text:
@article{Boyeau2022.05.27.493625,
 abstract = {Detecting differentially expressed genes is important for characterizing subpopulations of cells. In scRNA-seq data, however, nuisance variation due to technical factors like sequencing depth and RNA capture efficiency obscures the underlying biological signal. Deep generative models have been extensively applied to scRNA-seq data, with a special focus on embedding cells into a low-dimensional latent space and correcting for batch effects. However, little attention has been given to the problem of utilizing the uncertainty from the deep generative model for differential expression. Furthermore, the existing approaches do not allow controlling for the effect size or the false discovery rate. Here, we present lvm-DE, a generic Bayesian approach for performing differential expression from using a fitted deep generative model, while controlling the false discovery rate. We apply the lvm-DE framework to scVI and scSphere, two deep generative models. The resulting approaches outperform the state-of-the-art methods at estimating the log fold change in gene expression levels, as well as detecting differentially expressed genes between subpopulations of cells.},
 addendum = {\hrefhttps://www.biorxiv.org/content/early/2022/05/29/2022.05.27.493625\scriptsize [PDF]},
 author = {Boyeau, Pierre and Regier, Jeffrey and Gayoso, Adam and Jordan, Michael I. and \myname* and Yosef*, Nir},
 journal = {bioRxiv},
 keywords = {insubmission},
 month = {May},
 projects = {scVI},
 title = {An empirical Bayes method for differential expression analysis of single cells with deep generative models},
 url_pdf = {https://www.biorxiv.org/content/early/2022/05/29/2022.05.27.493625},
 year = {2022}
}

repository: romain-lopez/academic-kickstart

repo_name: romain-lopez/academic-kickstart


text:
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=751419260aa954499f7abaabaa882bbe"
DEPENDS = "db rasqal libtool libiodbc"
PR = "r2"

SRC_URI = "http://download.librdf.org/source/${BPN}-${PV}.tar.gz \
    file://No-docs-and-NOCONFIGURE.patch \
    "
SRC_URI[md5sum] = "b0deb87f3c7d3237a3d587c1e0f2f266"
SRC_URI[sha256sum] = "0e1f5825b6357c9b490da866c95ae1d895dbb5f445013d2511c37df822ee9ec6"

#see http://patches.openembedded.org/patch/33965/
SYSROOT_PREPROCESS_FUNCS += "redland_sysroot_preprocess"

inherit autotools gtk-doc

EXTRA_OECONF = "\
    --enable-maintainer-mode \
    --disable-gtk-doc \
    --with-raptor=system \
    --with-rasqal=system \
    --with-threestore=no \
    --with-mysql=no \
    --with-sqlite=no \
    --with-postgresql=no \
    --with-openssl-digests=no \
    --with-bdb=${STAGING_EXECPREFIXDIR} \
    --with-odbc-inc=${STAGING_INCDIR} \
    --with-odbc-lib=${STAGING_LIBDIR} \
    "

# Redland autogen.sh does not work properly, so let OE do the job
do_configure() {
    cd ${S}
    export NOCONFIGURE="no"; ./autogen.sh
    oe_runconf
}
do_install() {
    oe_runmake install DESTDIR=${D}
    install -d ${D}${bindir_crossscripts}
    install -m 755 ${D}${bindir}/redland-config ${D}${bindir_crossscripts}
}

RDEPENDS_${PN} = "rasqal raptor"

BBCLASSEXTEND = "native"

redland_sysroot_preprocess () {
       sysroot_stage_dir ${D}${bindir_crossscripts} ${SYSROOT_DESTDIR}${bindir_crossscripts}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bb


text:
DESCRIPTION = "ALSA Scenario Library"
HOMEPAGE = "http://opensource.wolfsonmicro.com/node/22"
SECTION = "console/utils"
LICENSE = "GPL"
DEPENDS = "alsa-lib ncurses"
SRCREV = "8bd7f83d847424eb44704cf1649974b2fda8d8f1"
PV = "0.2+gitr${SRCREV}"
PR = "r1"
PE = "1"

DEFAULT_PREFERENCE = "-1"

SRC_URI = "git://slimlogic.co.uk/alsa-scenario;branch=master;protocol=git"
S = "${WORKDIR}/git"

inherit autotools

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
require jsch_${PV}.bb

S = "${WORKDIR}/jsch-${PV}"

inherit java-native

DEPENDS = "fastjar-native jzlib-native"
RDEPENDS = ""

repository: demsey/openembedded

repo_name: demsey/openembedded


text:
@article{Gibson2009a,
 abstract = {Background: Non-steroidal anti-inflammatory drugs (NSAIDs) may be prothrombotic, may worsen hypertension or congestive heart failure and obstruct access to the binding site of aspirin to cyclooxygenase-1 and thereby interfere with aspirin's mechanism of action in reducing death and recurrent myocardial infarction (MI). We hypothesized that treatment with NSAIDs prior to an index MI would be associated with an increase in the risk of death, heart failure and recurrent MI among patients with ST-segment elevation MI (STEMI) treated with fibrinolytic therapy. Methods: In ExTRACT-TIMI 25, patients with STEMI were treated with aspirin and fibrinolytic therapy and randomized to either enoxaparin or unfractionated heparin. We included patients who had received NSAIDs within 7 days of enrollment and evaluated the incidence of MI, the composite of death and MI and the composite of death, MI, severe heart failure and shock through 30 days. Results: Of 20,479 patients enrolled, 572 (2.8%) received an NSAID within 7 days of enrollment. NSAID treatment prior to entry was associated with a higher incidence of 30-day death or nonfatal recurrent MI (15.9% vs. 10.8%, univariate P \textless 0.001). In multivariable models adjusting for randomization group and differences in baseline characteristics, NSAID use was associated with higher odds of MI (adjusted odds ratio [ORadj] 1.44, 95% confidence interval [CI] 1.01-2.07, P = 0.047), the composite of death and MI (ORadj 1.29, 95% CI 1.00-1.66, P = 0.051), and the composite of death, MI, severe heart failure and shock (ORadj 1.29, 95% CI 1.02-1.65, P = 0.037). Conclusions: Among STEMI patients treated with a fibrinolytic agent and aspirin, use of NSAIDs in the week preceding the incident event was associated with a higher incidence of MI, the composite of death and MI as well as the composite of death, MI, severe heart failure and shock at 30 days. \textcopyright Springer Science+Business Media, LLC 2008.},
 author = {Gibson, C.M. and Pride, Y.B. and Aylward, P.E. and Col, J.J. and Goodman, S.G. and Gulba, D. and Bergovec, M. and Kunadian, V. and Zorkun, C. and Buros, J.L. and Murphy, S.A. and Antman, E.M.},
 doi = {10.1007/s11239-008-0264-4},
 issn = {09295305},
 journal = {Journal of Thrombosis and Thrombolysis},
 keywords = {[Fibrinolytic therapy, Nonsteroidal antiinflammato},
 number = {1},
 title = {Association of non-steroidal anti-inflammatory drugs with outcomes in patients with ST-segment elevation myocardial infarction treated with fibrinolytic therapy: An ExTRACT-TIMI 25 analysis},
 volume = {27},
 year = {2009}
}

repository: jburos/another-biostats-blog

repo_name: jburos/another-biostats-blog

gha_license_id: MIT

gha_language: TeX

extension: bib


text:
@article{LeCun1998,
abstract = {Multilayer neural networks trained with the back-propagation algorithm constitute the best example of a successful gradient-based learning technique. Given an appropriate network architecture, gradient-based learning algorithms can be used to synthesize a complex decision surface that can classify high-dimensional patterns, such as handwritten characters, with minimal preprocessing. This paper reviews various methods applied to handwritten character recognition and compares them on a standard handwritten digit recognition task. Convolutional neural networks, which are specifically designed to deal with the variability of two dimensional (2-D) shapes, are shown to outperform all other techniques. Real-life document recognition systems are composed of multiple modules including field extraction, segmentation, recognition, and language modeling. A new learning paradigm, called graph transformer networks (GTN's), allows such multimodule systems to be trained globally using gradient-based methods so as to minimize an overall performance measure. Two systems for online handwriting recognition are described. Experiments demonstrate the advantage of global training, and the flexibility of graph transformer networks. A graph transformer network for reading a bank check is also described. It uses convolutional neural network character recognizers combined with global training techniques to provide record accuracy on business and personal checks. It is deployed commercially and reads several million checks per day. {\textcopyright} 1998 IEEE.},
author = {LeCun, Yann and Bottou, L{\'{e}}on and Bengio, Yoshua and Haffner, Patrick},
doi = {10.1109/5.726791},
file = {:home/artem/Mendeley/Unknown/Bengio, Haffner - 1998 - Gradient-Based Learning Applied to Document Recognition.pdf:pdf},
issn = {00189219},
journal = {Proceedings of the IEEE},
keywords = {Convolutional neural networks,Document recognition,Finite state transducers,Gradient-based learning,Graph transformer networks,Machine learning,Neural networks,Optical character recognition (OCR)},
number = {11},
pages = {2278--2323},
title = {{Gradient-based learning applied to document recognition}},
volume = {86},
year = {1998}
}

@online{Dataset,
  title = {Dataset and Dataloader},
  url = {https://pytorch.org/tutorials/beginner/basics/data_tutorial.html},
}

branch_name: refs/heads/main


text:
# Recipe to fetch/unpack sources used by ti-pdk-fetch recipes.
#
# Mimic gcc-source.inc from oe-core.

