboratory, the plantlets (M1V6) were individually grown in seedling bags under screen house conditions for 8 weeks, side-by-side with non-irradiated plantlets of the same clone. Once acclimatized, the banana plants were grown in an area confirmed positive of Foc TR4 (based on previous farm records stating that more than 50% of the plant population succumbed to the disease). Seedlings from each treatment (dose of radiation) were divided into four replicates, regardless of the number of plants. Each plant was given a unique identification code for traceability during disease monitoring, bunch and fruit quality evaluation.Incidences of Foc TR4, Moko disease (Ralstonia solanacearum) and virus diseases were monitored weekly. Plants found positive of any disease were eradicated immediately. The plant population for the succeeding generation was managed by removing the unwanted suckers, 12 weeks from planting using a spade gouge and keeping only one sucker per plant for the next generation. Agronomic characters of each plant were taken at the flowering stage. These included age to flower, height, pseudostem circumference, number of leaves and height of the sucker. The bunch was harvested 12 weeks from flowering. The number of hands in a bunch, the number of fingers and weight of a hand were recorded. The same agronomic characters of the plant were taken for the succeeding generations.Plants left standing in the field without any disease symptoms 3 years after planting were considered as putative mutants and were selected as candidate lines for multiplication and second-generation field screening. Only healthy suckers (free from viruses) were further multiplied via tissue culture technique to reach M1V6. Clean suckers from each line free of soil debris or dirt were sent to the laboratory for multiplication. At least 1000 plantlets were produced from each line for the second-generation field screening. These were grown in two locations – with and without records of Foc TR4. Field monitoring activities including plant population management, disease incidence assessment and fruit quality evaluation were carried out following the same protocols used in the establishment of the first-generation plants. Lines with population showing ≤10% Foc TR4 after the first harvest, with good vigor, fruit quality and productivity were considered as candidates for further multiplication, farmers distribution and field planting under semi-commercial scale.

Abío, Ignasi, Morgan Deters, Robert Nieuwenhuis, and Peter J. Stuckey. "Reducing Chaos in SAT-Like Search: Finding Solutions Close to a Given One." In Theory and Applications of Satisfiability Testing - SAT 2011, 273–86. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21581-0_22.

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Ankali, Sanjay B., and Latha Parthiban. "Development of Porting Analyzer to Search Cross-Language Code Clones Using Levenshtein Distance." In Smart Computing Techniques and Applications, 623–32. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-0878-0_60.

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Тези доповідей конференцій з теми "Clone search":

Lee, Mu-Woong, Jong-Won Roh, Seung-won Hwang, and Sunghun Kim. "Instant code clone search." In the eighteenth ACM SIGSOFT international symposium. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1882291.1882317.

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Balachandran, Vipin. "Reducing accidental clones using instant clone search in automatic code review." In 2020 IEEE International Conference on Software Maintenance and Evolution (ICSME). IEEE, 2020. http://dx.doi.org/10.1109/icsme46990.2020.00089.

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Schwarz, Niko. "Hot clones: Combining search-driven development, clone management, and code provenance." In 2012 34th International Conference on Software Engineering (ICSE 2012). IEEE, 2012. http://dx.doi.org/10.1109/icse.2012.6227221.

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Schwarz, Niko. "Hot Clones: A Shotgun Marriage of Search-Driven Development and Clone Management." In 2012 16th European Conference on Software Maintenance and Reengineering (CSMR). IEEE, 2012. http://dx.doi.org/10.1109/csmr.2012.67.

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Benoit, Tristan, Jean-Yves Marion, and Sébastien Bardin. "Scalable Program Clone Search through Spectral Analysis." In ESEC/FSE '23: 31st ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering. New York, NY, USA: ACM, 2023. http://dx.doi.org/10.1145/3611643.3616279.

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Keivanloo, Iman, Christopher Forbes, and Juergen Rilling. "Similarity search plug-in: Clone detection meets internet-scale code search." In 2012 4th International Workshop on Search-driven Development: Users, Infrastructure, Tools, and Evaluation (SUITE). IEEE, 2012. http://dx.doi.org/10.1109/suite.2012.6225474.

