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Journal articles on the topic '"a" loop'

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Published: 9 March 2023

Last updated: 10 March 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

Grigorian, Sergey. "Smooth loops and loop bundles." Advances in Mathematics 393 (December 2021): 108078. http://dx.doi.org/10.1016/j.aim.2021.108078.

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3

de Barros, Luiz G. X., and César Polcino Milies. "Loop algebras of code loops." Communications in Algebra 23, no. 13 (January 1995): 4781–90. http://dx.doi.org/10.1080/00927879508825500.

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4

Goodaire, Edgar G., and Rebecca G. Keeping. "Jordan loops and loop rings." Publicationes Mathematicae Debrecen 72, no. 1-2 (January 1, 2008): 173–87. http://dx.doi.org/10.5486/pmd.2008.3887.

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5

Johnson, K. W., and C. R. Leedham-Green. "Loop cohomology." Czechoslovak Mathematical Journal 40, no. 2 (1990): 182–94. http://dx.doi.org/10.21136/cmj.1990.102372.

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6

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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7

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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8

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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9

Sidana, Swati, and R. K. Sharma. "The unit loop of finite loop algebras of loops of order 32." Beiträge zur Algebra und Geometrie / Contributions to Algebra and Geometry 56, no. 1 (September 11, 2013): 339–49. http://dx.doi.org/10.1007/s13366-013-0166-2.

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10

Li, W., Z. Wang, and H. Li. "A Study on Determining Loops of Planar Kinematic Chains." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 208, no. 1 (January 1994): 59–63. http://dx.doi.org/10.1243/pime_proc_1994_208_098_02.

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This paper presents for the first time a method for the automatic generation of independent and peripheral loops of planar kinematic chains. In order to implement this method, three laws are considered and some new concepts, for instance same-position link, similar loop, loop-link vector and loop-joint vector, are defined. By using structural matrices of planar kinematic chains, independent loops are generated in the order from those with small length to those with large length. Next, one peripheral loop with the maximum length is generated. Finally a loop-link matrix and a loop-joint matrix are obtained to express all independent loops and the peripheral loop in a planar kinematic chain.

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11

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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12

Lawler, Gregory F. "Loops and Loop-Erased Random Walk." Notices of the American Mathematical Society 65, no. 07 (August 1, 2018): 788–89. http://dx.doi.org/10.1090/noti1702.

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13

Chein, Orin, and Edgar G. Goodaire. "Loops whose loop rings are alternative." Communications in Algebra 14, no. 2 (January 1986): 293–310. http://dx.doi.org/10.1080/00927878608823308.

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14

Debarros, L. G. X., and C. P. Milies. "Modular Loop Algebras of R.A. Loops." Journal of Algebra 175, no. 3 (August 1995): 1027–40. http://dx.doi.org/10.1006/jabr.1995.1225.

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15

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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16

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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17

Yamamoto, H., Y. Fukui, M. Fujishita, K. Torii, N. Kudo, S. Nozawa, K. Takahashi, et al. "Molecular loops in the Galactic centre; evidence for magnetic floatation accelerating molecular gas." Proceedings of the International Astronomical Union 2, S237 (August 2006): 501. http://dx.doi.org/10.1017/s174392130700289x.

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The new molecular image obtained by NANTEN telescope in the galactic center has revealed the existence of the two loop like structures, loop 1 and loop 2, which have never been seen before toward l = 355° to 358°. The velocities of loop 1 and loop 2 are −180 to −90 km s−1 and −90 and −40 km s−1, respectively, and these two loops have strong velocity gradients. The foot points of the loops show a very broad linewidth of ~40 to 80 km s−1 whose large velocity spans are characteristic of the molecular gas near the galactic center. Therefore, we classified the loops as being located in the galactic center and adopt a distance of 8.5 kpc. Then, the projected lengths of loop 1 and loop 2 were estimated as ~500 and ~300 pc, respectively and velocity gradients corresponds to ~80 km s−1 per 250 pc along loop 1 and ~60 km s−1 per 150 pc along loop 2. The heights of these loops are also estimated as ~220 to ~300 pc from the galactic plane, significantly higher than the typical scale height in the nuclear disk.

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18

Zhang, Yinxin, Massoud Motamed, Joachim Seemann, Michael S. Brown, and Joseph L. Goldstein. "Point Mutation in Luminal Loop 7 of Scap Protein Blocks Interaction with Loop 1 and Abolishes Movement to Golgi." Journal of Biological Chemistry 288, no. 20 (April 5, 2013): 14059–67. http://dx.doi.org/10.1074/jbc.m113.469528.

