Готові списки джерел за темами / EST clustering

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Добірка наукової літератури з теми "EST clustering"

Автор: Grafiati

Опубліковано: 11 березня 2023

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Статті в журналах з теми "EST clustering"

Wang, J. P. Z., B. G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W. C. Miller, and C. W. dePamphilis. "EST clustering error evaluation and correction." Bioinformatics 20, no. 17 (June 9, 2004): 2973–84. http://dx.doi.org/10.1093/bioinformatics/bth342.

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Hazelhurst, Scott, Winston Hide, Zsuzsanna Lipták, Ramon Nogueira, and Richard Starfield. "An overview of the wcd EST clustering tool." Bioinformatics 24, no. 13 (May 14, 2008): 1542–46. http://dx.doi.org/10.1093/bioinformatics/btn203.

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Mudhireddy, R., F. Ercal, and R. Frank. "Parallel Hash-Based EST Clustering Algorithm for Gene Sequencing." DNA and Cell Biology 23, no. 10 (October 2004): 615–23. http://dx.doi.org/10.1089/dna.2004.23.615.

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Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, et al. "TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets." Bioinformatics 19, no. 5 (March 22, 2003): 651–52. http://dx.doi.org/10.1093/bioinformatics/btg034.

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Kalyanaraman, A. "Efficient clustering of large EST data sets on parallel computers." Nucleic Acids Research 31, no. 11 (June 1, 2003): 2963–74. http://dx.doi.org/10.1093/nar/gkg379.

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Telles, Guilherme P., Marília D. V. Braga, Zanoni Dias, Lin Tzy-Li, José A. A. Quitzau, Felipe R. da Silva, and João Meidanis. "Bioinformatics of the sugarcane EST project." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 9–15. http://dx.doi.org/10.1590/s1415-47572001000100003.

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Анотація:

The Sugarcane EST project (SUCEST) produced 291,904 expressed sequence tags (ESTs) in a consortium that involved 74 sequencing and data mining laboratories. We created a web site for this project that served as a ‘meeting point’ for receiving, processing, analyzing, and providing services to help explore the sequence data. In this paper we describe the information pathway that we implemented to support this project and a brief explanation of the clustering procedure, which resulted in 43,141 clusters.

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Perseguini, Juliana Morini Küpper Cardoso, Lineu Roberto de Castro Romão, Boris Briñez, Erivaldo José Scaloppi Junior, Paulo de Souza Gonçalves, and Luciana Lasry Benchimol. "Genetic diversity of cultivated accessions and wild species of rubber tree using EST‑SSR markers." Pesquisa Agropecuária Brasileira 47, no. 8 (August 2012): 1087–94. http://dx.doi.org/10.1590/s0100-204x2012000800008.

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The objective of this work was to evaluate the efficiency of EST‑SSR markers in the assessment of the genetic diversity of rubber tree genotypes (Hevea brasiliensis) and to verify the transferability of these markers for wild species of Hevea. Forty‑five rubber tree accessions from the Instituto Agronômico (Campinas, SP, Brazil) and six wild species were used. Information provided by modified Roger's genetic distance were used to analyze EST‑SSR data. UPGMA clustering divided the samples into two major groups with high genetic differentiation, while the software Structure distributed the 51 clones into eight groups. A parallel could be established between both clustering analyses. The 30 polymorphic EST‑SSRs showed from two to ten alleles and were efficient in amplifying the six wild species. Functional EST‑SSR microsatellites are efficient in evaluating the genetic diversity among rubber tree clones and can be used to translate the genetic differences among cultivars and to fingerprint closely related materials. The accessions from the Instituto Agronômico show high genetic diversity. The EST‑SSR markers, developed from Hevea brasiliensis, show transferability and are able to amplify other species of Hevea.

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Lijoi, Antonio, Ramsés H. Mena, and Igor Prünster. "A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries." Journal of Computational Biology 15, no. 10 (December 2008): 1315–27. http://dx.doi.org/10.1089/cmb.2008.0043.

