Relevant bibliographies by topics / EF structure

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Academic literature on the topic 'EF structure'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "EF structure"

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Tsuda, K., and M. Tanaka. "Nanometer Crystal Structure Analysis by EF-CBED and EF-Microscopy." Microscopy and Microanalysis 6, S2 (August 2000): 152–53. http://dx.doi.org/10.1017/s1431927600033250.

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Crystal structure refinement by the convergent-beam electron diffraction (CBED) method has the following advantages: (i) Nanometer-size crystal structure refinement: CBED patterns can be obtained from specimen areas of a few nanometer in diameter, (ii) Dynamical diffraction effect: the CBED intensities contain phase information of crystal structure factors through the strong dynamical effect. (iii) Site-selective analysis: the use of Bloch states formed by incident electrons allows structure determination weighted for specific atom sites. Energy-filtering (EF) to revome inelastically scattered background is now getting necessary for such quantitative analysis of CBED patterns. Especially for the determination of atom positions and Debye-Waller factors, the use of energy-filtered higher-order Laue zone (HOLZ) CBED patterns is essential because small displacements of atoms can be sensitively detected using HOLZ reflections with large reciprocal vectors. For this purpose, we developed a new fl-filter transmission electron microscope (JEM-2010FEF) with a high acceptance angle [2] and a new analysis program “mbfit” to refine structural parameters using many-beam Bloch-wave calculations and least-square fitting [1].
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Wang, Yong, Youxing Jiang, Martina Meyering-Voss, Mathias Sprinzl, and Paul B. Sigler. "Crystal structure of the EF-Tu˙EF-Ts complex from Thermus thermophilus." Nature Structural Biology 4, no. 8 (August 1997): 650–56. http://dx.doi.org/10.1038/nsb0897-650.

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Merve Çağlar, N., and Erdal Şafak. "Energy Flux Approach for Dynamic Analysis of Structures." Bulletin of the Seismological Society of America 109, no. 5 (July 30, 2019): 1797–811. http://dx.doi.org/10.1785/0120180311.

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Abstract Dynamic response of structures can be analyzed in terms of the propagation of input energy within the structure. Energy propagation is quantified by energy flux (EF), which is the amount of energy transmitted per unit time through a cross section of a medium. The formulation of EF is similar to the formulation of wave propagation in structures. It involves tracking the propagation path of the input energy and the energy loss due to damping within the elements of the structure. The EF approach introduces a new tool to evaluate the dynamic response and the energy absorption capacity of structures, providing an alternative parameter for the design of structures for dynamic loads. This article presents the theoretical basis for the methodology and gives a numerical example for the EF analysis of a plane frame structure under earthquake loads.
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Anderson Jnr, A. G., S. C. Critchlow, L. C. Andrews, and R. D. Haddock. "Structure of dicyclopenta[ef,kl]heptalene (azupyrene)." Acta Crystallographica Section C Crystal Structure Communications 46, no. 3 (March 15, 1990): 439–41. http://dx.doi.org/10.1107/s0108270189007857.

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Mondal, Dibyendu, and Arieh Warshel. "EF-Tu and EF-G are activated by allosteric effects." Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): 3386–91. http://dx.doi.org/10.1073/pnas.1800054115.

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Many cellular processes are controlled by GTPases, and gaining quantitative understanding of the activation of such processes has been a major challenge. In particular, it is crucial to obtain reliable free-energy surfaces for the relevant reaction paths both in solution and in GTPases active sites. Here, we revisit the energetics of the activation of EF-G and EF-Tu by the ribosome and explore the nature of the catalysis of the GTPase reaction. The comparison of EF-Tu to EF-G allows us to explore the impact of possible problems with the available structure of EF-Tu. Additionally, mutational effects are used for a careful validation of the emerging conclusions. It is found that the reaction may proceed by both a two-water mechanism and a one-water (GTP as a base) mechanism. However, in both cases, the activation involves a structural allosteric effect, which is likely to be a general-activation mechanism for all GTPases.
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Kawashima, Takemasa, Carmen Berthet-Colominas, Michael Wulff, Stephen Cusack, and Reuben Leberman. "The structure of the Escherichia coli EF-Tu· EF-Ts complex at 2.5 Å resolution." Nature 379, no. 6565 (February 8, 1996): 511–18. http://dx.doi.org/10.1038/379511a0.

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Nizhnichenko, Vladimir A., Alexey V. Boyko, Talia T. Ginanova, and Igor Yu Dolmatov. "Muscle Regeneration in Holothurians without the Upregulation of Muscle Genes." International Journal of Molecular Sciences 23, no. 24 (December 16, 2022): 16037. http://dx.doi.org/10.3390/ijms232416037.

