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FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome. in Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome.
ERAI corresponding to NCEP initializations
<p>ERAI corresponding to NCEP initializations</p>
More Austro-Tai Comparisons and Observations on Vowel Correspondences
<p>In this presentation, 13 new comparisons between Kra-Dai and Austronesian are presented. The comparisons include terms like ‘rattan’, ‘to plant or transplant crops’, ‘derris root used as fish poison’, to be sick; in pain', ‘leech’, and other basic vocabulary terms. In addition, observations on vowel correspondences between final-syllable vowels are discussed. High-vowels in the penultimate syllable caused a split in reflexes of *a. Additionally, there was an unconditioned split affecting schwa, which appears in Kra-Dai and Austronesian examples for which several examples are given.</p>
Lemna minor annotation R package (org.Lminor.eg.db) and corresponding files behind the custom built
<p>This public repository containing the following files:</p> <ol> <li>Custom built annotation R package for the <em>Lemna minor </em>reference genome [<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/org.Lminor.eg.db.7z?versionId=c0a06176-0e46-4732-87ae-c6d9f9c68d0c">org.Lminor.eg.db.7z</a>]. The package was built via AnnotationForge using sequence homology of protein coding genes for functional characterisation (Description, PFAMs, GO terms). A combined approach using <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download">blastx </a>and <a href="http://eggnog5.embl.de/#/app/home">EMBL's eggNOG mapper</a> was used for this task. This package is compatible with <a href="https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html">clusterProfiler</a> for downstream functional enrichment analysis (ORA / GSEA) of <em>L. minor</em> transcriptomic / proteomic data.<br> <br> For <strong>how to install and use this package</strong> in your R session,<strong> check the R code example below</strong>.<br> </li> <li>Reference genome, genome annotation (gtf), gene coding sequences (cds) and cds translated peptide sequences (cds.pep) of the duckweed <em>Lemna minor </em>[<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/Lminor_refGenome_GTF_CDS.7z?versionId=c25b53a8-1fc3-4bfb-b559-718ab8b230a9">Lminor_refGenome_GTF_CDS.7z</a>].<br> The reference genome assembly fasta was downloaded from <a href="http://www.lemna.org">www.lemna.org</a>. Matching GTF annotation file was generated via '<em>gffread</em>', from the GFF<em> </em>annotation file available <a href="https://genomevolution.org/coge/LoadGenome.pl?wid=47218">here</a>.<br> </li> <li>With the cds translated peptide file, a blastp search was performed against a custom plant protein sequence database [<a href="https://zenodo.org/api/files/33f1633e-9232-4a1c-af07-5bcf19db9304/Lminor_ref.org.Db4blastp.7z?versionId=d1e69820-edfc-494d-9d44-f6624b190841">Lminor_ref.org.Db4blastp.7z</a>]. The custom database was built from the proteomes of well annotated reference plant species. (For details refer to the readme file within the compressed folder)</li> </ol> <p>For more details please refer to our publication in <a href="https://doi.org/10.1021/acs.est.2c01777">Environmental Science & Technology</a>:<br> Loll, Alexandra, Hannes Reinwald, Steve U. Ayobahan, Bernd Göckener, Gabriela Salinas, Christoph Schäfers, Karsten Schlich, Gerd Hamscher, and Sebastian Eilebrecht. <em><strong>“Short-Term Test for Toxicogenomic Analysis of Ecotoxic Modes of Action in Lemna Minor.”</strong></em> Environmental Science & Technology 56, no. 16 (August 16, 2022): 11504–15.