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Kim, N. "ECgene: Genome-based EST clustering and gene modeling for alternative splicing." Genome Research 15, no. 4 (March 21, 2005): 566–76. http://dx.doi.org/10.1101/gr.3030405.

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Kalyanaraman, A., S. Aluru, V. Brendel, and S. Kothari. "Space and time efficient parallel algorithms and software for EST clustering." IEEE Transactions on Parallel and Distributed Systems 14, no. 12 (December 2003): 1209–21. http://dx.doi.org/10.1109/tpds.2003.1255634.

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Більше джерел

Дисертації з теми "EST clustering"

Ptitsyn, Andrey. "New algorithms for EST clustering." Thesis, University of the Western Cape, 2000. http://etd.uwc.ac.za/index.php?module=etd&amp.

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Анотація:

Expressed sequence tag database is a rich and fast growing source of data for gene expression analysis and drug discovery. Clustering of raw EST data is a necessary step for further analysis and one of the most challenging problems of modem computational biology.

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Moler, James C. "Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1303482998.

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Lipták, Zsuzsanna. "Strings in proteomics and transcriptomics algorithmic and combinatorial questions in mass spectrometry and EST clustering /." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=979746566.

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Sczyrba, Alexander. "Genome analysis based on EST collections a clustering pipeline and a database on Xenopus laevis /." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=983938016.

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Gu, Yuhua. "Ant clustering with consensus." [Tampa, Fla] : University of South Florida, 2009. http://purl.fcla.edu/usf/dc/et/SFE0002959.

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Primo, Tiago Thompsen. "M?todos de clusteriza??o para apoio ? classifica??o est?tica de documentos." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2008. http://tede2.pucrs.br/tede2/handle/tede/5028.

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Made available in DSpace on 2015-04-14T14:49:01Z (GMT). No. of bitstreams: 1 406128.pdf: 16056423 bytes, checksum: d4b22e3a871de544238db5630e9a295f (MD5) Previous issue date: 2008-03-24
Neste trabalho ser?o abordados estudos referentes ? classifica??o de grande quantidade de documentos de conte?do vari?vel. Em tal processo quando um grande n?mero de documentos ? gerado, existe a necessidade de um usu?rio verific?-los um a um com a inten??o de separ?-los em bons (com pouco ou nenhum problema estrutural) ou ruins (que possuem problemas estruturais), processo este considerado lento e oneroso. Considerando este problema, neste trabalho foi desenvolvida uma ferramenta de classifica??o est?tica de documentos que visa reduzir esta interven??o humana. A ferramenta desenvolvida ? baseada em m?tricas que avaliam o quanto um documento automaticamente gerado difere de seu template, criando para cada um destes documentos uma assinatura baseada nas t?cnicas de fingerprint, objetivando primeiramente distingui-los entre si para ent?o utilizar t?cnicas de clusteriza??o criando grupos de documentos com caracter?sticas semelhantes. O algoritmo K-Med?ides ? usado para fazer tal agrupamento, tal algoritmo funciona criando grupos de objetos considerando um destes como base para a cria??o de cada cluster. A id?ia deste trabalho ? reduzir a interven??o humana fazendo com que um usu?rio classifique em bom ou ruim apenas determinados documentos de cada grupo formado pelo algoritmo de clusteriza??o. S?o tamb?m apresentados resultados de quatro experimentos realizados com esta ferramenta avaliando as contribui??es para diminuir a interven??o humana no processo de classifica??o de documentos.

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Arumugavelu, Shankar. "SIMD algorithms for single link and complete link pattern clustering." [Tampa, Fla.] : University of South Florida, 2007. http://purl.fcla.edu/usf/dc/et/SFE0001967.

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Hore, Prodip. "Scalable frameworks and algorithms for cluster ensembles and clustering data streams." [Tampa, Fla.] : University of South Florida, 2007. http://purl.fcla.edu/usf/dc/et/SFE0002135.