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The holothurian Eupentacta fraudatrix is capable of fully restoring its muscles after transverse dissection. Although the regeneration of these structures is well studied at the cellular level, the molecular basis of the process remains poorly understood. To identify genes that may be involved in the regulation of muscle regeneration, the transcriptome of the longitudinal muscle band of E. fraudatrix has been sequenced at different time periods post-injury. An analysis of the map of biological processes and pathways has shown that most genes associated with myogenesis decrease their expression during the regeneration. The only exception is the genes united by the GO term “heart valve development”. This may indicate the antiquity of mechanisms of mesodermal structure transformation, which was co-opted into various morphogeneses in deuterostomes. Two groups of genes that play a key role in the regeneration have been analyzed: transcription factors and matrix metalloproteinases. A total of six transcription factor genes (Ef-HOX5, Ef-ZEB2, Ef-RARB, Ef-RUNX1, Ef-SOX17, and Ef-ZNF318) and seven matrix metalloproteinase genes (Ef-MMP11, Ef-MMP13, Ef-MMP13-1, Ef-MMP16-2, Ef-MMP16-3, Ef-MMP24, and Ef-MMP24-1) showing differential expression during myogenesis have been revealed. The identified genes are assumed to be involved in the muscle regeneration in holothurians.
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Nordenswan, Elisabeth, Eeva-Leena Kataja, Kirby Deater-Deckard, Riikka Korja, Mira Karrasch, Matti Laine, Linnea Karlsson, and Hasse Karlsson. "Latent Structure of Executive Functioning/Learning Tasks in the CogState Computerized Battery." SAGE Open 10, no. 3 (July 2020): 215824402094884. http://dx.doi.org/10.1177/2158244020948846.

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This study tested whether executive functioning (EF)/learning tasks from the CogState computerized test battery show a unitary latent structure. This information is important for the construction of composite measures on these tasks for applied research purposes. Based on earlier factor analytic research, we identified five CogState tasks that have been labeled as EF/learning tasks and examined their intercorrelations in a new sample of Finnish birth cohort mothers ( N = 233). Using confirmatory factor analyses, we compared two single-factor EF/learning models. The first model included the recommended summative scores for each task. The second model exchanged summative scores for first test round results for the three tasks providing these data, as initial task performance is expected to load more heavily on EF. A single-factor solution provided a good fit for the present five EF/learning tasks. The second model, which was hypothesized to tap more onto EF, had slightly better fit indices, χ2(5) = 1.37, p = .93, standardized root mean square residual (SRMR) = .02, root mean square error of approximation (RMSEA) = .00, 90% CI = [.00–.03], comparative fit index (CFI) = 1.00, and more even factor loadings (.30–.56) than the first model, χ2(5) = 4.56, p = .47, SRMR = .03, RMSEA = .00, 90% CI = [.00–.09], CFI = 1.00, factor loadings (.20–.74), which was hypothesized to tap more onto learning. We conclude that the present CogState sum scores can be used for studying EF/learning in healthy adult samples, but call for further research to validate these sum scores against other EF tests.
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Himi, Samsad Afrin, Markus Bühner, and Sven Hilbert. "Advancing the Understanding of the Factor Structure of Executive Functioning." Journal of Intelligence 9, no. 1 (March 16, 2021): 16. http://dx.doi.org/10.3390/jintelligence9010016.

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There has been considerable debate and interest regarding the factor structure of executive functioning (EF). Therefore, the aim of the current study was to delve into this issue differently, by investigating EF and other cognitive constructs, such as working memory capacity (WMC), relational integration, and divided attention, which may contribute to EF. Here, we examined whether it is possible to provide evidence for a definite model of EF containing the components of updating, shifting, and inhibition. For this purpose, 202 young adults completed a battery of EF, three WMC tests, three relational integration tests, and two divided attention tests. A confirmatory factor analysis on all the cognitive abilities produced a five-factor structure, which included one factor predominately containing shifting tasks, the next factor containing two updating tasks, the third one predominately representing WMC, the fourth factor consisting of relational integration and antisaccade tasks, and finally, the last factor consisting of the divided attention and stop signal tasks. Lastly, a subsequent hierarchical model supported a higher-order factor, thereby representing general cognitive ability.
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Hirano, Yu, Kana Tsukamoto, Shingo Ariki, Yuki Naka, Mitsuhiro Ueda, and Taro Tamada. "X-ray crystallographic structural studies of α-amylase I from Eisenia fetida." Acta Crystallographica Section D Structural Biology 76, no. 9 (August 25, 2020): 834–44. http://dx.doi.org/10.1107/s2059798320010165.

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The earthworm Eisenia fetida possesses several cold-active enzymes, including α-amylase, β-glucanase and β-mannanase. E. fetida possesses two isoforms of α-amylase (Ef-Amy I and II) to digest raw starch. Ef-Amy I retains its catalytic activity at temperatures below 10°C. To identify the molecular properties of Ef-Amy I, X-ray crystal structures were determined of the wild type and of the inactive E249Q mutant. Ef-Amy I has structural similarities to mammalian α-amylases, including the porcine pancreatic and human pancreatic α-amylases. Structural comparisons of the overall structures as well as of the Ca2+-binding sites of Ef-Amy I and the mammalian α-amylases indicate that Ef-Amy I has increased structural flexibility and more solvent-exposed acidic residues. These structural features of Ef-Amy I may contribute to its observed catalytic activity at low temperatures, as many cold-adapted enzymes have similar structural properties. The structure of the substrate complex of the inactive mutant of Ef-Amy I shows that a maltohexaose molecule is bound in the active site and a maltotetraose molecule is bound in the cleft between the N- and C-terminal domains. The recognition of substrate molecules by Ef-Amy I exhibits some differences from that observed in structures of human pancreatic α-amylase. This result provides insights into the structural modulation of the recognition of substrates and inhibitors.
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Dissertations / Theses on the topic "EF structure"

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Minella, Odile. "Structure et phosphorylation du facteur d'elongation ef-1 au cours de la meiose. Caracterisation de ef-1 delta." Paris 6, 1996. http://www.theses.fr/1996PA066628.

