Bibliografie tematiche / Sequence selection

Letteratura scientifica selezionata sul tema "Sequence selection"

Autore: Grafiati

Pubblicato: 1 giugno 2024

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Articoli di riviste sul tema "Sequence selection":

Zhou, Haobo, G. Jonah Rainey, Swee-Kee Wong e John M. Coffin. "Substrate Sequence Selection by Retroviral Integrase". Journal of Virology 75, n. 3 (1 febbraio 2001): 1359–70. http://dx.doi.org/10.1128/jvi.75.3.1359-1370.2001.

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ABSTRACT Integration of retrovirus DNA is a specific process catalyzed by the integrase protein acting to join the viral substrate DNA (att) sequences of about 10 bases at the ends of the long terminal repeat (LTR) to various sites in the host target cell DNA. Although the interaction is sequence specific, the att sequences of different retroviruses are largely unrelated to one another and usually differ between the two ends of the viral DNA. To define substrate sequence specificity, we designed an “in vitro evolution” scheme to select an optimal substrate sequence by competitive integration in vitro from a large pool of partially randomized substrates. Integrated substrates are enriched by PCR amplification and then regenerated and subjected to subsequent cycles of selection and enrichment. Using this approach, we obtained the optimal substrate sequence of 5′-ACGACAACA-3′ for avian sarcoma-leukosis virus (ASLV) and 5′-AACA(A/C)AGCA-3′ for human immunodeficiency virus type 1, which differed from those found at both ends of the viral DNA. Clonal analysis of the integration products showed that ASLV integrase can use a wide variety of substrate sequences in vitro, although the consensus sequence was identical to the selected sequence. By a competition assay, the selected nucleotide at position 4 improved the in vitro integration efficiency over that of the wild-type sequence. Viral mutants bearing the optimal sequence replicated at wild-type levels, with the exception of some mutations disrupting the U5 RNA secondary structure important for reverse transcription, which were significantly impaired. Thus, maximizing the efficiency of integration may not be of major importance for efficient retrovirus replication.

Supina, Jaroslav. "On sequence selection properties". Filomat 27, n. 8 (2013): 1523–44. http://dx.doi.org/10.2298/fil1308523s.

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Wattis, Jonathan A. D., e Peter V. Coveney. "Sequence Selection during Copolymerization". Journal of Physical Chemistry B 111, n. 32 (agosto 2007): 9546–62. http://dx.doi.org/10.1021/jp071767h.

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ARLOTTO, ALESSANDRO, e J. MICHAEL STEELE. "Optimal Sequential Selection of a Unimodal Subsequence of a Random Sequence". Combinatorics, Probability and Computing 20, n. 6 (5 ottobre 2011): 799–814. http://dx.doi.org/10.1017/s0963548311000411.

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We consider the problem of selecting sequentially a unimodal subsequence from a sequence of independent identically distributed random variables, and we find that a person doing optimal sequential selection does so within a factor of the square root of two as well as a prophet who knows all of the random observations in advance of any selections. Our analysis applies in fact to selections of subsequences that have d+1 monotone blocks, and, by including the case d=0, our analysis also covers monotone subsequences.

Litviņenko, Anna, e Artūrs Āboltiņš. "Computationally Efficient Chaotic Spreading Sequence Selection for Asynchronous DS-CDMA". Electrical, Control and Communication Engineering 13, n. 1 (1 dicembre 2017): 75–80. http://dx.doi.org/10.1515/ecce-2017-0011.

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Abstract The choice of the spreading sequence for asynchronous direct-sequence code-division multiple-access (DS-CDMA) systems plays a crucial role for the mitigation of multiple-access interference. Considering the rich dynamics of chaotic sequences, their use for spreading allows overcoming the limitations of the classical spreading sequences. However, to ensure low cross-correlation between the sequences, careful selection must be performed. This paper presents a novel exhaustive search algorithm, which allows finding sets of chaotic spreading sequences of required length with a particularly low mutual cross-correlation. The efficiency of the search is verified by simulations, which show a significant advantage compared to non-selected chaotic sequences. Moreover, the impact of sequence length on the efficiency of the selection is studied.

Rowland, Lee A., e David R. Shanks. "Sequence learning and selection difficulty." Journal of Experimental Psychology: Human Perception and Performance 32, n. 2 (2006): 287–99. http://dx.doi.org/10.1037/0096-1523.32.2.287.

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Bukovský, Lev, e Jaroslav Šupina. "Modifications of sequence selection principles". Topology and its Applications 160, n. 18 (dicembre 2013): 2356–70. http://dx.doi.org/10.1016/j.topol.2013.07.030.

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SHAN, YING, HARPREET S. SAWHNEY e ART POPE. "CLUSTERING MULTIPLE IMAGE SEQUENCES WITH A SEQUENCE-TO-SEQUENCE SIMILARITY MEASURE". International Journal of Pattern Recognition and Artificial Intelligence 19, n. 04 (giugno 2005): 551–64. http://dx.doi.org/10.1142/s0218001405004149.