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Gupta, Upavan. "Utilitarian approaches for multi-metric optimization in VLSI circuit design and spatial clustering." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002584.

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Lundequist, Per. "Spatial clustering and industrial competitiveness : Studies in economic geography." Doctoral thesis, Uppsala : Department of Social and Economic Geography, Uppsala University, 2002. http://publications.uu.se/theses/99-2002-0429140456/.

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Книги з теми "EST clustering"

The clustering of America. New York: Harper & Row, 1989.

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Частини книг з теми "EST clustering"

Trivedi, Nishank, Kevin T. Pedretti, Terry A. Braun, Todd E. Scheetz, and Thomas L. Casavant. "Alternative Parallelization Strategies in EST Clustering." In Lecture Notes in Computer Science, 384–93. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-45145-7_36.

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Pedretti, Kevin, Todd Scheetz, Terry Braun, Chad Roberts, Natalie Robinson, and Thomas Casavant. "A Parallel Expressed Sequence Tag (EST) Clustering Program." In Lecture Notes in Computer Science, 490–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/3-540-44743-1_51.

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Brandes, Ulrik, Marco Gaertler, and Dorothea Wagner. "Experiments on Graph Clustering Algorithms." In Algorithms - ESA 2003, 568–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-39658-1_52.

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Hassin, Refael, and Einat Or. "Min Sum Clustering with Penalties." In Algorithms – ESA 2005, 167–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11561071_17.

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Kuhn, Fabian, Thomas Moscibroda, and Roger Wattenhofer. "Radio Network Clustering from Scratch." In Algorithms – ESA 2004, 460–71. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30140-0_42.

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Großwendt, Anna, and Heiko Röglin. "Improved Analysis of Complete-Linkage Clustering." In Algorithms - ESA 2015, 656–67. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-48350-3_55.

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Ailon, Nir, Noa Avigdor-Elgrabli, Edo Liberty, and Anke van Zuylen. "Improved Approximation Algorithms for Bipartite Correlation Clustering." In Algorithms – ESA 2011, 25–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23719-5_3.

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Chen, Danny Z., Michiel Smid, and Bin Xu. "Geometric Algorithms for Density-Based Data Clustering." In Algorithms — ESA 2002, 284–96. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45749-6_28.

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Hagauer, Johann, and Günter Rote. "Three-clustering of points in the plane." In Algorithms—ESA '93, 192–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/3-540-57273-2_55.

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Akhmetova, Anna V. "Transformation of Ethnocultural Development of Indigenous Peoples in the Conditions of Socialist Modernization of the Far East in 1920–1970s: Problems of Historiography." In Integration and Clustering for Sustainable Economic Growth, 553–58. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-45462-7_53.

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Тези доповідей конференцій з теми "EST clustering"

Kalyanaraman, A., S. Aluru, and S. Kothari. "Parallel EST clustering." In Proceedings 16th International Parallel and Distributed Processing Symposium. IPDPS 2002. IEEE, 2002. http://dx.doi.org/10.1109/ipdps.2002.1016587.

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Wang, Chunyu, Maozu Guo, and Yang Liu. "EST Clustering in Large Dataset with MapReduce." In 2010 First International Conference on Pervasive Computing, Signal Processing and Applications (PCSPA 2010). IEEE, 2010. http://dx.doi.org/10.1109/pcspa.2010.239.

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Das, Arunita, Daipayan Ghosal, and Krishna Gopal Dhal. "Leaf Segmentation of Rosette Plants using Rough K-Means in CIELab Color Space." In 7th Student Computer Science Research Conference. University of Maribor Press, 2021. http://dx.doi.org/10.18690/978-961-286-516-0.5.

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Segmentation of Plant Images plays an important role in modern agriculture where it can provide accurate analysis of a plant’s growth and possi-ble anomalies. In this paper, rough set based partitional clustering technique called Rough K-Means has been utilized in CIELab color space for the proper leaf segmentation of rosette plants. The eÿcacy of the proposed technique have been analysed by comparing it with the results of tra-ditional K-Means and Fuzzy C-Means clustering algorithms. The visual and numerical results re-veal that the RKM in CIELab provides the near-est result to the ideal ground truth, hence the most eÿcient one.