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Le facteur ef-1, intervenant dans la phase d'elongation de la synthese proteique, est constitue de deux elements : ef-1a, une proteine g et ef-1bgd, le complexe d'echange de gtp/gdp. La kinase cdc2, de la famille des proteines kinases cdk (dependantes des cyclines ; cdc2=cdk1) phosphoryle ef-1 pendant la transition g2/m. Nous avons etudie la structure et la phosphorylation de ef-1 dans l'ovocyte de xenope. Nous avons identifie deux nouvelles proteines ef-1 d1 et ef-1d2 appartenant au facteur ef-1. Ce sont deux nouvelles proteines d'echange de gtp/gdp, possedant un domaine c-terminal semblable a celui de la proteine ef-1b du meme complexe, et un motif d'interaction proteine-proteine de type leucine-zipper dans leur partie n-terminale. Elles sont toutes les deux presentes au sein des ovocytes, dans le complexe ef-1bgd. Nous avons determine que la valyl arnt synthetase de l'ovocyte est entierement presente dans le complexe d'echange de nucleotide, ef-1bgd. Il avait ete precedemment montre que ef-1g etait cible de la kinase cdc2/cyclineb. Nous avons determine que les deux proteines ef-1 d sont substrats in vivo de la kinase cdc2/ cycline b sur deux phospho-accepteurs une serine et une threonine. La threonine identifiee correspond a vt(92)paak dans ef-1d1 et vt(120)pak dans ef-1d2. Nous proposons en conclusion un modele de l'organisation de ef-1 a partir des observations chromatographiques, electrophoretiques et microscopiques du complexe purifie. Les etudes fonctionnelles de ef-1 et du role de ses phosphorylations devront tenir compte des progres realises dans la connaissance de la structure. Elles necessiteront de trouver de nouveaux modeles biologiques et de considerer non seulement l'activite multifonctionnelle proposee pour la proteine g, ef-1a, mais aussi la multitude des formes physiologiques du complexe ef-1bgd, et de ses sous-unites
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de, Laurentiis Evelina Ines, and University of Lethbridge Faculty of Arts and Science. "Two partners of the ribosome, EF-Tu and LepA." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, c2009, 2009. http://hdl.handle.net/10133/2515.

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The translational GTPases elongation factor Tu (EF-Tu) and LepA modulate the dynamics of tRNA on the ribosome. EF-Tu facilitates the delivery of aminoacyl-tRNA (aa-tRNA) to the translating ribosome and LepA catalyzes the retro-translocation of tRNA•mRNA from the E- and P-sites of the ribosome back to the P- and A-sites. Although an increasing body of structural and biochemical information is available, little is known about the functional cycle of LepA during retro-translocation, the kinetics of EF-Tu dissociation from the ribosome and the rate of EF-Tu conformational change during aa-tRNA delivery. This thesis reports the successful construction and biochemical characterisation of a mutant form of EF-Tu from Escherichia coli ideal for the specific incorporation of fluorescent labels, enabling measurements pivotal for uncovering the rate of EF-Tu conformational change and dissociation from the ribosome. Furthermore, to determine structural components critical for LepA’s function, mutant versions of the protein were constructed and biochemically characterised.
xii, 127 leaves : ill. (some col.) ; 29 cm
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KAWASHIMA, TAKEMASA. "Determination de la structure tridimensionnelle du complexe ef-tu : ef-ts, facteurs d'elongation polypeptidique d'escherichia coli, par la diffraction des rayons x." Paris 6, 1995. http://www.theses.fr/1995PA066633.

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Le complexe des facteurs de l'elongation polypeptidique ef-tu et ef-ts d'escherichia coli a ete cristallise afin d'etudier le mecanisme d'echange nucleotidique sur le plan structural, par la cristallographie aux rayons x. Les cristaux obtenus dans des solutions de peg 6000 peuvent se presenter sous deux formes morphologiquement similaires. L'une diffracte a basse resolution, l'autre a haute. La diffusion de vapeur d'eau peut convertir une forme en l'autre, et cette propriete faisait obstacle a la determination de la structure. La mise au point d'un protocole approprie de trempage et la collecte les donnees a temperature cryogenique, a permis d'obtenir des jeux de donnees complets de la forme diffractant a haute resolution, ce qui a conduit a la structure tridimensionnelle du complexe ef-tu:ef-ts a une resolution de 2. 5 angstroms. Le complexe est une molecule tetramerique contenant deux exemplaires de chaque facteur d'elongation. Les deux molecules de ef-ts forment un dimere et il n'y a que peu de contacts entre les deux molecules de ef-tu, ce qui est formule par 2ef-tu: ef-ts2. Ef-ts est en contact avec les domaines 1 et 3 de ef-tu. L'interaction de ef-ts avec ef-tu montre que le relargage du nucleotide guanidique est principalement du a l'alteration du site de fixation du magnesium par l'insertion de la chaine laterale d'une phenylalanine, appartenant a un motif conserve, dans la structure de ef-tu. Des sequences qui s'apparentent a ce motif peuvent etre identifiees dans d'autres facteurs d'echange nucleotidique
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Tossavainen, Helena. "NMR spectroscopic structure determination of calerythrin, and EF-hand protein from S. erythraea." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/kemia/vk/tossavainen/.

