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Journal articles on the topic 'Loops'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 September 2023

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1

Asai, Yukako, Tomokazu Shoji, Ikuro Kawagishi, and Michio Homma. "Cysteine-Scanning Mutagenesis of the Periplasmic Loop Regions of PomA, a Putative Channel Component of the Sodium-Driven Flagellar Motor in Vibrio alginolyticus." Journal of Bacteriology 182, no. 4 (February 15, 2000): 1001–7. http://dx.doi.org/10.1128/jb.182.4.1001-1007.2000.

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ABSTRACT The sodium-driven motor consists of the products of at least four genes, pomA, pomB, motX, andmotY, in Vibrio alginolyticus. PomA and PomB, which are homologous to the MotA and MotB components of proton-driven motors, have four transmembrane segments and one transmembrane segment, respectively, and are thought to form an ion channel. In PomA, two periplasmic loops were predicted at positions 21 to 36 between membrane segments 1 and 2 (loop1-2) and at positions 167 to 180 between membrane segments 3 and 4 (loop3-4). To characterize the two periplasmic loop regions, which may have a role as an ion entrance for the channel, we carried out cysteine-scanning mutagenesis. The T186 residue in the fourth transmembrane segment and the D71, D148, and D202 residues in the predicted cytoplasmic portion of PomA were also replaced with Cys. Only two mutations, M179C and T186C, conferred a nonmotile phenotype. Many mutations in the periplasmic loops and all of the cytoplasmic mutations did not abolish motility, though the five successive substitutions from M169C to K173C of loop3-4 impaired motility. In some mutants that retained substantial motility, motility was inhibited by the thiol-modifying reagents dithionitrobenzoic acid and N-ethylmaleimide. The profiles of inhibition by the reagents were consistent with the membrane topology predicted from the hydrophobicity profiles. Furthermore, from the profiles of labeling by biotin maleimide, we predicted more directly the membrane topology of loop3-4. None of the loop1-2 residues were labeled, suggesting that the environments around the two loops are very different. A few of the mutations were characterized further. The structure and function of the loop regions are discussed.

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2

Grosberg, Alexander Y. "Extruding Loops to Make Loopy Globules?" Biophysical Journal 110, no. 10 (May 2016): 2133–35. http://dx.doi.org/10.1016/j.bpj.2016.04.008.

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3

VanLehn, Kurt. "Regulative Loops, Step Loops and Task Loops." International Journal of Artificial Intelligence in Education 26, no. 1 (July 2, 2015): 107–12. http://dx.doi.org/10.1007/s40593-015-0056-x.

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4

deHaan, Jonathan. "Game loops, Game design loops, Game Terakoya loops and Ludic Language Pedagogy loops." Ludic Language Pedagogy 4 (January 17, 2022): 1–13. http://dx.doi.org/10.55853/llp_v4pg1.

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What is this? An exploration of well-designed games, game design “best practices,” solid steps in my Game Terakoya teaching, and straightforward questions for other teachers using games. I’ll loop back again and again ;) in this paper to the central concept of “loops:” sequences or systems that repeat and vary to different educational or entertaining effects. Why did you make it? I read and think a lot about games and game design. I also spend a lot of time designing and improving my teaching. I noticed the connections and wanted to create something that would help other teachers think about the loops in their teaching as well. Who is it for? It’s for experienced teachers: you’ve been teaching for “forever” … step back a bit from your work and think about whether your teaching is overly complex and not “loopy” enough. Let’s all aim for some elegant ludic language pedagogy!

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5

Liu, Xiao, and Yan Xu. "HnRNPA1 Specifically Recognizes the Base of Nucleotide at the Loop of RNA G-Quadruplex." Molecules 23, no. 1 (January 22, 2018): 237. http://dx.doi.org/10.3390/molecules23010237.

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Human telomere RNA performs various cellular functions, such as telomere length regulation, heterochromatin formation, and end protection. We recently demonstrated that the loops in the RNA G-quadruplex are important in the interaction of telomere RNA with heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Here, we report on a detailed analysis of hnRNPA1 binding to telomere RNA G-quadruplexes with a group of loop variants using an electrophoretic mobility shift assay (EMSA) and circular dichroism (CD) spectroscopy. We found that the hnRNPA1 binds to RNA G-quadruplexes with the 2’-O-methyl and DNA loops, but fails to bind with the abasic RNA and DNA loops. These results suggested that hnRNPA1 binds to the loop of the RNA G-quadruplex by recognizing the base of the loop’s nucleotides. The observation provides the first evidence that the base of the loop’s nucleotides is a key factor for hnRNPA1 specifically recognizing the RNA G-quadruplex.

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6

Chein, Orin, and Edgar G. Goodaire. "Code loops are RA2 loops." Journal of Algebra 130, no. 2 (May 1990): 385–87. http://dx.doi.org/10.1016/0021-8693(90)90088-6.

