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1,930 results for “Matrix”
WGSUniFrac experiment1 tree pairwise distance matrix
<p>Pairwise distance matrix generated from filtered nodes of gg_13_5 99_otus tree from Greengenes.</p>
Adjacency matrix (.csv) of wood industry project network
<p>Adjacency matrix (.csv) of wood industry project network exported from R code.</p>
Colombo-etal-Epyrinae - Combined matrix
<p>Combined matrix data with 232 morphological characters and 3367 molecular characters used in phylogenetics analysis by Colombo et al. </p>
FIGURE. Spring view of the open forests of Quercus faginea subsp. alpestris in a matrix of oromediterranean cushion endemic scrublands dominated by Astragalus nevadensis subsp. andres-molinae and Bupleurum spinosum. (Photo authors). in Vascular flora of the Sierra de las Nieves National Park and its surroundings (Andalusia, Spain)
FIGURE. Spring view of the open forests of Quercus faginea subsp. alpestris in a matrix of oromediterranean cushion endemic scrublands dominated by Astragalus nevadensis subsp. andres-molinae and Bupleurum spinosum. (Photo authors).
FIGURE. Graminoid vegetation with Festuca elegans in a matrix of spring-flowering Erinacea anthyllis subsp. anthyllis cushion scrub in the upper summits of the Rondeño sector. At the bottom, the peak La Torrecilla (1,918 m). (Photo authors). in Vascular flora of the Sierra de las Nieves National Park and its surroundings (Andalusia, Spain)
FIGURE. Graminoid vegetation with Festuca elegans in a matrix of spring-flowering Erinacea anthyllis subsp. anthyllis cushion scrub in the upper summits of the Rondeño sector. At the bottom, the peak La Torrecilla (1,918 m). (Photo authors).
Indonesian soil and litter Collembola species and trait matrix with environmental data
<p>Rainforest conversion and expansion of plantations in tropical regions is associated with changes in animal communities and biodiversity decline. In soil, Collembola are one of the most numerous invertebrate groups that control microbial processes and support arthropod predators. Despite that, information on the impact of changes in land use in the tropics on species and trait composition of Collembola communities is very limited. We investigated the response of Collembola to the conversion of rainforest into rubber agroforest ('junge rubber'), rubber and oil palm plantations in Jambi province (Sumatra, Indonesia), a region that experienced one of the strongest deforestation globally during the last decades. Collembola from litter and soil layers were collected in 2013 and 2016 using heat extraction. In the litter layer, density and species richness in plantation systems declined by 25-38% and 30-40%, respectively, compared to rainforest. By contrast, in the soil layer, density, species richness and trait diversity of Collembola were only slightly affected by land-use change contrasting the response of many other animal groups. Species and trait composition of Collembola communities in litter and soil layers differed between all land-use systems. Water content and pH were identified as main factors related to the differences in species and trait composition both in litter and soil layers, followed by the density of micro- and macropredators. Dominant Collembola species in rainforest and jungle rubber were characterized by small body size, absence of furca and absent or intense pigmentation, while in plantations larger species with long furca and diffuse or patterned coloration were more abundant. The trait-based responses were similar to those observed in Collembola from temperate regions and to those in a similar study on spiders at our study sites. Overall, land-use change negatively affected Collembola communities in the litter layer, but only little affected Collembola communities in soil. Several pantropical Collembola genera (i.e., <i>Isotomiella</i>, <i>Pseudosinella</i> and <i>Folsomides</i>) dominated across land-use systems, reflecting their high environmental adaptability or efficient dispersal calling for studies on their ecology and genetic diversity. The decline in species richness and density of litter-dwelling Collembola with the conversion of rainforest into plantation systems calls for management practices mitigating negative effects of the deterioration of the litter layer in rubber but in particular in oil palm plantations.</p>
Sirmione (BS), Grotte di Catullo, ipotesi ricostruttiva: piante, sezioni, prospetti ed Extended Matrix
<p>Nell'ambito del progetto e-Archeo, coordinato dalla società ALES e avente come obiettivo la valorizzazione di diversi siti archeologici italiani, l'Università di Verona si è occupata dello studio della Villa Romana di Desenzano e del sito "grotte di Catullo" di Sirmione, con la guida della prof.ssa Patrizia Basso. Sono qui presentati i risultati dei lavori volti a fornire un'ipotesi ricostruttiva del sito "grotte di Catullo". Si è proceduto con lo studio stilistico e comparato di edifici e contesti simili a quelli oggetto di studio che unito all’analisi delle fonti antiche ha permesso di dedurre le norme di proporzionamento dei diversi elementi architettonici e strutturali nonché di formulare delle ipotesi interpretative di come doveva apparire l’edificio all’epoca della sua costruzione. Ciò ha permesso di elaborare dei disegni ricostruttivi 2D propedeutici alla realizzazione dei modelli 3D della villa romana (Soriano). Contestualmente si è proceduto con la realizzazione dei contenuti scientifici, quali fonti (storiche, iconografiche e di confronto) e processi interpretativi, fondamentali per poter effettuare la mappatura dei livelli di affidabilità sulle ricostruzioni virtuali. La mappatura dei livelli di affidabilità è stata effettuata utilizzando il linguaggio Extended Matrix (sviluppato da E. Demetrescu, CNR) che permette di implementare in un modello tridimensionale per volumi semplificati le fonti ed i processi interpretativi che hanno condotto all’ipotesi ricostruttiva (Delbarba). A tutto ciò si è affiancato un lavoro di studio e confronto dei frammenti pittorici per permettere di proporre un'ipotesi della decorazione parietale originaria di due ambienti oggetto di ricostruzione (Bianchi).</p>