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Keivanloo, Iman. "Leveraging clone detection for Internet-scale source code search." In 2012 IEEE 20th International Conference on Program Comprehension (ICPC). IEEE, 2012. http://dx.doi.org/10.1109/icpc.2012.6240504.

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Ishio, Takashi, Yusuke Sakaguchi, Kaoru Ito, and Katsuro Inoue. "Source File Set Search for Clone-and-Own Reuse Analysis." In 2017 IEEE/ACM 14th International Conference on Mining Software Repositories (MSR). IEEE, 2017. http://dx.doi.org/10.1109/msr.2017.19.

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Keivanloo, Iman, Juergen Rilling, and Philippe Charland. "Internet-scale Real-time Code Clone Search Via Multi-level Indexing." In 2011 18th Working Conference on Reverse Engineering (WCRE). IEEE, 2011. http://dx.doi.org/10.1109/wcre.2011.13.

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Keivanloo, Iman, Juergen Rilling, and Philippe Charland. "SeClone - A Hybrid Approach to Internet-Scale Real-Time Code Clone Search." In 2011 IEEE 19th International Conference on Program Comprehension (ICPC). IEEE, 2011. http://dx.doi.org/10.1109/icpc.2011.29.

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Звіти організацій з теми "Clone search":

Riles, J. K. A search for close-mass lepton doublet. Office of Scientific and Technical Information (OSTI), April 1989. http://dx.doi.org/10.2172/6140588.

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Riles, John Keith. A Search for a Close-Mass Lepton Doublet. Office of Scientific and Technical Information (OSTI), June 2018. http://dx.doi.org/10.2172/1454047.

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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.

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Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically efficient, and environmentally sound means of controlling plant diseases, especially in small grain cereals. The systems selected for study in this proposal are barley (Hordeum vulgare ssp. vulgare, Hvv), its wild progenitor (Hordeum vulgare ssp. spontaneum, Hvs) and the powdery mildew (Blumeria graminis f. sp. hordei, Bgs) and leaf rust (Puccinia hordei, Ph) pathogens. We compiled a diverse panel of Hvs accessions (the Wild Barley Diversity Collection or WBDC; N = 314) from across its native range and evaluated it to 40 isolates of Bgs and 12 isolates of Ph. We obtained genomic DNA sequences enriched for Nucleotide Binding Site-Leucine Rich Repeat (NLR) type resistance genes for 203 WBDC accessions, plus cultivar Morex for which the first reference genome sequence of barley was based. We assembled the 250 bp Illumina sequencing reads into contigs using CLC assembly cell. From this effort, we successfully assembled the sequences of 201 WBDC accessions plus Morex and used NLR Parser to identify contigs containing NLR genes. AgRenSeq was then used to identify k-mers (short oligonucleotide sequences of length k) that were associated with resistance to each isolate of the two pathogens. This analysis was performed individually for all WBDC accessions and each individual pathogen race (9,898 host accession x pathogen race combinations). We visualized the results from these analyses in Manhattan plots and identified 311 and 144 peaks for powdery mildew and leaf rust resistance, respectively. The next step in the analysis was to identify the contigs associated with the peaks in the Manhattan plots. BLAST (Basic Local Alignment Search Tool) searches were employed to identify closely related contigs in other WBDC accessions or in Morex. We identified two candidate R genes that were only present in resistant WBDC accessions. One of these was present in seven WBDC lines and was associated with resistance to four leaf rust isolates. BLAST analysis of this gene revealed that it was Rph15, one of the most widely effective leaf rust resistance genes reported in Hordeum. This gene was cloned and functionally validated in association with our Australian colleagues (Cheng et al., 2021). We are currently in the process of cloning six of other resistance genes: four for powdery mildew and two for leaf rust. As the contigs do not contain much of the promoter sequences, we have employed a genome walking approach to identify 2,500 bp of promoter sequence. To speed up and simplify the cloning of resistance genes from the WBDC, the PI established the International Wild Barley Sequencing Consortium (IWBSC; https://iwbsc.umn.edu/) comprised of over 60 researchers from 14 different countries and raised over $150,000 through crowdfunding to pay for 10X depth sequence coverage. Genome-wide association study (GWAS) of whole genome sequencing (WGS) data identified extremely strong and clear signals of association for several resistance genes which will facilitate gene cloning in concert with a wild barley pan-genome currently under construction. The cloning of multiple resistance gene can facilitate the development of durably resistant cultivars by inserting, through transgenesis, cassettes of multiple resistance genes.

