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1,290 results for “Silva”
Silva SSU taxonomic training data formatted for DADA2 (Silva version 138)
<p>These DADA2-formatted training fasta files were derived from the Silva Project's version 138 release. See https://www.arb-silva.de/documentation/release-138/ for database and citation information. The Silva 138 database is licensed under Creative Commons Attribution 4.0 (CC-BY 4.0); see file "SILVA_LICENSE.txt". The fasta files were generated and checked for consistency with version 132 using the R code in the R-markdown document "silva-v138.Rmd".</p> <p>Version 2 removes the dependence on preprocessed files from mothur, which results in a greater number of bacterial and archeal sequences. It also includes a new version of the assignTaxonomy training set that goes through the species level for use with longer amplicons obtained from long-read amplicon sequencing.</p> <p>If you use these files, please cite one or both of the Silva references below (or at the above link) and the DADA2 paper (reference below). I also recommend citing or linking to the Zenodo record for this specific version in your Methods or published source code to record the specific taxonomic database files used in your analysis.</p> <p><strong>NOTE:</strong><strong> </strong>These Version 2 files are intended for use in classifying prokaryotic 16S sequencing data and are not appropriate for classifying eukaryotic ASVs. The new method implemented within DADA2 for constructing these files only includes 100 eukaryotic sequences for use as an outgroup.</p> <p><strong>NOTE:</strong> These Version 2 files have a known problem in 10/883 families and 114/3838 genera. See https://github.com/mikemc/dada2-reference-databases/blob/main/silva-138/v2/bad-taxa.csv for a list of affected taxa and https://github.com/benjjneb/dada2/issues/1293 for more information.</p>
Dataset gerado pela ferramenta pyHDB - Germano Lopes da Silva, Hemetério José dos Santos e Monteiro Lopes
<p>Esse dataset foi gerado pela <strong>pyHDB: Ferramenta heurística para a Hemeroteca Digital Brasileira </strong>a partir de três buscas realizadas no mês de outubro de 2021.</p> <p>A pyHDB é uma ferramenta de auxílio metodológico para pesquisa na interface da Hemeroteca Digital Brasileira da Biblioteca Nacional desenvolvida por <a href="https://github.com/ericbrasiln">Eric Brasil</a> como parte de pesquisa acadêmica da área de História Digital.</p> <p>As buscas utilizaram como parâmetros:</p> <p><strong>Busca 1: </strong></p> <ul> <li>Local da busca: <em>RJ</em>;</li> <li>Período da busca: <em>Todos</em>;</li> <li>Periódico da busca: <em>Todos</em>;</li> <li>Termo da busca: <em>“germano lopes da silva”</em></li> </ul> <p><strong>Busca 2:</strong></p> <ul> <li>Local da busca: <em>RJ</em>;</li> <li>Período da busca: <em>Todos</em>;</li> <li>Periódico da busca: <em>Todos</em>;</li> <li>Termo da busca: <em>“hemeterio jose dos santos”</em></li> </ul> <p><strong>Busca 3:</strong></p> <ul> <li>Local da busca:<em> RJ</em>;</li> <li>Período da busca: <em>1900 - 1909 & 1910 - 1919</em>;</li> <li>Periódico da busca: <em>Todos</em>;</li> <li>Termo da busca: <em>“monteiro lopes”</em></li> </ul> <p>Para maiores informações ver o o <a href="https://doi.org/10.5281/zenodo.5696670">repositório da ferramenta</a>.</p> <p>Esse dataset foi analisado em artigo científico que se encontra em fase de avaliação por pares.</p>
Figures 1–4 in A new species of Allomallodon Santos-Silva and Galileo, 2010 from Bolivia (Coleoptera: Cerambycidae: Prioninae: Macrotomini)
Figures 1–4. Allomallodon bolivianus sp. nov., holotype female. 1) Dorsal habitus. 2) Ventral habitus. 3) Head and prothorax, lateral view. 4) Labrum.
Figures 3–4 in Notes on the natural history of Enaphalodes archboldi Lingafelter and Chemsak, 2002 and E. bingkirki Lingafelter and Santos-Silva, 2018 (Coleoptera: Cerambycidae)
Figures 3–4. Signs of the workings of young larvae. 3) Crack in the bark where the larva circled the stem. 4) Subcortical gallery heading down the stem.
Figures 7–8 in Notes on the natural history of Enaphalodes archboldi Lingafelter and Chemsak, 2002 and E. bingkirki Lingafelter and Santos-Silva, 2018 (Coleoptera: Cerambycidae)
Figures 7–8. Expelled frass on the ground. 7) Severed stem next to a pile of frass. The bottom part is not apparent because it is covered by the frass and leaves. 8) Bottom part of the severed stem with regions of tightly packed granular frass. The red arrow points to the upper side of the stem.
Supplementary files for Silva et al. 2020 "Reptiles on the wrong track?": R Code, data and figures
<p>Datasets, R code and figures pertaining to the manuscript: Silva, I., Crane, M., Marshall, B.M., & Strine, C.T. (2020).<em> </em> <em>Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian Bridge Movement Models.</em> Movement Ecology 8, 43 DOI: 10.1186/s40462-020-00229-3</p> <p>Article available at: <a href="https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3">https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3</a></p>
FIG. 2 in Paleotropical distribution of the genus Neotropicomus A.C.Magnago, Alves-Silva & T.W.Henkel: a new species from India
FIG. 2. — Phylogram inferred from combined ITS and 28S dataset using IQTree program. BS ≥ 60% is indicated above or below the branches. Novel taxon is given in bold.
FIG. 1 in Paleotropical distribution of the genus Neotropicomus A.C.Magnago, Alves-Silva & T.W.Henkel: a new species from India
FIG. 1. — Neotropicomus indicus sp. nov. (from holotype): A-C, basidiomata; D, basidiospores; E, basidia; F, G, pleurocystidia; H, cheilocystidia; I, pileipellis; J, stipitipellis; K, terminal cells of pileipellis; L, caulocystidium. Scale bars: A-C, 20 mm; D-H, K, L, 10 μm; I, J, 20 μm.
Figure 6 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 6.Preserved specimen of Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000 from Buraco do Cão cave, Iraquara municipality, state of Bahia, Brazil (A) and live specimen of S. spinilacertus from Canoa Quebrada cave, municipality of Iraquara, state of Bahia, Brazil (B). Photograph: (A) Luciana B.R. Fernandes, (B) Adriano Gambarini.
Figure 4 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 4. Spelaeogammarus ginae sp. nov., Gruna da Serra Verde cave, Serra do Ramalho, state of Bahia, Brazil. Paratype male, body length 11.31 mm; pleopod 1 (A); pleopod 2 (B); pleopod 3 (C); uropod 1 (D); uropod 2 (E); uropod 3 (F); telson (G). Scale bars: A–F = 1 mm; G = 200 μm. Specimens of Spelaeogammarus ginae sp. nov. were found (C); map indicating the state of Bahia, the Gruna da Serra Verde cave, and the land use and land cover of the area (D). Photographs: M.E. Bichuette.
Figure 2 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 2. Spelaeogammarus ginae sp. nov., Gruna da Serra Verde cave, Serra do Ramalho, state of Bahia, Brazil. Paratype male, body length 11.31 mm; antenna 1 (A); antenna 2 (B); upper lip (C); lower lip (D); maxilla 1 (E); maxilla 2 (F); left mandible (G); right mandible (H); maxilliped (I); simple setae, present in various structures, the last one is more common on the uropods (J); aesthetasc, from antenna 1 (K); multicuspidate seta, from maxilla 1 outer plate (L); plumose setae, from antenna 1, maxilla 1 inner plate, maxilla 2 inner plate, mandibles and maxilliped, maxilliped and gnathopods, pleopods (M); (stout) cuspidate setae with accessory seta, present in various structures, first one more common on gnathopods and last one from telson (N); bifid and trifid setae, from maxilliped inner ramus, mandibles palp, gnathopods and uropod 3, pleopod 7, maxilliped palp (O). Scale bars: A, B = 600 μm; C–I = 200 μm; J–O = enlarged setae to see details.
Figure 5 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 5. Outcrops and pastures close to the Gruna da Serra Verde cave (A); cave gallery in the dry season (B) and detail of the small pool formed by the upper phreatic aquifer, where specimens of Spelaeogammarus ginae sp. nov. were found (C); map indicating the state of Bahia, the Gruna da Serra Verde cave, and the land use and land cover of the area (D). Photographs: M.E. Bichuette.
Figure 3 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 3. Spelaeogammarus ginae sp. nov., Gruna da Serra Verde cave, Serra do Ramalho, state of Bahia, Brazil. Paratype male, body length 11.31 mm; gnathopod 1 (A); gnathopod 2 (B); pereopod 3 (C); pereopod 4 (D); pereopod 5 (E); pereopod 6 (F); pereopod 7 (G). Scale bars: A, B = 400 μm; C–G = 1 mm.
Figure 7 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 7. Lake formed by upper phreatic aquifer at Canoa Quebrada cave (A); small pool of upper phreatic aquifer at Lapa Doce System (B); distribution of Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000, indicating caves with records of the species showing the land use and land cover of the area (C). Caption: LD = Lapa Doce System, GU = Gruta da Umburana cave, LS = Gruta da Lagoa Seca cave, BC = Buraco do Cão cave, CQ = Canoa Quebrada cave, BS = Baixa do Salitre cave, and BJ = Jaburu cave. Photographs: (A) Adriano Gambarini, (B) Jonas E. Gallão.
Figure 1 in A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000
Figure 1. Preserved (A) and live specimen (B) of Spelaeogammarus ginae sp. nov., Gruna da Serra Verde cave, Serra do Ramalho karst area, state of Bahia, Brazil. Photographs: (A) T. Zepon, (B) M.E. Bichuette.
Figs 1–4 in Validation of Eclipta dendensis Nascimento & Santos-Silva, 2017 (nomen nudum) (Coleoptera, Cerambycidae, Cerambycinae, Rhinotragini)
Figs 1–4. Eclipta dendensis sp. nov., holotype ♀, images copied from NASCIMENTO & SANTOS-SILVA (2017): 1, dorsal habitus; 2, ventral habitus; 3. lateral habitus; 4, head, frontal view. Total length: 8,55 mm.
Silva taxonomic training data formatted for DADA2 (Silva version 138.2)
<p>These DADA2-formatted training fasta files were derived from the Silva Project's version 138.2 release: https://www.arb-silva.de/</p> <p>These fastas were generated by the following commands (using the dada2 R package version 1.35.4):</p> <blockquote> <p>path <- "~/tax/Silva/v138_2"<br>fn.out.slv <- "~/Desktop/silva_nr99_v138.2_toGenus_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), <br> file.path(path, "tax_slv_ssu_138.2.txt"), <br> fn.out.slv)<br> <br>fn.out.spc.slv <- "~/Desktop/silva_nr99_v138.2_toSpecies_trainset.fa.gz"<br>dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), <br> file.path(path, "tax_slv_ssu_138.2.txt"), <br> fn.out.spc.slv, include.species=TRUE)</p> <p>fn.out.aS.slv <- "~/Desktop/silva_v138.2_assignSpecies.fa.gz"<br>dada2:::makeSpeciesFasta_Silva("~/tax/silva/v138_2/SILVA_138.2_SSURef_tax_silva.fasta.gz", <br> fn.out.aS.slv)</p> </blockquote>
Corpus de Notícias - Patriani, Silva (2025)
<p>Este arquivo compila o conjunto de notícias analisadas no trabalho de Patriani e Silva (2025), intitulado "Entre narrativas e justiça climática: cobertura da Globo e UOL sobre o ativismo nas COPs".</p> <p> </p> <p>This file the set of news analyzed in the work of Patriani and Silva (2025), entitled "Between Narratives and Climate Justice: Globo and UOL Coverage on Activism at the COPs".</p>
Fig. 1 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola
Fig. 1. – "Aspecto da embocadura do Rio Dande" [Aspect of the mouth of the River Dande] with Joaquim José da Silva (left) and José António (right). [a. "Forno da cal" [lime oven]; b. "Armazem de a-guardar" [storage]; c. "Sanzallas" [dwellings]; d. "Armazem da madeira" [timber storage]; e. "Igreja que foi dos Jesuitas" [church that was of the Jesuits]; f. "Ponta do Mussule(?)" [Mussule(?) Tip] [SILVA, J.J. (post. 1785: fig. 84); painting executed by José António] [© Arquivo Histórico dos Museus da Universidade de Lisboa]
Fig. 2 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola
Fig. 2. – Itinerary of Joaquim José da Silva in Angola from 1783 to 1810 according to TEIXEIRA (1962) in pink, SIMON (1983) in blue, and this work in red.
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