# These shources will be unpacked to a "work-shared" directory. Then each
# "ti-pdk-fetch" recipe will hard-link only the sources it requires.

deltask do_configure
deltask do_compile
deltask do_install
deltask do_populate_sysroot
deltask do_populate_lic

RM_WORK_EXCLUDE += "${PN}"
EXCLUDE_FROM_WORLD = "1"

inherit nopackages ti-pdk-fetch

LICENSE = "BSD-3-Clause"

PN = "${TI_PDK_SOURCE_PN}"
WORKDIR = "${TI_PDK_SOURCE_WORKDIR}"
SSTATE_SWSPEC = "sstate:ti-pdk::${PV}:${PR}::${SSTATE_VERSION}:"

STAMP = "${STAMPS_DIR}/work-shared/ti-pdk-${PV}"
STAMPCLEAN = "${STAMPS_DIR}/work-shared/ti-pdk-${PV}*"

INHIBIT_DEFAULT_DEPS = "1"
DEPENDS = ""
PACKAGES = ""

SRC_URI = "${TI_PDK_GIT_URI};branch=${TI_PDK_GIT_BRANCH};protocol=${TI_PDK_GIT_PROTOCOL}"
SRCREV = "${TI_PDK_SRCREV}"

repository: acrlinux/acrlinux-yocto

repo_name: acrlinux/acrlinux-yocto


text:
@article{Barb07,
  title = {Modularity and Community Detection in Bipartite Networks},
  author = {Barber, Michael J.},
  date = {2007-12-07},
  journaltitle = {Physical Review E},
  shortjournal = {Phys. Rev. E},
  volume = {76},
  pages = {066102},
  issn = {1539-3755, 1550-2376},
  doi = {10.1103/PhysRevE.76.066102},
  url = {http://arxiv.org/abs/0707.1616},
  urldate = {2020-09-09},
  abstract = {The modularity of a network quantifies the extent, relative to a null model network, to which vertices cluster into community groups. We define a null model appropriate for bipartite networks, and use it to define a bipartite modularity. The bipartite modularity is presented in terms of a modularity matrix B; some key properties of the eigenspectrum of B are identified and used to describe an algorithm for identifying modules in bipartite networks. The algorithm is based on the idea that the modules in the two parts of the network are dependent, with each part mutually being used to induce the vertices for the other part into the modules. We apply the algorithm to real-world network data, showing that the algorithm successfully identifies the modular structure of bipartite networks.},
  archivePrefix = {arXiv},
  eprint = {0707.1616},
  eprinttype = {arxiv},
  file = {C\:\\Users\\franc\\Zotero\\storage\\MAZWMVXM\\Barber - 2007 - Modularity and community detection in bipartite ne.pdf;C\:\\Users\\franc\\Zotero\\storage\\377GBS56\\0707.html},
  keywords = {Condensed Matter - Statistical Mechanics,Physics - Data Analysis; Statistics and Probability,Physics - Physics and Society},
  number = {6}
}

@article{BascJord03a,
  title = {The Nested Assembly of Plant–Animal Mutualistic Networks},
  author = {Bascompte, Jordi and Jordano, Pedro and Melián, Carlos J. and Olesen, Jens M.},
  date = {2003-08-05},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {PNAS},
  volume = {100},
  pages = {9383--9387},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1633576100},
  url = {https://www.pnas.org/content/100/16/9383},
  urldate = {2020-09-09},
  abstract = {Most studies of plant–animal mutualisms involve a small number of species. There is almost no information on the structural organization of species-rich mutualistic networks despite its potential importance for the maintenance of diversity. Here we analyze 52 mutualistic networks and show that they are highly nested; that is, the more specialist species interact only with proper subsets of those species interacting with the more generalists. This assembly pattern generates highly asymmetrical interactions and organizes the community cohesively around a central core of interactions. Thus, mutualistic networks are neither randomly assembled nor organized in compartments arising from tight, parallel specialization. Furthermore, nestedness increases with the complexity (number of interactions) of the network: for a given number of species, communities with more interactions are significantly more nested. Our results indicate a nonrandom pattern of community organization that may be relevant for our understanding of the organization and persistence of biodiversity.},
  eprint = {12881488},
  eprinttype = {pmid},
  file = {C\:\\Users\\franc\\Zotero\\storage\\U6LBW4ZU\\Bascompte et al. - 2003 - The nested assembly of plant–animal mutualistic ne.pdf;C\:\\Users\\franc\\Zotero\\storage\\T7WUWKBH\\9383.html},
  langid = {english},
  number = {16}
}

@article{DelmBess19,
  title = {Analysing Ecological Networks of Species Interactions},
  author = {Delmas, Eva and Besson, Mathilde and Brice, Marie Hélène and Burkle, Laura A. and Dalla Riva, Giulio V. and Fortin, Marie Josée and Gravel, Dominique and Guimarães, Paulo R. and Hembry, David H. and Newman, Erica A. and Olesen, Jens M. and Pires, Mathias M. and Yeakel, Justin D. and Poisot, Timothée},
  date = {2019},
  journaltitle = {Biological Reviews},
  doi = {10.1111/brv.12433},
  abstract = {Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems – such as communities – through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theory also provides numerous approaches and measures to analyze these objects and can offer new perspectives on established ecological theories as well as tools to address new challenges. However, prior to using these methods to test ecological hypotheses, it is necessary that we understand, adapt, and use them in ways that both allow us to deliver their full potential and account for their limitations. Here, we attempt to increase the accessibility of network approaches by providing a review of the tools that have been developed so far, with – what we believe to be – their appropriate uses and potential limitations. This is not an exhaustive review of all methods and metrics, but rather, an overview of tools that are robust, informative, and ecologically sound. After providing a brief presentation of species interaction networks and how to build them in order to summarize ecological information of different types, we then classify methods and metrics by the types of ecological questions that they can be used to answer from global to local scales, including methods for hypothesis testing and future perspectives. Specifically, we show how the organization of species interactions in a community yields different network structures (e.g., more or less dense, modular or nested), how different measures can be used to describe and quantify these emerging structures, and how to compare communities based on these differences in structures. Within networks, we illustrate metrics that can be used to describe and compare the functional and dynamic roles of species based on their position in the network and the organization of their interactions as well as associated new methods to test the significance of these results. Lastly, we describe potential fruitful avenues for new methodological developments to address novel ecological questions.},
  file = {C\:\\Users\\franc\\Zotero\\storage\\IVRZ5IP5\\DelmBess19-Analysing ecological networks of species interactions.pdf},
  keywords = {biogeography,community ecology,ecological networks,graph theory,interactions}
}

@article{DormGrub08,
  title = {Introducing the Bipartite {{Package}}: {{Analysing Ecological Networks}}},
  shorttitle = {Introducing the Bipartite {{Package}}},
  author = {Dormann, Carsten and Gruber, Bernd and Fründ, Jochen},
  date = {2008-01-01},
  journaltitle = {R News},
  shortjournal = {R News},
  volume = {8},
  file = {C\:\\Users\\franc\\Zotero\\storage\\K6BKFD2D\\Dormann et al. - 2008 - Introducing the bipartite Package Analysing Ecolo.pdf}
}

@article{DunnWill02c,
  title = {Network Structure and Biodiversity Loss in Food Webs: Robustness Increases with Connectance},
  shorttitle = {Network Structure and Biodiversity Loss in Food Webs},
  author = {Dunne, Jennifer A. and Williams, Richard J. and Martinez, Neo D.},
  date = {2002},
  journaltitle = {Ecology Letters},
  volume = {5},
  pages = {558--567},
  issn = {1461-0248},
  doi = {10.1046/j.1461-0248.2002.00354.x},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1461-0248.2002.00354.x},
  urldate = {2020-09-09},
  abstract = {Food-web structure mediates dramatic effects of biodiversity loss including secondary and `cascading' extinctions. We studied these effects by simulating primary species loss in 16 food webs from terrestrial and aquatic ecosystems and measuring robustness in terms of the secondary extinctions that followed. As observed in other networks, food webs are more robust to random removal of species than to selective removal of species with the most trophic links to other species. More surprisingly, robustness increases with food-web connectance but appears independent of species richness and omnivory. In particular, food webs experience `rivet-like' thresholds past which they display extreme sensitivity to removal of highly connected species. Higher connectance delays the onset of this threshold. Removing species with few trophic connections generally has little effect though there are several striking exceptions. These findings emphasize how the number of species removed affects ecosystems differently depending on the trophic functions of species removed.},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1461-0248.2002.00354.x},
  file = {C\:\\Users\\franc\\Zotero\\storage\\WJKWMY35\\Dunne et al. - 2002 - Network structure and biodiversity loss in food we.pdf;C\:\\Users\\franc\\Zotero\\storage\\LE86KMA4\\j.1461-0248.2002.00354.html},
  keywords = {Biodiversity,connectance,ecosystem function,food web,network structure,robustness,secondary extinctions,species loss,species richness,topology},
  langid = {english},
  number = {4}
}

@article{DunnWill02d,
  title = {Food-Web Structure and Network Theory: {{The}} Role of Connectance and Size},
  shorttitle = {Food-Web Structure and Network Theory},
  author = {Dunne, Jennifer A. and Williams, Richard J. and Martinez, Neo D.},
  date = {2002-10-01},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {PNAS},
  volume = {99},
  pages = {12917--12922},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.192407699},
  url = {https://www.pnas.org/content/99/20/12917},
  urldate = {2020-09-09},
  abstract = {Networks from a wide range of physical, biological, and social systems have been recently described as “small-world” and “scale-free.” However, studies disagree whether ecological networks called food webs possess the characteristic path lengths, clustering coefficients, and degree distributions required for membership in these classes of networks. Our analysis suggests that the disagreements are based on selective use of relatively few food webs, as well as analytical decisions that obscure important variability in the data. We analyze a broad range of 16 high-quality food webs, with 25–172 nodes, from a variety of aquatic and terrestrial ecosystems. Food webs generally have much higher complexity, measured as connectance (the fraction of all possible links that are realized in a network), and much smaller size than other networks studied, which have important implications for network topology. Our results resolve prior conflicts by demonstrating that although some food webs have small-world and scale-free structure, most do not if they exceed a relatively low level of connectance. Although food-web degree distributions do not display a universal functional form, observed distributions are systematically related to network connectance and size. Also, although food webs often lack small-world structure because of low clustering, we identify a continuum of real-world networks including food webs whose ratios of observed to random clustering coefficients increase as a power–law function of network size over 7 orders of magnitude. Although food webs are generally not small-world, scale-free networks, food-web topology is consistent with patterns found within those classes of networks.},
  eprint = {12235364},
  eprinttype = {pmid},
  file = {C\:\\Users\\franc\\Zotero\\storage\\FRKZUBPR\\Dunne et al. - 2002 - Food-web structure and network theory The role of.pdf;C\:\\Users\\franc\\Zotero\\storage\\M5W7ZZF8\\12917.html},
  langid = {english},
  number = {20}
}

