text:
reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.},
author = {Hansen, Kasper D. and Brenner, Steven E. and Dudoit, Sandrine},
doi = {10.1093/nar/gkq224},
file = {:home/fin/Documents/papers/mendeley/Hansen, Brenner, Dudoit\_2010\_Biases in Illumina transcriptome sequencing caused by random hexamer priming\_Nucleic Acids Research(2).pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {03051048},
journal = {Nucleic Acids Res.},
number = {12},
pages = {1--7},
pmid = {20395217},
title = {{Biases in Illumina transcriptome sequencing caused by random hexamer priming}},
volume = {38},
year = {2010}
}
@article{Hasegawa1985,
abstract = {A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 +/- 11.7, 13.3 +/- 1.5, 10.9 +/- 1.2, 3.7 +/- 0.6, and 2.7 +/- 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the pipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a proto-chimpanzee after the former had developed bipedalism.},
author = {Hasegawa, Masami and Kishino, Hirohisa and Yano, Taka Aki},
doi = {10.1007/BF02101694},
file = {:home/fin/Documents/papers/mendeley/Hasegawa, Kishino, Yano\_1985\_Dating of the human-ape splitting by a molecular clock of mitochondrial DNA\_Journal of Molecular Evolution.pdf:pdf},
isbn = {0022-2844},
issn = {00222844},
journal = {J. Mol. Evol.},
keywords = {Evolution of hominoids,Interspecies transfer of mitochondrial DNA,Phylogenetic position of Australopithecus afarensi},
pages = {160--174},
pmid = {3934395},
title = {{Dating of the human-ape splitting by a molecular clock of mitochondrial DNA}},
volume = {22},
year = {1985}
}
@article{Pound1893,
author = {Pound, Roscoe},
doi = {10.1086/275742},
file = {:home/fin/Documents/papers/mendeley/Pound\_1893\_Symbiosis and Mutualism\_The American Naturalist.pdf:pdf},
isbn = {00030147},
issn = {0003-0147},
journal = {Am. Nat.},
pages = {509},
title = {{Symbiosis and Mutualism}},
volume = {27},
year = {1893}
}
@article{Cho2011,
abstract = {Wolbachia pipientis are intracellular symbiotic bacteria extremely common in various organisms including Drosophila melanogaster, and are known for their ability to induce changes in host reproduction. These bacteria are present in astral microtubule-associated vesicular structures in host cytoplasm, but little is known about the identity of these vesicles. We report here that Wolbachia are restricted only to a group of Golgi-related vesicles concentrated near the site of membrane biogenesis and minus-ends of microtubules. The Wolbachia vesicles were significantly mislocalized in mutant embryos defective in cell/planar polarity genes suggesting that cell/tissue polarity genes are required for apical localization of these Golgi-related vesicles. Furthermore, two of the polarity proteins, Van Gogh/Strabismus and Scribble, appeared to be present in these Golgi-related vesicles. Thus, establishment of polarity may be closely linked to the precise insertion of Golgi vesicles into the new membrane addition site.},
author = {Cho, Kyung-Ok and Kim, Go-Woon and Lee, Ok-Kyung},
doi = {10.1371/journal.pone.0022703},
journal = {PLoS One},
number = {7},
pages = {e22703},
publisher = {Public Library of Science},
title = {{Wolbachia Bacteria Reside in Host Golgi-Related Vesicles Whose Position Is Regulated by Polarity Proteins}},
url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0022703},
volume = {6},
year = {2011}
}
@article{Adams1991,
abstract = {Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.},
author = {Adams, M D and Kelley, J M and Gocayne, J D and Dubnick, M and Polymeropoulos, M H and Xiao, H and Merril, C R and Wu, a and Olde, B and Moreno, R F},
doi = {10.1126/science.2047873},
file = {:home/fin/Documents/papers/mendeley/Adams et al.\_1991\_Complementary DNA sequencing expressed sequence tags and human genome project.\_Science (New York, N.Y.).pdf:pdf},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science},
number = {1990},
pages = {1651--1656},
pmid = {2047873},
title = {{Complementary DNA sequencing: expressed sequence tags and human genome project.}},
volume = {252},
year = {1991}
}
@article{Lepere2009,
author = {Lepere, G. and Nowacki, M. and Serrano, V. and Gout, J.-F. and Guglielmi, G. and Duharcourt, S. and Meyer, E.},
doi = {10.1093/nar/gkn1018},
file = {:home/fin/Documents/papers/mendeley/Lepere et al.\_2009\_Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia\_Nucleic Acids Research. Acids-: Acids-},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {3},
pages = {903--915},
title = {{Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn1018},
volume = {37},
year = {2009}
}
@article{Korfhage2013,
abstract = {DNA sequence analysis and genotyping of biological samples using next-generation sequencing (NGS), microarrays, or real-time PCR is often limited by the small amount of sample available. A single cell contains only one to four copies of the genomic DNA, depending on the organism (haploid or diploid organism) and the cell-cycle phase. The DNA content of a single cell ranges from a few femtograms in bacteria to picograms in mammalia. In contrast, a deep analysis of the genome currently requires a few hundred nanograms up to micrograms of genomic DNA for library formation necessary for NGS sequencing or labeling protocols (e.g., microarrays). Consequently, accurate whole-genome amplification (WGA) of single-cell DNA is required for reliable genetic analysis (e.g., NGS) and is particularly important when genomic DNA is limited. The use of single-cell WGA has enabled the analysis of genomic heterogeneity of individual cells (e.g., somatic genomic variation in tumor cells). This unit describes how the genome of single cells can be used for WGA for further genomic studies, such as NGS. Recommendations for isolation of single cells are given and common sources of errors are discussed.},
author = {Korfhage, Christian and Fisch, Evelyn and Fricke, Evelyn and Baedker, Silke and Loeffert, Dirk},
doi = {10.1002/0471142727.mb0714s104},
file = {:home/fin/Documents/papers/mendeley/Korfhage et al.\_2013\_Whole-genome amplification of single-cell genomes for next-generation sequencing\_Current Protocols in Molecular Bio.pdf:pdf},
isbn = {0471142727},
issn = {19343639},
journal = {Curr. Protoc. Mol. Biol.},
keywords = {Genome analysis,Next-generation sequencing,Single cell,Somatic genome variation},
number = {October},
pages = {1--11},
pmid = {24510298},
title = {{Whole-genome amplification of single-cell genomes for next-generation sequencing}},
year = {2013}
}
@article{Giordano2014,
abstract = {Nitrogen and sulfur are abundant constituents of plant and algal cells that are assimilated at the lowest oxidation number, as NH4+ and S2−, although they can (in the case of sulfur, usually must) be acquired with their highest oxidation number, as NO3− and SO42−. Some occasional differences and variants exists for transport and assimilation systems; the greatest differences in the way vascular plants and algae use N and S, however, most probably resides in regulation. For instance, nitrate assimilation in plants is strongly regulated by phosphorylation. In algae, redox regulation appears to be more important. Similarly, sulfate reduction has its main control step at the level of APS reductase in higher plants, whereas in algae a redox regulation has been recently been hypothesized for ATP sulfurylase, the first step in sulfate assimilation. Unfortunately, the information on the regulation of N and S acquisition and assimilation is limited to very few species (e.g. Chlamydomonas reinhardtii, Arabidopsis thaliana) this is especially true in the case of sulfur. This review attempts to highlight the points of divergence in N and S utilization by plants and algae, leaving aside the biochemical details and the features that do not show any obvious difference.},
author = {Giordano, Mario and Raven, John a.},
doi = {10.1016/j.aquabot.2014.06.012},
file = {:home/fin/Documents/papers/mendeley/Giordano, Raven\_2014\_Nitrogen and sulfur assimilation in plants and algae\_Aquatic Botany.pdf:pdf},
issn = {03043770},
journal = {Aquat. Bot.},
keywords = {Assimilation,Nitrogen,Nutrient,Signaling,Sulfur,Uptake},
pages = {45--61},
publisher = {Elsevier B.V.},
title = {{Nitrogen and sulfur assimilation in plants and algae}},
url = {http://www.sciencedirect.com/science/article/pii/S0304377014001016},
volume = {118},
year = {2014}
}
@article{Abou-Shanab2014,
abstract = {Coupling of advanced wastewater treatment with microalgae cultivation for low-cost lipid production was demonstrated in this study. The microalgal species Micractinium reisseri and Scenedesmus obliquus were isolated from municipal wastewater mixed with agricultural drainage. M. reisseri was selected based on the growth rate and cultivated in municipal wastewater (influent, secondary and tertiary effluents) which varied in nutrient concentration. M. reisseri showed an optimal specific growth rate ($\mu$opt) of 1.15, 1.04, and 1.01 1/day for the influent and the secondary and tertiary effluents, respectively. Secondary effluent supported the highest phosphorus removal (94\%) and saturated fatty acid content (40\%). The highest lipid content (40\%), unsaturated fatty acid content, including monounsaturated and polyunsaturated fatty acids (66\%), and nitrogen removal (80\%) were observed for tertiary effluent. Fatty acids accumulating in the microalgal biomass (M. reisseri) were mainly composed of palmitic acid, oleic acid, linoleic acid, and a-linolenic acid. Cultivation of M. reisseri using municipal wastewater served a dual function of nutrient removal and biofuel feedstock generation. © 2014 The Korean Society for Biotechnology and Bioengineering and Springer-Verlag.},
author = {Abou-Shanab, Reda a. I. and El-Dalatony, Marwa M. and EL-Sheekh, Mostafa M. and Ji, Min-Kyu and Salama, El-Sayed and Kabra, Akhil N. and Jeon, Byong-Hun},
doi = {10.1007/s12257-013-0485-z},
file = {:home/fin/Documents/papers/mendeley/Abou-Shanab et al.\_2014\_Cultivation of a new microalga, Micractinium reisseri, in municipal wastewater for nutrient removal, biomass, li.pdf:pdf},
issn = {1226-8372},
journal = {Biotechnol. Bioprocess Eng.},
keywords = {fatty acids,lipid,microalgae,municipal wastewater,nutrient,removal},
pages = {510--518},
title = {{Cultivation of a new microalga, Micractinium reisseri, in municipal wastewater for nutrient removal, biomass, lipid, and fatty acid production}},
url = {http://link.springer.com/10.1007/s12257-013-0485-z},
volume = {19},
year = {2014}
}
@article{Lartillot2004,
abstract = {Most current models of sequence evolution assume that all sites of a protein evolve under the same substitution process, characterized by a 20 x 20 substitution matrix. Here, we propose to relax this assumption by developing a Bayesian mixture model that allows the amino-acid replacement pattern at different sites of a protein alignment to be described by distinct substitution processes. Our model, named CAT, assumes the existence of distinct processes (or classes) differing by their equilibrium frequencies over the 20 residues. Through the use of a Dirichlet process prior, the total number of classes and their respective amino-acid profiles, as well as the affiliations of each site to a given class, are all free variables of the model. In this way, the CAT model is able to adapt to the complexity actually present in the data, and it yields an estimate of the substitutional heterogeneity through the posterior mean number of classes. We show that a significant level of heterogeneity is present in the substitution patterns of proteins, and that the standard one-matrix model fails to account for this heterogeneity. By evaluating the Bayes factor, we demonstrate that the standard model is outperformed by CAT on all of the data sets which we analyzed. Altogether, these results suggest that the complexity of the pattern of substitution of real sequences is better captured by the CAT model, offering the possibility of studying its impact on phylogenetic reconstruction and its connections with structure-function determinants.},