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We propose a novel similarity measure of two image sequences based on shapeme histograms. The idea of shapeme histogram has been used for single image/texture recognition, but is used here to solve the sequence-to-sequence matching problem. We develop techniques to represent each sequence as a set of shapeme histograms, which captures different variations of the object appearances within the sequence. These shapeme histograms are computed from the set of 2D invariant features that are stable across multiple images in the sequence, and therefore minimizes the effect of both background clutter, and 2D pose variations. We define sequence similarity measure as the similarity of the most similar pair of images from both sequences. This definition maximizes the chance of matching between two sequences of the same object, because it requires only part of the sequences being similar. We also introduce a weighting scheme to conduct an implicit feature selection process during the matching of two shapeme histograms. Experiments on clustering image sequences of tracked objects demonstrate the efficacy of the proposed method.

Feng, Chunyu, Yuting Liu, Guangqi Lyu, Songyang Shang, Hongyue Xia, Junpeng Zhang, David M. Irwin, Zhe Wang e Shuyi Zhang. "Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis". BioMed Research International 2022 (13 aprile 2022): 1–8. http://dx.doi.org/10.1155/2022/9627961.

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Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results. Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion. The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.

Chuzhanova, N. A., A. J. Jones e S. Margetts. "Feature selection for genetic sequence classification". Bioinformatics 14, n. 2 (1 marzo 1998): 139–43. http://dx.doi.org/10.1093/bioinformatics/14.2.139.

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Tesi sul tema "Sequence selection":

Tang, Fung Michael, e 鄧峰. "Sequence classification and melody tracks selection". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B29742973.

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Tang, Fung Michael. "Sequence classification and melody tracks selection /". Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25017470.

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Hoffman, Michael M. "Quantifying evolution and natural selection in vertebrate noncoding sequence". Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/245947.

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Abstract (sommario):

When studying genomic evolution, biologists find it important to identify varying patterns of natural selection. Many traditional methods of classifying directional selection have relied on models that categorize mutations as function-altering or neutral, and then comparing the rates of the two categories of mutations. The most well-known methods specifically compare nonsynonymous and synonymous substitutions in protein-coding sequence. The recent availability of whole genome sequences, especially those of various mammals and other vertebrates, enables us to develop alternative methods for analyzing molecular evolution and selection that rely on noncoding sequence. Furthermore, our greater understanding of the importance of noncoding DNA demands such methods. This thesis contains the results of the first in-depth genomic-scale analysis using intron substitutions to estimate the neutral rate of evolution. Performing this analysis across several genomes requires the development of a new model of gene evolution and related methods. I find strong correlation between estimates of the neutral rate made with intron methods and estimates made with synonymous coding nucleotides for both human–dog and mouse–rat comparisons. However, the two estimates cannot be considered directly equivalent. This thesis also describes a novel method that estimates a rate of function affecting evolution in promoter regions by inspecting the effect of simulated mutations on transcription factor binding. This involves the development and use of a probabilistic method that uses a hidden Markov model to predict the binding of transcription factors. I report the results of applying these new methods to the human genome for the identification of transcription factor binding sites, and for the identification of natural selection.

Garske, Tini. "Mutation-selection models of sequence evolution in population genetics". Thesis, Open University, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.412399.

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Buxton, David. "The impact of striatal neuropeptides and topography on action sequence selection". Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/22081/.

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Many common behaviours are a sequence of several actions. As action sequences are learned their activation often becomes habitual, allowing smooth, rapid, and semi-automatic execution; learning and performing action sequences is central to normal motor function. The striatum is the primary input nucleus for the basal ganglia and receives glutamatergic cortical afferents. These afferents innervate localised populations of medium spiny neurons (MSNs) and may encode 'action requests'. Striatal interactions ensure that only non-conflicting, high salience requests are selected, but the mechanisms enabling clean, rapid switching between sequential actions are poorly understood. Substance P (SP) and enkephalin are neuropeptides co-released with GABA by MSNs preferentially expressing D1 or D2 dopamine receptors respectively. SP facilitates subsequent glutamatergic inputs to target MSNs while enkephalin has an inhibitory effect. We construct models of these glutamatergic effects and integrate them into a basal ganglia model to demonstrate that diffuse neuropeptide connectivity enhances action selection. For action sequences with an ordinal structure, patterning SP connectivity to reflect this ordering enhances the selection of correctly–ordered actions and suppresses disordered selection. We also show that selectively pruning SP connections allows context–sensitive inhibition of specific undesirable requests that otherwise interfere with action group selection. We then construct a striatal microcircuit model with physical topography and show that inputs to this model generate oscillations in MSN spiking. Input salience and active neuronal density have differentiable impacts on oscillation amplitude and frequency, but the presence of oscillations has little effect on the mean MSN firing rate or action selection. Our model suggests that neuropeptide interactions enhance the contrast between selected and rejected action requests, and that patterned SP connectivity enhances the selection of ordered sequences. Our model further suggests that striatal topography does not directly impact action selection, but that evoked oscillations may represent an additional form of population coding that could bind together semantically related MSN groups.

Besenmatter, Werner. "Protein engineering with genetic selection : tolerance of enzyme activity to sequence change /". Zürich : ETH, 2007. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16912.

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Ibeh, Neke. "Inferring Viral Dynamics from Sequence Data". Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35317.

