text:
@Article{burke_2013_estimating,
  keywords = {permafrost},
  author = {Eleanor J. Burke and Chris D. Jones and Charles D. Koven},
  title = {Estimating the Permafrost-Carbon Climate Response in
                  the {CMIP5} Climate Models Using a Simplified
                  Approach},
  journal = {Journal of Climate},
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  number = {14},
  pages = {4897-4909},
  year = {2013},
  doi = {10.1175/jcli-d-12-00550.1},
  url = {https://doi.org/10.1175/jcli-d-12-00550.1},
  issn = {1520-0442},
  month = {Jul},
  publisher = {American Meteorological Society},
}

@Article{burke_2017_quantifying,
  keywords = {permafrost},
  author = {Eleanor J. Burke and Altug Ekici and Ye Huang and Sarah E. Chadburn and Chris Huntingford and Philippe Ciais and Pierre Friedlingstein and Shushi Peng and Gerhard Krinner},
  title = {Quantifying Uncertainties of Permafrost
                  Carbon-Climate Feedbacks},
  journal = {Biogeosciences Discussions},
  pages = {1-42},
  year = {2017},
  doi = {10.5194/bg-2016-544},
  url = {https://doi.org/10.5194/bg-2016-544},
  issn = {1810-6285},
  month = {Jan},
  publisher = {Copernicus GmbH},
}

@Article{camill_2001_changes,
  author = {Philip Camill and Jason A. Lynch and James S. Clark and J. Brad Adams and B. Jordan},
  title = {Changes in Biomass, Aboveground Net Primary
                  Production, and Peat Accumulation Following
                  Permafrost Thaw in the Boreal Peatlands of {Manitoba},
                  {Canada}},
  keywords = {permafrost},
  journal = {Ecosystems},
  volume = {4},
  number = {5},
  pages = {461-478},
  year = {2001},
  doi = {10.1007/s10021-001-0022-3},
  url = {https://doi.org/10.1007/s10021-001-0022-3},
  issn = {1435-0629},
  month = {Aug},
  publisher = {Springer Nature},
}

@Article{crichton_2016_permafrost,
  author = {K. A. Crichton and N. Bouttes and D. M. Roche and J. Chappellaz and G. Krinner},
  title = {Permafrost Carbon As a Missing Link To Explain {CO2}
                  Changes During the Last Deglaciation},
  keywords = {permafrost},
  journal = {Nature Geoscience},
  volume = {9},
  number = {9},
  pages = {683-686},
  year = {2016},
  doi = {10.1038/ngeo2793},
  url = {https://doi.org/10.1038/ngeo2793},
  issn = {1752-0908},
  month = {Aug},
  publisher = {Springer Nature},
}

@Article{drake_2015_ancient,
  author = {Travis W. Drake and Kimberly P. Wickland and Robert G. M. Spencer and Diane M. McKnight and Robert G. Striegl},
  title = {Ancient Low-Molecular-Weight Organic Acids in
                  Permafrost Fuel Rapid Carbon Dioxide Production Upon
                  Thaw},
  keywords = {permafrost},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {112},
  number = {45},
  pages = {13946-13951},
  year = {2015},
  doi = {10.1073/pnas.1511705112},
  url = {https://doi.org/10.1073/pnas.1511705112},
  issn = {1091-6490},
  month = {Oct},
  publisher = {Proceedings of the National Academy of Sciences},
}

@Article{elberling_2013_long,
  author = {Bo Elberling and Anders Michelsen and Christina Schädel and Edward A. G. Schuur and Hanne H. Christiansen and Louise Berg and Mikkel P. Tamstorf and Charlotte Sigsgaard},
  title = {Long-Term {CO2} Production Following Permafrost Thaw},
  keywords = {permafrost},
  journal = {Nature Climate Change},
  volume = {3},
  number = {10},
  pages = {890-894},
  year = {2013},
  doi = {10.1038/nclimate1955},
  url = {https://doi.org/10.1038/nclimate1955},
  issn = {1758-6798},
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  publisher = {Springer Nature},
}

@Article{harp_2016_effect,
  author = {D. R. Harp and A. L. Atchley and S. L. Painter and E. T. Coon and C. J. Wilson and V. E. Romanovsky and J. C. Rowland},
  title = {Effect of Soil Property Uncertainties on Permafrost
                  Thaw Projections: a Calibration-Constrained
                  Analysis},
  keywords = {permafrost},
  journal = {The Cryosphere},
  volume = {10},
  number = {1},
  pages = {341-358},
  year = {2016},
  doi = {10.5194/tc-10-341-2016},
  url = {https://doi.org/10.5194/tc-10-341-2016},
  issn = {1994-0424},
  month = {Feb},
  publisher = {Copernicus GmbH},
}

@Article{hartin_2015_simple,
  author = {C. A. Hartin and P. Patel and A. Schwarber and R. P. Link and B. P. Bond-Lamberty},
  title = {A Simple Object-Oriented and Open-Source Model for
                  Scientific and Policy Analyses of the Global Climate
                  System - {Hector} V1.0},
  journal = {Geoscientific Model Development},
  volume = {8},
  number = {4},
  pages = {939-955},
  year = {2015},
  doi = {10.5194/gmd-8-939-2015},
  url = {https://doi.org/10.5194/gmd-8-939-2015},
  issn = {1991-9603},
  month = {Apr},
  publisher = {Copernicus GmbH},
}

@Article{hartin_2016_ocean,
  author = {Corinne A. Hartin and Benjamin Bond-Lamberty and Pralit Patel and Anupriya Mundra},
  title = {Ocean Acidification Over the Next Three Centuries
                  Using a Simple Global Climate Carbon-Cycle Model:
                  Projections and Sensitivities},
  journal = {Biogeosciences},
  volume = {13},
  number = {15},
  pages = {4329-4342},
  year = {2016},
  doi = {10.5194/bg-13-4329-2016},
  url = {https://doi.org/10.5194/bg-13-4329-2016},
  issn = {1726-4189},
  month = {Aug},
  publisher = {Copernicus GmbH},
}

@Article{hope_2015_economic,
  author = {Chris Hope and Kevin Schaefer},
  title = {Economic Impacts of Carbon Dioxide and Methane
                  Released From Thawing Permafrost},
  keywords = {permafrost},
  journal = {Nature Climate Change},
  volume = {6},
  number = {1},
  pages = {56-59},
  year = {2015},
  doi = {10.1038/nclimate2807},
  url = {https://doi.org/10.1038/nclimate2807},
  issn = {1758-6798},
  month = {Sep},
  publisher = {Springer Nature},
}

@Article{hugelius_2014_estimated,
  author = {G. Hugelius and J. Strauss and S. Zubrzycki and J. W. Harden and E. A. G. Schuur and C.-L. Ping and L. Schirrmeister and G. Grosse and G. J. Michaelson and C. D. Koven and {et al.}},
  title = {Estimated stocks of circumpolar permafrost carbon with
                  quantified uncertainty ranges and identified data gaps},
  year = {2014},
  volume = {11},
  number = {23},
  month = {Dec},
  pages = {6573–6593},
  issn = {1726-4189},
  doi = {10.5194/bg-11-6573-2014},
  url = {http://dx.doi.org/10.5194/bg-11-6573-2014},
  journal = {Biogeosciences},
  publisher = {Copernicus GmbH},
  keywords = {permafrost, soil carbon},
}

@Article{ipcc_ar5_wg1,
  title = {Climate Change 2013 - The Physical Science Basis},
  author = {{IPCC}},
  year = {2013},
  doi = {10.1017/cbo9781107415324},
  url = {http://dx.doi.org/10.1017/CBO9781107415324},
  isbn = {9781107415324},
  publisher = {Cambridge University Press},
  journal = {UN Intergovernmental Panel on Climate Change: Fifth Assessment Report},
}

@Article{ito_2016_impacts,
  author = {Akihiko Ito and Kazuya Nishina and Hibiki M. Noda},
  title = {Impacts of Future Climate Change on the Carbon
                  Budget of Northern High-Latitude Terrestrial
                  Ecosystems: an Analysis Using {ISI-MIP} Data},
  journal = {Polar Science},
  volume = {10},
  number = {3},
  pages = {346-355},
  year = {2016},
  doi = {10.1016/j.polar.2015.11.002},
  url = {https://doi.org/10.1016/j.polar.2015.11.002},
  issn = {1873-9652},
  month = {Sep},
  publisher = {Elsevier BV},
}

@Article{jones_2005_global,
  author = {Chris Jones and Claire McConnell and Kevin Coleman and Peter Cox and Peter Falloon and David Jenkinson and David Powlson},
  title = {Global Climate Change and Soil Carbon Stocks;
                  Predictions From Two Contrasting Models for the
                  Turnover of Organic Carbon in Soil},
  journal = {Global Change Biology},
  volume = {11},
  number = {1},
  pages = {154-166},
  year = {2005},
  doi = {10.1111/j.1365-2486.2004.00885.x},
  url = {https://doi.org/10.1111/j.1365-2486.2004.00885.x},
  issn = {1365-2486},
  month = {Jan},
  publisher = {Wiley},
}

@Article{kessler_2017_estimating,
  author = {Louise Kessler},
  title = {Estimating the Economic Impact of the Permafrost
                  Carbon Feedback},
  journal = {Climate Change Economics},
  volume = {08},
  number = {02},
  pages = {1750008},
  year = {2017},
  doi = {10.1142/s2010007817500087},
  url = {https://doi.org/10.1142/s2010007817500087},
  issn = {2010-0086},
  month = {May},
  publisher = {World Scientific Pub Co Pte Lt},
  keywords = {permafrost, integrated assessment, economic impact, DICE},
}

@Article{kuhry_2010_potential,
  author = {P. Kuhry and E. Dorrepaal and G. Hugelius and E. A. G. Schuur and C. Tarnocai},
  title = {Potential Remobilization of Belowground Permafrost
                  Carbon Under Future Global Warming},
  keywords = {permafrost},
  journal = {Permafrost and Periglacial Processes},
  volume = {21},
  number = {2},
  pages = {208-214},
  year = {2010},
  doi = {10.1002/ppp.684},
  url = {https://doi.org/10.1002/ppp.684},
  issn = {1099-1530},
  month = {Jun},
  publisher = {Wiley},
}

