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Relevant bibliographies by topics / Sequence-Structure relationship

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Academic literature on the topic 'Sequence-Structure relationship'

Author: Grafiati

Published: 11 January 2025

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Journal articles on the topic "Sequence-Structure relationship"

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Dosztanyi, Z. "Servers for sequence-structure relationship analysis and prediction." Nucleic Acids Research 31, no. 13 (2003): 3359–63. http://dx.doi.org/10.1093/nar/gkg589.

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Morris, Kyle L., Alison Rodger, Matthew R. Hicks, et al. "Exploring the sequence–structure relationship for amyloid peptides." Biochemical Journal 450, no. 2 (2013): 275–83. http://dx.doi.org/10.1042/bj20121773.

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Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.

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Sadowski, M. I., and D. T. Jones. "The sequence–structure relationship and protein function prediction." Current Opinion in Structural Biology 19, no. 3 (2009): 357–62. http://dx.doi.org/10.1016/j.sbi.2009.03.008.

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Nekrasov, Alexei N., Yuri P. Kozmin, Sergey V. Kozyrev, Rustam H. Ziganshin, Alexandre G. de Brevern, and Anastasia A. Anashkina. "Hierarchical Structure of Protein Sequence." International Journal of Molecular Sciences 22, no. 15 (2021): 8339. http://dx.doi.org/10.3390/ijms22158339.

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Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs remains an actual research area. Here, we propose a mathematical method for revealing the hierarchical organization of protein sequences. The method is based on the pentapeptide as a unit of protein sequences. Employing the frequency of occurrence of pentapeptides in sequences of natural proteins and a special mathematical approach, this method revealed a hierarchical structure in the protein sequence. The method was applied to 24,647 non-homologous protein sequences with sizes ranging from 50 to 400 residues from the NRDB90 database. Statistical analysis of the branching points of the graphs revealed 11 characteristic values of y (the width of the inscribed function), showing the relationship of these multiple fragments of the sequences. Several examples illustrate how fragments of the protein spatial structure correspond to the elements of the hierarchical structure of the protein sequence. This methodology provides a promising basis for a mathematically-based classification of the elements of the spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used to solve biotechnological and medical problems.

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Nakamura, Shugo, and Kentaro Shimizu. "2P004 Analysis of sequence-structure relationship of protein loop regions(Proteins-structure and structure-function relationship,Poster Presentations)." Seibutsu Butsuri 47, supplement (2007): S114. http://dx.doi.org/10.2142/biophys.47.s114_1.

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Kuroda, D., H. Shirai, M. Kobori, and H. Nakamura. "Relationship between sequence and structure of CDR-H3 in antibodies." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C228. http://dx.doi.org/10.1107/s0108767308092684.

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Krissinel, E. "On the relationship between sequence and structure similarities in proteomics." Bioinformatics 23, no. 6 (2007): 717–23. http://dx.doi.org/10.1093/bioinformatics/btm006.

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Song, Jianxing. "Environment-transformable sequence–structure relationship: a general mechanism for proteotoxicity." Biophysical Reviews 10, no. 2 (2017): 503–16. http://dx.doi.org/10.1007/s12551-017-0369-0.

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Mansiaux, Yohann, Agnel Praveen Joseph, Jean-Christophe Gelly, and Alexandre G. de Brevern. "Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship." PLoS ONE 6, no. 3 (2011): e18401. http://dx.doi.org/10.1371/journal.pone.0018401.

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Leopold, P. E., M. Montal, and J. N. Onuchic. "Protein folding funnels: a kinetic approach to the sequence-structure relationship." Proceedings of the National Academy of Sciences 89, no. 18 (1992): 8721–25. http://dx.doi.org/10.1073/pnas.89.18.8721.

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Dissertations / Theses on the topic "Sequence-Structure relationship"

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Wang, Pam Shou-Ping. "Exploring the sequence-structure-function relationship in beta-peptide foldamers." Thesis, Yale University, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3580893.

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<p> The interplay between sequence, structure and function is an underlying theme in biological systems. Proteins, in particular, have evolved the ability to access a virtually infinite set of three-dimensional architectures from a small collection of building blocks; it is precisely this complexity of form that finely tunes their functional specificity. β-Peptides are a class of unnatural polyamides known to adopt structural motifs that are in many ways reminiscent of protein folds in nature. This dissertation first investigates the relationship between sequence and structure in self-assembling β-peptides, then demonstrates how the latter translates into function.</p><p> Chapter 1 provides an overview of the fundamental principles guiding β-peptide helix formation and self-assembly, and describes their applications both within and outside of the biological context. The ability of β-peptides to mimic natural α-helices while maintaining proteolytic resistance allows them to serve as therapeutic agents by targeting, for example, protein-protein interactions. Their unique stability in both aqueous and organic environments further enables the development of β-peptide-based nanomaterials and organocatalysts.</p><p> Chapter 2 elucidates the relationship between β-peptide primary sequence and quaternary structure based on the biophysical characterization of the Acid-3Y bundle. Acid-3Y was designed by substituting isoleucine for leucine side-chains in the sequence of the previously characterized octamer, Acid-1Y. The finding that Acid-3Y assembles into a tetrameric bundle suggests that branching at the γ-carbon of hydrophobic residues plays a critical role in determining β-peptide bundle stoichiometry.</p><p> Chapter 3 explores the potential of β-peptide bundles to mimic enzyme structure and function. The demonstration of β-peptide mutarotase activity in benzene highlights the importance of macromolecular preorganization in catalysis, while the ability of rationally designed β-peptide bundles to catalyze ester hydrolysis in water represents a crucial step towards the functionalization of these unnatural macromolecules. The dependence of catalytic activity on both active site geometry and bundle assembly, together with their substrate selectivity, underscores the unique biomimetic capacity of β-peptides. </p><p> Chapter 4 describes the rational design of a β-peptide ligand for the parathyroid hormone 1 receptor (PTH1R). Using previous strategies that led to the identification of p53 and GLP-1 mimics, a 12-member β-peptide library was constructed and tested <i>in vitro</i> for binding to the receptor protein. Although no hits were found from this initial screen, subsequently designed α/β-peptide chimeras showed promise as synthetic antagonists of PTH1R with improved pharmacokinetic properties.</p><p> Chapter 5 summarizes the key results of this dissertation and offers a perspective on possible future research directions. A breakthrough in the field of β-peptides would rely on the development of a method to synthesize genuine "β-proteins" with more sophisticated structure and function. </p>

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Mokrab, Younes. "Insights into sequence-structure relationship in helical transmembrane proteins : application to comparative modeling." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611915.