<br> DOI: <a href="https://doi.org/10.1021/acs.est.2c01777">https://doi.org/10.1021/acs.est.2c01777</a></p> <pre><code class="language-bash"># 1. Download and unzip (7zip format) the org.Lminor.eg.db package. # 2. Install the package via: orgDb = "path/to/org.Lminor.eg.db/" install.packages(orgDb, type="source", repos=NULL) # 3. Restart R session then load package require(org.Lminor.eg.db) require(AnnotationDbi) # to check for columns and keytypes: columns(org.Lminor.eg.db) keytypes(org.Lminor.eg.db) # query the org.Lminor.eg.db for particular Lemna gene IDs (GID) gid = keys(org.Lminor.eg.db, keytype="GID") col = columns(org.Lminor.eg.db)[c(5,17,9,15,1,8,14)] df = select(org.Lminor.eg.db, keys=gid[1000:1100], columns=col, keytype="GID") View(df) ### Running overrepresenation analysis in clusterProfiler using the Lminor annotation package ### # ORA for multiple gene sets via compareCluster() require(clusterProfiler) genLs = list(setA = gid[1:40], setB = gid[100:140], setC = gid[1000:1040]) res = compareCluster(genLs, fun = "enrichGO", OrgDb = "org.Lminor.eg.db", keyType = "GID", ont = "BP", universe = gid) # Compute semantic similiarities among GO terms: d = GOSemSim::godata('org.Lminor.eg.db', ont="BP", computeIC=FALSE, keytype = "GID") res = enrichplot::pairwise_termsim(res, method = "Wang", semData = d) # Rmv GO terms with redudant biological information resS = simplify(res, .8) # resort results after pvalues resS@compareClusterResult = resS@compareClusterResult[order(resS@compareClusterResult$pvalue),] View(res@compareClusterResult) # Network plot emapplot(resS, showCategory = 30)</code></pre>
FIGURE. Taphonomic process corresponding to the abundance of different kinds of plant remains in the three layers of "vegetational Pompeii" tuff bed. Single, double and triple repeated icons in different layers indicate rare, moderate and frequent occurrence respectively. Note that the thickness of the tuff bed is scaled but that of the two coal beds is neglected. in Discovery of coprolites in an Early Permian fern mesophyll
FIGURE. Taphonomic process corresponding to the abundance of different kinds of plant remains in the three layers of "vegetational Pompeii" tuff bed. Single, double and triple repeated icons in different layers indicate rare, moderate and frequent occurrence respectively. Note that the thickness of the tuff bed is scaled but that of the two coal beds is neglected.
Bathymetric and surface digital model of the river-floodplain system corresponding to the Duero river reach between Toro and Zamora (Castilla y León).
<p>Digitally edited digital model to represent correctly and with hydraulic criteria the bridges, weirs, dips, roads and walls present in the area.</p>
Bathymetric and terrain digital model (representative of the geomorphological reference condition) of the river-floodplain system corresponding to the Douro reach between Toro and Zamora (Castilla y León).
<p>Digitally edited digital model to represent the previous geomorphological situation in the Toro-Zamora section.</p>
Distribution. Known only from two localities in Central Province, SE Papua New Guinea, including type locality and Oio village, Abau district, ¢.120 km E of former. Former records are either misidentified Nyctophilus timoriensis or correspond to N. microdon. in Vespertilionidae
Distribution. Known only from two localities in Central Province, SE Papua New Guinea, including type locality and Oio village, Abau district, ¢.120 km E of former. Former records are either misidentified Nyctophilus timoriensis or correspond to N. microdon.
Subspecies and Distribution. C.s.salviniDobson,1878—fromEMexico(SVeracruz)SthroughCentralAmericatoNW&WSouthAmerica,includingN&WVenezuela,N&WColombia,Ecuador,NW&EPeru,NE&WBrazil(Tocantins,Rondo6nia,andMatoGrosso),andBolivia.Brazilianrecordsaredubious,theycouldrepresenttheHairyBig-eyedBat(Chirodermavillosum). C. s. scopaeum Handley, 1966 — W Mexico (from S Chihuahua S to Oaxaca). Records from Guatemala correspond to subspecies salvina. in Phyllostomidae
Subspecies and Distribution. C.s.salviniDobson,1878—fromEMexico(SVeracruz)SthroughCentralAmericatoNW&WSouthAmerica,includingN&WVenezuela,N&WColombia,Ecuador,NW&EPeru,NE&WBrazil(Tocantins,Rondo6nia,andMatoGrosso),andBolivia.Brazilianrecordsaredubious,theycouldrepresenttheHairyBig-eyedBat(Chirodermavillosum). C. s. scopaeum Handley, 1966 — W Mexico (from S Chihuahua S to Oaxaca). Records from Guatemala correspond to subspecies salvina.
