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12,393 results for “materiality”
Supplementary Material: Exposing Previously Undetectable Faults in Deep Neural Networks
<p>Supplementary material for ISSTA 2021 submission #58. The supplementary material is under 600MB and uploaded before the submission deadline, but uploading to the submission website did not work. Editing this supplementary material is not possible after upload.</p>
Supplementary material 1 from: Gómez-Domínguez H, Ortiz-Rodríguez AE, Velasco-Espino D, Hernández-Burguete R (2021) Taxonomic updates in Amphitecna (Bignoniaceae): A new Mexican species and the re-establishment of the giant-leaved A. megalophylla. PhytoKeys 171: 75-90. https://doi.org/10.3897/phytokeys.171.55397
Figure S1. Cophenetic correlation between clustering results from eight different linkage algorithms and Gower similarity index.
Data from: Real-time quantification of damage in structural materials during mechanical testing
A novel methodology is introduced for quantifying the severity and morphology of damage created during testing in composite components. The method utilises digital image correlation combined with image processing techniques to monitor the rate at which the strain field changes during mechanical tests. The methodology is demonstrated using two distinct experimental datasets, a ceramic matrix composite specimen loaded in tension at high temperature and nine polymer matrix composite specimens containing fibre-waviness defects loaded in bending. The changes in the strain field due to damage creation are shown to be a more effective indicator that the specimen has reached its proportional limit than using load-extension diagrams. The technique also introduces a new approach to using experimental data for creating maps showing the spatio-temporal distribution of damage in a component. These maps indicate where damage occurs in a component, its morphology and the time of occurrence. This presentation format is both easier and faster to interpret than the raw data which, for some tests, can consist of tens of thousands of images. This methodology has the potential to reduce the time taken to interpret large material test datasets whilst increasing the amount of knowledge that can be extracted from each test.
Data from: Comparative modelling of crack propagation in elastic-plastic materials using meshfree LRPIM and XFEM
<p>The modelling of crack propagation for elastic-plastic materials is critical in various engineering applications, such as safety analysis of concrete structures and stability analysis of rock slopes. Combined with elastic-plastic theory and fracture mechanics, the local radial basis point Interpolation method (LRPIM)has the ability to analyse crack propagation in elastic-plastic materials. Crack propagation in elastic-plastic materials is compared using the LRPIM and Extended Finite Element method (XFEM). The comparative investigation indicates that: (1) The LRPIM results are close to the model test results, which indicates that it is feasible for analysing crack growth of elastic-plastic materials. (2) Compared with the LRPIM, the XFEM results are closer to the experimental results, showing that the XFEM has higher accuracy and computational efficiency. (3) Compared with the XFEM, when the LRPIM method is used to analyse crack propagation, the propagation path is not smooth enough, which can be explained that the crack tip stress and strain not being accurate enough.</p>
Data from: The variation of grain size distribution in rock granular material in seepage process considering the mechanical-hydrological-chemical coupling effect: An experimental research
<p>As a common solid waste in geotechnical engineering, rock granular material should be properly treated and recycled. Rock granular material often coexists with water when it is used as the filling material in geotechnical engineering. Water flowing in rock granular materials is a complex progress with the mechanical-hydrological-chemical (MHC) coupling effect, i. e. the water scours in the gaps and spaces in the rock granular material structure, produces chemical reactions with rock grains, rock grains squeeze each other under the water pressure and compression leading re-breakage and producing secondary rock grains, the fine rock grains are migrated with water and rushed out. In this process, rock grain size distribution (GSD) changes, it affects the physical and mechanical characteristics of the rock granular materials, and even influences the seepage stability of the rock granular materials. To study the variation of GSD in the rock granular material considering the MHC coupling effect after the seepage process, seepage experiments of rock grain samples are carried out and analyzed in this paper. The result is expected to have a positive impact on further studies of the properties of the rock granular material.</p>
Data from: Examination of a historic collection of isolated cranial and appendicular hadrosaurid material from the lower Kirtland Formation of the San Juan Basin, New Mexico
The Field Museum of Natural History collection contains several isolated hadrosaurid specimens collected by Charles H. Sternberg from the lower Kirtland Formation of the San Juan Basin, New Mexico, that have been previously overlooked. Cranial elements described herein consist of a dentary and three jugals while appendicular material is limited to two humeri and two pubes. Many of the specimens preserve taxonomically informative characters that show strong affinities with Kritosaurini but are distinct from Kritosaurus navajovius (Brown, 1910) suggesting that the saurolophine-dominated San Juan Basin diversity is greater than currently recognized. Future examination of currently unprepared material will add to our developing understanding of the ambiguous hadrosaurid diversity of the San Juan Basin.
