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Backtracking-assisted multiplication

Houda Ferradi, Rémi Géraud, Diana Maimuţ, David Naccache, Hang Zhou
2017 Cryptography and Communications  
The method uses backtracking to find a multiplicationfriendly encoding of the operand known in advance.  ...  This paper describes a new multiplication algorithm, particularly suited to lightweight microprocessors when one of the operands is known in advance.  ...  Performance The algorithm has an offline step (backtracking) and an online step (multiplication), which are implemented on different devices.  ... 
doi:10.1007/s12095-017-0254-5 fatcat:2n4njxfqtvgcpghhog5jqfsoni

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms

V. Schweikhard, C. Meng, K. Murakami, C. D. Kaplan, R. D. Kornberg, S. M. Block
2014 Proceedings of the National Academy of Sciences of the United States of America  
that hinder transcription and a backtrack-independent activity under assisting loads.  ...  Pauses triggered by inosine triphosphate misincorporation led to backtracking, even under assisting loads, and their lifetimes were reduced by TFIIS, particularly when aided by TFIIF.  ...  that hinder transcription and a backtrack-independent activity under assisting loads.  ... 
doi:10.1073/pnas.1405181111 pmid:24733897 pmcid:PMC4020062 fatcat:aewpabrge5fyvh7x5jiukthkky

An exploratory study of backtracking strategies used by developers

Young Seok Yoon, Brad A. Myers
2012 2012 5th International Workshop on Co-operative and Human Aspects of Software Engineering (CHASE)  
However, little is known about when and how the developers backtrack, and modern IDEs do not provide much assistance for backtracking.  ...  As a first step towards gathering baseline knowledge about backtracking and designing more robust backtracking assistance tools in modern IDEs, we conducted an exploratory study with 12 professional developers  ...  Variation Management Backtracking becomes important when trying out multiple alternative solutions. There exist several tools that help with variation management.  ... 
doi:10.1109/chase.2012.6223012 dblp:conf/icse/YoonM12 fatcat:5mnjnaovkjcwblstbbrj55zoci

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

Jing Jin, Lu Bai, Daniel S Johnson, Robert M Fulbright, Maria L Kireeva, Mikhail Kashlev, Michelle D Wang
2010 Nature Structural & Molecular Biology  
When two RNAPs elongate in close proximity, the trailing RNAP apparently assists in the leading RNAP's elongation, reducing its backtracking and enhancing its transcription through a nucleosome by a factor  ...  Taken together, our data indicate that histone-DNA interactions dictate RNAP pausing behavior, and alleviation of nucleosome-induced backtracking by multiple polymerases may prove to be a mechanism for  ...  The trailing RNAP is capable of assisting the leading RNAP, likely by exerting an assisting force on it 43 , and facilitating the leading RNAP to exit the backtracked state and resume elongation.  ... 
doi:10.1038/nsmb.1798 pmid:20453861 pmcid:PMC2938954 fatcat:elb6p7f2grgpxai75riohuyagq

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

Joshua W. Shaevitz, Elio A. Abbondanzieri, Robert Landick, Steven M. Block
2003 Nature  
Our current system is capable of near-base-pair resolution in individual records of RNAP displacements, and achieves base-pair resolution (,0.3 nm) in averages of multiple records.  ...  The tension in the DNA was kept nearly constant (8.4^0.8 pN), for loads both opposing and assisting transcription, by feedback control of the position of the optical trap holding the larger bead.  ...  Both traces contain multiple short pauses (most are too short to be seen on this timescale); one includes a very long pause (410 s, red trace). b, In some records of long pauses, backtracking could be  ... 
doi:10.1038/nature02191 pmid:14634670 pmcid:PMC1483218 fatcat:cntorhl2n5cm3g3emvd773nvhy

Multiple personalities of the RNA polymerase active centre

N. Zenkin
2014 Microbiology  
Intriguingly, we showed that the reaction in the 1 bp backtracked state can be assisted by the 39 NMP of the RNA transcript -the phenomenon we referred to as transcript-assisted hydrolysis (Zenkin et  ...  Fig. 1 . 1 Multiple active centres of multi-subunit RNAPs.  ... 
doi:10.1099/mic.0.079020-0 pmid:24763425 fatcat:2rme2dtui5f3jgcabsgfazke2e

Multiple active centers of multi-subunit RNA polymerases

Yulia Yuzenkova, Mohammad Roghanian, Nikolay Zenkin
2012 Transcription  
2,10 Besides direct participation as an acidbase, the TL may also be involved in the transcript-assisted part of the cleavage by positioning the 3' NMPs in the active center. 10 Multiple functions of the  ...  Specific mechanisms exist to increase affinity for the labile Mg 2+ when hydrolysis becomes required for the resolution of backtracked or misincorporated complexes (see below). 2,3 Thus, the active center  ...  Transcription factor Gre assists hydrolysis of the transcript in the backtracked and misincorporated complexes.  ... 
doi:10.4161/trns.19887 pmid:22771945 pmcid:PMC3616080 fatcat:y74tgofz7zc6dcahxljrnlwnsi

Making Optimal and Justifiable Asset Maintenance Decisions [chapter]

Andrei Furda, Michael E. Cholette, Lin Ma, Colin Fidge, Wayne Hill, Warwick Robinson
2014 Lecture Notes in Mechanical Engineering  
To assist the asset manager in selecting between various policies, JOB also provides the capability of Multiple Criteria Decision Making.  ...  This decision support capability is realized through an efficient, scalable backtracking-based algorithm for the optimisation of maintenance policies, while enabling the user to view a number of solutions  ...  Multiple Criteria Optimisation Multiple Criteria Decision Making (MCDM) is a widely applied discipline used to support decision makers deal with multiple and often conflicting objectives.  ... 
doi:10.1007/978-3-319-09507-3_23 fatcat:utci4epi7je5xls5txmkihbaim