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7

Techalertpaisarn, Paiboon, and Antheunis Versluis. "Effect of apical portion of T-, sloped L-, and reversed L-closing loops on their force systems." Angle Orthodontist 87, no. 1 (July 19, 2016): 104–10. http://dx.doi.org/10.2319/020316-95.1.

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ABSTRACT Objective: To investigate the effect of the position of the apical portion of closing loops on the force system at both loop ends. Materials and Methods: T-loops were compared with backward-sloped L-loops (SL) and reversed L-loops (RL). SL-loops were directed toward the anterior side; RL-loops were directed toward the posterior side. Loop response to loop pulling was determined with finite element analysis at six positions of the apical loop portion for 12-mm interbracket distance and 8-mm loop length and height. Three-dimensional models of the closing loops were created using beam elements with the properties of stainless steel. Loop responses (horizontal load/deflection, vertical force, and moment-to-force ratio) at both loop ends were calculated as well as at 100 g and 200 g activation forces. Results: T-, SL-, and RL-loops with the same position of the apical portion showed approximately the same force system at both loop ends. This behavior was found across the investigated range through which the loops were moved (interbracket center to posterior bracket). Conclusions: The center of the apical portion determined the force system of the closing loops regardless of the position of the loop legs. The centers of the apical portion of the T-, SL-, and RL-loops acted like V-bend positions.

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8

Cozzo, Gabriele, Paolo Pagano, Antonino Petralia, and Fabio Reale. "Asymmetric Twisting of Coronal Loops." Symmetry 15, no. 3 (March 2, 2023): 627. http://dx.doi.org/10.3390/sym15030627.

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The bright solar corona entirely consists of closed magnetic loops rooted in the photosphere. Photospheric motions are important drivers of magnetic stressing, which eventually leads to energy release into heat. These motions are chaotic and obviously different from one footpoint to the other, and in fact, there is strong evidence that loops are finely stranded. One may also expect strong transient variations along the field lines, but at a glance, coronal loops ever appear more or less uniformly bright from one footpoint to the other. We aim to understand how much coronal loops can preserve their own symmetry against asymmetric boundary motions that are expected to occur at loop footpoints. We investigate this issue by time-dependent 2.5D MHD modelling of a coronal loop, including its rooting and beta-variation in the photosphere. We assume that the magnetic flux tube is stressed by footpoint rotation but also that the rotation has a different pattern from one footpoint to the other. In this way, we force strong asymmetries because we expect independent evolution along different magnetic strands. We found that until the Alfvén crossing-travel time relative to the entire loop length is much lower than the twisting period, the loop’s evolution depends only on the relative velocity between the boundaries, and the symmetry is efficiently preserved. We conclude that the very high Alfvén velocities that characterise the coronal environment can explain why coronal loops can maintain a very high degree of symmetry even when they are subjected to asymmetric photospheric motions for a long time.

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9

Tan, Baolin. "The Early Evolution of Solar Flaring Plasma Loops." Universe 7, no. 10 (October 11, 2021): 378. http://dx.doi.org/10.3390/universe7100378.

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Plasma loops are the elementary structures of solar flaring active regions and dominate the whole process of flaring eruptions. Standard flare models explain evolution and eruption after magnetic reconnection around the hot cusp-structure above the top of plasma loops very well; however, the early evolution of plasma loops before the onset of magnetic reconnection is poorly understood. Considering that magnetic gradients are ubiquitous in solar plasma loops, this work applies the magnetic-gradient pumping (MGP) mechanism to study the early evolution of flaring plasma loops. The results indicate that early evolution depends on the magnetic field distribution and the geometry of the plasma loops, which dominate the balance between the accumulation and dissipation of the energy around loop tops. Driven by MGP process, both of the density and temperature as well as the plasma β value around the looptop will increase in the early phase of the plasma loop’s evolution. In fact, the solar plasma loops will have two distinct evolutionary results: low, initially dense plasma loops with relatively strong magnetic fields tend to be stable for their maximum β value, which is always smaller than the critical value β<βc, while the higher, initially diluted solar plasma loops with relatively weak magnetic fields tend to be unstable for their β values, exceeding the critical value β>βc at a time of about one hour after the formation of the solar-magnetized plasma loop. The latter may produce ballooning instability and may finally trigger the following magnetic reconnection and eruptions. These physical scenarios may provide us with a new viewpoint to understand the nature and origin of solar flares.

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10

Ji, Wei Wei, Tao Wang, Yan Nie, and Rong Zhou Gong. "Numerical Study on Controllable Multi-Band Microwave Metamaterial Absorbers." Advanced Materials Research 239-242 (May 2011): 1260–64. http://dx.doi.org/10.4028/www.scientific.net/amr.239-242.1260.

