text:
epigenetically defined compartment structure.},
  language = {en},
  number = {29},
  journal = {PNAS},
  doi = {10.1073/pnas.1717730115},
  author = {Nuebler, Johannes and Fudenberg, Geoffrey and Imakaev, Maxim and Abdennur, Nezar and Mirny, Leonid A.},
  month = jul,
  year = {2018},
  keywords = {chromatin,Hi-C,genome architecture,polymer physics,active matter},
  pages = {E6697-E6706},
  file = {/home/bbeltr1/Documents/zotero/storage/RMPZWDTE/Nuebler et al. - 2018 - Chromatin organization by an interplay of loop ext.pdf;/home/bbeltr1/Documents/zotero/storage/PKLFYUHZ/E6697.html},
  pmid = {29967174}
}

@article{benedetti2017,
  title = {Transcription-Induced Supercoiling Explains Formation of Self-Interacting Chromatin Domains in {{S}}. Pombe},
  volume = {45},
  issn = {0305-1048},
  abstract = {Abstract.  The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukary},
  language = {en},
  number = {17},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gkx716},
  author = {Benedetti, Fabrizio and Racko, Dusan and Dorier, Julien and Burnier, Yannis and Stasiak, Andrzej},
  month = sep,
  year = {2017},
  pages = {9850-9859},
  file = {/home/bbeltr1/Documents/zotero/storage/RPLIWWT8/Benedetti et al. - 2017 - Transcription-induced supercoiling explains format.pdf;/home/bbeltr1/Documents/zotero/storage/C5Q3723K/4080665.html}
}

@article{sanborn2015,
  title = {Chromatin Extrusion Explains Key Features of Loop and Domain Formation in Wild-Type and Engineered Genomes},
  volume = {112},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic ``tension globule.'' In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.},
  language = {en},
  number = {47},
  journal = {PNAS},
  doi = {10.1073/pnas.1518552112},
  author = {Sanborn, Adrian L. and Rao, Suhas S. P. and Huang, Su-Chen and Durand, Neva C. and Huntley, Miriam H. and Jewett, Andrew I. and Bochkov, Ivan D. and Chinnappan, Dharmaraj and Cutkosky, Ashok and Li, Jian and Geeting, Kristopher P. and Gnirke, Andreas and Melnikov, Alexandre and McKenna, Doug and Stamenova, Elena K. and Lander, Eric S. and Aiden, Erez Lieberman},
  month = nov,
  year = {2015},
  keywords = {CTCF,genome architecture,molecular dynamics,chromatin loops,CRISPR},
  pages = {E6456-E6465},
  file = {/home/bbeltr1/Documents/zotero/storage/F2PHEN3U/Sanborn et al. - 2015 - Chromatin extrusion explains key features of loop .pdf;/home/bbeltr1/Documents/zotero/storage/RY4XMGFA/E6456.html},
  pmid = {26499245}
}

@article{macphersonInPress,
  title = {Bottom-up Modeling of Chromatin Segregation Due to Epigenetic Modifications},
  abstract = {We use a chromosome-scale simulation to show that the preferential
binding of HP1 to regions high in histone methylation (specifically
H3K9me3) results in phase segregation and reproduces features of
the observed Hi-C contact map. Specifically, we perform Monte-Carlo
simulations with one computational bead per nucleosome and an
H3K9me3 pattern based on published ChIP-seq signals. We implement
a binding model in which HP1 preferentially binds to trimethylated
histone tails and then oligomerizes to bridge together nucleosomes.
We observe a phase reminiscent of heterochromatin\textemdash{}dense
and high in H3K9me3\textemdash{}and another reminiscent of euchromatin\textemdash{}
less dense and lacking H3K9me3. This segregation results in a plaid
contact probability map that matches the general shape and position
of published Hi-C data. Analysis suggests that a roughly 20 kilobase
segment of H3K9me3 enrichment is required to drive segregation
into the heterochromatic phase.},
  journal = {PNAS},
  author = {MacPherson, Quinn and Beltran, Bruno and Spakowitz, Andrew J.},
  year = {In Press},
  file = {/home/bbeltr1/Documents/zotero/storage/MVKF3HND/_.pdf}
}

@article{bascom2017a,
  title = {Kilobase {{Pair Chromatin Fiber Contacts Promoted}} by {{Living}}-{{System}}-{{Like DNA Linker Length Distributions}} and {{Nucleosome Depletion}}},
  volume = {121},
  issn = {1520-6106, 1520-5207},
  abstract = {Nucleosome placement, or DNA linker length patterns, are believed to yield specific spatial features in chromatin fibers, but details are unknown. Here we examine by mesoscale modeling how kilobase (kb) range contacts and fiber looping depend on linker lengths ranging from 18 to 45 bp, with values modeled after living systems, including nucleosome free regions (NFRs) and gene encoding segments. We also compare artificial constructs with alternating versus randomly distributed linker lengths in the range of 18-72 bp. We show that nonuniform distributions with NFRs enhance flexibility and encourage kb-range contacts. NFRs between neighboring gene segments diminish short-range contacts between flanking nucleosomes, while enhancing kb-range contacts via hierarchical looping. We also demonstrate that variances in linker lengths enhance such contacts. In particular, moderate sized variations in fiber linker lengths ({$\sim$}27 bp) encourage long-range contacts in randomly distributed linker length fibers. Our work underscores the importance of linker length patterns, alongside bound proteins, in biological regulation. Contacts formed by kbrange chromatin folding are crucial to gene activity. Because we find that special linker length distributions in living systems promote kb contacts, our work suggests ways to manipulate these patterns for regulation of gene activity.},
  language = {en},
  number = {15},
  journal = {The Journal of Physical Chemistry B},
  doi = {10.1021/acs.jpcb.7b00998},
  author = {Bascom, Gavin D and Kim, Taejin and Schlick, Tamar},
  month = apr,
  year = {2017},
  pages = {3882-3894},
  file = {/home/bbeltr1/Documents/zotero/storage/NJ2J5QH8/Bascom et al. - 2017 - Kilobase Pair Chromatin Fiber Contacts Promoted by.pdf}
}

@article{mazur2007,
  title = {Wormlike {{Chain Theory}} and {{Bending}} of {{Short DNA}}},
  volume = {98},
  issn = {0031-9007, 1079-7114},
  language = {en},
  number = {21},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.98.218102},
  author = {Mazur, Alexey K.},
  month = may,
  year = {2007},
  file = {/home/bbeltr1/Documents/zotero/storage/CB6MLBRG/Mazur - 2007 - Wormlike Chain Theory and Bending of Short DNA.pdf}
}

@phdthesis{mergell2003,
  type = {{{PhD Thesis}}},
  title = {Thesis.Pdf},
  language = {eng},
  school = {Johannes Gutenberg-Universit\"at Mainz},
  author = {Mergell, Boris},
  month = jun,
  year = {2003},
  file = {/home/bbeltr1/Documents/zotero/storage/HDZEQNI2/thesis.pdf}
}