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One of the primary objectives of infectious disease research is uncovering the direct link that exists between viral population dynamics and molecular evolution. For RNA viruses in particular, evolution occurs at such a rapid pace that epidemiological processes become ingrained into gene sequences. Conceptually, this link is easy to make: as RNA viruses spread throughout a population, they evolve with each new host infection. However, developing a quantitative understanding of this connection is difficult. Thus, the emerging discipline of phylodynamics is centered on reconciling epidemiology and phylogenetics using genetic analysis. Here, we present two research studies that draw on phylodynamic principles in order to characterize the progression and evolution of the Ebola virus and the human immunodefficiency virus (HIV). In the first study, the interplay between selection and epistasis in the Ebola virus genome is elucidated through the ancestral reconstruction of a critical region in the Ebola virus glycoprotein. Hence, we provide a novel mechanistic account of the structural changes that led up to the 2014 Ebola virus outbreak. The second study applies an approximate Bayesian computation (ABC) approach to the inference of epidemiological parameters. First, we demonstrate the accuracy of this approach with simulated data. Then, we infer the dynamics of the Swiss HIV-1 epidemic, illustrating the applicability of this statistical method to the public health sector. Altogether, this thesis unravels some of the complex dynamics that shape epidemic progression, and provides potential avenues for facilitating viral surveillance efforts.

Sherborne, Amy Louise. "Balancing selection at the major histocompatibility complex (MHC) : sequence diversity and inbreeding avoidance". Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501605.

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The major histocompatibility complex (MHC) is a much studied region of the mammalian genome because of its uniquely high level of polymorphism. Both natural and sexual selection have been implicated in the maintenance of MHC diversity. The elevated heterozygosity observed at the MHC could reflect overdominant heterozygote advantage against pathogenic infection. Equally, MHC disassortative mating would lead to an excess of heterozygotes.

Al-Ouran, Rami. "Motif Selection: Identification of Gene Regulatory Elements using Sequence CoverageBased Models and Evolutionary Algorithms". Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1449003717.

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Niu, Jia. "Translation of DNA into Evolvable Sequence-Defined Synthetic Polymers". Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11351.

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Laboratory directed evolution have enabled the discovery of numerous functional natural and synthetic macromolecules with tailor-made functions. However, approaches that use enzymes to effect the crucial translation from an information carrier molecule such as DNA or RNA to synthetic polymers are limited to producing close analogs of nucleic acids, either due to a strict requirement to hybridize with a nucleic acid template or as a consequence of the limited substrate scope of polymerase enzymes.
Chemistry and Chemical Biology

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Libri sul tema "Sequence selection":

Krzyzanowski, Michel Szulc. Michel Szulc Krzyzanowski sequences: The ultimate selection. Antwerpen: Voetnoot, 2009.

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Rawlings, Christopher J. Software directory for molecular biologists: A complete guide to the selection of computer software for the management and analysis of molecular sequences. [New York, N.Y.]: Stockton Press, 1986.

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Cain, Stephen. Heart of the helix: Being a selection of five consecutive base pairs & thier complementary sequence from the centre of a collaborative work. Toronto: BookThug, Kitsch in Ink Press, 2002.

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Patel, Sejal. Characterisation of sequence selective binding of the pyrrolo[2,1-c][1,4]benzodiazepine dimers to DNA. Portsmouth: University of Portsmouth, Institute of Biomedical and Biomolecular Sciences, 2000.

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Crespellani, Teresa, a cura di. Terremoto e ricerca. Florence: Firenze University Press, 2008. http://dx.doi.org/10.36253/978-88-8453-819-2.

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The profound cultural transformation that has taken place in Italian seismic studies in the last ten years is distinguished by the growing interest in the problem of assessing the effects of earthquakes linked to local conditions, and in the related issue of a precise definition of the properties of the soil in the sphere of the dynamic and cyclical stresses induced by seismic actions. Despite the profound awareness of the extent to which the nature of the soil contributes to the destructive effects of earthquakes, we are still a long way from the possibility of a realistic forecast of the seismic behaviour of the Italian soils. This is because the identification of the dynamic properties calls for experimental equipment that is technologically complex and costly as well as lengthy observation and qualified personnel. The rare experimental data that have been acquired to date hence represent a fundamental element for scientific reflection. This book has been conceived with a view to setting at the disposal of a broader public the results of the tests conducted on site and in the laboratory on the soil of certain significant seismic areas using the dynamic-type apparatus of the Geotechnical Laboratory of the Department of Civil and Environmental Engineering (DICeA) of the University of Florence. It presents a selection of the works of the Geotechnical section of the DICeA that have been published in various specialist international and national ambits. These studies were largely launched following the seismic sequence in Umbria and the Marches, in collaboration with several Regional Authorities and Research Institutes for the reduction of the seismic risk in Italy (GNDT, IRRS, INGV). In addition to the experimental techniques and the results obtained, the models and the geotechnical procedures adopted for assessing the effects of site and soil instability in certain specific deposits of the Italian territory are also expounded.

Morris, Stephen James. Design, synthesis and evaluation of a sequence-selective DNA-cleaving agent based on the pyrrolo[2,1-c][1,4]benzodiazepine ring system: Investigation of the DNA-reactive species. Portsmouth: University of Portsmouth, Division of Medicinal Chemistry and Pharmacognosy, 1992.