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Based on the impedance matching and electromagnetic resonant characteristic of composite materials, we present a single-layer metamaterial absorber consisting of arch copper loop and substrate FR-4, of which the resonant frequency depended on the loop’s geometry perimeter. By combining resonant loops with different dimensions together, we can achieve multi-band absorption. The standard finite difference time domain method was used to calculate the magnitudes of reflectance, and then the induced surface current and power loss distributions were demonstrated to analyze the insight physical picture of the multi-band resonant feature. By optimizing the simulation results, the absorptivities of two absorption peaks are all above 98% when the number of copper loops is two, 95% for three absorption peaks of three loops, and 87% for four absorption peaks of four loops.

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11

Larson, Eric. "Program analysis too loopy? Set the loops aside." IET Software 7, no. 3 (June 2013): 131–49. http://dx.doi.org/10.1049/iet-sen.2012.0048.

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12

Romero Romero, Maria Luisa, Fan Yang, Yu-Ru Lin, Agnes Toth-Petroczy, Igor N. Berezovsky, Alexander Goncearenco, Wen Yang, et al. "Simple yet functional phosphate-loop proteins." Proceedings of the National Academy of Sciences 115, no. 51 (November 30, 2018): E11943—E11950. http://dx.doi.org/10.1073/pnas.1812400115.

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Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein’s scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop’s key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.

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13

Suryanto. "Dislocation Generated by Electron Irradiation." Advanced Materials Research 418-420 (December 2011): 744–47. http://dx.doi.org/10.4028/www.scientific.net/amr.418-420.744.

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Dislocation loop was generated by electron irradiation in nickel aluminum alloy. It is important to know dislocation characteristics obtained from a high energetic electron irradiation. If b is the Burger vector of a dislocation loop and g is the diffraction vector, dislocation loop will appear larger, smaller or disappear for g.b>0, g.b<0 or g.b=0, respectively. Dislocation loop was determined as follows – first, the appearance of dislocation loops is arranged in observation table. Second, based on type of dislocation loop, Burger vector and diffraction vector, appearance of dislocation loop is arranged in calculation table. Third, based on observation and calculation table, Burger vector and type of dislocation loop is determined. The results show that dislocation loops consist of perfect dislocation loops and Frank dislocation loops. The perfect dislocation loops have Burger vectors of ½[0 ] and ½[ 0] while Frank dislocation loops have Burger vectors of ⅓[1 1], ⅓[11 ], ⅓[ 11], ⅓[111], ⅓[1 1], ⅓[11 ] and ⅓[ 11]. All dislocation loops are interstitial types.

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14

Dockalova, Bara. "Loops." Scenario: A Journal of Performative Teaching, Learning, Research V, no. 1 (January 1, 2011): 66–74. http://dx.doi.org/10.33178/scenario.5.1.6.

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Our first Window of Practice contribution introduces a simple and effective language teaching technique called loops, which was developed as a part of the act and speak® method at Jeviste, a language school in Prague that specializes in using drama and theatre in language teaching. Loops allow for an intensive, focused, and engaging practice of narrowly selected language points, and they provide an easy start for improvisation and creative writing activities. The essence of loops lies in combining dramatic play with language drills in the form of repetitive dialogues. The dialogues must bear two important features: ambiguity and dramatic tension. The article provides suggestions on how teachers can create their own loops, and it describes the way loops can be used in the language classroom.

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15

Barfield, Lon. "Loops." ACM SIGCHI Bulletin - a supplement to interactions 2002 (January 2002): 15. http://dx.doi.org/10.1145/967135.967155.

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16

Young, Donovan. "BPS Wilson loops onS2at higher loops." Journal of High Energy Physics 2008, no. 05 (May 21, 2008): 077. http://dx.doi.org/10.1088/1126-6708/2008/05/077.

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17

Bassetto, Antonio, Luca Griguolo, Fabrizio Pucci, and Domenico Seminara. "Supersymmetric Wilson loops at two loops." Journal of High Energy Physics 2008, no. 06 (June 24, 2008): 083. http://dx.doi.org/10.1088/1126-6708/2008/06/083.

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18

Zizioli, Elena. "Fibered incidence loops and kinematic loops." Journal of Geometry 30, no. 2 (December 1987): 144–56. http://dx.doi.org/10.1007/bf01227812.

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19

Kreuzer, Alexander. "K-loops and Bruck loops on ?�?" Journal of Geometry 47, no. 1-2 (July 1993): 86–93. http://dx.doi.org/10.1007/bf01223807.

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20

Jaiyéọlá, T. G., A. A. Adeniregun, and M. A. Asiru. "Finite FRUTE loops." Journal of Algebra and Its Applications 16, no. 02 (February 2017): 1750040. http://dx.doi.org/10.1142/s0219498817500402.