@article{FlorPois16,
  title = {{{BiMat}}: A {{MATLAB}} Package to Facilitate the Analysis of Bipartite Networks},
  shorttitle = {{{BiMat}}},
  author = {Flores, Cesar O. and Poisot, Timothée and Valverde, Sergi and Weitz, Joshua S.},
  date = {2016},
  journaltitle = {Methods in Ecology and Evolution},
  volume = {7},
  pages = {127--132},
  issn = {2041-210X},
  doi = {10.1111/2041-210X.12458},
  url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12458},
  urldate = {2020-10-27},
  abstract = {Bipartite networks are ubiquitous in community ecology, including examples of facilitative interactions, such as plant-pollinator networks, and antagonistic interactions, such as virus–host infection networks. Statistical network analysis is increasingly used to identify emergent, nonrandom patterns of interaction and the effect of interaction patterns on ecological and evolutionary dynamics. Two recurring patterns are that of modularity and nestedness. Modularity is a feature of networks in which there are densely interacting subgroups. Nestedness is a feature of networks in which the interactions form ordered subsets. Here we describe BiMat, an open-source MATLAB package for the study of the structure of bipartite ecological networks. Unlike alternative tools, BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module-level) scales – and meta-analyses of many bipartite networks simultaneously. In common with other tools, BiMat calculates the degree to which a bipartite network is modular and/or nested, the statistical significance of these patterns, and enables visualization of latent structures in the network. BiMat is available as an open-source MATLAB package, with a quick-start guide and worked examples at: http://bimat.github.io/.},
  annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12458},
  file = {C\:\\Users\\franc\\Zotero\\storage\\PHAXW54C\\Flores et al. - 2016 - BiMat a MATLAB package to facilitate the analysis.pdf;C\:\\Users\\franc\\Zotero\\storage\\2IXGAMLE\\2041-210X.html},
  keywords = {community ecology,complex networks,ecological networks,host-parasite interactions,microbial ecology},
  langid = {english},
  number = {1}
}

@article{FortBasc06,
  title = {Habitat Loss and the Structure of Plant–Animal Mutualistic Networks},
  author = {Fortuna, Miguel A. and Bascompte, Jordi},
  date = {2006},
  journaltitle = {Ecology Letters},
  volume = {9},
  pages = {281--286},
  issn = {1461-0248},
  doi = {10.1111/j.1461-0248.2005.00868.x},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1461-0248.2005.00868.x},
  urldate = {2020-09-09},
  abstract = {Recent papers have described the structure of plant–animal mutualistic networks. However, no study has yet explored the dynamical implications of network structure for the persistence of such mutualistic communities. Here, we develop a patch-model of a whole plant–animal community and explore its persistence. To assess the role of network structure, we build three versions of the model. In the first version, we use the exact network of interactions of two real mutualistic communities. In the other versions, we randomize the observed network of interactions using two different null models. We show that the community response to habitat loss is affected by network structure. Real communities start to decay sooner than random communities, but persist for higher destruction levels. There is a destruction threshold at which the community collapses. Our model is the first attempt to describe the dynamics of whole mutualistic metacommunities interacting in realistic ways.},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2005.00868.x},
  file = {C\:\\Users\\franc\\Zotero\\storage\\LG3QAVQX\\Fortuna et Bascompte - 2006 - Habitat loss and the structure of plant–animal mut.pdf;C\:\\Users\\franc\\Zotero\\storage\\S5PIX6W9\\j.1461-0248.2005.00868.html},
  keywords = {Community structure,complex networks,habitat fragmentation,metacommunity,nestedness,pollination,seed dispersal},
  langid = {english},
  number = {3}
}

@article{FortStou10,
  title = {Nestedness versus Modularity in Ecological Networks: Two Sides of the Same Coin?},
  shorttitle = {Nestedness versus Modularity in Ecological Networks},
  author = {Fortuna, Miguel A. and Stouffer, Daniel B. and Olesen, Jens M. and Jordano, Pedro and Mouillot, David and Krasnov, Boris R. and Poulin, Robert and Bascompte, Jordi},
  date = {2010},
  journaltitle = {Journal of Animal Ecology},
  volume = {79},
  pages = {811--817},
  publisher = {{[Wiley, British Ecological Society]}},
  issn = {0021-8790},
  abstract = {1. Understanding the structure of ecological networks is a crucial task for interpreting community and ecosystem responses to global change. 2. Despite the recent interest in this subject, almost all studies have focused exclusively on one specific network property. The question remains as to what extent different network properties are related and how understanding this relationship can advance our comprehension of the mechanisms behind these patterns. 3. Here, we analysed the relationship between nestedness and modularity, two frequently studied network properties, for a large data set of 95 ecological communities including both plant-animal mutualistic and host-parasite networks. 4. We found that the correlation between nestedness and modularity for a population of random matrices generated from the real communities decreases significantly in magnitude and sign with increasing connectance independent of the network type. At low connectivities, networks that are highly nested also tend to be highly modular; the reverse happens at high connectivities. 5. The above result is qualitatively robust when different null models are used to infer network structure, but, at a finer scale, quantitative differences exist. We observed an important interaction between the network structure pattern and the null model used to detect it. 6. A better understanding of the relationship between nestedness and modularity is important given their potential implications on the dynamics and stability of ecological communities.},
  eprint = {40835468},
  eprinttype = {jstor},
  number = {4}
}

@article{Guim20,
  title = {The {{Structure}} of {{Ecological Networks Across Levels}} of {{Organization}}},
  author = {Guimarães, Paulo R.},
  date = {2020-11-02},
  journaltitle = {Annual Review of Ecology, Evolution, and Systematics},
  shortjournal = {Annu. Rev. Ecol. Evol. Syst.},
  volume = {51},
  pages = {annurev-ecolsys-012220-120819},
  issn = {1543-592X, 1545-2069},
  doi = {10.1146/annurev-ecolsys-012220-120819},
  url = {https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-012220-120819},
  urldate = {2020-09-02},
  abstract = {Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.             Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
  langid = {english},
  number = {1}
}

@article{HagbSchu08,
  title = {Exploring {{Network Structure}}, {{Dynamics}}, and {{Function}} Using {{NetworkX}}},
  author = {Hagberg, Aric A and Schult, Daniel A and Swart, Pieter J},
  date = {2008},
  pages = {5},
  file = {C\:\\Users\\franc\\Zotero\\storage\\BNK6RQ98\\Hagberg et al. - 2008 - Exploring Network Structure, Dynamics, and Functio.pdf},
  langid = {english}
}

@article{HudsEmer13,
  title = {Cheddar: Analysis and Visualisation of Ecological Communities in {{R}}},
  shorttitle = {Cheddar},
  author = {Hudson, Lawrence N. and Emerson, Rob and Jenkins, Gareth B. and Layer, Katrin and Ledger, Mark E. and Pichler, Doris E. and Thompson, Murray S. A. and O'Gorman, Eoin J. and Woodward, Guy and Reuman, Daniel C.},
  date = {2013},
  journaltitle = {Methods in Ecology and Evolution},
  volume = {4},
  pages = {99--104},
  issn = {2041-210X},
  doi = {10.1111/2041-210X.12005},
  url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12005},
  urldate = {2020-10-27},
  abstract = {There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies. We introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance. The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples. This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development.},
  annotation = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12005},
  file = {C\:\\Users\\franc\\Zotero\\storage\\XAS9UDMM\\Hudson et al. - 2013 - Cheddar analysis and visualisation of ecological .pdf;C\:\\Users\\franc\\Zotero\\storage\\I6DQIJT4\\2041-210X.html},
  keywords = {allometry,body mass,ecological network,food chain,food web,mass–abundance,predator–prey,resource–consumer,trophic height,trophic level},
  langid = {english},
  number = {1}
}

@article{MacDBanv20a,
  title = {Revisiting the {{Links}}-{{Species Scaling Relationship}} in {{Food Webs}}},
  author = {MacDonald, Arthur Andrew Meahan and Banville, Francis and Poisot, Timothée},
  date = {2020-07-29},
  journaltitle = {Patterns},
  shortjournal = {PATTER},
  volume = {0},
  publisher = {{Elsevier}},
  issn = {2666-3899},
  doi = {10.1016/j.patter.2020.100079},
  url = {https://www.cell.com/patterns/abstract/S2666-3899(20)30107-0},
  urldate = {2020-09-11},
  file = {C\:\\Users\\franc\\Zotero\\storage\\8Q95IAQF\\MacDonald et al. - 2020 - Revisiting the Links-Species Scaling Relationship .pdf;C\:\\Users\\franc\\Zotero\\storage\\DV9C3TIM\\S2666-3899(20)30107-0.html},
  keywords = {and tested for one domain/problem,Bayesian methods,constant connectance,DSML 2: Proof-of-Concept: Data science output has been formulated,food webs,implemented,link-species scaling,power law,probabilistic programming},
  langid = {english},
  number = {0}
}

@article{Newm06,
  title = {Modularity and Community Structure in Networks},
  author = {Newman, M. E. J.},
  date = {2006-06-06},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proceedings of the National Academy of Sciences},
  volume = {103},
  pages = {8577--8582},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0601602103},
  url = {http://arxiv.org/abs/physics/0602124},
  urldate = {2020-09-09},
  abstract = {Many networks of interest in the sciences, including a variety of social and biological networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure has attracted considerable recent attention. One of the most sensitive detection methods is optimization of the quality function known as "modularity" over the possible divisions of a network, but direct application of this method using, for instance, simulated annealing is computationally costly. Here we show that the modularity can be reformulated in terms of the eigenvectors of a new characteristic matrix for the network, which we call the modularity matrix, and that this reformulation leads to a spectral algorithm for community detection that returns results of better quality than competing methods in noticeably shorter running times. We demonstrate the algorithm with applications to several network data sets.},
  archivePrefix = {arXiv},
  eprint = {physics/0602124},
  eprinttype = {arxiv},
  file = {C\:\\Users\\franc\\Zotero\\storage\\GNL5SZSW\\Newman - 2006 - Modularity and community structure in networks.pdf;C\:\\Users\\franc\\Zotero\\storage\\TWQU7ZDN\\0602124.html},
  keywords = {Condensed Matter - Statistical Mechanics,Physics - Data Analysis; Statistics and Probability,Physics - Physics and Society},
  number = {23}
}