@Article{lawrence_2005_projection,
  author = {David M. Lawrence and Andrew G. Slater},
  title = {A projection of severe near-surface permafrost degradation
                  during the 21st century},
  year = {2005},
  volume = {32},
  number = {24},
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  url = {http://dx.doi.org/10.1029/2005GL025080},
  journal = {Geophysical Research Letters},
  publisher = {American Geophysical Union (AGU)},
}

@Article{lebauer_2013_facilitating,
  author = {David S. LeBauer and Dan Wang and Katherine T. Richter and Carl C. Davidson and Michael C. Dietze},
  title = {Facilitating Feedbacks Between Field Measurements
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  journal = {Ecological Monographs},
  volume = {83},
  number = {2},
  pages = {133-154},
  year = {2013},
  doi = {10.1890/12-0137.1},
  url = {https://doi.org/10.1890/12-0137.1},
  issn = {0012-9615},
  month = {May},
  publisher = {Wiley},
}

@Article{lee_2011_rate,
  author = {Hanna Lee and Edward A. G. Schuur and Kanika S. Inglett and Martin Lavoie and Jeffrey P. Chanton},
  title = {The Rate of Permafrost Carbon Release Under Aerobic
                  and Anaerobic Conditions and Its Potential Effects
                  on Climate},
  keywords = {permafrost},
  journal = {Global Change Biology},
  volume = {18},
  number = {2},
  pages = {515-527},
  year = {2011},
  doi = {10.1111/j.1365-2486.2011.02519.x},
  url = {https://doi.org/10.1111/j.1365-2486.2011.02519.x},
  issn = {1354-1013},
  month = {Sep},
  publisher = {Wiley},
}

@Article{macdougall_2012_significant,
  author = {Andrew H. MacDougall and Christopher A. Avis and Andrew J. Weaver},
  title = {Significant Contribution To Climate Warming From the
                  Permafrost Carbon Feedback},
  keywords = {permafrost},
  journal = {Nature Geoscience},
  volume = {5},
  number = {10},
  pages = {719-721},
  year = {2012},
  doi = {10.1038/ngeo1573},
  url = {https://doi.org/10.1038/ngeo1573},
  issn = {1752-0908},
  month = {Sep},
  publisher = {Springer Nature},
}

@Article{macdougall_2013_if,
  author = {Andrew H. MacDougall and Michael Eby and Andrew J. Weaver},
  title = {If Anthropogenic {CO2} emissions Cease, Will
                  Atmospheric {CO2} concentration Continue To Increase?},
  journal = {Journal of Climate},
  volume = {26},
  number = {23},
  pages = {9563-9576},
  year = {2013},
  doi = {10.1175/jcli-d-12-00751.1},
  url = {https://doi.org/10.1175/jcli-d-12-00751.1},
  issn = {1520-0442},
  month = {Dec},
  publisher = {American Meteorological Society},
}

@Article{meinshausen_2011_emulating,
  author = {M. Meinshausen and S. C. B. Raper and T. M. L. Wigley},
  title = {Emulating Coupled Atmosphere-Ocean and Carbon Cycle
                  Models With a Simpler Model, Magicc6 - Part 1: Model
                  Description and Calibration},
  journal = {Atmospheric Chemistry and Physics},
  volume = {11},
  number = {4},
  pages = {1417-1456},
  year = {2011},
  doi = {10.5194/acp-11-1417-2011},
  url = {https://doi.org/10.5194/acp-11-1417-2011},
  issn = {1680-7324},
  month = {Feb},
  publisher = {Copernicus GmbH},
}

@Article{qian_2010_enhanced,
  author = {Haifeng Qian and Renu Joseph and Ning Zeng},
  title = {Enhanced Terrestrial Carbon Uptake in the {Northern}
                  {High} {Latitudes} in the 21st Century From the {Coupled}
                  {Carbon} {Cycle} {Climate} {Model} {Intercomparison} {Project}
                  Model Projections},
  journal = {Global Change Biology},
  volume = {16},
  number = {2},
  pages = {641-656},
  year = {2010},
  doi = {10.1111/j.1365-2486.2009.01989.x},
  url = {https://doi.org/10.1111/j.1365-2486.2009.01989.x},
  issn = {1365-2486},
  month = {Feb},
  publisher = {Wiley},
}

@Article{schaefer_2011_amount,
  author = {Kevin Schaefer and Tingjun Zhang and Lori Bruhwiler and Andrew P. Barrett},
  title = {Amount and Timing of Permafrost Carbon Release in
                  Response To Climate Warming},
  keywords = {permafrost},
  journal = {Tellus B},
  volume = {63},
  number = {2},
  pages = {165-180},
  year = {2011},
  doi = {10.1111/j.1600-0889.2011.00527.x},
  url = {https://doi.org/10.1111/j.1600-0889.2011.00527.x},
  issn = {0280-6509},
  month = {Feb},
  publisher = {Informa UK Limited},
}

@Article{schaefer_2014_impact,
  author = {Kevin Schaefer and Hugues Lantuit and Vladimir E Romanovsky and Edward A G Schuur and Ronald Witt},
  title = {The Impact of the Permafrost Carbon Feedback on
                  Global Climate},
  keywords = {permafrost},
  journal = {Environmental Research Letters},
  volume = {9},
  number = {8},
  pages = {085003},
  year = {2014},
  doi = {10.1088/1748-9326/9/8/085003},
  url = {https://doi.org/10.1088/1748-9326/9/8/085003},
  issn = {1748-9326},
  month = {Aug},
  publisher = {IOP Publishing},
}

@Article{schneider_2012_estimating,
  author = {T. {Schneider von Deimling} and M. Meinshausen and A. Levermann and V. Huber and K. Frieler and D. M. Lawrence and V. Brovkin},
  title = {Estimating the Near-Surface Permafrost-Carbon
                  Feedback on Global Warming},
  keywords = {permafrost},
  journal = {Biogeosciences},
  volume = {9},
  number = {2},
  pages = {649-665},
  year = {2012},
  doi = {10.5194/bg-9-649-2012},
  url = {https://doi.org/10.5194/bg-9-649-2012},
  issn = {1726-4189},
  month = {Feb},
  publisher = {Copernicus GmbH},
}

@Article{schneider_2015_observation,
  author = {T. {Schneider von Deimling} and G. Grosse and J. Strauss and L. Schirrmeister and A. Morgenstern and S. Schaphoff and M. Meinshausen and J. Boike},
  title = {Observation-Based Modelling of Permafrost Carbon
                  Fluxes With Accounting for Deep Carbon Deposits and
                  Thermokarst Activity},
  keywords = {permafrost},
  journal = {Biogeosciences},
  volume = {12},
  number = {11},
  pages = {3469-3488},
  year = {2015},
  doi = {10.5194/bg-12-3469-2015},
  url = {https://doi.org/10.5194/bg-12-3469-2015},
  issn = {1726-4189},
  month = {Jun},
  publisher = {Copernicus GmbH},
}

@Article{schuur_2009_effect,
  author = {Edward A. G. Schuur and Jason G. Vogel and Kathryn G. Crummer and Hanna Lee and James O. Sickman and T. E. Osterkamp},
  title = {The Effect of Permafrost Thaw on Old Carbon Release
                  and Net Carbon Exchange From Tundra},
  keywords = {permafrost},
  journal = {Nature},
  volume = {459},
  number = {7246},
  pages = {556-559},
  year = {2009},
  doi = {10.1038/nature08031},
  url = {https://doi.org/10.1038/nature08031},
  issn = {1476-4687},
  month = {May},
  publisher = {Springer Nature},
}

@Article{schuur_2011_climate_change,
  author = {Edward A. G. Schuur and Benjamin Abbott},
  title = {Climate Change: High Risk of Permafrost Thaw},
  keywords = {permafrost},
  journal = {Nature},
  volume = {480},
  number = {7375},
  pages = {32-33},
  year = {2011},
  doi = {10.1038/480032a},
  url = {https://doi.org/10.1038/480032a},
  issn = {1476-4687},
  month = {Nov},
  publisher = {Springer Nature},
}

@Article{schuur_2015_climate,
  author = {E. A. G. Schuur and A. D. McGuire and C. Schädel and G. Grosse and J. W. Harden and D. J. Hayes and G. Hugelius and C. D. Koven and P. Kuhry and D. M. Lawrence and {et al.}},
  title = {Climate Change and the Permafrost Carbon Feedback},
  keywords = {permafrost},
  journal = {Nature},
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  number = {7546},
  pages = {171-179},
  year = {2015},
  doi = {10.1038/nature14338},
  url = {https://doi.org/10.1038/nature14338},
  issn = {1476-4687},
  month = {Apr},
  publisher = {Springer Nature},
}

@Article{tarnocai_2009_soil,
  author = {C. Tarnocai and J. G. Canadell and E. A. G. Schuur and P. Kuhry and G. Mazhitova and S. Zimov},
  title = {Soil Organic Carbon Pools in the Northern
                  Circumpolar Permafrost Region},
  keywords = {permafrost},
  journal = {Global Biogeochemical Cycles},
  volume = {23},
  number = {2},
  pages = {n/a-n/a},
  year = {2009},
  doi = {10.1029/2008gb003327},
  url = {https://doi.org/10.1029/2008gb003327},
  issn = {0886-6236},
  month = {Jun},
  publisher = {American Geophysical Union (AGU)},
}

@Article{treat_2013_permafrost_carbon_bomb,
  author = {Claire C. Treat and Steve Frolking},
  title = {A Permafrost Carbon Bomb?},
  keywords = {permafrost},
  journal = {Nature Climate Change},
  volume = {3},
  number = {10},
  pages = {865-867},
  year = {2013},
  doi = {10.1038/nclimate2010},
  url = {https://doi.org/10.1038/nclimate2010},
  issn = {1758-6798},
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  publisher = {Springer Nature},
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@Article{turetsky_2002_boreal,
  author = {Merritt R Turetsky and R.Kelman Wieder and Dale H Vitt},
  title = {Boreal Peatland {C} Fluxes Under Varying Permafrost
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  keywords = {permafrost},
  journal = {Soil Biology and Biochemistry},
  volume = {34},
  number = {7},
  pages = {907-912},
  year = {2002},
  doi = {10.1016/s0038-0717(02)00022-6},
  url = {https://doi.org/10.1016/s0038-0717(02)00022-6},
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@Article{whiteman_2013_vast,
  author = {Gail Whiteman and Chris Hope and Peter Wadhams},
  title = {Vast costs of Arctic change},
  year = {2013},
  volume = {499},
  number = {7459},
  month = {Jul},
  pages = {401–403},
  issn = {1476-4687},
  doi = {10.1038/499401a},
  url = {http://dx.doi.org/10.1038/499401a},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
}