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ABDALLAH, BASSIMA, and André Mazabraud. "Les genes specifiant les facteurs d'elongation ef-1 alpha chez le xenope. Expression dans les lignees germinales et tumorales. Structure du gene ef-1 alpha oocytaire." Paris 6, 1993. http://www.theses.fr/1993PA066001.

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Nous avons etudie l'expression des genes specifiant plusieurs elements du systeme de synthese proteique pendant la gametogenese et l'embryogenese de xenopus laevis. Les genes etudies sont ceux qui codent pour le facteur d'elongation 1 alpha (ef-1 alpha), la thesaurine a et la thesaurine b. Ces deux dernieres proteines sont impliquees dans le stockage a long terme du rna 5s et du trna dans les oocytes. Elles ne sont pas detectables dans les cellules somatiques. Ef-1 alpha existe sous deux formes: une forme somatique (ef-1 alphas) et une forme oocytaire (ef-1 alphao). On demontre ici que le rna messager de ef-1 alphas est indetectable dans les oocytes et les spermatocytes, mais qu'il est present dans les cellules embryonnaires a partir du stade neurula. Le rna messager de ef-1 alphao est present non seulement dans les oogonies et les oocytes de tous les stades, mais aussi dans les spermatogonies et les spermatocytes primaires. Les rna messagers codant pour la thesaurine a et la thesaurine b sont egalement specifiques des cellules germinales. Ils sont traduits en proteines dans le testicule comme ils le sont dans l'ovaire. Cette etude revele une similitude frappante dans le programme d'expression des genes durant l'oogenese et la spermatogenese. Les produits des genes ef-1 alphao, thesaurine a et la thesaurine b peuvent etre consideres comme des marqueurs de la differenciation des cellules germinales
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Cai, Jinghan. "Two essays on the study of capital structure in Chinese stock market /." access full-text access abstract and table of contents, 2005. http://libweb.cityu.edu.hk/cgi-bin/ezdb/thesis.pl?phd-ef-b19887681a.pdf.

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Thesis (Ph.D.)--City University of Hong Kong, 2005.
"Submitted to Department of Economics and Finance in partial fulfillment of the requirements for the degree of Doctor of Philosophy" Includes bibliographical references (leaves 84-89)
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Franchini, Patrick Lorenzo Angelo. "Structure/Function in the CD site of parvalbumin : understanding calcium affinity using synthetic single site EF-hand peptides." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0020/NQ46344.pdf.

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Liboz, Thierry. "Structure et expression des genes codant pour le facteur d'elongation de la traduction ef-1 alpha chez arabidopsis thaliana." Toulouse 3, 1991. http://www.theses.fr/1991TOU30010.

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Les genes codant pour le facteur d'elongation de la tranduction ef-1 alpha d'arabidopsis thaliana ont ete clones et caracterises. Le facteur d'elongation ef-1 alpha est code par une petite famille multigenique de quatre membres chez cette espece. Les quatre genes, denommes a1, a2, a3 et a4, sont fonctionnels et codent pour une proteine identique, tres homologue aux divers facteurs d'elongation ef-1 alpha caracterises chez d'autres especes. L'analyse structurale a permis de montrer que les genes a1, a2 et a3 d'une part, et a4 d'autre part, doivent constituer deux sous-familles distinctes dans le genome d'arabidopsis thaliana. Les quatre genes sont interrompus par deux introns dont l'un est situe dans la region 5 non codante. Ils possedent tous dans leur promoteur plusieurs sequences susceptibles de jouer un role dans la regulation de leur expression. Des etudes d'analyse des transcrits ef-1 alpha effectuees dans differents organes de la plante et dans des conditions physiologiques variees (choc thermique, obscurite) indiquent que les quatre genes s'expriment de facon constitutive
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VALAGUSSA, STEFANIA. "Executive Function in children with typical and atypical development: toward an ecological assessment." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2015. http://hdl.handle.net/10281/68848.