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Keng-Hoong Ng, Somnuk Phon-Amnuaisuk, and Chin-Kuan Ho. "Clustering of Expressed Sequence Tag (EST) with Markov models and self-organizing maps: An exploratory study." In 2008 International Symposium on Information Technology. IEEE, 2008. http://dx.doi.org/10.1109/itsim.2008.4631585.

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Ma, Ruicheng, Dandan Hu, Ya Deng, Limin Zhao, and Shu Wang. "Integrated Semi-Supervised Clustering Method and Its Application in Rock-Typing in AA Reservoir." In SPE Middle East Oil & Gas Show and Conference. SPE, 2021. http://dx.doi.org/10.2118/204777-ms.

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Abstract Rock-typing is complicated and critical for numerical simulation. Therefore, some researchers proposed several clustering methods to make classification automatic and convenient. However, traditional methods only focus in specific area such as lithofacies or petrophysical data instead of integrated clustering. Besides, all the clustering method are related to classification interval determined subjectively. Therefore, a new clustering method for rock-typing integrated different disciplines is critical for modelling and reservoir simulation. In this paper, we proposed a novel semi-supervised clustering method integrated with data from different disciplines, which can divide rock type automatically and precisely. Considering AA reservoir is a porous carbonate reservoir with seldom fracture and vug, FZI (Flow Zone Indicator) and RQI (Reservoir Quality Index) is utilized as the corner stone of the clustering method after collection and plotting for porosity and permeability data for cores from AA reservoir. Then lithofacies, sedimentary facies and petrophysical data are applied as constraints to improve FZI method. Hamming distance and earth mover distance are imported to build integrated function for clustering method. Finally, based on output results of integrated clustering method from experimental data, grid properties of model in Petrel software are imported as the input parameter for further procession. Therefore, saturation region for numerical simulation built by rock-typing is constructed. The results show that new method could make classification accurately and easily. History matching results for watercut indicate that new saturation regions improve the numerical simulation performance.

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El-Bathy, Naser, Ghassan Azar, Mohammed El-Bathy, and Gordon Stein. "Intelligent Extended Clustering Genetic Algorithm." In 2011 IEEE International Conference on Electro/Information Technology (EIT 2011). IEEE, 2011. http://dx.doi.org/10.1109/eit.2011.5978607.

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Thang, Vu Viet, D. V. Pantiukhin, and A. I. Galushkin. "A Hybrid Clustering Algorithm: The FastDBSCAN." In 2015 International Conference on Engineering and Telecommunication (EnT). IEEE, 2015. http://dx.doi.org/10.1109/ent.2015.31.

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Mirzaei, Golrokh, Mohsin M. Jamali, Jeremy D. Ross, Peter V. Gorsevski, and Verner P. Bingman. "Fuzzy clustering in avian infrared imagery application." In 2014 IEEE International Conference on Electro/Information Technology (EIT). IEEE, 2014. http://dx.doi.org/10.1109/eit.2014.6871768.

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Chang, Edward Y., Chen Li, James Z. Wang, Peter Mork, and Gio Wiederhold. "Searching near-replicas of images via clustering." In Photonics East '99, edited by Sethuraman Panchanathan, Shih-Fu Chang, and C. C. Jay Kuo. SPIE, 1999. http://dx.doi.org/10.1117/12.360433.

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Xiong, Xiao, Jie Zhang, and Qingwei Shi. "An efficient fractal dimension based clustering algorithm." In Optics East 2007, edited by Sergey I. Balandin. SPIE, 2007. http://dx.doi.org/10.1117/12.752680.

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Звіти організацій з теми "EST clustering"

Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, December 2002. http://dx.doi.org/10.32747/2002.7587232.bard.

