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Source data of the lithologic indicators of climate for NC
<p>Source data are the ~290 Ma (Figure 4a) and ~280 Ma (Figure 4b) lithologic indicators of climate from Boucot et al. (2013).</p>
Association between exposure to ecotoxicants and clinical and laboratory indices at clinical and preclinical stages of rheumatoid arthritis
Open the record for dataset details and reuse information.
An evidence map of research assessing the effects of timber harvesting on water quality, biotic and biodiversity indicators in running waters: Data and R code
<p>These are the data and R code that accompany the Forest Ecology and Management publication titled "An evidence map of research assessing the effects of timber harvesting on water quality, biotic and biodiversity indicators in running waters". </p>
Replication package of the Paper "On the Relationships between the Initial Ecology Indicators of OSS Projects and Their Long-Term Popularity: An Exploratory Study on GitHub"
<p>The dataset is collected from GitHub API and GitHub GHTorrent dataset. A brief description of each folder is provided below:</p> <p><strong>1. "Dataset_and_Code" folder</strong></p> <p>Contains the final dataset and algorithms</p> <p><strong>2. "Test_parameters" folders </strong></p> <p>Includes datasets under different parameters and the corresponding reproduction code, which corresponds to the first experiment of RQ1</p> <p><strong>3. "Compare_baseline"folder</strong></p> <p>Includes the dataset used by our method, the dataset used by the baseline method, and the reproduction code, corresponding to the second experiment of RQ1</p> <p><strong>4. "PLS" folder</strong></p> <p>Includes the dataset used by PLS and the corresponding reproduction code, which corresponds to experiment of RQ2</p> <p><strong>5. " Indicator_Calculation " folder</strong><br>It contains the calculation methods for various metrics in the paper, as well as the corresponding key files. </p> <p><span><strong>6. " Appendix " folder</strong><br></span><span>It includes supplementary materials such as the methodology for metric calculations to address the reviewers' questions.</span> </p> <p><strong>Note</strong></p> <p>We have provided a corresponding README file in each folder to help others reproduce our results</p>
Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
<p>This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the <i>Valenzuela flavidus </i>(Psocodea: Psocomorpha: Caeciliusidae) Species Complex".</p> <p><i>Valenzuela flavidus</i> is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, <i>Valenzuela aurantiacus</i> was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of <i>V. flavidus</i> providing insight for future studies to understand patterns of asexuality reported within the complex.</p> <p>The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.</p>
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.
Subspecies and Distribution. T.n.napuF.Cuvier,1822—SMyanmar,Thai/MalayPeninsula,islandsoffWMalayPeninsula(Langkawi&Pangkor),Borneo,SSumatra,BangkaI,islandsoffBorneo(Laut&Serasan). T.n.bangue:Chasen&Kloss,1931—BanggiIandBalembanganI,offNBorneo. T.n.bunguranensisMiller,1901—NatunaIs(=Bunguran),oftWBorneo. T.n.neubronneriSody,1931—NSumatra. T.n.nmiasisLyon,1916—NiasI,offWSumatra. T.n.rufulusMiller,1900—TiomanI,offEMalayPeninsula,RiauandLinggaArchipelagos. T. n. terutus Thomas & Wroughton, 1909 — Terutau I, off W Malay Peninsula. The species was recently reconfirmed for Singapore. Maps that include Vietnam, Cambodia, and Laos in the distribution range are based on the earlier assumption that 7. versicolor was a subspecies of 1. napu. Subsequent studies have indicated that 7. versicolor is a distinct species, and that the range of 1. napu therefore does not extend into Cambodia, Laos, and Vietnam. The northern limit on the Thai-Malay peninsula is not well defined. Specimens of 1. napu have been collected from as far north as Bankachon in southern Myanmar (10° 08" N), but despite fairly intensive camera-trapping in Kui Buri National Park, Thailand (12° N), 7. napu has not been photographed there. At the northern margin ofits range, it is generally rare. It has been reported, for example, that during the flooding of the Chiew Larn Reservoir (Surat Thani Province; about 9° N, 98° 45' E), only six 7. napu were rescued compared with 172 71. kanchil. This area is the transition zone from wetter evergreen forest to drier deciduous types, and it might be that 7° napu is not well adapted to the drier forest types towards the northern limit ofits range. There are unconfirmed reports of the species on Java, where it may have been confused with one of the two color morphs of 7. javanicus. As explained in the Taxonomy section, the subspecific status of the populations of several islands remains unclear. in Tragulidae