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Scap is a polytopic protein of the endoplasmic reticulum (ER) that controls cholesterol homeostasis by transporting sterol regulatory element-binding proteins (SREBPs) from the ER to the Golgi complex. Scap has eight transmembrane helices (TM) joined by four small hydrophilic loops and three large loops. Two of the large loops (Loops 1 and 7) are in the ER lumen, and the other large loop (Loop 6) faces the cytosol where it binds COPII proteins that initiate transport to Golgi. Cholesterol binding to Loop 1 alters the configuration of Loop 6, precluding COPII binding and preventing the exit of Scap from the ER. Here, we create a point mutation (Y640S) in luminal Loop 7 that prevents Scap movement to Golgi. Trypsin cleavage assays show that Loop 6 of Scap(Y640S) is always in the configuration that precludes COPII binding, even in the absence of cholesterol. When expressed separately by co-transfection, the NH2-terminal portion of Scap (containing TM helices 1–6, including Loop 1) binds to the COOH-terminal portion (containing TM helices 7–8 and Loop 7) as determined by co-immunoprecipitation. This binding does not occur when Loop 7 contains the Y640S mutation. Co-immunoprecipitation is also abolished by a point mutation in Loop 1 (Y234A) that also prevents Scap movement. These data suggest that Scap Loop 1 must interact with Loop 7 to maintain Loop 6 in the configuration that permits COPII binding. These results help explain the operation of Scap as a sterol sensor.

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19

Cross, Rod. "Loop the loop experiments." Physics Education 57, no. 6 (September 20, 2022): 065018. http://dx.doi.org/10.1088/1361-6552/ac8dd9.

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Abstract A loop-the-loop experiment is described to show how sliding friction affects motion of the ball. Conservation of energy can be used to explain the basic physics, but significant energy loss is observed in practice and expands the usefulness of this apparatus as a teaching tool.

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20

Koshy, Ommen, and Sanjay Azad. "Loop within a Loop." Plastic and Reconstructive Surgery 117, no. 3 (March 2006): 1075–76. http://dx.doi.org/10.1097/01.prs.0000201316.82383.23.

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21

Cook, Anne, D. Wong, and B. McNeela. "Vascular loop the loop." Eye 12, no. 2 (March 1998): 323. http://dx.doi.org/10.1038/eye.1998.76.

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22

Karandikar, Girish Ramchandra, Azeem Sajjad Patel, VK Ravindranath, and Anil S. Malik. "Comparative Assessment of Efficacy of Four Different Designs of Retraction Loops made of Beta Titanium Archwire: A Finite Element Study." Journal of Contemporary Dentistry 4, no. 1 (2014): 6–9. http://dx.doi.org/10.5005/jp-journals-10031-1060.

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ABSTRACT Objective To compare the forces, moments and moment/ force (M/F) ratio and load deflection rate of T-loop, keyhole loop, teardrop loop and mushroom loop with the finite element method (FEM). Materials and Methods FEM was used to compare 3D models of closing loops in rectangular (0.017 × 0.025 inch) beta titanium wire. The T-loop, mushroom loop, keyhole loop and teardrop loop were 7 mm in height. The forces, the moments and the M/F ratios at each tooth node were recorded with an activation of 2 mm. Results The highest force and moments was produced by the keyhole loop and the lowest force was produced by the mushroom loop. Conclusion All the four retraction loops exerted the greatest force levels at the molar node. The maximum value for M/F ratio is seen at the central incisor followed by lateral incisor, molar and canine node. The keyhole loop demonstrated the least load deflection rate making it the most efficient design. How to cite this article Patel AS, Ravindranath VK, Karandikar GR, Malik AS. Comparative Assessment of Efficacy of Four Different Designs of Retraction Loops made of Beta Titanium Archwire: A Finite Element Study. J Contemp Dent 2014;4(1): 6-9.

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23

Liu, Xingbo, Xiao-Biao Lin, Yuzhen Bai, and Deming Zhu. "Loop Numbers for the Stability of Homoclinic Loops of Planar Vector Fields." International Journal of Bifurcation and Chaos 28, no. 08 (July 2018): 1850101. http://dx.doi.org/10.1142/s0218127418501018.

