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Relevant bibliographies by topics / Sequence profiles

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Academic literature on the topic 'Sequence profiles'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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Journal articles on the topic "Sequence profiles"

1

Popovic, Tatjana, Aleksandra Jelusic, Petar Mitrovic, Renata Ilicic, and Sanja Markovic. "Allelic profile of Serbian Xanthomonas campestris pv. campestris isolates from cabbage." Pesticidi i fitomedicina 35, no. 1 (2020): 19–26. http://dx.doi.org/10.2298/pif2001019p.

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Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot disease of cabbage (Brassica oleracea var. capitata L.), is one of the most important bacteria which affect proper cabbage growth, leading to head weight and quality losses and thereby drastically reducing its marketing value. The pathogen is genetically diverse, which is evident from the presence of eleven races worldwide and more than thirty combinations of allelic profiles. Therefore, this study aimed to determine the allelic profiles of Serbian cabbage Xcc strains obtained in 2014. The analysis was done on three selected Xcc strains whose DNA was first amplified using polymerase chain reaction (PCR) with four housekeeping genes - P-XdnaK, fyuA, gyrB, and rpoD, then sequenced, and the obtained sequences were finally used to determine allelic profiles. Allelic profiles were determined by comparison with 33 Xcc strains obtained from different hosts and regions, whose allelic profiles had been determined previously. A non-redundant database (NRDB) from the pubMLST was used for allelic profile determination and Phyloviz software for constructing a minimum spanning tree. The obtained allelic profile of all Serbian Xcc cabbage strains was 1, 3, 1, 1 for the P-X-dnaK, fyuA, gyrB and rpoD genes, respectively. This profile is assigned as sequence type 2 (ST2) and it coincides with a Portuguese B. oleracea Xcc strain, CPBF 213, originating from B. oleracea var. costata. No connection between sequence type (ST) and the host was detected.

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Kiah, Han Mao, Gregory J. Puleo, and Olgica Milenkovic. "Codes for DNA Sequence Profiles." IEEE Transactions on Information Theory 62, no. 6 (June 2016): 3125–46. http://dx.doi.org/10.1109/tit.2016.2555321.

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Rozemuller, E. H., B. Chadwick, D. Charron, L. A. Baxter-Lowe, J. F. Eliaou, L. Johnston-Dow, and M. G. J. Tilanus. "Sequenase sequence profiles used for HLA-DPB1 sequencing-based typing." Tissue Antigens 47, no. 1 (January 1996): 72–79. http://dx.doi.org/10.1111/j.1399-0039.1996.tb02516.x.

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FREITAS, A. D., and S. COUTINHO. "MULTIFRACTALITY OF GENERALIZED FIBONACCI PROFILES." Fractals 01, no. 03 (September 1993): 694–701. http://dx.doi.org/10.1142/s0218348x93000721.

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The multifractal properties of a class of one parameter generalized Fibonacci sequences are studied. This class of recursion relations, which is defined by an infinite set of sequences similar to the original Fibonacci’s one, appears for the first time in the study of the Ising model by the real space Migdal-Kadanoff renormalization group approach. The whole set of numbers generated by these equations, when properly arranged over the interval [0,1], gives the exact local magnetization profile of the Ising model on generalized hierarchical lattices at the critical temperature. This profile has a multifractal structure showing that an infinite set of exponents is required to describe how its singularities are distributed. The F(α)-function for the measure defined by the normalized profile is numerically obtained and analyzed. Each value of α characterizes the set of numbers generated by one sequence with arbitrary initial conditions. The exact lower (αmin) and upper (αmax) bounds of the spectra are analytically calculated. For a particular value of the parameter, the original Fibonacci sequence appears, generating a set of numbers diverging with the αmin exponent.

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Hirons, Linda, Eleanor J. Gardiner, Christopher A. Hunter, and Peter Willett. "Structural DNA Profiles: Single Sequence Queries." Journal of Chemical Information and Modeling 46, no. 2 (March 2006): 743–52. http://dx.doi.org/10.1021/ci050385a.

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Gil, Nelson, and Andras Fiser. "Identifying functionally informative evolutionary sequence profiles." Bioinformatics 34, no. 8 (December 1, 2017): 1278–86. http://dx.doi.org/10.1093/bioinformatics/btx779.