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La presente ricerca è stata realizzata con l’intento di approfondire alcuni temi cardine nello studio delle Funzioni Esecutive (FE). Il termine FE si riferisce a processi neurocognitivi, deliberati e top-down necessari per esercitare controllo volontario su pensieri ed emozioni e per la messa in atto di comportamenti finalizzati al raggiungimento di un obiettivo. Si tratta di abilità indispensabili in situazioni nuove ed ambigue. Al dominio esecutivo vengono ascritte non solo abilità puramente cognitive. Tra le FF figurano: controllo degli impulsi ed autoregolazione, attenzione, memoria di lavoro, iniziativa, pianificazione ed organizzazione, flessibilità cognitiva, problem solving, decision making affettivo, teoria della mente ed empatia. Ad oggi non esiste un punto di vista condiviso su alcuni temi che sono stati oggetto del nostro interesse: la valutazione, la struttura e lo sviluppo delle FE, i deficit esecutivi presenti in alcuni disturbi specifici dello sviluppo. Per quanto concerne la valutazione delle FE, uno dei nodi critici è la scarsa validità ecologica degli strumenti tradizionalmente utilizzati nella ricerca e nella clinica. Al fine di superare questo problema metodologico sono state proposte modalità alternative di valutazione basate sia sulla performance che su report di insegnanti e genitori. Nella presente ricerca abbiamo proposto una nuova batteria neuropsicologica volta a fornire una panoramica globale del dominio esecutivo mettendo il bambino davanti a problemi analoghi a quelli che la quotidianità elicita. La batteria include: Battersea Multitasking Paradigm Task, Test di Ragionamento visuo-spaziale, Test di Pianificazione Quotidiano, Junior Gambling Task e Test del Clacson. È stato inoltre elaborato un questionario, il Questionario per la valutazione delle Funzioni Esecutive, QuFE, del quale sono indagate struttura, attendibilità ed utilità clinica. A tale scopo il questionario è stato somministrato a genitori ed insegnanti di bambini con sviluppo tipico o atipico di età compresa tra gli 8 ed i 13 anni. I risultati suggeriscono una struttura a 5 fattori per la versione genitori ed una a 3 per la versione insegnanti. Le abilità che sembrerebbero essere indagate sono: abilità metacognitive, regolazione delle emozioni e del comportamento, organizzazione dei materiali, adattamento ed iniziativa. Entrambe le versioni del QuFE si caratterizzano per una elevata validità interna. Per quanto concerne l’utilità clinica, lo strumento sembrerebbe distinguere in modo efficace soggetti con sviluppo tipico da soggetti clinici, minore è la capacità di differenziare tra i profili di soggetti con differenti disturbi dello sviluppo. Lo sviluppo e la struttura delle FE sono stati esaminati somministrando ad un campione di 343 soggetti con sviluppo tipico di età compresa tra gli 8 ed i 13 anni la batteria presentata sopra. Sono stati documentati significativi cambiamenti nei profili di performance in tutti test somministrati. Dall’analisi fattoriale è emersa una struttura a 4 fattori distinti ma interdipendenti: vigilanza, comportamento strategico, inibizione/flessibilità cognitiva e memoria. La struttura è stabile nel tempo e non presenta differenze legate al genere. Infine sono stati indagati i profili esecutivi in bambini con Disturbo da Deficit dell’Attenzione ed Iperattività (ADHD) e Disturbi Specifici dell’Apprendimento (DSA). Sono state oggetto di valutazione le performance di bambini con sviluppo tipico (207) o atipico (65) di età compresa tra gli 8 ed i 13 anni. I nostri dati suggeriscono che i bambini con ADHD e DSA hanno competenze strategiche ed inibitorie sovrapponibili. In entrambi i gruppi si è osservato un deficit della vigilanza e della memoria, di estensione maggiore nel gruppo ADHD. Si conferma la presenza di un deficit esecutivo nelle due popolazioni oggetto di interesse, deficit però circoscritto e non generalizzato.
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Cacan, Ercan. "Evolutionary synthetic biology: structure/function relationships within the protein translation system." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45838.

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Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.
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Books on the topic "EF structure"

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Berchtold, Martin W. Structure and expression of genes for parvalbumin and other EF-hand type CA2 - binding proteins. Zürich: Hartung-Gorre, 1990.

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Berchtold, Martin W. Structure and expression of genes for parvalbumin and other EF-hand type CA²⁺--binding proteins. Zürich: Hartung-Gorre, 1990.

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3

Carrión, Victor G., John A. Turner, and Carl F. Weems. Executive Function. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190201968.003.0001.

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In the first chapter, the relationship between traumatic stress and the broad domain of executive function (EF) and their neurofunctional correlates is discussed. The phenomenology of this relationship is reviewed in terms of the preclinical lesion and adult neuroimaging studies that have established a link between stress and deficits in executive functions. The myriad executive functions that have demonstrated vulnerability to traumatic stress are categorized as either updating, inhibiting, or shifting. Considerations from each domain establish clearly that the experience of trauma and the manifestation of posttraumatic stress symptoms can lead to or predispose individuals to deficits throughout the brain, resulting in slower processing speed, the formation of negative decision-making biases, and difficulties in emotional regulation, attention regulation, and response inhibition. The transition from psychometric cognitive tests to structural and functional neuroimaging and future directions for the study of executive function are also discussed.
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Book chapters on the topic "EF structure"

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Perret, Christine, Nourredine Lomri, and Monique Thomasset. "Structure of the Rat Vitamin D-Induced Calbindin-D9K Gene and Evolution of the EF-Hand Calcium-Binding Protein Family." In Calcium Protein Signaling, 241–50. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-5679-0_26.