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Viklund, Håkan. "Formalizing life : Towards an improved understanding of the sequence-structure relationship in alpha-helical transmembrane proteins." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7144.

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<p>Genes coding for alpha-helical transmembrane proteins constitute roughly 25% of the total number of genes in a typical organism. As these proteins are vital parts of many biological processes, an improved understanding of them is important for achieving a better understanding of the mechanisms that constitute life.</p><p>All proteins consist of an amino acid sequence that fold into a three-dimensional structure in order to perform its biological function. The work presented in this thesis is directed towards improving the understanding of the relationship between sequence and structure for alpha-helical transmembrane proteins. Specifically, five original methods for predicting the topology of alpha-helical transmembrane proteins have been developed: PRO-TMHMM, PRODIV-TMHMM, OCTOPUS, Toppred III and SCAMPI. </p><p>A general conclusion from these studies is that approaches that use multiple sequence information achive the best prediction accuracy. Further, the properties of reentrant regions have been studied, both with respect to sequence and structure. One result of this study is an improved definition of the topological grammar of transmembrane proteins, which is used in OCTOPUS and shown to further improve topology prediction. Finally, Z-coordinates, an alternative system for representation of topological information for transmembrane proteins that is based on distance to the membrane center has been introduced, and a method for predicting Z-coordinates from amino acid sequence, Z-PRED, has been developed.</p>

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Viklund, Håkan. "Formalizing life : towards an improved understanding of the sequence-structure relationship in alpha-helical transmembrane proteins /." Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7144.

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Zheng, Ying. "Functional divergence after gene duplication and sequence-structure relationship a case-study of G-protein alpha subunits /." [Ames, Iowa : Iowa State University], 2007.

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Shafqat, Naeem. "Substrate specificities and functional properties of human short-chain dehydrogenases/reductases /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-829-7.

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Chevallier, Sylvie. "Relations structure-fonction de l'oligopeptidase proline-spécifique (EC 3. 4. 21. 26) de Flavobacterium meningosepticum." Grenoble 1, 1993. http://www.theses.fr/1993GRE10076.

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L'oligopeptidase proline-specifique (pop) de f. Meningosepticum coupe presque exclusivement du cote c-terminal des prolines et des hydroxyprolines. Le remplacement d'une proline par un acide pipecolique transforme un substrat en un inhibiteur, ce qui confirme la forte stereospecificite de la pop au niveau du sous-site s1. La sequence proteique a ete determinee par sequencage chimique de la pop, et clonage et sequencage de son gene (2115 pb). La pop mature periplasmique comporte 685 residus pour une masse moleculaire de 76784 da et montre des homologies de sequence uniquement avec la pop de cerveau de porc (38%) et la protease ii d'e. Coli (24%). La sequence grsng comprenant la serine 536 du site actif marquee par le diisopropylfluorophosphate tritie est distincte de celle du site actif des proteases a serine connues, bien qu'elle soit en correlation avec la sequence consensus gxsxg/a. Les residus presumes de la triade catalytique de la pop (s536, d621, h655) sont disposes dans un ordre different de ceux de la chymotrypsine (h57, d102, s195) et de la subtilisine (d32, h64, s221), mais similaire a celui de la carboxypeptidase y (s146, d338, h397). L'existence de trois domaines n-terminaux structuralement analogues a l'immunophiline humaine fkbp-12 et d'un domaine catalytique c-terminal de structure alpha-beta hydrolase fold a ete demontree par analyse hca de la pop. Les pops et la protease ii d'e. Coli forment donc une nouvelle famille de proteases a serine structuralement proches de la dienelactone hydrolase et de la carboxypeptidase ii dont les domaines catalytiques montrent un repliement de type alpha-beta hydrolase

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Vignoud, Lucile. "Étude du rôle des motifs NPXY dans la fonction de l'intégrine alpha 5/beta 1." Grenoble 1, 1996. http://www.theses.fr/1996GRE10274.

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Le travail presente concerne l'etude du role joue par les deux motifs peptidiques npxy localises dans le domaine cytoplasmique de la sous-unite beta 1 des integrines. Par analogie avec le recepteur des ldl, ces deux motifs etaient assimiles au signal d'internalisation npxy permettant une association au complexe d'adaptines ha-2 et une internalisation dependante des puits a clathrine. En generant des lignees stables exprimant des integrines a sous-unite beta 1 mutees, nous avons montre que contrairement a d'autres recepteurs, les motifs npxy n'intervenaient pas dans l'internalisation de l'integrine alpha 5/beta 1. En revanche, nous avons observe que chacun des motifs npxy etait indispensable a l'assemblage des adherences focales. L'affinite pour le ligand extracellulaire n'etant pas affectee par les mutations realisees, nos resultats attribuent aux deux motifs npxy un role en tant que sites d'interaction, ou permettant la formation de sites d'interaction, avec une ou plusieurs proteines cytoplasmiques necessaires a l'assemblage des adherences focales. L'analyse de la fixation in vitro de la taline sur les chaines beta 1 mutees au niveau des sequences npxy, indique que cette proteine, pourtant necessaire a l'etablissement des adherences focales, n'est pas la proteine cible qui interagit avec les motifs npxy des integrines pour permettre leur recrutement au sein de ces adherences. La taline n'est pas suffisante a elle seule pour permettre l'assemblage des adherences focales. L'identite des proteines interagissant avec la sous-unite beta 1 de maniere dependante des motifs npxy, reste a determiner. L'immunoprecipitation des integrines a sous-unite beta 1 humaine dans des conditions menagees, a mis en evidence leur association avec diverses proteines cellulaires, controlee par le premier motif npxy (tyr 783). Ces proteines, non identifiees, pourraient jouer un role essentiel dans l'organisation des adherences focales, dependante du premier motif npxy de la sous-unite beta 1 des integrines, et/ou dans la signalisation cellulaire