Granot, David, Richard Amasino, and Avner Silber. Mutual effects of hexose phosphorylation enzymes and phosphorous on plant development. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7587223.bard.

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Research objectives 1) Analyze the combined effects of hexose phosphorylation and P level in tomato and Arabidopsis plants 2) Analyze the combined effects of hexose phosphorylation and P level in pho1 and pho2 Arabidopsis mutants 3) Clone and analyze the PHO2 gene 4) Select Arabidopsis mutants resistant to high and low P 5) Analyze the Arabidopsis mutants and clone the corresponding genes 6) Survey wild tomato species for growth characteristics at various P levels Background to the topic Hexose phosphorylating enzymes, the first enzymes of sugar metabolism, regulate key processes in plants such as photosynthesis, growth, senescence and vascular transport. We have previously discovered that hexose phosphorylating enzymes might regulate these processes as a function of phosphorous (P) concentration, and might accelerate acquisition of P, one of the most limiting nutrients in the soil. These discoveries have opened new avenues to gain fundamental knowledge about the relationship between P, sugar phosphorylation and plant development. Since both hexose phosphorylating enzymes and P levels affect plant development, their interaction is of major importance for agriculture. Due to the acceleration of senescence caused by the combined effects of hexose phosphorylation and P concentration, traits affecting P uptake may have been lost in the course of cultivation in which fertilization with relatively high P (30 mg/L) are commonly used. We therefore intended to survey wild tomato species for high P-acquisition at low P soil levels. Genetic resources with high P-acquisition will serve not only to generate a segregating population to map the trait and clone the gene, but will also provide a means to follow the trait in classical breeding programs. This approach could potentially be applicable for other crops as well. Major conclusions, solutions, achievements Our results confirm the mutual effect of hexose phosphorylating enzymes and P level on plant development. Two major aspects of this mutual effect arose. One is related to P toxicity in which HXK seems to play a major role, and the second is related to the effect of HXK on P concentration in the plant. Using tomato plants we demonstrated that high HXK activity increased leaf P concentration, and induced P toxicity when leaf P concentration increases above a certain high level. These results further support our prediction that the desired trait of high-P acquisition might have been lost in the course of cultivation and might exist in wild species. Indeed, in a survey of wild species we identified tomato species that acquired P and performed better at low P (in the irrigation water) compared to the cultivated Lycopersicon esculentum species. The connection between hexose phosphorylation and P toxicity has also been shown with the P sensitive species VerticordiaplumosaL . in which P toxicity is manifested by accelerated senescence (Silber et al., 2003). In a previous work we uncovered the phenomenon of sugar induced cell death (SICD) in yeast cells. Subsequently we showed that SICD is dependent on the rate of hexose phosphorylation as determined by Arabidopsis thaliana hexokinase. In this study we have shown that hexokinase dependent SICD has many characteristics of programmed cell death (PCD) (Granot et al., 2003). High hexokinase activity accelerates senescence (a PCD process) of tomato plants, which is further enhanced by high P. Hence, hexokinase mediated PCD might be a general phenomena. Botrytis cinerea is a non-specific, necrotrophic pathogen that attacks many plant species, including tomato. Senescing leaves are particularly susceptible to B. cinerea infection and delaying leaf senescence might reduce this susceptibility. It has been suggested that B. cinerea’s mode of action may be based on induction of precocious senescence. Using tomato plants developed in the course of the preceding BARD grant (IS 2894-97) and characterized throughout this research (Swartzberg et al., 2006), we have shown that B. cinerea indeed induces senescence and is inhibited by autoregulated production of cytokinin (Swartzberg et al., submitted). To further determine how hexokinase mediates sugar effects we have analyzed tomato plants that express Arabidopsis HXK1 (AtHXK1) grown at different P levels in the irrigation water. We found that Arabidopsis hexokinase mediates sugar signalling in tomato plants independently of hexose phosphate (Kandel-Kfir et al., submitted). To study which hexokinase is involved in sugar sensing we searched and identified two additional HXK genes in tomato plants (Kandel-Kfir et al., 2006). Tomato plants have two different hexose phosphorylating enzymes; hexokinases (HXKs) that can phosphorylate either glucose or fructose, and fructokinases (FRKs) that specifically phosphorylate fructose. To complete the search for genes encoding hexose phosphorylating enzymes we identified a forth fructokinase gene (FRK) (German et al., 2004). The intracellular localization of the four tomato HXK and four FRK enzymes has been determined using GFP fusion analysis in tobacco protoplasts (Kandel-Kfir et al., 2006; Hilla-Weissler et al., 2006). One of the HXK isozymes and one of the FRK isozymes are located within plastids. The other three HXK isozymes are associated with the mitochondria while the other three FRK isozymes are dispersed in the cytosol. We concluded that HXK and FRK are spatially separated in plant cytoplasm and accordingly might play different metabolic and perhaps signalling roles. We have started to analyze the role of the various HXK and FRK genes in plant development. So far we found that LeFRK2 is required for xylem development (German et al., 2003). Irrigation with different P levels had no effect on the phenotype of LeFRK2 antisense plants. In the course of this research we developed a rapid method for the analysis of zygosity in transgenic plants (German et al., 2003).