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Bortolani, Ljuba Merlina, e Michael Palma. The Siege: A Sequence of Poems (Lannan Translations Selection Series, No. 1). BOA Editions, 2002.

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Sequence dancing: 66 old time dancing favourites : a selection of both social and medal test dances. Nort Star publishers, 1985.

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Walsh, Bruce, e Michael Lynch. Using Molecular Data to Detect Selection: Signatures from Recent Single Events. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0009.

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Abstract (sommario):

Different types and phases of a selective sweep (hard, soft, partial, polygenic) generate different patterns of departures from neutrality, and hence require different tests. It is thus not surprising that a large number of tests have been proposed that use sequence information to detect ongoing, or very-recently completed, episodes of selection. This chapter critically reviews over 50 such tests, which use information on allele-frequency change, linkage disequilibrium patterns, spatial allele-frequency patterns, site-frequency spectrum data, allele-frequency spectrum data, and haplotype structure. This chapter discusses the domain of applicability for each test, and their strengths and weaknesses. Finally, this chapter examines application of these methods in the search for recent, or ongoing, selection in humans and for genes involved in the domestication process in plants and animals.

Walsh, Bruce, e Michael Lynch. Using Molecular Data to Detect Selection: Signatures from Multiple Historical Events. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0010.

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This chapter examines the search for a pattern of repetitive adaptive substitutions over evolutionary time. In contrast with the previous chapter, only a modest number of tests toward this aim have been proposed. The HKA and McDonald-Kreitman tests contrast the polymorphism to divergence ratio between different genomic classes (such as different genes or silent versus replacement sites within the same gene). These approaches can detect an excess of substitutions, which allows one to estimate the fraction of adaptive sites. This chapter reviews the empirical data on estimates of this fraction and discusses some of the sources of bias it its estimation. Over an even longer time scale, one can contrast the rate of change of sites in a sequence over a phylogeny. These tests require a rather special type of selection, wherein the same specific site (usually a codon) experiences multiple adaptive substitutions over a phylogeny, such as might occur in arms-race genes.

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Capitoli di libri sul tema "Sequence selection":

Delahaye, Jean-Paul. "Automatic Selection of Sequence Transformations". In Sequence Transformations, 223–48. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-61347-0_7.

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Ohta, Tomoko. "Drift and Selection in Evolving Interacting Systems". In Structural Approaches to Sequence Evolution, 285–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-35306-5_13.

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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.

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Qiu, Xing, e Lev Klebanov. "Gene Selection with the δ-Sequence Method". In Methods in Molecular Biology, 57–71. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-60327-337-4_4.

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Maccaferri, Marco, Martina Bruschi e Roberto Tuberosa. "Sequence-Based Marker Assisted Selection in Wheat". In Wheat Improvement, 513–38. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-90673-3_28.

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AbstractWheat improvement has traditionally been conducted by relying on artificial crossing of suitable parental lines followed by selection of the best genetic combinations. At the same time wheat genetic resources have been characterized and exploited with the aim of continuously improving target traits. Over this solid framework, innovations from emerging research disciplines have been progressively added over time: cytogenetics, quantitative genetics, chromosome engineering, mutagenesis, molecular biology and, most recently, comparative, structural, and functional genomics with all the related -omics platforms. Nowadays, the integration of these disciplines coupled with their spectacular technical advances made possible by the sequencing of the entire wheat genome, has ushered us in a new breeding paradigm on how to best leverage the functional variability of genetic stocks and germplasm collections. Molecular techniques first impacted wheat genetics and breeding in the 1980s with the development of restriction fragment length polymorphism (RFLP)-based approaches. Since then, steady progress in sequence-based, marker-assisted selection now allows for an unprecedently accurate ‘breeding by design’ of wheat, progressing further up to the pangenome-based level. This chapter provides an overview of the technologies of the ‘circular genomics era’ which allow breeders to better characterize and more effectively leverage the huge and largely untapped natural variability present in the Triticeae gene pool, particularly at the tetraploid level, and its closest diploid and polyploid ancestors and relatives.

Tamboli, Mubin Shoukat, e Rajesh S. Prasad. "Authorship Identification with Multi Sequence Word Selection Method". In Advances in Intelligent Systems and Computing, 653–61. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-16657-1_61.

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Liang, Yuzhi, Jia Zhu, Yupeng Li, Min Yang e Siu Ming Yiu. "Relevant Fact Selection for QA via Sequence Labeling". In Knowledge Science, Engineering and Management, 399–409. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-63558-3_34.

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Gupta, Mayetri. "Model selection and sensitivity analysis for sequence pattern models". In Beyond Parametrics in Interdisciplinary Research: Festschrift in Honor of Professor Pranab K. Sen, 390–407. Beachwood, Ohio, USA: Institute of Mathematical Statistics, 2008. http://dx.doi.org/10.1214/193940307000000301.

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Saeys, Yvan, e Yves Van de Peer. "Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection". In Knowledge Discovery and Emergent Complexity in Bioinformatics, 107–18. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-71037-0_7.