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This paper is devoted to the study of stability and bifurcations of homoclinic loops for planar vector fields. For a given homoclinic loop, a sequence of loop numbers can be defined such that the stability and bifurcations of the loop are determined by the first nonzero term of the sequence. Formulas for the first several loop numbers were established in the past. In this paper, we will introduce general formulas for the loop numbers for both the single and double homoclinic loops.

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24

Minge, Erik, and Scott Petersen. "Sensor Performance in Measuring Vehicle Length." Transportation Research Record: Journal of the Transportation Research Board 2339, no. 1 (January 2013): 47–56. http://dx.doi.org/10.3141/2339-06.

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Although most vehicle classification conducted in the United States is axle based, some applications could be supplemented or replaced by length-based data. Common length-based methods, including loop detectors and several types of nonloop sensors (both side-fire and in-road sensors), are more widespread and can be less expensive. The most frequently deployed data collection method is by loop detector, and most dual-loop installations can report vehicle length. This paper examines field and laboratory tests of loop detectors and nonloop sensors for their performance in determining vehicle length and vehicle speed. Field testing was conducted at four locations in Minnesota and South Dakota. Ten commercially available sensors were evaluated. The testing results indicated that across a variety of detection technologies, the loop detectors and nonloop sensors generally reported comparable length and speed data. The research also examined various loop configurations and found that 6- x 6-ft loops performed similarly to 6- x 8-ft loops, although 6- x 6-ft quadrupole loops performed poorly for vehicles with high beds because of the loops’ relatively small magnetic field. Loop detector performance was found not to degrade with the variety of lead-in wire lengths that were tested. Laboratory testing conducted with a loop simulator confirmed the field testing and found that loop detector data are generally repeatable.

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25

GEBSER, MARTIN, JOOHYUNG LEE, and YULIYA LIERLER. "On elementary loops of logic programs." Theory and Practice of Logic Programming 11, no. 6 (May 24, 2011): 953–88. http://dx.doi.org/10.1017/s1471068411000019.

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AbstractUsing the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR'05), 53–65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, using a graph-theoretic characterization of an elementary loop, we show that the problem of recognizing an elementary loop is tractable. On the other hand, we also show that the corresponding problem is coNP-complete for a disjunctive program. Based on the notion of an elementary loop, we present the class of Head-Elementary-loop-Free (HEF) programs, which strictly generalizes the class of Head-Cycle-Free (HCF) programs attributable to Ben-Eliyahu and Dechter (1994. Annals of Mathematics and Artificial Intelligence 12, 53–87). Like an HCF program, an HEF program can be turned into an equivalent nondisjunctive program in polynomial time by shifting head atoms into the body.

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26

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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27

Dong, Sicong, and Gary W. Blissard. "Functional Analysis of the Autographa californica Multiple Nucleopolyhedrovirus GP64 Terminal Fusion Loops and Interactions with Membranes." Journal of Virology 86, no. 18 (June 27, 2012): 9617–28. http://dx.doi.org/10.1128/jvi.00813-12.

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TheAutographa californicamultiple nucleopolyhedrovirus (AcMNPV) glycoprotein GP64 is the major envelope protein of the budded virus (BV). GP64 is a class III fusion protein that mediates BV attachment to the cell surface and low-pH-triggered membrane fusion between the BV envelope and the endosome membrane during entry. Class III fusion proteins contain terminal looped structures that are believed to interact with membranes. To examine the functions of 3 loops found at the apex of the GP64 postfusion structure, we generated 2-alanine substitutions that scanned the two so-called fusion loops (loop 1 and loop 2) plus an adjacent loop structure (loop 3) that is closely attached to loop 2 and is also found at the apex of the GP64 postfusion structure. We identified essential residues from Y75 to T86 (loop 1) and N149 to H156 (loop 2) that are required for fusion activity, but no essential residues in loop 3. Further analysis revealed that critical fusion loop residues fall within two groups that are associated with either membrane merger (hemifusion) or fusion pore expansion. We next examined the interactions of soluble GP64 proteins and BV with membranes composed of various phospholipids. BV interacted directly with small unilamellar vesicles (SUVs) comprised of phospholipids phosphatidylcholine and phosphatidic acid (PC/PA) or phosphatidylcholine and phosphatidylserine (PC/PS) under neutral and acidic pH. We also examined the interactions of soluble GP64 constructs containing substitutions of the most hydrophobic residues within each of the two fusion loops. We found that a 2-residue substitution in either single loop (loop 1 [positions 81 and 82] or loop 2 [positions 153 and 154]) was not sufficient to substantially reduce the GP64-liposome interaction, but the same substitutions in both fusion loops severely reduced the GP64-liposome association at neutral pH. These results suggest that critical hydrophobic residues in both fusion loops may be involved in the interaction of GP64 with host cellular membranes and direct GP64-membrane interactions may represent a receptor-binding step prior to a low-pH-triggered conformational change.