@Article{wickland_2006_effects,
  author = {Kimberly P. Wickland and Robert G. Striegl and Jason C. Neff and Torsten Sachs},
  title = {Effects of Permafrost Melting on {CO2} and {CH4} exchange
                  of a Poorly Drained Black Spruce Lowland},
  keywords = {permafrost},
  journal = {Journal of Geophysical Research: Biogeosciences},
  volume = {111},
  number = {G2},
  pages = {n/a-n/a},
  year = {2006},
  doi = {10.1029/2005jg000099},
  url = {https://doi.org/10.1029/2005jg000099},
  issn = {0148-0227},
  month = {Jun},
  publisher = {American Geophysical Union (AGU)},
}

@Article{zimov_2006_climate_change,
  author = {S. A. Zimov and Edward A. G. Schuur and F. Stuart Chapin},
  title = {Climate Change: Permafrost and the Global Carbon
                  Budget},
  keywords = {permafrost},
  journal = {Science},
  volume = {312},
  number = {5780},
  pages = {1612-1613},
  year = {2006},
  doi = {10.1126/science.1128908},
  url = {https://doi.org/10.1126/science.1128908},
  issn = {1095-9203},
  month = {Jun},
  publisher = {American Association for the Advancement of Science
                  (AAAS)},
}


text:
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  abbr={YArch},
  author = {Levine, Reese and Sorensen, Tyler},
  title = {Probabilistic Memory Consistency Specifications},
  year = {2023},
  booktitle = {Young Architect Workshop},
  publisher = {ACM},
  pdf={yarch_pmcs.pdf}
}

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text:
@article{mckinnon_science_2016,
	title = {Science, {Twitter} and election campaigns: {Tracking} \#auspol in the {Australian} federal elections.},
	volume = {15},
	copyright = {All rights reserved},
	url = {https://jcom.sissa.it/},
	doi = {10.22323/2.15060204},
	abstract = {Social media is increasingly being used by science communicators, journalists and government agencies to engage in discourse with a range of publics. Despite a growing body of literature on Twitter use, the communication of science via Twitter is comparatively under explored. This paper examines the prominence of scientific issues in political debate occurring on Twitter during the 2013 and 2016 Australian federal election campaigns. Hashtracking of the umbrella political hashtag auspol was used to capture tweets during the two campaign periods. The 2013 campaign was particularly relevant as a major issue for both parties was climate change mitigation, a controversial and partisan issue. Therefore, climate change discussion on Twitter during the 2013 election was used as a focal case study in this research. Subsamples of the 2013 data were used to identify public sentiment and major contributors to the online conversation, specifically seeking to see if scientific, governmental, media or ‘public' sources were the more dominant instigators. We compare the prominence of issues on Twitter to mainstream media polls over the two campaign periods and argue that the potential of Twitter as an effective public engagement tool for science, and for politicised scientific issues in particular, is not being realised.},
	number = {06},
	journal = {JCOM},
	author = {McKinnon, Merryn and Semmens, David and Moon, Brenda and Amarasekara, Inoka and Bolliet, Léa},
	year = {2016},
	pages = {A04--A04},
}

repository: brendam/academic-kickstart

repo_name: brendam/academic-kickstart


text:
SUMMARY = "big LITTLE task placement experiment"
HOMEPAGE = "https://github.com/BayLibre/bLsched"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=b0df75b2edb80ee98b732ee0514a265c"

SRC_URI = "git://github.com/baylibre/blsched.git"
SRCREV = "${AUTOREV}"

S = "${WORKDIR}/git"

inherit autotools

repository: BayLibre/meta-baylibre-agl-blsched

repo_name: BayLibre/meta-baylibre-agl-blsched


text:
@InProceedings{richard13,
  pdf = {http://jmlr.org/proceedings/papers/v28/richard13.pdf},
  supplementary = {Supplementary:richard13-supp.pdf},
  number = {3},
  section = {cycle-3},
  title = {Intersecting singularities for multi-structured estimation},
  author = {Richard, Emile and BACH, Francis and Vert, Jean-Philippe},
  pages = {1157-1165},
  abstract = {We address the problem of designing a convex nonsmooth regularizer encouraging multiple structural effects simultaneously. Focusing on the inference of sparse and low-rank matrices we suggest a new complexity index and a convex penalty approximating it. The new penalty term can be written as the trace norm of a linear function of the matrix. By analyzing theoretical properties of this family of regularizers  we come up with oracle inequalities and compressed sensing results ensuring the quality of our regularized estimator. We also provide algorithms and supporting numerical experiments.},
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_license_id: MIT

gha_language: TeX


text:
DESCRIPTION = "Vexed levels for qpe-vexed"
SECTION = "opie/games"
PRIORITY = "optional"
MAINTAINER = "Marcin Juszkiewicz <openembedded@hrw.one.pl>"
LICENSE = "GPL"
AUTHOR = "The Vexed Development Team"
HOMEPAGE = "http://vexed.sourceforge.net/"
PACKAGE_ARCH = "all"
PR = "r1"

SRC_URI = "cvs://anonymous@cvs.sourceforge.net/cvsroot/vexed/;module=vexed/levelpacks"

S = "${WORKDIR}"

do_install () {
	install -d ${D}${palmtopdir}/etc/qpe-vexed

	for level in ${WORKDIR}/levelpacks/*.ini;
	do
	    install -m 0664 "$level" "${D}${palmtopdir}/etc/qpe-vexed/`basename "$level" .ini`.lvl";
	done
}

FILES_${PN} = "${palmtopdir}/etc/qpe-vexed/*.lvl"

repository: Terentyev/familiar-linux

repo_name: Terentyev/familiar-linux


text:
@article{Pearson:2017,
  	url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P},
  	Archiveprefix = {arXiv},
  	Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.},
  	Eprint = {1703.04627},
  	Journal = {ArXiv e-prints},
  	Keywords = {Astrophysics - Astrophysics of Galaxies},
  	Month = mar,
  	Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}},
  	Year = 2017
}

@book{Binney:2008,
  	url = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
  	Author = {{Binney}, J. and {Tremaine}, S.},
  	Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.},
  	Publisher = {Princeton University Press},
  	Title = {{Galactic Dynamics: Second Edition}},
  	Year = 2008
}

@article{gaia,
    author = {{Gaia Collaboration}},
    title = "{The Gaia mission}",
    journal = {Astronomy and Astrophysics},
    archivePrefix = "arXiv",
    eprint = {1609.04153},
    primaryClass = "astro-ph.IM",
    keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
    year = 2016,
    month = nov,
    volume = 595,
    doi = {10.1051/0004-6361/201629272},
    url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
}

@article{astropy,
    author = {{Astropy Collaboration}},
    title = "{Astropy: A community Python package for astronomy}",
    journal = {Astronomy and Astrophysics},
    archivePrefix = "arXiv",
    eprint = {1307.6212},
    primaryClass = "astro-ph.IM",
    keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
    year = 2013,
    month = oct,
    volume = 558,
    doi = {10.1051/0004-6361/201322068},
    url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
}

@misc{fidgit,
  author = {A. Smith},
  title = {Fidgit: An ungodly union of GitHub and Figshare},
  year = {2020},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/arfon/fidgit}
}

@article{moura_de_sousa_genome_2020,
	title = {Genome diversification via genetic exchanges between temperate and virulent bacteriophages},
	url = {http://biorxiv.org/lookup/doi/10.1101/2020.04.14.041137},
	doi = {10.1101/2020.04.14.041137},
	abstract = {Bacteriophages (henceforth phages) evolve by mutation and recombination. Temperate phages are known to evolve rapidly by genetic exchanges. In contrast, recombination events between virulent and between temperate and virulent phages have rarely been reported. A gene flow barrier between these two large distinct groups of phages could affect the ability of phages to acquire novel functions. Here, we show that genomes of temperate and virulent phages are very distinct but often have a few almost identical genes. These cases are due to recent genetic exchanges of both phage-like and bacterial-like genes. These exchanges were probably mediated by phage recombinases with low homology requirements and mechanisms of non-homologous end joining, since both were over-represented in recombinant phages and their hosts. When assessing the impact of gene flow across the two populations of phages we realized that temperate phages have narrower host ranges than virulent phages. This suggests, and we find some evidence, that gene flow between temperate phages infecting distant bacterial hosts might be mediated by recombination with the broader host virulent phages. Hence, gene flow across phages with distinct lifestyles could drastically increase the gene repertoire available for phage evolution, including the transfer of functional innovations across taxa. These results also have implications for bacterial evolution because of the impact of phage predation in bacterial population dynamics and the contribution of temperate phages to the evolution of bacterial gene repertoires.},
	language = {en},
	number = {10.1101/709758},
	urldate = {2020-04-16},
	journal = {bioRxiv},
	author = {Moura de Sousa, Jorge A. and Pfeifer, Eugen and Touchon, Marie and Rocha, Eduardo P. C.},
	month = apr,
	year = {2020},
	file = {Sousa et al. - 2020 - Genome diversification via genetic exchanges betwe.pdf:/Users/adamhockenberry/Zotero/storage/HLT638GZ/Sousa et al. - 2020 - Genome diversification via genetic exchanges betwe.pdf:application/pdf}
}

@article{mcnair_phacts_2012,
	title = {{PHACTS}, a computational approach to classifying the lifestyle of phages},
	volume = {28},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts014},
	doi = {10.1093/bioinformatics/bts014},
	abstract = {Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.},
	language = {en},
	number = {5},
	urldate = {2020-04-22},
	journal = {Bioinformatics},
	author = {McNair, Katelyn and Bailey, Barbara A. and Edwards, Robert A.},
	month = mar,
	year = {2012},
	pages = {614--618},
	file = {McNair et al. - 2012 - PHACTS, a computational approach to classifying th.pdf:/Users/adamhockenberry/Zotero/storage/V92V33PH/McNair et al. - 2012 - PHACTS, a computational approach to classifying th.pdf:application/pdf}
}