author = {Lartillot, Nicolas and Philippe, Herv\'{e}},
doi = {10.1093/molbev/msh112},
file = {:home/fin/Documents/papers/mendeley/Lartillot, Philippe\_2004\_A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process\_Molecular Biolog.pdf:pdf},
isbn = {0737-4038},
issn = {07374038},
journal = {Mol. Biol. Evol.},
keywords = {Amino-acid replacement,Bayes,Bayes factor,Dirichlet process mixtures,Phylogeny,Posterior predictive resampling},
number = {6},
pages = {1095--1109},
pmid = {15014145},
title = {{A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process}},
volume = {21},
year = {2004}
}
@article{AliagaGoltsman2014,
author = {{Aliaga Goltsman}, Daniela S and Comolli, Luis R and Thomas, Brian C and Banfield, Jillian F},
doi = {10.1038/ismej.2014.200},
file = {:home/fin/Documents/papers/mendeley/Aliaga Goltsman et al.\_2014\_Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities\_The.pdf:pdf},
issn = {1751-7362},
journal = {ISME J.},
number = {4},
pages = {1014--1023},
publisher = {Nature Publishing Group},
title = {{Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities}},
url = {http://www.nature.com/doifinder/10.1038/ismej.2014.200},
volume = {9},
year = {2014}
}
@article{Pyrkosz2013,
abstract = {Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in the inferred expression levels can result. In this study, we use simulated reads generated from real transcriptomes to determine the accuracy of read mapping, and measure the error resulting from using an incomplete transcriptome. We show that the two primary sources of count- ing error are 1) alternative splice variants that share reads and 2) missing transcripts from the reference. Alternative splice variants increase the false positive rate of mapping while incomplete reference tran- scriptomes decrease the true positive rate, leading to inaccurate transcript expression levels. Grouping transcripts by gene or read sharing (similar to mapping to a reference genome) significantly decreases false positives, but only by improving the reference transcriptome itself can the missing transcript problem be addressed. We also demonstrate that employing different mapping software does not yield substantial increases in accuracy on simulated data. Finally, we show that read lengths or insert sizes must increase past 1kb to resolve mapping ambiguity.},
archivePrefix = {arXiv},
arxivId = {1303.2411},
author = {Pyrkosz, Alexis Black and Cheng, Hans and Brown, C Titus},
eprint = {1303.2411},
file = {:home/fin/Documents/papers/mendeley/Pyrkosz, Cheng, Brown\_2013\_RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates\_arXiv1303.2411.pdf:pdf},
journal = {arXiv:1303.2411},
pages = {1--17},
title = {{RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates}},
url = {http://arxiv.org/abs/1303.2411},
year = {2013}
}
@article{Sijen2007,
author = {Sijen, Titia and Steiner, Florian A and Thijssen, Karen L and Plasterk, Ronald H A},
file = {:home/fin/Documents/papers/mendeley/Sijen et al.\_2007\_Secondary siRNAs Result from Unprimed RNA Synthesis and Form a Distinct Class\_Science.pdf:pdf},
journal = {Science (80-. ).},
pages = {244--247},
title = {{Secondary siRNAs Result from Unprimed RNA Synthesis and Form a Distinct Class}},
volume = {315},
year = {2007}
}
@article{Fiehn2002,
author = {Fiehn, O},
doi = {10.1023/A:1013713905833},
file = {:home/fin/Documents/papers/mendeley/Fiehn\_2002\_Metabolomics – the link between genotypes and phenotypes\_Plant Molecular Biology.pdf:pdf},
isbn = {978-94-010-3903-1},
issn = {01674412},
journal = {Plant Mol. Biol. },
keywords = {functional genomics,mass spectrometry,metabolism,metabolite profiling},
pages = {155--171},
pmid = {11860207},
title = {{Metabolomics – the link between genotypes and phenotypes}},
volume = {48},
year = {2002}
}
@article{Hosoya1995a,
author = {Hosoya, H and Kimura, K and Matsuda, S and Kitaura, M and Takahashi, T and Kosaka, T},
file = {:home/fin/Documents/papers/mendeley//Hosoya et al.\_1995\_Symbiotic Algae-free Strains of The Green Paramecium Paramecium bursaria produced by the Herbicide Paraquat\_Zoologica.pdf:pdf},
journal = {Zoolog. Sci.},
pages = {807--810},
title = {{Symbiotic Algae-free Strains of The Green Paramecium Paramecium bursaria Produced by the Herbicide Paraquat}},
volume = {12},
year = {1995}
}
@article{Darriba2011c,
abstract = {UNLABELLED: We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities. AVAILABILITY: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/). CONTACT: dposada@uvigo.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
author = {Darriba, Diego and Taboada, Guillermo L and Doallo, Ram\'{o}n and Posada, David},
doi = {10.1093/bioinformatics/btr088},
file = {:home/fin/Documents/papers/mendeley/Darriba et al.\_2011\_ProtTest 3 fast selection of best-fit models of protein evolution.\_Bioinformatics.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Evolution,Models,Molecular,Phylogeny,Protein,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,Statistical},
month = apr,
number = {8},
pages = {1164--5},
pmid = {21335321},
title = {{ProtTest 3: fast selection of best-fit models of protein evolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21335321},
volume = {27},
year = {2011}
}
@article{Horton2007a,
author = {Horton, P. and Park, K.-J. and Obayashi, T. and Fujita, N. and Harada, H. and Adams-Collier, C.J. and Nakai, K.},
doi = {10.1093/nar/gkm259},
file = {:home/fin/Documents/papers/mendeley/Horton et al.\_2007\_WoLF PSORT protein localization predictor\_Nucleic Acids Research.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
number = {17},
pages = {W585--W587},
title = {{WoLF PSORT: protein localization predictor}},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkm259},
volume = {35},
year = {2007}
}
@article{Neil2013c,
author = {Neil, Shawn T O and Emrich, Scott J},
file = {:home/fin/Documents/papers/mendeley/Neil, Emrich\_2013\_Assessing De Novo transcriptome assembly metrics for consistency and utility\_BMC genomics.pdf:pdf},
journal = {BMC Genomics},
title = {{Assessing De Novo transcriptome assembly metrics for consistency and utility}},
year = {2013}
}
@article{Gough2002,
abstract = {The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genomes. Given an amino acid or nucleotide query sequence the server will return the domain architecture and SCOP classification. The server produces alignments of the query sequences with sequences of known structure, and includes multiple alignments of genome and PDB sequences. The structural assignments are carried out on all complete genomes (currently 59) covering approximately half of the soluble protein domains. The assignments, superfamily breakdown and statistics on them are available from the server. The database is currently used by this group and others for genome annotation, structural genomics, gene prediction and domain-based genomic studies.},
author = {Gough, Julian and Chothia, Cyrus},
doi = {10.1093/nar/30.1.268},
file = {:home/fin/Documents/papers/mendeley/Gough, Chothia\_2002\_SUPERFAMILY HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignm.pdf:pdf},
isbn = {1362-4962},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
keywords = {Amino Acid Sequence,Animals,Base Sequence,Databases, Protein,Evolution, Molecular,Genome,Humans,Information Storage and Retrieval,Internet,Molecular Sequence Data,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Proteins: genetics,Sequence Alignment},
number = {1},
pages = {268--72},
pmid = {11752312},
title = {{SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=99153\&tool=pmcentrez\&rendertype=abstract},
volume = {30},
year = {2002}
}
@article{Kircher2009,
abstract = {The Illumina Genome Analyzer generates millions of short sequencing reads. We present Ibis (Improved base identification system), an accurate, fast and easy-to-use base caller that significantly reduces the error rate and increases the output of usable reads. Ibis is faster and more robust with respect to chemistry and technology than other publicly available packages. Ibis is freely available under the GPL from http://bioinf.eva.mpg.de/Ibis/.},
author = {Kircher, Martin and Stenzel, Udo and Kelso, Janet},
doi = {10.1186/gb-2009-10-8-r83},
file = {:home/fin/Documents/papers/mendeley/Kircher, Stenzel, Kelso\_2009\_Improved base calling for the Illumina Genome Analyzer using machine learning strategies.\_Genome biology.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$n1465-6906 (Linking)},
issn = {1465-6906},
journal = {Genome Biol.},
number = {8},
pages = {R83},
pmid = {19682367},
title = {{Improved base calling for the Illumina Genome Analyzer using machine learning strategies.}},
volume = {10},
year = {2009}
}
@article{Wehrens2014,
author = {Wehrens, Ron and Weingart, Georg and Mattivi, Fulvio},
doi = {10.1016/j.jchromb.2014.02.051},
file = {:home/fin/Documents/papers/mendeley/Wehrens, Weingart, Mattivi\_2014\_metaMS An open-source pipeline for GC–MS-based untargeted metabolomics\_Journal of Chromatography B.pdf:pdf},
issn = {15700232},
journal = {J. Chromatogr. B},
pages = {109--116},
publisher = {Elsevier B.V.},
title = {{metaMS: An open-source pipeline for GC–MS-based untargeted metabolomics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1570023214001548},
volume = {966},
year = {2014}
}
@misc{Thomas2003,
abstract = {The \{PANTHER\} database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models \{(Hidden\} Markov Models, or \{HMMs)\} are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, \{HMMs\} are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the \{PANTHER\} database includes training sequences from all organisms in the \{GenBank\} non-redundant protein database, and the \{HMMs\} have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. \{PANTHER\} is publicly available on the web at http://panther.celera.com.},
author = {Thomas, Paul D and Kejariwal, Anish and Campbell, Michael J and Mi, Huaiyu and Diemer, Karen and Guo, Nan and Ladunga, Istvan and Ulitsky-Lazareva, Betty and Muruganujan, Anushya and Rabkin, Steven and Vandergriff, Jody a and Doremieux, Olivier},
booktitle = {Nucleic Acids Res.},
doi = {10.1093/nar/gkg115},
file = {:home/fin/Documents/papers/mendeley/Thomas et al.\_2003\_\{PANTHER\} a browsable database of gene products organized by biological function, using curated protein family and s.html:html},
isbn = {1362-4962 (Linking)},
issn = {1362-4962},
pages = {334--341},
pmid = {12520017},
title = {{\{PANTHER:\} a browsable database of gene products organized by biological function, using curated protein family and subfamily classification}},
url = {http://dx.doi.org/10.1093/nar/gkg115},
volume = {31},
year = {2003}
}
@article{Takahashi2007,