Collection of pXRF Data Corresponding to Study Spectral Samples | Southwest Australia Acid Saline Sediments | Radwin 2022
<p>This file contains pXRF data from a portable Bruker XRF instrument using mudrock calibration settings, where each sample was scanned for 90 seconds to alternate through energy spectrums. This data has at tab displaying associated file numbers that correspond to sample ID's. These sample ID's all correspond to spectra of the same sample location used for the pXRF measurements. This data was collected for the completion of a masters thesis at the University of Utah Department of Geology & Geophysics. </p>
Cross-modal correspondences: different modes, common codes? Investigating musical engagement with an Ecological cognitive approach
<p>This folder refers to my thesis entitled "Crossmodal correspondences: different modes, common codes? Investigating musical engagement with an Ecological cognitive approach."</p>
Subspecies and Distribution. pos sagitta Pallas, 1773 — S Russia (Altai Krai) and right bank of Irtysh River in Kazakhstan (Pavlodar and East Kazakhstan regions). D.s.aksuensisWangSung,1964—NWChina(NTarimBasininXinjiang). D.s.austrouralensisShenbrot,1991—NWKazakhstan(WestKazakhstan,Atyrau,andAktoberegionsbetweenUralandEmbarivers). D.s.bulganensisShenbrot,1991—EKazakhstan(ELakeZaysaninEastKazakhstanRegion),NWChina(DzungarianBasininXinjiang),andMongolia(SKhovdandSWGovi-Altai). D.s.deasyiBarret-Hamilton,1900—NWChina(STarimBasininXinjiangandS&WQaidamBasininQinghai). D. s. fuscocanus Wang Sung, 1964 — W China (S foothills of E Tian Shan in Xinjiang). D. s. halli Sowerby, 1920 — China (NE Inner Mongolia [= Nei Mongol], SW Heilongjiang, NWJilin, and N Liaoning) and SE Mongolia (Stikhbaatar). D. s. innae Ognev, 1930 — S Russia (Astrakhan Region E of Volga River) and NW Kazakhstan (West Kazakhstan and Atyrau regions W of Ural River). D. s. lagopus Lichtenstein, 1823 — WC Kazakhstan (E of Emba and N of Syrdarya rivers). D. s. megacranius Shenbrot, 1991 — SE Kazakhstan (Moinkum Sands in Jambyl Region). D. s. nogai Satunin, 1907 — S European Russia (Volgograd and Astrakhan regions E of Volga River, Kalmykia, and Dagestan). D. s. sowerbyi Thomas, 1908 — N China (NE Xinjiang, N Qaidam Basin in Qinghai, Gansu, SW Inner Mongolia, N Ningxia, and N Shaanxi) and Mongolia. D. s. turanicus Shenbrot, 1991 — SW Kazakhstan (S Kyzylorda S of Syrdarya River and Mangystau regions), Uzbekistan, and Turkmenistan; it probably occurs in adjacent W Afghanistan. D. s. ubsanensis Bannikov, 1947 — NW Mongolia (N Uvs) and adjacent Russia (extreme S Tuva). D. s. usuni Shenbrot, 1991 — SE Kazakhstan (Almaty Region); it probably occurs in adjacent China (sands of Ili Valley of W Xinjiang). D. s. zaissanensis Selevin, 1934 — E Kazakhstan (NW Lake Zaysan Basin on the left bank of Irtysh River). Isolated population in N Iran (Turan Desert in E Semnan Province) may belong to turanicus or correspond to a yet undescribed subspecies. in Dipodidae