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A loop [Formula: see text] is called a FRUTE loop if it obeys the identity [Formula: see text]. Interestingly, a FRUTE loop is a Moufang loop but not necessarily an extra loop or a group (and vice versa). In this paper, algebraic properties of the left (right) regular representation set of a FRUTE loop are deduced. A FRUTE loop is shown to be universal and an [Formula: see text]-loop for all [Formula: see text]. A Moufang loop is shown to be a FRUTE loop if and only if it is nuclear cube if and only if it is an [Formula: see text]-loop. It is established that: the smallest, associative, non-commutative FRUTE loop is of order [Formula: see text] (the quaternion group [Formula: see text]); for any [Formula: see text], there exists at least a non-commutative group of order [Formula: see text] that is a FRUTE loop; there exists [Formula: see text]-groups of orders [Formula: see text] that are non-commutative FRUTE loops; there are no non-commutative groups that are FRUTE loops of the following range of orders [Formula: see text]; there are two non-associative FRUTE loops of order [Formula: see text] up to isomorphism and there are six non-isomorphic, non-associative FRUTE loops of order [Formula: see text]. It is noted that there exists a non-associative and non-commutative FRUTE loop of order [Formula: see text]. The study is concluded with some questions, conjectures and problem.

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21

Grishkov, Alexander, and Rosemary Miguel Pires. "Variety of loops generated by code loops." International Journal of Algebra and Computation 28, no. 01 (February 2018): 163–77. http://dx.doi.org/10.1142/s021819671850008x.

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In this work, we construct free infinitely generated Moufang loop in the variety generated by code loops and find the minimal set of identities that define this variety. We apply this construction to the study of code loops.

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22

Mitusińska, Karolina, Tomasz Skalski, and Artur Góra. "Simple Selection Procedure to Distinguish between Static and Flexible Loops." International Journal of Molecular Sciences 21, no. 7 (March 26, 2020): 2293. http://dx.doi.org/10.3390/ijms21072293.

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Loops are the most variable and unorganized elements of the secondary structure of proteins. Their ability to shift their shape can play a role in the binding of small ligands, enzymatic catalysis, or protein–protein interactions. Due to the loop flexibility, the positions of their residues in solved structures show the largest B-factors, or in a worst-case scenario can be unknown. Based on the loops’ movements’ timeline, they can be divided into slow (static) and fast (flexible). Although most of the loops that are missing in experimental structures belong to the flexible loops group, the computational tools for loop reconstruction use a set of static loop conformations to predict the missing part of the structure and evaluate the model. We believe that these two loop types can adopt different conformations and that using scoring functions appropriate for static loops is not sufficient for flexible loops. We showed that common model evaluation methods, are insufficient in the case of flexible solvent-exposed loops. Instead, we recommend using the potential energy to evaluate such loop models. We provide a novel model selection method based on a set of geometrical parameters to distinguish between flexible and static loops without the use of molecular dynamics simulations. We have also pointed out the importance of water network and interactions with the solvent for the flexible loop modeling.

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23

Jaíyéolá, Tèmítòpé Gbóláhàn, Benard Osoba, and Anthony Oyem. "Isostrophy Bryant-Schneider Group-Invariant of Bol Loops." Buletinul Academiei de Ştiinţe a Republicii Moldova. Matematica, no. 2(99) (January 2023): 3–18. http://dx.doi.org/10.56415/basm.y2022.i2.p3.

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In the recent past, Grecu and Syrbu (in no order of preference) have jointly and individually reported some results on isostrophy invariants of Bol loops. Also, the Bryant-Schneider group of a loop has been found important in the study of the isotopy-isomorphy of some varieties of loops (e.g. Bol loops, Moufang loops, Osborn loops). In this current work, the Bryant-Schneider group of a middle Bol loop was linked with some of the isostrophy-group invariance results of Grecu and Syrbu. In particular, it was shown that some subgroups of the Bryant-Schneider group of a middle Bol loop are equal (or isomorphic) to the automorphism and pseudo-aumorphism groups of its corresponding right (left) Bol loop. Some elements of the Bryant-Schneider group of a middle Bol loop were shown to induce automorphisms and middle pseudo-automorphisms. It was discovered that if a middle Bol loop is of exponent 2, then, its corresponding right (left) Bol loop is a left (right) G-loop.

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24

Yudo, Hartono, Sarjito Jokosisworo, Wilma Amiruddin, Pujianto Pujianto, Tuswan Tuswan, and Mohamad Djaeni. "Numerical evaluation of expansion loops for pipe subjected to thermal displacements." Curved and Layered Structures 9, no. 1 (December 4, 2021): 72–80. http://dx.doi.org/10.1515/cls-2022-0007.