@article{PoisBeli19a,
  title = {{{EcologicalNetworks}}.Jl: Analysing Ecological Networks of Species Interactions},
  shorttitle = {{{EcologicalNetworks}}.Jl},
  author = {Poisot, Timothée and Bélisle, Zachary and Hoebeke, Laura and Stock, Michiel and Szefer, Piotr},
  date = {2019},
  journaltitle = {Ecography},
  volume = {42},
  pages = {1850--1861},
  issn = {1600-0587},
  doi = {10.1111/ecog.04310},
  url = {https://www.onlinelibrary.wiley.com/doi/abs/10.1111/ecog.04310},
  urldate = {2020-09-01},
  abstract = {Networks are a convenient way to represent many interactions among ecological entities. The analysis of ecological networks is challenging for two reasons. First, there is a plethora of measures that can be applied (and some of them measure the same property). Second, the implementation of these measures is sometimes difficult. We present ’EcologicalNetworks.jl’, a package for the ‘Julia’ programming language. Using a layered system of types to represent several types of ecological networks, this packages offers a solid library of basic functions which can be chained together to perform the most common analyses of ecological networks.},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.04310},
  file = {C\:\\Users\\franc\\Zotero\\storage\\U7AK75LU\\Poisot et al. - 2019 - EcologicalNetworks.jl analysing ecological networ.pdf;C\:\\Users\\franc\\Zotero\\storage\\CU8DBDRY\\ecog.html},
  keywords = {ecological networks,graph theory,Julia},
  langid = {english},
  number = {11}
}

@article{PoisCirt16,
  title = {The Structure of Probabilistic Networks},
  author = {Poisot, Timothée and Cirtwill, Alyssa R. and Cazelles, Kévin and Gravel, Dominique and Fortin, Marie Josée and Stouffer, Daniel B.},
  date = {2016},
  journaltitle = {Methods in Ecology and Evolution},
  doi = {10.1111/2041-210X.12468},
  abstract = {There is a growing realization among community ecologists that interactions between species vary across space and time and that this variation needs to be quantified. Our current numerical framework to analyse the structure of species interactions, based on graph-theoretical approaches, usually do not consider the variability of interactions. As this variability has been show to hold valuable ecological information, there is a need to adapt the current measures of network structure so that they can exploit it. We present analytical expressions of key measures of network structured, adapted so that they account for the variability of ecological interactions. We do so by modelling each interaction as a Bernoulli event; using basic calculus allows expressing the expected value, and when mathematically tractable, its variance. When applied to non-probabilistic data, the measures we present give the same results as their non-probabilistic formulations, meaning that they can be generally applied. We present three case studies that highlight how these measures can be used, in re-analysing data that experimentally measured the variability of interactions, to alleviate the computational demands of permutation-based approaches, and to use the frequency at which interactions are observed over several locations to infer the structure of local networks. We provide a free and open-source implementation of these measures. We discuss how both sampling and data representation of ecological networks can be adapted to allow the application of a fully probabilistic numerical network approach.},
  file = {C\:\\Users\\franc\\Zotero\\storage\\3IN2SR5Y\\PoisCirt16-The structure of probabilitic networks.pdf},
  keywords = {Connectance,Degree distribution,Ecological networks,Modularity,Nestedness,Species interactions}
}

@article{PoisGrav14,
  title = {When Is an Ecological Network Complex? {{Connectance}} Drives Degree Distribution and Emerging Network Properties},
  author = {Poisot, Timothée and Gravel, Dominique},
  date = {2014},
  journaltitle = {PeerJ},
  doi = {10.7717/peerj.251},
  abstract = {Connectance and degree distributions are important components of the structure of ecological networks. In this contribution, we use a statistical argument and simple network generating models to show that properties of the degree distribution are driven by network connectance.We discuss the consequences of this finding for (1) the generation of random networks in null-model analyses, and (2) the interpretation of network structure and ecosystem properties in relationship with degree distribution. ©2014 Poisot et al.},
  file = {C\:\\Users\\franc\\Zotero\\storage\\DFBIZPCZ\\PoisGrav14-Connectance drives degree distribution and emerging network properties.pdf},
  keywords = {Connectance,Degree distribution,Ecological networks,Food webs,Network theory,Niche model,Null models,Power-law}
}

@article{StanKopp13,
  title = {The Ghost of Nestedness in Ecological Networks},
  author = {Staniczenko, Phillip P.A. and Kopp, Jason C. and Allesina, Stefano},
  date = {2013-01},
  journaltitle = {Nature Communications},
  volume = {4},
  pages = {1--6},
  publisher = {{Nature Publishing Group}},
  doi = {10.1038/ncomms2422},
  abstract = {Ecologists are fascinated by the prevalence of nestedness in biogeographic and community data, where it is thought to promote biodiversity in mutualistic systems. Traditionally, nestedness has been treated in a binary sense: species and their interactions are either present or absent, neglecting information on abundances and interaction frequencies. Extending nestedness to quantitative data facilitates the study of species preferences, and we propose a new detection method that follows from a basic property of bipartite networks: large dominant eigenvalues are associated with highly nested configurations. We show that complex ecological networks are binary nested, but quantitative preferences are non-nested, indicating limited consumer overlap of favoured resources. The spectral graph approach provides a formal link to local dynamical stability analysis, where we demonstrate that nested mutualistic structures are minimally stable. We conclude that, within the binary constraint of interaction plausibility, species preferences are partitioned to avoid competition, thereby benefiting system-wide resource allocation. © 2013 Macmillan Publishers Limited. All rights reserved.},
  file = {C\:\\Users\\franc\\Zotero\\storage\\SXPDLBNY\\Staniczenko, Kopp, Allesina - 2013 - The ghost of nestedness in ecological networks.pdf},
  keywords = {Ecological networks,Theoretical ecology},
  number = {1}
}

@article{Theb13,
  title = {Identifying Compartments in Presence–Absence Matrices and Bipartite Networks: Insights into Modularity Measures},
  shorttitle = {Identifying Compartments in Presence–Absence Matrices and Bipartite Networks},
  author = {Thébault, Elisa},
  date = {2013},
  journaltitle = {Journal of Biogeography},
  volume = {40},
  pages = {759--768},
  issn = {1365-2699},
  doi = {10.1111/jbi.12015},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.12015},
  urldate = {2020-09-09},
  abstract = {Aim The identification of compartments (i.e. clusters of overlapping species ranges across an environmental gradient) is an important methodological challenge for biogeographical studies. Recent developments in network theory offer promising perspectives on this issue using the measurement of modularity. A presence–absence matrix is modular if particular subgroups of species are mainly linked to particular subgroups of sites. Modularity is still rarely considered in biogeographical studies. Here, I compare different modularity indices to investigate which is the most appropriate for studying presence–absence matrices and similar types of networks, such as bipartite networks. Location Evaluation was based on 279 data sets from around the world. Methods I consider the three most commonly used modularity indices. One was developed for unipartite networks and the other two for bipartite networks. The performance of these indices (detection of a modular pattern, quality of compartment identification) is evaluated on test matrices of known compartmentalization levels with varying sizes and fills. Modularity patterns are then evaluated for 279 presence–absence matrices. Results The three modularity measures differ mainly in the identification of the compartments, and less in the statistical significance of the observed modularity. The modularity measure Q3 tends to perform best, whereas Q2 usually performs less well, especially for highly diverse and highly connected networks that include a few extremely well-connected nodes. These modularity indices all reveal the presence of modular patterns in presence–absence matrices. Main conclusions The choice of an appropriate modularity index is particularly important when we are interested in the composition of the different compartments. This analysis suggests that compartmentalized structures can be widespread in presence–absence matrices (about 40\% of the matrices considered here). Modularity should thus offer interesting perspectives on the understanding of biogeographical patterns.},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jbi.12015},
  file = {C\:\\Users\\franc\\Zotero\\storage\\4XTA7NU2\\jbi.html},
  keywords = {Biogeography,compartmentalization,modularity,nestedness,network theory,networks,power analysis,presence–absence matrices},
  langid = {english},
  number = {4}
}

@misc{Bromberger17,
  author       = {Seth Bromberger, James Fairbanks, and other contributors},
  title        = {JuliaGraphs/LightGraphs.jl: an optimized graphs package for the Julia programming language},
  year         = 2017,
  doi          = {10.5281/zenodo.889971},
  url          = {https://doi.org/10.5281/zenodo.889971}
}

@Article{CsarNepu06,
   title = {The igraph software package for complex network research},
   author = {Gabor Csardi and Tamas Nepusz},
   journal = {InterJournal},
   volume = {Complex Systems},
   pages = {1695},
   year = {2006},
   url = {https://igraph.org},
 }

gha_license_id: NOASSERTION


text:
@InProceedings{dawid10a,
  section = {theory},
  title = {Beware of the DAG!},
  author = {A. Philip Dawid},
  pages = {59--86},
  abstract = {Directed acyclic graph (DAG) models are popular tools for describing causal relationships and for guiding attempts to learn them from data.  They appear to supply a means of extracting causal conclusions from probabilistic conditional independence properties inferred from purely observational data.  I take a critical look at  this enterprise, and suggest that it is in need of more, and more explicit, methodological and philosophical justification than it typically receives. In particular, I argue for the value of a clean separation between formal causal language and intuitive causal assumptions.},
  pdf = {http://jmlr.org/proceedings/papers/v6/dawid10a/dawid10a.pdf},
}

repository: mreid/papersite

repo_name: mreid/papersite


text:
DESCRIPTION = "A Python binding for the v4l2 (video4linux2) userspace api, using ctypes"

LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://LICENSE;md5=751419260aa954499f7abaabaa882bbe"

SRC_URI = "git://github.com/qtec/python-v4l2"
SRCREV = "a185ceac598547fa5626ebfb71bfd5e5c53d60db"

PV = "1.3+git${SRCPV}"