@article{popov2005,
  title = {Effects of Kinks on {{DNA}} Elasticity},
  volume = {71},
  issn = {1539-3755, 1550-2376},
  language = {en},
  number = {5},
  journal = {Physical Review E},
  doi = {10.1103/PhysRevE.71.051905},
  author = {Popov, Yuri O. and Tkachenko, Alexei V.},
  month = may,
  year = {2005},
  file = {/home/bbeltr1/Documents/zotero/storage/DLPXPBW4/Popov and Tkachenko - 2005 - Effects of kinks on DNA elasticity.pdf}
}

@article{koslover2013a,
  title = {Discretizing Elastic Chains for Coarse-Grained Polymer Models},
  volume = {9},
  language = {en},
  number = {29},
  journal = {Soft Matter},
  doi = {10.1039/C3SM50311A},
  author = {Koslover, Elena and Spakowitz, Andrew J.},
  year = {2013},
  pages = {7016-7027},
  file = {/home/bbeltr1/Documents/zotero/storage/3T2QQ4JN/F. Koslover and J. Spakowitz - 2013 - Discretizing elastic chains for coarse-grained pol.pdf;/home/bbeltr1/Documents/zotero/storage/TH9VWUWE/c3sm50311a.html}
}

@article{fudenberg2012,
  title = {Higher Order Chromatin Structure: Bridging Physics and Biology},
  volume = {22},
  issn = {0959-437X},
  shorttitle = {Higher Order Chromatin Structure},
  abstract = {Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interphase chromatin organization. By taking into account topological constraints acting on the chromatin fiber, recently-developed polymer models of interphase chromatin can reproduce the observed scaling of distances between genomic loci, chromosomal territories, and probabilities of contacts between loci measured by chromosome conformation capture methods. Polymer models provide a framework for the interpretation of experimental data as ensembles of conformations rather than collections of loops, and will be crucial for untangling functional implications of chromosomal organization.},
  number = {2},
  journal = {Curr Opin Genet Dev},
  doi = {10.1016/j.gde.2012.01.006},
  author = {Fudenberg, Geoffrey and Mirny, Leonid A.},
  month = apr,
  year = {2012},
  pages = {115-124},
  file = {/home/bbeltr1/Documents/zotero/storage/673HMXTF/Fudenberg and Mirny - 2012 - Higher order chromatin structure bridging physics.pdf},
  pmid = {22360992},
  pmcid = {PMC3697851}
}

@article{liu2011a,
  title = {Statistical Mechanics of Helical Wormlike Chain Model},
  volume = {134},
  issn = {0021-9606, 1089-7690},
  language = {en},
  number = {6},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.3548885},
  author = {Liu, Ya and P\'erez, Toni and Li, Wei and Gunton, J. D. and Green, Amanda},
  month = feb,
  year = {2011},
  pages = {065107},
  file = {/home/bbeltr1/Documents/zotero/storage/MY942XJC/Liu et al. - 2011 - Statistical mechanics of helical wormlike chain mo.pdf}
}

@article{wiggins2005,
  title = {Exact Theory of Kinkable Elastic Polymers},
  volume = {71},
  issn = {1539-3755},
  abstract = {The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection angles, many rod systems exhibit a high-curvature softening. The signature behavior of these rod systems is a kinking transition in which the bending is localized. Recent DNA cyclization experiments by Cloutier and Widom have offered evidence that the linear-elastic bending theory fails to describe the high-curvature mechanics of DNA. Motivated by this recent experimental work, we develop a simple and exact theory of the statistical mechanics of linear-elastic polymer chains that can undergo a kinking transition. We characterize the kinking behavior with a single parameter and show that the resulting theory reproduces both the low-curvature linear-elastic behavior which is already well described by the wormlike chain model, as well as the high-curvature softening observed in recent cyclization experiments.},
  number = {2 Pt 1},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  author = {Wiggins, Paul A. and Phillips, Rob and Nelson, Philip C.},
  month = feb,
  year = {2005},
  pages = {021909},
  file = {/home/bbeltr1/Documents/zotero/storage/RBJLJWKB/Wiggins et al. - 2005 - Exact theory of kinkable elastic polymers.pdf},
  pmid = {15783354},
  pmcid = {PMC3496790}
}

@article{le2014,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1405.0509},
  title = {Probing the Elastic Limit of {{DNA}} Bending},
  volume = {42},
  issn = {1362-4962, 0305-1048},
  abstract = {Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics. Although the thermomechanical behavior of long dsDNA is well described by the worm-like chain (WLC) model, the length limit of such elastic behavior remains controversial. To investigate the energetics of strong dsDNA bending, we measured the opening rate of small dsDNA loops with contour lengths of 40-200 bp using Fluorescence Resonance Energy Transfer (FRET). From the measured relationship of loop stability to loop size, we observed a transition between two separate bending regimes at a critical loop size below 100 bp. Above this loop size, the loop lifetime decreased with decreasing loop size in a manner consistent with an elastic bending stress. Below the critical loop size, however, the loop lifetime became less sensitive to loop size, indicative of softening of the double helix. The critical loop size was measured to be \textasciitilde{}60 bp with sodium only and \textasciitilde{}100 bp with 5 mM magnesium, which suggests that magnesium facilitates the softening transition. We show that our results are in quantitative agreement with the kinkable worm-like chain model. Furthermore, the model parameters constrained by our data can reproduce previously measured J factors between 50 and 200 bp. Our work provides powerful means to study dsDNA bending in the strong bending regime.},
  language = {en},
  number = {16},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gku735},
  author = {Le, Tung T. and Kim, Harold D.},
  month = sep,
  year = {2014},
  keywords = {Condensed Matter - Soft Condensed Matter,Physics - Biological Physics,Quantitative Biology - Biomolecules},
  pages = {10786-10794},
  file = {/home/bbeltr1/Documents/zotero/storage/5RHFE9GG/Le and Kim - 2014 - Probing the elastic limit of DNA bending.pdf}
}

@phdthesis{hasan2003,
  address = {Cambridge},
  type = {Masters},
  title = {Prediction and {{Analysis}} of {{Nucleosome Positioning}} in {{Genomic Sequences}}},
  abstract = {A nucleosome is the resultant structure formed when 1.6 left-handed turns of DNA (\textasciitilde{}146 bp)
are wound around a basic complex of histone proteins (the histone octamer). Nucleosomes
occur naturally and ubiquitously in all eukaryotic genomes; the histone proteins themselves
are highly conserved in eukaryotes. Experimental evidence suggests that specific DNA
sequences may exhibit high or low nucleosome-forming tendencies compared to random
DNA. This could mean that nucleosomes, whose positions are influenced by the underlying
DNA sequence, can in turn govern the accessibility of regulatory DNA sequences such as
transcription initiation and replication origin sites. This forms the need to search for evidence
of nucleosome positioning and consequently build models to predict and investigate such
locations.
One theory suggests that DNA sequences, which are intrinsically ``curved'', can
position nucleosomes. In a previous study, using ``cyclical'' hidden-markov models, it had
been suggested that a 10 periodic occurrence of the [VWG] motif could have such an effect
and could help nucleosomes to be positioned in human exons. This work was extended in
this thesis. 60\% of human genomic sequences were seen to be covered in apparently weak 9-
10 bp periodic patches of [CWG]. [CWG]-dense regions were seen to alternate with regions
which were rich in [W] motifs in human. However, the pattern was not the same in mouse.
Another theory suggests that highly flexible or highly rigid DNA sequences may
favour or disfavour nucleosome formation respectively. The locations of such patterns were
investigated in human sequences using the wavelet technique. This approach identified
confined periodic patterns (in the range of 80-200 bp) of rigidity in human genomic
sequences; the patterns themselves were, however, mainly consequences of alu repeatclustering.
However, the same analysis in the mouse genome indicated that such a
mechanism for positioning nucleosomes was not conserved and therefore unlikely.
A different approach to model nucleosomes was to train weighted DNA matrices
from experimentally-mapped nucleosome datasets. This technique gave some encouraging
results (one model showing 100\% accuracy at 40\% coverage), but was restricted by the
limited size of the datasets.
 Overall the conclusion is that there is some evidence for sequence specific
nucleosome positioning, but that more experimental data is needed to build and evaluate
practical and predictive computational models.},
  language = {eng},
  school = {University of Cambridge},
  author = {Hasan, Samiul},
  year = {Apris 2003},
  file = {/home/bbeltr1/Documents/zotero/storage/2Q3RDT6R/Hasan - 2003 - Prediction and Analysis of Nucleosome Positioning .pdf}
}