abstract = {A green ciliate Paramecium bursaria, bearing several hundreds of endosymbiotic algae, demonstrates rotational microtubule-based cytoplasmic streaming, in which cytoplasmic granules and endosymbiotic algae flow in a constant direction. However, its physiological significance is still unknown. We investigated physiological roles of cytoplasmic streaming in P. bursaria through host cell cycle using video-microscopy. Here, we found that cytoplasmic streaming was arrested in dividing green paramecia and the endosymbiotic algae proliferated only during the arrest of cytoplasmic streaming. Interestingly, arrest of cytoplasmic streaming with pressure or a microtubule drug also induced proliferation of endosymbiotic algae independently of host cell cycle. Thus, cytoplasmic streaming may control the algal proliferation in P. bursaria. Furthermore, confocal microscopic observation revealed that a division septum was formed in the constricted area of a dividing paramecium, producing arrest of cytoplasmic streaming. This is a first report to suggest that cytoplasmic streaming controls proliferation of eukaryotic cells.},
author = {Takahashi, Toshiyuki and Shirai, Yohji and Kosaka, Toshikazu and Hosoya, Hiroshi},
doi = {10.1371/journal.pone.0001352},
file = {:home/fin/Documents/papers/mendeley/Takahashi et al.\_2007\_Arrest of cytoplasmic streaming induces algal proliferation in green paramecia.\_PloS One.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Animals,Confocal,Cytoplasm,Cytoplasm: drug effects,Eukaryota,Eukaryota: cytology,Eukaryota: physiology,Fluorescence,Microscopy,Microtubules,Microtubules: drug effects,Nocodazole,Nocodazole: pharmacology,Paramecium,Paramecium: physiology,Symbiosis},
month = jan,
number = {12},
pages = {e1352},
pmid = {18159235},
title = {{Arrest of cytoplasmic streaming induces algal proliferation in green paramecia.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2131778\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2007}
}
@article{Zhou2009,
author = {Zhou, Shiguo and Wei, Fusheng and Nguyen, John and Bechner, Mike and Potamousis, Konstantinos and Goldstein, Steve and Pape, Louise and Mehan, Michael R. and Churas, Chris and Pasternak, Shiran and Forrest, Dan K. and Wise, Roger and Ware, Doreen and Wing, Rod a. and Waterman, Michael S. and Livny, Miron and Schwartz, David C.},
doi = {10.1371/journal.pgen.1000711},
file = {:home/fin/Documents/papers/mendeley/Zhou et al.\_2009\_A Single Molecule Scaffold for the Maize Genome\_PLoS Genetics.pdf:pdf},
issn = {1553-7404},
journal = {PLoS Genet.},
number = {11},
pages = {e1000711},
title = {{A Single Molecule Scaffold for the Maize Genome}},
url = {http://dx.plos.org/10.1371/journal.pgen.1000711},
volume = {5},
year = {2009}
}
@article{hotelling1933analysis,
author = {Hotelling, Harold},
journal = {J. Educ. Psychol.},
number = {6},
pages = {417},
publisher = {Warwick \& York},
title = {{Analysis of a complex of statistical variables into principal components.}},
volume = {24},
year = {1933}
}
@article{Buchan2002,
abstract = {We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30\% and 40\% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.},
author = {Buchan, Daniel W a and Shepherd, Adrian J and Lee, David and Pearl, Frances M G and Rison, Stuart C G and Thornton, Janet M and Orengo, Christine a},
doi = {10.1101/gr.213802},
file = {:home/fin/Documents/papers/mendeley/Buchan et al.\_2002\_Gene3D structural assignment for whole genes and genomes using the CATH domain structure database\_Genome Research.pdf:pdf},
isbn = {1088-9051 (Print)$\backslash$r1088-9051},
issn = {1088-9051},
journal = {Genome Res.},
keywords = {Animals,Archaeal,Archaeal Proteins,Archaeal Proteins: genetics,Archaeal: genetics,Bacterial,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial: genetics,Databases,Genes,Genes: genetics,Genetic,Genetic: statistics \& numerical data,Genome,Internet,Nucleic Acid,Protein,Protein Structure,Proteins,Proteins: genetics,Sequence Homology,Software,Software: statistics \& numerical data,Tertiary},
pages = {503--14},
pmid = {11875040},
title = {{Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=155287\&tool=pmcentrez\&rendertype=abstract},
volume = {12},
year = {2002}
}
@article{Chen2010a,
abstract = {Sugar efflux transporters are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. Despite broad biological importance, the identity of sugar efflux transporters has remained elusive. Using optical glucose sensors, we identified a new class of sugar transporters, named SWEETs, and show that at least six out of seventeen Arabidopsis, two out of over twenty rice and two out of seven homologues in Caenorhabditis elegans, and the single copy human protein, mediate glucose transport. Arabidopsis SWEET8 is essential for pollen viability, and the rice homologues SWEET11 and SWEET14 are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter. Bacterial symbionts and fungal and bacterial pathogens induce the expression of different SWEET genes, indicating that the sugar efflux function of SWEET transporters is probably targeted by pathogens and symbionts for nutritional gain. The metazoan homologues may be involved in sugar efflux from intestinal, liver, epididymis and mammary cells.},
author = {Chen, Li-Qing and Hou, Bi-Huei and Lalonde, Sylvie and Takanaga, Hitomi and Hartung, Mara L and Qu, Xiao-Qing and Guo, Woei-Jiun and Kim, Jung-Gun and Underwood, William and Chaudhuri, Bhavna and Chermak, Diane and Antony, Ginny and White, Frank F and Somerville, Shauna C and Mudgett, Mary Beth and Frommer, Wolf B},
doi = {10.1038/nature09606},
file = {:home/fin/Documents/papers/mendeley/Chen et al.\_2010\_Sugar transporters for intercellular exchange and nutrition of pathogens.\_Nature.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$n0028-0836 (Linking)},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Arabidopsis,Arabidopsis Proteins,Arabidopsis Proteins: genetics,Arabidopsis Proteins: metabolism,Arabidopsis: genetics,Arabidopsis: metabolism,Arabidopsis: microbiology,Biological Transport,Biological Transport: genetics,Gene Expression Profiling,Gene Expression Regulation, Plant,Glucose,Glucose: metabolism,HEK293 Cells,Host-Pathogen Interactions,Host-Pathogen Interactions: physiology,Humans,Membrane Transport Proteins,Membrane Transport Proteins: metabolism,Models, Biological,Oryza sativa,Oryza sativa: genetics,Oryza sativa: metabolism,Oryza sativa: microbiology,RNA, Messenger,RNA, Messenger: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Xenopus,Xenopus: genetics},
number = {7323},
pages = {527--32},
pmid = {21107422},
publisher = {Nature Publishing Group},
title = {{Sugar transporters for intercellular exchange and nutrition of pathogens.}},
url = {http://dx.doi.org/10.1038/nature09606},
volume = {468},
year = {2010}
}
@article{Keeling2008a,
author = {Keeling, Patrick J. and Palmer, Jeffrey D.},
doi = {10.1038/nrg2386},
file = {:home/fin/Documents/papers/mendeley/Keeling, Palmer\_2008\_Horizontal gene transfer in eukaryotic evolution\_Nature Reviews Genetics.pdf:pdf},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
number = {august},
pages = {605--618},
title = {{Horizontal gene transfer in eukaryotic evolution}},
url = {http://www.nature.com/doifinder/10.1038/nrg2386},
volume = {9},
year = {2008}
}
@article{Ding2015,
abstract = {This paper presents Yinyang K-means, a new algorithm for K-means clustering. By cluster-ing the centers in the initial stage, and lever-aging efficiently maintained lower and upper bounds between a point and centers, it more effectively avoids unnecessary distance calcula-tions than prior algorithms. It significantly out-performs prior K-means algorithms consistently across all experimented data sets, cluster num-bers, and machine configurations. The consis-tent, superior performance—plus its simplicity, user-control of overheads, and guarantee in pro-ducing the same clustering results as the stan-dard K-means—makes Yinyang K-means a drop-in replacement of the classic K-means with an order of magnitude higher performance.},
author = {Ding, Yufei and Zhao, Yue and {Xipeng Shen}, Ncsuedu and Musuvathi, Madanlal and {Todd Mytkowicz}, Microsoftcom},
file = {:home/fin/Documents/papers/mendeley/Ding et al.\_2015\_Yinyang K-Means A Drop-In Replacement of the Classic K-Means with Consistent Speedup\_Unknown.pdf:pdf},
title = {{Yinyang K-Means: A Drop-In Replacement of the Classic K-Means with Consistent Speedup}},
volume = {37},
year = {2015}
}
@article{Prell2006,
abstract = {Bacteria have evolved a wide variety of metabolic strategies to cope with varied environments. Some are specialists and only able to survive in restricted environments; others are generalists and able to cope with diverse environmental conditions. Rhizobia (e.g. Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium and Azorhizobium species) can survive and compete for nutrients in soil and the plant rhizosphere but can also form a beneficial symbiosis with legumes in a highly specialized plant cell environment. Inside the legume-root nodule, the bacteria (bacteroids) reduce dinitrogen to ammonium, which is secreted to the plant in exchange for a carbon and energy source. A new and challenging aspect of nodule physiology is that nitrogen fixation requires the cycling of amino acids between the bacteroid and plant. This review aims to summarize the metabolic plasticity of rhizobia and the importance of amino acid cycling. ?? 2006 Elsevier Ltd. All rights reserved.},
author = {Prell, Juergen and Poole, Philip},
doi = {10.1016/j.tim.2006.02.005},
file = {:home/fin/Documents/papers/mendeley/Prell, Poole\_2006\_Metabolic changes of rhizobia in legume nodules\_Trends in Microbiology.pdf:pdf},
isbn = {0966-842X (Print)},
issn = {0966842X},
journal = {Trends Microbiol.},
number = {4},
pages = {161--168},
pmid = {16520035},
title = {{Metabolic changes of rhizobia in legume nodules}},
volume = {14},
year = {2006}
}
@article{Sagan1967,
author = {Sagan, Lynn},
file = {:home/fin/Documents/papers/mendeley/Sagan\_1967\_On the Origin of Mitosing Cells\_Journal of Theoretical Biology.pdf:pdf},
journal = {J. Theor. Biol.},
pages = {225--274},
title = {{On the Origin of Mitosing Cells}},
volume = {14},
year = {1967}
}
@article{Ikawa1997,
abstract = {The activity of the degradation products of linoleic and Linolenic acids in inhibiting the growth of the green alga Chlorella pyrenoidosa was determined using the paper disk-agar plate method. Although hydroperoxides derived from these acids and aldehyde biodegradation products and other related aldehydes and alcohols showed inhibitory activity, it is concluded from the weakness of the activities that the inhibitory effects of polyunsaturated fatty acids (PUFAs) on Chlorella growth is due mainly to the acids themselves and not their degradation products. The evidence for the possible ecological role of PUFAs as toxic agents against phytoplankton is presented.},
author = {Ikawa, Miyoshi and Sasner, John J and Haney, James F},
doi = {10.1023/A:1003103726520},
file = {:home/fin/Documents/papers/mendeley/Ikawa, Sasner, Haney\_1997\_Inhibition of Chlorella growth by degradation and related products of linoleic and linolenic acids and the pos.pdf:pdf},
isbn = {0018-8158},
issn = {00188158},
journal = {Hydrobiologia},
keywords = {Chlorella pyrenoidosa,Growth inhibition,Hydroperoxides,Linoleic acid,Linolenic acid,Polyunsaturated fatty acids},
number = {1967},
pages = {143--148},
pmid = {1409},
title = {{Inhibition of Chlorella growth by degradation and related products of linoleic and linolenic acids and the possible significance of polyunsaturated fatty acids in phytoplankton ecology}},