S = "${WORKDIR}/git/v4l2wrapper"

inherit setuptools3

RDEPENDS_${PN} += "python3-logging python3-ctypes python3-v4l2 python3-fcntl python3-numbers python3-numpy python3-mmap"

repository: qtec/meta-qtec-core

repo_name: qtec/meta-qtec-core


text:
% This file was created with JabRef 2.9.2.
% Encoding: UTF-8

@MISC{Eagle2013,
  author = {Bob Eagle},
  title = {Einstein's Field Equations - For Beginners!},
  howpublished = {Youtube Video},
  year = {2013},
  note = {http://www.bobeagle.co.uk/drphysicsa.html},
  keywords = {Einstein's Field Equations for General Relativity - including the
	Metric Tensor, Christoffel symbols, Ricci Cuvature Tensor, Curvature
	Scalar, Stress Energy Momentum Tensor and Cosmological Constant.},
  owner = {kkunzelm},
  timestamp = {2014.05.18},
  url = {https://www.youtube.com/watch?v=foRPKAKZWx8}
}

@MISC{Gebhardt2014,
  author = {Thomas Gebhardt},
  title = {Einführung in die Kombinatorik},
  year = {2014},
  owner = {kkunzelm},
  timestamp = {2014.05.23},
  url = {http://www.zum.de/Faecher/Materialien/gebhardt/stochastik/Kombin.html}
}

@BOOK{Grinfeld2013,
  title = {Introduction to Tensor Analysis and the Calculus of Moving Surfaces},
  publisher = {Springer},
  year = {2013},
  author = {Pavel Grinfeld},
  owner = {kkunzelm},
  timestamp = {2014.05.18}
}

@ARTICLE{Poessel2010,
  author = {Markus Pössel},
  title = {Vom Äquivalenzprinzip zur Lichtablenkung},
  journal = {Einstein Online},
  year = {2010},
  volume = {04},
  pages = {1120},
  owner = {kkunzelm},
  timestamp = {2014.05.22},
  url = {http://www.einstein-online.info/vertiefung/AequivalenzLicht}
}

@ARTICLE{Poessel2010a,
  author = {Markus Pössel},
  title = {Kabine, Schwerkraft und Rakete: Das Äquivalenzprinzip},
  journal = {Einstein Online},
  year = {2010},
  volume = {04},
  pages = {1111},
  owner = {kkunzelm},
  timestamp = {2014.05.22},
  url = {http://www.einstein-online.info/vertiefung/Aequivalenzprinzip?set_language=de}
}

@MISC{Ratcliffe2004,
  author = {Philip G. Ratcliffe},
  title = {The Tensor Package for {LATEX2e}},
  year = {2004},
  owner = {kkunzelm},
  timestamp = {2014.05.18},
  url = {http://get-software.net/macros/latex2e/contrib/tensor/tensor.pdf}
}

@MISC{Rupaner2009,
  author = {Julia Rupaner},
  title = {{LATEX-Kurs: Mathematische Formeln}},
  howpublished = {Technische Universität München. 15. April 2009.},
  year = {2009},
  owner = {kkunzelm},
  timestamp = {2014.05.18},
  url = {http://www.ma.tum.de/foswiki/pub/Ferienkurse/WiSe0809/LaTeX/2_Mathematik_print.pdf}
}

@MISC{Susskind2008,
  author = {Leonard Susskind},
  title = {The Theoretical Minimum: General Relativity},
  year = {2008},
  note = {Video lectures.},
  keywords = {The theoretical minimum. Einstein. General Relativity.},
  owner = {kkunzelm},
  timestamp = {2014.05.18},
  url = {http://theoreticalminimum.com/courses/general-relativity/2008/fall}
}

@MISC{MetricTensor,
  title = {{M}etrischer {T}ensor},
  year = {2014},
  owner = {kkunzelm},
  timestamp = {2014.05.23},
  url = {https://de.wikipedia.org/wiki/Metrischer_Tensor}
}

@MISC{WikipediaAequivalenzprinzip2014,
  title = {Äquivalenzprinzip ({P}hysik)},
  year = {2014},
  owner = {kkunzelm},
  timestamp = {2014.05.22},
  url = {http://de.wikipedia.org/wiki/Äquivalenzprinzip_(Physik)}
}

@comment{jabref-meta: selector_publisher:}

@comment{jabref-meta: selector_author:}

@comment{jabref-meta: selector_journal:}

@comment{jabref-meta: selector_keywords:}

repository: kkunzelm/ART-Skript

repo_name: kkunzelm/ART-Skript


text:
@article{Patrick2021,
 abstract = {River managers strive to use the best available science to sustain biodiversity and ecosystem function. To achieve this goal requires consideration of processes at different scales. Metacommunity theory describes how multiple species from different communities potentially interact with local-scale environmental drivers to influence population dynamics and community structure. However, this body of knowledge has only rarely been used to inform management practices for river ecosystems. In this article, we present a conceptual model outlining how the metacommunity processes of local niche sorting and dispersal can influence the outcomes of management interventions and provide a series of specific recommendations for applying these ideas as well as research needs. In all cases, we identify situations where traditional approaches to riverine management could be enhanced by incorporating an understanding of metacommunity dynamics. A common theme is developing guidelines for assessing the metacommunity context of a site or region, evaluating how that context may affect the desired outcome, and incorporating that understanding into the planning process and methods used. To maximize the effectiveness of management activities, scientists, and resource managers should update the toolbox of approaches to riverine management to reflect theoretical advances in metacommunity ecology. This article is categorized under: Water and Life > Nature of Freshwater Ecosystems Water and Life > Conservation, Management, and Awareness Water and Life > Methods. © 2021 The Authors. WIREs Water published by Wiley Periodicals LLC.},
 affiliation = {Department of Biological Sciences, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, United States; Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States; Department of Biological Sciences, Virginia Tech, Virginia, United States; Department of Watershed Sciences, Ecology Center, and National Aquatic Monitoring Center, Utah State University, Logan, UT, United States; United States Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, AZ, United States; Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States; Institute of Biosciences, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil; University of Maryland, Baltimore, MD, United States; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; United States Environmental Protection Agency – Office of Water, Washington, DC, United States},
 art_number = {e1557},
 author = {Patrick, C.J. and Anderson, K.E. and Brown, B.L. and Hawkins, C.P. and Metcalfe, A. and Saffarinia, P. and Siqueira, T. and Swan, C.M. and Tonkin, J.D. and Yuan, L.L.},
 author_keywords = {biomonitoring;  conservation;  dispersal;  invasive species;  local sorting;  network connectivity;  restoration;  spatial},
 document_type = {Review},
 doi = {10.1002/wat2.1557},
 journal = {Wiley Interdisciplinary Reviews: Water},
 note = {cited By 0},
 number = {6},
 source = {Scopus},
 title = {The application of metacommunity theory to the management of riverine ecosystems},
 url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114452825&doi=10.1002%2fwat2.1557&partnerID=40&md5=a3047821242657e8da0e6fdb1622ba28},
 volume = {8},
 year = {2021}
}

repository: tonkinlab/tonkinlab

repo_name: tonkinlab/tonkinlab


text:
require videoplayer.inc

SRC_URI[md5sum] = "1956b3e2234107fda908fd0d73bf33a2"
SRC_URI[sha256sum] = "72fb707b0bc71c006a38d14c9b7c918cb0edd54756c1e820b52dad12ec7e77c5"

SRC_URI += "file://videoplayer-gstreamer-no-fb1.patch"
SRC_URI += "file://videoplayer-gst-launch-adapt-screen.patch"

repository: rousis/meta-atmel

repo_name: rousis/meta-atmel


text:
import React from "react";

import Principle from "../../components/WCAGPrinciple1";

import Wrapper from "../../components/Wrapper";
import SlideHeading from "../../components/SlideHeading";
import EnglishS from "../../components/EnglishS";

export default class WCAGPrinciple1 extends React.Component {
  render() {
    return (
      <Wrapper>
        <SlideHeading style={{ fontWeight: "normal" }}>
          ۴ اصل <EnglishS>WCAG 2.0</EnglishS>
        </SlideHeading>
        <Principle large />
      </Wrapper>
    );
  }
}

repository: ardalann/InclusiveIran

repo_name: ardalann/InclusiveIran

gha_language: JavaScript

extension: js


text:
DESCRIPTION = "Qt embedded interface for choosing which configured network \
to connect to. It also provides a method for browsing 802.11 SSID scan \
results, an event history log of messages generated by wpa_supplicant, and \
a method to add or edit wpa_supplicant networks."
SECTION = "network"
LICENSE = "GPL BSD"
HOMEPAGE = "http://hostap.epitest.fi/wpa_supplicant/"
RDEPENDS_${PN} = "wpa-supplicant"

SRCREV = "653c4893be17d12ef7bc6e941b765c92c1e4a161"
PR = "r4"
PV = "0.7.3+0.8.0-rc"
PR_append = "+gitr${SRCPV}"

DEFAULT_PREFERENCE = "-1"

SRC_URI = "git://w1.fi/srv/git/hostap.git;protocol=git \
          file://0001-wpa_gui-make-the-networkconfig-dialog-scrollable.patch \
          file://0002-wpa-gui-e-fix-display-issue-on-small-screen.patch \
          file://0003-wpa-gui-trigger-udhcpc-on-connection-to-new-access-p.patch \
          file://connection_script.sh"

S = "${WORKDIR}/git/wpa_supplicant/wpa_gui-qt4"

inherit qt4e
ARM_INSTRUCTION_SET = "arm"

do_install () {
       install -d ${D}${bindir}
       install -d ${D}${datadir}/wpa_gui
       install -d ${D}${datadir}/applications
       install -m 755 wpa_gui ${D}/${bindir}/wpa_gui-e
       install -m 0755 ${WORKDIR}/connection_script.sh ${D}${datadir}/wpa_gui
}