@article{mavrich_bacteriophage_2017,
	title = {Bacteriophage evolution differs by host, lifestyle and genome},
	volume = {2},
	issn = {2058-5276},
	url = {http://www.nature.com/articles/nmicrobiol2017112},
	doi = {10.1038/nmicrobiol.2017.112},
	language = {en},
	number = {9},
	urldate = {2020-04-22},
	journal = {Nature Microbiology},
	author = {Mavrich, Travis N. and Hatfull, Graham F.},
	month = sep,
	year = {2017},
	pages = {17112},
	file = {Mavrich and Hatfull - 2017 - Bacteriophage evolution differs by host, lifestyle.pdf:/Users/adamhockenberry/Zotero/storage/ZYYGZJVG/Mavrich and Hatfull - 2017 - Bacteriophage evolution differs by host, lifestyle.pdf:application/pdf}
}

@article{pope_whole_2015,
	title = {Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity},
	volume = {4},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.06416},
	doi = {10.7554/eLife.06416},
	abstract = {The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.},
	urldate = {2020-04-22},
	journal = {eLife},
	author = {Pope, Welkin H and Bowman, Charles A and Russell, Daniel A and Jacobs-Sera, Deborah and Asai, David J and Cresawn, Steven G and Jacobs, Jr, William R and Hendrix, Roger W and Lawrence, Jeffrey G and Hatfull, Graham F and {Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science} and {Phage Hunters Integrating Research and Education} and {Mycobacterial Genetics Course}},
	editor = {Kolter, Roberto},
	month = apr,
	year = {2015},
	keywords = {bacteriophage, evolution, genomic},
	pages = {e06416},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/SXGYEBDX/Pope et al. - 2015 - Whole genome comparison of a large collection of m.pdf:application/pdf}
}

@article{deng_viral_2014,
	title = {Viral tagging reveals discrete populations in {Synechococcus} viral genome sequence space},
	volume = {513},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature13459},
	doi = {10.1038/nature13459},
	language = {en},
	number = {7517},
	urldate = {2020-04-22},
	journal = {Nature},
	author = {Deng, Li and Ignacio-Espinoza, J. Cesar and Gregory, Ann C. and Poulos, Bonnie T. and Weitz, Joshua S. and Hugenholtz, Philip and Sullivan, Matthew B.},
	month = sep,
	year = {2014},
	pages = {242--245},
	file = {Deng et al. - 2014 - Viral tagging reveals discrete populations in Syne.pdf:/Users/adamhockenberry/Zotero/storage/YQX3XC4Q/Deng et al. - 2014 - Viral tagging reveals discrete populations in Syne.pdf:application/pdf}
}

@article{roux_viral_2015,
	title = {Viral dark matter and virus–host interactions resolved from publicly available microbial genomes},
	volume = {4},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.08490},
	doi = {10.7554/eLife.08490},
	abstract = {The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38\% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.},
	urldate = {2020-04-22},
	journal = {eLife},
	author = {Roux, Simon and Hallam, Steven J and Woyke, Tanja and Sullivan, Matthew B},
	editor = {Neher, Richard A},
	month = jul,
	year = {2015},
	keywords = {phage, prophage, virus, virus-host adaptation},
	pages = {e08490},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/HHY4U6KD/Roux et al. - 2015 - Viral dark matter and virus–host interactions reso.pdf:application/pdf}
}

@article{li_when_2019,
	title = {When to be {Temperate}: {On} the {Fitness} {Benefits} of {Lysis} vs. {Lysogeny}},
	shorttitle = {When to be {Temperate}},
	url = {http://biorxiv.org/lookup/doi/10.1101/709758},
	doi = {10.1101/709758},
	abstract = {Bacterial viruses, i.e., ‘bacteriophage’ or ‘phage’, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e., ‘temperate’ bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, i.e., the ‘prophage’, can induce and restart the lytic pathway. Here, we explore the relationship between infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage-bacteria dynamics spanning both explicit and implicit representations of intracellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses – notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.},
	language = {en},
	number = {10.1101/709758},
	urldate = {2020-04-22},
	journal = {bioRxiv},
	author = {Li, Guanlin and Cortez, Michael H. and Dushoff, Jonathan and Weitz, Joshua S.},
	month = jul,
	year = {2019},
	file = {Li et al. - 2019 - When to be Temperate On the Fitness Benefits of L.pdf:/Users/adamhockenberry/Zotero/storage/SFB7DK83/Li et al. - 2019 - When to be Temperate On the Fitness Benefits of L.pdf:application/pdf}
}

@article{tisza_discovery_2020,
	title = {Discovery of several thousand highly diverse circular {DNA} viruses},
	volume = {9},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.51971},
	doi = {10.7554/eLife.51971},
	abstract = {Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.},
	urldate = {2020-04-22},
	journal = {eLife},
	author = {Tisza, Michael J and Pastrana, Diana V and Welch, Nicole L and Stewart, Brittany and Peretti, Alberto and Starrett, Gabriel J and Pang, Yuk-Ying S and Krishnamurthy, Siddharth R and Pesavento, Patricia A and McDermott, David H and Murphy, Philip M and Whited, Jessica L and Miller, Bess and Brenchley, Jason and Rosshart, Stephan P and Rehermann, Barbara and Doorbar, John and Ta'ala, Blake A and Pletnikova, Olga and Troncoso, Juan C and Resnick, Susan M and Bolduc, Ben and Sullivan, Matthew B and Varsani, Arvind and Segall, Anca M and Buck, Christopher B},
	editor = {Kirkegaard, Karla and Pride, David},
	month = feb,
	year = {2020},
	keywords = {metagenomics, microbiome, viral evolution},
	pages = {e51971},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/AHYM2ZL3/Tisza et al. - 2020 - Discovery of several thousand highly diverse circu.pdf:application/pdf}
}

@article{carey_phage_2019,
	title = {Phage integration alters the respiratory strategy of its host},
	volume = {8},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.49081},
	doi = {10.7554/eLife.49081},
	abstract = {Temperate bacteriophages are viruses that can incorporate their genomes into their bacterial hosts, existing there as prophages that refrain from killing the host cell until induced. Prophages are largely quiescent, but they can alter host phenotype through factors encoded in their genomes (often virulence factors) or by disrupting host genes as a result of integration. Here we describe another mechanism by which a prophage can modulate host phenotype. We show that a temperate phage that integrates in Escherichia coli reprograms host regulation of an anaerobic respiratory system, thereby inhibiting a bet hedging strategy. The phage exerts this effect by upregulating a host-encoded signal transduction protein through transcription initiated from a phage-encoded promoter. We further show that this phenomenon occurs not only in a laboratory strain of E. coli, but also in a natural isolate that contains a prophage at this site.},
	urldate = {2020-04-22},
	journal = {eLife},
	author = {Carey, Jeffrey N and Mettert, Erin L and Fishman-Engel, Daniel R and Roggiani, Manuela and Kiley, Patricia J and Goulian, Mark},
	editor = {Laub, Michael T and Storz, Gisela},
	month = oct,
	year = {2019},
	keywords = {bacteriophage, bet hedging, trimethylamine N-oxide, two-component signaling},
	pages = {e49081},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/ZY42SIHR/Carey et al. - 2019 - Phage integration alters the respiratory strategy .pdf:application/pdf}
}

@article{brum_patterns_2015,
	title = {Patterns and ecological drivers of ocean viral communities},
	volume = {348},
	copyright = {Copyright © 2015, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/348/6237/1261498},
	doi = {10.1126/science.1261498},
	abstract = {Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.},
	language = {en},
	number = {6237},
	urldate = {2020-04-22},
	journal = {Science},
	author = {Brum, Jennifer R. and Ignacio-Espinoza, J. Cesar and Roux, Simon and Doulcier, Guilhem and Acinas, Silvia G. and Alberti, Adriana and Chaffron, Samuel and Cruaud, Corinne and Vargas, Colomban de and Gasol, Josep M. and Gorsky, Gabriel and Gregory, Ann C. and Guidi, Lionel and Hingamp, Pascal and Iudicone, Daniele and Not, Fabrice and Ogata, Hiroyuki and Pesant, Stéphane and Poulos, Bonnie T. and Schwenck, Sarah M. and Speich, Sabrina and Dimier, Celine and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Coordinators, Tara Oceans and Bork, Peer and Bowler, Chris and Sunagawa, Shinichi and Wincker, Patrick and Karsenti, Eric and Sullivan, Matthew B.},
	month = may,
	year = {2015},
	file = {Snapshot:/Users/adamhockenberry/Zotero/storage/AXCI2NL3/1261498.html:text/html;Submitted Version:/Users/adamhockenberry/Zotero/storage/XGGH9WV2/Brum et al. - 2015 - Patterns and ecological drivers of ocean viral com.pdf:application/pdf}
}

@article{simmonds_virus_2017,
	title = {Virus taxonomy in the age of metagenomics},
	volume = {15},
	issn = {1740-1526, 1740-1534},
	url = {http://www.nature.com/articles/nrmicro.2016.177},
	doi = {10.1038/nrmicro.2016.177},
	abstract = {The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.},
	language = {en},
	number = {3},
	urldate = {2020-04-22},
	journal = {Nature Reviews Microbiology},
	author = {Simmonds, Peter and Adams, Mike J. and Benkő, Mária and Breitbart, Mya and Brister, J. Rodney and Carstens, Eric B. and Davison, Andrew J. and Delwart, Eric and Gorbalenya, Alexander E. and Harrach, Balázs and Hull, Roger and King, Andrew M.Q. and Koonin, Eugene V. and Krupovic, Mart and Kuhn, Jens H. and Lefkowitz, Elliot J. and Nibert, Max L. and Orton, Richard and Roossinck, Marilyn J. and Sabanadzovic, Sead and Sullivan, Matthew B. and Suttle, Curtis A. and Tesh, Robert B. and van der Vlugt, René A. and Varsani, Arvind and Zerbini, F. Murilo},
	month = mar,
	year = {2017},
	pages = {161--168},
	file = {Simmonds et al. - 2017 - Virus taxonomy in the age of metagenomics.pdf:/Users/adamhockenberry/Zotero/storage/UVDBTIJK/Simmonds et al. - 2017 - Virus taxonomy in the age of metagenomics.pdf:application/pdf}
}