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Abstract The thermal expansion can lead to the high stress on the pipe. The problem can be overcome using expansion loops in a certain length depending on the material’s elastic modulus, diameter, the amount of expansion, and the pipe’s allowable stresses. Currently, there is no exact definition for the dimension of expansion loops design both for loop width (W) and loop footing height (H) sizes. In this study, expansion loops were investigated with using ratio of width and height (W/H) variations to understand pipe stress occurring on the expansion loops and the expansion loops’ safety factor. Relationship between non dimensional stress on the expansion loop pipe was studied numerically by finite element software on several working temperatures of 400oF, 500oF, 600oF, and 700oF. It can be found that stress occurring on the pipes increases as the increases of W/H of the expansion loops and results in a lower safety factor. The safety factor of the expansion loops pipe has a value of 1 when the ratio of loop width and loop footing height (W/H) value was 1.2 for a 16-inch diameter pipe. Stress occurring on the pipe increases with the increase of the working temperature. Expansion loops pipe designed for 400oF can still work well to handle thermal extension pipe occurring on 500oF.

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25

Hermoso, Antoni, Jordi Espadaler, E. Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, Baldomero Oliva, and Narcis Fernandez-Fuentes. "Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)." Bioinformatics and Biology Insights 1 (January 2007): 117793220700100. http://dx.doi.org/10.1177/117793220700100004.

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Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB ( http://sbi.imim.es/archdb ) is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ~40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the comparative study of loops, the analysis of loops involved in protein function and to obtain templates for loop modeling.

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26

Schlessinger, Avner, Jinfeng Liu, and Burkhard Rost. "Natively Unstructured Loops Differ from Other Loops." PLoS Computational Biology 3, no. 7 (July 20, 2007): e140. http://dx.doi.org/10.1371/journal.pcbi.0030140.

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27

Schlessinger, Avner, Jinfeng Liu, and Burkhard Rost. "Natively Unstructured Loops Differ from Other Loops." PLoS Computational Biology preprint, no. 2007 (2005): e140. http://dx.doi.org/10.1371/journal.pcbi.0030140.eor.

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28

Konrad, Angelika. "Hyperbolische Loops Über Oktaven und K-Loops." Results in Mathematics 25, no. 3-4 (May 1994): 331–38. http://dx.doi.org/10.1007/bf03323414.

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29

Van Den Oord, G. H. J., and F. Zuccarello. "Coronal loops and their modeling." Symposium - International Astronomical Union 176 (1996): 433–48. http://dx.doi.org/10.1017/s0074180900083455.

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We discuss the theory of quasi-static coronal loops, introducing a phase plane representation to study loop solutions independently of specific boundary conditions. Emphasis is put on the effects of loop expansion, heat input and gravitational stratification on the differential emission measure, and on the intrinsic limitations of spectroscopic observations for deriving loop parameters. We show that certain classes of published loop solutions cannot actually exist. For expanding loops new classes of loop solutions, with rather special properties, are presented. Special attention is paid to loops in binary systems and on rapidly rotating stars.

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30

Sivaraks, Jesada, and Settapong Malisuwan. "Multiband Antenna Formed of Superimposed Compressed Loops." Applied Mechanics and Materials 548-549 (April 2014): 780–84. http://dx.doi.org/10.4028/www.scientific.net/amm.548-549.780.

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A compressed multiple band loop antenna that has multiple superimposed compressed loops. Each compressed loop is formed from numerous segments arrayed in multiple diverse directions so that the enclosed area of that loop and the overall size of the antenna are decreased. Multiple loops are arrayed and superimposed to provide multiple frequency bands of operation and are used to broaden the useful bandwidth of individual-bands. The small size of the compressed antenna facilitates its use in small mobile communications devices requiring internal antennas that operate in close proximity to conductive surfaces. Multiple loops are arrayed in several configurations that include nested and non-nested loops as well as closely located and spatially separated superimposed loops.

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31

Bougie, Daniel W., Julie A. Peterson, Adam Kanack, Brian R. Curtis, and Richard H. Aster. "Antibodies Specific For Human Neutrophil Antigen 3a (HNA-3a) Recognize Complex Epitopes On Choline Transporter Protein 2 (CTL2): Implications For HNA-3a Antibody Detection." Blood 122, no. 21 (November 15, 2013): 3662. http://dx.doi.org/10.1182/blood.v122.21.3662.3662.

