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294 results for “data discovery”
Data from: Unexpected discovery: A new 3,3'-bipyrazolo[3,4-b]pyridine scaffold and its comprehensive analysis
<p>A novel 3,3'-bipyrazolo[3,4-b]pyridine scaffold was obtained as a product of serendipity. This article describes the synthesis and characterization this new compound, 3,3'-dimethyl-1,1'-diphenyl-1H,1'H-[6,6'-bipyrazolo[3,4-b]pyridine]-5-carbaldehyde, using various analytical techniques such as NMR, IR, HRMS and melting point measurements. The compound was synthesized by reacting Acetamidopyrazole 2 with the Vilsmeier-Haack reagent, resulting in a 40% yield of the final product. From a theoretical viewpoint, the conformational barrier of the compound was studied using ab-initio calculation methodology based on density functional theory. The equilibrium structures associated with the barrier were optimized at a reasonable calculation level (B3LYP/6-311+G(2d,p)), and subsequently, the energy profile corresponding to the conformational barrier was constructed (energies were obtained at the CAM-B3LYP/aug-ccpVTZ level of calculation). Once the most probable structures were identified, theoretical IR and NMR spectra for these structures were obtained for comparison with the corresponding experimental spectra.</p>
Data used in "Biologically informed deep neural network for prostate cancer discovery" publication
<p>Data used in the publication titled "<strong>Biologically informed deep neural network for prostate cancer discovery </strong>" </p> <p>Elmarakeby, Haitham A., et al. "Biologically informed deep neural network for prostate cancer discovery." <em>Nature</em> 598.7880 (2021): 348-352.</p> <p>These datasets were derived from the following public domain resources:</p> <ol> <li>Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, et al. The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018;50: 645–651. DOI: <a href="https://doi.org/10.1038/s41588-018-0078-z">10.1038/s41588-018-0078-z</a></li> <li>Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, et al. Genomic hallmarks of localized, non-indolent prostate cancer. Nature. 2017;541: 359–364. https://doi.org/10.1038/nature20788</li> <li>Robinson DR, Wu Y-M, Lonigro RJ, Vats P, Cobain E, Everett J, et al. Integrative clinical genomics of metastatic cancer. Nature. 2017;548: 297–303. https://doi.org/10.1038/nature23306</li> <li>Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, et al. The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018;46: D649–D655. DOI: <a href="https://doi.org/10.1093/nar/gkv1351">10.1093/nar/gkv1351</a></li> </ol> <p> </p>
Unleashing the power of data through organization: Structure and connections for meaning, learning, and discovery
<p><span>Knowledge organization is needed everywhere. Its importance is marked by its pervasiveness. This paper will show many areas, tasks, and functions where proper use of Knowledge Organization, construed as broadly as the term implies, provides support for learning and understanding, for sensemaking and meaning making, for inference, and for discovery by people and computer programs and thereby will make the world a better place. The paper focuses not on metadata but rather on structuring and representing the actual data or knowledge itself and argues for more communication between the largely separated KO, Ontology, Data Modeling, and Semantic Web communities to address the many problems that need better solutions. In particular, the paper discusses the application of knowledge organization in Knowledge bases for question answering and cognitive systems; Knowledge bases for information extraction from text or multimedia; Linked data; Big data and data analytics; Electronic health records as one example; Influence diagrams (causal maps), dynamic system models, process diagrams, concept maps, and other node-link diagrams; Information systems in organizations; Knowledge organization for understanding and learning; and Knowledge transfer between domains. The paper argues for moving beyond triples to a more powerful representation using entities and multi-way relationships but not attributes.</span></p>
Data from: Whole-genome phylogeography of the Blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome
<p>Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the Blue-faced honeyeater (<em>Entomyzon cyanotis</em>), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within <em>E. cyanotis</em> across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3 – 1.7 MYA). Evidence for introgression between non-sister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and explore its diversity, divergence and introgression landscape. We show that, as in some Sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome, with the ancestral pseudoautosomal region (PAR) appearing to become non-recombinant between Z and W, along with most of the fused chromosome 5 (~37.2 Mbp). The added non-recombinant portion of the neo-Z displays reduced heterozygosity and faster population genetic differentiation compared with the ancestral Z. Yet, the new PAR shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.</p>
Data from: The patterns of vascular plant discoveries in China
<p>Aim</p> <p>1. To understand geographic patterns of species discovery by examining the effect of growth form, range size, and geographic distribution on discovery probability of vascular plant species in China.</p> <p>2. To find out which taxa harbor the largest number of undiscovered species and where those species locate.</p> <p>3. To find out the determinants of province-level mean discovery time and inventory completeness.</p> <p>Location: China</p> <p>Methods</p> <p>We compiled the discovery time and province-level geographic distributions of ~31000 vascular plant species described between 1753 and 2013 from Flora of China. We used a Cox proportional hazard model to determine the biological and geographic correlates of discovery probability. Accumulation curves of species discoveries were fitted by a logistic discovery model to estimate inventory completeness of different growth forms and of different provinces. We then used linear regression to identify the determinants of mean discovery time, and beta regression to identify the determinants of inventory completeness.</p> <p>Results</p> <p>We found that species with larger range size and distributed in northeastern part of China have a higher discovery probability. Coastal species were discovered earlier than inland species. Trees and shrubs of seed plants have the highest discovery probability while ferns have the lowest discovery probability. Herbs have the largest number of undiscovered species in China. Most undiscovered species will be found in southwest China, where three global biodiversity hotspots locate. Spatial patterns of mean discovery time and inventory completeness are mainly driven by the total number of species, human population density in an area, latitude and longitude of a province.</p> <p>Main conclusions</p> <p>Socio-economic factors primarily determine the discovery patterns of vascular plants in China. Undiscovered species are most likely to be narrow-ranged, inconspicuous endemic species such as herbs and ferns, which are prone to extinctions and locate in biodiversity hotspots in southwestern China.</p>
Multi-omics data for ischemic stroke etiology biomarker discovery
<p>Multi-omics data for ischemic stroke etiology biomarker discovery</p>
Test and Train data for the retrieval experiment in "A molecule generation-oriented lead compound optimization architecture: discovery of potent, selective, oral NLRP3 inflammasome inhibitors"
Open the record for dataset details and reuse information.
