Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,696
datasets available to search
ShareScore release 0.9.0
Dataset results
3,696 results for “reference”
An Investigation on Usage of Code References in Pull Requests on GitHub
<p>Review for ICPC 2025</p>
Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.
megahit reference files for ANASTASIA
<p>Reference files for using ANASTASIA tools and pipelines</p>
Figures 63-74 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 63-74 Bardaxima , Stragulodonta, Elasmia, male genitalia, aedoeagus, 8th male abdominal segment, ventral view: (63–65) B. dissona; (66–68) B. terminalba; (69–71) S. stragula; (72–74) E. perses.
Figures 19-30 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 19-30 Bardaxima , Stragulodonta and Elasmia specimens, dorsal view: (19) B. ionia, female, Turrialba, Cartago, Costa Rica; (20) B. dissona, male holotype, Peru; (21, 22) B. subrutila male, female, Camacan, Bahia, Brasil. (23–25) B. terminalba: (23, 24) male, female, Campos do Jordão, São Paulo, Brazil; (25) male holotype, São Paulo, São Paulo, Brazil. (26–28) S. stragula: (26) male, Jenaro Herrera, Loreto, Peru; (27) female, Vilhena, Rondônia, Brazil; (28) male holotype, Surinam. (29, 30) E. perses: (29) male, Cacaulândia, Rondônia, Brazil; (30) female, Planaltina, Distrito Federal, Brazil.
Figures 51-62 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 51-62 Bardaxima , male genitalia, aedoeagus, 8th male abdominal segment, ventral view: (51–53) B. marcida; (54–56) B. subrutila; (57–59) B. procne; (60–62) B. sambana.
Figures 9-18 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 9-18 Bardaxima specimens, dorsal view: (9, 10) B. donatian: (9) male, Porto Seguro, Bahia, Brazil; (10) female, Porto Seguro, Bahia, Brazil. (11–13) B. marcida: (11) female, Camacan, Bahia, Brazil; (12) male, Camacan, Bahia, Brazil; (13) female holotype, Colombia. (14–18) B. ionia: (14) male, Planaltina, Distrito Federal, Brazil; (15) female, Camacan, Bahia, Brazil; (16) male lectotype, Brazil; (17) female, Sete Lagoas, Minas Gerais, Brazil; (18) male, Camacan, Bahia, Brazil.
Figures 1-8 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 1-8 Bardaxima specimens, dorsal view: (1–3) B. lucilinea: (1) male, Porto Seguro, Bahia, Brazil; (2) female, Açailândia, Maranhão, Brazil; (3) male holotype, Rio de Janeiro, Brazil. (4–8) B. fulgurifera: (4) female, Bijagua, Alajuela, Costa Rica; (5) male, Monteverde, Puntarenas, Costa Rica; (6) female, Los Bancos, Pichincha, Ecuador; (7) male, Porto Velho, Rondônia, Brazil; (8) female holotype, Honduras.
Figures 39-50 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 39-50 Bardaxima , male genitália, aedoeagus, 8th male abdominal segment, ventral view: (39–41) B. lucilinea; (42–44) B. fulgurifera; (45–47) B. donatian; (48–50) B. ionia.
Figures 31-38 from: Becker VO (2021) A review of the Neotropical moth genus Bardaxima (Lepidoptera: Notodontidae: Nystaleinae), with special reference to the species occurring in Brazil. Zoologia 38: 1-14. https://doi.org/10.3897/zoologia.38.e63526
Figures 31-38 Bardaxima specimens, dorsal view: (31–33) B. procne: (31) male, Vilhena, Rondônia, Brazil; (32) female, Cacaulândia, Rondônia, Brazil; (33) female, Jenaro Herrera, Loreto, Peru. (34–38) B. sambana: (34) male holotype, Costa Rica; (35) male, Porto Seguro, Bahia, Brazil; (36) female, Guaramiranga, Ceará. Brazil; (37) male, Los Bancos, Pichuincha, Ecuador; (38) male, Esquipulas, Chiquimula, Guatemala.