@article{lowary1997,
  title = {Nucleosome Packaging and Nucleosome Positioning of Genomic {{DNA}}},
  volume = {94},
  copyright = {Copyright \textcopyright{} 1997, The National Academy of Sciences of the USA},
  issn = {0027-8424, 1091-6490},
  abstract = {{$<$}p{$>$}The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95\% of bulk DNA sequences have an affinity for histone octamer in nucleosomes that is similar to that of randomly synthesized DNA; they contribute little to their own packaging at the level of individual nucleosomes. An equation was developed that relates the measured free energy to the fractional occupancy of specific nucleosome positions. Evidently, the bulk of eukaryotic genomic DNA is also not evolved or constrained for significant sequence-directed nucleosome positioning at the level of individual nucleosomes. Implications for gene regulation \emph{in vivo} are discussed.{$<$}/p{$>$}},
  language = {en},
  number = {4},
  journal = {PNAS},
  doi = {10.1073/pnas.94.4.1183},
  author = {Lowary, P. T. and Widom, J.},
  month = feb,
  year = {1997},
  keywords = {chromatin,gene regulation,transcriptional activation},
  pages = {1183-1188},
  file = {/home/bbeltr1/Documents/zotero/storage/HCA6FUQX/Lowary and Widom - 1997 - Nucleosome packaging and nucleosome positioning of.pdf;/home/bbeltr1/Documents/zotero/storage/PRX8FQA8/1183.html},
  pmid = {9037027}
}

@article{widlund1997,
  title = {Identification and Characterization of Genomic Nucleosome-Positioning {{sequences11Edited}} by {{T}}. {{Richmond}}},
  volume = {267},
  issn = {0022-2836},
  abstract = {Positioned nucleosomes are believed to play important roles in transcriptional regulation and for the organization of chromatin in cell nuclei. Here, we have isolated the DNA segments in the mouse genome that form the most stable nucleosomes yet characterized. In separate molecules we find phased runs of three to four adenine nucleotides, extensive CA repeats, and in a few cases phased TATA tetranucleotides. The latter forms the most stable nucleosome yet characterized. One sequence with CAG repeats was also found. By fluorescence in situ hydridization the selected sequences are shown to be localized at the centromeric regions of mouse metaphase chromosomes.},
  number = {4},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.1997.0916},
  author = {Widlund, Hans R and Cao, Hui and Simonsson, Stina and Magnusson, Elisabet and Simonsson, Tomas and Nielsen, Peter E and Kahn, Jason D and Crothers, Donald M and Kubista, Mikael},
  month = apr,
  year = {1997},
  keywords = {stability,chromatin,centromeres,nucleosome,positioning},
  pages = {807-817},
  file = {/home/bbeltr1/Documents/zotero/storage/YIHAZ3FA/Widlund et al. - 1997 - Identification and characterization of genomic nuc.pdf;/home/bbeltr1/Documents/zotero/storage/Z32VP88H/S0022283697909165.html}
}

@article{thastrom1999,
  title = {Sequence Motifs and Free Energies of Selected Natural and Non-Natural Nucleosome Positioning {{DNA sequences11Edited}} by {{T}}. {{Richmond}}},
  volume = {288},
  issn = {0022-2836},
  abstract = {Our laboratories recently completed SELEX experiments to isolate DNA sequences that most-strongly favor or disfavor nucleosome formation and positioning, from the entire mouse genome or from even more diverse pools of chemically synthetic random sequence DNA. Here we directly compare these selected natural and non-natural sequences. We find that the strongest natural positioning sequences have affinities for histone binding and nucleosome formation that are sixfold or more lower than those possessed by many of the selected non-natural sequences. We conclude that even the highest-affinity sequence regions of eukaryotic genomes are not evolved for the highest affinity or nucleosome positioning power. Fourier transform calculations on the selected natural sequences reveal a special significance for nucleosome positioning of a motif consisting of {$\sim$}10 bp periodic placement of TA dinucleotide steps. Contributions to histone binding and nucleosome formation from periodic TA steps are more significant than those from other periodic steps such as AA (=TT), CC (=GG) and more important than those from the other YR steps (CA (=TG) and CG), which are reported to have greater conformational flexibility in protein-DNA complexes even than TA. We report the development of improved procedures for measuring the free energies of even stronger positioning sequences that may be isolated in the future, and show that when the favorable free energy of histone-DNA interactions becomes sufficiently large, measurements based on the widely used exchange method become unreliable.},
  number = {2},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.1999.2686},
  author = {Th\aa{}str\"om, A and Lowary, P. T and Widlund, H. R and Cao, H and Kubista, M and Widom, J},
  month = apr,
  year = {1999},
  keywords = {chromatin,nucleosome,histone,positioning,affinity},
  pages = {213-229},
  file = {/home/bbeltr1/Documents/zotero/storage/VLQSEYQQ/Thåström et al. - 1999 - Sequence motifs and free energies of selected natu.pdf;/home/bbeltr1/Documents/zotero/storage/H7RPPEGL/S0022283699926864.html}
}

@article{shimada1984,
  title = {Ring-Closure Probabilities for Twisted Wormlike Chains. {{Application}} to {{DNA}}},
  volume = {17},
  issn = {0024-9297},
  number = {4},
  journal = {Macromolecules},
  doi = {10.1021/ma00134a028},
  author = {Shimada, Jiro and Yamakawa, Hiromi},
  month = apr,
  year = {1984},
  pages = {689-698},
  file = {/home/bbeltr1/Documents/zotero/storage/NEBMJTLB/Shimada and Yamakawa - 1984 - Ring-closure probabilities for twisted wormlike ch.pdf;/home/bbeltr1/Documents/zotero/storage/IWMFTKIT/ma00134a028.html}
}