Subspecies and Distribution. T.n.napuF.Cuvier,1822—SMyanmar,Thai/MalayPeninsula,islandsoffWMalayPeninsula(Langkawi&Pangkor),Borneo,SSumatra,BangkaI,islandsoffBorneo(Laut&Serasan). T.n.bangue:Chasen&Kloss,1931—BanggiIandBalembanganI,offNBorneo. T.n.bunguranensisMiller,1901—NatunaIs(=Bunguran),oftWBorneo. T.n.neubronneriSody,1931—NSumatra. T.n.nmiasisLyon,1916—NiasI,offWSumatra. T.n.rufulusMiller,1900—TiomanI,offEMalayPeninsula,RiauandLinggaArchipelagos. T. n. terutus Thomas & Wroughton, 1909 — Terutau I, off W Malay Peninsula. The species was recently reconfirmed for Singapore. Maps that include Vietnam, Cambodia, and Laos in the distribution range are based on the earlier assumption that 7. versicolor was a subspecies of 1. napu. Subsequent studies have indicated that 7. versicolor is a distinct species, and that the range of 1. napu therefore does not extend into Cambodia, Laos, and Vietnam. The northern limit on the Thai-Malay peninsula is not well defined. Specimens of 1. napu have been collected from as far north as Bankachon in southern Myanmar (10° 08" N), but despite fairly intensive camera-trapping in Kui Buri National Park, Thailand (12° N), 7. napu has not been photographed there. At the northern margin ofits range, it is generally rare. It has been reported, for example, that during the flooding of the Chiew Larn Reservoir (Surat Thani Province; about 9° N, 98° 45' E), only six 7. napu were rescued compared with 172 71. kanchil. This area is the transition zone from wetter evergreen forest to drier deciduous types, and it might be that 7° napu is not well adapted to the drier forest types towards the northern limit ofits range. There are unconfirmed reports of the species on Java, where it may have been confused with one of the two color morphs of 7. javanicus. As explained in the Taxonomy section, the subspecific status of the populations of several islands remains unclear.
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
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).
Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera
<p><em>Juniperus flaccida</em> (drooping juniper) and <em>Pinus cembroides</em> (pinyon pine) are conifers native to North America, spanning Mexico and the Southwestern region of the United States. Although from two different lineages, both species exhibit heteroblastic growth. Morphologically, their leaves undergo a change between the juvenile and adult life stage. <em>J. flaccida</em> leaves appear needle-like at youth and scale-like at maturity, whereas the <em>P. cembroides</em> will transition from needle-like leaves to brown scale-like leaves. The objective was to perform a comparative transcriptomic analysis to quantify and examine differential expression in juvenile and adult individuals from both species. RNA from twelve samples was sequenced on HiSeq 1500 (100bp PE) and analyzed with available software. Because there are no reference genomes for these species, they were assembled<em> de novo </em>from the RNA-Seq reads. Following assembly, the coding regions were identified and redundant transcripts were removed. Quality filtered reads were aligned to the reference transcriptomes (one for each species), counts were generated from the alignment files, and differential expression analysis was performed with DESeq2 via Kallisto. Up and down-regulated genes (padj<0.1) across both age classes (juvenile vs adult) were observed in each species and compared.</p>
FIGURE. Microscopic structures of Gliophorus roseus (PAN612, holotype). a. Upper part of pileipellis, gelatinous matrix not indicated. b. Basidiospores. c. Ixo-cheilocystidia in a gelatinous matrix (not indicated). d. Basidia at different developmental stages. Bars = 10 µm. Drawings by K. Reschke. in New and interesting species of Agaricomycetes from Panama
FIGURE. Microscopic structures of Gliophorus roseus (PAN612, holotype). a. Upper part of pileipellis, gelatinous matrix not indicated. b. Basidiospores. c. Ixo-cheilocystidia in a gelatinous matrix (not indicated). d. Basidia at different developmental stages. Bars = 10 µm. Drawings by K. Reschke.