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28

Nishikino, Tatsuro, Hiroto Iwatsuki, Taira Mino, Seiji Kojima, and Michio Homma. "Characterization of PomA periplasmic loop and sodium ion entering in stator complex of sodium-driven flagellar motor." Journal of Biochemistry 167, no. 4 (November 18, 2019): 389–98. http://dx.doi.org/10.1093/jb/mvz102.

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Abstract The bacterial flagellar motor is a rotary nanomachine driven by ion flow. The flagellar stator complex, which is composed of two proteins, PomA and PomB, performs energy transduction in marine Vibrio. PomA is a four transmembrane (TM) protein and the cytoplasmic region between TM2 and TM3 (loop2–3) interacts with the rotor protein FliG to generate torque. The periplasmic regions between TM1 and TM2 (loop1–2) and TM3 and TM4 (loop3–4) are candidates to be at the entrance to the transmembrane ion channel of the stator. In this study, we purified the stator complex with cysteine replacements in the periplasmic loops and assessed the reactivity of the protein with biotin maleimide (BM). BM easily modified Cys residues in loop3–4 but hardly labelled Cys residues in loop1–2. We could not purify the plug deletion stator (ΔL stator) composed of PomBΔ41–120 and WT-PomA but could do the ΔL stator with PomA-D31C of loop1–2 or with PomB-D24N of TM. When the ion channel is closed, PomA and PomB interact strongly. When the ion channel opens, PomA interacts less tightly with PomB. The plug and loop1–2 region regulate this activation of the stator, which depends on the binding of sodium ion to the D24 residue of PomB.

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29

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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Gatti-Bono, Caroline, and N. C. Perkins. "Effect of Loop Shape on the Drag-Induced Lift of Fly Line." Journal of Applied Mechanics 71, no. 5 (September 1, 2004): 745–47. http://dx.doi.org/10.1115/1.1778414.

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This note explains why casting a loop with a positive angle of attack is advantageous in distance fly casting. Several loop shapes, one with a positive angle of attack, one with a negative angle of attack, and two symmetrical loops with zero angle of attack are studied. For each loop, we compute the vertical drag component, i.e., the “lift.” It is found that a loop with a positive angle of attack generates lift about four times larger than a symmetrical loop. Thus, loops with positive angles of attack stay “aerialized longer” which is consistent with observations made by (competition) distance fly casters.

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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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Wang, Xue Yu. "On Constructing 2-Connected2-Dominating Set Using Distributed Algorithm." Advanced Materials Research 850-851 (December 2013): 588–91. http://dx.doi.org/10.4028/www.scientific.net/amr.850-851.588.

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This paper proposes a distributed algorithm to construct a 2-connected 2-dominating set. The main ingredient of this algorithm is that the nodes in the loop are 2-vertex connected. It starts from any node, and forms a localized loop made by dominating nodes. The nodes in the loop are 2-vertex connected. Basing on this loop, the algorithm continue to construct other loops formed by dominating nodes until the nodes out loops are 2-dominated.

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Jaiteh, Mariama, Antoine Taly, and Jérôme Hénin. "Evolution of Pro-Loop Channels: A Fresh Look at the Former Cys-Loop Family." Biophysical Journal 108, no. 2 (January 2015): 432a. http://dx.doi.org/10.1016/j.bpj.2014.11.2361.

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Antonov, D. V. "Stochastic Loop Equations." International Journal of Modern Physics A 12, no. 11 (April 30, 1997): 2047–59. http://dx.doi.org/10.1142/s0217751x97001298.

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Stochastic quantization is applied to derivation of the equations for the Wilson loops and generating functionals of the Wilson loops in the N = ∞ limit. These equations are treated both in the coordinate and momentum representations. In the first case the connection of the suggested approach with the problem of random closed contours and supersymmetric quantum mechanics is established, and the equation for the Quenched Master Field Wilson loop is derived. The regularized version of one of the obtained equations is presented and applied to derivation of the equation for the bilocal field correlator. The momentum loop dynamics is also investigated.