@article{macpherson2018,
  title = {Bottom\textendash{}up Modeling of Chromatin Segregation Due to Epigenetic Modifications},
  copyright = {Copyright \textcopyright{} 2018 the Author(s). Published by PNAS.. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).},
  issn = {0027-8424, 1091-6490},
  abstract = {We use a chromosome-scale simulation to show that the preferential binding of heterochromatin protein 1 (HP1) to regions high in histone methylation (specifically H3K9me3) results in phase segregation and reproduces features of the observed Hi-C contact map. Specifically, we perform Monte Carlo simulations with one computational bead per nucleosome and an H3K9me3 pattern based on published ChIP-seq signals. We implement a binding model in which HP1 preferentially binds to trimethylated histone tails and then oligomerizes to bridge together nucleosomes. We observe a phase reminiscent of heterochromatin\textemdash{}dense and high in H3K9me3\textemdash{}and another reminiscent of euchromatin\textemdash{}less dense and lacking H3K9me3. This segregation results in a plaid contact probability map that matches the general shape and position of published Hi-C data. Analysis suggests that a roughly 20-kb segment of H3K9me3 enrichment is required to drive segregation into the heterochromatic phase.},
  language = {en},
  journal = {PNAS},
  doi = {10.1073/pnas.1812268115},
  author = {MacPherson, Quinn and Beltran, Bruno and Spakowitz, Andrew J.},
  month = nov,
  year = {2018},
  keywords = {Hi-C,genomic architecture,chromosomal organization,epigenetic regulation,polymer simulation},
  pages = {201812268},
  file = {/home/bbeltr1/Documents/zotero/storage/9JVG9GEH/MacPherson et al. - 2018 - Bottom–up modeling of chromatin segregation due to.pdf;/home/bbeltr1/Documents/zotero/storage/ZKCBKJYV/1812268115.html},
  pmid = {30478042}
}

@article{korolev2018,
  title = {A Systematic Analysis of Nucleosome Core Particle and Nucleosome-Nucleosome Stacking Structure},
  volume = {8},
  issn = {2045-2322},
  language = {en},
  number = {1},
  journal = {Scientific Reports},
  doi = {10.1038/s41598-018-19875-0},
  author = {Korolev, Nikolay and Lyubartsev, Alexander P. and Nordenski\"old, Lars},
  month = dec,
  year = {2018},
  file = {/home/bbeltr1/Documents/zotero/storage/J6C98IEG/Korolev et al. - 2018 - A systematic analysis of nucleosome core particle .pdf}
}

@article{kilic2018,
  title = {Single-Molecule {{FRET}} Reveals Multiscale Chromatin Dynamics Modulated by {{HP1$\alpha$}}},
  volume = {9},
  issn = {2041-1723},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-017-02619-5},
  author = {Kilic, Sinan and Felekyan, Suren and Doroshenko, Olga and Boichenko, Iuliia and Dimura, Mykola and Vardanyan, Hayk and Bryan, Louise C. and Arya, Gaurav and Seidel, Claus A. M. and Fierz, Beat},
  month = dec,
  year = {2018},
  file = {/home/bbeltr1/Documents/zotero/storage/79QNX6RV/Kilic et al. - 2018 - Single-molecule FRET reveals multiscale chromatin .pdf}
}

@article{hagerman1988,
  title = {Flexibility of {{DNA}}},
  volume = {17},
  number = {1},
  journal = {Annual Review of Biophysics and Biophysical Chemistry},
  doi = {10.1146/annurev.bb.17.060188.001405},
  author = {Hagerman, Paul J.},
  year = {1988},
  pages = {265-286},
  file = {/home/bbeltr1/Documents/zotero/storage/NMLCZD3I/Hagerman - 1988 - Flexibility of DNA.pdf},
  pmid = {3293588}
}

@article{rittman2009,
  title = {Is {{DNA}} a Worm-like Chain in {{Couette}} Flow?: "{{In}} Search of Persistence Length, a Critical Review"},
  volume = {92},
  issn = {0036-8504},
  shorttitle = {Is {{DNA}} a Worm-like Chain in {{Couette}} Flow?},
  abstract = {[Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of B-DNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.]},
  number = {2},
  journal = {Science Progress (1933-)},
  author = {RITTMAN, MARTYN and GILROY, EMMA and KOOHY, HASHEM and RODGER, ALISON and RICHARDS, ADAIR},
  year = {2009},
  pages = {163-204}
}

@article{bryant2003,
  title = {Structural Transitions and Elasticity from Torque Measurements on {{DNA}}},
  volume = {424},
  copyright = {2003 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Knowledge of the elastic properties of DNA is required to understand the structural dynamics of cellular processes such as replication and transcription. Measurements of force and extension on single molecules of DNA1,2,3 have allowed direct determination of the molecule's mechanical properties, provided rigorous tests of theories of polymer elasticity4, revealed unforeseen structural transitions induced by mechanical stresses3,5,6,7, and established an experimental and conceptual framework for mechanical assays of enzymes that act on DNA8. However, a complete description of DNA mechanics must also consider the effects of torque, a quantity that has hitherto not been directly measured in micromanipulation experiments. We have measured torque as a function of twist for stretched DNA\textemdash{}torsional strain in over- or underwound molecules was used to power the rotation of submicrometre beads serving as calibrated loads. Here we report tests of the linearity of DNA's twist elasticity, direct measurements of the torsional modulus (finding a value {$\sim$}40\% higher than generally accepted), characterization of torque-induced structural transitions, and the establishment of a framework for future assays of torque and twist generation by DNA-dependent enzymes. We also show that cooperative structural transitions in DNA can be exploited to construct constant-torque wind-up motors and force\textendash{}torque converters.},
  language = {en},
  number = {6946},
  journal = {Nature},
  doi = {10.1038/nature01810},
  author = {Bryant, Zev and Stone, Michael D. and Gore, Jeff and Smith, Steven B. and Cozzarelli, Nicholas R. and Bustamante, Carlos},
  month = jul,
  year = {2003},
  pages = {338-341},
  file = {/home/bbeltr1/Documents/zotero/storage/C3MZ88ZV/Bryant et al. - 2003 - Structural transitions and elasticity from torque .pdf;/home/bbeltr1/Documents/zotero/storage/QQ7YCI6M/nature01810.html}
}

@article{kilanowski2017,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1711.04032},
  primaryClass = {math},
  title = {Convergence of the {{Freely Rotating Chain}} to the {{Kratky}}-{{Porod Model}} of {{Semi}}-Flexible {{Polymers}}},
  abstract = {The freely rotating chain is one of the classic discrete models of a polymer in dilute solution. It consists of a broken line of N straight segments of fixed length such that the angle between adjacent segments is constant and the N-1 torsional angles are independent, identically distributed, uniform random variables. We provide a rigorous proof of a folklore result in the chemical physics literature stating that under an appropriate scaling, as N tends to infinity, the freely rotating chain converges to a random curve defined by the property that its derivative with respect to arclength is a brownian motion on the unit sphere. This is the Kratky-Porod model of semi-flexible polymers. We also investigate limits of the model when a stiffness parameter, called the persistence length, tends to zero or infinity. The main idea is to introduce orthogonal frames adapted to the polymer and to express conformational changes in the polymer in terms of stochastic equations for the rotation of these frames.},
  journal = {arXiv:1711.04032 [math]},
  author = {Kilanowski, Philip and March, Peter and Samara, Marko},
  month = nov,
  year = {2017},
  keywords = {Mathematics - Probability},
  file = {/home/bbeltr1/Documents/zotero/storage/8VT7XXVH/Kilanowski et al. - 2017 - Convergence of the Freely Rotating Chain to the Kr.pdf;/home/bbeltr1/Documents/zotero/storage/UPD2YC7S/1711.html}
}