Flabbi, Luca, and Mauricio Tejada. Gender Gaps in Education and Labor Market Outcomes in the United States: The Impact of Employers` Prejudice. Inter-American Development Bank, December 2012. http://dx.doi.org/10.18235/0011443.

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This paper makes three contributions to the existing literature. First, it provides descriptive evidence on gender differentials by education level in the US labor market over the last twenty years. Second, it uses the structural estimation of a search model of the labor market to identify and quantify the impact of employers' prejudice on labor market gender differentials. Third, it connects both the descriptive and the analytical findings to recent policy interventions in the US labor market and presents some policy experiments. The results show that prejudice may still have a role in explaining the evidence on gender differentials and there is at least one scenario where the possibility of the presence of prejudiced employers in the labor market has substantial effects. In particular, it is responsible for the reversal of the returns to schooling ranking in recent years and it may explain up to 44% of the gender wage gap of the top education group (Master and PhD) in 2005. Since prejudice is still important, policy interventions may be effective in attaining both efficiency and welfare gains. The paper is in favor of implementing an affirmative action policy because it is frequently able to close the gender gap without reducing overall welfare and because it is effective in targeting the group that should take center stage in the future debate about gender differentials: high-skilled, high-earners workers, who also have family responsibilities.

Prusky, Dov, Noel Keen, and John Browse. Modulation of the synthesis of the main preformed antifungal compound as abasis for the prevention of postharvest disease of C. gloeosporioides in avocado fruits. United States Department of Agriculture, December 2001. http://dx.doi.org/10.32747/2001.7575273.bard.