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35

Huo, Yarui, and Faridah Binti Sahari. "Analysis on the Common Quality Problems and Production Methods of Jeans Belt Loop Knot." Scientific and Social Research 4, no. 11 (November 30, 2022): 28–35. http://dx.doi.org/10.26689/ssr.v4i11.4535.

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The belt loop is an important part of a standard five-pocket jeans, integrating functionality and aesthetics. Because of common problems such as skewed belt loop, unequal lengths, improper slackness, double lines at the front pocket of the belt loop cover, exposed bottom of the belt loop, asymmetry, too low or too high position of the belt loop, and no light in the back, we tracked the sewing of the belt loop in the jeans production line, analyzed the causes of the problems, and came out with targeted solutions. We analyzed the operation steps of knotting jeans belt loops and then develop daily maintenance measures for knotting machines, provide technical guidance for seamstresses/seamsters and team leaders to enhance the maintenance ability to knot machines, enhance the ability of knotting machines to run well, ensure the stability of jeans belt loops quality, and provide technical reference for quality control of belt loops in the same type of jeans production lines.

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Roncagliolo, Pedro A., Javier G. García, and Carlos H. Muravchik. "Optimized Carrier Tracking Loop Design for Real-Time High-Dynamics GNSS Receivers." International Journal of Navigation and Observation 2012 (June 3, 2012): 1–18. http://dx.doi.org/10.1155/2012/651039.

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Carrier phase estimation in real-time Global Navigation Satellite System (GNSS) receivers is usually performed by tracking loops due to their very low computational complexity. We show that a careful design of these loops allows them to operate properly in high-dynamics environments, that is, accelerations up to 40 g or more. Their phase and frequency discriminators and loop filter are derived considering the digital nature of the loop inputs. Based on these ideas, we propose a new loop structure named Unambiguous Frequency-Aided Phase-Locked Loop (UFA-PLL). In terms of tracking capacity and noise resistance UFA-PLL has the same advantages of frequently used coupled-loop schemes, but it is simpler to design and to implement. Moreover, it can keep phase lock in situations where other loops cannot. The loop design is completed selecting the correlation time and loop bandwidth that minimize the pull-out probability, without relying on typical rules of thumb. Optimal and efficient ways to smooth the phase estimates are also presented. Hence, high-quality phase measurements—usually exploited in offline and quasistatic applications—become practical for real-time and high-dynamics receivers. Experiments with fixed-point implementations of the proposed loops and actual radio signals are also shown.

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Rovelli, Carlo. "A new look at loop quantum gravity." Classical and Quantum Gravity 28, no. 11 (May 20, 2011): 114005. http://dx.doi.org/10.1088/0264-9381/28/11/114005.

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Brégier, Frédéric, Marie-Christine Counilh, and Jean Roman. "Scheduling loops with partial loop-carried dependencies." Parallel Computing 26, no. 13-14 (December 2000): 1789–806. http://dx.doi.org/10.1016/s0167-8191(00)00055-7.

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TAVARES, J. N. "CHEN INTEGRALS, GENERALIZED LOOPS AND LOOP CALCULUS." International Journal of Modern Physics A 09, no. 26 (October 20, 1994): 4511–48. http://dx.doi.org/10.1142/s0217751x94001795.

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We use Chen iterated line integrals to construct a topological algebra [Formula: see text] of separating functions on the group of loopsLℳp. [Formula: see text] has a Hopf algebra structure which allows the construction of a group structure on its spectrum. We call this topological group the group of generalized loops [Formula: see text] Then we develop a loop calculus, based on the end point and area derivative operators, providing a rigorous mathematical treatment of the early heuristic ideas of Gambini, Trias and also Mandelstam, Makeenko and Migdal. Finally, we define a natural action of the “pointed” diffeomorphism group Diff p(ℳ) on [Formula: see text], and consider a variational derivative which allows the construction of homotopy invariants. This formalism is useful for constructing a mathematical theory of loop representation of gauge theories and quantum gravity.

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Goodaire, Edgar G., and César Polcino Milies. "Alternative Loop Rings with Solvable Unit Loops." Journal of Algebra 240, no. 1 (June 2001): 25–39. http://dx.doi.org/10.1006/jabr.2000.8662.

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Stolz, Robert, Shaheen Sulthana, Stella R. Hartono, Maika Malig, Craig J. Benham, and Frederic Chedin. "Interplay between DNA sequence and negative superhelicity drives R-loop structures." Proceedings of the National Academy of Sciences 116, no. 13 (March 8, 2019): 6260–69. http://dx.doi.org/10.1073/pnas.1819476116.