volume = {356},
year = {1997}
}
@article{Batista2011,
author = {Batista, Thiago Mafra and Marques, Jo\~{a}o Trindade},
doi = {10.1016/j.jprot.2011.02.032},
file = {:home/fin/Documents/papers/mendeley/Batista, Marques\_2011\_RNAi pathways in parasitic protists and worms\_Journal of Proteomics.pdf:pdf},
issn = {18743919},
journal = {J. Proteomics},
keywords = {Argonaute,Non-coding RNA,Parasitic worms,Protists,RNA interference,Tropical diseases},
number = {9},
pages = {1504--1514},
publisher = {Elsevier B.V.},
title = {{RNAi pathways in parasitic protists and worms}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1874391911000881},
volume = {74},
year = {2011}
}
@article{Schulz2015,
author = {Schulz, Frederik and Horn, Matthias},
doi = {10.1016/j.tcb.2015.01.002},
file = {:home/fin/Documents/papers/mendeley/Schulz, Horn\_2015\_Intranuclear bacteria inside the cellular control center of eukaryotes\_Trends in Cell Biology.pdf:pdf},
issn = {09628924},
journal = {Trends Cell Biol.},
keywords = {endonuclear,nucleus,rickettsia,symbiosis},
pages = {1--8},
publisher = {Elsevier Ltd},
title = {{Intranuclear bacteria: inside the cellular control center of eukaryotes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0962892415000136},
year = {2015}
}
@book{Fayyad2001,
address = {San Francisco, CA, USA},
author = {Fayyad, Usama and Grinstein, Georges G and Wierse, Andreas},
isbn = {1-55860-689-0},
publisher = {Morgan Kaufmann Publishers Inc.},
title = {{Information Visualization in Data Mining and Knowledge Discovery}},
year = {2001}
}
@article{Sanderson2010,
author = {Sanderson, Conrad},
journal = {NICTA},
title = {{Conrad Sanderson. Armadillo: An Open Source C++ Linear Algebra Library for Fast Prototyping and Computationally Intensive Experiments}},
volume = {Technical },
year = {2010}
}
@article{Welsh2000,
abstract = {The osmoadaptation of most micro-organisms involves the accumulation of K+ ions and one or more of a restricted range of low molecular mass organic solutes, collectively termed 'compatible solutes'. These solutes are accumulated to high intracellular concentrations, in order to balance the osmotic pressure of the growth medium and maintain cell turgor pressure, which provides the driving force for cell extension growth. In this review, I discuss the alternative roles which compatible solutes may also play as intracellular reserves of carbon, energy and nitrogen, and as more general stress metabolites involved in protection of cells against other environmental stresses including heat. desiccation and freezing. Thus, the evolutionary selection for the accumulation of a specific compatible solute may nor depend solely upon its function during osmoadaptation, but also upon the secondary benefits its accumulation provides, such as increased tolerance of other environmental stresses prevalent in the organism's niche or even anti-herbivory or dispersal functions in the case of dimethylsulfoniopropionate (DMSP). In the second part of the review, I discuss the ecological consequences of the release of compatible solutes to the environment, where they can provide sources of compatible solutes, carbon, nitrogen and energy for other members of the micro-flora. Finally, at the global scale the metabolism of specific compatible solutes (betaines and DMSP) in brackish water, marine and hypersaline environments may influence global climate, due to the production of the trace gases, methane and dimethylsulfide (DMS) and in the case of DMS, also couple the marine and terrestrial sulfur cycles. (C) 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
author = {Welsh, D T},
doi = {10.1111/j.1574-6976.2000.tb00542.x},
file = {:home/fin/Documents/papers/mendeley/Welsh\_2000\_Ecological significance of compatible solute accumulation by micro-organisms from single cells to global climate.\_FEMS microb.pdf:pdf},
isbn = {0168-6445},
issn = {1574-6976},
journal = {FEMS Microbiol. Rev.},
keywords = {AEROBIC METHANE,CLOUD CONDENSATION NUCLEI,GLYCINE BETAINE TRANSPORT,MEMBRANE PHASE-TRANSITIONS,METHYLATED SULFUR-COMPOUNDS,OXIDATION,SALT-MARSH SEDIMENTS,SULFATE-REDUCING BACTERIUM,TERTIARY SULFONIUM COMPOUNDS,TROPICAL SOUTH-ATLANTIC,UPPER WATER COLUMN,climate,climate regulation,compatible solute,de,desiccation,desiccation resistance,dimethylsul,dimethylsulfide,dimethylsulfoniopropionate,glycine betaine,methanogenesis,osmoadaptation,regulation,resistance,stress tolerance,thermotolerance,trehalose},
pages = {263--290},
pmid = {10841973},
title = {{Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate.}},
url = {<Go to ISI>://000087800400003},
volume = {24},
year = {2000}
}
@article{VanEtten1983,
author = {{Van Etten}, James L and Burbank, D E and Kuczmarski, D and Meints, R H},
file = {:home/fin/Documents/papers/mendeley/Van Etten et al.\_1983\_Virus Infection of Culturable Chlorella-Like Algae and Dlevelopment of a Plaque Assay\_Science.pdf:pdf},
journal = {Science (80-. ).},
pages = {994--996},
title = {{Virus Infection of Culturable Chlorella-Like Algae and Dlevelopment of a Plaque Assay}},
volume = {219},
year = {1983}
}
@article{Talavera2007,
abstract = {Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.},
author = {Talavera, Gerard and Castresana, Jose},
doi = {10.1080/10635150701472164},
file = {:home/fin/Documents/papers/mendeley/Talavera, Castresana\_2007\_Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence align.pdf:pdf},
isbn = {1063-5157 (Print)$\backslash$n1063-5157 (Linking)},
issn = {1063-5157},
journal = {Syst. Biol.},
number = {4},
pages = {564--577},
pmid = {17654362},
title = {{Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.}},
volume = {56},
year = {2007}
}
@article{Scott1979,
abstract = {In this paper the formula for the optimal histogram bin width is derived which asymptotic- ally minimizes the integrated mean squared error. Monte Carlo methods are used to verify the usefulness of this formula for small samples. A data-based procedure for choosing the bin width parameter is proposed, which assumes a Gaussian reference standard and requires only the sample size and an estimate of the standard deviation. The sensitivity of the procedure is investigated using several probability models which violate the Gaussian assumption.},
author = {Scott, D W},
doi = {10.1093/biomet/66.3.605},
file = {:home/fin/Documents/papers/mendeley/Scott\_1979\_On optimal and data-based histograms\_Biometrika.pdf:pdf},
isbn = {00063444},
issn = {0006-3444},
journal = {Biometrika},
keywords = {Sturge's rule,histograms},
number = {3},
pages = {605--610},
title = {{On optimal and data-based histograms}},
volume = {66},
year = {1979}
}
@article{Schatz2012a,
author = {Schatz, M C and Delcher, a L and Roberts, M and Marc\c{c}ais, G and Pop, M and Yorke, J a},
doi = {10.1101/gr.131383.111},
file = {:home/fin/Documents/papers/mendeley/Schatz et al.\_2012\_GAGE A critical evaluation of genome assemblies and assembly algorithms Steven L. Salzberg, Adam M. Phillippy, Ale(2).pdf:pdf},
isbn = {1549-5469 (Electronic) 1088-9051 (Linking)},
issn = {1549-5469},
journal = {Genome Res.},
pages = {557--567},
pmid = {22147368},
title = {{GAGE: A critical evaluation of genome assemblies and assembly algorithms Steven L. Salzberg, Adam M. Phillippy, Aleksey Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J. Treangen}},
volume = {22},
year = {2012}
}
@article{Grabherr2011,
abstract = {Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.},
author = {Grabherr, Manfred G and Haas, Brian J and Yassour, Moran and Levin, Joshua Z and Thompson, Dawn a and Amit, Ido and Adiconis, Xian and Fan, Lin and Raychowdhury, Raktima and Zeng, Qiandong and Chen, Zehua and Mauceli, Evan and Hacohen, Nir and Gnirke, Andreas and Rhind, Nicholas and di Palma, Federica and Birren, Bruce W and Nusbaum, Chad and Lindblad-Toh, Kerstin and Friedman, Nir and Regev, Aviv},
doi = {10.1038/nbt.1883},
file = {:home/fin/Documents/papers/mendeley/Grabherr et al.\_2011\_Full-length transcriptome assembly from RNA-Seq data without a reference genome.\_Nature biotechnology.pdf:pdf},
issn = {1546-1696},
journal = {Nat. Biotechnol.},
month = may,
number = {7},
pmid = {21572440},
title = {{Full-length transcriptome assembly from RNA-Seq data without a reference genome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21572440},
volume = {29},
year = {2011}
}
@article{Wiens2008,
abstract = {The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that in- complete taxa can be accurately placed as long as the overall number of characters in the analysis is large. How- ever, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95\% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses. Key words accuracy, Bayesian analysis, missing data, phylogenetic analysis. The},
author = {Wiens, John J. and Moen, Daniel S.},
doi = {10.3724/SP.J.1002.2008.08040},
file = {:home/fin/Documents/papers/mendeley/Wiens, Moen\_2008\_Missing data and the accuracy of Bayesian phylogenetics\_Journal of Systematics and Evolution.pdf:pdf},
isbn = {0529-1526},
issn = {05291526},
journal = {J. Syst. Evol.},
keywords = {accuracy,analyses,bayesian analysis,data is a potentially,im-,missing data,of life,particularly if,phylogenetic analysis,portant issue in phylogenetic,reconstruct a comprehensive tree,the goal is to,the impact of missing},
pages = {307--314},
title = {{Missing data and the accuracy of Bayesian phylogenetics}},
volume = {46},
year = {2008}
}
@article{Paez2004,
abstract = {Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however, limited by the paucity of genomic DNA available. Here we have tested the fidelity and genome representation of phi29 polymerase-based genome amplification (phi29MDA) using direct sequencing and high density oligonucleotide arrays probing >10,000 SNP alleles. Genome representation was comprehensive and estimated to be 99.82\% complete, although six regions encompassing a maximum of 5.62 Mb failed to amplify. There was no degradation in the accuracy of SNP genotyping and, in direct sequencing experiments sampling 500,000 bp, the estimated error rate (9.5 x 10(-6)) was the same as in paired unamplified samples. The detection of cancer-associated loss of heterozygosity and copy number changes, including homozygous deletion and gene amplification, were similarly robust. These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis.},
author = {Paez, J Guillermo and Lin, Ming and Beroukhim, Rameen and Lee, Jeffrey C and Zhao, Xiaojun and Richter, Daniel J and Gabriel, Stacey and Herman, Paula and Sasaki, Hidefumi and Altshuler, David and Li, Cheng and Meyerson, Matthew and Sellers, William R},
doi = {10.1093/nar/gnh069},
file = {:home/fin/Documents/papers/mendeley/Paez et al.\_2004\_Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.pdf:pdf},
isbn = {0305-1048},
issn = {1362-4962},
journal = {Nucleic Acids Res.},
number = {9},
pages = {e71},
pmid = {15150323},
title = {{Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.}},
volume = {32},
year = {2004}
}
@article{Schussler1992,
abstract = {After treatment with the carboxylic ionophore monensin the Chlorella containing perialgal vacuoles of the "green" Paramecium bursaria swell. The Paramecium cells remain motile at this concentration for at least one day. The swelling is only observed in illuminated cells and can be inhibited by DCMU. We assume that during photosynthesis the perialgal vacuoles are acidified and that monensin exchanges H+ ions against monovalent cations (here K+). In consequence the osmotic value of the vacuoles increases. The proton gradient is believed to drive the transport of maltose from the symbiont into the host. Another but light independent effect of the monensin treatment is the swelling of peripheral alveoles of the ciliates, likewise indicating that the alveolar membrane contains an active proton pump.},