Subspecies and Distribution. pos sagitta Pallas, 1773 — S Russia (Altai Krai) and right bank of Irtysh River in Kazakhstan (Pavlodar and East Kazakhstan regions). D.s.aksuensisWangSung,1964—NWChina(NTarimBasininXinjiang). D.s.austrouralensisShenbrot,1991—NWKazakhstan(WestKazakhstan,Atyrau,andAktoberegionsbetweenUralandEmbarivers). D.s.bulganensisShenbrot,1991—EKazakhstan(ELakeZaysaninEastKazakhstanRegion),NWChina(DzungarianBasininXinjiang),andMongolia(SKhovdandSWGovi-Altai). D.s.deasyiBarret-Hamilton,1900—NWChina(STarimBasininXinjiangandS&WQaidamBasininQinghai). D. s. fuscocanus Wang Sung, 1964 — W China (S foothills of E Tian Shan in Xinjiang). D. s. halli Sowerby, 1920 — China (NE Inner Mongolia [= Nei Mongol], SW Heilongjiang, NWJilin, and N Liaoning) and SE Mongolia (Stikhbaatar). D. s. innae Ognev, 1930 — S Russia (Astrakhan Region E of Volga River) and NW Kazakhstan (West Kazakhstan and Atyrau regions W of Ural River). D. s. lagopus Lichtenstein, 1823 — WC Kazakhstan (E of Emba and N of Syrdarya rivers). D. s. megacranius Shenbrot, 1991 — SE Kazakhstan (Moinkum Sands in Jambyl Region). D. s. nogai Satunin, 1907 — S European Russia (Volgograd and Astrakhan regions E of Volga River, Kalmykia, and Dagestan). D. s. sowerbyi Thomas, 1908 — N China (NE Xinjiang, N Qaidam Basin in Qinghai, Gansu, SW Inner Mongolia, N Ningxia, and N Shaanxi) and Mongolia. D. s. turanicus Shenbrot, 1991 — SW Kazakhstan (S Kyzylorda S of Syrdarya River and Mangystau regions), Uzbekistan, and Turkmenistan; it probably occurs in adjacent W Afghanistan. D. s. ubsanensis Bannikov, 1947 — NW Mongolia (N Uvs) and adjacent Russia (extreme S Tuva). D. s. usuni Shenbrot, 1991 — SE Kazakhstan (Almaty Region); it probably occurs in adjacent China (sands of Ili Valley of W Xinjiang). D. s. zaissanensis Selevin, 1934 — E Kazakhstan (NW Lake Zaysan Basin on the left bank of Irtysh River). Isolated population in N Iran (Turan Desert in E Semnan Province) may belong to turanicus or correspond to a yet undescribed subspecies.
Subspecies and Distribution. D. m. microps Merriam, 1904 — SW USA (Owens River drainage of W Mojave Desert, S California). D. m. alfredi Goldman, 1937 — W USA (Gunnison I, Great Salt Lake, Utah). D. m. aquilonius Willett, 1935 — W USA (lower elevations of the Great Basin Desert of NE California and NW Nevada). D. m. bonneuvillei Goldman, 1937 — W USA (Great Basin Desert of NE Nevada and NW Utah, corresponding closely with the former outline of Pleistocene Lake Bonneville). D. m. celsus Goldman, 1924 — SW USA (possibly disjunct distribution in Virgin River Valley of SW Utah and adjacent NW Arizona). D. m. centralis Hall & Dale, 1939 — W USA (Great Basin Desert of C & E Nevada). D. m. idahoensis Hall & Dale, 1939 — W USA (restricted to the Snake River Valley, SW Idaho). D. m. leucotis Goldman, 1931 — SW USA (restricted distribution between the Vermilion Cliffs and the brink of Marble Canyon of the Colorado River in N Arizona). D. m. levipes Merriam, 1904 — SW USA (restricted to Panamint Valley, S California). D. m. occidentalis Hall & Dale, 1939 — SW USA (Great Basin Desert in W & S Nevada and disjunct, restricted populations in the W Mojave Desert, SE California). D. m. preblei Goldman, 1921 — W USA (Great Basin Desert of SE Oregon and NW Nevada). D. m. russeolus Goldman, 1939 — W USA (Dolphin I, Great Salt Lake, Utah). D. m. subtenuis Goldman, 1939 -W USA (Badger, Carrington, and Stansbury Is, Great Salt Lake, and S on the mainland to Cedar Valley, NC Utah). in Heteromyidae