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R-loops are abundant three-stranded nucleic-acid structures that formin cisduring transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms—junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription.

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Tran, Huyen-Thi, Myoung-Ki Hong, Ho-Phuong-Thuy Ngo, Kim-Hung Huynh, Yeh-Jin Ahn, Zhong Wang, and Lin-Woo Kang. "Structure ofD-alanine-D-alanine ligase fromYersinia pestis: nucleotide phosphate recognition by the serine loop." Acta Crystallographica Section D Structural Biology 72, no. 1 (January 1, 2016): 12–21. http://dx.doi.org/10.1107/s2059798315021671.

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D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL fromYersinia pestis(YpDDL) were determined at 1.7–2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5′-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.

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Lin, Ruoyao, Xiaoming Zhong, Yongli Zhou, Huichao Geng, Qingxi Hu, Zhihao Huang, Jun Hu, Xiang-Dong Fu, Liang Chen, and Jia-Yu Chen. "R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation." Nucleic Acids Research 50, no. D1 (November 18, 2021): D303—D315. http://dx.doi.org/10.1093/nar/gkab1103.

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Abstract R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.

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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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45

Swinbanks, David. "Carp to loop the loop?" Nature 315, no. 6020 (June 1985): 531. http://dx.doi.org/10.1038/315531b0.

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Nian, J., and H. J. Pirner. "Wilson loop–loop correlators in." Nuclear Physics A 833, no. 1-4 (February 2010): 119–37. http://dx.doi.org/10.1016/j.nuclphysa.2009.12.003.

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Roberts, Roland G. "Watching Genes Loop the Loop." PLoS Biology 11, no. 6 (June 18, 2013): e1001592. http://dx.doi.org/10.1371/journal.pbio.1001592.

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Hansen, R. C., and J. R. Moser. "Loop-shield-loop shielding effectiveness." IEEE Transactions on Electromagnetic Compatibility 41, no. 2 (May 1999): 144–46. http://dx.doi.org/10.1109/15.765104.

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Li, Hanshuang, Chunshen Long, Yan Hong, Lemuge Chao, Yong Peng, and Yongchun Zuo. "The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming." International Journal of Molecular Sciences 23, no. 3 (January 29, 2022): 1567. http://dx.doi.org/10.3390/ijms23031567.

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R-loop, a three-stranded RNA/DNA structure, plays important roles in modulating genome stability and gene expression, but the molecular mechanism of R-loops in cell reprogramming remains elusive. Here, we comprehensively profiled the genome-wide landscape of R-loops during cell reprogramming. The results showed that the R-loop formation on most different types of repetitive elements is stage-specific in cell reprogramming. We unveiled that the cumulative deposition of an R-loop subset is positively correlated with gene expression during reprogramming. More importantly, the dynamic turnover of this R-loop subset is accompanied by the activation of the pluripotent transcriptional regulatory network (TRN). Moreover, the large accumulation of the active histone marker H3K4me3 and the reduction in H3K27me3 were also observed in these R-loop regions. Finally, we characterized the dynamic network of R-loops that facilitates cell fate transitions in reprogramming. Together, our study provides a new clue for deciphering the interplay mechanism between R-loops and HMs to control cell reprogramming.

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Adewumi, Tosin P. "Inner loop program construct: A faster way for program execution." Open Computer Science 8, no. 1 (July 1, 2018): 115–22. http://dx.doi.org/10.1515/comp-2018-0004.

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Abstract Loops are repetitive control structures in programming languages. They are used extensively in many algorithms. The for-loop and while-loop exist, where the former is repeated a number of times while the latter is repeated until a condition is met. Some have asked if re-arranging loops in certain ways can change a program’s speed to produce machine-independent optimisation. Therefore, this research sought to find out if there is any speed difference in a single loop of computations and a loop with an inner loop of same computations. Greater focus is on inner for-loop. The research used a comparative study method in order to evaluate the primary data obtained from running several tests in four popular programming languages: C, C#, Python and R. The Python implementations were further tested on Ubuntu 16 for comparison with results from Windows 10. Results established that, across all languages, there were more computations performed per unit time with an inner for-loop than no inner loop, meaning, given the same number of computations to perform, a loop with an inner for-loop will finish faster. The inner while-loop didn’t perform so well, though. This study will help developers in making better choices with programming language and style.

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