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Fig. 1 in Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
Fig. 1. Sequence identification by matching a peptide fragmentation pattern to a predicted tryptic peptide sequence. (A) Example of the chicken weighted simple consensus (CWSC) sequence algorithm for predicting a tryptic collagen peptide sequence from a previously unsequenced taxon (ostrich) based on three related organisms with one weighted organism (chicken). If a consensus of at least two organisms was present at amino add residues that diverged (positions 11, 15, and 23), the consensus residue was chosen in the predicted tryptic peptide sequence. For residues that diverged where no consensus was present (positions 2 and 3), the residue from the weighted organism (chicken) was chosen for the predicted sequence. Amino acid residues that aligned through all three organisms were left unchanged in the predicted sequence. (B) The experimental MS/MS spectrum from the LC/MS/MS analysis of a triply charged peptide from ostrich bone protein extract that matched to the predicted sequence GPAGP (OH)PGKNGDDGEAGKP(OH)GRP(OH)GER and contained three hydroxyproline residues. (C) The MS/MS spectrum of the synthetically derived triply charged peptide of the same sequence for confirmation. The typical b- and y- fragment ions from the fragmentation pattern of the experimental peptide align very well with the synthetic peptide, validating the sequence interpretation
Fig. 2 in Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
Fig. 2. Collagen peptide sequences unique to extinct mastodon identified by LC/MS/MS. (A) The four collagen altl peptide sequences found by the approach that are unique to ancient mastodon. Xcorr (cross-correlation score) and Sp (preliminary score) represent the scores resulting from database searching against protein databases using Sequest. The asterisk represents the hydroxylation site after the posttranslationally modified residue. (B) An example of the experimental MS/MS spectrum of a doubly charged tryptic peptide for the collagen altl peptide sequence GSEGPQGTR from the LC/MS/MS analysis of mastodon fossilized bone extract identified from a Sequest search against a theoretical collagen protein database. (C) The synthetic version of the same peptide sequence. All major ions from the experimental spectrum align very well with the ions from the synthetic version, validating the sequence.
Fig. 2 in Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis.
Figure 1 in A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination
Figure 1. Tandem mass spectrum from high-resolution (HCD) fragmentation analysis of the peptide sequence (GPPGESGAVGPAGPIGSR) matched from our analysis of ostrich bone collagen that is homologous to the peptide proposed as unique to T. rex and B. canadensis.
Figure 2 in A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination
Figure 2. Tandem mass spectrum of the peptide sequence claimed as being endogenous to both dinosaurs with sequence (GLPGESGAVGPAGPPGSR) downloaded from the B. canadensis analysis by Schweitzer et al. [14].
RTPR_rnrdb_tara_full-length_amino_acid_sequences
<p>RTPR amino acid sequences used as reference for framshift corrections</p>
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
Sequence Tagging of FA-KES Dataset
<p>We used the BIOE Sequence Tagging strategy which was utilized in OpenTag [1] in the aim of getting every word in the dataset<br> associated with a label called ‘tag’. A tag consists of one of these letters B, I, O, or E, that stand respectively for beginning, inside, outside, or end of an attribute, followed by a ‘-’ sign, followed by three letters that represent the type of information that was initially extracted. Tokens were labeled with one of the following tags: ‘B-LOC’, ‘I-LOC’, ‘E-LOC’, ‘B-CIV’, ‘I-CIV’, ‘E-CIV’, ‘B-NCV’, ‘I-NCV’, ‘E-NCV’, ‘B-WMN’, ‘I-WMN’, ‘E-WMN’, ‘B-CHD’, ‘I-CHD’, ‘E-CHD’, ‘B-ACT’, ‘I-ACT’,‘E-ACT’, ‘B-COD’, ‘I-COD’, ‘E-COD’, ‘B-DAT’, ‘I-DAT’, ‘E-DAT’, or ‘O’ (where O stands for words outside the scope, LOC for the incident location, CIV for the number of civilians dead, NCV for the number of non-civilians dead, WMN for the number of women targeted, CHD for the number of children killed, ACT for actor/authority responsible for the incident, COD for the cause of death, and DAT for date of incident). This was done by creating a parser that would automatically tag each word with the appropriate tag.</p> <p>We created three subsets of the FA-KES dataset. The first one consists of the articles' titles, the second one of the articles' titles concatenated with the articles' first paragraphs, and the third one consists of the articles' titles along with their contents. The first column in each of the three CSV files represents the article number in the dataset, the second column contains the sequence of words for each article and the third one holds the tags linked to the tokens of the previous column.</p> <p>[1]: G. Zheng, S. Mukherjee, X. L. Dong, and F. Li, “Opentag: Open attribute value extraction from product profiles,” CoRR, vol. abs/1806.01264, 2018.</p>
The data of complete chloroplast genome sequence of Sorbus amabilis (Rosaceae) in China
<p>This dataset includes the complete chloroplast genome of <em>Sorbus amabilis </em> in China.</p>
FIGURE 32 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURE 32. Neighbor joining tree showing the clustering of similar COI sequences in Cyclocephala taxa. Parentheses after the taxon name indicate the number of sequences represented in that cluster. Parentheses are followed by a three-letter country code. CRI = Costa Rica, GLP = Guadeloupe, GTM = Guatemala, HND = Honduras, KNA = St. Kitts and Nevis, MEX = Mexico, NIC = Nicaragua, PAN = Panama, SLV = El Salvador, VEN = Venezuela. Colored branches highlight taxa of the C. mafaffa species complex (green = C. deceptor; red = C. mafaffa mafaffa; blue = C. mafaffa grandis).