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Lombard, Valentin. "Geometric deep manifold learning combined with natural language processing for protein movies." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS379.

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Les protéines jouent un rôle central dans les processus biologiques, et comprendre comment elles se déforment et se déplacent est essentiel pour élucider leurs mécanismes fonctionnels. Malgré les récentes avancées dans les technologies à haut débit, qui ont élargi nos connaissances sur les structures protéiques, la prédiction précise de leurs différents états conformationnels et mouvements reste un défi majeur. Nous présentons deux approches complémentaires pour relever le défi de la compréhension et de la prédiction de l'ensemble de la variabilité conformationnelle des protéines. La première approche, appelée Dimensionality Analysis for protein Conformational Exploration (DANCE), permet une description systématique et complète de la variabilité conformationnelle des familles de protéines. DANCE prend en compte à la fois les structures expérimentales et prédites. Elle est adaptée à l'analyse des protéines individuelles jusqu'aux superfamilles. En l'utilisant, nous avons regroupé toutes les structures protéiques résolues expérimentalement disponibles dans la banque de données Protein Data Bank en collections conformationnelles et les avons caractérisées comme des ensembles de mouvements linéaires. Cette ressource facilite l'accès et l'exploitation des multiples états adoptés par une protéine et ses homologues. Au-delà de l'analyse descriptive, nous avons évalué des techniques classiques de réduction de la dimensionnalité pour échantillonner des états non observés sur un banc d'essai représentatif. Ce travail améliore notre compréhension de la manière dont les protéines se déforment pour accomplir leurs fonctions et ouvre la voie à une évaluation standardisée des méthodes conçues pour échantillonner et générer des conformations protéiques. La deuxième approche repose sur l'apprentissage profond pour prédire des représentations continues du mouvement des protéines directement à partir de séquences, sans avoir besoin de données structurelles. Ce modèle, appelé SeaMoon, utilise des embeddings de modèles de langage protéique (pLM) comme entrées dans un réseau neuronal convolutif léger comptant environ un million de paramètres entraînables. SeaMoon atteint un taux de réussite de 40 % lorsqu'il est évalué sur environ 1 000 collections de conformations expérimentales, capturant des mouvements au-delà de la portée des méthodes traditionnelles comme l'analyse des modes normaux, qui repose uniquement sur la géométrie 3D. De plus, SeaMoon se généralise à des protéines n'ayant aucune similitude de séquence détectable avec son ensemble d'entraînement et peut être facilement réentraîné avec des pLM mis à jour. Ces deux approches offrent un cadre unifié pour faire progresser notre compréhension de la dynamique des protéines. DANCE fournit une exploration détaillée des mouvements protéiques basée sur des données structurelles, tandis que SeaMoon démontre le potentiel des modèles d'apprentissage profond basés sur les séquences pour capturer des mouvements complexes sans dépendre d'informations structurelles explicites. Ensemble, elles ouvrent la voie à une compréhension plus complète de la variabilité conformationnelle des protéines et de son rôle dans la fonction biologique<br>Proteins play a central role in biological processes, and understanding how they deform and move is essential to elucidating their functional mechanisms. Despite recent advances in high-throughput technologies, which have broadened our knowledge of protein structures, accurate prediction of their various conformational states and motions remains a major challenge. We present two complementary approaches to address the challenge of understanding and predicting the full range of protein conformational variability. The first approach, Dimensionality Analysis for protein Conformational Exploration (DANCE) for a systematic and comprehensive description of protein families conformational variability. DANCE accommodates both experimental and predicted structures. It is suitable for analyzing anything from single proteins to superfamilies. Employing it, we clustered all experimentally resolved protein structures available in the Protein Data Bank into conformational collections and characterized them as sets of linear motions. The resource facilitates access and exploitation of the multiple states adopted by a protein and its homologs. Beyond descriptive analysis, we assessed classical dimensionality reduction techniques for sampling unseen states on a representative benchmark. This work improves our understanding of how proteins deform to perform their functions and opens ways to a standardized evaluation of methods designed to sample and generate protein conformations. The second approach relies on deep learning to predict continuous representations of protein motion directly from sequences, without the need for structural data. This model, SeaMoon, uses protein language model (pLM) embeddings as inputs to a lightweight convolutional neural network with around 1 million trainable parameters. SeaMoon achieves a success rate of 40% when evaluated against around 1,000 collections of experimental conformations, capturing movements beyond the reach of traditional methods such as normal mode analysis, which relies solely on 3D geometry. In addition, SeaMoon generalizes to proteins that have no detectable sequence similarity with its training set and can be easily retrained with updated pLMs. These two approaches offer a unified framework for advancing our understanding of protein dynamics. DANCE provides a detailed exploration of protein movements based on structural data, while SeaMoon demonstrates the potential of sequence-based deep learning models to capture complex movements without relying on explicit structural information. Together, they pave the way for a more comprehensive understanding of protein conformational variability and its role in biological function

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Pauly, Marc. "Etude structurale et fonctionnelle de la sequence tata du promoteur precoce du virus simien sv40." Université Louis Pasteur (Strasbourg) (1971-2008), 1989. http://www.theses.fr/1989STR13043.