Building EU common indicators on migrant integration: The role of survey data on EMMs
<p>In May-June 2021, <a href="http://cost.eu/actions/CA16111/">ETHMIGSURVEYDATA</a>—a COST Action and research network dedicated to quantitative surveys on ethnic and migrant minorities' (EMMs') integration and inclusion—organized a <em>Policy Dialogue Webinar Series </em>to share ETHMIGSURVEYDATA’s main results, as well as to showcase EMM projects that are ongoing in policy-relevant institutions. These webinars have included presentations by the European Asylum Support Office (EASO), the European Commission Joint Research Centre (JRC), the International Organization for Migration (IOM), and the Organisation for Economic Co-operation and Development (OECD).</p> <p>This is the video recording for the <em>Policy Dialogue Webinar Series' </em>kick-off webinar held on 04.05.2021: “Building EU common indicators on migrant integration: The role of survey data on migrants and ethnic minorities.” This video recording has also been made available on <a href="https://www.youtube.com/watch?v=cq1zdxvlisU">ETHMIGSURVEYDATA's Youtube channel</a>.</p> <p>The full program for this webinar can be found below:</p> <ul> <li>Welcoming remarks (Elena Ambrosetti, Sapienza University Rome; Guido Tintori, JRC-EC)</li> <li>EU-wide surveys: What use for policymaking (Béatrice d’Hombres, JRC-EC)</li> <li>Survey-based indicators on attitudes towards immigration (Marco Scipioni, JRC-EC)</li> <li>The EthMigSurveyDataHub: facilitating knowledge sharing and transfer of migrant and ethnic minorities survey data across Europe (Laura Morales, ETHMIGSURVEYDATA)</li> <li>Commentary (Franz Eiffe, Eurofound)</li> <li>Q&A</li> </ul>
Quartz rheology constrained from constant-load experiments indicate lower strength of the continental crust
<p>Raw mechanical data.</p> <p>Raw EBSD data of the sample OR90.</p>
Indices for mm10 for local version of HTSstation (mapping and 4Cseq)
<p>In order to perform analyses the same way it was done on htsstation.epfl.ch, the bowtie2 indices, fasta and 4C libraries were grouped into a tar archive.</p>
Fossilized pollen malformations as indicators of past environmental stress and meiotic disruption: insights from modern conifers
<p>Pollen malformations have been proposed as a paleoenvironmental stress proxy. However, the frequency and variability of pollen malformations under near-optimal conditions and environmental stress, as well as their developmental origins, remain unclear. To bridge these gaps, we compared pollen malformation frequencies and assemblages of 14 extant conifer genera of Pinaceae and Podocarpaceae producing saccate (winged) grains grown under near-optimal conditions. These baseline pollen yields were compared with those produced by <i>Pinus mugo</i> 'Columnaris' cultured under an abiotic stress—three experimentally heightened UV-B regimes proposed for the end-Permian crisis. We additionally reviewed previous cytological literature of abnormal microsporogenesis in conifers. Under near-optimal conditions, malformations comprise <3% of pollen yields in 12 out of 13 bisaccate genera and >10% of yields in the naturally trisaccate <i>Dacrycarpus dacrydioides</i>. We detected no phylogenetic pattern in malformation assemblages of the baseline comparisons. UV-B irradiated <i>P. mugo</i> produced significantly higher malformation frequencies and different assemblage compositions when compared with baseline bisaccate lineages. We propose that pollen malformations originate during the meiotic and tetrad stages of microsporogenesis and present a framework for the ontogeny of different malformation types seen in the fossil record. Malformations comprising >3% of bisaccate pollen yields can be used as a paleoenvironmental stress proxy, but rare, naturally trisaccate lineages are not suitable for such assessments. Furthermore, heightened UV-B not only increases pollen malformation production, but also alters the types of abnormalities trees produce. Different environmental stresses may therefore leave behind distinct fingerprints in the fossil record.</p>
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications.
<p>The datasets used in the publications titled "Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications"</p>
FIGURE. Scatter plots (N=200) and linear regression lines of the length and diameter of termite coprolites from the Lower Cretaceous Huolinhe Formation in eastern Inner Mongolia, China. The grey shading represents the 95% confidence interval of linear relationship. Note scatter plots depicting a k-means clustering analysis reveals three groups, indicated by circles of different colours; stars of different colour mean the clusters centroids which are the average length and diameter. in Termite coprolites (Blattodea: Isoptera) from the Early Cretaceous of eastern Inner Mongolia, Northeast China
FIGURE. Scatter plots (N=200) and linear regression lines of the length and diameter of termite coprolites from the Lower Cretaceous Huolinhe Formation in eastern Inner Mongolia, China. The grey shading represents the 95% confidence interval of linear relationship. Note scatter plots depicting a k-means clustering analysis reveals three groups, indicated by circles of different colours; stars of different colour mean the clusters centroids which are the average length and diameter.
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.
FIGURE. Distribution of Thalictrum atriplex. Blue arrow indicates the type locality of T. atriplex, i.e. Kangding county in western Sichuan, China; black arrow indicates the type locality of T. spiristylum (= T. atriplex), i.e. Ninglang county in northwestern Yunnan, China. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Distribution of Thalictrum atriplex. Blue arrow indicates the type locality of T. atriplex, i.e. Kangding county in western Sichuan, China; black arrow indicates the type locality of T. spiristylum (= T. atriplex), i.e. Ninglang county in northwestern Yunnan, China.
Data set of studies and indicators on the impacts of crop diversification through coffee agroforestry.
<p>The dataset contains information about 215 papers that were included in the review study. </p>
ScienceDex guides
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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.