@article{dedrick_engineered_2019,
	title = {Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant {Mycobacterium} abscessus},
	volume = {25},
	issn = {1078-8956, 1546-170X},
	url = {http://www.nature.com/articles/s41591-019-0437-z},
	doi = {10.1038/s41591-019-0437-z},
	language = {en},
	number = {5},
	urldate = {2020-04-22},
	journal = {Nature Medicine},
	author = {Dedrick, Rebekah M. and Guerrero-Bustamante, Carlos A. and Garlena, Rebecca A. and Russell, Daniel A. and Ford, Katrina and Harris, Kathryn and Gilmour, Kimberly C. and Soothill, James and Jacobs-Sera, Deborah and Schooley, Robert T. and Hatfull, Graham F. and Spencer, Helen},
	month = may,
	year = {2019},
	pages = {730--733},
	file = {Dedrick et al. - 2019 - Engineered bacteriophages for treatment of a patie.pdf:/Users/adamhockenberry/Zotero/storage/KZU6GLTU/Dedrick et al. - 2019 - Engineered bacteriophages for treatment of a patie.pdf:application/pdf}
}

@article{rodriguez-gonzalez_quantitative_2020,
	title = {Quantitative {Models} of {Phage}-{Antibiotic} {Combination} {Therapy}},
	volume = {5},
	issn = {2379-5077},
	doi = {10.1128/mSystems.00756-19},
	language = {en},
	number = {1},
	urldate = {2020-04-22},
	journal = {mSystems},
	author = {Rodriguez-Gonzalez, Rogelio A. and Leung, Chung Yin and Chan, Benjamin K. and Turner, Paul E. and Weitz, Joshua S.},
	editor = {Whiteson, Katrine L.},
	month = feb,
	year = {2020},
	pages = {e00756--19},
	file = {Rodriguez-Gonzalez et al. - 2020 - Quantitative Models of Phage-Antibiotic Combinatio.pdf:/Users/adamhockenberry/Zotero/storage/8U5M2NCA/Rodriguez-Gonzalez et al. - 2020 - Quantitative Models of Phage-Antibiotic Combinatio.pdf:application/pdf}
}

@article{ofir_contemporary_2018,
	title = {Contemporary {Phage} {Biology}: {From} {Classic} {Models} to {New} {Insights}},
	volume = {172},
	issn = {0092-8674},
	doi = {10.1016/j.cell.2017.10.045},
	language = {en},
	number = {6},
	urldate = {2020-04-22},
	journal = {Cell},
	author = {Ofir, Gal and Sorek, Rotem},
	month = mar,
	year = {2018},
	pages = {1260--1270},
	file = {ScienceDirect Full Text PDF:/Users/adamhockenberry/Zotero/storage/8Q82NSJD/Ofir and Sorek - 2018 - Contemporary Phage Biology From Classic Models to.pdf:application/pdf;ScienceDirect Snapshot:/Users/adamhockenberry/Zotero/storage/5X2AXJRV/S0092867417313053.html:text/html}
}

@article{daly_viruses_2019,
	title = {Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing},
	volume = {4},
	issn = {2058-5276},
	url = {http://www.nature.com/articles/s41564-018-0312-6},
	doi = {10.1038/s41564-018-0312-6},
	language = {en},
	number = {2},
	urldate = {2020-04-22},
	journal = {Nature Microbiology},
	author = {Daly, Rebecca A. and Roux, Simon and Borton, Mikayla A. and Morgan, David M. and Johnston, Michael D. and Booker, Anne E. and Hoyt, David W. and Meulia, Tea and Wolfe, Richard A. and Hanson, Andrea J. and Mouser, Paula J. and Moore, Joseph D. and Wunch, Kenneth and Sullivan, Matthew B. and Wrighton, Kelly C. and Wilkins, Michael J.},
	month = feb,
	year = {2019},
	pages = {352--361},
	file = {Daly et al. - 2019 - Viruses control dominant bacteria colonizing the t.pdf:/Users/adamhockenberry/Zotero/storage/JGIT2XJI/Daly et al. - 2019 - Viruses control dominant bacteria colonizing the t.pdf:application/pdf}
}

@article{emerson_host-linked_2018,
	title = {Host-linked soil viral ecology along a permafrost thaw gradient},
	volume = {3},
	issn = {2058-5276},
	url = {http://www.nature.com/articles/s41564-018-0190-y},
	doi = {10.1038/s41564-018-0190-y},
	abstract = {Rapidly thawing permafrost harbors ϳ30 to 50\% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-ampliﬁed) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire ﬁeld site in northern Sweden. Only 15\% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ϳ30\% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-viruslike assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identiﬁed and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these ﬁndings suggest that these soil viruses have distinct ecology, impact hostmediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic.},
	language = {en},
	number = {8},
	urldate = {2020-04-22},
	journal = {Nature Microbiology},
	author = {Emerson, Joanne B. and Roux, Simon and Brum, Jennifer R. and Bolduc, Benjamin and Woodcroft, Ben J. and Jang, Ho Bin and Singleton, Caitlin M. and Solden, Lindsey M. and Naas, Adrian E. and Boyd, Joel A. and Hodgkins, Suzanne B. and Wilson, Rachel M. and Trubl, Gareth and Li, Changsheng and Frolking, Steve and Pope, Phillip B. and Wrighton, Kelly C. and Crill, Patrick M. and Chanton, Jeffrey P. and Saleska, Scott R. and Tyson, Gene W. and Rich, Virginia I. and Sullivan, Matthew B.},
	month = aug,
	year = {2018},
	pages = {870--880},
	file = {Emerson et al. - 2018 - Host-linked soil viral ecology along a permafrost .pdf:/Users/adamhockenberry/Zotero/storage/9V3SW5M5/Emerson et al. - 2018 - Host-linked soil viral ecology along a permafrost .pdf:application/pdf}
}

@article{nishimura_environmental_2017,
	title = {Environmental {Viral} {Genomes} {Shed} {New} {Light} on {Virus}-{Host} {Interactions} in the {Ocean}},
	volume = {2},
	issn = {2379-5042},
	url = {https://mSphere.asm.org/lookup/doi/10.1128/mSphere.00359-16},
	doi = {10.1128/mSphere.00359-16},
	abstract = {Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral “dark matter.” However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genuslevel operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efﬁcient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for speciﬁc viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes.},
	language = {en},
	number = {2},
	urldate = {2020-04-22},
	journal = {mSphere},
	author = {Nishimura, Yosuke and Watai, Hiroyasu and Honda, Takashi and Mihara, Tomoko and Omae, Kimiho and Roux, Simon and Blanc-Mathieu, Romain and Yamamoto, Keigo and Hingamp, Pascal and Sako, Yoshihiko and Sullivan, Matthew B. and Goto, Susumu and Ogata, Hiroyuki and Yoshida, Takashi},
	editor = {Tamaki, Hideyuki},
	month = apr,
	year = {2017},
	pages = {e00359--16},
	file = {Nishimura et al. - 2017 - Environmental Viral Genomes Shed New Light on Viru.pdf:/Users/adamhockenberry/Zotero/storage/Z67JUDM9/Nishimura et al. - 2017 - Environmental Viral Genomes Shed New Light on Viru.pdf:application/pdf}
}

@article{touchon_genetic_2016,
	title = {Genetic and life-history traits associated with the distribution of prophages in bacteria},
	volume = {10},
	issn = {1751-7362, 1751-7370},
	url = {http://www.nature.com/articles/ismej201647},
	doi = {10.1038/ismej.2016.47},
	language = {en},
	number = {11},
	urldate = {2020-04-22},
	journal = {The ISME Journal},
	author = {Touchon, Marie and Bernheim, Aude and Rocha, Eduardo PC},
	month = nov,
	year = {2016},
	pages = {2744--2754},
	file = {Touchon et al. - 2016 - Genetic and life-history traits associated with th.pdf:/Users/adamhockenberry/Zotero/storage/ZESTVSIU/Touchon et al. - 2016 - Genetic and life-history traits associated with th.pdf:application/pdf}
}

@article{jain_high_2018,
	title = {High throughput {ANI} analysis of {90K} prokaryotic genomes reveals clear species boundaries},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-07641-9},
	doi = {10.1038/s41467-018-07641-9},
	language = {en},
	number = {1},
	urldate = {2020-04-28},
	journal = {Nature Communications},
	author = {Jain, Chirag and Rodriguez-R, Luis M. and Phillippy, Adam M. and Konstantinidis, Konstantinos T. and Aluru, Srinivas},
	month = dec,
	year = {2018},
	pages = {5114},
	file = {Jain et al. - 2018 - High throughput ANI analysis of 90K prokaryotic ge.pdf:/Users/adamhockenberry/Zotero/storage/KTNGMG8I/Jain et al. - 2018 - High throughput ANI analysis of 90K prokaryotic ge.pdf:application/pdf}
}

@article{eddy_accelerated_2011,
	title = {Accelerated {Profile} {HMM} {Searches}},
	volume = {7},
	issn = {1553-7358},
	url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002195},
	doi = {10.1371/journal.pcbi.1002195},
	abstract = {Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.},
	language = {en},
	number = {10},
	urldate = {2020-04-28},
	journal = {PLOS Computational Biology},
	author = {Eddy, Sean R.},
	month = oct,
	year = {2011},
	keywords = {Algorithms, BLAST algorithm, Database searching, Heuristic alignment procedure, Hidden Markov models, Multiple alignment calculation, Sequence alignment, Sequence databases},
	pages = {e1002195},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/WYQDDSLI/Eddy - 2011 - Accelerated Profile HMM Searches.pdf:application/pdf;Snapshot:/Users/adamhockenberry/Zotero/storage/45QMQKZF/article.html:text/html}
}