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Gardiner, Don L., Alison M. Goodfellow, Diana R. Martin, and Kadaba S. Sriprakash. "Group A Streptococcal Vir Types Are M-Protein Gene (emm) Sequence Type Specific." Journal of Clinical Microbiology 36, no. 4 (1998): 902–7. http://dx.doi.org/10.1128/jcm.36.4.902-907.1998.

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The M-protein genes (emm genes) of 103 separate impetiginous Streptococcus pyogenes isolates were sequenced and the sequence types were compared to the types obtained by Vir typing. Vir typing is based on restriction fragment length polymorphism (RFLP) analysis of a 4- to 7-kb pathogenicity island encodingemm and other virulence genes. By using bothHaeIII and HinfI to generate RFLP profiles, complete concordance between Vir type and emm sequence type was found. Comparison of the emm sequences with those in GenBank revealed new sequence types sharing less than 90% identity with known types. Diversity in the emm sequence was generated by corrected frameshift mutations, point mutations, and small in-frame mutations.

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Rychlewski, Leszek, Weizhong Li, Lukasz Jaroszewski, and Adam Godzik. "Comparison of sequence profiles. Strategies for structural predictions using sequence information." Protein Science 9, no. 2 (December 31, 2008): 232–41. http://dx.doi.org/10.1110/ps.9.2.232.

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Kim, Byoung-Jun, Jae-Myung Kim, Bo-Ram Kim, So-Young Lee, GaNa Kim, Yun-Ho Jang, Soyoon Ryoo, et al. "Mycobacterium anyangense sp. nov., a rapidly growing species isolated from blood of Korean native cattle, Hanwoo (Bos taurus coreanae)." International Journal of Systematic and Evolutionary Microbiology 65, Pt_7 (July 1, 2015): 2277–85. http://dx.doi.org/10.1099/ijs.0.000255.

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From the whole blood of Korean native cattle, Hanwoo (Bos taurus coreanae), a previously undescribed, rapidly growing, scotochromogenic isolate of the genus Mycobacterium is reported. Its 16S rRNA gene sequence, and the sequences of three other genes (hsp65, recA and rpoB) were unique and phylogenetic analysis based on 16S rRNA gene sequence (1420 bp) placed the organism into the rapidly growing Mycobacterium group close to Mycobacterium smegmatis (98.5 % sequence similarity). However, phylogenetic analyses based on three different gene sequences (hsp65, recA and rpoB) revealed its location to be distinct from the branch of rapidly growing species. Culture and biochemical characteristics were generally similar to those of Mycobacterium fortuitum. Unique matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS profiles of lipids, unique fatty acid profile, unique mycolic acids profiles and a low DNA–DNA relatedness to M. fortuitum (23.6 %) and M. smegmatis (39.7 %) strongly supported the taxonomic status of this strain as a representative of a novel species of rapidly growing mycobacteria named Mycobacterium anyangense. The type strain is strain QIA-38T ( = JCM 30275T = KCTC 29443T).

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Xiong, Yi, Juan Liu, Wen Zhang, and Tao Zeng. "Prediction of heme binding residues from protein sequences with integrative sequence profiles." Proteome Science 10, Suppl 1 (2012): S20. http://dx.doi.org/10.1186/1477-5956-10-s1-s20.

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Dissertations / Theses on the topic "Sequence profiles"

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Chan, Yin-leung. "Identification of bacteria with ambiguous biochemical profiles by 16S ribosomal RNA gene sequencing." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23373209.

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陳賢良 and Yin-leung Chan. "Identification of bacteria with ambiguous biochemical profiles by 16S ribosomal RNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B3197028X.

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Menlove, Kit J. "Model Detection Based upon Amino Acid Properties." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2253.

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Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most basic and fundamental problems at the heart of bioinformatics. It is central to problems currently under intense investigation in protein structure prediction, phylogenetic analyses, and computational drug development. Currently discriminative methods for homology detection, which are not readily interpretable, are substantially more powerful than their more interpretable counterparts, particularly when sequence identity is very low. Here I present a computational graph-based framework for homology inference using physiochemical amino acid properties which aims to both reduce the gap in accuracy between discriminative and generative methods and provide a framework for easily identifying the physiochemical basis for the structural similarity between proteins. The accuracy of my method slightly improves on the accuracy of PSI-BLAST, the most popular generative approach, and underscores the potential of this methodology given a more robust statistical foundation.