author = {Schussler, a and Schnepf, E},
doi = {10.1007/bf01322784},
file = {:home/fin/Documents/papers/mendeley/Schussler, Schnepf\_1992\_Photosynthesis Dependent Acidification of Perialgal Vacuoles in the Paramecium-Bursaria Chlorella Symbiosis - Vi.pdf:pdf},
isbn = {0033-183X},
issn = {0033-183X},
journal = {Protoplasma},
keywords = {endosymbiontic chlorella,gal vacuoles,mo-,paramecium bursaria,perial-,photosynthesis,proton pumps,sugar transport},
pages = {218--222},
title = {{Photosynthesis Dependent Acidification of Perialgal Vacuoles in the Paramecium-Bursaria Chlorella Symbiosis - Visualization By Monensin}},
url = {<Go to ISI>://WOS:A1992HK38500010},
volume = {166},
year = {1992}
}
@article{Richards2009g,
abstract = {Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. The role of HGT in plant evolutionary history is, however, largely unexplored. Here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. We constructed a phylogeny for all 1689 genes identified and all homolog groups available from the rice (Oryza sativa) genome (3177 gene families) and used these to define 14 candidate plant-fungi HGT events. Comprehensive phylogenetic analyses of these 14 data sets, using methods that account for site rate heterogeneity, demonstrated support for nine HGT events, demonstrating an infrequent pattern of HGT between plants and fungi. Five HGTs were fungi-to-plant transfers and four were plant-to-fungi HGTs. None of the fungal-to-plant HGTs involved angiosperm recipients. These results alter the current view of organismal barriers to HGT, suggesting that phagotrophy, the consumption of a whole cell by another, is not necessarily a prerequisite for HGT between eukaryotes. Putative functional annotation of the HGT candidate genes suggests that two fungi-to-plant transfers have added phenotypes important for life in a soil environment. Our study suggests that genetic exchange between plants and fungi is exceedingly rare, particularly among the angiosperms, but has occurred during their evolutionary history and added important metabolic traits to plant lineages.},
author = {Richards, Thomas a and Soanes, Darren M and Foster, Peter G and Leonard, Guy and Thornton, Christopher R and Talbot, Nicholas J},
doi = {10.1105/tpc.109.065805},
file = {:home/fin/Documents/papers/mendeley/Richards et al.\_2009\_Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi..pdf:pdf},
isbn = {1040-4651 (Print)},
issn = {1040-4651},
journal = {Plant Cell},
number = {July},
pages = {1897--1911},
pmid = {19584142},
title = {{Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.}},
volume = {21},
year = {2009}
}
@article{Arisue2014,
abstract = {The phylum Apicomplexa includes many parasitic genera of medical and veterinary importance including Plasmodium (causative agent of malaria), Toxoplasma (toxoplasmosis), and Babesia (babesiosis). Most of the apicomplexan parasites possess a unique, essential organelle, the apicoplast, which is a plastid without photosynthetic ability. Although the apicoplast is considered to have evolved through secondary endosymbiosis of a red alga into the common ancestral cell of apicomplexans, its evolutionary history has been under debate until recently. The apicoplast has a genome around 30-40kb in length. Repertoire and arrangement of the apicoplast genome-encoded genes differ among apicomplexan genera, although within the genus Plasmodium these are almost conserved. Genes in the apicoplast genome may be useful markers for Plasmodium phylogeny, because these are single copy (except for the inverted repeat region) and may have more phylogenetic signal than the mitochondrial genome that have been most commonly used for Plasmodium phylogeny. This review describes recent studies concerning the evolutionary origin of the apicoplast, presents evolutionary comparison of the primary structures of apicoplast genomes from apicomplexan parasites, and summarizes recent findings of malaria phylogeny based on apicoplast genome-encoded genes.},
author = {Arisue, Nobuko and Hashimoto, Tetsuo},
doi = {10.1016/j.parint.2014.10.005},
file = {:home/fin/Documents/papers/mendeley/Arisue, Hashimoto\_2014\_Phylogeny and evolution of apicoplasts and apicomplexan parasites.\_Parasitology international.pdf:pdf},
issn = {1873-0329},
journal = {Parasitol. Int.},
keywords = {Apicoplast,Evolution,Phylogeny,Plasmodium},
month = oct,
pmid = {25451217},
publisher = {Elsevier B.V.},
title = {{Phylogeny and evolution of apicoplasts and apicomplexan parasites.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25451217},
year = {2014}
}
@incollection{Kodama2009a,
author = {Kodama, Yuuki and Fujishima, Masahiro},
booktitle = {Endosymbionts in Paramecium},
chapter = {2},
doi = {10.1007/978-3-540-92677-1},
editor = {Fujishima, Masahiro},
file = {:home/fin/Documents/papers/mendeley/Kodama, Fujishima\_2009\_Infection of Paramecium bursaria by Symbiotic Chlorella Species\_Endosymbionts in Paramecium.pdf:pdf},
isbn = {978-3-540-92676-4},
pages = {31--55},
publisher = {Springer},
series = {Microbiology Monographs},
title = {{Infection of Paramecium bursaria by Symbiotic Chlorella Species}},
url = {http://link.springer.com/10.1007/978-3-540-92677-1},
volume = {12},
year = {2009}
}
@misc{Li2015,
author = {Li, Heng},
title = {{Seqtk}},
url = {https://github.com/lh3/seqtk},
year = {2015}
}
@article{Vijay2013,
abstract = {Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism $\pi$, alternative splicing), technological processing (sequencing error $\epsilon$, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (EdgeR vs. BaySeq software) works well even in the absence of a reference genome and is robust across a broad range of parameters. We advise against library normalization and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, Soapdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.},
author = {Vijay, Nagarjun and Poelstra, Jelmer W. and K\"{u}nstner, Axel and Wolf, Jochen B W},
doi = {10.1111/mec.12014},
file = {:home/fin/Documents/papers/mendeley/Vijay et al.\_2013\_Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive i.pdf:pdf},
isbn = {1365-294X},
issn = {09621083},
journal = {Mol. Ecol.},
keywords = {RNA-seq,bioinformatics,comparative genomics,differential gene expression,simulation,systems biology,transcriptome assembly},
pages = {620--634},
pmid = {22998089},
title = {{Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments}},
volume = {22},
year = {2013}
}
@article{Zdobnov2001a,
author = {Zdobnov, Evgeni M and Apweiler, Rolf},
file = {:home/fin/Documents/papers/mendeley/Zdobnov, Apweiler\_2001\_signature-recognition methods in InterPro\_Unknown.pdf:pdf},
number = {9},
pages = {847--848},
title = {{signature-recognition methods in InterPro}},
volume = {17},
year = {2001}
}
@article{Niess1982a,
abstract = {The endosymbiotic unit of Paramecium bursaria and Chlorella spec. shows two types of photobehaviour: 1) A step-up photophobic response which possibly depends on photosensitive agents in the ciliate cell itself - as is also shown by alga-free Paramecium bursaria - and can be drastically enhanced by photosynthetic activity of symbiotic algae; and 2) a step-down photophobic response. The step-down response leads to photoaccumulation of green paramecia. Both types of photobehaviour in Paramecium bursaria do not depend on any special kind of algal partners: The infection of alga-free Paramecium bursaria with different Chlorella species results in new ciliatealgae-associations. They are formed not only by combination of the original symbiotic algae with their host, but also by infection with other symbiotic or free-living (aposymbiotic) chlorellae, respecitively. Systems with other than the original algae are not permanently stable - algae are lost under stress conditions - but show the same types of photobehaviour. Photoaccumulation in general requires algal photosynthesis and occurs only with ciliates containing more than fifty algae/cell. It is not mediated by a chemotactic response to oxygen in the medium, since it occurs at light fluence rates not sufficient for a release of oxygen by the symbiotic system, e.g., below its photosynthetic compensation point. Photoresponses can be inhibited by 3-(3',4'-dichlorophenyl)-1,1-dimethylurea (DCMU). Sensory transduction does not depend on any special symbiotic features of the algae, e.g., sugar excretion. The participation of oxygen in the Paramecium cell, of its cytoplasmic pH and of ions released or taken up by endosymbiotic algae in sensory transduction is discussed.},
author = {Niess, D and Reisser, W and Wiessner, W},
doi = {10.1007/BF00393320},
issn = {0032-0935 (Print)},
journal = {Planta},
language = {eng},
month = dec,
number = {5},
pages = {475--480},
pmid = {24272662},
title = {{Photobehaviour of Paramecium bursaria infected with different symbiotic and aposymbiotic species of Chlorella.}},
volume = {156},
year = {1982}
}
@article{Smith1986,
author = {Smith, L.M. and Sanders, J.Z. and Kaiser, R.J. and Hughes, P. and Dodd, C. and Connell, C.R. and Heiner, C. and Kent, S.B.H. and Hood, L.E},
file = {:home/fin/Documents/papers/mendeley/Smith et al.\_1986\_Fluorescence Detection in Automated DNA Sequence Analysis\_Nature.pdf:pdf},
journal = {Nature},
number = {June},
pages = {674--679},
title = {{Fluorescence Detection in Automated DNA Sequence Analysis}},
volume = {321},
year = {1986}
}
@article{Milinkovitch1996,
author = {Milinkovitch, Michel C and Leduc, G and Ada, Jun and Farnir, Frederic and Georgest, Michel and Hasegawa, Masami},
file = {:home/fin/Documents/papers/mendeley/Milinkovitch et al.\_1996\_Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction A Case Study Based on DNA Seque.pdf:pdf},
journal = {Genetics},
pages = {1817--1833},
title = {{Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans}},
volume = {144},
year = {1996}
}
@article{Nikolenko2013,
abstract = {Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.},
archivePrefix = {arXiv},
arxivId = {1211.2756},
author = {Nikolenko, Sergey I and Korobeynikov, Anton I and Alekseyev, Max a},
doi = {10.1186/1471-2164-14-S1-S7},
eprint = {1211.2756},
file = {:home/fin/Documents/papers/mendeley/Nikolenko, Korobeynikov, Alekseyev\_2013\_BayesHammer Bayesian clustering for error correction in single-cell sequencing.\_BMC genomics.pdf:pdf},
isbn = {1471-2164 (Electronic)$\backslash$n1471-2164 (Linking)},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Algorithms,Bayes Theorem,Cluster Analysis,Escherichia coli,Escherichia coli: genetics,Sequence Analysis, DNA,Single-Cell Analysis},
number = {Suppl 1},
pages = {S7},
pmid = {23368723},
publisher = {BioMed Central Ltd},
title = {{BayesHammer: Bayesian clustering for error correction in single-cell sequencing.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3549815\&tool=pmcentrez\&rendertype=abstract},
volume = {14 Suppl 1},
year = {2013}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
SUMMARY = "The qml application launcher for the Luna Next webOS UI platform."
LICENSE = "GPL-3.0"
LIC_FILES_CHKSUM = "file://COPYING;md5=4ddd17b0c9241d7b24a4960caefe8e40"