FIGURE 1 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 1. Portrait of CharlesJoseph Panckoucke.
Table e-1 and e-references for: Neurogenic dysphagia: a systematic review and proposal of a classification system
<p><b>Objective:</b> Introduction of a phenotypic classification of dysphagia with differential diagnostic implications and its validation in different disease groups using videos of flexible endoscopic evaluation of swallowing (FEES).</p> <p><b>Methods: </b>A systematic literature review was performed to summarize disease-typical FEES-findings.<b> </b>In an interdisciplinary team, a FEES-based classification of neurogenic dysphagia was developed which distinguishes different dysphagia phenotypes. The classification was validated using 1012 randomly selected FEES videos of patients with various neurological disorders. Chi-square tests were applied to investigate the relationship between the disease groups and each dysphagia phenotype.</p> <p><b>Results: </b>Seven dysphagia phenotypes were defined and all phenotypes were significantly associated with specific neurological disease groups: (1) "Premature bolus spillage" and (2) "delayed swallowing reflex" occurred mainly in stroke patients, (3) "predominance of residue in the valleculae" was most common in Parkinson's disease, (4) "predominance of residue in the piriform sinus" occurred only in myositis, motoneuron disease and brainstem stroke patients, (5) "pharyngolaryngeal movement disorder" was found in atypical Parkinsonian syndromes and stroke patients, (6) "fatigable swallowing weakness" was common in patients with myasthenia gravis, and (7) "complex disorder" with a heterogeneous dysphagia pattern was the leading mechanism in amyotrophic later sclerosis. The interrater reliability showed a strong agreement (kappa = 0.84).</p> <p><b>Conclusion: </b>Neurogenic dysphagia is not a mere symptom, but a multi-etiological syndrome with different phenotypic patterns depending on the underlying disease. Dysphagia phenotypes can facilitate differential diagnosis in patients with dysphagia of unclear etiology.</p>
Supplementary references from: Thrombus composition, imaging, and outcome prediction in acute ischemic stroke
<p><strong>Purpose of the Review</strong>: <span>This article reviews the biochemical, structural, and imaging characteristics of intracranial thrombi in acute ischemic stroke; the relationship between thrombus composition and response to lytic and endovascular therapies; and current and future directions for improving outcomes in acute stroke patients based on thrombus characteristics.</span><br> <br> <span><strong>Recent Findings:</strong> New imaging techniques have advanced our ability to capture thrombus characteristics and burden in real-time, An improved understanding of recanalization rates with thrombolysis and endovascular thrombectomy based on thrombi has spurred interest in new acute therapies for acute stroke.</span></p> <p><strong><span>Summary</span></strong><span><strong>: </strong>Thrombus composition, size, location, and timing from stroke onset correlate with imaging findings in acute ischemic stroke and are associated with clinical outcome. Further research across multiple domains could assist in better applying our knowledge of thrombi to patient selection and individualization of acute therapies.</span></p>
FIGURE 17 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 17. Holotype of V. ×ruggerii Ardenghi, Galasso, Banfi & Lastrucci (MSNM).
FIGURE 14 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 14. Holotype of V. ×koberi Ardenghi, Galasso, Banfi & Lastrucci (MSNM).
FIGURE 5 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 5. Vitis riparia. Leaf blade variability: a–b, d) adaxial surface; c) abaxial surface.
FIGURE 10 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 10. Vitis vinifera. Leaf blade variability: a–c, e–f) adaxial surface; d) abaxial surface.
FIGURE 16 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 16. Geographical distribution in Elba Island of V. ×koberi and V. ×ruggerii.
FIGURE 12 in A taxonomic survey of the genus Vitis L. (Vitaceae) in Italy, with special reference to Elba Island (Tuscan Archipelago)
FIGURE 12. Holotype of V. ×instabilis Ardenghi, Galasso, Banfi & Lastrucci (MSNM).
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.