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Savel, Daniel M. "Towards a Human Genomic Coevolution Network." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1524241451267546.

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Chen, Sharon S. "Peptide sequence assignments by probabilistic peptide profile matching to an annotated peptide database /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/8084.

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Reysset, Aurelien. "Conception préliminaire d'actionneurs électromécaniques - outils d'aide à la spécification et à la génération de procédures de dimensionnement pour l'optimisation." Thesis, Toulouse, INSA, 2015. http://www.theses.fr/2015ISAT0003/document.

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Cette thèse a pour objectif d’apporter un ensemble d’outils logiciels s’inscrivant dans une méthodologie globale de conception de systèmes mécatroniques. Elle arrive en complément de travaux déjà menés au sein du laboratoire sur le pré-dimensionnement d’actionneurs aéronautiques de nouvelle génération : les actionneurs électromécaniques (EMA). Cette technologie apporte de nouvelles problématiques qui forcent les ingénieurs à modifier leur processus de développement et ce dès la phase de spécification où des profils de mission devront être générés/transformés/analysés de manière à simplifier la conception et assurer leur validation. Une toolbox Simulink a donc été créée dans cette thèse pour répondre à ce besoin de transformation de l’information entre avionneur et systémier. Comme tout système embarqué, le concepteur fait face à des compromis entre performances, durée de vie et intégration, qui peuvent se résumer à un problème d’optimisation décrit par un ensemble d’équations et de contraintes. Un effort particulier de description a été mené sur le conditionnement de ces équations sous la forme d’un séquencement de calculs explicites adaptés aux algorithmes d’optimisation. La méthode et son implémentation logicielle, toutes deux basées sur la théorie des graphes, interagissent avec le concepteur de manière à l’informer des erreurs de singularité ou de bouclages algébriques apparaissant dans son problème et à lui fournir des pistes de résolution. Pour finir, des études de pré-dimensionnement d’actionneurs de train d’atterrissage et de surfaces de vol primaires (aileron et spoiler), réalisées dans le cadre de cette thèse, dresseront les possibilités offertes par cette approche innovante : conception intégrée avec une cinématique complexe, conception collaborative pluri-partenaires découplée, utilisation de surfaces de réponse pour accélérer l’optimisation
The aim of this thesis is to bring a package of software tools included in a whole methodology dealing with mechatronic systems design. It comes as an add-on to the work already carried out at the laboratory in the field of the new generation of aircraft actuation systems: electromechanical actuators (EMA). This technology triggers new problematics leading the engineers to modify their development process as early as the specification phase, when mission profiles have to be generated/transformed/analyzed in order to simplify the design and ensure the validation step. Thus a Simulink toolbox has been created to meet the need for an information translator working as an intermediate between airframer and system-supplier. As for all the embedded systems, the designer has to face some performance-lifetime-integration trade-off, which can be considered as an optimization problem described by a set of equations and constraints. Particular attention is paid here to the conditioning of those explicit equations in order to obtain a standardized calculation sequence adapted to many optimization algorithms. The method and implemented software, both based on the graph theory, interact with the designer to inform him on the possible singularity and algebraic loop issues, providing some leads for their resolution. Finally, some preliminary sizing studies of landing gear and primary flight control surfaces (aileron and spoiler) actuation systems are presented to highlight the possibilities brought out by this innovative approach: integrated design with complex kinematics, collaborative multi-partners design, use of response surfaces to speed up the optimization

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Zhang, Yue. "Detection copy number variants profile by multiple constrained optimization." HKBU Institutional Repository, 2017. https://repository.hkbu.edu.hk/etd_oa/439.