Supplemental material for: Morphological phylogenetics evaluated using novel evolutionary simulations
<p></p><p>Evolutionary inferences require reliable phylogenies. Morphological data has traditionally been analysed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here we investigate phylogenetic methods using two novel simulation models – one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees – measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics – demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differs between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, towards identifying modes of morphological evolution and using these to build models for probabilistic search methods.</p><p></p>
The last pteraspids (Agnatha, Heterostraci): New material from the Middle Devonian of Alberta and Idaho
<p>This report documents the last pteraspids, (armored, jawless members of the Heterostraci), which are otherwise only known from the Early Devonian of the Old Red Sandstone Continent. Tuberculate pteraspid heterostracans are described from the Middle Devonian beds of two formations in western North America. The late Givetian Yahatinda Formation of Alberta and British Columbia consists of channels cut into lower Paleozoic rocks and represents deposition in marine to littoral environments. Clavulaspis finis new genus new combination, is redescribed from additional material from the Yahatinda Formation and renamed, as the original genus name has proved to be invalid. The Eifelian Spring Mountain beds of Idaho consist of a large channel that represents a clastic dominated estuarine environment. It contains Scutellaspis wilsoni new genus new species, and the previously described species from the Spring Mountain beds is redescribed as Ecphymaspis idahoensis new genus new combination, prompted by new material and a review of the validity of the original genus name. Phylogenetic analysis shows that these three new taxa form part of the derived clade Protaspididae.</p>
Data from: Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
Data from: A redescription and phylogenetic analysis based on new material of the fossil newts Taricha oligocenica Van Frank, 1955 and Taricha lindoei Naylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon.
Complete body fossils of salamanders are relatively rare, but provide critical information on the evolutionary roots of extant urodele clades. We describe new specimens of the fossil salamandrids Taricha oligocenica Van Frank, 1955, and Taricha lindoei Naylor, 1979, from the Oligocene Mehama and John Day Formations of Oregon that illustrate aspects of skeletal morphology previously unseen in these taxa, and contribute to our understanding of population-level variation. Morphological analysis of these specimens supports the classification of T. oligocenica and T. lindoei as two different species, distinct from extant Taricha. Parsimony-based, heuristic analysis of phylogeny using 108 morphological characters for 40 taxa yields different results from a phylogenetic analysis that excludes four taxa known only via vertebrae. Our smaller analysis generally agrees with molecular phylogenies of the family Salamandridae, but with poorer resolution for molgin newts, especially between Taricha and Notophthalmus. The analysis including all taxa produced polytomies mostly related to complications from several fossil taxa. The presence or absence of dorsally expanded, sculptured neural spine tables on trunk vertebrae, an important character in past descriptions of fossil salamandrids, appears to be either homoplastic within the Salamandridae, or requires an expansion of characters or character states. T. oligocenica and T. lindoei are separate species of an at least 33 million-year-old clade, but their relationships with each other and extant North American salamandrids remain unclear with current levels of morphological data. Salamandrid research requires additional morphological data, particularly for the vertebrae and ribs, to better resolve salamandrid evolutionary history through morphological characters.
Data from: Studies in Lichens and Lichenicolous Fungi – no. 18: resolution of three names introduced by Degelius and Magnusson based on material from the Great Smoky Mountains
Arthonia biseptata is shown to be a species of Mycoporum, likely narrowly endemic to high elevations of the southern Appalachian Mountains and the new combination M. biseptatum is proposed. Lecidea degelii is shown to apply to the sorediate morphotype of Porpidia albocaerulescens. The results of molecular phylogenetic analyses of nrITS and mtSSU sequence data of sorediate and esorediate populations of P. albocaerulescens are presented. These analyses recovered the sorediate and esorediate morophotypes together in a single clade as strongly-supported monophyletic entities. As a result the new combination Porpidia degelii is proposed, the species illustrated, and the North American distribution of P. degelii with respect to P. albocaerulescens is discussed. These data strongly refute the notion that "species pairs" do not exist in Porpidia. Lecidea subtilis is placed in synonymy with Pyrrhospora varians.
Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
Data from: Population history provides foundational knowledge for utilizing and developing native plant restoration materials
A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.
Data from: Wall structure and material properties cause viscous damping of swimbladder sounds in the oyster toadfish Opsanus tau
Despite rapid damping, fish swimbladders have been modelled as underwater resonant bubbles. Recent data suggest that swimbladders of sound-producing fishes use a forced rather than a resonant response to produce sound. The reason for this discrepancy has not been formally addressed, and we demonstrate, for the first time, that the structure of the swimbladder wall will affect vibratory behaviour. Using the oyster toadfish Opsanus tau, we find regional differences in bladder thickness, directionality of collagen layers (anisotropic bladder wall structure), material properties that differ between circular and longitudinal directions (stress, strain and Young's modulus), high water content (80%) of the bladder wall and a 300-fold increase in the modulus of dried tissue. Therefore, the swimbladder wall is a viscoelastic structure that serves to damp vibrations and impart directionality, preventing the expression of resonance.
Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.
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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.
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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.