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The most important pathological factor limiting fruit life after harvest in subtropical fruits are quiescent infections of anthracnose caused by Colletotrichum gloeosporioides. Prusky and Keen elucidated the mechanism of resistance in avocado fruits to quiescent infections of C. gloeosporioides and determined that the major biocide involved is the preformed compound,1-acetoxy-2-hydroxy-4-oxo-heneicosa-13, 15 diene. Two possibilities exist for maintaining fungitoxic levels of antifungal compounds in the tissue of ripening fruits: (i). Prevention of catabolism (ii). Induction of synthesis. Previous work has demonstrated that increased fruit susceptibility after fruit harvest occurs through diene catabolism mediated by oxidation of the antifungal compound by the enzyme lipoxygenase. Levels of a non-specific inhibitor, epicatechin, in turn, regulate activity of lipoxygenase, present in the peel of unripe but not ripe fruit. In this proposal, we examined the possibility of exploiting induced synthesis of the antifungal compound for the study of the synthetic pathway. The general objective of the present research was to study the mechanism of biosynthesis of natural antifungal compounds in order to regulate the process of resistance to postharvest diseases in ripening avocado fruits. The specific objectives of the research were: 1. To localize synthesis of the antifungal diene and modulate the process by biotic or a biotic elicitors. 2. To determine the relation between synthesis of the diene and accumulation in the peel and fruit resistance to decay 3. To characterize the biosynthetic pathway and the diene and the genes involved. The analysis of the antifungal compounds in avocado resulted in the detection of a new antifungal compound (E, Z, Z)-1-acetoxy-2-hydroxy-4-oxo- heneicosa-5, 12,15-triene. This new compound was shown to inhibit spore germination of C. gloeosporioides similarly as the antifungal diene. We had localized one of the biosynthetic places of these antifungal compounds in specialized idioblast cells (oil cells) in the mesocarp that can be easily enhanced by elicitors as ethylene. Results have also suggested that the antifungal compounds can be "exported" from the mesocarp to the pericarp where its main activity takes place. The search for the biosynthesis of antifungal compounds and the genes involved took two directions i. direct search for specific genes involved in the synthesis of the diene and ii. Indirect selection of genes using the differential display library. We have cloned , The most important pathological factor limiting fruit life after harvest in subtropical fruits are quiescent infections of anthracnose caused by Colletotrichum gloeosporioides. Prusky and Keen elucidated the mechanism of resistance in avocado fruits to quiescent infections of C. gloeosporioides and determined that the major biocide involved is the preformed compound,1-acetoxy-2-hydroxy-4-oxo-heneicosa-13, 15 diene. Two possibilities exist for maintaining fungitoxic levels of antifungal compounds in the tissue of ripening fruits: (i). Prevention of catabolism (ii). Induction of synthesis. Previous work has demonstrated that increased fruit susceptibility after fruit harvest occurs through diene catabolism mediated by oxidation of the antifungal compound by the enzyme lipoxygenase. Levels of a non-specific inhibitor, epicatechin, in turn, regulate activity of lipoxygenase, present in the peel of unripe but not ripe fruit. In this proposal, we examined the possibility of exploiting induced synthesis of the antifungal compound for the study of the synthetic pathway. The general objective of the present research was to study the mechanism of biosynthesis of natural antifungal compounds in order to regulate the process of resistance to postharvest diseases in ripening avocado fruits. The specific objectives of the research were: 1. To localize synthesis of the antifungal diene and modulate the process by biotic or a biotic elicitors. 2. To determine the relation between synthesis of the diene and accumulation in the peel and fruit resistance to decay 3. To characterize the biosynthetic pathway and the diene and the genes involved. The analysis of the antifungal compounds in avocado resulted in the detection of a new antifungal compound (E, Z, Z)-1-acetoxy-2-hydroxy-4-oxo- heneicosa-5, 12,15-triene. This new compound was shown to inhibit spore germination of C. gloeosporioides similarly as the antifungal diene. We had localized one of the biosynthetic places of these antifungal compounds in specialized idioblast cells (oil cells) in the mesocarp that can be easily enhanced by elicitors as ethylene. Results have also suggested that the antifungal compounds can be "exported" from the mesocarp to the pericarp where its main activity takes place. The search for the biosynthesis of antifungal compounds and the genes involved took two directions i. direct search for specific genes involved in the synthesis of the diene and ii. Indirect selection of genes using the differential display library. We have cloned D9 and D12 desaturase, a protein kinase and a elongase that their transcriptional activation is significantly enhanced during the enhanced synthesis of the antifungal diene. Although we are far away from a complete elucidation of the synthesis of the antifungal compound we have stepped forward determining some of the key steps that might be involved in its synthesis.

Adam, Zach, and Eran Pichersky. Degradation of Abnormal Proteins in Chloroplasts of Higher Plants. United States Department of Agriculture, August 1994. http://dx.doi.org/10.32747/1994.7568768.bard.

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In this study we attempted to get a better understanding of processes involved in the degradation of abnormal proteins i chloroplasts. To achieve this goal, we used a number of complementary approaches. We first characterized the expression of the two subunits of Clp protease. We demonstrated that both of them were expressed in chloroplasts in a constitutive fashion, but the expression of the regulatory subunit ClpC was enhanced by light. We generated a mutant the lumenal protein OEE33 which was targeted to the stroma in in vitro experiments. In the wrong compartment it was found unstable, and characterization of its degradation revealed that it was degraded by a soluble, ATP-dependent serine protease, which are also the characteristics of Clp protease. In search of other homologues of bacterial proteases, we found that chloroplasts contain a homologue of the FtsH protease. It is an ATP-dependent metallo-protease, bound to the stromal side of the thylakoid membrane, whose expression is dependent on light. The gene encodig this protease was cloned and characterized. In attempt to generate Arabidopsis mutant plants impaired in their capability to degrade abnormal chloroplast proteins, we fused the gene for mistargeted OEE33 to the streptomycin-detoxifying gene. This chimeric gene was introduced into Arabodipsis plants, to generate transformed plants. This transformants plants were sensitive to streptomycin due to the rapid turn-over of the chimeric protein. Seeds from these plants were then chemically mutagenised, and seedlings were selected for their capability to grow on streptomycin. The ability of these mutant transformants to grow on streptomycin is presumably due to stabilization of the chimeric protein. These plants will allow us in the future to identify the effected genes, which are likely to be involved in the protein degradation process.