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Abstract Transfusion-related acute lung injury (TRALI), the leading cause of mortality associated with blood transfusion, usually results from passive transfer of antibodies present in donated blood to a patient. TRALI can be triggered by antibodies specific for Class I or Class II HLA antigens, human neutrophil antigens (HNA) and possibly other targets. For reasons not well understood, antibodies specific for the leukocyte antigen HNA-3a cause particularly severe, often fatal TRALI. It would be highly desirable therefore to be able to screen blood donors routinely for HNA-3a antibodies. HNA-3a/b antigens are carried on choline transporter-like protein 2 (CTL2), an apparent 10 membrane-spanning protein with 5 extracellular loops and N and C intracellular termini. The HNA-3a/b polymorphism is created by an R/Q substitution at position 154 in the first of these extracellular loops (Loop 1). In solid phase assays, about one-half of HNA-3a antibodies implicated in TRALI recognize Loop 1 peptides containing R154 (Type 1 antibodies). The remaining antibodies (Type 2) are non-reactive with peptides despite reacting well against full length CTL2. We studied reactions of Type 1 and Type 2 HNA-3a antibodies against soluble recombinant CTL2 fragments, human CTL2, mouse CTL2, and human/mouse CTL2 chimeras expressed in HEK293 cells to characterize the basis for HNA-3a antibody heterogeneity. The following observations were made:1) Only Type 1 antibodies react with detergent-solublized CTL2 in solid phase assays.2) A soluble recombinant fragment derived from the first extracellular (EC) loop (R154) of human CTL2 reacts only with Type 1 antibodies.3) Mouse CTL2 is 91% identical to human CTL2 and contains the R154 residue critical for HNA-3a expression. Type 1 antibodies recognize mouse CTL2, but Type 2 antibodies do not.4) Chimeric CTL2 containing human sequence in EC Loop 1 and mouse sequence in Loops 2-5 (H1M) reacts only with Type 1 antibodies. The reciprocal construct with mouse sequence in EC loop 1 and human sequence in Loops 2-5 (M1H) reacts with both Type 1 and Type 2 antibodies.5) Chimeric CTL2 containing human sequence in EC Loops 1-2 and mouse sequence in Loops 3-5 (H2M) reacts only with Type 1 antibodies.6) Chimeric CTL2 containing human sequence in EC Loops 1-3 and mouse sequence in Loops 4-5 (H3M) reacts with both Type 1 and Type 2 antibodies. These findings show that Loop 1 peptides containing R154 are sufficient for Type 1 antibodies to recognize CTL2 and the Type 1 epitope survives detergent solubilization of the protein. However, Type 2 antibodies require human sequence in EC Loops 1-3 for binding and the epitope they recognize does not survive detergent treatment. Moreover both Type 1 and Type 2 recognize the M1H chimera with the entire EC loop 1 sequence derived from mouse. The simplest explanation for these observations is that Type 2 HNA-3a antibodies need to contact human amino acid residues in EC Loop 3 in addition to Loop 1 for tight binding to CTL2. An alternative possibility is both Type 1 and 2 antibodies recognize only Loop1, but EC Loops 2 and 3 are required to hold Loop 1 in a configuration suitable for Type 2 antibody binding. In either case, it appears that at least the first 3 EC loops of CTL2 (R154) need to be in a configuration that closely mimics their natural state in the cell membrane in order to be recognized by Type 2 HNA-3a antibodies. Considerable ingenuity will be required to engineer a target capable of detecting both Type 1 and Type 2 HNA-3a antibodies in a format suitable for large-scale blood donor screening. Disclosures: No relevant conflicts of interest to declare.

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Carrasco-Salas, Yeraldinne, Amélie Malapert, Shaheen Sulthana, Bastien Molcrette, Léa Chazot-Franguiadakis, Pascal Bernard, Frédéric Chédin, Cendrine Faivre-Moskalenko, and Vincent Vanoosthuyse. "The extruded non-template strand determines the architecture of R-loops." Nucleic Acids Research 47, no. 13 (May 8, 2019): 6783–95. http://dx.doi.org/10.1093/nar/gkz341.

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Abstract Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.

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33

Karampelas, K., and T. Van Doorsselaere. "Simulations of fully deformed oscillating flux tubes." Astronomy & Astrophysics 610 (February 2018): L9. http://dx.doi.org/10.1051/0004-6361/201731646.

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Context. In recent years, a number of numerical studies have been focusing on the significance of the Kelvin–Helmholtz instability in the dynamics of oscillating coronal loops. This process enhances the transfer of energy into smaller scales, and has been connected with heating of coronal loops, when dissipation mechanisms, such as resistivity, are considered. However, the turbulent layer is expected near the outer regions of the loops. Therefore, the effects of wave heating are expected to be confined to the loop’s external layers, leaving their denser inner parts without a heating mechanism. Aim. In the current work we aim to study the spatial evolution of wave heating effects from a footpoint driven standing kink wave in a coronal loop. Methods. Using the MPI-AMRVAC code, we performed ideal, three dimensional magnetohydrodynamic simulations of footpoint driven transverse oscillations of a cold, straight coronal flux tube, embedded in a hotter environment. We have also constructed forward models for our simulation using the FoMo code. Results. The developed transverse wave induced Kelvin–Helmholtz (TWIKH) rolls expand throughout the tube cross-section, and cover it entirely. This turbulence significantly alters the initial density profile, leading to a fully deformed cross section. As a consequence, the resistive and viscous heating rate both increase over the entire loop cross section. The resistive heating rate takes its maximum values near the footpoints, while the viscous heating rate at the apex. Conclusions. We conclude that even a monoperiodic driver can spread wave heating over the whole loop cross section, potentially providing a heating source in the inner loop region. Despite the loop’s fully deformed structure, forward modelling still shows the structure appearing as a loop.