Improving the evidence base for services working with youth at-risk of involvement in the criminal justice system: developing a standardised program approach

Alice Knight, Myfanwy Maple, Anthony Shakeshaft, Bernie Shakehsaft, Tania Pearce
2018 Health & Justice  
Young people who engage in multiple risk behaviour (high-risk young people) such as substance abuse, antisocial behaviour, low engagement in education and employment, self-harm or suicide ideation are  ...  Financial contributors to the BackTrack program are provided on their website (http://www.backtrack.org.au/).  ...  Acknowledgements We would like to thank the staff and participants of BackTrack, a youth program based in the rural NSW town of Armidale, for participating in this study.  ... 
doi:10.1186/s40352-018-0066-5 pmid:29658091 pmcid:PMC5899965 fatcat:lycotwguoveypiskquxqjts56a

Residence Time Analysis of RNA Polymerase Transcription Dynamics: A Bayesian Sticky HMM Approach [article]

Zeliha Kilic, Ioannis Sgouralis, Steve Pressé
2020 bioRxiv   pre-print
find: no emergent separation between long and short residence times warranted by the data; force dependent average residence time transcription elongation dynamics; limited effects of GreB on average backtracking  ...  the assisting forces with 75% confidence.  ...  First, we start with the analysis of the effect of RNaseA on the average backtracking durations under both assisting and opposing force geometries.  ... 
doi:10.1101/2020.07.28.132373 fatcat:tqm75e5kcfd5bgerezji4ekliq

Ubiquitous Transcriptional Pausing Is Independent of RNA Polymerase Backtracking

Keir C. Neuman, Elio A. Abbondanzieri, Robert Landick, Jeff Gelles, Steven M. Block
2003 Cell  
During backtracking, the 3Ј end of the nascent RNA protrudes from a pore in the enzyme thought to be the  ...  investigated the mechpause is characterized by two empirical parameters: the anism of transcription by measuring the effect of both efficiency (equivalently, the pause probability or frehindering and assisting  ...  The backtracking hypothesis predicts that the equilibrium between the active and paused (backtracked) states should be shifted by forces that either assist or oppose translocation.  ... 
doi:10.1016/s0092-8674(03)00845-6 pmid:14622598 fatcat:p4voehj6kfalhp7ja6ouznzcuy

A longitudinal study of programmers' backtracking

Young Seok Yoon, Brad A. Myers
2014 2014 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC)  
Using this method, we detected a total of 15,095 backtracking instances, which gives an average backtracking rate of 10.3/hour.  ...  Programming often involves reverting source code to an earlier state, which we call backtracking.  ...  multiple, which means that more than one type of editing commands were used to accomplish the backtracking.  ... 
doi:10.1109/vlhcc.2014.6883030 dblp:conf/vl/YoonM14 fatcat:4or7praddjctncdkolzs3bfh7a

Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics

Toyotaka Ishibashi, Manchuta Dangkulwanich, Yves Coello, Troy A. Lionberger, Lucyna Lubkowska, Alfred S. Ponticelli, Mikhail Kashlev, Carlos Bustamante
2014 Proceedings of the National Academy of Sciences of the United States of America  
We showed that TFIIF mainly prevents Pol II from pause entering, whereas TFIIS assists with pause recovery, and quantitatively described these effects on the kinetics of transcription elongation by Pol  ...  TFIIS rescues backtracked Pol II molecules by stimulating the intrinsic endonucleolytic activity of Pol II (7).  ...  Cesar Díaz Celis for experimental assistance. We also thank Dr. Chen Yang for providing us a fraction of purified TFIIF.  ... 
doi:10.1073/pnas.1401611111 pmid:24550488 pmcid:PMC3948276 fatcat:ljr3ypikkrazha3d2yvzb2yzay

Crystallization and preliminary X-ray crystallographic analyses ofThermus thermophilusbacktracked RNA polymerase

Yuko Murayama, Shun-ichi Sekine, Shigeyuki Yokoyama
2013 Acta Crystallographica. Section F : Structural Biology and Crystallization Communications  
To study the structural basis of the backtracked state and its cleavage activity, two backtracked RNAP complexes were reconstituted by assembling Thermus thermophilus RNAP with designed nucleic acid scaffolds  ...  The reconstituted backtracked complexes were active in the transcript-cleavage reaction.  ...  We thank the beamline staff of BL41XU at SPring-8 and NE3A at the Photon Factory for assistance with data collection. This work was supported in part by a Japan Society for the Promotion of Science (  ... 
doi:10.1107/s1744309113000055 pmid:23385762 pmcid:PMC3564623 fatcat:xmzl2f5xvrf2zjinec2wsoehlq

The transcription fidelity factor GreA impedes DNA break repair

Priya Sivaramakrishnan, Leonardo A. Sepúlveda, Jennifer A. Halliday, Jingjing Liu, María Angélica Bravo Núñez, Ido Golding, Susan M. Rosenberg, Christophe Herman
2017 Nature  
GreA restarts backtracked RNA polymerase (RNAP) and hence promotes transcription fidelity.  ...  Our findings suggest that increased RNAP backtracking promotes break repair by instigating RecA loading by RecBCD, without the influence of canonical Chi signals.  ...  RecJ can compensate for the nuclease function and RecF aids in RecA filament formation, resulting in a hybrid resection machine composed of RecB helicase, RecJ exonuclease and RecF assisted RecA loading  ... 
doi:10.1038/nature23907 pmid:28976965 pmcid:PMC5654330 fatcat:gafdwr7dm5g4rdm3xajmsccu7a
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