@article{lu_cddsparcle_2020,
	title = {{CDD}/{SPARCLE}: the conserved domain database in 2020},
	volume = {48},
	issn = {0305-1048, 1362-4962},
	shorttitle = {{CDD}/{SPARCLE}},
	url = {https://academic.oup.com/nar/article/48/D1/D265/5645006},
	doi = {10.1093/nar/gkz991},
	abstract = {As NLM’s Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classiﬁcations of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesisdriven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a signiﬁcant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/ cdd/cdd.shtml.},
	language = {en},
	number = {D1},
	urldate = {2020-04-28},
	journal = {Nucleic Acids Research},
	author = {Lu, Shennan and Wang, Jiyao and Chitsaz, Farideh and Derbyshire, Myra K and Geer, Renata C and Gonzales, Noreen R and Gwadz, Marc and Hurwitz, David I and Marchler, Gabriele H and Song, James S and Thanki, Narmada and Yamashita, Roxanne A and Yang, Mingzhang and Zhang, Dachuan and Zheng, Chanjuan and Lanczycki, Christopher J and Marchler-Bauer, Aron},
	month = jan,
	year = {2020},
	pages = {D265--D268},
	file = {Lu et al. - 2020 - CDDSPARCLE the conserved domain database in 2020.pdf:/Users/adamhockenberry/Zotero/storage/IIXYFEQP/Lu et al. - 2020 - CDDSPARCLE the conserved domain database in 2020.pdf:application/pdf}
}

@article{bobay_adaptation_2013,
	title = {The {Adaptation} of {Temperate} {Bacteriophages} to {Their} {Host} {Genomes}},
	volume = {30},
	issn = {1537-1719, 0737-4038},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mss279},
	doi = {10.1093/molbev/mss279},
	abstract = {Rapid turnover of mobile elements drives the plasticity of bacterial genomes. Integrated bacteriophages (prophages) encode host-adaptive traits and represent a sizable fraction of bacterial chromosomes. We hypothesized that natural selection shapes prophage integration patterns relative to the host genome organization. We tested this idea by detecting and studying 500 prophages of 69 strains of Escherichia and Salmonella. Phage integrases often target not only conserved genes but also intergenic positions, suggesting purifying selection for integration sites. Furthermore, most integration hotspots are conserved between the two host genera. Integration sites seem also selected at the large chromosomal scale, as they are nonrandomly organized in terms of the origin–terminus axis and the macrodomain structure. The genes of lambdoid prophages are systematically co-oriented with the bacterial replication fork and display the host high frequency of polarized FtsK-orienting polar sequences motifs required for chromosome segregation. matS motifs are strongly avoided by prophages suggesting counter selection of motifs disrupting macrodomains. These results show how natural selection for seamless integration of prophages in the chromosome shapes the evolution of the bacterium and the phage. First, integration sites are highly conserved for many millions of years favoring lysogeny over the lytic cycle for temperate phages. Second, the global distribution of prophages is intimately associated with the chromosome structure and the patterns of gene expression. Third, the phage endures selection for DNA motifs that pertain exclusively to the biology of the prophage in the bacterial chromosome. Understanding prophage genetic adaptation sheds new lights on the coexistence of horizontal transfer and organized bacterial genomes.},
	language = {en},
	number = {4},
	urldate = {2020-05-12},
	journal = {Molecular Biology and Evolution},
	author = {Bobay, Louis-Marie and Rocha, Eduardo P.C. and Touchon, Marie},
	month = apr,
	year = {2013},
	pages = {737--751},
	file = {Bobay et al. - 2013 - The Adaptation of Temperate Bacteriophages to Thei.pdf:/Users/adamhockenberry/Zotero/storage/TNSC5R5D/Bobay et al. - 2013 - The Adaptation of Temperate Bacteriophages to Thei.pdf:application/pdf}
}

@article{gregory_marine_2019,
	title = {Marine {DNA} {Viral} {Macro}- and {Microdiversity} from {Pole} to {Pole}},
	volume = {177},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(19)30341-1},
	doi = {10.1016/j.cell.2019.03.040},
	language = {English},
	number = {5},
	urldate = {2020-07-08},
	journal = {Cell},
	author = {Gregory, Ann C. and Zayed, Ahmed A. and Conceição-Neto, Nádia and Temperton, Ben and Bolduc, Ben and Alberti, Adriana and Ardyna, Mathieu and Arkhipova, Ksenia and Carmichael, Margaux and Cruaud, Corinne and Dimier, Céline and Domínguez-Huerta, Guillermo and Ferland, Joannie and Kandels, Stefanie and Liu, Yunxiao and Marec, Claudie and Pesant, Stéphane and Picheral, Marc and Pisarev, Sergey and Poulain, Julie and Tremblay, Jean-Éric and Vik, Dean and Acinas, Silvia G. and Babin, Marcel and Bork, Peer and Boss, Emmanuel and Bowler, Chris and Cochrane, Guy and Vargas, Colomban de and Follows, Michael and Gorsky, Gabriel and Grimsley, Nigel and Guidi, Lionel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Kandels-Lewis, Stefanie and Karp-Boss, Lee and Karsenti, Eric and Not, Fabrice and Ogata, Hiroyuki and Pesant, Stéphane and Poulton, Nicole and Raes, Jeroen and Sardet, Christian and Speich, Sabrina and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Babin, Marcel and Bowler, Chris and Culley, Alexander I. and Vargas, Colomban de and Dutilh, Bas E. and Iudicone, Daniele and Karp-Boss, Lee and Roux, Simon and Sunagawa, Shinichi and Wincker, Patrick and Sullivan, Matthew B.},
	month = may,
	year = {2019},
	pmid = {31031001},
	note = {Publisher: Elsevier},
	keywords = {metagenomics, community ecology, diversity gradients, marine biology, population ecology, species, viruses},
	pages = {1109--1123.e14},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/9MAGFEBE/Gregory et al. - 2019 - Marine DNA Viral Macro- and Microdiversity from Po.pdf:application/pdf;Snapshot:/Users/adamhockenberry/Zotero/storage/WX9PXHDE/S0092-8674(19)30341-1.html:text/html}
}

@article{paez-espino_uncovering_2016,
	title = {Uncovering {Earth}’s virome},
	volume = {536},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature19094},
	doi = {10.1038/nature19094},
	language = {en},
	number = {7617},
	urldate = {2020-07-08},
	journal = {Nature},
	author = {Paez-Espino, David and Eloe-Fadrosh, Emiley A. and Pavlopoulos, Georgios A. and Thomas, Alex D. and Huntemann, Marcel and Mikhailova, Natalia and Rubin, Edward and Ivanova, Natalia N. and Kyrpides, Nikos C.},
	month = aug,
	year = {2016},
	pages = {425--430},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/WIRI8GHI/Paez-Espino et al. - 2016 - Uncovering Earth’s virome.pdf:application/pdf;Snapshot:/Users/adamhockenberry/Zotero/storage/A4R9XBBY/nature19094.html:text/html}
}

@article{forterre_manipulation_2011,
	title = {Manipulation of cellular syntheses and the nature of viruses: {The} virocell concept},
	volume = {14},
	issn = {1631-0748},
	shorttitle = {Manipulation of cellular syntheses and the nature of viruses},
	url = {http://www.sciencedirect.com/science/article/pii/S1631074810001724},
	doi = {10.1016/j.crci.2010.06.007},
	language = {en},
	number = {4},
	urldate = {2020-07-08},
	journal = {Comptes Rendus Chimie},
	author = {Forterre, Patrick},
	month = apr,
	year = {2011},
	keywords = {Bacteriophage, Bactériophage, Biologie synthétique, Cellule virale, Evolution, Évolution, Mimivirus, Synthetic biology, Usine virale, Viral factory, Virocell, Virus},
	pages = {392--399},
	file = {ScienceDirect Full Text PDF:/Users/adamhockenberry/Zotero/storage/W55GDT94/Forterre - 2011 - Manipulation of cellular syntheses and the nature .pdf:application/pdf;ScienceDirect Snapshot:/Users/adamhockenberry/Zotero/storage/KMBAVVJD/S1631074810001724.html:text/html}
}

@book{abedon_bacteriophage_2008,
	address = {Cambridge},
	series = {Advances in {Molecular} and {Cellular} {Microbiology}},
	title = {Bacteriophage {Ecology}},
	isbn = {978-0-521-85845-8},
	shorttitle = {Bacteriophage {Ecology}},
	abstract = {Bacteriophages, or phages, are viruses that infect bacteria and are believed to be the most abundant and genetically diverse organisms on Earth. As such, their ecology is vast both in quantitative and qualitative terms. Their abundance makes an understanding of phage ecology increasingly relevant to bacterial ecosystem ecology, bacterial genomics and bacterial pathology. Abedon provides the first text on phage ecology for almost 20 years. Written by leading experts, synthesizing the three key approaches to studying phage ecology, namely studying them in natural environments (in situ), experimentally in the lab, or theoretically using mathematical or computer models. With strong emphasis on microbial population biology and distilling cutting-edge research into basic principles, this book will complement other currently available volumes. It will therefore serve as an essential resource for graduate students and researchers, particularly those with an interest in phage ecology and evolutionary biology.},
	urldate = {2020-07-08},
	publisher = {Cambridge University Press},
	editor = {Abedon, Stephen T.},
	year = {2008},
	file = {Snapshot:/Users/adamhockenberry/Zotero/storage/P4DCZ4JI/17FAA5647551E145800AA39AA237932E.html:text/html}
}

@article{dion_phage_2020,
	title = {Phage diversity, genomics and phylogeny},
	volume = {18},
	issn = {1740-1534},
	doi = {10.1038/s41579-019-0311-5},
	language = {en},
	number = {3},
	urldate = {2020-07-08},
	journal = {Nature Reviews Microbiology},
	author = {Dion, Moïra B. and Oechslin, Frank and Moineau, Sylvain},
	month = mar,
	year = {2020},
	pages = {125--138},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/DJ9MLJIM/Dion et al. - 2020 - Phage diversity, genomics and phylogeny.pdf:application/pdf;Snapshot:/Users/adamhockenberry/Zotero/storage/EYARUPU3/s41579-019-0311-5.html:text/html}
}