FIGURES 25–30 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 25–30. Stigmalia deficiens Casey, lectotype male and paralectotype female. 25, Stigmalia deficiens Casey lectotype male, dorsal habitus. 26, Stigmalia deficiens Casey paralectotype female, dorsal habitus. 27, Parameres of lectotype male, caudal view. 28, Aedeagus of lectotype male, lateral view. 29, Lectotype male specimen labels. 30, paralectotype female specimen labels.
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 17–20. Stigmalia cuernavacana Casey, holotype female. 17, Stigmalia cuernavacana Casey holotype female, dorsal habitus. 18, Elytral epipleural flange of holotype female, dorsal view. 19, Elytral epipleural flange of holotype female, lateral view. 20, Holotype female specimen labels.
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 21–24. Stigmalia fallaciosa Casey, holotype male. 21, Stigmalia fallaciosa Casey holotype male, dorsal habitus. 22, Parameres of holotype male, caudal view. 23, Aedeagus of holotype male, lateral view. 24, Holotype male specimen labels.
FIGURES 11–16 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 11–16. Stigmalia deceptor Casey, lectotype male and paralectotype female. 11, Stigmalia deceptor Casey lectotype male, dorsal habitus. 12, Stigmalia deceptor Casey paralectotype female, dorsal habitus. 13, Parameres of lectotype male, caudal view. 14, Aedeagus of lectotype male, lateral view. 15, Lectotype male specimen labels. 16, Paralectotype female specimen labels.
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 7–10. Stigmalia mafaffa histrionica Casey, holotype female. 7, Stigmalia mafaffa histrionica Casey holotype female, dorsal habitus. 8, Holotype female, elytral epipleural flange in dorsal view. 9, Holotype female, elytral epipleural flange in lateral view. 10, Holotype female specimen labels.
FIGURES 1–2. Cyclocephala deceptor and C in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 1–2. Cyclocephala deceptor and C. mafaffa, basal margin of the pronotum. 1, Cyclocephala deceptor with pronotal basal bead medially complete. 2, Cyclocephala mafaffa with pronotal basal bead medially incomplete.
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3 in Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)
FIGURES 3–6. Cyclocephala mafaffa Burmeister, lectotype male from MLUH. 3, Lectotype male, dorsal habitus. 4, Lectotype male, ventral habitus. 5, Lectotype male, lateral habitus. 6, Lectotype male specimen labels and aedeagus. Photographs courtesy of Matthias Seidel (Department of Entomology, National Museum, Prague, Czech Republic).
Data sets for: EMA-amplicon-based sequencing of untreated and SODIS treated rainwater
<p>Data sets for the EMA-amplicon-based sequencing of untreated and treated rainwater collected from an informal settlement and rural farming community in South Africa. The data sets were used for the publication: EMA-amplicon-based sequencing informs risk assessment analysis of water treatment systems (Submitted to Science of the Total Environment).</p>
TAASRAD19 Radar Sequences 2010-2019 NetCDF
<p>TAASRAD19 (Trentino-Alto Adige/Südtirol Radar 2019) is a high-resolution radar reflectivity dataset collected by the Civil Protection weather radar of the Trentino South Tyrol Region, in the Italian Alps.<br> The dataset includes 894,916 time steps of precipitation from more than 9 years of data, offering a novel resource to develop and benchmark analog ensemble models and machine learning solutions for precipitation nowcasting. Data are expressed as 2D images, considering the maximum reflectivity on the vertical section and 5 minutes sampling rate, covering an area of 240km of diameter at 500m horizontal resolution. The TAASRAD19 distribution also includes a curated set of 1,732 sequences, for a total of 362,233 radar images, labeled with precipitation type tags assigned by expert meteorologists. We validated TAASRAD19 as a benchmark for nowcasting using deep learning model to forecast reflectivity and a procedure based on the UMAP dimensionality reduction method for interactive exploration.<br> Software methods for data pre-processing, model training and inference, and a pre-trained model are<br> publicly available at https://github.com/MPBA/TAASRAD19 for replication and reproducibility.</p>
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
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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.