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20,299 results for “Systematic”
Systematic creation and phenotyping of Mendelian disease models in C. elegans: towards large-scale drug repurposing
<p>Data collected for the eLife OpenAccess paper: Systematic creation and phenotyping of Mendelian disease models in <em>C. elegans</em>: towards large-scale drug repurposing. (doi: 10.7554/eLife.92491.1)</p> <p>Contains: extracted features, calculated stats, normalised z-scores and timerseries data of all the disease model mutants generated. In addition, there is a static .html file that allows for mousing over the clustermaps to easily view differences in strains compared to the N2 wild-type. Dataset also contains, metadata and feature summary/file name information of FDA-library drug screen and the confirmation screen of the hit from this (i.e., all data collected in published in the associated paper). </p>
The efficacy of hemoglobin spray in wound management: a systematic review and network meta-analysis of comparative studies
<p>Dataset</p>
Topology Bench: Systematic Graph Based Benchmarking for Optical Networks
<p>TopologyBench is a systematic graph theoretical approach to benchmarking optical network topologies. Network datasets are combined with their corresponding graph theoretical analysis to provide a systematic methodology for selecting diverse sets of optical networks for benchmarking. This topology benchmark is comprised of a network dataset and a systematic graph theoretic analysis. The dataset provides (a) 105 real optical networks and (b) synthetic topologies, generated by the SNR-BA model, divided into (i) Syn-small of 900 synthetic networks and (ii) Syn-large of 270,000 synthetic networks. The systematic graph theoretical analysis identifies and analyses structural, spatial and spectral properties of both the real world and synthetic networks. The graph theoretical correlation analysis reveal network design strategies leading to sparse yet efficient networks. An outlier analysis identifies networks that deviate from standard network designs. The analysis also identifies the limitations of real data in terms of network diversity and provides a justification for using synthetic data to complement the real dataset. We conclude the paper by providing a systematic methodology to cluster networks based on unsupervised machine learning and to select a diverse set of topologies for benchmarking. TopologyBench is a novel, high-quality and unified benchmark designed to facilitate research collaborations in long-haul fibre infrastructure by providing a systematic graph theoretical approach to benchmarking optical networks.</p> <p> </p> <p>If you use any of the data provided, please cite our paper:</p> <p> </p> <pre>@article{matzner2024topology, title={Topology Bench: systematic graph-based benchmarking for core optical networks}, author={Matzner, Robin and Ahuja, Akanksha and Sadeghi, Rasoul and Doherty, Michael and Beghelli, Alejandra and Savory, Seb J and Bayvel, Polina}, journal={Journal of Optical Communications and Networking}, volume={17}, number={1}, pages={7--27}, year={2024}, publisher={IEEE} }<br><br></pre>
Change Impact Analysis in Microservice Systems A Systematic Literature Review
<p>Reproduction package for Change Impact Analysis in Microservice Systems A Systematic Literature Review</p>
Can Machine Learning Support the Selection of Studies for Systematic Literature Review Updates?
<p>Artifacts for "Can Machine Learning Support the Selection of Studies for Systematic Literature Review Updates?".</p> <p>File used to answer RQ1:</p> <ul> <li>RQ1-RF-predictions.csv</li> <li>RQ1-RQ3-best-configuration-RF.csv</li> </ul> <p>File used to answer RQ2:</p> <ul> <li>RQ2-SVM-predictions.csv</li> <li>RQ2-best-configuration-SVM.csv</li> </ul> <p>File used to answer RQ3:</p> <ul> <li>RQ3-RF-normalized-predictions.csv</li> <li>RQ1-RQ3-best-configuration-RF.csv</li> </ul> <p> </p> <p>The file assessment-team-votes.csv contains the title of each study, a bolean indicating if it was included or not and the individual marks of each reviewer before applying the agreement criteria.</p> <p> </p> <p>The .bib files used in our experiment are available at:</p> <ul> <li> <div>Our testing set: 'Testing set - Excluded.bib' (513 studies) and 'Testing set - Included.bib' (38 studies). All of the 551 studies we used, were obtained from the actual SLR Update</div> </li> <li>Our training set: 'Training set - Excluded.bib' (83 studies - obtained by performing the backward snowballing using the Original SLR) and 'Training set - Included.bib' (45 studies - all studies that were included in the Original SLR).</li> </ul> <p>All of our code is available in the .zip file. Besides our pipeline, there's also some jupyter notebooks in code/analysis showing illustrating how we answered each of our questions.</p>
Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation
Advances in sequencing technology and phylogenetics have revolutionised avian biology by providing an evolutionary framework for studying natural groupings. In the parrots (Psittaciformes), DNA-based studies have led to a reclassification of clades, yet substantial gaps remain in the data gleaned from genetic information. Here we provide an overview of published genetic data of parrots, characterise sampling depth across the phylogeny, and evaluate support for existing systematic treatments. We inferred a concatenated tree with 307 species from a 30-gene supermatrix. We recovered well-supported relationships among recently proposed clades. Taxonomic groups were more stable towards the base of the tree and increased sampling will be required to clarify relationships at the tips, particularly below the generic level. Only a third of species have been sampled intraspecifically in population genetic or phylogeographic surveys. Intraspecific sampling has not been geographically or phylogenetically even across Psittaciformes, especially poor in the cockatoos, Southeast Asia, and parts of Australo-Papua. Threatened species are poorly sampled in the Neotropics. We highlight where effort should be focused to improve sampling based on geography and conservation status. In sum, phylogenetic relationships among the major parrot clades are robust, but relationships within and between genera and species provide opportunities for future investigations.