@article{kirchberger_resurrection_2020,
	title = {Resurrection of a global, metagenomically defined gokushovirus},
	volume = {9},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.51599},
	doi = {10.7554/eLife.51599},
	abstract = {Gokushoviruses are single-stranded, circular DNA bacteriophages found in metagenomic datasets from diverse ecosystems worldwide, including human gut microbiomes. Despite their ubiquity and abundance, little is known about their biology or host range: Isolates are exceedingly rare, known only from three obligate intracellular bacterial genera. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced gokushoviruses in an experimentally tractable model system, allowing us to investigate their features and biology. We demonstrate that virions can reliably infect and lysogenize hosts by hijacking a conserved chromosome-dimer resolution system. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses; however, we show that even partial motifs enable phages to persist cytoplasmically without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae.},
	urldate = {2020-07-28},
	journal = {eLife},
	author = {Kirchberger, Paul C and Ochman, Howard},
	editor = {Zambrano, María Mercedes and Kirkegaard, Karla and Breitbart, Mya},
	month = feb,
	year = {2020},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {bacteriophage, integrative elements, metagenomes, Microviridae, virome},
	pages = {e51599},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/STV6ZYT5/Kirchberger and Ochman - 2020 - Resurrection of a global, metagenomically defined .pdf:application/pdf}
}

@article{tynecki_phageai_2020,
	title = {{PhageAI} - {Bacteriophage} {Life} {Cycle} {Recognition} with {Machine} {Learning} and {Natural} {Language} {Processing}},
	copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2020.07.11.198606v1},
	doi = {10.1101/2020.07.11.198606},
	abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}As antibiotic resistance is becoming a major problem nowadays in a treatment of infections, bacteriophages (also known as phages) seem to be an alternative. However, to be used in a therapy, their life cycle should be strictly lytic. With the growing popularity of Next Generation Sequencing (NGS) technology, it is possible to gain such information from the genome sequence. A number of tools are available which help to define phage life cycle. However, there is still no unanimous way to deal with this problem, especially in the absence of well-defined open reading frames. To overcome this limitation, a new tool is definitely needed.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}We developed a novel tool, called PhageAI, that allows to access more than 10 000 publicly available bacteriophages and differentiate between their major types of life cycles: lytic and lysogenic. The tool included life cycle classifier which achieved 98.90\% accuracy on a validation set and 97.18\% average accuracy on a test set. We adopted nucleotide sequences embedding based on the Word2Vec with Ship-gram model and linear Support Vector Machine with 10-fold cross-validation for supervised classification. PhageAI is free of charge and it is available at https://phage.ai/. PhageAI is a REST web service and available as Python package.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}Machine learning and Natural Language Processing allows to extract information from bacteriophages nucleotide sequences for lifecycle prediction tasks. The PhageAI tool classifies phages into either virulent or temperate with a higher accuracy than any existing methods and shares interactive 3D visualization to help interpreting model classification results.{\textless}/p{\textgreater}},
	language = {en},
	urldate = {2021-01-26},
	journal = {bioRxiv},
	author = {Tynecki, Piotr and Guziński, Arkadiusz and Kazimierczak, Joanna and Jadczuk, Michał and Dastych, Jarosław and Onisko, Agnieszka},
	month = jul,
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2020.07.11.198606},
	file = {Full Text PDF:/Users/adamhockenberry/Zotero/storage/P7K7HJFC/Tynecki et al. - 2020 - PhageAI - Bacteriophage Life Cycle Recognition wit.pdf:application/pdf;Snapshot:/Users/adamhockenberry/Zotero/storage/3A4IF2V3/2020.07.11.html:text/html}
}

repository: liupfskygre/bacphlip

repo_name: liupfskygre/bacphlip


text:
require qt5-git.inc
require ${PN}.inc

# qtwayland wasn't released yet, last tag before this SRCREV is 5.0.0-beta1
# qt5-git PV is only to indicate that this recipe is compatible with qt5 5.2.1

SRCREV = "98dca3b54f52f08117c1e0d3a1b4826ed12ef23f"
QT_MODULE_BRANCH = "5.4"

# wayland-scanner and qtwaylandscanner must be in same path to work properly
do_install_append() {
    ln -sf ${D}${OE_QMAKE_PATH_QT_BINS}/qtwaylandscanner ${D}${bindir}/qtwaylandscanner
}


text:
DESCRIPTION = "Control Gembird SIS-PM programmable power outlet strips"
HOMEPAGE = "http://sispmctl.sourceforge.net/"
LICENSE = "GPL-2.0-only"
LIC_FILES_CHKSUM = "file://COPYING;md5=b234ee4d69f5fce4486a80fdaf4a4263"
DEPENDS = "libusb"

inherit autotools pkgconfig

PACKAGECONFIG[web] = "--disable-webless,--enable-webless,"

SRC_URI = "https://sourceforge.net/projects/sispmctl/files/sispmctl/sispmctl-${PV}/sispmctl-${PV}.tar.gz"

SRC_URI[sha256sum] = "6a9ec7125e8c01bb45d4a3b56f07fb41fc437020c8dcd8c0f29ebb98dc55a647"

repository: labgrid-project/meta-labgrid

repo_name: labgrid-project/meta-labgrid

gha_language: BitBake


text:
@article{scott_association_2016,
 author = {Scott, Kate M. and Lim, Carmen and Al-Hamzawi, Ali and Alonso, Jordi and Bruffaerts, Ronny and Caldas-de-Almeida, José Miguel and Florescu, Silvia and de Girolamo, Giovanni and Hu, Chiyi and de Jonge, Peter and Kawakami, Norito and Medina-Mora, Maria Elena and Moskalewicz, Jacek and Navarro-Mateu, Fernando and O’Neill, Siobhan and Piazza, Marina and Posada-Villa, José and Torres, Yolanda and Kessler, Ronald C.},
 doi = {10.1001/jamapsychiatry.2015.2688},
 issn = {2168-622X},
 journal = {JAMA Psychiatry},
 language = {en},
 month = {February},
 number = {2},
 pages = {150},
 shorttitle = {Association of Mental Disorders With Subsequent Chronic Physical Conditions},
 title = {Association of Mental Disorders With Subsequent Chronic Physical Conditions: World Mental Health Surveys From 17 Countries},
 url = {http://archpsyc.jamanetwork.com/article.aspx?doi=10.1001/jamapsychiatry.2015.2688},
 urldate = {2021-03-27},
 volume = {73},
 year = {2016}
}


text:
@Article{leppik_85,
  title = {A double-blind crossover evaluation of progabide in partial seizures: 3: 15 PM8},
  author = {Leppik, Ilo and Dreifuss, Fritz and Bowman, Terri and Santilli, Nancy and Jacobs, Margaret and Crosby, Coral and Cloyd, James and Stockman, Judy and Graves, Nina and Sutula, Tom and others},
  journal = {Neurology},
  year = {1985},
  volume={35}
}

@Article{inouye_17,
  title = {A review of multivariate distributions for count data derived from the Poisson distribution},
  author = {Inouye, David I and Yang, Eunho and Allen, Genevera I and Ravikumar, Pradeep},
  journal = {Wiley Interdisciplinary Reviews: Computational Statistics},
  year = {2017},
  volume = {9},
  pages = {e1398}
}

@Article{ferguson_73,
  author =       {Ferguson, T S},
  title =        {A {B}ayesian  analysis of some nonparametric problems},
  journal =      {Annals of Statistics},
  year =         {1973},
  volume =       {1},
  pages =        {209--230}
}

@Article{ferguson_74,
  author =       {Ferguson, T S},
  title =        {Prior distribution on the spaces of probability measures},
  journal =      {Annals of Statistics},
  year =         {1974},
  volume =       {2},
  pages =        {615--629},
}

@Article{lo_84,
  author =       {Lo, A Y},
  title =        {On a class of {B}ayesian nonparametric estimates {I}: Density estimates},
  journal =      {The Annals of Statistics},
  year =         {1984},
  volume =       {12},
  pages =        {351--357},
}

@Article{escobar_94,
  author =       {Escobar, M D},
  title =        {{Estimating normal means with a {D}irichlet process prior}},
  journal =      {Journal of the American Statistical Association},
  year =         {1994},
  volume =       {89},
  pages =        {268--277},
}

@Article{escobar_west_95,
  author =       {Escobar, M D and West, M},
  title =        {{Bayesian density estimation and inference using mixtures}},
  journal =      {Journal of the American Statistical Association},
  year =         {1995},
  volume =       {90},
  pages =        {577--588},
}

@Article{blackwell_mcqueen_73,
  author =       {Blackwell, D and MacQueen, J},
  title =        {Ferguson distributions via {P}\'olya urn schemes},
  journal =      {The Annals of Statistics},
  year =         {1973},
  volume =       {1},
  pages =        {353--355},
}

@Article{sethuraman_94,
  author =       {Sethuraman, J},
  title =        {A constructive definition of {D}irichlet prior},
  journal =      {Statistica Sinica},
  year =         {1994},
  volume =       {2},
  pages =        {639--650},
}

@Article{neal_2000,
  author =       {Neal, R},
  title =        {{Markov chain sampling methods for {D}irichlet process mixture models}},
  journal =      {Journal of Computational and Graphical Statistics},
  year =         {2000},
  volume =       {9},
  pages =        {249--265},
}

@article{ishwaran_2001,
  title={Gibbs sampling methods for stick-breaking priors},
  author={Ishwaran, Hemant and James, Lancelot F},
  journal={Journal of the American Statistical Association},
  volume={96},
  number={453},
  pages={161--173},
  year={2001},
  publisher={Taylor \& Francis}
}

@Article{ishwaran_james_2002,
  author =       {Ishwaran, H and James, L F},
  title =        {Approximate {D}irichlet process computing in finite normal mixtures: smoothing and prior information},
  journal =      {Journal of Computational and Graphical Statistics},
  year =         {2002},
  volume =       {11},
  pages =        {508--532},
}

repository: nimble-dev/nimble-demos

repo_name: nimble-dev/nimble-demos

gha_language: HTML


text:
KBRANCH ?= "dev-5.3"
LINUX_VERSION ?= "5.3.1"