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Atti di convegni sul tema "Sequence selection":

Qian, Chao, Chao Feng e Ke Tang. "Sequence Selection by Pareto Optimization". In Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. California: International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/206.

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The problem of selecting a sequence of items from a universe that maximizes some given objective function arises in many real-world applications. In this paper, we propose an anytime randomized iterative approach POSeqSel, which maximizes the given objective function and minimizes the sequence length simultaneously. We prove that for any previously studied objective function, POSeqSel using a reasonable time can always reach or improve the best known approximation guarantee. Empirical results exhibit the superior performance of POSeqSel.

Yu, Qiang, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter e Jun Huan. "Reference sequence selection for motif searches". In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359745.

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Kaneshige, John, Kalmanje KrishnaKumar e Felix Shung. "Tactical Maneuvering Using Immunized Sequence Selection". In 2nd AIAA "Unmanned Unlimited" Conf. and Workshop & Exhibit. Reston, Virigina: American Institute of Aeronautics and Astronautics, 2003. http://dx.doi.org/10.2514/6.2003-6640.

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Shechtman, Slava, David Haws e Raul Fernandez. "Stable Checkpoint Selection and Evaluation in Sequence to Sequence Speech Synthesis". In ICASSP 2021 - 2021 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE, 2021. http://dx.doi.org/10.1109/icassp39728.2021.9414402.

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D’Souza, Roshan M., Paul K. Wright e Carlo Se´quin. "Handling Tool Holder Collision in Optimal Tool Sequence Selection for 2.5-D Pocket Machining". In ASME 2002 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2002. http://dx.doi.org/10.1115/detc2002/cie-34475.

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Significant cycle time saving can be achieved in 2.5-D milling by intelligently selecting tool sequences. The problem of finding the optimal tool sequence was reduced to finding the shortest path in a single-source single-sink directed acyclic graph. The nodes in the graph represented the state of the stock after the tool named in the node was done machining and the edges represented the cost of machining. In this paper a novel method for handling tool holder collision in the graph-based algorithm for optimal tool sequence selection has been developed. The method consists of iteratively solving the graph for the shortest path, validating the solution by checking for tool holder collisions and eliminating problematic edges in the graph. Also described is a method to intelligently build the graph such that in presence of tool holder collisions, the complexity of building the graph is greatly reduced.

Villeval, Shahar, Joseph Tabrikian e Igal Bilik. "Optimal Antenna Selection Sequence for MIMO Radar". In 2019 53rd Asilomar Conference on Signals, Systems, and Computers. IEEE, 2019. http://dx.doi.org/10.1109/ieeeconf44664.2019.9049069.

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Cho, Jaemin, Minjoon Seo e Hannaneh Hajishirzi. "Mixture Content Selection for Diverse Sequence Generation". In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). Stroudsburg, PA, USA: Association for Computational Linguistics, 2019. http://dx.doi.org/10.18653/v1/d19-1308.

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Wang, Yiding, Yuanshu Li e Zhulei Wang. "Code sequence selection for SAR radiometric calibration". In IGARSS 2010 - 2010 IEEE International Geoscience and Remote Sensing Symposium. IEEE, 2010. http://dx.doi.org/10.1109/igarss.2010.5651086.

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Lowe, G., e B. Shirinzadeh. "Dynamic assembly sequence selection using reinforcement learning". In IEEE International Conference on Robotics and Automation, 2004. Proceedings. ICRA '04. 2004. IEEE, 2004. http://dx.doi.org/10.1109/robot.2004.1307458.

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Brzus, Michal, Cavan J. Riley, Joel Bruss, Aaron Boes, Randall Jones e Hans J. Johnson. "DICOM sequence selection for medical imaging applications". In Imaging Informatics for Healthcare, Research, and Applications, a cura di Shandong Wu e Hiroyuki Yoshida. SPIE, 2024. http://dx.doi.org/10.1117/12.3006568.

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Rapporti di organizzazioni sul tema "Sequence selection":

Gelb, Jr., Jack, Yoram Weisman, Brian Ladman e Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, dicembre 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.

Lippolis, Nicolas. Diagnostics for Industrialisation: Growth, Sectoral Selection, and Constraints on Firms. Digital Pathways at Oxford, marzo 2022. http://dx.doi.org/10.35489/bsg-dp-wp_2022/03.

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This paper reviews methods that have been suggested by the development literature on diagnostics. We subdivide the variety of diagnostics into three types: revealing the most binding constraints to economy-wide growth; selecting sectors in which to diversify; and identifying sources of sectoral underperformance. Each diagnostic method is judged on whether it: provides a structured way of performing diagnostics; directs analysts towards the right questions; and is efficient in its use of data and resources. After reviewing a variety of methods, we argue that, with respect to growth diagnostics, the best approach is to combine Hausmann’s, Rodrik and Velasco’s Growth Diagnostics with more encompassing and forward-looking methods. In sectoral selection, Hausmann and Hidalgo’s 'Product Space' analysis can serve as an adequate base for choosing sectors in which to diversify, but this method must be tempered by a much more diverse set of indicators that matter for sectoral choice. Finally, diagnostics at the sectoral level can be performed through a sequence of methods: starting from easily collectable perceptions data and progressing to more data-heavy techniques, depending on the time and resources available.