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Plath, Thomas, Charlotte R. Knudsen, Nese Bilgin, Carsten Lindschau, Volker A. Erdmann, and Corinna Lippmann. "Structural requirements for the EF-Tu-directed kinase." In Interacting Protein Domains, 231–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60848-3_35.

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Heizmann, Claus W., and Katharina Braun. "Structures of EF-Hand Ca2+-Binding Proteins and Annexins." In Calcium Regulation by Calcium-Binding Proteins in Neurodegenerative Disorders, 13–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-662-21689-7_2.

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Heizmann, Claus W., and Katharina Braun. "Gene Structures and Chromosomal Assignments of EF-Hand Ca2+-Binding Proteins." In Calcium Regulation by Calcium-Binding Proteins in Neurodegenerative Disorders, 41–46. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-662-21689-7_3.

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Hilgenfeld, Rolf, Jeroen Mesters, and Tanis Hogg. "Insights into the GTPase Mechanism of EF-Tu from Structural Studies." In The Ribosome, 347–57. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818142.ch28.

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Jurnak, Frances, Michelle Nelson, Marilyn Yoder, Susan Heffron, and Suet Miu. "Progress on the Three-Dimensional Structural Determination of Trypsin-Modified EF-TU-GDP." In The Guanine — Nucleotide Binding Proteins, 15–25. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2_2.

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Sheu, Gwo-Tarng, and Jolinda A. Traugh. "A structural model for elongation factor 1 (EF-1) and phosphorylation by protein kinase CKII." In A Molecular and Cellular View of Protein Kinase CK2, 181–86. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4419-8624-5_22.

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Pingoud, Alfred, Uwe Pieper, Roger Busche, Hans-Jürgen Ehbrecht, Matthias Wehrmann, Frank-Ulrich Gast, Jürgen Feuerstein, et al. "Structural And Functional Studies on c-P21, v-P21 and the Genetically Engineered Guanine Nucleotide Binding Domain of EF-Tu." In The Guanine — Nucleotide Binding Proteins, 215–27. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2_21.

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Szebenyi, Doletha M. E., and Keith Moffat. "SOME THOUGHTS REGARDING EF-HANDS AND THE STRUCTURE OF CALBINDINS." In Calcium-Binding Proteins in Health and Disease, 323–32. Elsevier, 1987. http://dx.doi.org/10.1016/b978-0-12-521040-9.50058-9.

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Tomii, Kentaro, and Minoru Kanehisa. "Systematic Detection of Protein Structural Motifs." In Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.003.0012.

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It is widely believed that the prediction of the 3D structure of a protein from its amino acid sequence is important because the structure will help understand the function. As the number of protein structures resolved is increasing, most predictive methods have become based on the knowledge of the repertoire of 3D folds taken by actual proteins. We must emphasize, however, that this type of structure prediction, or fold recognition, concerns the overall folding of the polypeptide chain. Since two similar folds could be due to entirely different sequences and even two similar sequences could have different functions, it is unlikely that successful fold recognition will uncover any functional clue that cannot otherwise be obtained by sequence analysis alone. In contrast to the global feature of 3D folds, the concept of structural motifs or local structures is far more important in understanding protein function. It has been revealed that there are common local folding patterns that appear in many proteins of globally different structures and that are involved in conserved function. In addition, the local sequence patterns associated with these local structures are also often conserved, though the whole sequences can be quite different. At the supersecondary structure level there are, for example, βαβ -unit, EF hand, and helix-turn-helix motifs. Various dehydrogenases have a common structural motif called Rossman fold, which is composed of two consecutive βαβ -units, and most of those proteins also have the sequence motif GxGxxG around the nucleotide binding region (Wierenga and Hol, 1983; Wierenga et al., 1986). The EF hand consisting of the helix-loop-helix structure (Tufty and Kretsinger, 1975) occurs in many calcium-binding domains, and the residues that participate in ligand binding are well conserved. The helix-turn-helix motif that involves about 20 residues appears in a class of DNA-binding domains, and glycine tends to be conserved at a special position in the turn whose conformation corresponds to the left-handed helix. A number of known sequence motifs are registered in the motif libraries such as PROSITE (Bairoch and Bucher, 1994) that compile the relationships between sequence patterns and functions.
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Conference papers on the topic "EF structure"

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Hu, Yurui, Guangte Xiang, Jianfeng Shi, and Jinyang Zheng. "Influence of Resistor Wire on the Maximum Stress In Electrofusion Joint." In ASME 2021 Pressure Vessels & Piping Conference. American Society of Mechanical Engineers, 2021. http://dx.doi.org/10.1115/pvp2021-62123.