Subspecies and Distribution. D. m. microps Merriam, 1904 — SW USA (Owens River drainage of W Mojave Desert, S California). D. m. alfredi Goldman, 1937 — W USA (Gunnison I, Great Salt Lake, Utah). D. m. aquilonius Willett, 1935 — W USA (lower elevations of the Great Basin Desert of NE California and NW Nevada). D. m. bonneuvillei Goldman, 1937 — W USA (Great Basin Desert of NE Nevada and NW Utah, corresponding closely with the former outline of Pleistocene Lake Bonneville). D. m. celsus Goldman, 1924 — SW USA (possibly disjunct distribution in Virgin River Valley of SW Utah and adjacent NW Arizona). D. m. centralis Hall & Dale, 1939 — W USA (Great Basin Desert of C & E Nevada). D. m. idahoensis Hall & Dale, 1939 — W USA (restricted to the Snake River Valley, SW Idaho). D. m. leucotis Goldman, 1931 — SW USA (restricted distribution between the Vermilion Cliffs and the brink of Marble Canyon of the Colorado River in N Arizona). D. m. levipes Merriam, 1904 — SW USA (restricted to Panamint Valley, S California). D. m. occidentalis Hall & Dale, 1939 — SW USA (Great Basin Desert in W & S Nevada and disjunct, restricted populations in the W Mojave Desert, SE California). D. m. preblei Goldman, 1921 — W USA (Great Basin Desert of SE Oregon and NW Nevada). D. m. russeolus Goldman, 1939 — W USA (Dolphin I, Great Salt Lake, Utah). D. m. subtenuis Goldman, 1939 -W USA (Badger, Carrington, and Stansbury Is, Great Salt Lake, and S on the mainland to Cedar Valley, NC Utah).
FIGURE 14 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 14. Erythraeus (Zaracarus) rupestris (Linnaeus, 1758), larva: Legs I–III. Details of tarsus (ta) I–III (normal setae omitted). Abbreviations: elcI—supracoxal seta, z—accompanying seta, ω—solenidion on tarsus, ζ—eupathidium, φ—solenidion on tibia, ε—famulus, κ—microseta, σ—solenidion on genu.
FIGURE 11 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 11. Erythraeus (Zaracarus) rupestris (Linnaeus, 1758), larva: Habitus of unfed larva in dorsal view.
FIGURE 13 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 13. Erythraeus (Zaracarus) rupestris (Linnaeus, 1758), larva: a—scutum. b—gnathosoma, ventral view. Abbreviations: AL—anterior lateral seta, ASens—anterior sensillum (AM of other authors), PL—posterior lateral seta, PSens—posterior sensillum, as—oral spine like seta, bs—hypostomal seta, cs—adoral seta, elcp—supracoxala, ω—solenidion, ζ—eupathidium.
FIGURE 15 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 15. Erythraeus (Zaracarus) rupestris (Linnaeus, 1758), Phenology based on cumulated data of regular field samplings 2000–2001 in the National Park 'Lower Odra Valley'. LA—larva (n=85), PN—protonymph (n=4), DN—deutonymph (n=13), TN—tritonymph (n=5), AD—adult (n=48).
FIGURE 9 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 9. Erythraeus (Zaracarus) rupestris (Linnaeus, 1758), adult: a—palp genu, tibia and tarsus (lateral view) and medial view of palp tibia and tarsus, b—scutum with crista metopica and position of lateral eyes, c—posterior dorsal body setae.
FIGURE 5 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 5. Erythraeus (Zaracarus) budapestensis Fain and Ripka, 1998, larva: a—leg I (basifemur—genu, dorsolateral view), b—leg II (basifemur—genu, ventral view), c—leg III (basifemur—genu, ventral view). Abbreviations: κ—microseta, σ—solenidion on genu.
FIGURE 6 in Correspondence of larval and postlarval instars in two species of the subgenus Zaracarus (Acari: Erythraeidae: Erythraeus) established with laboratory rearing
FIGURE 6. Erythraeus (Zaracarus) budapestensis Fain and Ripka, 1998, larva: a—leg I (tibia—tarsus, dorsolateral view), b—leg II (tibia—tarsus, ventral view), c—leg III (tibia—tarsus, ventral view). Abbreviations: ε—famulus, κ—microseta, ω— solenidion on tarsus, ζ—eupathidium, φ—solenidion on tibia, z—accompanying seta.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.