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The Khovanov homology of 3-strand pretzels, revisited [article]

Andrew Manion
2013 arXiv   pre-print
We compute the reduced Khovanov homology of 3-stranded pretzel links. The coefficients are the integers with the "even" sign assignment.  ...  In particular, we show that the only homologically thin, non-quasi-alternating 3-stranded pretzels are P(-p,p,r) with p an odd integer and r greater than or equal to p (these were shown to be homologically  ...  Order the crossings so that those in the p-strand come first, then those in the q-strand, then those in the r-strand.  ... 
arXiv:1303.3303v2 fatcat:a3ja7jw2pncqjkncqjdman6fgy

Library construction for ancient genomics: Single strand or double strand?

E. Andrew Bennett, Diyendo Massilani, Giulia Lizzo, Julien Daligault, Eva-Maria Geigl, Thierry Grange
2014 BioTechniques  
strand or double strand?  ...  incapable of double-stranded ligation.  ... 
doi:10.2144/000114176 pmid:24924389 fatcat:2w5tdvmrq5hibfg3mumxbx42p4

Strands algebras and Ozsváth-Szabó's Kauffman-states functor [article]

Andrew Manion, Marco Marengon, Michael Willis
2019 arXiv   pre-print
We also show how Ozsv\'ath-Szab\'o's gradings on B(n,k,S) arise naturally from the general framework of group-valued gradings on strands algebras.  ...  We define new differential graded algebras A(n,k,S) in the framework of Lipshitz-Ozsv\'ath-Thurston's and Zarev's strands algebras from bordered Floer homology.  ...  strand in s ′ .  ... 
arXiv:1903.05655v1 fatcat:z54z3qccibc35e5ui4lpovnxyy

Stranded Irrigation Assets

Productivity Commission, Heather Roper, Chris Sayers, Andrew Smith
2006 Social Science Research Network  
consequences of stranded assets.  ...  Will stranded assets be a 'problem'?  ... 
doi:10.2139/ssrn.925773 fatcat:a5rky5w5tbabdarg5xyuw5xduu

Extreme Scaling of Supercomputing with Stranded Power: Costs and Capabilities [article]

Fan Yang, Andrew A. Chien
2016 arXiv   pre-print
We proposes to exploit stranded power, renewable energy that has no value to the power grid, for scaling supercomputers, Zero-Carbon Cloud (ZCCloud), and showing that stranded power can be employed effectively  ...  We build on those results with a new analysis of stranded power, characterizing temporal, geographic, and interval properties.  ...  ZCCloud uses stranded power as its only power source, and thus only operates when stranded power is available and shut down when there is no stranded power.  ... 
arXiv:1607.02133v1 fatcat:psbxxdvrwvd7lnewxgqqrtz244

A 1,3-phenyl-linked hydantoin oligomer scaffold as a β-strand mimetic

Andrew G. Jamieson, David Russell, Andrew D. Hamilton
2012 Chemical Communications  
All experiments were carried out under an atmosphere of nitrogen, using anhydrous solvents, unless otherwise stated. All chemicals were purchased from Sigma-Aldrich and used as received. Analytical thin layer chromatography was carried out on Merck Kieselgel 60 F 254 plates with visualisation by ultraviolet light. Flash column chromatography was performed using Merck Kieselgel 60 (230-400 mesh). Infra-red spectra were recorded on a Perkin Elmer System 100 with a Universal ATR attachment
more » ... y as neat films. Maximum absorbances (ν max ) are quoted in wavenumbers (cm -1 ) and the abbreviations used are: w, weak; m, medium; s, strong. NMR spectra were recorded on Brucker DPX 300 ( 1 H, 300 MHz; 13 C, 75 MHz), Brucker DPX 400 ( '1H, 400 MHz; 13 C, 100 MHz) or Brucker Avance III 500 ( 1 H, 500 MHz; 13 C, 125 MHz) spectrometers as indicated. NMR chemical shifts (δ) are quoted in ppm relative to the residual non-deuterated solvent peak of chloroform ( 1 H δ 7.26, 13 C δ 77.0) and coupling constants (J) are quoted to the nearest 0.1 Hertz (Hz). Spectral data is reported as follows: chemical shift, integration, multiplicity (s, singlet; d, doublet; t, triplet; m, multiplet; or as a combination of these), coupling constant(s) and assignment. 1 H assignment is supported by COSY spectra where necessary. 13 C assignment is supported by APT and HSQC spectra correlations where necessary. Melting points were recorded on a Reichert Köfler micro heating stage melting point apparatus and are uncorrected. Highresolution mass spectra were recorded on a Kratos Concept 1H spectrometer using peak matching to stable reference.
doi:10.1039/c2cc30295k pmid:22399148 fatcat:fszuh37txbcndodgcibnkhhm2y

Data Centers as Dispatchable Loads to Harness Stranded Power [article]

Kibaek Kim, Fan Yang, Victor M. Zavala, Andrew A. Chien
2016 arXiv   pre-print
Our analysis reveals that significant spillage and stranded power will be observed in power grids as wind power levels are increased.  ...  In contrast, optimally placing data centers that are dispatchable (with flexible loads) provides system-wide flexibility, reduces stranded power, and improves efficiency.  ...  Fan Yang and Andrew A. Chien are with the Department of Computer Science at the University of Chicago. Victor M.  ... 
arXiv:1606.00350v1 fatcat:fgkg7qln2zhi3avaubjhkm65ci