DEPENDS = "qtbase qtdeclarative qtwebengine luna-sysmgr-common libwebos-application"
RDEPENDS_${PN} += "qtwebengine-qmlplugins qtdeclarative-qmlplugins"

PV = "0.1.0-6+git${SRCPV}"
SRCREV = "02a6b2cf8a57182a86dc27cb074db9f98e30d918"

inherit webos_ports_repo
inherit webos_system_bus
inherit webos_cmake_qt5

SRC_URI = "${WEBOS_PORTS_GIT_REPO_COMPLETE}"
S = "${WORKDIR}/git"

repository: Tofee/meta-webos-ports

repo_name: Tofee/meta-webos-ports

gha_license_id: MIT

gha_language: BitBake

extension: bb


text:
package main

import (
	"bytes"
	"crypto/ecdsa"
	"crypto/md5"
	"crypto/rand"
	"encoding/hex"
	"fmt"
	"io/ioutil"
	"log"
	"math/big"
	"mime/multipart"
	"net/http"
	"strings"
)

// Sign 签名
// 参数：
//      priKey ：私钥
//      data   ：待签名的数据
// 返回值：
//      签名后的数据
func Sign(priKey, data []byte) ([]byte, error) {
	Md5Inst := md5.New()
	Md5Inst.Write(data)
	hash := Md5Inst.Sum([]byte(""))

	x, y := SECP256K1().ScalarBaseMult(priKey)
	sk := ecdsa.PrivateKey{
		PublicKey: ecdsa.PublicKey{
			Curve: SECP256K1(),
			X:     x,
			Y:     y,
		},
		D: new(big.Int).SetBytes(priKey),
	}
	r, s, err := ecdsa.Sign(rand.Reader, &sk, hash)
	if err != nil {
		return nil, err
	}

	rBytes := r.Bytes()
	sBytes := s.Bytes()
	sign := make([]byte, 64)
	copy(sign[32-len(rBytes):32], rBytes)
	copy(sign[64-len(sBytes):64], sBytes)

	return sign, nil
}

// Verify 验证签名
// 参数：
//      sign   ：签名数据
//      data   ：待签名的数据
//      pubKey ：公钥
// 返回值：
//      验证结果
func Verify(sign, data []byte, pubKey string) (bool, error) {
	Md5Inst := md5.New()
	Md5Inst.Write(data)
	hash := Md5Inst.Sum([]byte(""))

	var pk = strings.TrimPrefix(pubKey, "04")
	x, err := hex.DecodeString(pk[:64])
	if err != nil {
		return false, err
	}
	y, err := hex.DecodeString(pk[64:])
	if err != nil {
		return false, err
	}
	publicKey := ecdsa.PublicKey{
		Curve: SECP256K1(),
		X:     new(big.Int).SetBytes(x),
		Y:     new(big.Int).SetBytes(y),
	}

	if !ecdsa.Verify(&publicKey, hash, new(big.Int).SetBytes(sign[:32]), new(big.Int).SetBytes(sign[32:])) {
		return false, nil
	}

	return true, nil
}

// CreatePubKey 由私钥生成公钥
// 参数：
//      sk   ：16进制私钥
// 返回值：
//      公钥
func CreatePubKey(sk string) string {
	k, err := hex.DecodeString(sk)
	if err != nil {
		log.Fatalln(err)
	}
	x, y := SECP256K1().ScalarBaseMult(k)

	publicKey := ecdsa.PublicKey{
		Curve: SECP256K1(),
		X:     x,
		Y:     y,
	}

	pubKey := append([]byte{0x04}, publicKey.X.Bytes()...)
	pubKey = append(pubKey, publicKey.Y.Bytes()...)
	return hex.EncodeToString(pubKey)
}

// TranPost 转账
// 参数：
//      data   ：待签名的数据
//      sign   ：签名数据
//      url    ：请求地址
func TranPost(data, sign []byte, url string) {
	// Prepare a form that you will submit to that URL.
	var b bytes.Buffer
	w := multipart.NewWriter(&b)

	// Add the other fields
	fw, err := w.CreateFormField("data")
	if err != nil {
		log.Fatalln(err)
	}

	if _, err = fw.Write(data); err != nil {
		log.Fatalln(err)
	}

	// Add the other fields
	fw, err = w.CreateFormField("sign")
	if err != nil {
		log.Fatalln(err)
	}

	if _, err = fw.Write(sign); err != nil {
		log.Fatalln(err)
	}

	// Don't forget to close the multipart writer.
	// If you don't close it, your request will be missing the terminating boundary.
	w.Close()

	// Now that you have a form, you can submit it to your handler.
	req, err := http.NewRequest("POST", url, &b)
	if err != nil {
		log.Fatalln(err)
	}
	// Don't forget to set the content type, this will contain the boundary.
	req.Header.Set("Content-Type", w.FormDataContentType())

	// Submit the request
	client := &http.Client{}
	res, err := client.Do(req)
	if err != nil {
		log.Fatalln(err)
	}

	defer res.Body.Close()
	// Check the response
	if res.StatusCode != http.StatusOK {
		log.Fatalln("StatusCode", res.StatusCode)
	}

	body, err := ioutil.ReadAll(res.Body)
	if err != nil {
		log.Fatalln(err)
	}

	fmt.Println(string(body))
}

extension: go


text:
@article{harris2015,
 abstract = {BACKGROUND: Annually, more than 11 million patients are admitted to hospital overnight in England, but the UK is ranked 24 of 31 European countries with respect to per head provision of intensive care unit (ICU) beds. This lack of beds places strain on the capacity to admit patients from the ward because of high ICU occupancy. Such delay can cause harm, but the effect of such harm is difficult to measure. Prompt admissions are prompt precisely because these patients are severely unwell. Measured severity is unlikely to completely capture the clinical judgment used to allocate early admission, and therefore risk-adjusted outcomes will be biased against the early admission. We aimed to evaluate the effect of delayed admission to critical care without this treatment selection bias. METHODS: We did a prospective cohort study of deteriorating ward patients assessed for critical care admission in National Health Service hospitals in the UK. Early admission was defined as within 4 h of assessment. The primary endpoint was 90-day survival. We used critical care occupancy as an instrumental variable, assuming that a full ICU could only affect outcome of a ward patient by deflecting or delaying admission. FINDINGS: 12 495 patients from 48 hospitals were available for analysis of whom 3797 (30·4%) died within 90 days. 4494 (36·0%) patients were admitted to critical care of whom 2492 (55·5%) were admitted early. The median time to admission was 2 h (IQR 1-3) with a bedside decision to admit, and 12 h otherwise (5-29). 991 patients (7·9%) were assessed when the critical care unit was fully occupied. Compared with those assessed when more than one bed was available, these patients were admitted less often (odds ratio [OR] 0·37, 95% CI 0·28-0·48), experienced greater delays (median increase 2 h, IQR 1-3), and deteriorated further while waiting (1·4 ICNARC physiology points, 95% CI 0·4-2·5). Early admission reduced mortality (OR 0·49, 95% CI 0·27-0·89). When averaged across the full population, absolute mortality fell by 13·9% (95% CI 25-23·0). INTERPRETATION: Our study has shown that the deteriorating ward patient is vulnerable with a high short-term mortality (none of these patients had treatment limitations). Delays to admission were large and common, and arose both from our inability to perfectly triage these patients, and from limits to the capacity of the system. That these delays cause harm is very likely. FUNDING: Wellcome Trust, National Institute for Health Research Service Support Costs, Intensive Care National Audit & Research Centre.},
 author = {Harris, S and Singer, M and Rowan, K and Sanderson, C},
 editor = {},
 journal = {Lancet},
 keywords = {},
 location = {London School of Hygiene & Tropical Medicine, London, UK. Electronic address: doc@steveharris.me. University College London, London, UK. Intensive Care National Audit & Research Centre, London, UK. London School of Hygiene & Tropical Medicine, London, UK.},
 number = {},
 pages = {S40},
 title = {Delay to admission to critical care and mortality among deteriorating ward patients in UK hospitals: a multicentre, prospective, observational cohort study.},
 volume = {385 Suppl 1},
 year = {2015}
}

repository: docsteveharris/harris-data-lab

repo_name: docsteveharris/harris-data-lab

branch_name: refs/heads/main

gha_language: TeX


text:
# Copyright (C) 2021 Khem Raj <raj.khem@gmail.com>
# Released under the MIT license (see COPYING.MIT for the terms)

SUMMARY = "execnet: rapid multi-Python deployment"
HOMEPAGE = "https://execnet.readthedocs.io/en/latest/"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://LICENSE;md5=772fcdaca14b378878d05c7d857e6c3e"

DEPENDS += "\
    python3-pip-native \
    python3-hatch-vcs-native \
"

SRC_URI += "file://run-ptest \
           "
SRC_URI[sha256sum] = "cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af"

inherit ptest pypi python_hatchling

do_install_ptest() {
    install -d ${D}${PTEST_PATH}/tests
    cp -rf ${S}/testing/* ${D}${PTEST_PATH}/tests/
}

RDEPENDS:${PN}-ptest += "\
    python3-pytest \
"

RDEPENDS:${PN} += "python3-core python3-crypt python3-ctypes python3-fcntl python3-io python3-shell python3-threading"

BBCLASSEXTEND = "native nativesdk"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded


text:
DESCRIPTION = "gdb - GNU debugger"
LICENSE="GPL"
SECTION = "devel"
PRIORITY = "optional"
PR = "r1"
MAINTAINER = "Pawel Osiczko <p.osiczko@tetrapyloctomy.org>"
DEPENDS = "ncurses readline"

PACKAGES =+ 'gdbserver '
FILES_gdbserver = '${bindir}/gdbserver'

inherit autotools gettext

SRC_URI = "${GNU_MIRROR}/gdb/gdb-${PV}.tar.gz \
	   file://uclibc.patch;patch=1"

LDFLAGS_append = " -s"
export CC_FOR_BUILD = "${BUILD_CC}"
export CXX_FOR_BUILD = "${BUILD_CXX}"
export CPP_FOR_BUILD = "${BUILD_CPP}"
export CFLAGS_FOR_BUILD = "${BUILD_CFLAGS}"
export CXXFLAGS_FOR_BUILD = "${BUILD_CXXFLAGS}"
export CPPFLAGS_FOR_BUILD = "${BUILD_CPPFLAGS}"
export CFLAGS_append=" -L${STAGING_LIBDIR}"
EXTRA_OEMAKE = "'SUBDIRS=intl mmalloc libiberty opcodes bfd sim gdb etc utils'"