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Анотація:

The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel sequences involved in these processes B. Comparing expression profiles following the perception of various artificial as well as natural signals known to induce dormancy release, and searching for gene showing similar expression patterns, as candidates for further study of pathways having potential to play a central role in dormancy release. We first created targeted EST collections from V. vinifera and V. riparia mature buds. Clones were randomly selected from cDNA libraries prepared following controlled dormancy release and controlled dormancy induction and from respective controls. The entire collection (7920 vinifera and 1194 riparia clones) was sequenced and subjected to bioinformatics analysis, including clustering, annotations and GO classifications. PCR products from the entire collection were used for printing of cDNA microarrays. Bud tissue in general, and the dormant bud in particular, are under-represented within the grape EST database. Accordingly, 59% of the our vinifera EST collection, composed of 5516 unigenes, are not included within the current Vitis TIGR collection and about 22% of these transcripts bear no resemblance to any known plant transcript, corroborating the current need for our targeted EST collection and the bud specific cDNA array. Analysis of the V. riparia sequences yielded 814 unigenes, of which 140 are unique (keilin et al., manuscript, Appendix B). Results from computational expression profiling of the vinifera collection suggest that oxidative stress, calcium signaling, intracellular vesicle trafficking and anaerobic mode of carbohydrate metabolism play a role in the regulation and execution of grape-bud dormancy release. A comprehensive analysis confirmed the induction of transcription from several calcium–signaling related genes following HC treatment, and detected an inhibiting effect of calcium channel blocker and calcium chelator on HC-induced and chilling-induced bud break. It also detected the existence of HC-induced and calcium dependent protein phosphorylation activity. These data suggest, for the first time, that calcium signaling is involved in the mechanism of dormancy release (Pang et al., in preparation). We compared the effects of heat shock (HS) to those detected in buds following HC application and found that HS lead to earlier and higher bud break. We also demonstrated similar temporary reduction in catalase expression and temporary induction of ascorbate peroxidase, glutathione reductase, thioredoxin and glutathione S transferase expression following both treatments. These findings further support the assumption that temporary oxidative stress is part of the mechanism leading to bud break. The temporary induction of sucrose syntase, pyruvate decarboxylase and alcohol dehydrogenase indicate that temporary respiratory stress is developed and suggest that mitochondrial function may be of central importance for that mechanism. These finding, suggesting triggering of identical mechanisms by HS and HC, justified the comparison of expression profiles of HC and HS treated buds, as a tool for the identification of pathways with a central role in dormancy release (Halaly et al., in preparation). RNA samples from buds treated with HS, HC and water were hybridized with the cDNA arrays in an interconnected loop design. Differentially expressed genes from the were selected using R-language package from Bioconductor project called LIMMA and clones showing a significant change following both HS and HC treatments, compared to control, were selected for further analysis. A total of 1541 clones show significant induction, of which 37% have no hit or unknown function and the rest represent 661 genes with identified function. Similarly, out of 1452 clones showing significant reduction, only 53% of the clones have identified function and they represent 573 genes. The 661 induced genes are involved in 445 different molecular functions. About 90% of those functions were classified to 20 categories based on careful survey of the literature. Among other things, it appears that carbohydrate metabolism and mitochondrial function may be of central importance in the mechanism of dormancy release and studies in this direction are ongoing. Analysis of the reduced function is ongoing (Appendix A). A second set of hybridizations was carried out with RNA samples from buds exposed to short photoperiod, leading to induction of bud dormancy, and long photoperiod treatment, as control. Analysis indicated that 42 genes were significant difference between LD and SD and 11 of these were unique.

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Anke, Juliane, Angela Francke, and Tibor Petzoldt. RadVerS - Mit Smartphones generierte Verhaltensdaten im Verkehr – Differenzierung des Nutzerverhaltens unterschiedlicher RadfahrerInnengruppen : Teil 1 des Abschlussberichts. Technische Universität Dresden, September 2021. http://dx.doi.org/10.26128/2021.240.