@article{bustamante1994,
  title = {Entropic Elasticity of Lambda-Phage {{DNA}}},
  volume = {265},
  copyright = {\textcopyright{} 1994},
  issn = {0036-8075, 1095-9203},
  language = {en},
  number = {5178},
  journal = {Science},
  doi = {10.1126/science.8079175},
  author = {Bustamante, C. and Marko, J. F. and Siggia, E. D. and Smith, S.},
  month = sep,
  year = {1994},
  pages = {1599-1600},
  file = {/home/bbeltr1/Documents/zotero/storage/GMEPVJS6/Bustamante et al. - 1994 - Entropic elasticity of lambda-phage DNA.pdf;/home/bbeltr1/Documents/zotero/storage/XQRD4WYL/1599.html},
  pmid = {8079175}
}

@article{marko1995,
  title = {Stretching {{DNA}}},
  volume = {28},
  issn = {0024-9297},
  number = {26},
  journal = {Macromolecules},
  doi = {10.1021/ma00130a008},
  author = {Marko, John F. and Siggia, Eric D.},
  month = dec,
  year = {1995},
  pages = {8759-8770},
  file = {/home/bbeltr1/Documents/zotero/storage/3E7TE597/Marko and Siggia - 1995 - Stretching DNA.pdf;/home/bbeltr1/Documents/zotero/storage/365ICYVF/ma00130a008.html}
}

@article{efremov2017,
  title = {Theoretical {{Methods}} for {{Studying DNA Structural Transitions}} under {{Applied Mechanical Constraints}}},
  volume = {9},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  abstract = {Recent progress in single-molecule manipulation technologies has made it possible to exert force and torque on individual DNA biopolymers to probe their mechanical stability and interaction with various DNA-binding proteins. It was revealed in these experiments that the DNA structure and formation of nucleoprotein complexes by DNA-architectural proteins can be strongly modulated by an intricate interplay between the entropic elasticity of DNA and its global topology, which is closely related to the mechanical constraints applied to the DNA. Detailed understanding of the physical processes underlying the DNA behavior observed in single-molecule experiments requires the development of a general theoretical framework, which turned out to be a rather challenging task. Here, we review recent advances in theoretical methods that can be used to interpret single-molecule manipulation experiments on DNA.},
  language = {en},
  number = {2},
  journal = {Polymers},
  doi = {10.3390/polym9020074},
  author = {Efremov, Artem K. and Winardhi, Ricksen S. and Yan, Jie},
  month = feb,
  year = {2017},
  keywords = {DNA,equilibrium thermodynamics,force-spectroscopy,phase transition},
  pages = {74},
  file = {/home/bbeltr1/Documents/zotero/storage/HBUD38UA/Efremov et al. - 2017 - Theoretical Methods for Studying DNA Structural Tr.pdf;/home/bbeltr1/Documents/zotero/storage/JP2PHJ6V/74.html}
}

@article{efremov2016,
  title = {Transfer-Matrix Calculations of {{DNA}} Polymer Micromechanics under Tension and Torque Constraints},
  volume = {94},
  abstract = {Recent development of single-molecule manipulation technologies has made it possible to exert constant force and torque on individual DNA biopolymers to probe their elastic characteristics and structural stability. It has been previously shown that depending on the nature of applied mechanical constraints, DNA can exist in several forms including B-, L-, and P-DNA. However, there is still a lack of understanding of how structural heterogeneity of DNA, which may naturally arise due to sequence-dependent DNA properties, protein binding, or DNA damage, influences local stability of the above DNA states. To provide a more complete and detailed description of the DNA mechanics, we developed a theoretical framework based on transfer-matrix calculations and demonstrated how it can be used to predict the DNA behavior upon application of a wide range of force and torque constraints. The resulting phase diagram shows DNA structural transitions that are in good agreement with previous experimental and theoretical studies. We further discuss how the constructed formalism can be extended to include local inhomogeneities in the DNA physical properties, thus making it possible to investigate the effect of DNA sequence as well as protein binding on DNA structural stability.},
  number = {3},
  journal = {Phys. Rev. E},
  doi = {10.1103/PhysRevE.94.032404},
  author = {Efremov, Artem K. and Winardhi, Ricksen S. and Yan, Jie},
  month = sep,
  year = {2016},
  pages = {032404},
  file = {/home/bbeltr1/Documents/zotero/storage/9649EQAI/Efremov et al. - 2016 - Transfer-matrix calculations of DNA polymer microm.pdf;/home/bbeltr1/Documents/zotero/storage/YS6WLEH6/PhysRevE.94.html}
}

@article{efremov2018,
  title = {Transfer-Matrix Calculations of the Effects of Tension and Torque Constraints on {{DNA}}\textendash{}Protein Interactions},
  volume = {46},
  issn = {0305-1048, 1362-4962},
  abstract = {Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA\textendash{}protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA\textendash{}protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNAbinding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA\textendash{}protein interactions.},
  language = {en},
  number = {13},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gky478},
  author = {Efremov, Artem K and Yan, Jie},
  month = jul,
  year = {2018},
  pages = {6504-6527},
  file = {/home/bbeltr1/Documents/zotero/storage/FT68EE9P/Efremov and Yan - 2018 - Transfer-matrix calculations of the effects of ten.pdf}
}

@article{dekker2002,
  title = {Capturing {{Chromosome Conformation}}},
  volume = {295},
  issn = {0036-8075, 1095-9203},
  abstract = {We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.},
  language = {en},
  number = {5558},
  journal = {Science},
  doi = {10.1126/science.1067799},
  author = {Dekker, Job and Rippe, Karsten and Dekker, Martijn and Kleckner, Nancy},
  month = feb,
  year = {2002},
  pages = {1306-1311},
  file = {/home/bbeltr1/Documents/zotero/storage/IZXPGGAJ/Dekker et al. - 2002 - Capturing Chromosome Conformation.pdf;/home/bbeltr1/Documents/zotero/storage/4JQXYP6W/1306.html},
  pmid = {11847345}
}

@article{spadafora1976,
  title = {The {{DNA}} Repeat Lengths in Chromatins from Sea Urchin Sperm and Gastrula Cells Are Markedly Different},
  volume = {69},
  issn = {0014-5793},
  number = {1},
  journal = {FEBS Letters},
  doi = {10.1016/0014-5793(76)80704-1},
  author = {Spadafora, Corrado and Bellard, Maria and Lee Compton, J. and Chambon, Pierre},
  month = oct,
  year = {1976},
  pages = {281-285},
  file = {/home/bbeltr1/Documents/zotero/storage/246A82YR/Spadafora et al. - 1976 - The DNA repeat lengths in chromatins from sea urch.pdf;/home/bbeltr1/Documents/zotero/storage/45BYJJI9/0014579376807041.html}
}