EXTRA_OECONF = "--disable-gdbtk --disable-tui --disable-x \
                --with-curses --disable-multilib --with-readline --disable-sim \
                --program-prefix=''"

S = "${WORKDIR}/gdb-${PV}"
B = "${WORKDIR}/build-${TARGET_SYS}"

do_configure () {
# override this function to avoid the autoconf/automake/aclocal/autoheader
# calls for now
	(cd ${S} && gnu-configize) || die "failure in running gnu-configize"
        CPPFLAGS="" oe_runconf
}

do_install () {
	make -C bfd/doc chew LDFLAGS= CFLAGS=-O2
	oe_runmake install \
	    'prefix=${D}' 'exec_prefix=${D}' 'bindir=${D}${base_bindir}' \
	    'sbindir=${D}${base_sbindir}' 'infodir=${D}/share/info' 'libdir=${D}${base_libdir}' \
	    'mandir=${D}/share/man' 'includedir=${D}/include'
	install -d ${D}${bindir}
	install -m 0755 gdb/gdbserver/gdbserver ${D}${bindir}
}


text:
package country_ip

import (
	"github.com/stretchr/testify/assert"
	"testing"
)

func TestIP_From(t *testing.T) {
	cases := []struct {
		ip   string
		c    string
		want bool
	}{
		{
			"114.114.114.114",
			"CN",
			true,
		},
		{
			"192.168.1.183",
			"LAN",
			true,
		},
		{
			"1.1.1.1",
			"AU",
			true,
		},
	}

	for _, cs := range cases {
		r, err := IP(cs.ip).From(cs.c)
		assert.NoError(t, err)
		assert.Equal(t, r, cs.want)
	}
}

repository: ruijzhan/country-ip

repo_name: ruijzhan/country-ip


text:
package model

import "time"

type Dataset struct {
	Owner     string    `dynamodbav:"owner" json:"owner"`
	DatasetId string    `dynamodbav:"dataset_id" json:"dataset_id"`
	Created   time.Time `dynamodbav:"created" type:"timestamp" timestampFormat:"unix" json:"created"`
}

type Metadata struct {
	DatasetId   string    `dynamodbav:"dataset_id" json:"dataset_id"`
	MetadataId  string    `dynamodbav:"metadata_id" json:"metadata_id"`
	DescribedBy string    `dynamodbav:"described_by" json:"described_by"`
	Created     time.Time `dynamodbav:"created" type:"timestamp" timestampFormat:"unix" json:"created"`
}

type ValidationResult struct {
	Valid   bool     `json:"valid"`
	Message string   `json:"message"`
	Errors  []string `json:"errors"`
}

type ErrorMessage struct {
	Message string `json:"message"`
}

var DefaultOwner = "dan"

type MetadataSuccessMessage struct {
	Info Metadata `json:"info"`
	File string   `json:"file"`
}

repository: codetaming/indy-ingest

repo_name: codetaming/indy-ingest

gha_language: Go


text:
package gb

type interrupt uint8

const (
	vblankInterrupt interrupt = 1 << iota
	lcdStatInterrupt
	timerInterrupt
	serialInterrupt
	joypadInterrupt

	anyInterrupt = 0xff
)

func (i interrupt) String() string {
	buf := []byte{'-', '-', '-', '-', '-', '-', '-', '-'}

	if i&vblankInterrupt > 0 {
		buf[0] = 'V'
	}
	if i&lcdStatInterrupt > 0 {
		buf[1] = 'L'
	}
	if i&timerInterrupt > 0 {
		buf[2] = 'T'
	}
	if i&serialInterrupt > 0 {
		buf[3] = 'S'
	}
	if i&joypadInterrupt > 0 {
		buf[4] = 'J'
	}

	return string(buf)
}

type interruptCtrl struct {
	IME    bool
	IF, IE interrupt
}

func (ic *interruptCtrl) clock(gb *GameBoy) {}

func (ic *interruptCtrl) write(addr uint16, v uint8) {
	switch addr {
	case ioRegs.IF:
		ic.IF = interrupt(v)
	case ioRegs.IE:
		ic.IE = interrupt(v)
	default:
		unmappedWrite("interrupt controller", addr, v)
	}
}

func (ic *interruptCtrl) read(addr uint16) uint8 {
	switch addr {
	case ioRegs.IF:
		return 0xe0 | uint8(ic.IF)
	case ioRegs.IE:
		return uint8(ic.IE)
	default:
		unmappedRead("interrupt controller", addr)
		return 0
	}
}

func (ic *interruptCtrl) raised(interrupt interrupt) interrupt {
	return ic.IE & ic.IF & interrupt
}

func (ic *interruptCtrl) raise(interrupt interrupt) {
	ic.IF |= interrupt
}

func (ic *interruptCtrl) enabled(interrupt interrupt) interrupt {
	return ic.IE & interrupt
}

func (ic *interruptCtrl) enable(interrupt interrupt) {
	ic.IE |= interrupt
}

func (ic *interruptCtrl) ack(interrupt interrupt) {
	ic.IF &^= interrupt
}

license: Unlicense

repository: flga/gb

repo_name: flga/gb


text:
// Copyright © 2009--2013 The Web.go Authors
// Use of this source code is governed by a MIT-style
// license that can be found in the LICENSE file.

// Simple web framework.
//
// At the core of web.go are request handlers:
//
//     func helloworld() string {
//         return "hello, world"
//     }
//
// These are hooked up to the routing table using web.go:
//
//     func main() {
//         web.Get("/", helloworld)
//         web.Run("127.0.0.1:9999")
//     }
//
// Now visit http://127.0.0.1:9999 to see the greeting
//
// The routing table is based on regular expressions and allows parameter
// groups:
//
//     func hello(name string) string {
//         return "hello, " + name
//     }
//
//     func main() {
//         web.Get("/(.*)", hello)
//         web.Run("127.0.0.1:9999")
//     }
//
// Visit http://127.0.0.1:9999/fidodido to see 'hello, fidodido'
//
// Route handlers may contain a pointer to web.Context as their first parameter.
// This variable serves many purposes -- it contains information about the
// request, and it provides methods to control the http connection.
//
// See the examples directory for more examples.
package web

repository: hraban/web

repo_name: hraban/web


text:
package dome9

import "time"

// Finding holds information pertaining to rule violations
type Finding struct {
	//FindingID string  `json:"id"`
	//FindingKey string `json:"findingKey"`

	assessmentID int // not populated by endpoint

	EntityType       string `json:"entityType"`
	EntityName       string `json:"entityName"`
	EntityExternalID string `json:"entityExternalId"`

	FindingDescription string `json:"description"`
	Remediation        string `json:"remediation"`

	RuleName  string `json:"ruleName"`
	RuleLogic string `json:"ruleLogic"`
	RuleHash  string // Not populated by endpoint

	Severity string `json:"severity"`

	//CreatedTime  time.Time `json:"createdTime"`
	//UpdatedTime  time.Time `json:"updatedTime"`
	//LastSeenTime time.Time `json:"lastSeenTime"`

	//CloudAccountType string `json:"cloudAccountType"`
	CloudAccountID           string `json:"cloudAccountId"`
	externalCloudAccountID   string
	externalCloudAccountName string

	// bundleID is not returned by the API, but is populated by the api wrapper
	bundleID string

	// dueDate is not returned by the API, and must be set manually
	dueDate time.Time
}

// Bundle holds the rules associated to a particular binding, which are then used to get findings that violate the rule
type Bundle struct {
	Rules     []Rule `json:"rules"`
	AccountID int    `json:"accountId"`
	//CreatedTime      time.Time `json:"createdTime"`
	//UpdatedTime      time.Time `json:"updatedTime"`
	ID               int    `json:"id"`
	Name             string `json:"name"`
	Description      string `json:"description"`
	IsTemplate       bool   `json:"isTemplate"`
	HideInCompliance bool   `json:"hideInCompliance"`
	MinFeatureTier   string `json:"minFeatureTier"`
	Section          int    `json:"section"`
	TooltipText      string `json:"tooltipText"`
	ShowBundle       bool   `json:"showBundle"`
	SystemBundle     bool   `json:"systemBundle"`
	CloudVendor      string `json:"cloudVendor"`
	Version          int    `json:"version"`
	Language         string `json:"language"`
	RulesCount       int    `json:"rulesCount"`
}

// Rule holds information pertaining to compliance in a CIS engine
type Rule struct {
	Name          string `json:"name"`
	Severity      string `json:"severity"`
	Logic         string `json:"logic"`
	Description   string `json:"description"`
	Remediation   string `json:"remediation"`
	ComplianceTag string `json:"complianceTag"`
	Domain        string `json:"domain"`
	Priority      string `json:"priority"`
	ControlTitle  string `json:"controlTitle"`
	RuleID        string `json:"ruleId"`
	LogicHash     string `json:"logicHash"`
	IsDefault     bool   `json:"isDefault"`
}

// CloudAccount ... TODO:
type CloudAccount struct {
	ID                    string `json:"id"`
	Vendor                string `json:"vendor"`
	Name                  string `json:"name"`
	ExternalAccountNumber string `json:"externalAccountNumber"`
	Error                 string `json:"error"`
	//CreationDate          time.Time `json:"creationDate"`
	//Credentials           struct {
	//	Apikey     string `json:"apikey"`
	//	Arn        string `json:"arn"`
	//	Secret     string `json:"secret"`
	//	IamUser    string `json:"iamUser"`
	//	Type       string `json:"type"`
	//	IsReadOnly bool   `json:"isReadOnly"`
	//} `json:"credentials"`
	//IamSafe struct {
	//	AwsGroupArn         string `json:"awsGroupArn"`
	//	AwsPolicyArn        string `json:"awsPolicyArn"`
	//	Mode                string `json:"mode"`
	//	State               string `json:"state"`
	//	ExcludedIamEntities struct {
	//		RolesArns []string `json:"rolesArns"`
	//		UsersArns []string `json:"usersArns"`
	//	} `json:"excludedIamEntities"`
	//	RestrictedIamEntities struct {
	//		RolesArns []string `json:"rolesArns"`
	//		UsersArns []string `json:"usersArns"`
	//	} `json:"restrictedIamEntities"`
	//} `json:"iamSafe"`
	//NetSec struct {
	//	Regions []struct {
	//		Region           string `json:"region"`
	//		Name             string `json:"name"`
	//		Hidden           bool   `json:"hidden"`
	//		NewGroupBehavior string `json:"newGroupBehavior"`
	//	} `json:"regions"`
	//} `json:"netSec"`
	//Magellan               bool   `json:"magellan"`
	//FullProtection         bool   `json:"fullProtection"`
	//AllowReadOnly          bool   `json:"allowReadOnly"`
	//OrganizationalUnitID   string `json:"organizationalUnitId"`
	//OrganizationalUnitPath string `json:"organizationalUnitPath"`
	//OrganizationalUnitName string `json:"organizationalUnitName"`
	//LambdaScanner          bool   `json:"lambdaScanner"`
}


text:
package main

import "fmt"

//当前size不超过1024，按每次2倍增长，否则按当前大小的1/4增长。
// slice will inherit array's capacity and length.
//func main() {
//	data := [7]int{0, 1, 2, 3, 4, 5,}
//	fmt.Println(data, len(data), cap(data))
//	a := data[:3]
//	fmt.Println(a, len(a), cap(a))
//	a = append(a, a[:3]...) // output [0 1 2 100]
//	fmt.Println(a, len(a), cap(a))
//	a = append(a, 100)
//	fmt.Println(a, len(a), cap(a))
//
//}

func main() {
	a := []int{1} // after initialization len=1 cap=1
	test(a)       // call test to append slice, but a is [1], not [1 2]
	fmt.Println(a, len(a), cap(a))
}
func test(a []int) {
	a = append(a, 2)
	fmt.Println(a, len(a), cap(a))
}

//----output----
//[1 2] 2 2
//[1] 1 1

repository: FrankHitman/playGo

repo_name: FrankHitman/playGo


text:
package repository_test

import (
	"github.com/stone1549/product-admin-service/repository"
	"testing"
)

func makeNewImRepo(t *testing.T) repository.ProductRepository {
	repo, err := repository.MakeInMemoryRepository(inMemorySmall)

	ok(t, err)
	return repo
}


text:
require recipes-kernel/linux/linux.inc

KERNEL_IMAGETYPE = "uImage"

COMPATIBLE_MACHINE = "bug20"

MACHINE_KERNEL_PR_append = "+gitr${SRCREV}"

SRCREV = "37efe9e3ef0e12a207a92da21f28fe7d295c4aba"

SRC_URI = "git://github.com/buglabs/bug20-2.6.35-linaro.git;branch=master;protocol=git"

S = "${WORKDIR}/git"

do_configure_prepend() {
	cp arch/arm/configs/omap3_buglabs_defconfig ${WORKDIR}/defconfig
}

do_configure_append() {
	sed -i -e "s/CONFIG_LOCALVERSION=\"\"/CONFIG_LOCALVERSION=\"-${PR}\"/g" ${S}/.config
	sed -i "/CONFIG_ARM_UNWIND[ =]/d" ${S}/.config
	echo "# CONFIG_ARM_UNWIND is not set" >> ${S}/.config
}

# Make BMI header files available for JNI
do_install_append() {
	install -d ${D}${includedir}/linux/bmi/
	install -m 0644 ${S}/include/linux/bmi/*.h ${D}${includedir}/linux/bmi/

	install -d ${D}${sysconfdir}/
	echo "BUG Kernel Information" > ${D}${sysconfdir}/kernelinfo
	date >> ${D}${sysconfdir}/kernelinfo
	whoami >> ${D}${sysconfdir}/kernelinfo
	echo "git rev: ${SRCREV}" >> ${D}${sysconfdir}/kernelinfo
}

PACKAGES += "kernel-headers"
FILES_kernel-headers = "${includedir}/linux/bmi"
FILES_kernel-image += "${sysconfdir}/kernelinfo"

module_conf_g_file_storage = "options g_file_storage file=/dev/mmcblk1 removable=y"
module_autoload_g_file_storage = "g_file_storage"

module_autoload_bmi_li3m02cm = "bmi_camera \
iommu2 \
omap3-iommu \
omap3-isp \
omap34xxcam \
"
# Perf in 2.6.35 doesn't build, so disable it
do_compile_perf() {
    :
}

do_install_perf() {
    :
}

repository: GNUtoo/meta-bug

repo_name: GNUtoo/meta-bug


text:
@InProceedings{tran11,
  title = {Mixed-Variate Restricted Boltzmann Machines},
  author = {T. Tran and D. Phung  and  S. Venkatesh},
  pages = {213--229},
  abstract = {Modern datasets are becoming heterogeneous. To this end, we present in this paper Mixed-Variate Restricted Boltzmann Machines for simultaneously modelling variables of multiple types and modalities, including binary and continuous responses, categorical options, multicategorical choices, ordinal assessment and category-ranked preferences. Dependency among variables is modeled using latent binary variables, each of which can be interpreted as a particular hidden aspect of the data. The proposed model, similar to the standard RBMs, allows fast evaluation of the posterior for the latent variables. Hence, it is naturally suitable for many common tasks including, but not limited to, (a) as a pre-processing step to convert complex input data into a more convenient vectorial representation through the latent posteriors, thereby offering a dimensionality reduction capacity, (b) as a classifier supporting binary, multiclass, multilabel, and label-ranking outputs, or a regression tool for continuous outputs and (c) as a data completion tool for multimodal and heterogeneous data. We evaluate the proposed model on a large-scale dataset using the world opinion survey results on three tasks: feature extraction and visualization, data completion and prediction.},
  pdf = {http://jmlr.org/proceedings/papers/v20/tran11/tran11.pdf},
}

repository: mreid/papersite

repo_name: mreid/papersite


text:
package validator

import (
	"errors"
	"fmt"
	"reflect"
	"strconv"
	"strings"
)

type IValidator interface {
	Validate(field string, value reflect.Value, isRequired bool, args ...string) error
}

var validatorsMap = map[string]IValidator{
	"required": &RequiredValidator{},
	"string":   &StringValidator{},
	"number":   &NumberValidator{},
	"multi":    &MultiValidator{},
	"in":       &InValidator{},
	"len":      &LenValidator{},
}

/*
RequiredValidator
*/
type RequiredValidator struct {
}

func (rv *RequiredValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] is must required"

	if checkIsZoreValue(value) {
		return formatError(eMsg, field)
	}

	return nil
}

/*
StringValidator
*/
type StringValidator struct {
	Equal
	Range
}

func (sv *StringValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] is not a string"

	if value.Kind() != reflect.String {
		return formatError(eMsg, field)
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}

	argsLen := len(args)
	if argsLen == 1 {
		return sv.ValueEqual(field, value, args[0])
	}

	if argsLen == 2 {
		sv.InitRange(field, args...)
		return sv.CompareStringRange(value)
	}

	return nil
}

/*
NumberValidator
*/
type NumberValidator struct {
	Equal
	Range
}

func (nv *NumberValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] is not a number"

	if !checkIsNumberKind(value.Kind()) {
		return formatError(eMsg, field)
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}

	argsLen := len(args)
	if argsLen == 1 {
		return nv.ValueEqual(field, value, args[0])
	}

	if argsLen == 2 {
		nv.InitRange(field, args...)
		return nv.CompareNumberRange(value)
	}

	return nil
}

/*
MultiValidator
*/
type MultiValidator struct {
	Equal
	Range
}

func (av *MultiValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] is not a array/slice/map"

	if !checkIsMultiKind(value.Kind()) {
		return formatError(eMsg, field)
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}

	if len(args) == 1 {
		return av.MultiEqual(field, value, args...)
	}

	if len(args) == 2 {
		av.InitRange(field, args...)
		return av.CompareMultiRange(value)
	}

	return nil
}

/*
BoolValidator
*/
type BoolValidator struct {
	Equal
}

func (bv *BoolValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] is not a bool"

	if value.Kind() != reflect.Bool {
		return formatError(eMsg, field)
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}

	if len(args) == 1 {
		return bv.ValueEqual(field, value, args[0])
	}

	return nil
}

/*
	InValidator
	仅支持 string,float,int,bool 类型
	或值类型为 string,float,int,bool 类型的array,slice,map
*/
type InValidator struct {
	Equal
}

func (iv *InValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) (err error) {
	eMsg := "[name] is not in [value]"

	if len(args) == 0 {
		return errors.New("[InValidator] validator must have params")
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}

	isIn := false

	switch kind := value.Kind(); {
	case !checkIsMultiKind(kind):
		s := fmt.Sprint(value.Interface())
		if strings.Index(args[0], s) >= 0 {
			isIn = true
		}
		break
	case kind == reflect.Array || kind == reflect.Slice:
		s := fmt.Sprint(value.Interface())
		argsArr := strings.Split(args[0], ",")
		for _, v := range argsArr {
			if strings.Index(s, v) >= 0 {
				isIn = true
				break
			}
		}
		break
	case kind == reflect.Map:
		ks := value.MapKeys()
		for _, v := range ks {
			s := fmt.Sprint(value.MapIndex(v))
			if strings.Index(args[0], s) >= 0 {
				isIn = true
				break
			}
		}
		break
	}

	if !isIn {
		return formatMapError(eMsg, map[string]string{"name": field, "value": args[0]})
	}

	return nil
}

/*
	LenValidator
*/
type LenValidator struct {
	Equal
}

func (lv *LenValidator) Validate(field string, value reflect.Value, isRequired bool, args ...string) error {
	eMsg := "[name] length should be equal [value]"

	if len(args) != 1 {
		return errors.New("[LenValidator] validator must have 1 param")
	}

	if !checkIsLen(value.Kind()) && !checkIsNumberKind(value.Kind()) {
		return formatError(TYPE_INVALID, field)
	}

	if !isRequired && checkIsZoreValue(value) {
		return nil
	}
	l, err := strconv.ParseInt(args[0], 10, 64)
	if err != nil {
		return errors.New("len args must be a int")
	}

	le := 0
	if checkIsNumberKind(value.Kind()) {
		s := numberToString(value)
		le = len(s)
	} else {
		le = value.Len()
	}

	if le != int(l) {
		return formatMapError(eMsg, map[string]string{"name": field, "value": args[0]})
	}

	return nil
}

repository: baxiang/soldiers-sortie

repo_name: baxiang/soldiers-sortie


text:
require pulseaudio.inc

SRCREV = "f834150aceccd753e3ac5bab9f7d64bed9993624"
PV = "0.9.22+git"
PR = "${INC_PR}.1-r${SRCPV}"

DEPENDS += "orc gdbm speex"

DEFAULT_PREFERENCE = "-1"

FILESPATHPKG =. "pulseaudio-0.9.21:"

inherit gettext

SRC_URI = "git://git.0pointer.de/pulseaudio.git;protocol=git \
           file://gcc4-compile-fix.patch \
           file://volatiles.04_pulse \
           file://autoconf_version.patch \
           file://tls_m4.patch \
"

S = "${WORKDIR}/git"

EXTRA_OECONF += " --with-module-dir=${libdir}/pulse-${PV}/modules"

do_configure_prepend() {
	touch config.rpath
	echo "${PV}" >.tarball-version
	echo "${PV}" >.version
}

# orc.m4 calls pkg-config ----variable=orcc orc-0.4 to get the path to orcc,
# resulting in /usr/bin/orcc. Force it to use the staged orcc.
do_configure_append() {
    for i in $(find ${S} -name "Makefile") ; do
        sed -i -e s:${bindir}/orcc:${STAGING_BINDIR_NATIVE}/orcc:g $i
    done
}

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
/*
 * Early Access
 *
 * API Reference — v2
 *
 * API version: 2.2
 * Generated by: OpenAPI Generator (https://openapi-generator.tech)
 */

package twitapi
// TweetNonPublicMetrics Nonpublic engagement metrics for the Tweet at the time of the request.
type TweetNonPublicMetrics struct {
	// Number of times this Tweet has been viewed.
	ImpressionCount int32 `json:"impression_count,omitempty"`
}

repository: kylebevans/twitapi

repo_name: kylebevans/twitapi