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded -- double-stranded DNA junctions by 2D fluorescence spectroscopy [article]

Dylan Heussman, Justin Kittell, Peter H. von Hippel, Andrew H. Marcus
2021 bioRxiv   pre-print
DNA replication, and the related processes of genome expression, require binding, assembly, and function of protein complexes at and near single-stranded (ss) -- double-stranded (ds) DNA junctions.  ...  studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands  ...  in the direction towards the single-stranded region.  ... 
doi:10.1101/2021.10.21.465365 fatcat:wjsdex4txjaxvfw3ide2w5r7xa

Deep Reads: Strands in the History of Molecular Genetics

Andrew D. Chisholm
2014 PLoS Genetics  
I end these recommendations with a brief look at another important strand in modern genetics, chromosome structure, and dynamics.  ...  Photo courtesy of Andrew D. Chisholm. doi:10.1371/journal.pgen.1004887.g001 , complete with Perutz's ''commonplace book'' of inspiring quotations.  ... 
doi:10.1371/journal.pgen.1004887 pmid:25521096 pmcid:PMC4270799 fatcat:52ib4yfs7zespfi3szcjckm4x4

C. elegans Telomeres Contain G-Strand and C-Strand Overhangs that Are Bound by Distinct Proteins

Marcela Raices, Ramiro E. Verdun, Sarah A. Compton, Candy I. Haggblom, Jack D. Griffith, Andrew Dillin, Jan Karlseder
2008 Cell  
Single-strand extensions of the G strand of telomeres are known to be critical for chromosomeend protection and length regulation.  ...  Here, we report that in C. elegans, chromosome termini possess 3 0 G-strand overhangs as well as 5 0 C-strand overhangs.  ...  strand breaks.  ... 
doi:10.1016/j.cell.2007.12.039 pmid:18329362 fatcat:yaushreasrcchm2wj7b2vfqdtq

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Douglas W. Fadrosh, Cynthia Andrews-Pfannkoch, Shannon J. Williamson
2011 Journal of Visualized Experiments  
doi:10.3791/3146 pmid:21989424 pmcid:PMC3230181 fatcat:7er5n46jibhefc3hdtw3gu5cwm

Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

C. Andrews-Pfannkoch, D. W. Fadrosh, J. Thorpe, S. J. Williamson
2010 Applied and Environmental Microbiology  
Here, we report the use of hydroxyapatite chromatography to efficiently fractionate double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, and ssRNA genomes from known bacteriophages.  ...  The majority of viral metagenomic studies to date have focused on double-stranded DNA (dsDNA) viruses (11, 19, 27) .  ...  The second reaction synthesizes a DNA strand complementary to the linear ssDNA copy created in the first reaction.  ... 
doi:10.1128/aem.00204-10 pmid:20543058 pmcid:PMC2916501 fatcat:uhho37bbpngz3lo5w7afnnij2a

2–strand twisting and knots with identical quantum knot homologies

Andrew Lobb
2014 Geometry and Topology  
Given a knot, we ask how its Khovanov and Khovanov-Rozansky homologies change under the operation of introducing twists in a pair of strands.  ...  One such ad hoc construction is based on pure Brunnian braids (pure braids that become equivalent to a trivial braid when any strand is removed).  ...  Introduction and results In this paper we consider sl.n/ Khovanov-Rozansky homology [6] (Khovanov homology appears as n D 2) under the operation of adding twists in a pair of strands.  ... 
doi:10.2140/gt.2014.18.873 fatcat:kgfs4o4phveozhv7mgvz2oxxmi

Pervasive off-target and double-stranded DNA nicking by CRISPR-Cas12a [article]

Karthik Murugan, Arun Seetharam, Andrew J. Severin, Dipali G Sashital
2019 bioRxiv   pre-print
Interestingly, several of these deleterious mismatches were located in the region where the non-target strand is cut (position 16 -18 from the 5' end of the target on the non-target strand) (Zetsche et  ...  Cas12a has a single active site, and it cleaves the dsDNA target in a sequential order with the nicking of non-target strand (NTS) followed by target-strand (TS) (Swarts and Jinek 2019; Jeon et al. 2018  ... 
doi:10.1101/657791 fatcat:z7tsx7zylrdpha4zbvpncqwuae

Multiple classes of bactericidal antibiotics cause DNA double strand breaks in Staphylococcus aureus [article]

Rebecca S Clarke, Andrew M Edwards
2021 bioRxiv   pre-print
However, antibiotic-triggered DNA damage led to double strand breaks, the processing of which by the RexAB helicase/nuclease complex triggered the SOS response and reduced staphylococcal susceptibility  ...  We conclude that DNA double strand breaks are a common occurrence during bacterial exposure to several different antibiotic classes and that repair of this damage by the RexAB complex promotes bacterial  ... 
doi:10.1101/2021.03.05.434095 fatcat:53iktiggajfxxfvpucgzhslvkm
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