@article{langowski2006a,
  title = {Polymer Chain Models of {{DNA}} and Chromatin},
  volume = {19},
  issn = {1292-8941, 1292-895X},
  abstract = {Many properties of the genome in the cell nucleus can be understood by modeling DNA and chromatin as a flexible polymer chain. This article introduces into current models for such a coarse-grained description and reviews some recent results from our own group. Examples given are the unrolling of DNA from the histone core and the response of the 30 nm chromatin fiber to mechanical stretching.},
  language = {en},
  number = {3},
  journal = {The European Physical Journal E},
  doi = {10.1140/epje/i2005-10067-9},
  author = {Langowski, J.},
  month = mar,
  year = {2006},
  pages = {241-249},
  file = {/home/bbeltr1/Documents/zotero/storage/ZCT7FNR5/Langowski - 2006 - Polymer chain models of DNA and chromatin.pdf}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
@inproceedings{lawson_persistent_spie_2019,
 abstract = {In this study, we present an automated approach to classify prostate cancer (PCa) whole slide images (WSIs) as high or low cancer aggressiveness using features derived from persistent homology, a tool of topological data analysis (TDA). This extends previous work on the use of these features for representing the characteristics of prostate cancer architecture in region of interest (ROI) images, and demonstrates the value of features derived from persistent homology to predict cancer aggressiveness of WSIs on an ROI basis. We compute persistence on ROI images and summarize persistence as a persistence image. Using this summary we construct a random forest classifier to predict cancer aggressiveness. We demonstrate the potential of persistent homology to capture the architectural differences between low and high grade prostate cancers in a feature representation that lends itself well to machine learning approaches.},
 author = {Lawson, Peter and Schupbach, Jordan and Fasy, Brittany Terese and Sheppard, John W.},
 booktitle = {Medical Imaging 2019: Digital Pathology},
 doi = {10.1117/12.2513137},
 file = {Full Text PDF:/Users/geekypete/Zotero/storage/QL2YKMU5/Lawson et al. - 2019 - Persistent homology for the automatic classificati.pdf:application/pdf;Snapshot:/Users/geekypete/Zotero/storage/R3ZKD6TE/12.2513137.html:text/html},
 month = {March},
 pages = {109560G},
 publisher = {International Society for Optics and Photonics},
 title = {Persistent homology for the automatic classification of prostate cancer aggressiveness in histopathology images},
 url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10956/109560G/Persistent-homology-for-the-automatic-classification-of-prostate-cancer-aggressiveness/10.1117/12.2513137.short},
 urldate = {2019-04-04},
 volume = {10956},
 year = {2019}
}

repository: pete-lawson/academic-kickstart

repo_name: pete-lawson/academic-kickstart


text:
@book{Achananuparp2008a,
 abstract = {Digital reference services normally rely on human experts to provide quality answers to the user requests via online communication tools. As the services gain more popularity, more experts are needed to keep up with a growing demand. Alternatively, automated question answering module can help shorten the question-answering cycle. When the system receives a new user submitted question, the similarity of the user's request and the existing questions in the archive can be compared. If the appropriate match is found, the system then uses the associated answer to response to such request. Since a question is relatively short and two questions might contain very few words in common, the challenge is how to effectively identify the similarity of questions. In this paper, we focus on the problem of identifying questions that convey the similar information need. That is, our goal is to find paraphrases of the original questions. To achieve this, we propose a hybrid approach that combines semantic, syntactic, and question category to judge question similarity. Semantic and syntactic information is measured by taking into account word similarity, word order, and part of speech information. Information about the types of question is derived from a Support Vector Machine classifier. The experimental results demonstrate that our combined measures are highly effective in distinguishing original questions and their paraphrases, thus improving the potency of question matching task.},
 author = {Achananuparp, Palakorn and Hu, Xiaohua and Zhou, Xiaohua and Zhang, Xiaodan},
 booktitle = {Proceedings of the 11th International Conference on Asian Digital Libraries - ICADL '08},
 doi = {10.1007/978-3-540-89533-6-21},
 isbn = {3540895329},
 issn = {03029743},
 keywords = {Answer reuse,Factoid questions,Question answering,Question categories,Question similarity,Semantic and syntactic techniques,Sentence similarity},
 title = {Utilizing Semantic, Syntactic, and Question category Information for Automated Digital Reference Services},
 volume = {5362 LNCS},
 year = {2008}
}

repository: aekpalakorn/academic-kickstart

repo_name: aekpalakorn/academic-kickstart

gha_license_id: MIT


text:
DESCRIPTION = "High-level C Binding for ZeroMQ"
HOMEPAGE = "http://czmq.zeromq.org/"
LICENSE = "LGPLv3+"
LIC_FILES_CHKSUM = "file://LICENSE;md5=9741c346eef56131163e13b9db1241b3"

DEPENDS = "zeromq util-linux systemd"

SRC_URI = "http://github.com/zeromq/czmq/releases/download/v${PV}/czmq-${PV}.tar.gz"

SRC_URI[md5sum] = "6d3a6fdd25c2bb29897c53670dce97bf"
SRC_URI[sha256sum] = "f00ff419881dc2a05d0686c8467cd89b4882677fc56f31c0e2cc81c134cbb0c0"

#S = "${WORKDIR}/czmq-${PV}"

EXTRA_OECONF += "--disable-drafts"

inherit autotools pkgconfig

FILES_${PN}-dev += "${datadir}/zproject"

RDEPENDS_${PN}-dev = "zeromq-dev"

extension: bb


text:
# SPDX-License-Identifier: MIT
require mion-onie-image.inc
require recipes-core/images/mion-image-core.inc

ONLPV="onlpv1"
IMAGE_INSTALL_append = " \
    ${ONLPV} \
    packagegroup-onl-python2 \
"

repository: NetworkGradeLinux/meta-mion

repo_name: NetworkGradeLinux/meta-mion

branch_name: refs/heads/dunfell

gha_language: C


text:
package bot

import (
	"os/exec"
	"strconv"
)

// Song contains information about song
type Song struct {
	Media    string
	Title    string
	Duration *string
	Id       string
}

// Ffmpeg returns ffmpeg executable command
func (song Song) Ffmpeg() *exec.Cmd {
	return exec.Command("ffmpeg", "-i", song.Media, "-f", "s16le", "-ar", strconv.Itoa(FRAME_RATE), "-ac",
		strconv.Itoa(CHANNELS), "pipe:1")
}

// NewSong creates and returns new song
func NewSong(media, title, id string) *Song {
	song := new(Song)
	song.Media = media
	song.Title = title
	song.Id = id
	return song
}

extension: go


text:
@article{Abbara-universlity-2020,
 abstract = {In a noiseless linear estimation problem, the goal is to reconstruct a vector  from the knowledge of its linear projections . There have been many theoretical works concentrating on the case where the matrix  is a random i.i.d. one, but a number of heuristic evidence suggests that many of these results are universal and extend well beyond this restricted case. Here we revisit this problem through the prism of development of message passing methods, and consider not only the universality of the -transition, as previously addressed, but also the one of the optimal Bayesian reconstruction. We observed that the universality extends to the Bayes-optimal minimum mean-squared (MMSE) error, and to a range of structured matrices.},
 author = {Alia Abbara and Antoine Baker and Florent Krzakala and Lenka Zdeborová},
 doi = {10.1088/1751-8121/ab59ef},
 journal = {Journal of Physics A: Mathematical and Theoretical},
 month = {mar},
 number = {16},
 pages = {164001},
 publisher = {IOP Publishing},
 title = {On the universality of noiseless linear estimation with respect to the measurement matrix},
 url = {https://doi.org/10.1088%2F1751-8121%2Fab59ef},
 volume = {53},
 year = {2020}
}

repository: krzakala/academic-kickstart

repo_name: krzakala/academic-kickstart


text:
require findutils.inc
LICENSE = "GPLv2"