FILES_${PN} += "${datadir}/wpa_gui/connection_script.sh"


text:
@article{DiasIoT2022,
  title   = {Designing and Constructing Internet-of-Things Systems: An Overview of the Ecosystem},
  journal = {Internet of Things},
  year    = {2022},
  issn    = {2542-6605},
  author  = {João Pedro Dias and André Restivo and Hugo Sereno Ferreira}
}

gha_language: HTML


text:
@MISC{Rafelsberger2007,
  author = {Walter Rafelsberger},
  title = {3D family tree visualization using Rhizome Navigation},
  howpublished = {part of a documentary by Benedikt Bjarnason},
  year = {2007},
  abstract = {For an upcoming documentary by Benedikt Bjarnason, Rhizome Navigation was used to create animated visualizations of large genealogy data sets. The graph layout was done using an adapted force-directed algorithm and features more than 3300 persons. What set's it apart from similar visualizations is the capability to show far more complex relationships by breaking up the classic tree structure and following a more rhizome-like approach - and of course the sheer amount of relationships shown.},
  url = {http://www.rafelsberger.at/node/genealogy-visualization}
}

repository: vis-au/treevisnet

repo_name: vis-au/treevisnet


text:
@article{Stefanini_etal14,
 author = {Stefanini, F. and Neftci, E. and Sheik, S. and Indiveri, G.},
 journal = {Frontiers in Neuroinformatics},
 keyword = {own},
 link = {http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00073/pdf},
 month = {July},
 note = {(equal contrib. FS, EN, SS)},
 title = {PyNCS: a kernel for high-level configuration and definition of neuromorphic electronic systems},
 volume = {8},
 year = {2014}
}

repository: eneftci/academic-kickstart

repo_name: eneftci/academic-kickstart


text:
import React from "react";
import { Box, Container, Modal, Typography } from "@material-ui/core";
import { makeStyles } from "@material-ui/core/styles";
import { kvStrings, getSaves } from "../utilities/helpers";
import Scores from "./Scores";
import Stat from "./Stat";
import Ability from "./Ability";

const useStyles = makeStyles((theme) => ({
  title: {
    color: "#501e0e",
    fontFamily: "Times, 'Times New Roman', Georgia, serif",
    fontVariant: "small-caps",
    letterSpacing: ".01em",
  },
  divider: {
    borderBottom: "2px solid #a40b07",
  },
}));

const MonsterView = (props) => {
  const { data } = props;
  const classes = useStyles();
  const {
    actions,
    alignment,
    armor_class,
    armor_desc,
    challenge_rating,
    condition_immunities,
    damage_immunities,
    damage_resistances,
    damage_vulnerabilities,
    hit_dice,
    hit_points,
    languages,
    legendary_actions,
    legendary_desc,
    name,
    reactions,
    senses,
    special_abilities,
    size,
    type,
  } = data;

  const speed = kvStrings(data.speed);
  const saving_throws = getSaves(data);
  const skills = kvStrings(data.skills);

  return (

      <Box component="header" className={classes.divider}>
        <Typography
          id="monster-title"
          className={classes.title}
          variant="h5"
          component="h1"
        >
          {name}
        </Typography>
        <Box component="p" mt={0} fontStyle="oblique" id="monster-description">
          {`${size} ${type}, ${alignment}`}
        </Box>
      </Box>
      <Box component="section" className={classes.divider}>

          <Stat data={{ armor_class: [`${armor_class} (${armor_desc})`] }} />
          <Stat data={{ hit_points: [`${hit_points} (${hit_dice})`] }} />
          <Stat data={{ speed }} />

      </Box>
      <Box component="section" className={classes.divider}>
        <Scores scores={data} />
      </Box>
      <Box component="section" className={classes.divider}>

          <Stat data={{ saving_throws }} />
          <Stat data={{ skills }} />
          <Stat data={{ damage_vulnerabilities }} />
          <Stat data={{ damage_resistances }} />
          <Stat data={{ damage_immunities }} />
          <Stat data={{ condition_immunities }} />
          <Stat data={{ senses }} />
          <Stat data={{ languages }} />
          <Stat data={{ challenge_rating }} />

      </Box>
      <Ability data={{ special_abilities }} hide={true} />
      <Ability data={{ actions }} />
      <Ability data={{ legendary_actions }}>

{legendary_desc}

      </Ability>
      <Ability data={{ reactions }} />

  );
};

export default MonsterView;

repository: jkrayer/summoner

repo_name: jkrayer/summoner


text:
require bug-app.inc

DESCRIPTION = "A set of test cases for the Camera module. Works with Blueback  test runner."
HOMEPAGE = "http://buglabs.net/applications/CameraTestCase"

DEPENDS += "com.buglabs.app.blueback com.buglabs.bug.menu com.buglabs.bug.module.camera com.buglabs.common "

PV = "7"

SRC_LINK = "http://buglabs.net/program_version/download/610"

APIVERSION = ""

COMPATIBLE_MACHINE = "bug"
PACKAGE_ARCH = "${MACHINE_ARCH}"


text:
@article{Blagov2018,
	title = {Financial crises and time-varying risk premia in a small open economy: a {Markov}-switching {DSGE} model for {Estonia}},
	volume = {54},
	issn = {0377-7332},
	url = {http://link.springer.com/10.1007/s00181-017-1256-z},
	doi = {10.1007/s00181-017-1256-z},
	number = {3},
	journal = {Empirical Economics},
	author = {Blagov, Boris},
	month = may,
	year = {2018},
	note = {Publisher: Springer Berlin Heidelberg
ISBN: 0018101712},
	keywords = {currency board, Currency board, Estonia, exchange rate credibility, Exchange rate credibility, Exchange Rate Credibility, markov-switching dsge, Markov-switching DSGE, Markov-Switching DSGE},
	pages = {1017--1060}
}


text:
@inproceedings{2022-DPRB-CHIUW,
 author = {Zhihui Du and Joseph Patchett and Oliver Alvarado Rodriguez and David A. Bader},
 booktitle = {The 9th Annual {Chapel} Implementers and Users Workshop ({CHIUW})}},
 groups = {Edited},
 title = {Truss Analytics Algorithms and Integration in {Arkouda}},
 year = {2022},
 url       = {},
 doi={},
 abstract = {The K-Truss of a graph is a cohesive subgraph that has been widely used for community detection in applications such as social networks and security analysis. In this paper, we first propose one optimized triangle search kernel with a few operations that can be used in both triangle counting and triangle search to replace the existing list intersection method. Based on the optimized kernel, three truss analytics algorithms, an optimized K-Truss parallel algorithm, a maximal K-Truss parallel algorithm, and a Truss decomposition parallel algorithm, are developed to efficiently enable different kinds of graph analysis. Moreover, all proposed parallel algorithms have been implemented in the highly-productive parallel language Chapel and integrated into the open-source framework Arkouda. Experimental results compared with the existing list intersection-based method show that for both synthetic and real-world graphs, the proposed method can significantly improve the performance of truss analysis on large graphs. The implemented method is publicly available from GitHub.}
}

gha_language: Shell


text:
require nodejs5.inc

INC_PR = "r1"

LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://LICENSE;md5=ee90ba97d933fc8d56e97812b7dd62e9"

SRC_URI[src.md5sum] = "285e108abd8f5048c82ee7cdb11825f1"
SRC_URI[src.sha256sum] = "25b2d3b7dd57fe47a483539fea240a3c6bbbdab4d89a45a812134cf1380ecb94"

repository: siemens/meta-nodejs

repo_name: siemens/meta-nodejs


text:
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://${COREBASE}/meta/files/common-licenses/GPL-2.0;md5=801f80980d171dd6425610833a22dbe6"

#FILESEXTRAPATHS_prepend := "${THISDIR}/service_file:"

SRC_URI = " \
    git://github.com/rockchip-linux/rkwifibt.git \
    file://config.txt \
"
#SRCREV = "456b6008e495d40793eba5c8abcad8d09c65f6ea"
SRCREV = "bcfe5dc630ec1a0d129101bc3abae208ba848ccc"
#RDEPENDS_${PN} += "linux-firmware-rtl8723b"

S = "${WORKDIR}/git/firmware/broadcom"

#PN=rkwifi-${PV}
TARGET_CC_ARCH += "${LDFLAGS}"
#PACKAGES =+ "${PN}-rkwifi"
#inherit systemd

#SYSTEMD_SERVICE_${PN} = "bluetooth_rk.service"

do_install () {
        install -d ${D}/lib/firmware
#        cp -rf ${S} ${D}/lib/firmware
#        install -m 0755 ${S}/all/wifi/fw_bcm43438a0.bin ${D}/lib/firmware/fw_bcm43438a0.bin
#        install -m 0755 ${S}/all/wifi/nvram_ap6212.txt ${D}/lib/firmware/nvram_ap6212.txt
        install -m 0755 ${S}/AP6236/wifi/fw_bcm43436b0.bin ${D}/lib/firmware/fw_bcm43438a0.bin
        install -m 0755 ${S}/AP6236/wifi/nvram_ap6236.txt ${D}/lib/firmware/nvram_ap6212.txt
        install -m 0755 ${WORKDIR}/config.txt ${D}/lib/firmware/config.txt
        install -m 0755 ${S}/AP6236/wifi/fw_bcm43436b0.bin ${D}/lib/firmware/fw_bcm43436b0.bin
        install -m 0755 ${S}/AP6236/wifi/nvram_ap6236.txt ${D}/lib/firmware/nvram_ap6236.txt

#        install -m 0755 ${S}/fw_bcm43436b0_apsta.bin ${D}/lib/firmware/fw_bcm43436b0.bin
}
FILES_SOLIBSDEV = ""
FILES_${PN} += " /lib /lib/firmware  /lib/firmware/* "

#PACKAGES = "${PN}-rkwifi"
#FILES_${PN} += " ${D}/lib/firmware/* "

repository: clodpi/meta-rockchip

repo_name: clodpi/meta-rockchip


text:
@ARTICLE{ADA03,
  author = {{American Diabetes Association}},
  title = {Diabetes Update},
  journal = {Nursing},
  year = 2003,
  month = nov,
  volume = {Suppl},
  pages = {19--20, 24}}

@BOOK{AG98,
  editor = {S. V. Ambudkar and M. M. Gottesman},
  title = {{ABC} Transporters: Biomedical, Cellular, and Molecular Aspects},
  publisher = {Academic Press},
  address = {San Diego (CA)},
  year = 1998,
  volume = 292,
  series = {Methods in enzymology}}

@PRESENTATION{Ant03,
  author = {Antani, S. and Long, L. R. and Thoma, G. R. and Lee, D. J.},
  title = {Anatomical Shape Representation in Spine X-ray Images. {P}aper presented at: {VIIP 2003}. {P}roceedings of the 3rd {IASTED} {I}nternational {C}onference on {V}isualization, {I}maging and {I}mage {P}rocessing},
  month = {2003 Sep~8--10},
  address = {Benalmadena, Spain}}