Granot, David, and Richard Amasino. Regulation of Senescence by Sugar Metabolism. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7585189.bard.

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Research objectives a. Analyze transgenic plants that undergo rapid senescence due to increased expression of hexokinase. b. Determine if hexokinase-induced senescence accelerates natural senescence using senescence specific promoters that drive expression of a reporter gene (GUS) and a cytokinin producing gene (IPT - isopentyl transferase). c. Isolate and analyze plant genes that suppress sugar-induced cell death (SICD) in yeast, genes that potentially are involved in programmed cell death and senescence in plants. Background to the topic Leaf senescence is a regulated process of programmed cell death (PCD) in which metabolites are recycled to other active parts of the plant. Senescence associated genes (SAGs) are expressed throughout leaf senescence. Sugar flux and metabolism is thought to playa fundamental regulatory role in senescence. We found that transgenic tomato plants with high hexokinase activity, the initial enzymatic step of sugar (hexose) metabolism, undergo rapid leaf senescence, directly correlated with hexokinase activity. These plants provide a unique opportunity to analyze the regulatory role of sugar metabolism in senescence, and its relation to cytokinin, a senescence-inhibiting hormone. In addition, we found that sugar induces programmed cells death of yeast cells in direct correlation to hexokinase activity. We proposed to use the sugar induced cell death (SICD) to isolate Arabidopsis genes that suppress SICD. Such genes could potentially be involved in senescence induced PCD in plants. Major conclusions The promoters of Arabidopsis senescence-associated genes, SAG12 and SAGI3, are expressed in senescing tomato leaves similar to their expression in Arabidopsis leaves, indicating that these promoters are good senescence markers for tomato plants. Increased hexokinase activity accelerated senescence and induced expression of pSAG12 and pSAG13 promoters in tomato plants, suggesting that sugar regulate natural senescence via hexokinase. Expression of IPT, a cytokinin producing gene, under pSAG12 and pSAG13 promoters, delayed senescence of tomato leaves. Yet, senescence accelerated by hexokinase was epistatic over cytokinin, indicating that sugar regulation of senescence is dominant over the senescence-inhibiting hormone. A gene designated SFP1, which is similar to the major super family monosaccharide transporters, is induced during leaf senescence in Arabidopsis and may be involved in sugar transport during senescence. Accordingly, adult leaves accumulate sugars that may accelerate hexokinase activity. Light status of the entire plant affects the senescence of individual leaves. When individual leaves are darkened, senescence is induced in the covered leaves. However, whole adult plant placed in darkness show delayed senescence. In a search for Arabidopsis genes that suppress SICD we isolated 8 cDNA clones which confer partial resistance to SICD. One of the clones encodes a vesicle associated membrane protein - VAMP. This is the first evidence that vesicle trafficking might be involved in cell death. Implications Increased hexokinase activity accelerates senescence. We hypothesized that, reduced hexokinase activity may delay senescence. Preliminary experiments using a hexokinase inhibitor support this possible implication. Currently we are analyzing various practical approaches to delay leaf senescence via hexokinase inhibition. .

Rafaeli, Ada, Russell Jurenka, and Daniel Segal. Isolation, Purification and Sequence Determination of Pheromonotropic-Receptors. United States Department of Agriculture, July 2003. http://dx.doi.org/10.32747/2003.7695850.bard.