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Abstract Polyethylene (PE) pipes are widely used in oil and gas transportation, municipal construction. Electrofusion (EF) welding is one of the most commonly used connection method for PE pipes. The welding quality of EF joints is crucial to the safety of PE pipeline. Resistor wire is an important part of pipe fittings, and has great influence in final welding quality and strength of EF joints. In this paper, we discussed the influence of resistor wire for EF fittings in the aspect of selection of resistor wire materials and determination of structural dimensions. Resistivity and temperature coefficient of resistance (TCR) are two factors for material selection. In addition, the influence of resistor wire structure, i.e., resistor wire spacing, resistor wire diameter, on the stress distribution of EF joint was discussed through finite element analysis. The results revealed that the maximum stress in EF joint increase with the diameter of resistor wire, and is barely affected by resistor wire spacing.
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Chang, Y., N. G. Stoffel, Ming Tang, R. Zanoni, M. Onellion, Robert Joynt, D. L. Huber, et al. "Temperature effects in the near-EF electronic structure of Bi4Ca3Sr3Cu4O16+x." In Topical conference on high tc superconducting thin films, devices, and applications. AIP, 1989. http://dx.doi.org/10.1063/1.37955.

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Zheng, Jinyang, Xiangpeng Luo, Jianfeng Shi, and Sijia Zhong. "Study on the Failure Mode of Cracking Through the Fitting of Electrofusion Joint." In ASME 2013 Pressure Vessels and Piping Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/pvp2013-97172.

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Electrofusion (EF) technique has been widely used in polyethylene and its composite pipeline system. The strength of the EF joint is regarded as higher than that of present pipe, for the EF joints are usually failed at the pipe when subjected to internal pressure. However, several recent studies from different researchers have revealed that the EF joint may fail by cracking through the fitting in the long-term hydraulic pressure tests. In this study, the structure parameter and loading condition were taken into consideration to investigate the failure mechanism of this failure mode. The progress of crack initiation and propagation was studied by FEA method and linear elastic fracture mechanics theory. EF joints with different structure and welding parameters were analyzed to find out the design factors which would have major influence on the failure mode of cracking through the fitting. The analytical results show a reasonable agreement with experimental observations, and also reveal that the length of inner cold welding zone has a great influence and should be carefully determined in the designation of EF fittings.
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Guo, Rong, Xiaochen Wu, and Tong Wu. "Research on the compilation of low carbon planning guidelines for Changxing County, China." In Post-Oil City Planning for Urban Green Deals Virtual Congress. ISOCARP, 2020. http://dx.doi.org/10.47472/tsmz5166.

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In the past 40 years since China's reform and opening up, the city has been developing rapidly. Small towns are faced with the challenges of extensive development, degradation of human settlements and dif iculty in retaining local characteristics. Therefore, in the development process of small towns, we should not only pay attention to economic development, but also energy conservation and emission reduction, and pay attention to the protection of local characteristics.This paper calculates the carbon emissions of energy consumption in Changxing County from 2002 to 2017, and analyzes the main factors and degree of carbon emissions in Changxing County by using Kaya identities based on the carbon emissions decomposition model. The results show that the carbon emissions of Changxing County increased year by year, but the growth rate showed a downward trend. The ef ect of economic development and energy intensity has a great contribution to the carbon emissions of Changxing County. Industrial structure ef ect, energy structure ef ect and population size ef ect have little contribution to carbon emissions. Combined with the current situation and main factors of carbon emissions in Changxing County, this paper puts forward the compilation ideas and framework of low-carbon planning guidelines of Changxing County from six characteristic spaces , so as to provide the thinking and practical basis for the low-carbon construction of small towns.
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Marti, Kurt. "Stochastic Approximation Methods in Optimal Structural Design: The Use of Intermediate Variables." In ASME 1996 Design Engineering Technical Conferences and Computers in Engineering Conference. American Society of Mechanical Engineers, 1996. http://dx.doi.org/10.1115/96-detc/dac-1458.

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Abstract Reliability-based optimization methods in optimal structural design use mostly the following basic design criteria: I) Minimal weight (volume or costs) and II) high or reliability of the structure. Since, in practice, several parameters of the structure, e.g. elastic moduli, tolerances of structural dimensions, loads, are not given, fixed quantities, but random variables having a certain probability distribution P, a stochastic optimization problem will result from criteria (I), (II), which can be represented min F(x) with F(x) := Ef(ω, x). (1) x∇D Stochastic approximation methods are considered for solving (1): The gradient estimators are obtained by the response surface methodology (RSM) where especially the improvement of the estimators by using so-called “intermediate” or “intervening” variables is considered.
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Jhun, Choon-Sik, Mark B. Ratcliffe, and Julius M. Guccione. "Ventricular Wall Stress and Pump Function of Ventricular Septal Defect of Congenital Heart Defects." In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206320.