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Dans le but d'elucider les mecanismes moleculaires de la regulation de l'expression des genes, une etude structurale et fonctionnelle detaillee de la sequence tata du promoteur precoce du virus sv40 est realisee. La mutagenese dirigee utilisant des oligodesoxynucleotides de synthese permet la localisation des domaines fonctionnels de deux elements tata situes dans la region d'origine de replication virale. Chacun des elements dirige independamment l'initiation precise et efficace de la transcription precoce in vivo a partir d'un groupe de sites definis

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Books on the topic "Sequence-Structure relationship"

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International Symposium on Protein Structure-Function Relationship (1988 Karachi, Pakistan). Protein structure-function relationship: Proceedings of the International Symposium on Protein Structure-Function Relationship, held in Karachi, Pakistan, 18-20 January 1988, and of the Protein Sequencing Workshop, held subsequently in Karachi, Pakistan, 21-30 January 1988. Edited by Zaidi Zafar H and Protein Sequencing Workshop (1988 : Karachi, Pakistan). Elsevier Science Publishers, 1988.

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W, Shriver John, ed. Protein structure, stability, and interactions. Humana, 2009.

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Harren, Jhoti, and Leach Andrew R, eds. Structure-based drug discovery. Springer, 2007.

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I, Chasman Daniel, ed. Protein structure: Determination, analysis, and applications for drug discovery. Marcel Dekker, 2003.

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Nir, Ben-Tal, ed. Introduction to proteins: Structure, function, and motion. CRC Press, 2011.

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Protein Structure Determination. Wiley-Interscience, 1991.

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R, Leach· Andrew, and Harren Jhoti. Structure-based Drug Discovery. Springer, 2010.

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(Editor), Harren Jhoti, and Andrew R. Leach (Editor), eds. Structure-based Drug Discovery. Springer, 2007.

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Chasman, Daniel. Protein Structure: Determination, Analysis, and Applications for Drug Discovery. Taylor & Francis Group, 2003.

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Chasman, Daniel. Protein Structure: Determination, Analysis, and Applications for Drug Discovery. Taylor & Francis Group, 2003.

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Book chapters on the topic "Sequence-Structure relationship"

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Lesk, Arthur M. "Proteins: Relationship Among Divergence of Sequence, Structure, and Function." In Encyclopedia of Biophysics. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_145.

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Holder, Jerry Ryan, Rayna M. Bauzo, Zhimin Xiang, and Carrie Haskell-Luevano. "Structure-Activity Relationship Studies (SAR) of Melanocortin Agonists Central His-Phe-Arg-Trp Sequence." In Peptides: The Wave of the Future. Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_329.

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Ji, Rongju, and Haoqi Ren. "A New Prefetching Unit for Digital Signal Processor." In Proceeding of 2021 International Conference on Wireless Communications, Networking and Applications. Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-2456-9_94.

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AbstractIn this paper, a new structure of instruction prefetching unit is proposed. The prefetching is achieved by building the relationship between the branch source and its branch target and the relationship between the branch target and the first branch in its following instruction sequence. With the help of the proposed structure, it is easy to know whether the instruction block of branch target blocks exist in the instruction cache based on the recorded branch information. The two-level depth target prefetching can be performed to eliminate or reduce the instruction cache miss penalty. Experimental results demonstrate that the proposed instruction prefetching scheme can achieve lower cache miss rate and miss penalty than the traditional next-line prefetching technique.

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Upadhyay, Upashna, Poonam Kaithal, Preetam Verma, Rohit Lall, and Poonam Singh. "Analysis of Pectin in Different Citrus Fruits and Evolutionary Relationship." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022). Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_26.

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AbstractPectin is a polysaccharide present in fruit cell walls can be extracted from fruit wastes obtained after processing. The objective of the present investigation was to study the potential of citrus fruit peels to be a source of pectin as it is of great importance in food and medical industry. This study aimed at comparing the characteristics of different pectin and to see which one is more suitable for industrial application. Pectin was extracted using alcohol precipitation method from peels of grapefruit, mousambi, and orange so that the use of pectin can be applied to a wider range. According to the study, the pectin extracted by mousambi on wet basis (17.1%) was higher in comparison to the pectin extraction of orange and grapefruit. The pectin can be used in many fields like food and medicines so the improvement in quality and production is very important. MicroRNAs have the main function of guiding the base pairing with target mRNA to negatively regulate its expression for gene silencing via mRNA clevage. In the present study we also found the phylogenetic relationship among the citrus fruits by multiple sequence alignment of microRNAs stem-loop sequence from the miRbase database of the citrus fruits and after getting phylogenetic tree we got the common ancestors. In recent years, the center of production has moved to Europe and to citrus- producing countries like Mexico and Brazil. Further changes of structure and location of the industry continue, but are constrained by the need for large capital investment to setup Plant of economic size, and the need for a large-scale source or sources of raw material.

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Song, Zhiyu, Yafei Zhai, and Guangkun Liu. "Analysis of Dynamic Response Characteristics of Towering Intake Towers Under the Action of Main-Aftershock Sequences." In Lecture Notes in Civil Engineering. Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-97-9184-2_22.

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AbstractAfter a strong earthquake occurs, it can cause a certain degree of damage to the structure, and the strong aftershock effect can cause secondary damage to the already damaged structure. In this study, taking a actual project of intake tower in the district of western strong earthquake as an example, the acoustic unit is used to simulate the dynamic effect of reservoir water on the tower body, and the overall nonlinear model of the water-intake tower-foundation is established. Combined with the site and seismic motion characteristics of the engineering area, the seismic motion sequence of the main-aftershocks was constructed based on the statistical relationship between the main shocks and strong aftershocks, as well as the NGA seismic motion attenuation model. The effects of main shock, aftershock, and main-aftershock on the structural damage evolution of intake towers in strong earthquake zones were investigated separately. The results show that after considering the aftershock effect, the damage and failure of the intake tower structure intensify, and its dissipation energy and residual displacement increase by about 20%~25%. Compared with the main shock, the aftershock alone causes less damage to the tower structure. However, for the intake tower structure that is damaged after the main shock, the aftershock can cause larger secondary residual deformation of the tower.

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Stoeva, Stanka, Krasimira Idakieva, Wolfgang Voelter, and Nicolay Genov. "Isolation, Characterization and Amino Acid Sequence of the N-Terminal Functional Unit from the Rapana thomasiana grosse (Marine Snail, Gastropod) Hemocyanin." In Protein Structure — Function Relationship. Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-0359-6_24.

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Hunter, C. A., and M. J. Packer. "Computational Approaches to Predicting Sequence-Structure Relationships in DNA." In Solid Mechanics and Its Applications. Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-015-9930-6_34.

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Steipe, Boris, and Bhooma Thiruv. "schematikon: Detailed Sequence-Structure Relationships from Mining a Non-redundant Protein Structure Database." In Bioinformatics Research and Applications. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-08171-7_32.

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Howard, S. P., and L. Lindsay. "Structure/Function Relationships in the Signal Sequence of the Colicin A Lysis Protein." In Bacteriocins, Microcins and Lantibiotics. Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-76974-0_28.

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Estess, Pila, Ann B. Begovich, Patricia P. Jones, and Hugh O. McDevitt. "Structure/Function Relationships Among Murine Class II Molecules: Sequence Analysis of I-A cDNA Clones." In Regulation of Immune Gene Expression. Humana Press, 1986. http://dx.doi.org/10.1007/978-1-4612-5014-2_1.

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Conference papers on the topic "Sequence-Structure relationship"

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Li, Minghui, Lei Lin, Xiaolong Wang, Qiwen Dong, and Tao Liu. "Study on Relationship between Protein Sequence Pattern and Protein Secondary Structure." In 2005 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1615533.

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Nicosia, Giuseppe, Eva Sciacca, and Luca Zammataro. "Detecting constituent sequences by means of HP pattern-based grammars to synthesize proteins: Inferring sequence-structure-function relationship." In 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops. IEEE, 2007. http://dx.doi.org/10.1109/bibmw.2007.4425400.

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Jenewein, Oswald. "Designing Towards Ecological Environments: A Modular Approach to Structure a Design Studio Sequence." In 2019 ACSA Teachers Conference. ACSA Press, 2019. http://dx.doi.org/10.35483/acsa.teach.2019.53.

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Architecture is a process that forms the physical background of every-day life. Both in academia and practice, a contemporary design studio must tackle ecological topics as architecture materializes itself within the rapidly changing natural environment. The premise for this paper are three timely challenges that the world is facing collectively in this stage of Post-Industrialization.First and foremost, the challenges arising from the Epoch of the Anthropocene. As the repercussions of climate change have started to materialize, the built environment needs to adapt to changing conditions, from sea-level-rise to extreme weather and cultural shifts, as climate migrants need to find new lands.Second, the challenges correlated with globalized economies and networks which have been a major force causing environmental threats and change. Capitalist democracies in the western world have developed complex logistical processes shipping commodities, goods, and thoughts around the world. These processes have shaped the (built) environment and life especially in urban areas. The relationship between the individual and the collective undergoes change as a consequence of how (political) regimes organize their economies and distribute wealth.Third, the challenges and opportunities digitalization offers to society. The dematerialization of (urban) landscapes through digital media enables the (re)distribution and access to information, education, and labor. Urban environments need to address these challenges as opportunities to create fairer and healthier places to live.These three challenges form the context of the studio modules presented here and link the contemporary discourse of architecture to a global cross-disciplinary discourse.

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Grzebieta, Raphael, David Young, Andrew McIntosh, and Michael Bambach. "Occupant Injuries and Roof Strength in Rollover Crashes." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-68739.

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This paper shows how a mathematical relationship can be derived linking serious neck injuries to excessive roof deformation and that this relationship depends on the vehicle’s Centre of Gravity (COG) lateral velocity at the moment of touchdown of the vehicle’s roof structure. The relationships have been greatly simplified for an idealized condition to facilitate derivation of the equations. In the case of a very strong roof, occupant neck loading resulting from torso augmentation reaches a threshold value that depends on the coefficient of friction between the road surface and the vehicle’s steel body or tires and the height the vehicle’s COG drops during a quarter turn impact sequence.

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Ramaswamy, Shri, Shuiyuan Huang, Amit Goel, et al. "The 3D Structure of Paper and its Relationship to Moisture Transport in Liquid and Vapor Forms." In The Science of Papermaking, edited by C. F. Baker. Fundamental Research Committee (FRC), Manchester, 2001. http://dx.doi.org/10.15376/frc.2001.2.1289.

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The three dimensional structure of paper materials plays a critical role in the paper manufacturing process especially via its impact on the transport properties for fluids. Dewatering of the wet web, pressing and drying will benefit from knowledge of the relationships between the web structure and its transport coefficients. Among transport, moisture diffusion in paper is central to the understanding and optimal design of paper products for their performance in different environmental conditions. Our recent research of moisture sorption in paper has indicated that diffusion of water vapor through the pore space is an important mechanism for transport [1,2]. The effect of the three dimensional structure of the paper sheet on the diffusion of moisture is significant. The structure of the pore space within a paper sheet is imaged in serial sections using x-ray microtomography. The three dimensional structure is reconstructed from these sections using digital image processing techniques. The structure is then analyzed by measuring traditional descriptors for the pore space such as specific surface area and porosity. In addition, morphometric and quantitative stereological techniques are used to characterize the structure. Techniques of mathematical morphology [3] used include erosion, dilation, closing, opening and binarization with subsequent skeletonization. A sequence of microtomographs was imaged at approximately 2 μm intervals and the three-dimensional pore-fiber structure was reconstructed. The pore size distributions for both in-plane as well as transverse pores were measured. Significant differences in the in-plane (X-Y) and the transverse directions in pore characteristics are found and may help partly explain the different liquid and vapor transport properties in the in-plane and transverse directions. The results from the mathematical morphological study show that the pore space and the fiber space are bicontinuous. Some network measures of both these spaces are the network nodal density and bond co-ordination number distribution, both of which are determined. Significant transport properties for the pore space include the saturated water permeability and water vapor diffusivity. Due to the anisotropic nature of the structure, these are three-dimensional tensors in general.

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Sonalkar, Neeraj, Kathryn Jablokow, Jonathan Edelman, Ade Mabogunje, and Larry Leifer. "Design Whodunit: The Relationship Between Individual Characteristics and Interaction Behaviors in Design Concept Generation." In ASME 2017 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/detc2017-68239.

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This paper investigates the relationship between interaction behaviors and the cognitive characteristics of participating individuals in engineering design teams engaged in concept generation. Individual characteristics were measured using the Kirton Adaption-Innovation inventory (KAI), which assesses an individual’s cognitive preference for structure in seeking and responding to change. Team interactions were measured using the Interaction Dynamics Notation (IDN), which allows interaction behaviors to be quantitatively analyzed. A correlation analysis revealed statistically significant correlations between individual characteristics and specific interaction behaviors, and ideation utterances. An interaction sequence analysis of the team data also revealed specific interaction sequences associated with greater probabilities of idea occurrence within the team. These findings serve as a first step towards building a cognitive-behavioral model of engineering design team performance.

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Miwa, Toshiharu, Hideki Aoyama, and Kosuke Ishii. "Probabilistic Evaluation of Product Development Task Planning Using Worth Flow Analysis." In ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/detc2008-49142.

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The acceleration of the product development cycle continues to be a significant challenge for manufacturing firms around the world. The present paper describes a task planning method that takes the uncertain relationships among the product components into consideration in order to reduce the development time in large-scale and complicated product development with uncertainty at the early stage of product development. We developed a probabilistic worth flow analysis to evaluate each product component for task prioritization with an uncertain relationship among product components. The method calculates the probabilistic distribution of worth flow of each product component based on the probabilistic relationship among product components with the Monte Carlo simulation and determines the development sequence of each component so as to minimize the possibility with the highest feedback information across the task groups. The present paper describes an example of a generic hair drier with a simple mechanical structure developed using the proposed method in order to reduce the uncertainty of feedback information across the task groups while maintaining the uncertainty within same task groups in case the uncertainty has an asymmetric distribution.

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Wang, Tianming, Xiaojun Wan, and Shaowei Yao. "Better AMR-To-Text Generation with Graph Structure Reconstruction." In Twenty-Ninth International Joint Conference on Artificial Intelligence and Seventeenth Pacific Rim International Conference on Artificial Intelligence {IJCAI-PRICAI-20}. International Joint Conferences on Artificial Intelligence Organization, 2020. http://dx.doi.org/10.24963/ijcai.2020/542.

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AMR-to-text generation is a challenging task of generating texts from graph-based semantic representations. Recent studies formalize this task a graph-to-sequence learning problem and use various graph neural networks to model graph structure. In this paper, we propose a novel approach that generates texts from AMR graphs while reconstructing the input graph structures. Our model employs graph attention mechanism to aggregate information for encoding the inputs. Moreover, better node representations are learned by optimizing two simple but effective auxiliary reconstruction objectives: link prediction objective which requires predicting the semantic relationship between nodes, and distance prediction objective which requires predicting the distance between nodes. Experimental results on two benchmark datasets show that our proposed model improves considerably over strong baselines and achieves new state-of-the-art.

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Ganian, Robert, Viktoriia Korchemna, and Stefan Szeider. "Revisiting Causal Discovery from a Complexity-Theoretic Perspective." In Thirty-Third International Joint Conference on Artificial Intelligence {IJCAI-24}. International Joint Conferences on Artificial Intelligence Organization, 2024. http://dx.doi.org/10.24963/ijcai.2024/374.

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Causal discovery seeks to unveil causal relationships (represented as a so-called causal graph) from observational data. This paper investigates the complex relationship between the graph structure and the efficiency of constraint-based causal discovery algorithms. Our main contributions include (i) a near-tight characterization of which causal graphs admit a small d-separating set for each pair of vertices and thus can potentially be efficiently recovered by a constraint-based causal discovery algorithm, (ii) the explicit construction of a sequence of causal graphs on which the influential PC algorithm might need exponential time, although there is a small d-separating set between every pair of variables, and (iii) the formulation of a new causal discovery algorithm which achieves fixed-parameter running time by considering the maximum number of edge-disjoint paths between variables in the (undirected) super-structure as the parameter. A distinguishing feature of our investigation is that it is carried out within a more fine-grained model which more faithfully captures the infeasibility of performing accurate independence tests for large sets of conditioning variables.

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Qiao, Jie, Ruichu Cai, Siyu Wu, Yu Xiang, Keli Zhang, and Zhifeng Hao. "Structural Hawkes Processes for Learning Causal Structure from Discrete-Time Event Sequences." In Thirty-Second International Joint Conference on Artificial Intelligence {IJCAI-23}. International Joint Conferences on Artificial Intelligence Organization, 2023. http://dx.doi.org/10.24963/ijcai.2023/633.