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Copy number variation, causing by the genome rearrangement, generally refers to the copy numbers increased or decreased of large genome segments whose lengths are more than 1kb. Such copy number variations mainly appeared as the sub-microscopic level of deletion and duplication. Copy number variation is an important component of genome structural variation, and is one of pathogenic factors of human diseases. Next generation sequencing technology is a popular CNV detection method and it has been widely used in various fields of life science research. It possesses the advantages of high throughput and low cost. By tailoring NGS technology, it is plausible to sequence individual cells. Such single cell sequencing can reveal the gene expression status and genomic variation profile of a single-cell. Single cell sequencing is promising in the study of tumor, developmental biology, neuroscience and other fields. However, there are two challenging problems encountered in CNV detection for NGS data. The first one is that since single-cell sequencing requires a special genome amplification step to accumulate enough samples, a large number of bias is introduced, making the calling of copy number variants rather challenging. The performances of many popular copy number calling methods, designed for bulk sequencings, are not consistent and cannot be applied on single-cell sequenced data directly. The second one is to simultaneously analyze genome data for multiple samples, thus achieving assembling and subgrouping similar cells accurately and efficiently. The high level of noises in single-cell-sequencing data negatively affects the reliability of sequence reads and leads to inaccurate patterns of variations. To handle the problem of reliably finding CNVs in NGS data, in this thesis, we firstly establish a workflow for analyzing NGS and single-cell sequencing data. The CNVs identification is formulated as a quadratic optimization problem with both constraints of sparsity and smoothness. Tailored from alternating direction minimization (ADM) framework, an efficient numerical solution is designed accordingly. The proposed model was tested extensively to demonstrate its superior performances. It is shown that the proposed approach can successfully reconstruct CNVs especially somatic copy number alteration patterns from raw data. By comparing with existing counterparts, it achieved superior or comparable performances in detection of the CNVs. To tackle this issue of recovering the hidden blocks within multiple single-cell DNA-sequencing samples, we present an permutation based model to rearrange the samples such that similar ones are positioned adjacently. The permutation is guided by the total variational (TV) norm of the recovered copy number profiles, and is continued until the TV-norm is minimized when similar samples are stacked together to reveal block patterns. Accordingly, an efficient numerical scheme for finding this permutation is designed, tailored from the alternating direction method of multipliers. Application of this method to both simulated and real data demonstrates its ability to recover the hidden structures of single-cell DNA sequences.

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Houston, Alice Elizabeth Dashwood. "On binary sequences with specific linear complexity and correlation properties." Thesis, Royal Holloway, University of London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.307031.

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For many applications, such as cryptography and digital communications, binary sequences with certain specific properties are required. These include a balance of 0's and 1's in a period, ideal runs frequencies, good auto- and cross-correlation spectra, and high linear complexity. Perfect Linear Complexity Profile sequences (PLCPs) have the linear complexity of all subsequences (starting with the first bit) equal to half the length of the subsequence (this is the expected value for a random sequence). We investigate the density - proportion of ones - of finite length PLCPs, both in general and for specific examples. We gain results on the average, maximal and minimal densities, as well as their limits as the length tends to infinity. We also study whether the PLCP property is preserved under various decimations. PLCPs are characterised by a simple linear recurrence modulo 2. We look at similar "nearly" perfect profiles and characterise sequences with these profiles in terms of similar recurrences. Also sequences with a PLCP up to a point and then constant complexity are characterised in terms of the convergents in the continued fraction expansion of the generating function of PLCPs, and we look briefly at their corresponding periods. Sequences with bounded jumps in their linear complexity are discussed and a method of generating them is suggested. The interleaving of shifts of a sequence with out-of-phase auto-correlation equal to -1 and balance, in a specific order, seems to be a fundamental method of generating longer sequences with this auto-correlation property. It is shown that two pairs of families of these sequences, derived in different ways, are in fact equivalent. The analysis highlights the general method mentioned above, and so provides examples of families of sequences with 2-valued auto-correlation by changing the ingredients in the interleaving pattern. We also look at the cross-correlation of sequences with this interleaved structure.

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Ohlson, Tomas. "The use of evolutionary information in protein alignments and homology identification." Doctoral thesis, Stockholm : Stockholm Bioinformatics Center, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-812.

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Guney, Tacettin Dogacan. "Prediction Of Protein-protein Interactions From Sequence Using Evolutionary Relations Of Proteins And Species." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12611058/index.pdf.