SRCREV="3a98193d306d77a1d650c59e7f5b5743acec9b60"

require linux-aspeed.inc

repository: HCL-BMC/openbmc

repo_name: HCL-BMC/openbmc

gha_license_id: NOASSERTION


text: @inbook{Cardoso10IoSPlatSLAmodel,	abstract = {The Internet of Services (IoS) embraces new business and technological	models that can radically change the way day-to-day services are	provisioned and contracted. Within the IoS, services which were traditionally	not created based on an established science and operated without	a systematic approach, will be digitalized using proper methodologies,	standards, and tools. The digital specification of services will	enable their trading over the Internet using electronic marketplaces.	This paper provides four main contributions to the IoS research:	a definition and characterization for the concept of IoS-based service,	the role and importance of platform services for the IoS, the challenges	of managing SLA dependencies between IoS-based services in compositions,	and a model-based approach for service engineering that can be used	to design IoS-based services.},	author = {Cardoso, Jorge and Winkler, Matthias and Voigt, Konrad and Berthold, Henrike},	booktitle = {Software and Data Technologies},	date-added = {2018-04-25 20:02:07 +0000},	date-modified = {2018-04-25 20:02:07 +0000},	editor = {Cordeiro, Jos{\'e} and Ranchordas, AlpeshKumar and Shishkov, Boris},	isbn = {978-3-642-20116-5},	owner = {Jorge Cardoso},	pages = {3-17},	publisher = {Springer Berlin Heidelberg},	refid = {211},	series = {Communications in Computer and Information Science},	timestamp = {2010.08.26},	title = {IoS-Based Services, Platform Services, SLA and Models for the Internet of Services},	url = {http://dx.doi.org/10.1007/978-3-642-20116-5_1},	volume = {50},	webpdf = {/Papers/BC-2009-029-Springer-CCIS-Selec-Papers-ICSOFT09-IoS.pdf},	year = {2011},	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-20116-5_1}}


text:
DESCRIPTION = "NETCP PA firmware for Keystone"

LICENSE = "TI-TFL"
LIC_FILES_CHKSUM = "file://LICENCE.ti-keystone;md5=3a86335d32864b0bef996bee26cc0f2c"

PV = "3.0.2.3"
PR = "r1"

CLEANBROKEN = "1"

COMPATIBLE_MACHINE = "k2hk|k2l-evm|k2e"

PACKAGE_ARCH = "${MACHINE_ARCH}"

SRCREV = "953ab647b0b6af411965242ecd919b1cb0e570d6"
BRANCH ?= "ti-linux-firmware-4.1.y"

SRC_URI = "git://git.ti.com/processor-firmware/ti-linux-firmware.git;protocol=git;branch=${BRANCH}"

S = "${WORKDIR}/git"

FWBASENAME = " \
ks2_pa_eg0_pdsp0 \
ks2_pa_eg0_pdsp1 \
ks2_pa_eg0_pdsp2 \
ks2_pa_eg1_pdsp0 \
ks2_pa_eg2_pdsp0 \
ks2_pa_in0_pdsp0 \
ks2_pa_in0_pdsp1 \
ks2_pa_in1_pdsp0 \
ks2_pa_in1_pdsp1 \
ks2_pa_in2_pdsp0 \
ks2_pa_in3_pdsp0 \
ks2_pa_in4_pdsp0 \
ks2_pa_in4_pdsp1 \
ks2_pa_post_pdsp0 \
ks2_pa_post_pdsp1 \
"

FWBASENAME_k2hk = " \
ks2_pa_pdsp0_classify1 \
ks2_pa_pdsp1_classify1 \
ks2_pa_pdsp2_classify1 \
ks2_pa_pdsp3_classify2 \
ks2_pa_pdsp4_pam \
ks2_pa_pdsp5_pam \
"

do_install() {
	install -d ${D}${base_libdir}/firmware
	for f in ${FWBASENAME}; do
		install -m 0644 ${S}/ti-keystone/$f.bin ${D}${base_libdir}/firmware/$f.bin
	done
}

FILES_${PN} = "${base_libdir}/firmware"


text:
/*------------
Font
------------*/
@import url("https://fonts.googleapis.com/css2?family=Roboto:wght@300;400;500;700;900&display=swap");
@font-face {
  font-family: steelfish;
  src: url(../font/stelfish.ttf);
}

/*------------
Resset Css
------------*/
*, ::after, ::before, h1, h2, p {
  box-sizing: border-box;
  margin: 0;
  padding: 0;
  font-family: 'Roboto', sans-serif;
  outline: none;
}

/*------------
Variables
------------*/
/*------------
Styling
------------*/
.onScrolled {
  position: fixed;
  top: 0;
}

#mainHeader {
  padding-top: 1rem;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary {
  display: flex;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data {
  display: flex;
  align-items: center;
  justify-content: center;
  flex-direction: column;
  background-color: #fff;
  box-shadow: 0px 0px 11px rgba(0, 0, 0, 0.25);
  border-radius: 15px;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .arrow {
  position: absolute;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon {
  width: 100%;
  display: flex;
  justify-content: center;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .wrapperChart canvas {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData {
  font-size: 18px;
  text-align: center;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData .valueData {
  color: #DC3545;
}

.mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p {
  text-align: center;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana {
  display: flex;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic {
  box-shadow: 0px 0px 11px rgba(0, 0, 0, 0.25);
  border-radius: 15px;
  display: flex;
  align-items: center;
  margin: 1rem 1rem;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .valueDana {
  font-weight: 700;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart canvas {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana {
  display: flex;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic {
  box-shadow: 0px 0px 11px rgba(0, 0, 0, 0.25);
  border-radius: 15px;
  display: flex;
  align-items: center;
  margin: 1rem 1rem;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .valueDana {
  font-weight: 700;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart canvas {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab {
  background: #fff;
  box-shadow: 0px 0px 11px rgba(0, 0, 0, 0.25);
  border-radius: 15px;
  margin: 1rem 1rem;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart {
  display: flex;
  align-items: center;
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperChart {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperChart canvas {
  width: 100%;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperInfo {
  display: flex;
  position: relative;
  justify-content: space-between;
}

.mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperInfo .info {
  position: relative;
}

@media screen and (min-width: 0px) {
  #mainHeader .navbar {
    margin-bottom: 1rem;
  }
  .mainContent {
    padding: 2rem 1rem;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data {
    margin: 1rem 1rem;
    padding: 2rem 2rem;
    position: relative;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .arrow {
    right: 10%;
    top: 10%;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .arrow img {
    max-width: 15px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon {
    margin-bottom: 2rem;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon img {
    max-width: 120px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .wrapperChart {
    max-width: 110px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData {
    font-size: 14px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .btnStyle {
    margin-top: .5rem;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p {
    font-size: 12px;
    margin-top: .3rem;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p .month {
    margin-right: .2rem;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic {
    padding: 2rem 2rem;
    margin: 1rem 1rem;
    flex-direction: column-reverse;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .nameValue {
    font-size: 14px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .valueDana {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart {
    max-width: 130px;
    margin-bottom: 1.5rem;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic {
    padding: 2rem 2rem;
    margin: 1rem 1rem;
    flex-direction: column-reverse;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .nameValue {
    font-size: 14px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .valueDana {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart {
    max-width: 130px;
    margin-bottom: 1.5rem;
  }
  .mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab {
    padding: 2rem 1rem;
  }
  .mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart {
    display: flex;
    align-items: center;
    flex-direction: column;
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperChart {
    margin-bottom: 2rem;
  }
  .mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperInfo {
    width: 100%;
  }
  .mainContent .container-fluid .wrapperContent .statisticAllDataEbaltab .containerChart .wrapperInfo .info {
    font-size: 12px;
    text-align: center;
  }
}

@media screen and (min-width: 992px) {
  .mainContent {
    padding: 4rem 3rem;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary {
    justify-content: center;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon img {
    max-width: 150px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .wrapperChart {
    max-width: 135px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData {
    font-size: 14px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p {
    font-size: 12px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .nameValue {
    font-size: 16px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .valueDana {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart {
    max-width: 150px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .nameValue {
    font-size: 16px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .valueDana {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart {
    max-width: 150px;
  }
}

@media screen and (min-width: 1200px) {
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon img {
    max-width: 160px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .wrapperChart {
    max-width: 140px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p {
    font-size: 14px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic {
    flex-direction: row;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .nameValue {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .valueDana {
    font-size: 22px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart {
    max-width: 160px;
    margin-bottom: 0;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic {
    flex-direction: row;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .nameValue {
    font-size: 18px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .valueDana {
    font-size: 22px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart {
    max-width: 160px;
    margin-bottom: 0;
  }
}

@media screen and (min-width: 1400px) {
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .icon img {
    max-width: 200px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .wrapperChart {
    max-width: 155px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data .titleData {
    font-size: 24px;
  }
  .mainContent .container-fluid .wrapperContent .wrapperDataSummary .data p {
    font-size: 18px;
    margin-top: .5rem;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic {
    flex-direction: row;
    padding: 2rem 3rem;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue {
    width: 70%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .nameValue {
    font-size: 24px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .contentValue .valueDana {
    font-size: 32px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .alokasiDana .cardStatistic .wrapperChart {
    max-width: 300px;
    width: 30%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic {
    flex-direction: row;
    padding: 2rem 3rem;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue {
    width: 70%;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .nameValue {
    font-size: 24px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .contentValue .valueDana {
    font-size: 32px;
  }
  .mainContent .container-fluid .wrapperContent .container-danaAlokasi-penyaluranDana .penyaluranDana .cardStatistic .wrapperChart {
    max-width: 300px;
    width: 30%;
  }
}

repository: Akumagami-s/KPRS

repo_name: Akumagami-s/KPRS

branch_name: refs/heads/main

extension: css


text:
SUMMARY = "Basic utility library for Xfce4"
SECTION = "x11/libs"
LICENSE = "LGPL-2.0-or-later"
LIC_FILES_CHKSUM = "file://COPYING;md5=4cf66a4984120007c9881cc871cf49db"
DEPENDS = "intltool-native xfce4-dev-tools-native glib-2.0"

inherit xfce gtk-doc gobject-introspection vala

SRC_URI[sha256sum] = "8a52063a5adc66252238cad9ee6997909b59983ed21c77eb83c5e67829d1b01f"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded