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46 results for “LSU”
Linked collectors and determiners for: LSUMZ (LSU MNS) Fishes Collection.
Natural history specimen data linked to collectors and determiners held within, "LSUMZ (LSU MNS) Fishes Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8a1073ce-54a4-4712-89a6-e14d82836d9e">https://bionomia.net/dataset/8a1073ce-54a4-4712-89a6-e14d82836d9e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8a1073ce-54a4-4712-89a6-e14d82836d9e">https://gbif.org/dataset/8a1073ce-54a4-4712-89a6-e14d82836d9e</a>. Formatted as a Frictionless Data package.
RDP LSU taxonomic training data formatted for DADA2 (trainingset 11)
<p>#Format RDP taxonomic training set for DADA2<br> #1 Wrangle the RDP trainingsets and unaligned data into the downloads folder by executing this from a terminal and move the file somewhere with >30GB free<br> wget https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata.zip/download<br> wget http://rdp.cme.msu.edu/download/current_Fungi_unaligned.fa.gz<br> #2 Unzip the trainingset file and replace Us with Ts in the fasta by executing in terminal<br> awk 'NR%2==0 {gsub(/[uU]/,"T"); print} NR%2==1' /media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014.fa > /media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa<br> #3 Summon the dada2 pkg<br> library(dada2);packageVersion("dada2")<br> #4 Transform the DADA2 formatted training fastas<br> path<-"/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata"<br> dada2:::makeTaxonomyFasta_RDP(file.path(path, "fungiLSU_train_012014_lsu_fixed_v2.fa"), file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa",compress=FALSE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa", compress=FALSE)</p> <p>#5 Make the compressed DADA2 formatted training fastas in gz and zip format<br> dada2:::makeTaxonomyFasta_RDP("/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa", file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa.gz",compress=TRUE)<br> dada2:::makeTaxonomyFasta_RDP("/media/lauren/96BA-19E6/RDPClassifier_fungiLSU_trainsetNo11_rawtrainingdata/fungiLSU_train_012014_lsu_fixed_v2.fa", file.path(path, "fungiLSU_taxid_012014.txt"),"/media/lauren/96BA-19E6/Upload/RDP_LSU_fixed_train_set_v2.fa.zip",compress=TRUE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa.gz", compress=TRUE)<br> dada2:::makeSpeciesFasta_RDP("/media/lauren/96BA-19E6/RDPClassifierLSU/current_Fungi_unaligned.fa", "/media/lauren/96BA-19E6/Upload/rdp_species_assignment_LSU_v2.fa.zip", compress=TRUE)</p> <p> </p>
Simulated electron scattering volume of 6Q8Y_whole_LSU
<p>Electron scattering density of a parsed large ribosomal subunit (pdb identifier: 6Q8Y) for comparison during unit tests of the ttsim3d Python package. See the <a href="https://github.com/teamtomo/ttsim3d">ttsim3d GitHub page</a> and testing scripts for further information.</p> <p>Reference data here has been updated to reflect a bugfix in the underlying simulation code when applying dose weighting to the simulated structure.</p>
LSU_AIM2024
<p>This <strong>zip</strong> file contains a subset of the image sequences and all YOLOv5 neural networks used in the "Solving Short-Term Relocalization Problems in Monocular Keyframe Visual SLAM Using Spatial and Semantic Data" paper. This paper was presented in 2024 IEEE/ASME International Conference on Advanced Intelligent Mechatronics (AIM) held in Boston, MA, USA.</p> <p>The proposed framework, along with links to the preprint paper and presentation slides is made publicly available in this GitHub repository: https://github.com/RKinDLab/ros2_psd_pcb_reloc</p> <p>UPDATE: 07/30/2024</p> <p>After careful consideration, we have decided to remove the image sequences from the EuRoC MAV and TUM RGBD SLAM datasets to avoid future confusion with redistribution. Only the image sequenecs from our in-house UGV dataset (LSU-iCORE-Mono) have been provided along with the neural network weights.</p> <p>Please follow the updated instructions in the GitHub repo regarding how to setup sequences from EuRoC MAV and TUM RGBD SLAM (Robot SLAM category) datasets.</p>
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa
List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon if known.
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in Laimaphelenchus persicus n. sp. (Nematoda: Aphelenchoididae) from Iran
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in Laimaphelenchus hyrcanus n. sp. (Nematoda: Aphelenchoididae), a new species from northern Iran
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank accession numbers are listed for each taxon.
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Zhejiang Province, eastern China
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322). in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322).
Supplementary material 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data
Supplementary material 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S1. Accession numbers corresponding with the reference sequences used to build the phylogenetic trees
Supplementary material 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S3. Maximum-likelihood tree constructed in IQ-Tree2 based on three-gene (LSU D1-D2, SSU, ITS2) reference sequence alignments and OTUs for both markers (clustering thresholds: 99% LSU D1-D2 and 98% ITS2)
Supplementary material 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S2. Species accumulation curves of the OTUs generated from the ITS (panel right) and LSU (panel left) metabarcodes
ITS and LSU sequences, phylogenetic trees
<p>Russula kashmiriana sp. nov (<em>subg. Tenellula, sect. Laricinae</em>) has been collected and described from Himalayan coniferous forest of Azad Jammu and Kashmir (AJ&K), Pakistan. The taxon is characterized by bright reddish orange pileus with cracked margins and obvious reddish orange circle on the pileus, yellow context and light olive to yellowish amyloid basidiospores. Micro and macroscopic features along with molecular phylogenetic analysis based on large subunit (LSU) and internal transcribed spacer (ITS) sequences data confirmed the status of <em>Russula kashmiriana</em> as a distinct species. AJ&K, LSU, Phylogeny, Russulaceae.</p>
Fig. 1 in A short LSU rRNA fragment as a standard marker for integrative taxonomy in calcareous sponges (Porifera: Calcarea)
Fig. 1 Overview of the alignment and consensus of ITS sequences. For each specimen, 2–3 clones were sequenced
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 in A new species of Naematelia (Tremellales, Basidiomycota) from India
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 are indicated above branches. The new species is indicated in bold. Holotype is represented in red color. Cryptococcus depauperatus was set as the outgroup.
FIGURE 2 in Detecting the phylogenetic position of Bovista acuminata (Agaricales, Basidiomycota) by an ITS-LSU combined analysis: the new genus Bryoperdon and revisitation of Lycoperdon subgen. Apioperdon
FIGURE 2. Bryoperdon acuminatum. Fresh basidiomes (TO HG191016). a in field; b in studio; c particular of the exoperidium; d particular of the exoperidium and ellipsoid-lacerate stoma. Scale bars: a, b = 10 mm; c = 5 mm; d = 2 mm. Pictures by A. Vizzini.
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