Data for "Beyond theory driven discovery: hot random search and datum derived structures"
<p>Data associated with "Beyond theory driven discovery: hot random search and datum derived structures"</p> <p>contributed to: FD 2025: Data-driven discovery in the chemical sciences</p> <p><code>.</code><br><code>├── README</code><br><code>├── b</code><br><code>│ ├── collection</code><br><code>│ ├── eddp</code><br><code>│ ├── test-105-111</code><br><code>│ ├── test-192</code><br><code>│ └── test-56</code><br><code>├── c</code><br><code>│ ├── collection</code><br><code>│ ├── collection-0.5eV</code><br><code>│ ├── collection-1eV</code><br><code>│ ├── manifest-dia</code><br><code>│ ├── test-dia-25-48</code><br><code>│ ├── test-dia-8-24</code><br><code>│ └── test-dia-nosymm-8</code><br><code>└── pyrope</code><br><code> ├── airss</code><br><code> ├── collection-gamma-relax</code><br><code> ├── manifest</code><br><code> └── test</code></p> <p><br>C J Pickard, 2024<br>Cambridge</p>
FIGURE 12. Single cladogram recovered for the data from Tables 1–2 in New Species, Host Record, and Male Discovery for Three Messatoporus Cushman (Hymenoptera, Ichneumonidae, Cryptinae) from Brazil
FIGURE 12. Single cladogram recovered for the data from Tables 1–2, using exact search with implicit enumeration (in 15752.34 secs). Score: 98.628
Simulation data for "Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing"
<p>Simulation data used in analysis of single cell variant calling softwares in manuscript "Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing"</p> <p>Two sets of simulation experiments were performed, one with varying sequencing depth (simulation.tar.gz) and one with a fixed depth at 30 (simulation_fixedDP.tar.gz).</p> <p> </p>
Datasets for "A classification-based approach to override cross-domain data bias in materials discovery"
<p>This repository provides the featurized versions of the specialized datasets, SuperCon and ESTM, utilized in the study titled 'Classification-based detection and quantification of cross-domain data bias in<br>materials discovery'.</p>
Data from: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea and Q. robur) and three natural populations from south-western France that included two additional interfertile white oak species (Q. pubescens and Q. pyrenaica). The genotyping success rate in mapping populations was 80.4% overall and 72.4% for polymorphic SNPs. In natural populations, these figures were lower (54.8% and 51.9%, respectively). Illumina genotype clusters with compression (shift of clusters on the normalized x-axis) were detected in ~25% of the successfully genotyped SNPs and may be due to the presence of paralogues. Compressed clusters were significantly more frequent for SNPs showing a priori incorrect Illumina genotypes, suggesting that they should be considered with caution or discarded. Altogether, these results show a high experimental error rate for the Infinium array (between 15% and 20% of SNPs potentially unreliable and 10% when excluding all compressed clusters), and recommendations are proposed when applying this type of high-throughput technique. Finally, results on diversity levels and shared polymorphisms across targeted white oaks and more distant species of the Quercus genus are discussed, and perspectives for future comparative studies are proposed.