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Prediction of protein-protein interactions is an important part in understanding the biological processes in a living cell. There are completely sequenced organisms that do not yet have experimentally verified protein-protein interaction networks. For such organisms, we can not generally use a supervised method, where a portion of the protein-protein interaction network is used as training set. Furthermore, for newly-sequenced organisms, many other data sources, such as gene expression data and gene ontology annotations, that are used to identify protein-protein interaction networks may not be available. In this thesis work, our aim is to identify and cluster likely protein-protein interaction pairs using only sequence of proteins and evolutionary information. We use a protein&rsquo
s phylogenetic profile because the co-evolutionary pressure hypothesis suggests that proteins with similar phylogenetic profiles are likely to interact. We also divide phylogenetic profile into smaller profiles based on the evolutionary lines. These divided profiles are then used to score the similarity between all possible protein pairs. Since not all profile groups have the same number of elements, it is a difficult task to assess the similarity between such pairs. We show that many commonly used measures do not work well and that the end result greatly depends on the type of the similarity measure used. We also introduce a novel similarity measure. The resulting dense putative interaction network contains many false-positive interactions, therefore we apply the Markov Clustering algorithm to cluster the protein-protein interaction network and filter out the weaker edges. The end result is a set of clusters where proteins within the clusters are likely to be functionally linked and to interact. While this method does not perform as well as supervised methods, it has the advantage of not requiring a training set and being able to work only using sequence data and evolutionary information. So it can be used as a first step in identifying protein-protein interactions in newly-sequenced organisms.

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Books on the topic "Sequence profiles"

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L, Kohring Lisa, and United States. Environmnetal Protection Agency., eds. Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. [Washington, D.C.?: Environmental Protection Agency], 1994.

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L, Kohring Lisa, and United States. Environmental Protection Agency, eds. Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. [Washington, D.C.?: Environmental Protection Agency], 1994.

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1941-, Linsky J. L., Ayres Thomas R, and United States. National Aeronautics and Space Administration., eds. Evaluating possible heating mechanisms using the transition region line profiles of late-type stars. [Washington, DC: National Aeronautics and Space Administration, 1997.

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1941-, Linsky J. L., Ayres Thomas R, and United States. National Aeronautics and Space Administration., eds. Evaluating possible heating mechanisms using the transition region line profiles of late-type stars. [Washington, DC: National Aeronautics and Space Administration, 1997.

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Hemmelgarn, Anthony L., and Charles Glisson. Conclusion and Future Challenges for Improving Human Service Organizations. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190455286.003.0014.

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This concluding chapter suggests that future research and development efforts focus on four interrelated areas. These four areas, together, describe how more specific information about the ARC strategies can increase the capacity for improving human services. The authors argue that the emphasis on evidence-based practices should be expanded to include strategies that focus on the organization’s social context. Knowing which strategies are most effective to alter specific OSC profiles and knowing the sequence of strategies that are most effective for targeted outcomes will allow organizations to tailor improvement efforts with the greatest efficiency. The chapter calls for more information about how an array of strategies can be used most efficiently by an organization to target outcomes over an extended period and how to determine, a priori, the optimal application of the various strategies necessary to achieve success with the least amount of resources.

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Risk profile - Group B Streptococcus (GBS) – Streptococcus agalactiae sequence type (ST) 283 in freshwater fish. FAO, 2021. http://dx.doi.org/10.4060/cb5067en.

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Divan, Aysha, and Janice A. Royds. 8. Molecular forensics. Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198723882.003.0008.

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A key challenge for molecular biology is to use research outcomes to meet the demands of modern society. ‘Molecular forensics’ shows that molecular markers are having a substantial impact; from bench to boardroom or even courtroom. DNA profiling plays a role in helping to solve crimes and miscarriages of justice. Although 99.5 per cent of the human DNA sequence is the same for everyone, there are small regions of variability that are specific to each individual giving each person a unique DNA profile, or fingerprint. DNA profile applications are increasing and are now used to identify food counterfeits and contamination of food; to tackle pandemics and epidemics; and in biosecurity measures.

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Weiss, Meredith L. Prejudice before Pride. University of Illinois Press, 2017. http://dx.doi.org/10.5406/illinois/9780252037726.003.0007.

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This chapter presents evidence for the so-called homophobic anticipatory countermovement, with reference primarily to Southeast Asian cases—particularly Singapore, Malaysia, Indonesia, and the Philippines—and considers the roots and implications of such a sequence. These cases are chosen for their proximity, which is useful for evaluating the extent of global and regional discursive circuits, but also for their diversity. Indonesia and Malaysia are both Muslim-majority states, but Indonesia today is far more democratic than Malaysia; the Philippines is a Catholic-majority democracy; while Singapore is a single-party-dominant state with important Muslim and evangelical Christian minorities. While all but prosperous Singapore are developing states, all are highly exposed to global trade, media, and other circuits. Moreover, all four states offer recent examples of high-profile homophobia, all with roots in Christian or Islamist discourse.