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Arakawa, K., and Hirotaro Mori. "Process of the One-Dimensional Motion of Small Interstitial-Type Dislocation Loops in Iron." Materials Science Forum 512 (April 2006): 103–6. http://dx.doi.org/10.4028/www.scientific.net/msf.512.103.

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Extensive simulations based on classical molecular dynamics have shown that small interstitial-type perfect dislocation loops in various metals and alloys have the structure of bundles of crowdions and a loop can easily makes the one-dimensional glide motion due to almost independent motion of crowdions in the loop. However, the experimental knowledge on the motion of loops is not enough. The present study dynamically examined the motion process of loops in pure iron under 1000 keV electron irradiation and thermal annealing by using transmission electron microscopy under which loops could move. Two types of loops were formed by irradiation. Loops of one type possessed the Burgers vector of 1/2<111> and the habit plane of {011}, and loops of the other type were <001> {001}. Loops of the former type made back-andforth glide motion and expansion towards the direction along their Burgers vectors when they were smaller than about a few-ten nanometers in diameter. This strongly suggests that these small 1/2<111> loops have the structure of the bundle of crowdions. Loops of the latter type only rarely moved less frequently when they were smaller than about the same size. When loops of two types grew larger than about 50 nm, the characteristics of the motion of loops changed drastically. Dislocation segments of each large loop made long-distance glide independently of their opposite segments, and the habit plane deviated from the original ones. This kind of motion means that selfinterstitial atoms at the central region of such large loops are no longer the crowdions.

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CHEE, WING LOON, STEPHEN M. GAGOLA, and ANDREW RAJAH. "CLASSIFICATION OF MINIMAL NONASSOCIATIVE MOUFANG LOOPS OF ORDER pq3." International Journal of Algebra and Computation 23, no. 08 (December 2013): 1895–908. http://dx.doi.org/10.1142/s0218196713500483.

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An open problem in the theory of Moufang loops is to classify those loops which are minimally nonassociative, that is, loops which are nonassociative but where all proper subloops are associative. A related question is to classify all integers n for which a minimally nonassociative loop exists. In [Possible orders of nonassociative Moufang loops, Comment. Math. Univ. Carolin.41(2) (2000) 237–244], O. Chein and the third author showed that a minimal nonassociative Moufang loop of order 2q3can be constructed by using a non-abelian group of order q3. In [Moufang loops of odd order pq3, J. Algebra235 (2001) 66–93], the third author also proved that for odd primes p < q, a nonassociative Moufang loop of order pq3exists if and only if q ≡ 1 ( mod p). Here we complete the classification of minimally nonassociative Moufang loops of order pq3for primes p < q.

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LONG, LING, and JONATHAN D. H. SMITH. "Catalan loops." Mathematical Proceedings of the Cambridge Philosophical Society 149, no. 3 (July 19, 2010): 445–53. http://dx.doi.org/10.1017/s0305004110000393.

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AbstractMotivated by a problem from number theory about the relationship between Fermat curves and modular curves, a new class of loops is introduced, the Catalan loops. In the number-theoretic context, these loops turn out to be abelian precisely when the Fermat curves and modular curves coincide. General Catalan loops arise on certain transversals to diagonal subgroups in special linear groups over rings with a topologically nilpotent element. The transversals consist of products of certain affine shears. In a Catalan loop, the multiplication and right division are given by rational functions. The left division is algebraic, corresponding to a quadratic irrationality. The left division embodies generating functions for the Catalan numbers. Structurally, Catalan loops are shown to be residually nilpotent.

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Ferdowsifard, Kasra, Shraddha Barke, Hila Peleg, Sorin Lerner, and Nadia Polikarpova. "LooPy: interactive program synthesis with control structures." Proceedings of the ACM on Programming Languages 5, OOPSLA (October 20, 2021): 1–29. http://dx.doi.org/10.1145/3485530.