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About 36,000 infants are born each year with a congenital heart defect (CHD) and charges for treatment surpass $2.2 billion for inpatient surgery alone. Of many different types of CHDs, ventricular septal defect (VSD) is the most common class (∼1/3 of CHDs) of heart deformity present at birth. Though many close spontaneously and rarely require treatment, VSD still accounts for ∼15% of defects requiring an invasive procedure within the first year of life [1]. Generally, the ventricular performance is indexed by geometry, shape, diastolic and systolic function, and myocardial contractility [2]. Ejection fraction (EF) and end-systolic (ES) wall stress also used to assess the ventricular function [3–5]. Ratcliffe and Guy suggested that the assessment of LV function focusing on indices of systolic function, such as EF and contractility (EES), is misleading because the shift of end-systolic pressure-volume relationship (ESPVR) and increase/decrease in EES and coincident shift of end-diastolic pressure-volume relationship (EDPVR) may result in pseudo increase/decrease of EF even though there may not be any significant change in true LV function (i.e., Starling relationship) [6]. Though Sagawa and associates proposed the ESPVR as a reliable index of intrinsic systolic function [7], it requires derivation of the pressure-volume relationship at different loading conditions by using a noninotropic vasoconstrictor or vasodilator. This may consequently enforce a significant burden on infants with a failing heart. Moreover, irreversible complication of muscle structure can be generated [8–10]. Thus, rigorous quantification of the pump function associated with mechanics has been hindered especially for infants.
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Shi, Jianfeng, Jinyang Zheng, and Weican Guo. "Formation Mechanism and Micro-Structure of Eigen-Line in Electrofusion Joints of Polyethylene Pipes." In ASME 2010 Pressure Vessels and Piping Division/K-PVP Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/pvp2010-25574.

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Cold welding is the most dangerous defect in the electro-fusion (EF) joint of polyethylene (PE) pipes. A proprietary method was developed to detect the degree of cold welding by using an Eigen-line which was discovered in our previous study. To understand when, where and how the Eigen-line occurs, the forming mechanism was investigated in this paper. Three factors, i.e., micro-air-bubbles, difference of acoustic impendence of PE in the melted and un-melted region and small-crowded crystals may cause the appearance of the Eigen-line. It was found that the number of Eigen-lines was the same as that of welding times when re-welded with decreasing welding time, and only one Eigen-line could be observed when re-welded with increasing welding time. The result showed that small-crowded crystals may be the dominating factor. This was then verified by the temperature analysis and differential scanning calorimeter (DSC) tests, and the forming process of the small-crowded crystals was discussed in detail.
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polyphemus, Limulus, T. Muta, T. Miyata, F. Tokunaga, T. Nakamura, and S. Iwanaga. "PRIMARY STRUCTURE OF ANTI-LIPOPOLYSACCHARIDE FACTOR ISOLATED FROM AMERICAN HORSESHOE CRAB." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644608.

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In 1982, a protein component that inhibits the limulus coagulation cascade was found in the hemocyte lysates from Japanese and American horseshoe crabs and named anti-lipopolysaccharide (LPS) factor. This protein specifically inhibited the LPS-mediated activation of limulus factor C and had a strong anti-bacterial effect on the growth of Gram-negative R-type bacteria. Moreover, it had a hemolytic activity on the red blood cells sensitized with LPS.In the present study, the complete amino acid sequence of anti-LPS factor purified from the Limulus (L) polyphemus hemocytes was determined by characterization of the NH2-terminal sequence and the peptides generated after digestion of the protein with lysyl endopeptidase, clostripain, and Staphylococcus aureus V8 protease. Upon sequencing the peptides by the automated Edman method, the following primary structure was obtained:During the sequence analysis, two species of the protein, which differed from each other at one locus, were found and characterized. L. polyphemus anti-LPS factor was a basic protein consisting of a single polypeptide chain of 101 residues and a calculated molecular weight of 11,786 or 11,800. The hydrophobic NH2-terminal sequence and positive charges found in the disulfide loop yielded a typical amphipathic character of this protein. Moreover, L. polyphemus anti-LPS factor showed 83% sequence identity with the Tachypleus tridentatus protein (J. Aketagawa, et al. (1986) J. Biol. Chem. 261, 7357-7365), and the sequence similar to that observed in the EF-hand structure was found to contain in the COOH-terminal portions of these proteins, although its function is unknown.
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Cheng, Yu-Chen, and Pen-Hsiu Grace Chao. "A Model for Ligament Fibroblast Migration Into Provisional Matrix." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53858.

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Many strategies have been proposed to enhance the healing capability of the anterior cruciate ligament (ACL). A novel treatment option, called enhanced primary repair, places a provisional matrix at the tear site to promote cell infiltration of the wound and aims to reestablish the structure-function relationship of the ACL [1]. This approach of guided tissue regeneration offers great potential benefits of retaining the complex native tissue matrix structure, innervation, and vascularization as compared with grafts. A major aspect of this procedure is enhancing ligament fibroblast infiltration into the matrix material and promoting matrix synthesis. We have previously demonstrated that applied electric fields (EFs) enhance knee ligament fibroblast migration, alignment, and collagen gene expressions on planar substrates [2]. In the current study, we developed a new system to simulate cell infiltration from the tissue to a provisional collagen matrix. An EF was applied across the construct to investigate its effects of on ACL fibroblast migration into the provisional matrix.
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Wang, Tzu-Han, Ruowei Wu, Vasu Gupta, and Shaolan Li. "27.3 A 13.8-ENOB 0.4pF-CIN 3rd-Order Noise-Shaping SAR in a Single-Amplifier EF-CIFF Structure with Fully Dynamic Hardware-Reusing kT/C Noise Cancelation." In 2021 IEEE International Solid- State Circuits Conference (ISSCC). IEEE, 2021. http://dx.doi.org/10.1109/isscc42613.2021.9365990.

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