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Book chapters on the topic "Sequence profiles"

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Dworkin, Jonathan E., and George D. Rose. "Hydrophobicity Profiles Revisited." In Methods in Protein Sequence Analysis · 1986, 573–86. Totowa, NJ: Humana Press, 1987. http://dx.doi.org/10.1007/978-1-59259-480-1_49.

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Werner, Helmut. "The Nineteenth Century: A Sequence of Accidental Discoveries." In Profiles in Inorganic Chemistry, 1–16. New York, NY: Springer New York, 2008. http://dx.doi.org/10.1007/978-0-387-09848-7_3.

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Aguiar, Orlando G. "The Implications of the Conceptual Profile in Science Teaching: An Example from a Teaching Sequence in Thermal Physics." In Conceptual Profiles, 235–59. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-90-481-9246-5_9.

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Kim, Tai Hyo, and Sung Deok Cha. "Timed High-Level Message Sequence Charts for Real-Time System Design." In System Analysis and Modeling: Language Profiles, 82–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11951148_6.

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Lv, Yanping, Shaozi Li, Changle Zhou, Wenzhong Guo, and Zhengming Xu. "Improved Genetic Algorithm for Multiple Sequence Alignment Using Segment Profiles (GASP)." In Advanced Data Mining and Applications, 388–95. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11811305_43.

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St. Arnaud, R. J., and E. P. Whiteside. "Morphology and Genesis of a Chernozemic to Podzolic Sequence of Soil Profiles in Saskatchewan." In Selected Papers in Soil Formation and Classification, 350–64. Madison, Wisconsin, USA: Soil Science Society of America, Inc., 2015. http://dx.doi.org/10.2136/sssaspecpub1.c29.

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Graham, Alister W., and Mercedes Prieto. "On the Light-Profiles of Spiral Galaxy Bulges and the Hubble Sequence for Spirals." In Toward a New Millennium in Galaxy Morphology, 653–54. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4114-7_71.

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Sarker, Bandhan, Md Matiur Rahaman, Suman Khan, Priyanka Bosu, and Md Nurul Haque Mollah. "Bioinformatic Analysis of Differentially Expressed Genes (DEGs) Detected from RNA-Sequence Profiles of Mouse Striatum." In Data Science and SDGs, 101–22. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-1919-9_9.

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Gribskov, Michael. "Profile Analysis." In Computer Analysis of Sequence Data, 247–66. Totowa, NJ: Humana Press, 1994. http://dx.doi.org/10.1385/0-89603-276-0:247.

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Pirincci Ercan, Deniz, and Frank Uhlmann. "Analysis of Cell Cycle Progression in the Budding Yeast S. cerevisiae." In Methods in Molecular Biology, 265–76. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1538-6_19.

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AbstractThe cell cycle is an ordered series of events by which cells grow and divide to give rise to two daughter cells. In eukaryotes, cyclin–cyclin-dependent kinase (cyclin–Cdk) complexes act as master regulators of the cell division cycle by phosphorylating numerous substrates. Their activity and expression profiles are regulated in time. The budding yeast S. cerevisiae was one of the pioneering model organisms to study the cell cycle. Its genetic amenability continues to make it a favorite model to decipher the principles of how changes in cyclin-Cdk activity translate into the intricate sequence of substrate phosphorylation events that govern the cell cycle. In this chapter, we introduce robust and straightforward methods to analyze cell cycle progression in S. cerevisiae. These techniques can be utilized to describe cell cycle events and to address the effects of perturbations on accurate and timely cell cycle progression.

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Conference papers on the topic "Sequence profiles"

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Kiah, Han Mao, Gregory J. Puleo, and Olgica Milenkovic. "Codes for DNA sequence profiles." In 2015 IEEE International Symposium on Information Theory (ISIT). IEEE, 2015. http://dx.doi.org/10.1109/isit.2015.7282568.

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Hartmann, Stephan, Thorsten Nagel, Thomas Rauch, and Klaus Werner. "Asymmetric Line Profiles in Spectra of Gaseous Metal Disks around Single White Dwarfs." In PLANETARY SYSTEMS BEYOND THE MAIN SEQUENCE: Proceedings of the International Conference. AIP, 2011. http://dx.doi.org/10.1063/1.3556204.