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Learning causal structure among event types from discrete-time event sequences is a particularly important but challenging task. Existing methods, such as the multivariate Hawkes processes based methods, mostly boil down to learning the so-called Granger causality which assumes that the cause event happens strictly prior to its effect event. Such an assumption is often untenable beyond applications, especially when dealing with discrete-time event sequences in low-resolution; and typical discrete Hawkes processes mainly suffer from identifiability issues raised by the instantaneous effect, i.e., the causal relationship that occurred simultaneously due to the low-resolution data will not be captured by Granger causality. In this work, we propose Structure Hawkes Processes (SHPs) that leverage the instantaneous effect for learning the causal structure among events type in discrete-time event sequence. The proposed method is featured with the Expectation-Maximization of the likelihood function and a sparse optimization scheme. Theoretical results show that the instantaneous effect is a blessing rather than a curse, and the causal structure is identifiable under the existence of the instantaneous effect. Experiments on synthetic and real-world data verify the effectiveness of the proposed method.

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Reports on the topic "Sequence-Structure relationship"

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Montville, Thomas J., and Roni Shapira. Molecular Engineering of Pediocin A to Establish Structure/Function Relationships for Mechanistic Control of Foodborne Pathogens. United States Department of Agriculture, 1993. http://dx.doi.org/10.32747/1993.7568088.bard.

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This project relates the structure of the bacteriocin molecule (which is genetically determined) to its antimicrobial function. We have sequenced the 19,542 bp pediocin plasmid pMD136 and developed a genetic transfer system for pediococci. The pediocin A operon is complex, containing putative structural, immunity, processing, and transport genes. The deduced sequence of the pediocin A molecule contains 44 amino acids and has a predicted PI of 9.45. Mechanistic studies compared the interaction of pediocin PA-1 and nisin with Listeria monocytgenes cells and model lipid systems. While significant nisin-induced intracellular ATP depletion is caused by efflux, pediocin-induced depletion is caused exclusively by hydrolysis. Liposomes derived from L. monocytogenes phospholipids were used to study the physical chemistry of pediocin and nisin interactions with lipids. Their different pH optima are the results of different specific ionizable amino acids. We generated a predicted 3-D structural model for pediocin PA-1 and used a variety of mutant pediocins to demonstrate that the "positive patch" at residues 11 and 12 (and not the YGNGV consensus sequence) is responsible for the binding step of pediocin action. This structure/function understanding gained here provides necessary prerequisites to the more efficacious use of bacteriocins to control foodborne pathogens.

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Mevarech, Moshe, Jeremy Bruenn, and Yigal Koltin. Virus Encoded Toxin of the Corn Smut Ustilago Maydis - Isolation of Receptors and Mapping Functional Domains. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7613022.bard.

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Ustilago maydis is a fungal pathogen of maize. Some strains of U. maydis encode secreted polypeptide toxins capable of killing other susceptible strains of U. maydis. Resistance to the toxins is conferred by recessive nuclear genes. The toxins are encoded by genomic segments of resident double-strande RNA viruses. The best characterized toxin, KP6, is composed of two polypeptides, a and b, which are not covalently linked. It is encoded by P6M2 dsRNA, which has been cloned, sequenced and expressed in a variety of systems. In this study we have shown that the toxin acts on the membranes of sensitive cells and that both polypeptides are required for toxin activity. The toxin has been shown to function by creating new pores in the cell membrane and disrupting ion fluxes. The experiments performed on artificial phospholipid bilayers indicated that KP6 forms large voltage-independent, cation-selective channels. Experiments leading to the resolution of structure-function relationship of the toxin by in vitro analysis have been initiated. During the course of this research the collaboration also yielded X-ray diffracion data of the crystallized a polypeptide. The effect of the toxin on the pathogen has been shown to be receptor-mediated. A potential receptor protein, identified in membrane fractions of sensitive cells, was subjected to tryptic hydrolysis followed by amino-acid analysis. The peptides obtained were used to isolate a cDNA fragment by reverse PCR, which showed 30% sequence homology to the human HLA protein. Analysis of other toxins secreted by U. maydis, KP1 and KP4, have demonstrated that, unlike KP6, they are composed of a single polypeptide. Finally, KP6 has been expressed in transgenic tobacco plants, indicating that accurate processing by Kex2p-like activity occurs in plants as well. Using tobacco as a model system, we determined that active antifungal toxins can be synthesized and targeted to the outside of transgenic plant cells. If this methodology can be applied to other agronomically crop species, then U. maydis toxins may provide a novel means for biological control of pathogenic fungi.

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McElwain, Terry, Eugene Pipano, Guy Palmer, Varda Shkap, Stephen Hines, and Douglas Jasmer. Protection of Cattle Against Babesiosis: Immunization with Recombinant DNA Derived Apical Complex Antigens of Babesia bovis. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7612835.bard.