Funkenstein, Bruria, e Cunming Duan. GH-IGF Axis in Sparus aurata: Possible Applications to Genetic Selection. United States Department of Agriculture, novembre 2000. http://dx.doi.org/10.32747/2000.7580665.bard.

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Many factors affect growth rate in fish: environmental, nutritional, genetics and endogenous (physiological) factors. Endogenous control of growth is very complex and many hormone systems are involved. Nevertheless, it is well accepted that growth hormone (GH) plays a major role in stimulating somatic growth. Although it is now clear that most, if not all, components of the GH-IGF axis exist in fish, we are still far from understanding how fish grow. In our project we used as the experimental system a marine fish, the gilthead sea bream (Sparus aurata), which inhabits lagoons along the Mediterranean and Atlantic coasts of Europe, and represents one of the most important fish species used in the mariculture industry in the Mediterranean region, including Israel. Production of Sparus is rapidly growing, however, in order for this production to stay competitive, the farming of this fish species has to intensify and become more efficient. One drawback, still, in Sparus extensive culture is that it grows relatively slow. In addition, it is now clear that growth and reproduction are physiological interrelated processes that affect each other. In particular sexual maturation (puberty) is known to be closely related to growth rate in fish as it is in mammals, indicating interactions between the somatotropic and gonadotropic axes. The goal of our project was to try to identify the rate-limiting components(s) in Sparus aurata GH-IGF system which might explain its slow growth by studying the ontogeny of growth-related genes: GH, GH receptor, IGF-I, IGF-II, IGF receptor, IGF-binding proteins (IGFBPs) and Pit-1 during early stages of development of Sparus aurata larvae from slow and fast growing lines. Our project was a continuation of a previous BARD project and could be divided into five major parts: i) obtaining additional tools to those obtained in the previous project that are necessary to carry out the developmental study; ii) the developmental expression of growth-related genes and their cellular localization; iii) tissue-specific expression and effect of GH on expression of growth-related genes; iv) possible relationship between GH gene structure, growth rate and genetic selection; v) the possible role of the IGF system in gonadal development. The major findings of our research can be summarized as follows: 1) The cDNAs (complete or partial) coding for Sparus IGFBP-2, GH receptor and Pit-1 were cloned. Sequence comparison reveals that the primary structure of IGFBP-2 protein is 43-49% identical to that of zebrafish and other vertebrates. Intensive efforts resulted in cloning a fragment of 138 nucleotides, coding for 46 amino acids in the proximal end of the intracellular domain of GH receptor. This is the first fish GH receptor cDNA that had been cloned to date. The cloned fragment will enable us to complete the GH - receptor cloning. 2) IGF-I, IGF-II, IGFBP-2, and IGF receptor transcripts were detected by RT-PCR method throughout development in unfertilized eggs, embryos, and larvae suggesting that these mRNAs are products of both the maternal and the embryonic genomes. Preliminary RT-PCR analysis suggest that GH receptor transcript is present in post-hatching larvae already on day 1. 3) IGF-1R transcripts were detected in all tissues tested by RT-PCR with highest levels in gill cartilage, skin, kidney, heart, pyloric caeca, and brain. Northern blot analysis detected IGF receptor only in gonads, brain and gill cartilage but not in muscle; GH increased slightly brain and gill cartilage IGF-1R mRNA levels. 4) IGFBP-2 transcript were detected only in liver and gonads, when analyzed by Northern blots; RT-PCR analysis revealed expression in all tissues studied, with the highest levels found in liver, skin, gonad and pyloric caeca. 5) Expression of IGF-I, IGF-II, IGF-1R and IGFBP-2 was analyzed during gonadal development. High levels of IGF-I and IGFBP-2 expression were found in bisexual young gonads, which decreased during gonadal development. Regardless of maturational stage, IGF-II levels were higher than those of IGF-L 6) The GH gene was cloned and its structure was characterized. It contains minisatellites of tandem repeats in the first and third introns that result in high level of genetic polymorphism. 7) Analysis of the presence of IGF-I and two types of IGF receptor by immunohistochemistry revealed tissue- and stage-specific expression during larval development. Immunohistochemistry also showed that IGF-I and its receptors are present in both testicular and ovarian cells. Although at this stage we are not able to pinpoint which is the rate-limiting step causing the slow growth of Sparus aurata, our project (together with the previous BARD) yielded a great number of experimental tools both DNA probes and antibodies that will enable further studies on the factors regulating growth in Sparus aurata. Our expression studies and cellular localization shed new light on the tissue and developmental expression of growth-related genes in fish.

Medrano, Juan, Adam Friedmann, Moshe (Morris) Soller, Ehud Lipkin e Abraham Korol. High resolution linkage disequilibrium mapping of QTL affecting milk production traits in Israel Holstein dairy cattle. United States Department of Agriculture, marzo 2008. http://dx.doi.org/10.32747/2008.7696509.bard.