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Bondugula, Rajkumar, and Dong Xu. "COMBINING SEQUENCE AND STRUCTURAL PROFILES FOR PROTEIN SOLVENT ACCESSIBILITY PREDICTION." In Proceedings of the CSB 2008 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2008. http://dx.doi.org/10.1142/9781848162648_0017.

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Santos, Jehiel, Wenjie Wang, and Ross Murch. "Imaging Transmission Line Impedance Profiles using Passband Signals and Adaptive Sequence Design." In 2020 IEEE International Symposium on Circuits and Systems (ISCAS). IEEE, 2020. http://dx.doi.org/10.1109/iscas45731.2020.9181120.

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Benabdellah, Naoual Chaouni, Mourad Gharbi, and Mostafa Bellafkih. "Ant colony algorithm and new pheromone to adapt units sequence to learners' profiles." In 2014 9th International Conference on Intelligent Systems: Theories and Applications (SITA). IEEE, 2014. http://dx.doi.org/10.1109/sita.2014.6847300.

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Chang, Zuling, Johan Chrisnata, Martianus Frederic Ezerman, and Han Mao Kiah. "On the number of DNA sequence profiles for practical values of read lengths." In 2016 IEEE International Symposium on Information Theory (ISIT). IEEE, 2016. http://dx.doi.org/10.1109/isit.2016.7541780.

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van den Berg, E. A., E. Sprengers, M. Jaye, W. Burgess, and V. W. M. van Hinsbergh. "REGULATION OF PLASMINOGEN ACTIVATOR INHIBITOR-1 mRNA IN HUMAN ENDOTHELIAL CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642856.

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Cultured human endothelial cells (HEC) increase their production of plasminogen activator inhibitor (PAI-1) upon stimulation with endotoxin and IL-1, agents that are known to cause an increase in PAI-1 levels in vivo. In order to study the regulation of PAI-1 synthesis at the mRNA level, we isolated a cDNA clone for the human PAI-1 gene from an endothelial expression cDNA library in λ gt 11 by screening with a PAI-1 specific antibody. Three positive cross-hybridizing clones were isolated. The longest insert (1500 bp) was partially sequenced (1000 bp). The sequence was identical to the PAI-1 sequence recently reported by others. The identity of the cDNA clone was further confirmed by comparison with part of the amino acid sequence of PAI-1. For that purpose t-PA-PAI-1 complex was purified from HEC conditioned medium by immunoadsorption to anti-t-PA IgG, and a suitable peptide was sequenced after comparison of the HPLC elution profiles of CNBr digests of t-PA and t-PA-PAI-1 complex. The amino acid sequence (M)FRQFQADFT completely matches the sequence predicted from the cDNA sequence.By hybridization of the cDNA probe to Northern blots of total cellular RNA from human umbilical vein and artery EC (HUVEC, HUAEC), two transcripts of 2.3 and 3 kb were found. Primary HUAEC, incubated for 18 hours in growth medium, produced considerable although variable levels of PAI-1 activity and contained PAI-1 mRNA levels comparable to those found in subcultured HUAEC. When subcultured HUEC were incubated for 6 h with endotoxin, IL-1 or TNF, a 2-fold increase in PAI-1 mRNA was found with each of these mediators. Stimulation of the cells in the presence of cycloheximide resulted in a further increase of the 3 kb PAI-1 transcript. The 3’ end of this transcript contains a 75 bp AT-rich sequence. Similar 3’ AT-rich sequences have been found in mRNA’s for a number of inflammatory mediators and cellular oncogenes, and in some cases it has been shown that removal of the sequence increased mRNA stability. The influence of cyclohex-imid on the larger PAI-1 transcript might be explained by inhibition of synthesis of a specific nuclease that controls the level of mRNA’s harbouring such an AT rich sequence.

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Rahman, Mosfequr, Saheem Absar, F. N. U. Aktaruzzaman, Abdur Rahman, and N. M. Awlad Hossain. "Effect of Ply Stacking Sequence on Structural Response of Symmetric Composite Laminates." In ASME 2014 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/imece2014-37217.