FIG. 8 in Systematics of Neotropical Spiny Mice, Genus Neacomys Thomas, 1900 (Rodentia: Cricetidae), from Southeastern Amazonia, with Descriptions of Three New Species
FIG. 8. Dorsal and ventral views of the skin of Neacomys vossi (UFPA 1583, holotype).
FIG. 4 in Systematics of Neotropical Spiny Mice, Genus Neacomys Thomas, 1900 (Rodentia: Cricetidae), from Southeastern Amazonia, with Descriptions of Three New Species
FIG. 4. The holotype of Neacomys marajoara, (MPEG 40432) in life. Photo by Rogério V. Rossi.
FIG. 11 in Systematics of Neotropical Spiny Mice, Genus Neacomys Thomas, 1900 (Rodentia: Cricetidae), from Southeastern Amazonia, with Descriptions of Three New Species
FIG. 11. Dorsal and ventral views of the skin of Neacomys xingu (UFMT 1268, holotype).
FIG. 10. Robert S in Systematics of Neotropical Spiny Mice, Genus Neacomys Thomas, 1900 (Rodentia: Cricetidae), from Southeastern Amazonia, with Descriptions of Three New Species
FIG. 10. Robert S. Voss in the field (Venezuela, 1979; photo by Paul Kaarakka).
Skin eruptions in acute hemorrhagic edema of young children: systematic review of the literature
<p><strong>Background:</strong> Acute hemorrhagic edema is a skin limited small-vessel leukocytoclastic vasculitis, which affects infants 4 weeks to 2 years of age and remits within 3 weeks. The diagnosis is made clinically in not-ill appearing children with acute onset of raised annular or nummular eruptions and edema. In this vasculitis, type, distribution and evolution of the rash have never been systemically investigated. To address this issue, we employed the data contained in the Acute Hemorrhagic Edema Bibliographic Database, which incorporates all reports on acute hemorrhagic edema. <strong>Summary:</strong> Key features of rash were documented in 383 children. Annular eruptions in strict sense, usually targetoid, were reported in 375 (98%) cases (many children also presented polycyclic or arciform eruptions). Nummular eruptions were also very common (N=358; 93%). Purpuric eruptions and ecchymoses were reported in the vast majority of cases. Macules and wheals were described in a minority of cases. Edema, detected in all cases, was mostly painful, indurated and non-pitting. Following regions were affected, in decreasing order, by annular or nummular eruptions: legs, feet, face, arms, ears, trunk, and genitals. With the exception of feet, which were very often affected, the same distribution was reported for edema. The initial eruption was often a wheal or a macule that evolved into a nummular or an annular eruption. Nummular eruptions successively evolved into annular ones<strong>. Key message</strong>: this study carefully characterizes type, distribution and evolution of skin eruption in acute hemorrhagic edema. The data help physicians to rapidly and noninvasively make the clinical diagnosis of this vasculitis.</p>
A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack‐bearer moths
<p>The frenulum is a wing coupling structure that is found on the wings of most families of Lepidoptera. It is a single bristle or set of bristles that originate from the base of the hindwing that often interlocks with the forewing during flight. This wing coupling mechanism is thought to have been a major evolutionary innovation that allowed for enhanced flight in Lepidoptera. The sack-bearer moths (Mimallonidae) are unusual among Lepidoptera in that not all species within the family have a frenulum. We test the hypothesis that the frenulum is not necessary and is therefore lost in mimallonids that have longer male forewings because such wings are perhaps better suited to be coupled by other means. To understand the evolution of the frenulum, we inferred the most taxonomically and genetically sampled anchored hybrid enrichment-based phylogeny of Mimallonidae, including 604 loci from all 41 genera and from 120 species, covering about 40% of the described species in the family. The maximum likelihood tree robustly supports major relationships within the family, and ancestral state reconstruction clearly recovers the frenulum as the plesiomorphic condition in Mimallonidae. Our results show that the frenulum is more often observed in species that have shorter, rather than longer, male forewings. The frenulum has historically been used as an important character for intrafamilial classification in Mimallonidae, but our results conclusively show that this character system is more variable than previously thought. Based on our results, we erect two new subfamilies, Roelofinae St Laurent & Kawahara, <b>subfam. n.</b> and Meneviinae St Laurent, Herbin, & Kawahara, <b>subfam. n.</b>, for four genera previously considered <i>incertae sedis.</i> In the predominantly frenulum-lacking clade Cicinninae, we describe a new genus, <i>Cerradocinnus </i>St Laurent, Mielke, & Kawahara, <b>gen. n.</b>, and the genus <i>Gonogramma </i><b>stat. rev.</b> is revalidated to include many species previously placed in <i>Cicinnus sensu lato</i>. With these changes, <i>Cicinnus </i>can now be considered monophyletic. Thirty-three species are transferred to <i>Gonogramma </i>from <i>Cicinnus sensu lato</i>.</p>