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Original objectives: To create BAC contigs covering two QTL containing chromosomal regions (QTLR) and obtain BAC end sequence information as a platform for SNP identification. Use the SNPs to search for marker-QTL linkage disequilibrium (LD) in the test populations (US and Israel Holstein cattle). Identify candidate genes, test for association with dairy cattle production and functional traits, and confirm any associations in a secondary test population. Revisions in the course of the project: The selective recombinant genotyping (SRG) methodology which we implemented to provide moderate resolution QTL mapping turned out to be less effective than expected, due to problems introduced by incomplete marker informativity. This required a no-cost one-year extension of the project. Aside from this, the project was implemented essentially as envisaged, but only with respect to a single QTLR and single population association-test. Background to the topic. Dairy cattle breeders are looking to marker-assisted selection (MAS) as a means of identifying genetically superior sires and dams. MAS based on population-wide LD can be many times more effective than MAS based on within-family linkage mapping. In this proposal we developed a protocol leading from family based QTL mapping to population-wide LD between markers and the QTL Major conclusions, solutions, achievements. The critical importance of marker informativity for application of the SRG design in outcrossing random mating populations was identified, and an alternative Fractioned Pool Design (FPD) based on selective DNA pooling was developed. We demonstrated the feasibility of constructing a BAC contig across a targeted chromosomal region flanking the marker RM188 on bovine chromosome BTA4, which was shown in previous work to contain a QTL affecting milk production traits. BAC end sequences were obtained and successfully screened for SNPs. LD studies of these SNPs in the Israel population, and of an independent set of SNPs taken across the entire proximal region of BTA4 in the USA population, showed a much lower degree of LD than previously reported in the literature. Only at distances in the sub-cM level did an appreciable fraction of SNP marker-pairs show levels of LD useful for MAS. In contrast, studies in the Israel population using microsatellite markers, presented an equivalent degree of LD at a 1-5 separation distance. SNP LD appeared to reflect historical population size of Bostaurus (Ne=5000- 10,000), while microsatellite LD appeared to be in proportion to more recent effective population size of the Holstein breed (Ne=50-100). An appreciable fraction of the observed LD was due to Family admixture structure of the Holstein population. The SNPs MEOX2/IF2G (found within the gene SETMAR at 23,000 bp from RM188) and SNP23 were significantly associated with PTA protein, Cheese dollars and Net Merit Protein in the Davis bull resource population, and were also associated with protein and casein percentages in the Davis cow resource population. Implications. These studies document a major difference in degree of LD presented by SNPs as compared to microsatellites, and raise questions as to the source of this difference and its implications for QTL mapping and MAS. The study lends significant support to the targeted approach to fine map a previously identified QTL. Using high density genotyping with SNP discovered in flanking genes to the QTL, we have identified important markers associated with milk protein percentage that can be tested in markers assisted selection programs.

Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu e George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, gennaio 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.

Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir e Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, dicembre 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.

Taylor, Palmer. The Primary Sequence of Acetylcholinesterase and Selective Antibodies for the Detection of Organophosphate Toxicity. Fort Belvoir, VA: Defense Technical Information Center, novembre 1989. http://dx.doi.org/10.21236/ada225175.

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Seroussi, Eyal, e George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, settembre 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.

Leach, Roland M., Mark Pines, Carol V. Gay e Shmuel Hurwitz. In vivo and in vitro Chondrocyte Metabolism in Relationship to the Developemnt of Tibial Dyschondroplasia in Broiler Chickens. United States Department of Agriculture, luglio 1993. http://dx.doi.org/10.32747/1993.7568090.bard.

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Skeletal deformities are a significant financial and welfare problem for the world poultry industry. Tibial dyschondroplasia (TD) is the most prevalent skeletal abnormality found in young broilers, turkeys and ducks. Tibial dyschondroplasia results from a perturbation of the sequence of events in the epiphyseal growth plate, the tissue responsible for longitudinal bone growth. The purpose of this investigation was to test the hypothesis that TD was the result of a failure of growth plate chondrocytes to differentiate and express the chemotactic molecules required for cartilage vascularization. In this investigation in situ hybridization and immunocytochemical techniques were used to study chondrocyte gene products associated with cartilage maturation and vascularization such as osteopontin, osteonectin, type X collagen, and alkaline phosphatase. All markers were present in the growth plate tissue anter or to the TD lesion but were greatly diminished in the TD lesion. Thus, rather than not acquiring the markers for hypertrophy, it appears that the growth plate chondrocytes reach a certain stage of hypertrophy and then de-differentiate into cells which resemble chondrocytes in the prehypertrophic zone. Similar patterns were observed in all TD tissues examined whether the lesions were spontaneous or induced by dietary treatments or genetic selection. The decrease in gene expression can at least be partially explained by the fact that many of the dysplastic chondrocytes show classic signs of apoptosis. These results provide an explanation for the observation that a variety of genes show reduced expression in the TD lesion when examined by in situ hybridization. This would suggest that future research should focus on the earliest detectable stages in the development of TD and examine endocrine and autocrine factors which cause chondrocytes to de-differentiate and undergo premature apoptosis.