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Bovine babesiosis caused by Babesia bovis continues to be a significant deterrent to global livestock production. Current control methods have both biological and technical drawbacks that have stimulated research on improved methods of vaccination. This BARD project has focused on characterization of candidate Babesia bovis vaccine antigens located in the apical complex, a unique group of subcellular organelles - including rhoptries, micronemes, and spherical bodies - involved in the invation of erythrocytes. Spherical bodies and rhoptries were partially purified and their contents characterized using monoclonal antibodies. Existing and newly developed monoclonal antibodies bound to antigens in the spherical body, rhoptry, merozoite membrane, and infected erythrocyte membrane. In an initial immunization study using biologically cloned strains, it was demonstrated that strain-common epitopes are important for inducing immune protection against heterologous challenge. Rhoptry-associated antigen 1 (RAP-1) had been demonstrated previously to induce partial immune protection, fulfilled criteria of broad interstrain B and T cell epitope conservation, and thus was further characterized. The RAP-1 gene family consists of at least two gene copies, is homologous to the RAP-1 gene family in B. bigemina, and contains significant sequence similarity to other erythroparasitic protozoan candidate vaccine antigens, including the apical membrane antigen of Plasmodium falciparum. A new RAP-1 monoclonal antibody was developed that inhibits merozoite growth in vitro, demonstrating the presence of a RAP-1 neutralization sensitive domain. Based on these observations, cattle were immunized with Mo7 (Mexico) strain recombinant RAP-1 representing one of the two gene copies. All cattle responded with variable levels of serum antibodies inhibitory to heterologous Israel strain merozoite growth in vitro, and RAP-1 specific T lymphocytes that proliferated when stimulated with either homologous or heterologous native parasite antigen. Minimal protection from clinical disease was present after virulent Israel (heterologous) strain B. bovis challenge. In total, the results support the continued development of RAP-1 as a vaccine antigen, but indicate that additional information about the native structure and function of both RAP-1 gene copies, including the relationship of conserved and polymorphic sequences to B and T cell lepitopes relevant for protection, is necessary for optimization of RAP-1 as a vaccine component.

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Funkenstein, Bruria, and Cunming Duan. GH-IGF Axis in Sparus aurata: Possible Applications to Genetic Selection. United States Department of Agriculture, 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.

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Hunter, Fraser, and Martin Carruthers. Iron Age Scotland. Society for Antiquaries of Scotland, 2012. http://dx.doi.org/10.9750/scarf.09.2012.193.

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The main recommendations of the panel report can be summarised under five key headings:  Building blocks: The ultimate aim should be to build rich, detailed and testable narratives situated within a European context, and addressing phenomena from the longue durée to the short-term over international to local scales. Chronological control is essential to this and effective dating strategies are required to enable generation-level analysis. The ‘serendipity factor’ of archaeological work must be enhanced by recognising and getting the most out of information-rich sites as they appear. o There is a pressing need to revisit the archives of excavated sites to extract more information from existing resources, notably through dating programmes targeted at regional sequences – the Western Isles Atlantic roundhouse sequence is an obvious target. o Many areas still lack anything beyond the baldest of settlement sequences, with little understanding of the relations between key site types. There is a need to get at least basic sequences from many more areas, either from sustained regional programmes or targeted sampling exercises. o Much of the methodologically innovative work and new insights have come from long-running research excavations. Such large-scale research projects are an important element in developing new approaches to the Iron Age.  Daily life and practice: There remains great potential to improve the understanding of people’s lives in the Iron Age through fresh approaches to, and integration of, existing and newly-excavated data. o House use. Rigorous analysis and innovative approaches, including experimental archaeology, should be employed to get the most out of the understanding of daily life through the strengths of the Scottish record, such as deposits within buildings, organic preservation and waterlogging. o Material culture. Artefact studies have the potential to be far more integral to understandings of Iron Age societies, both from the rich assemblages of the Atlantic area and less-rich lowland finds. Key areas of concern are basic studies of material groups (including the function of everyday items such as stone and bone tools, and the nature of craft processes – iron, copper alloy, bone/antler and shale offer particularly good evidence). Other key topics are: the role of ‘art’ and other forms of decoration and comparative approaches to assemblages to obtain synthetic views of the uses of material culture. o Field to feast. Subsistence practices are a core area of research essential to understanding past society, but different strands of evidence need to be more fully integrated, with a ‘field to feast’ approach, from production to consumption. The working of agricultural systems is poorly understood, from agricultural processes to cooking practices and cuisine: integrated work between different specialisms would assist greatly. There is a need for conceptual as well as practical perspectives – e.g. how were wild resources conceived? o Ritual practice. There has been valuable work in identifying depositional practices, such as deposition of animals or querns, which are thought to relate to house-based ritual practices, but there is great potential for further pattern-spotting, synthesis and interpretation. Iron Age Scotland: ScARF Panel Report v  Landscapes and regions:  Concepts of ‘region’ or ‘province’, and how they changed over time, need to be critically explored, because they are contentious, poorly defined and highly variable. What did Iron Age people see as their geographical horizons, and how did this change?  Attempts to understand the Iron Age landscape require improved, integrated survey methodologies, as existing approaches are inevitably partial.  Aspects of the landscape’s physical form and cover should be investigated more fully, in terms of vegetation (known only in outline over most of the country) and sea level change in key areas such as the firths of Moray and Forth.  Landscapes beyond settlement merit further work, e.g. the use of the landscape for deposition of objects or people, and what this tells us of contemporary perceptions and beliefs.  Concepts of inherited landscapes (how Iron Age communities saw and used this longlived land) and socal resilience to issues such as climate change should be explored more fully.  Reconstructing Iron Age societies. The changing structure of society over space and time in this period remains poorly understood. Researchers should interrogate the data for better and more explicitly-expressed understandings of social structures and relations between people.  The wider context: Researchers need to engage with the big questions of change on a European level (and beyond). Relationships with neighbouring areas (e.g. England, Ireland) and analogies from other areas (e.g. Scandinavia and the Low Countries) can help inform Scottish studies. Key big topics are: o The nature and effect of the introduction of iron. o The social processes lying behind evidence for movement and contact. o Parallels and differences in social processes and developments. o The changing nature of houses and households over this period, including the role of ‘substantial houses’, from crannogs to brochs, the development and role of complex architecture, and the shift away from roundhouses. o The chronology, nature and meaning of hillforts and other enclosed settlements. o Relationships with the Roman world

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