Dataset (46 analyzed core studies) of the publication "Conservation perspectives of small-scale private forest owners in Europe: A systematic review"
<p>The dataset contains the data collected to conduct the review "Conservation perspectives of small-scale private forest owners in Europe: A systematic review".</p>
Systematic Mapping Study Results
<p>This is a CSV-file containing the results from a systematic mapping study tiltled "Edge computing for cyber-physical systems -- A systematic mapping study emphasizing trustworthiness" submittied for review to ACM Transactions on Cyber-Physical Systems.</p>
Data from: Assessing the usefulness of Citizen Science Data for habitat suitability modelling: opportunistic reporting versus sampling based on a systematic protocol
<p><strong>Aim:</strong> To evaluate the potential of models based on opportunistic reporting (OR) compared to models based on data from a systematic protocol (SP) for modelling species distributions. We compared model performance for eight forest bird species with contrasting spatial distributions, habitat requirements, and rarity. Differences in the reporting of species were also assessed. Finally, we tested potential improvement of models when inferring high quality absences from OR based on questionnaires sent to observers.</p> <p><strong>Location:</strong> Both datasets cover the same large area (Sweden) and time period (2000 -2013).</p> <p><strong>Methods:</strong> Species distributions were modelled using logistic regression. Predictive performance of OR models to predict SP data were assessed based on AUC. We quantified the congruence in spatial predictions using Spearman's rank correlation coefficient. We related these results to species characteristics and reporting behaviour of observers. We also assessed the gain in predictive performance of OR models by adding inferred absences. Finally, we investigated the potential impact of sampling bias in OR.</p> <p><strong>Results:</strong> For all species, and despite the sampling biases, results from OR overall agreed well with those of SP, for the nationwide spatial congruence of habitat suitability maps and the selection and directions of species-environment relationships. The OR models also performed well in predicting the SP data. The predictive performance of the OR models increased with species rarity and even outperformed the SP model for the rarest species. No significant impact of observer behaviour was found.</p> <p><strong>Main Conclusions:</strong> Relatively simple analyses with inferred absences could produce reliable spatial predictions of habitat suitability. This was especially true for rare species. OR data should be seen as a complement to SP, as the weakness of one is the strength of the other, and OR may be especially useful at large spatial scales or where no systematic data collection protocols exist.</p>
Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis (Dataset)
<p>Raw data used for statistical analysis of our paper "Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis". </p>
Figure 2 in Contribution to systematics of the genus Eustigmaeus (Acari: Stigmaeidae) of Russia
Figure 2 Eustigmaeus bochkovin. sp., female: left palp in dorsal view.
Figure 3 in Charles Immanuel Forsyth Major's expedition to Madagascar, 1894 to 1896: beginnings of modern systematic study of the island's mammalian fauna
Figure 3. Map showing region of Madagascar visited by Major.
Figure 2 in Charles Immanuel Forsyth Major's expedition to Madagascar, 1894 to 1896: beginnings of modern systematic study of the island's mammalian fauna
Figure 2. Examples of original specimen labels.
Figure 1 in Charles Immanuel Forsyth Major's expedition to Madagascar, 1894 to 1896: beginnings of modern systematic study of the island's mammalian fauna
Figure 1. Photograph of Charles Immanuel Forsyth Major from Stehlin (1925).
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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.