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Moths constitute a major group of pest insects in agriculture. Pheromone blends are utilised by a variety of moth species to attract conspecific mates, which is under circadian control by the neurohormone, PBAN (pheromone-biosynthesis-activating neuropeptide). Our working hypothesis was that, since the emission of sex-pheromone is necessary to attract a mate, then failure to produce and emit pheromone is a potential strategy for manipulating adult moth behavior. The project aimed at identifying, characterising and determining the sequence of specific receptors responsible for the interaction with pheromonotropic neuropeptide/s using two related moth species: Helicoverpa armigera and H. lea as model insects. We established specific binding to a membrane protein estimated at 50 kDa in mature adult females using a photoaffinity-biotin probe for PBAN. We showed that JH is required for the up-regulation of this putative receptor protein. In vitro studies established that the binding initiates a cascade of second messengers including channel opening for calcium ions and intracellular cAMP production. Pharmacological studies (using sodium fluoride) established that the receptor is coupled to a G-protein, that is, the pheromone-biosynthesis-activating neuropeptide receptor (PBAN-R) belongs to the family of G protein-coupled receptor (GPCR)'s. We showed that PBAN-like peptides are present in Drosophila melanogaster based on bioassay and immunocytochemical data. Using the annotated genome of D. melanogaster to search for a GPCR, we found that some were similar to neuromedin U- receptors of vertebrates, which contain a similar C-terminal ending as PBAN. We established that neuromedin U does indeed induce pheromone biosynthesis and cAMP production. Using a PCR based cloning strategy and mRNA isolated from pheromone glands of H. zea, we successfully identified a gene encoding a GPCR from pheromone glands. The full-length PBAN-R was subsequently cloned and expressed in Sf9 insect cells and was shown to mobilize calcium in response to PBAN in a dose-dependent manner. The successful progress in the identification of a gene, encoding a GPCR for the neurohormone, PBAN, provides a basis for the design of a novel battery of compounds that will specifically antagonize pheromone production. Furthermore, since PBAN belongs to a family of insect neuropeptides with more than one function in different life stages, this rationale may be extended to other physiological key-regulatory processes in different insects.

Michaels, Trevor. Red-tailed boa (Boa constrictor) surveys at Salt River Bay National Park, St. Croix U.S. Virgin Islands: 2023 report of activities. National Park Service, 2024. http://dx.doi.org/10.36967/2303799.

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St. Croix is home to a variety of threatened and endangered (T&E) species that are at risk for predation by the invasive red-tailed boa (Boa constrictor), such as the St. Croix ground lizard (Amevia polyps), the ground-nesting least tern (Sterna antillarum), and the hawksbill sea turtle (Eretmochelys imbricata). Genetic analysis determined the original red-tailed boa population on St. Croix sourced from a single female released by a pet owner and its range expands every year. Presently, the main population of red-tailed boa is established on the west end of St. Croix and extends as far east as Salt River. One individual was found in Salt River Marina and additional sightings have occurred in Salt River Bay National Historical Park and Ecological Preserve (SARI) more recently. This inventory aims to search for red-tailed boas in two focal areas that park staff are actively restoring. The park will use information from this inventory to develop a boa removal program and protect sensitive native species like the ground-nesting least tern, the St. Croix ground lizard and the hawksbill sea turtle nests and increase the success of restoration. Snakes are cryptic species, often occurring in low density, and utilize complex habitat patterns. To increase the likelihood of detecting red-tailed boa, the Maryland/Delaware/D.C. Wildlife Services detector dog handling team partnered with the USDA-APHIS National Detector Dog Training Center to train and develop detector dogs to assist in determining the presence/absence of red-tailed boa for this project. Canines were trained to locate red-tailed boa and indicate its presence to the handler via barking three times near the identified target. Two dog detector teams traveled to Salt River Bay National Park (SARI) in St. Croix to conduct surveys for red-tailed boa in habitats likely to contain red-tailed boa in June 2023. Habitat varied throughout the surveys. Close to the bay, mangrove forests dominated and, as elevation increased, transects took place in almost exclusively dry tropical shrub forest. Each transect was surveyed by one dog team. The canine teams had no red-tailed boa detections within SARI. Canines showed proficiency at surveying for red-tailed boa populations in SARI. Given the proximity of confirmed detections to SARI, it is likely red-tailed boa will be in the park in the future, if they are not already. Additional surveys, whether by humans, canines, or both, are recommended in areas of the park that have not been previously surveyed.