Mazzoni, Silvia, Nicholas Gregor, Linda Al Atik, Yousef Bozorgnia, David Welch e Gregory Deierlein. Probabilistic Seismic Hazard Analysis and Selecting and Scaling of Ground-Motion Records (PEER-CEA Project). Pacific Earthquake Engineering Research Center, University of California, Berkeley, CA, novembre 2020. http://dx.doi.org/10.55461/zjdn7385.

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This report is one of a series of reports documenting the methods and findings of a multi-year, multi-disciplinary project coordinated by the Pacific Earthquake Engineering Research Center (PEER) and funded by the California Earthquake Authority (CEA). The overall project is titled “Quantifying the Performance of Retrofit of Cripple Walls and Sill Anchorage in Single-Family Wood-Frame Buildings,” henceforth referred to as the “PEER–CEA Project.” The overall objective of the PEER–CEA Project is to provide scientifically based information (e.g., testing, analysis, and resulting loss models) that measure and assess the effectiveness of seismic retrofit to reduce the risk of damage and associated losses (repair costs) of wood-frame houses with cripple wall and sill anchorage deficiencies as well as retrofitted conditions that address those deficiencies. Tasks that support and inform the loss-modeling effort are: (1) collecting and summarizing existing information and results of previous research on the performance of wood-frame houses; (2) identifying construction features to characterize alternative variants of wood-frame houses; (3) characterizing earthquake hazard and ground motions at representative sites in California; (4) developing cyclic loading protocols and conducting laboratory tests of cripple wall panels, wood-frame wall subassemblies, and sill anchorages to measure and document their response (strength and stiffness) under cyclic loading; and (5) the computer modeling, simulations, and the development of loss models as informed by a workshop with claims adjustors. This report is a product of Working Group 3 (WG3), Task 3.1: Selecting and Scaling Ground-motion records. The objective of Task 3.1 is to provide suites of ground motions to be used by other working groups (WGs), especially Working Group 5: Analytical Modeling (WG5) for Simulation Studies. The ground motions used in the numerical simulations are intended to represent seismic hazard at the building site. The seismic hazard is dependent on the location of the site relative to seismic sources, the characteristics of the seismic sources in the region and the local soil conditions at the site. To achieve a proper representation of hazard across the State of California, ten sites were selected, and a site-specific probabilistic seismic hazard analysis (PSHA) was performed at each of these sites for both a soft soil (Vs30 = 270 m/sec) and a stiff soil (Vs30=760 m/sec). The PSHA used the UCERF3 seismic source model, which represents the latest seismic source model adopted by the USGS [2013] and NGA-West2 ground-motion models. The PSHA was carried out for structural periods ranging from 0.01 to 10 sec. At each site and soil class, the results from the PSHA—hazard curves, hazard deaggregation, and uniform-hazard spectra (UHS)—were extracted for a series of ten return periods, prescribed by WG5 and WG6, ranging from 15.5–2500 years. For each case (site, soil class, and return period), the UHS was used as the target spectrum for selection and modification of a suite of ground motions. Additionally, another set of target spectra based on “Conditional Spectra” (CS), which are more realistic than UHS, was developed [Baker and Lee 2018]. The Conditional Spectra are defined by the median (Conditional Mean Spectrum) and a period-dependent variance. A suite of at least 40 record pairs (horizontal) were selected and modified for each return period and target-spectrum type. Thus, for each ground-motion suite, 40 or more record pairs were selected using the deaggregation of the hazard, resulting in more than 200 record pairs per target-spectrum type at each site. The suites contained more than 40 records in case some were rejected by the modelers due to secondary characteristics; however, none were rejected, and the complete set was used. For the case of UHS as the target spectrum, the selected motions were modified (scaled) such that the average of the median spectrum (RotD50) [Boore 2010] of the ground-motion pairs follow the target spectrum closely within the period range of interest to the analysts. In communications with WG5 researchers, for ground-motion (time histories, or time series) selection and modification, a period range between 0.01–2.0 sec was selected for this specific application for the project. The duration metrics and pulse characteristics of the records were also used in the final selection of ground motions. The damping ratio for the PSHA and ground-motion target spectra was set to 5%, which is standard practice in engineering applications. For the cases where the CS was used as the target spectrum, the ground-motion suites were selected and scaled using a modified version of the conditional spectrum ground-motion selection tool (CS-GMS tool) developed by Baker and Lee [2018]. This tool selects and scales a suite of ground motions to meet both the median and the user-defined variability. This variability is defined by the relationship developed by Baker and Jayaram [2008]. The computation of CS requires a structural period for the conditional model. In collaboration with WG5 researchers, a conditioning period of 0.25 sec was selected as a representative of the fundamental mode of vibration of the buildings of interest in this study. Working Group 5 carried out a sensitivity analysis of using other conditioning periods, and the results and discussion of selection of conditioning period are reported in Section 4 of the WG5 PEER report entitled Technical Background Report for Structural Analysis and Performance Assessment. The WG3.1 report presents a summary of the selected sites, the seismic-source characterization model, and the ground-motion characterization model used in the PSHA, followed by selection and modification of suites of ground motions. The Record Sequence Number (RSN) and the associated scale factors are tabulated in the Appendices of this report, and the actual time-series files can be downloaded from the PEER Ground-motion database Portal (https://ngawest2.berkeley.edu/)(link is external).