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In this work, the effect of ply stacking sequence on the structural response of multi-ply unidirectional fiber-reinforced composite laminates was evaluated using finite element analysis. The objective of this study was to develop a computational model to analyze the stress response of individual plies in a composite laminate for a given stacking sequence. A laminated composite plate structure under tensile loading was modeled in ANSYS. Stress profiles of the individual plies were obtained for each lamina. An Epoxy matrix with both unidirectional Graphite and Kevlar fibers was considered for the model. Three dimensional sectioned shell elements (SHELL181) were used for meshing the model. Several sets of stacking sequences were implemented, symmetrical to the mid-plane of the laminate. Symmetric stacking configurations of 6 layers stacked in ply angles of [0/45/-45]s, [0/60/-60]s, [0/45/90]s, and an 8-layered arrangement of [0/45/60/90]s were modeled for the analysis. The layer thickness was maintained at 0.1 mm. The results were compared against an analytical model based on the generalized Hooke’s law for orthotropic materials and classical laminate theory. A numerical formulation of the analytical model was implemented in MATLAB to evaluate the constitutive equations for each lamina. The stress distributions obtained using finite element analysis have shown good agreement with the analytical models in some of the cases.

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Dhaka, Pankaj, and Raghu V. Prakash. "Finite Element Study of the Effect of Load Sequence on the Fretting Wear." In ASME 2020 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/imece2020-23275.

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Abstract Understanding the effect of load sequence is important in the context of a blade-disc dovetail joint in an aero-engine and many other such applications where, the mating surfaces undergo fretting wear under variable slip amplitude loading conditions. In the present work, a two-dimensional finite element analysis is carried out for a cylinder-on-plate configuration. The cylinder is modeled as deformable whereas the plate is modelled as rigid. An incremental wear modelling algorithm is used to model the wear of cylindrical pad while the plate is assumed as un-worn. This simulates a practical scenario where, generally one of the mating surfaces is sufficiently hardened or an interfacial harder/sacrificial element is inserted to restrict the wear to only one of the surfaces. A Fortran-based ABAQUS® subroutine UMESHMOTION is used to simulate the wear profile for the cylinder. A constant extrapolation technique is used to simulate 18000 cycles of fretting. The finite element analysis results are validated with the analytical solutions and literature data. The fretting wear modelling is carried out for two different slip amplitudes viz., 25 μm and 150 μm, to simulate the low and high slip amplitude loading respectively. Two blocks of alternate low and high slip amplitudes are applied to understand the influence of load sequence. Important contact parameters viz., contact pressure, contact stresses and contact slip are extracted. A comparison is made between the low-high and high-low load sequence based on the contact tractions and worn out profiles.

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García, Samira, Edgardo Paternina, Oscar R. Pupo, Antonio Bula, and Francisco Acuña. "CFD Simulation of Multiphase Flow in an Airlift Column Photobioreactor for the Cultivation of Microalgae." In ASME 2012 6th International Conference on Energy Sustainability collocated with the ASME 2012 10th International Conference on Fuel Cell Science, Engineering and Technology. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/es2012-91297.

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Due to their better operational advantages, such as good scalability, operational flexibility, high mass and heat transfer characteristics, homogenous shear stress, good mixing and better control over fluid circulation, airlift column photobioreactors (PBR) have become a promising design alternative for microalgae culture, among bubble column and other types of photobioreactors. The good hydrodynamic environment for fragile microorganisms in airlift columns have led to numerous investigations in order to understand the hydrodynamic phenomena of multiphase flow, particularly gas-liquid, inside this type of PBR. In the present paper, a CFD (Computer Fluid Dynamics) simulation in CFX, ANSYS Inc. 11.0, is developed following a multiphase flow model with an Eulerian-Eulerian approach. For evaluating turbulence, the modified k–ε model is chosen. Gas holdup, gas superficial velocity and liquid velocity profiles for different heights column are obtained by varying air volumetric flow rates at 2, 5 and 8 L/min. Also gas holdup, gas superficial velocity and liquid velocity contours are obtained for a sequence of five step times. An experimental video validation to compare the multiphase flow behavior has been made with a high-resolution video camera. The experiments are carried out by using an airlift column photobioreactor with air supply by a porous sparger. The profiles of the hydrodynamic variables made for 5 different column heights show that the trends of gas holdup and gas superficial velocity are very similar and do not depend on the variation of inlet air flow. For the liquid velocity profiles, the trends don’t show the same behavior, the profiles at lower heights are off-centered and less symmetric and the maximum velocities are reached at h = 0.2 m. The time sequences with the variable contours are made to enhance the visualization and understanding of the hydrodynamic behavior, especially when air supply begins and the bubble plume starts to form.

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