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Ziel der vorliegenden Studie war es, eine Typologie von RadfahrerInnen in Deutschland zu erarbeiten und diese zu beschreiben. Zu diesem Zweck wurde auf Basis einer umfassenden Literaturrecherche eine groß angelegte Online-Befragung vom 20.11.2017 bis 07.01.2018 durchgeführt. Insgesamt wurden dabei 10.294 auswertbare Datensätze gewonnen. Durch Hauptkomponenten- und Faktorenanalyse wurden neun Faktoren (symbolische Motive, affektive Motive, instrumentelle Motive, subjektive Sicherheit, Identifikation als RadfahrerIn, zeitliche Distanz, Nutzungshäufigkeit, Wetter/Komfort und Regeltreue) extrahiert, die anschließend zur Clusterung der RadfahrerInnen genutzt wurden. Mit Hilfe dieser Faktoren ließen sich vier Typen von RadfahrerInnen identifizieren: passionierter, pragmatischer, funktioneller und ambitionierter Radfahrtyp. Die Typen unterscheiden sich dabei sowohl hinsichtlich der Typologisierungsfaktoren als auch bezüglich infrastruktureller Präferenzen, Unfallhistorie und der Radfahrhäufigkeit für bestimmte Wegezwecke. Die Einbeziehung motivationaler Faktoren erbrachte wichtige Einblicke in die Eigenschaften von RadfahrerInnen. Für den passionierten Radfahrtyp spielen sowohl Faktoren, wie die soziale Anerkennung bzw. Identifikation mit dem Umfeld, die Freude am Fahren als auch Faktoren wie Flexibilität oder Umweltschutz eine wichtige Rolle. Der Pragmatische wird dagegen v.a. instrumentell motiviert, d.h. das Rad wird genutzt, weil es flexibel ist, gut für die eigene Fitness und man damit schnell vorankommt. Insgesamt am wenigsten zum Radfahren motiviert ist der/die funktionelle RadfahrerIn. Für diesen Typ stehen z.B. ökonomische Gründe bei der Radnutzung im Vordergrund und das Fahrrad wird eher als „Mittel zum Zweck“ gesehen. Der Spaß am Fahren sowie die Zugehörigkeit zu oder das Kennenlernen von Personen sind für die ambitionierten RadfahrerInnen Hauptmotive für die Radnutzung. Aus den Kenntnissen der Eigenschaften der vier Radfahrtypen lassen sich u.a. Implikationen für die Radverkehrsförderung ableiten. So könnten z.B. Kampagnen vermitteln, dass das Fahrrad mehr sein kann als nur „Mittel zum Zweck“, um funktionelle und pragmatische Typen zu einer (Mehr-) Nutzung zu ermutigen. Die Arbeit schließt mit einem Ausblick auf Teil 2 des Projektes, bei dem die gewonnenen Erkenntnisse über die Radfahrtypen mit realem Fahrverhalten verknüpft wurden.

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Weinberg, Zwi G., Adegbola Adesogan, Itzhak Mizrahi, Shlomo Sela, Kwnag Jeong, and Diwakar Vyas. effect of selected lactic acid bacteria on the microbial composition and on the survival of pathogens in the rumen in context with their probiotic effects on ruminants. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598162.bard.