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One vision for program synthesis, and specifically for programming by example (PBE), is an interactive programmer's assistant, integrated into the development environment. To make program synthesis practical for interactive use, prior work on Small-Step Live PBE has proposed to limit the scope of synthesis to small code snippets, and enable the users to provide local specifications for those snippets. This paradigm, however, does not work well in the presence of loops. We present LooPy, a synthesizer integrated into a live programming environment, which extends Small-Step Live PBE to work inside loops and scales it up to synthesize larger code snippets, while remaining fast enough for interactive use. To allow users to effectively provide examples at various loop iterations, even when the loop body is incomplete, LooPy makes use of live execution , a technique that leverages the programmer as an oracle to step over incomplete parts of the loop. To enable synthesis of loop bodies at interactive speeds, LooPy introduces Intermediate State Graph , a new data structure, which compactly represents a large space of code snippets composed of multiple assignment statements and conditionals. We evaluate LooPy empirically using benchmarks from competitive programming and previous synthesizers, and show that it can solve a wide variety of synthesis tasks at interactive speeds. We also perform a small qualitative user study which shows that LooPy's block-level specifications are easy for programmers to provide.

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Nagy, Péter T., and Karl Strambach. "Loops as Invariant Sections in Groups, and their Geometry." Canadian Journal of Mathematics 46, no. 5 (October 1, 1994): 1027–56. http://dx.doi.org/10.4153/cjm-1994-059-8.

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AbstractWe investigate left conjugacy closed loops which can be given by invariant sections in the group generated by their left translations. These loops are generalizations of the conjugacy closed loops introduced in [13] just as Bol loops generalize Moufang loops. The relations of these loops to common classes of loops are studied. For instance on a connected manifold we construct proper topological left conjugacy closed loops satisfying the left Bol condition but show that any differentiable such loop must be a group. We show that the configurational condition in the 3-net corresponding to an isotopy class of left conjugacy closed loops has the same importance in the geometry of 3-nets as the Reidemeister or the Bol condition.

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39

Rennick, Stephanie. "Self-Fulfilling Prophecies." Philosophies 6, no. 3 (September 18, 2021): 78. http://dx.doi.org/10.3390/philosophies6030078.

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Causal loops are a recurring feature in the philosophy of time travel, where it is generally agreed that they are logically possible but may come with a theoretical cost. This paper introduces an unfamiliar set of causal loop cases involving knowledge or beliefs about the future: self-fulfilling prophecy loops (SFP loops). I show how and when such loops arise and consider their relationship to more familiar causal loops.

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40

Halperin, Tavi, Hanit Hakim, Orestis Vantzos, Gershon Hochman, Netai Benaim, Lior Sassy, Michael Kupchik, Ofir Bibi, and Ohad Fried. "Endless loops." ACM Transactions on Graphics 40, no. 4 (August 2021): 1–12. http://dx.doi.org/10.1145/3476576.3476719.

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41

Halperin, Tavi, Hanit Hakim, Orestis Vantzos, Gershon Hochman, Netai Benaim, Lior Sassy, Michael Kupchik, Ofir Bibi, and Ohad Fried. "Endless loops." ACM Transactions on Graphics 40, no. 4 (August 2021): 1–12. http://dx.doi.org/10.1145/3450626.3459935.

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42

Pickering, M. Ruth. "Guilt Loops." Canadian Journal of Psychiatry 36, no. 6 (August 1991): 447–51. http://dx.doi.org/10.1177/070674379103600612.

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43

Phillips, J. D., and V. A. Shcherbacov. "Cheban loops." Journal of Generalized Lie Theory and Applications 4 (2010): 58–62. http://dx.doi.org/10.4303/jglta/g100501.

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44

Remensnyder, Linda S. "Hearing Loops." Hearing Journal 67 (February 2014): 1. http://dx.doi.org/10.1097/01.hj.0000444154.82696.b0.

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Remensnyder, Linda S. "Hearing Loops." Hearing Journal 67, no. 3 (March 2014): 24. http://dx.doi.org/10.1097/01.hj.0000445226.52606.b6.

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Sterkens, Juliëtte P. M. "HEARING LOOPS." Hearing Journal 67, no. 3 (March 2014): 28. http://dx.doi.org/10.1097/01.hj.0000445227.60229.8a.

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47

Powell, Corey S. "Super Loops." Scientific American 271, no. 3 (September 1994): 14. http://dx.doi.org/10.1038/scientificamerican0994-14a.

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48

Schönemann, Peter H. "Untangling Loops." Contemporary Psychology: A Journal of Reviews 32, no. 7 (July 1987): 619–21. http://dx.doi.org/10.1037/027301.

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Weitzman, Jonathan B. "Autocrine loops." Genome Biology 2 (2001): spotlight—20011101–01. http://dx.doi.org/10.1186/gb-spotlight-20011101-01.

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50

Whitchurch, Celia. "Closing loops." Perspectives: Policy and Practice in Higher Education 6, no. 1 (January 2002): 1–2. http://dx.doi.org/10.1080/13603100120118931.

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