@INPROCEEDINGS{Are05,
  author = {Arendt, T.},
  title = {Alzheimer's Disease as a Disorder of Dynamic Brain Self-Organization},
  editor = {van Pelt, J. and Kamermans, M. and Levelt, C. N. and van Ooyen, A. and Ramakers, G. J. and Roelfsema, P. R.},
  booktitle = {Development, dynamics, and pathology of neuronal networks: from molecules to functional circuits. Proceedings of the 23rd International Summer School of Brain Research},
  month = {2003 Aug~25--29},
  organization = {Royal Netherlands Academy of Arts and Sciences},
  address = {Amsterdam, the Netherlands},
  publisher = {Amsterdam (Netherlands): Elsevier},
  year = 2005,
  pages = {355--378}}

@BOOK{Ber01,
  editor = {Bergstresser, P. R. and Takashima, A.},
  title = {Gamma-delta T cells},
  address = {New York (NY)},
  publisher = {Karger},
  year = 2001,
  series = {Chemical immunology},
  volume = 79}

@ARTICLE{BGC04,
  author = {Berrino, F. and Gatta, G. and Crosignani, P.},
  year = 2004,
  title = {[{C}ase-control Evaluation of Screening Efficacy]},
  journal = {Epidemiol. Prev.},
  volume = 28,
  pages = {354--359},
  note = {Italian}}

@ARTICLE{Bla89,
  author =  {Black, H. R.},
  title = 	{Evaluation of the Elderly Hypertensive},
  journal = {Geriatrics},
  year = 	1989,
  volume = 	{44 Suppl B},
  pages = 	{15--19}}

@BOOK{Bra04,
  editor = {Bradley, W. G. and Daroff, R. B. and Fenichel, G. M. and Jankovic, J.},
  title = {Neurology in Clinical Practice},
  publisher = {Butterworth-Heinemann},
  year = 2004,
  volume = {1, Principles of diagnosis and management},
  address = {Philadelphia (PA)},
  edition = {Fourth}}

@MANUAL{CEN05,
  author = {{European Committee for Electrotechnical Standardization (CENELEC)}},
  title = {Measurement and Assessment of Personal Exposures to Incoherent Optical Radiation -- Part 2: Visible and Infrared Radiation Emitted by Artificial Sources in the Workplace},
  address = {Brussels},
  organization = {CENELEC},
  year = 2005,
  note = {Standard No. EN 14255-2:2005}}

@PRESENTATION{Cha06,
  author = {Chasman, J. and Kaplan, R. F.},
  title = {The effects of occupation on preserved cognitive functioning in dementia. Poster session presented at: Excellence in clinical practice. 4th Annual Conference of the American Academy of Clinical Neuropsychology},
  month = {2006 Jun~15--17},
  address = {Philadelphia, PA}}

@INPROCEEDINGS{deT98,
  author = {de The, G.},
  title = {Les priorit{\'e}s de sant{\'e} dans les pays en d{\'e}veloppement},
  booktitle = {Colloque Energie Solaire et Sant{\'e} dans les Pays en D{\'e}veloppement = Conference on Solar Energy and Health Care in Developing Countries},
  month = {1991 Nov~4--7},
  address = {Paris},
  publisher = {London: Tec \& Doc},
  year = {c1998},
  pages = {19--29},
  note = {French}}

@PROCEEDINGS{DCK03,
  editor = {Dostorovsky, J. O. and Carr, D. B. and Koltzenburg, M.},
  title = {Proceedings of the 10th World Congress on Pain},
  month = {2002 Aug~17--22},
  address = {San Diego, CA},
  publisher = {Seattle (WA): IASP Press},
  year = 2003}

@ARTICLE{ElP05,
  title = {La ``gripe del pollo'' vuela can las aves silvestres [{T}he ``bird flu'' flies with the wild birds]},
  journal = {El Pais (Madrid) (Ed. Europa)},
  year = 2005,
  month = jul # "~17",
  pages = {28 (col.~1)},
  note = {Spanish}}

@BOOK{Eva04,
  editor = {Evans, L. K. and Lang, N. M.},
  title = {Academic Nursing Practice},
  address = {New York (NY)},
  publisher = {Springer},
  year = {c2004},
  series = {Springer series on the teaching of nursing}}

@BOOK{Fla04,
  author = {{Flaws B, translator}},
  title = {The Classic of Difficulties: A Translation of the {N}an {J}ing},
  edition = {Third},
  address = {Boulder (CO)},
  publisher = {Blue Poppy Press},
  year = 2004}

@ARTICLE{FM97,
  title = {Neue {N}ifedipin-{Z}ubereitung erm{\"o}glicht t{\"a}gliche {E}inmalgabe [{N}ew nifedipine preparation makes single daily dose possible]},
  journal = {Fortschr. Med.},
  year = 1997,
  month = nov # "~30",
  volume = 115,
  number = 33,
  pages = {[following p. 54]},
  note = {German}}

@BOOK{FBW04,
  title = {Models and Perspectives in Health Psychology},
  publisher = {American Psychological Association},
  year = 2004,
  editor = {Frank, R. G and Baum, A. and Wallander, J. L.},
  volume = 3,
  series = {Boll TJ, editor. Handbook of clinical health psychology},
  address = {Washington (DC)}}

@ARTICLE{Gau05,
  author = {Gaul, G.},
  title = {When Geography Influences Treatment Options},
  journal = {Washington Post (Maryland Ed.)},
  year = 2005,
  month = jul # "~24",
  note = {Sect.~A:12 (col.~1)}}

@ARTICLE{HN05,
  title = {Pelvic Floor Exercise Can Reduce Stress Incontinence},
  journal = {Health News},
  year = 2005,
  volume = 11,
  number = 4,
  pages = {11}}

@INPROCEEDINGS{Hor98,
  author = {Horrobin, D. F. and Lampinskas, P.},
  title = {The commercial development of food plants used as medicines},
  editor = {Prendergast, H. D. and Etkin, N. L. and Harris, D. R. and Houghton, P. J.},
  booktitle = {Plants for food and medicine. Proceedings of the Joint Conference of the Society for Economic Botany and the International Society for Ethnopharmacology},
  month = {1996 Jul~1--6},
  address = {London},
  publisher = {London: Royal Botanic Gardens, Kew},
  year = 1998,
  pages = {75--81}}

@BOOK{Ind01,
  author = {Indryan, A. and Sarmukaddam, S. B.},
  title = {Medical Biostatistics},
  address = {New York (NY)},
  publisher = {Marcel Dekker},
  year = 2001,
  series = {Biostatistics},
  number = 7}

@BOOK{Jen05,
  author = {Jenkins, P. F.},
  title = {Making Sense of the Chest X-ray: A Hands-on Guide},
  address = {New York (NY)},
  publisher = {Oxford University Press},
  year = 2005}

@ARTICLE{KKZ06,
  author = {Klose, R. J. and Kallin, E. M. and Zhang, Y.},
  title = {{JmjC}-domain-containing proteins and histone demethylation},
  journal = {Nat. Rev. Genet.},
  year = 2006,
  volume = 7,
  pages = {715--727}}

@INPROCEEDINGS{Leo04,
  author = {Leonard, K. J. and Winkelman, W.},
  title = {Developing Electronic Patient Records: Employing Interactive Methods to Ensure Patient Involvement},
  editor = {Ferreira de Oliveira, M. J.},
  booktitle = {Accessibility and quality of health services. Proceedings of the 28th Meeting of the European Working Group on Operational Research Applied to Health Services (ORAHS)},
  month = {2002 Jul~28--Aug~2},
  address = {Rio de Janeiro, Brazil},
  publisher = {Frankfurt (Germany): Peter Lang},
  year = {c2004},
  pages = {241--255}}

@BOOK{Luz85,
  author = {Luzikov, V. N.},
  title = {Mitochondrial Biogenesis and Breakdown. {Galkin~AV, translator; Roodyn~DB, editor}},
  address = {New York (NY)},
  publisher = {Consultants Bureau},
  year = 1985}

@ARTICLE{Lyd08,
  author = {Lyderson, K},
  title = {Risk of Disease Rises with Water Temperatures},
  journal = {Washington Post [Internet]},
  year = {{2008 Oct~20 [cited 2008 Dec~19]}},
  pages = {A08},
  url = {http://www.washingtonpost.com/wp-dyn/content/article/2008/10/19/AR2008101901533.html},
  note = {Article includes a correction}}

@ARTICLE{Mac04,
  author = {MacGregor, R. J.},
  title = {A Functional View of Consciousness and its Relations in Brain},
  journal = {J. Integr. Neurosci.},
  year = 2004,
  volume = 3,
  number = 3,
  pages = {253--266}}

@ARTICLE{Men05,
  author = {Meneton, P. and Jeunemaitre, X. and de Wardener, H. E. and MacGregor, G. A.},
  title = {Links Between Dietary Salt Intake, Renal Salt Handling, Blood Pressure, and Cardiovascular Diseases},
  journal = {Physiol. Rev.},
  year = 2005,
  month = apr,
  volume = 85,
  pages = {679--715}}

@ARTICLE{NBK07,
  author = {Nallamothu, B. K. and Bradley, E. H. and Krumholz, H. M.},
  title = {Time to treatment in primary percutaneous coronary intervention},
  journal = {N. Engl. J. Med.},
  year = 2007,
  volume = 357,
  number = {},
  pages = {1631--1638},
  month = oct # "~18"}

@TECHREPORT{HBPEP,
  author = {{National High Blood Pressure Education Program (US)}},
  title = {The Fourth Report on the Diagnosis of High Blood Pressure in Children. {R}ev. ed.},
  address = {Bethesda (MD)},
  institution = {National Heart, Lung, and Blood Institute (US)},
  year = 2005,
  note = {(NIH publication; no.~05-5267)}}

@ARTICLE{NYT05,
  author = {},
  title = {Taking Steps Back to Normal after Novel Rabies Therapy},
  journal = {New York Times (National Ed.)},
  year = 2005,
  month = dec # "~25",
  volume = 155,
  number = 53439,
  pages = {23 (col.~3)},
  note = {Milwaukee, Dec~24}}