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This research project was performed in context of the apparent probiotic effect of selected lactic acid bacteria (LAB) silage inoculants on the performance of ruminants (improved feed intake, faster live-weight gain, higher milk yields and improved feed efficiency). The overall objective was to find out how LAB affect ruminant performance. The project included several “chapters” as follows: 1. The effect of LAB silage inoculants on the survival of detrimental bacteria in rumen fluid, in vitro study (Weinberg et al., The Volcani Center). An in vitro model was developed to study the interaction between selected LAB and an E. coli strain tagged with green fluorescence protein (GFP) in buffered RF. Results indicated that both LAB inoculants and E. coli survived in the RF for several days; both LAB inoculants and LAB-treated silages did not affect survival of E. coli in rumen fluid in vitro. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the performance of high-lactating cows (Weinberg et al., The Volcani Center). Treatments included control (no additive), Lacobacillusbuchneri40788 (LB), Lactobacillus plantarumMTD1 40027 (LP) and Pediococcuspentosaceus30168 (PP), each applied at 10⁶ cfu/g FM. The silages were included in the TMR of 32 high milking Holstein cows in a controlled feeding experiment. All baled silages were of good quality. The LB silage had the numerically highest acetic acid and were the most stable upon aerobic exposure. The cows fed the LB silages had the highest daily milk yields, percent milk fat and protein. The microbiome of baled wheat silages and changes during ensiling of wheat and corn (Sela et al., The Volcani Center). Bacterial community of the baled silages was dominated mainly of two genera in total, dominated by Lactobacillus and Clostridium_sensu_stricto_12 with 300 other genera at very low abundance. Fungal community was composed mainly of two genera in total, dominated by Candida and Monascuswith 20 other genera at very low abundance. In addition, changes in the microbiome during ensiling of wheat and corn with and without addition of L. plantarumMTD1 was studied in mini-silos. Overall 236 bacterial genera were identified in the fresh corn but after 3 months Lactobacillus outnumbered all other species by acquiring 95% of relative abundance. The wheat silage samples are still under analysis. The effect of applying LAB inoculants at ensiling on survival of E. coli O157:H7 in alfalfa and corn silages(Adesogan et al., University of Florida). E. coli (10⁵ cfu/g) was applied to fresh alfalfa and corn at ensiling with or without L. plantarumor L. buchneri. The pathogen was added again after about 3 moths at the beginning of an aerobic exposure period. The inoculants resulted in faster decrease in pH as compared with the control (no additives) or E. coli alone and therefore, the pathogen was eliminated faster from these silages. After aerobic exposure the pathogen was not detected in the LAB treated silages, whereas it was still present in the E. coli alone samples. 5. The effect of feeding corn silage treated with or without L. buchnerion shedding of E. coli O157:H7 by dairy cows (Adesogan et al., UFL). BARD Report - Project 4704 Page 2 of 12 Five hundred cows from the dairy herd of the University of Florida were screened for E. coli shedding, out of which 14 low and 13 high shedders were selected. These cows were fed a total mixed ration (TMR) which was inoculated with E. coli O157:H7 for 21 days. The TMR included corn silage treated with or without L. buchneri. The inoculated silages were more stable upon aerobic exposure than the control silages; the silage inoculant had no significant effect on any milk or cow blood parameters. However, the silage inoculant tended to reduce shedding of E. coli regardless of high or low shedders (p = 0.06). 6. The effect of feeding baled wheat silages treated with or without three selected LAB silage inoculants on the rumen microbiome (Mizrahi et al., BGU). Rumen fluid was sampled throughout the feeding experiment in which inoculated wheat silages were included in the rations. Microbial DNA was subsequently purified from each sample and the 16S rRNA was sequenced, thus obtaining an overview of the microbiome and its dynamic changes for each experimental treatment. We observed an increase in OTU richness in the group which received the baled silage inoculated with Lactobacillus Plantarum(LP). In contrast the group fed Lactobacillus buchneri(LB) inoculated silage resulted in a significant decrease in richness. Lower OTU richness was recently associated in lactating cows with higher performance (Ben Shabatet al., 2016). No significant clustering could be observed between the different inoculation treatments and the control in non metric multi-dimentional scaling, suggesting that the effect of the treatments is not the result of an overall modulation of the microbiome composition but possibly the result of more discrete interactions. Significant phylum level changes in composition also indicates that no broad changes in taxa identity and composition occurred under any treatment A more discrete modulation could be observed in the fold change of several taxonomic groups (genus level analysis), unique to each treatment, before and after the treatment. Of particular interest is the LB treated group, in which several taxa significantly decreased in abundance. BARD Report - Project 4704 Page 3 of 12

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