PR = "${INC_PR}.0"

SRC_URI += "file://mkinstalldirs.patch"

EXTRA_OECONF += " ac_cv_path_SORT=/usr/bin/sort "

SRC_URI[archive.md5sum] = "24e76434ca74ba3c2c6ad621eb64e1ff"
SRC_URI[archive.sha256sum] = "1a9ed8db0711f8419156e786b6aecd42dd05df29e53e380d8924e696f7071ae0"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
require ${PN}.inc

PR = "r1"

SRC_URI = "http://sources.openembedded.org/opie-1.2.4-split_noncore_apps_dagger.tar.bz2 \
           http://sources.openembedded.org/opie-1.2.4-split_pics.tar.bz2 \
           http://sources.openembedded.org/opie-1.2.4-split_apps.tar.bz2"


text:
DESCRIPTION = "CHMLIB is a library for dealing with Microsoft ITSS/CHM format files."
LICENSE = "GPLv2"
HOMEPAGE = "http://66.93.236.84/~jedwin/projects/chmlib/"

SRC_URI = "${DEBIAN_MIRROR}/main/c/chmlib/chmlib_0.380.orig.tar.gz \
	   file://arm-guess.patch"

S = "${WORKDIR}/chmlib-0.380"

inherit autotools pkgconfig

SRC_URI[md5sum] = "2282c228ab3776c828e79b7b51f2ccc1"
SRC_URI[sha256sum] = "36645bb9e89ba63c303591a4c365f1819a1dd435d46f227140640f4089bfe6f0"


text:
/**
 * @fileOverview {@link Menu}クラスを記述したファイルです。
 */

/**
 * @class Menu
 * メニュークラス。
 *

 * このクラスに対応するHTMLの記述は以下のようなものになります。
 * 以下の例はid="menu"の場合です。
 *
 * 	<div id="menu" style="width:100%;">
 *		<table id="menu[0]" style="width:100%;">
 *			<thead>
 *				<tr>
 *					<th id="menu[0].name" colspan="2"></th>
 *				</tr>
 *			</thead>
 *			<tbody id="menu[0].pageList">
 *				<tr>
 *					<td style="width:150px;">
 *						<a id="menu[0].pageList[0].url">
 *							<span id="menu[0].pageList[0].name">Menu item</span>
 *						</a>
 *					</td>
 *					<td>
 *						<span id="menu[0].pageList[0].description">Description</span>
 *					</td>
 *				</tr>
 *			</tbody>
 *		</table>
 *	</div>
 *
 *
 *

 * @extends WebComponent
 */
Menu = createSubclass("Menu", {}, "WebComponent");

/**
 * メニューのレイアウト情報を取得します。
 */
Menu.prototype.getMenuLayout = function() {
	this.menuLayout = this.get().html();
}

/**
 * HTMLエレメントとの対応付けを行います。
 */
Menu.prototype.attach = function() {
	WebComponent.prototype.attach.call(this);
	this.getMenuLayout();
	this.update();
}

/**
 * メニューの表示内容を更新します。
 */
Menu.prototype.update = function() {
	var mglist = this.menuGroupList;
	var menuHtml = this.getMenuHtml(mglist);
	var menu = this.get();
	menu.html(menuHtml);
}

/**
 * メニューの内容を展開したHTML作成します。
 * @param {Array} mglist メニューグループリスト.
 * @returns {String} HTML.
 */
Menu.prototype.getMenuHtml = function(mglist) {
    logger.dir(mglist);
    var ret = "";
	var pat = new RegExp(this.id + "\\[0\\]", "g");
	var patl = new RegExp("pageList\\[0\\]", "g");
	for (var i = 0; i < mglist.length; i++) {
		var mg = this.menuLayout.replace(pat, this.id + "[" + i + "]")
		var q = $("
" + mg + "
");
		var menu = $(q.find("[id$='\\.pageList']").get()[0]).html();
		var plist = q.find("[id$='\\.pageList']");
		plist.empty();
		for (var j = 0; j < mglist[i].pageList.length; j++) {
			plist.append(menu.replace(patl, "pageList[" + j +"]"));
		}
		q.find("#" + this.id + "\\[" + i + "\\]\\.name").html(mglist[i].name);
		q.find("#" + this.id + "\\[" + i + "\\]\\.name").attr("data-menu-group-id", mglist[i].id);
		for (var j = 0; j < mglist[i].pageList.length; j++) {
            plist.find("[id$='\\.pageList\\[" + j + "\\]\\.url']").attr("href", mglist[i].pageList[j].url);
            if (mglist[i].pageList[j].menuTarget != null) {
                plist.find("[id$='\\.pageList\\[" + j + "\\]\\.url']").attr("target", mglist[i].pageList[j].menuTarget);
            }
			plist.find("[id$='\\.pageList\\[" + j + "\\]\\.name']").html(mglist[i].pageList[j].menuName);
			plist.find("[id$='\\.pageList\\[" + j + "\\]\\.description']").html(mglist[i].pageList[j].description);
		}
		ret += q.html();
	}
	return ret;
}

extension: js


text:
/*
Copyright 2020-2021 Gravitational, Inc.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/

package jira

// Jira REST API resources

type ErrorResult struct {
	ErrorMessages []string `url:"errorMessages"`
	Errors        []string `url:"errors"`
}

type GetMyPermissionsQueryOptions struct {
	ProjectKey  string   `url:"projectKey,omitempty"`
	Permissions []string `url:"permissions,comma,omitempty"`
}

type GetIssueQueryOptions struct {
	Fields     []string `url:"fields,comma,omitempty"`
	Expand     []string `url:"expand,comma,omitempty"`
	Properties []string `url:"properties,comma,omitempty"`
}

type GetIssueCommentQueryOptions struct {
	StartAt    int      `url:"startAt,omitempty"`
	MaxResults int      `url:"maxResults,omitempty"`
	OrderBy    string   `url:"orderBy,omitempty"`
	Expand     []string `url:"expand,comma,omitempty"`
}

type Permission struct {
	ID             string `json:"id"`
	Key            string `json:"key"`
	Name           string `json:"name"`
	Type           string `json:"type"`
	Description    string `json:"description"`
	HavePermission bool   `json:"havePermission"`
}

type Permissions struct {
	Permissions map[string]Permission `json:"permissions"`
}

type Project struct {
	Expand      string `json:"expand,omitempty"`
	Self        string `json:"self,omitempty"`
	ID          string `json:"id,omitempty"`
	Key         string `json:"key,omitempty"`
	Description string `json:"description,omitempty"`
	URL         string `json:"url,omitempty"`
	Email       string `json:"email,omitempty"`
	Name        string `json:"name,omitempty"`
}