Data from: Discovery of proteinaceous moieties in Late Cretaceous dinosaur eggshells
<p>The documentation of proteinaceous soft tissues in fossils from deep time remains controversial. Often this has been attributed to the laboratory or other modes of modern contamination. Here we provide incontrovertible evidence for the preservation of proteinaceous moieties in the Maastrichtian dinosaur eggshells using pyrolysis-GC×GC-TOFMS. The presence of nitrogen-bearing organic molecules along with diketodipyrrole suggest that the proteinaceous moieties can survive diagenesis. The preservation of these proteinaceous moieties has been attributed to deposition in a palustrine flat environment under subaerial conditions and entrapment of organic material by the eggshell calcitic units. The present study demonstrates that the preservation of nitrogen-bearing macromolecules in Mesozoic fossil remains is not impossible provided the depositional environments and diagenetic processes are propitious. The survival of nitrogen-bearing macromolecule in deep time under subaerial depositional settings will open a new avenue to the research on soft tissue preservation.</p>
Data from: Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics
New technologies for imaging and analysis of morphological characters offer opportunities to enhance revisionary taxonomy and better integrate it with the rest of biology. In this study, we revise the Afrotropical fauna of the ant genus Zasphinctus Wheeler, and use high-resolution X-ray microtomography (micro-CT) to analyse a number of morphological characters of taxonomic and biological interest. We recognise and describe three new species: Z. obamai sp. n., Z. sarowiwai sp. n., and Z. wilsoni sp. n. The species delimitations are based on the morphological examination of all physical specimens in combination with 3D scans and volume reconstructions. Based on this approach, we present a new taxonomic discrimination system for the regional fauna that consists of a combination of easily observable morphological characters visible at magnifications of around 80–100 ×, less observable characters that require higher magnifications, as well as characters made visible through virtual dissections that would otherwise require destructive treatment. Zasphinctus are rarely collected ants and the material available to us is comparatively scarce. Consequently, we explore the use of micro-CT as a non-invasive tool for the virtual examination, manipulation, and dissection of such rare material. Furthermore, we delineate the treated species by providing a diagnostic character matrix illustrated by numerous images and supplement that with additional evidence in the form of stacked montage images, 3D PDFs and 3D rotation videos of scans of major body parts and full body (in total we provide 16 stacked montage photographs, 116 images of 3D reconstructions, 15 3D rotation videos, and 13 3D PDFs). In addition to the comparative morphology analyses used for species delimitations, we also apply micro-CT data to examine certain traits, such as mouthparts, cuticle thickness, and thoracic and abdominal muscles in order to assess their taxonomic usefulness or gain insights into the natural history of the genus. The complete datasets comprising the raw micro-CT data, 3D PDFs, 3D rotation videos, still images of 3D models, and coloured montage photos have been made available online as cybertypes (Dryad, http://dx.doi.org/10.5061/dryad.4s3v1).
Data from: SNP discovery in European lobster (Homarus gammarus) using RAD sequencing
The European lobster (Homarus gammarus) is a decapod crustacean with a high market value and therefore their fisheries are of major importance to the economies they support. However, over-exploitation has led to profound stock declines in some regions such as Scandinavia and the Mediterranean. To manage this resource sustainably, knowledge of population structure and connectivity is crucial to inform management about dispersal, recruitment, stock identification and food traceability. We used restriction-site associated DNA sequencing to develop novel SNP markers from 55 individuals encompassing much of the species range; SNPs were quality filtered, ranked using F-statistics and the top 96 SNPs adequate for primer design were retained. SNP markers were developed with the aim of maximising the power to detect genetic differentiation between: (i) Atlantic and Mediterranean lobsters and (ii) Atlantic lobsters. This panel of SNPs provides a useful resource for future studies of population genetic structure and assignment in H. gammarus.
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</p>
Replication data and theory code for: Discovery of segmented Fermi surface induced by Cooper pair momentum
<p>Replication data and theory code for: Discovery of segmented Fermi surface induced by Cooper pair momentum</p>
Supplementary Data: Discovery of natural non-circular permutations in non-coding RNAs
<p><strong>Supplementary File 1</strong>. RNAMotif Rnamotif / DARN! search patterns for the new permutations of the hammerhead ribozyme and analogous twister ribozyme permutations.</p> <p><strong>Supplementary File 2</strong>. Alignments of novel RNA motifs detected in this work (Supplementary Table 2). The alignments are stored in Stockholm format, which is a text format that can be viewed with a fixed-width font and can also be interpreted by several computer programs. Only unique sequences are supplied.</p> <p><strong>Supplementary File 3</strong>. Printable alignments of novel RNA motifs detected in this work (Supplementary Table 2), in PDF format. Only unique sequences are shown.</p> <p><strong>Supplementary File 4</strong>. Frequencies of RNA motifs in different environmental datasets. This data is a basis for relevant columns in Supplementary Table 2. The first worksheet describes the data format.</p> <p> </p>
Digitizing Chemical Discovery with a Bayesian Explorer for Interpreting Reactivity Data
<p>Dataset for the work entitled Digitizing Chemical Discovery with a Bayesian Explorer for Interpreting Reactivity Data</p>
Data Driven Discovery of MOFs for Hydrogen Gas Adsorption
<p>This data is in accordance with the submitted article to <strong>The Journal of Chemical Theory and Computation. </strong>This article is entitled, “<strong>Data Driven Discovery of MOFs for Hydrogen Gas Adsorption</strong>” by Samrendra K. Singh, Abhishek T. Sose, Fangxi Wang, Karteek K. Bejagam, and Sanket A. Deshmukh; to be published in the special issue on “Machine Learning for Molecular Simulation” in Journal of Chemical Theory and Computation.</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.