@ARTICLE{NYT06,
  author = {},
  title = {Major Decline in {U.S.} Deaths is Recorded},
  journal = {New York Times (Washington Final)},
  year = 2006,
  month = apr # "~20",
  note = {Sect.~A:14 (col.~6)}}

@BOOK{Och00,
  author = {Ochoa, S.},
  title = {Base molecular de la expresion del mensaje genetico [{M}olecular Basis of Gene Expression]},
  address = {Madrid},
  publisher = {Consejo Superior de Investigaciones Cientificas},
  year = 2000,
  note = {Spanish}}

@PRESENTATION{Pat03,
  author = {Patrias, K.},
  title = {Computer-compatible writing and editing. Paper presented at: Interacting with the digital environment: modern scientific publishing. 46th Annual Meeting of the Council of Science Editors},
  month = {2003 May~3--6},
  address = {Pittsburgh, PA}}

@ARTICLE{PTP03,
  author = {Prokai-Tatrai, K. and Prokai, L.},
  title = {Modifying Peptide Properties by Prodrug Design for Enhanced Transport into the {CNS}},
  journal = {Prog. Drug Res.},
  year = 2003,
  volume = 61,
  pages = {155--188}}

@INPROCEEDINGS{Ric03,
  author = {Rice, A. S. and Farquhar-Smith, W. P. and Bridges, D. and Brooks, J. W.},
  title = {Canabinoids and Pain},
  editor = {Dostorovsky, J. O. and Carr, D. B. and Koltzenburg, M.},
  booktitle = {Proceedings of the 10th World Congress on Pain},
  month = {2002 Aug~17--22},
  address = {San Diego, CA},
  publisher = {Seattle (WA): IASP Press},
  year = 2003,
  pages = {437--468}}

@INBOOK{Rif06,
  author = {Riffenburgh, R. H.},
  title = {Statistics in Medicine},
  edition = {Second},
  address = {Amsterdam (Netherlands)},
  publisher = {Elsevier Academic Press},
  year = 2006,
  chapter = {24, Regression and correlation methods},
  pages = {447--486}}

@MASTERSTHESIS{Rog05,
  author = {Roguskie, J. M.},
  title = {The role of \emph{Pseudomonas aeruginosa} 1244 pilin glycan in virulence},
  address = {Pittsburgh (PA)},
  school = {Duquesne University},
  year = 2005}

@PROCEEDINGS{SSM03,
  editor = {Satoh, K. and Suzuki, S. and Matsunaga, M.},
  title = {Advances in brain research: cerebrovascular disorders and neurodegeneration. Proceedings of the 6th Hirosaki International Forum of Medical Science},
  month = {2002 Oct~15--16},
  address = {Hirosaki, Japan},
  publisher = {Amsterdam (Netherlands): Elsevier},
  year = 2003,
  series = {Excerpta Medica international congress series},
  number = 1251}

@INCOLLECTION{Sum03,
  author = {Sumner, P. and Mollon, J. D.},
  title = {Did Primate Trichromacy Evolve for Frugivory or Folivory?},
  editor = {Mollon, J. D. and Pokorny, J. and Knoblauch, K.},
  booktitle = {Normal and Defective Colour Vision},
  address = {New York (NY)},
  publisher = {Oxford University Press},
  year = 2003,
  pages = {21--30}}

@PROCEEDINGS{vP05,
  editor = {van Pelt, J. and Kamermans, M. and Levelt, C. N. and van Ooyen, A. and Ramakers, G. J. A. and Roelfsema, P. R.},
  title = {Development, dynamics, and pathology of neuronal networks: from molecules to functional circuits. Proceedings of the 23rd International Summer School of Brain Research},
  month = {2003 Aug~25--29},
  organization = {Royal Netherlands Academy of Arts and Sciences},
  address = {Amsterdam, the Netherlands},
  publisher = {Amsterdam: Elsevier},
  year = 2005,
  series = {Progress in brain research},
  volume = 147}

@ARTICLE{Ved06,
  author = {Vedantam, S.},
  title = {When Staying Cool Seems Better Than Being Bad},
  journal = {Washington Post (Final Ed.)},
  year = 2006,
  month = aug # "~7",
  note = {Sect.~A:2 (col.~3 ). Part of a weekly series of stories about the sociology and psychology behind news events}}

@ARTICLE{VMD07,
  author = {Veronesi, U. and Maisonneuve, P. and Decensi, A.},
  title = {Tamoxifen: an enduring star},
  journal = {J. Natl Cancer Inst.},
  year = 2007,
  volume = 99,
  number = 4,
  pages = {258--260},
  month = feb # "~21"}

@BOOK{Wen95,
  author = {Wenger, N. K. and Sivarajan Froelicher, E. and Smith, L. K. and Ades, P. A. and Berra, K. and Blumenthal, J. A. and Certo, C. M. E. and Dattilo, A. M. and Davis, D. and DeBusk, R. F. and others},
  title = {Cardiac Rehabilitation},
  publisher = {Agency for Health Care Policy and Research (US)},
  address = {Rockville (MD)},
  year = 1995}

@ARTICLE{Wil04,
  author = {Wilkniss, S. M. and Hunter, R. H. and Silverstein, S. M.},
  title = {Traitement multimodal de l'agressivit{\'e} et de la violence chez des personnes souffrant de psychose [{M}ultimodal Treatment of Aggression and Violence in Individuals with Psychosis]},
  journal = {Sante Ment Que},
  year = {2004 Autumn},
  volume = 29,
  number = 2,
  pages = {143--174},
  note = {French}}

@PHDTHESIS{Zha05,
  author = {Zhao, C.},
  title = {Development of Nanoelectrospray and Application to Protein Research and Drug Discovery},
  address = {Buffalo (NY)},
  school = {State University of New York at Buffalo},
  year = 2005}

repository: gilberto-sassi/geo-okfd

repo_name: gilberto-sassi/geo-okfd


text:
DESCRIPTION = "QCOM Firmware for Google Pixel 5a 5G"

FW_QCOM_NAME = "barbet"
AOSP_BUILD = "sp2a.220405.003"
CHECKSUM_vendor = "c3cdaef9"

SRC_URI[vendor.sha256sum] = "93b12611038f8c54d3a57f95906839ed1c3315a6b47e0883cf1890dfca6eb728"

require recipes-bsp/firmware-nexus/firmware-qcom-pixel.inc

repository: vchong/meta-qcom

repo_name: vchong/meta-qcom

gha_language: BitBake


text:
@inproceedings{Le13,
  pdf = {http://jmlr.org/proceedings/papers/v29/Le13.pdf},
  title = {Generalized Aitchison Embeddings for Histograms},
  author = {Le, Tam and Cuturi, Marco},
  pages = {293-308},
  abstract = {Learning distances that are specifically designed to compare histograms in the probability simplex has recently attracted the attention of the community. Learning such distances is important because most machine learning problems involve bags of features rather than simple vectors. Ample empirical evidence suggests that the Euclidean distance in general and Mahalanobis metric learning in particular may not be suitable to quantify distances between points in the simplex. We propose in this paper a new contribution to address this problem by generalizing a family of embeddings proposed by Aitchison (1982) to map the probability simplex onto a suitable Euclidean space. We provide algorithms to estimate the parameters of such maps, and show that these algorithms lead to representations that outperform alternative approaches to compare histograms.},
}


text:
DESCRIPTION = ""Net::Server" is an extensible, generic Perl server engine."

SECTION = "libs"
LICENSE = "Artistic-1.0 | GPL-1.0-or-later"
PR = "r0"

MAINTAINER=	"Poky <poky@yoctoproject.org>"
HOMEPAGE=	"https://metacpan.org/release/Net-Server"

LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Artistic-1.0;md5=cda03bbdc3c1951996392b872397b798 \
file://${COMMON_LICENSE_DIR}/GPL-1.0-or-later;md5=30c0b8a5048cc2f4be5ff15ef0d8cf61"

SRC_URI = "https://cpan.metacpan.org/authors/id/R/RH/RHANDOM/Net-Server-2.010.tar.gz"

SRC_URI[md5sum] = "d97171b4b2f0ebfea1d5fa03207eaaf6"
SRC_URI[sha256sum] = "95fc380abc32eaef84406ecc4b01612c7215f6375318fdb95901be1babd1a6e1"

S = "${WORKDIR}/Net-Server-${PV}"

inherit cpan allarch

BBCLASSEXTEND = "native"

repository: rehsack/meta-cpan

repo_name: rehsack/meta-cpan


text:
inherit features_check

REQUIRED_MACHINE_FEATURES = "common"

inherit esw python3native

DEPENDS += "xilstandalone "

PACKAGECONFIG ?= "${@bb.utils.contains("MACHINE_FEATURES", "clockps", "clockps", "", d)} \
		  ${@bb.utils.contains("MACHINE_FEATURES", "scugic", "scugic", "", d)} \
		  ${@bb.utils.contains("MACHINE_FEATURES", "intc", "intc", "", d)}"
PACKAGECONFIG[clockps] = "${RECIPE_SYSROOT}/usr/lib/libclockps.a,,clockps,,"
PACKAGECONFIG[scugic] = "${RECIPE_SYSROOT}/usr/lib/libscugic.a,,scugic,,"
PACKAGECONFIG[intc] = "${RECIPE_SYSROOT}/usr/lib/libintc.a,,intc,,"

ESW_COMPONENT_SRC = "/XilinxProcessorIPLib/drivers/common/src/"
ESW_COMPONENT_NAME = "libcommon.a"

do_configure:prepend() {
    LOPPER_DTC_FLAGS="-b 0 -@" lopper ${DTS_FILE} -- baremetalconfig_xlnx.py ${ESW_MACHINE} ${S}/XilinxProcessorIPLib/drivers/intc/src/
    LOPPER_DTC_FLAGS="-b 0 -@" lopper ${DTS_FILE} -- baremetalconfig_xlnx.py ${ESW_MACHINE} ${S}/XilinxProcessorIPLib/drivers/scugic/src/
    install -m 0755 *.cmake ${S}/${ESW_COMPONENT_SRC}/
}

repository: Xilinx/meta-xilinx

repo_name: Xilinx/meta-xilinx

gha_language: C