type Issue struct {
	Expand      string                 `json:"expand"`
	Self        string                 `json:"self"`
	ID          string                 `json:"id"`
	Key         string                 `json:"key"`
	Fields      IssueFields            `json:"fields"`
	Changelog   PageOfChangelogs       `json:"changelog"`
	Properties  map[string]interface{} `json:"properties"`
	Transitions []IssueTransition      `json:"transitions"`
}

type IssueFields struct {
	Status      StatusDetails  `json:"status"`
	Comment     PageOfComments `json:"comment"`
	Project     Project        `json:"project"`
	Type        IssueType      `json:"issuetype"`
	Summary     string         `json:"summary,omitempty"`
	Description string         `json:"description,omitempty"`
}

type IssueTransition struct {
	ID   string        `json:"id,omitempty"`
	Name string        `json:"name,omitempty"`
	To   StatusDetails `json:"to,omitempty"`
}

type IssueType struct {
	Self        string `json:"self,omitempty"`
	ID          string `json:"id,omitempty"`
	Description string `json:"description,omitempty"`
	IconURL     string `json:"iconUrl,omitempty"`
	Name        string `json:"name,omitempty"`
}

type IssueFieldsInput struct {
	Type        *IssueType `json:"issuetype,omitempty"`
	Project     *Project   `json:"project,omitempty"`
	Summary     string     `json:"summary,omitempty"`
	Description string     `json:"description,omitempty"`
}

type IssueInput struct {
	Fields     IssueFieldsInput `json:"fields,omitempty"`
	Properties []EntityProperty `json:"properties,omitempty"`
}

type IssueTransitionInput struct {
	Transition IssueTransition `json:"transition"`
}

type CreatedIssue struct {
	ID   string `json:"id"`
	Key  string `json:"key"`
	Self string `json:"self"`
}

type EntityProperty struct {
	Key   string `json:"key"`
	Value string `json:"value"`
}

type StatusDetails struct {
	Self        string `json:"self"`
	Description string `json:"description"`
	IconURL     string `json:"iconUrl"`
	Name        string `json:"name"`
	ID          string `json:"id"`
}

type UserDetails struct {
	Self         string `json:"self"`
	AccountID    string `json:"accountId"`
	EmailAddress string `json:"emailAddress"`
	DisplayName  string `json:"displayName"`
	Active       bool   `json:"active"`
	TimeZone     string `json:"timeZone"`
	AccountType  string `json:"accountType"`
}

type Changelog struct {
	ID      string          `json:"id"`
	Author  UserDetails     `json:"author"`
	Created string          `json:"created"`
	Items   []ChangeDetails `json:"items"`
}

type ChangeDetails struct {
	Field      string `json:"field"`
	FieldType  string `json:"fieldtype"`
	FieldID    string `json:"fieldId"`
	From       string `json:"from"`
	FromString string `json:"fromString"`
	To         string `json:"to"`
	ToString   string `json:"toString"`
}

type Comment struct {
	Self    string      `json:"self"`
	ID      string      `json:"id"`
	Author  UserDetails `json:"author"`
	Body    string      `json:"body"`
	Created string      `json:"created"`
}

type CommentInput struct {
	Body       string           `json:"body,omitempty"`
	Properties []EntityProperty `json:"properties,omitempty"`
}

type PageOfChangelogs struct {
	StartAt    int         `json:"startAt"`
	MaxResults int         `json:"maxResults"`
	Total      int         `json:"total"`
	Histories  []Changelog `json:"histories"`
}

type PageOfComments struct {
	StartAt    int       `json:"startAt"`
	MaxResults int       `json:"maxResults"`
	Total      int       `json:"total"`
	Comments   []Comment `json:"comments"`
}

repository: gravitational/teleport

repo_name: gravitational/teleport

gha_language: Go


text:
@article{odaly_amphetamine_2014-1,
 abstract = {Amphetamine sensitisation (AS) is an established animal model of the hypersensitivity to psychostimulants seen in patients with schizophrenia. AS also models the dysregulation of mesolimbic dopamine signalling which has been implicated in the development of psychotic symptoms. Recent data suggest that the enhanced excitability of mesolimbic dopamine neurons in AS is driven by a hyperactivity of hippocampal (subiculum) neurons, consistent with a strong association between hippocampal dysfunction and schizophrenia. While AS can be modelled in human volunteers, its functional consequences on dopaminoceptive brain regions (i.e. striatum and hippocampus) remains unclear. Here we describe the effects of a sensitising dosage pattern of dextroamphetamine on the neural correlates of motor sequence learning in healthy volunteers, within a randomised, double-blind, parallel-groups design. Behaviourally, sensitisation was characterised by enhanced subjective responses to amphetamine but did not change  performance (i.e. learning rate) during an explicit sequence learning task. In contrast, functional magnetic resonance imaging (fMRI) measurements showed that repeated intermittent amphetamine exposure was associated with increased blood-oxygen-level dependent (BOLD) signal within the medial temporal lobe (MTL)  (subiculum/entorhinal cortex) and midbrain, in the vicinity of the substantia nigra/ventral tegmental area (SN/VTA) during sequence encoding. Importantly, MTL  hyperactivity correlated with the sensitisation of amphetamine-induced attentiveness. The MTL-midbrain hyperactivity reported here mirrors observations  in sensitised rodents and is consistent with contemporary models of schizophrenia and behavioural sensitisation. These findings of meso-hippocampal hyperactivity during AS thus link pathophysiological concepts of dopamine dysregulation to cognitive models of psychosis.},
 author = {O'Daly, Owen G. and Joyce, Daniel and Tracy, Derek K. and Stephan, Klaas E. and Murray, Robin M. and Shergill, Sukhwinder},
 copyright = {(c) The Author(s) 2014.},
 doi = {10.1177/0269881114527360},
 issn = {1461-7285 0269-8811},
 journal = {Journal of psychopharmacology (Oxford, England)},
 keywords = {Humans, Magnetic Resonance Imaging, Healthy Volunteers, Double-Blind Method, dopamine, Amphetamine, Attention/drug effects/physiology, Central Nervous System Sensitization/*drug effects/*physiology, Central Nervous System Stimulants/pharmacology, Dextroamphetamine/*pharmacology, Functional Neuroimaging, medial temporal lobe, Memory/drug effects/*physiology, Mesencephalon/drug effects/*physiology, midbrain, motor learning, sensitisation, Serial Learning/drug effects/physiology, Temporal Lobe/drug effects/*physiology},
 language = {eng},
 month = {September},
 note = {Place: United States},
 number = {9},
 pages = {857--865},
 pmid = {24671338},
 title = {Amphetamine sensitisation and memory in healthy human volunteers: a functional magnetic resonance imaging study.},
 volume = {28},
 year = {2014}
}

repository: danwjoyce/technical-blog

repo_name: danwjoyce/technical-blog


text:
@article{marconi2021disentangling,
 author = {Marconi, Sergio and Weinstein, Benjamin G and Lichstein, Jeremy W and Bohlman, Stephanie A and Singh, Aditya and White, Ethan P},
 journal = {bioRxiv},
 pages = {2021--04},
 publisher = {Cold Spring Harbor Laboratory},
 title = {Disentangling the roles of inter and intraspecific variation on leaf trait distributions across the eastern United States},
 year = {2021}
}

repository: weecology/website

repo_name: weecology/website

branch_name: refs/heads/main

gha_language: TeX