Carpophiline-ID: An interactive matrix-based key to the carpophiline sap beetles (Coleoptera, Nitidulidae) of Eastern North America
<p>We present Carpophiline-ID, a matrix-based Lucid<sup>TM</sup> key, for the adult stage of the known species of Carpophilinae (<em>Coleoptera: Nitidulidae</em>) of North America, east of the Mississippi River. We provide an overview of the features and technical specifications used to build the key. The list of terminal taxa used in the key represents the most current regional account for Carpophilinae, a beetle subfamily of agricultural and ecological importance. We discuss the value of matrix-based, free access keys for the identification of difficult taxa.</p>
Data for Performance-Portable Solid Mechanics via Matrix-Free p-Multigrid
<p>Data, scripts to make the figures, and tex source for the paper: https://arxiv.org/abs/2204.01722</p>
Matrix of sources for decOM
<p>Matrix of sources used by decOM</p>
Ranked distance matrix for WGSUniFrac experiments - Grinder with matched primer
<p>Distance matrix for generating 16s and WGS grinder inputs.</p>
Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests: Complete matrix
<p>We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike <i>Sakesphorus luctuosus</i> (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of <i>S. luctuosus</i>, we identified independent lineages and estimated their differentiation, divergence times and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that <i>S. luctuosus</i> consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (<i>S. l.</i> <i>araguayae</i>), and gathered circumstantial evidence indicating that the taxon <i>S. hagmanni</i> may represent a highly introgressed population between 3 distinct phylogroups of <i>S. luctuosus</i>. Divergence time estimates between populations seem to be recent, occurring during the last 183 kya. Signs of population expansions were detected for populations attributed to subspecies <i>S. l. luctuosus</i>, but the <i>S. l. araguayae </i>population had probably maintained its effective size through time. Our results support<b> </b>that <i>S. luctuosus</i> has had a complex population history, resulting from a high dependence on southeastern "clear-water" habitats and their availability through time. Spatial and demographic expansions towards the western "white water" flooded forests might still be ongoing. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between <i>várzeas</i> ("white water" floodplains, mostly in southwestern Amazonia) and <i>igapós</i> ("clear- water" floodplains, especially located in the east) should be further explored as powerful drivers of micro-evolution.</p>
Data from: Improvement of genomic predictions in small breeds by construction of genomic relationship matrix through variable selection
<p>Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value—which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models—especially those using XGBoost—in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds.</p>
Phylogenetic matrix from: Osteology and neuroanatomy of a Miocene phasianid (Aves: Galliformes) from the Miocene of Nebraska
<p>Tetraoninae (grouse) and Meleagridinae (turkeys) are conspicuous representatives of the modern North American avifauna. The pre-Pleistocene fossil record of these clades has historically been limited to fragmentary remains, in some cases contributing to confusion rather than improving our understanding of how these charismatic landfowl evolved. We report an exquisitely preserved partial skeleton representing a new species of Late Miocene phasianid from the Ash Hollow Formation of Nebraska. <em>Centuriavis lioae</em> is a phasianid species close in size to modern sage-grouse that diverged prior to the grouse-turkey split and thus offers insight into the early history of this radiation. The cranial endocast resembles other North American phasianids and differs from odontophorids in exhibiting a strongly projected Wulst bordered by a well-defined vallecula. Phylogenetic analyses indicate that <em>Centuriavis</em> <em>lioae</em> gen. et sp. nov. forms a clade with Tetraoninae, Meleagridinae, and <em>Pucrasia</em> <em>macrolopha</em> (Koklass pheasant). The new fossil species provides a late Miocene minimum calibration for the divergence of these extant taxa from other Galliformes and supports the hypothesis of a single dispersal from Asia to North America by a lineage that later gave rise to grouse and turkeys.</p>
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I in New species of Trichomycterus (Siluriformes: Trichomycteridae) lacking pelvic fins from Paranapanema basin, southeastern Brazil
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I (COI) and 16S genes, showing the relationships of Trichomycterus pascuali within Trichomycterinae. Numbers on branches of tree denote bootstrap (B) values.
Supplementary material 1 from: Rousse P, van Noort S (2014) Afrotropical Ophioninae (Hymenoptera, Ichneumonidae): an update of Gauld and Mitchell's revision, including two new species and an interactive matrix identification key. ZooKeys 456: 59-73. https://doi.org/10.3897/zookeys.456.8140
Afrotropical Ophioninae: coordinates of the new distribution records.: Explanation note: Summary of the collection localities and their geographical data listed as new distribution records for Afrotropical Ophioninae
Kernel matrix for PPInfer
<p>Kernel matrices for eight organisms</p> <p>K10090.rds for mouse</p> <p>K3702.rds for A. thaliana</p> <p>K4932.rds for yeast</p> <p>K511145.rds for E. coli</p> <p>K6239.rds for C. elegans</p> <p>K7227.rds for D. melanogaster</p> <p>K7955.rds for zebra fish</p> <p>K9606.rds for human</p>
Estimation of the road traffic sound levels based on Non-Negative Matrix Factorization dataset
<p>Sound database to compute the NonnegMatrixFact experience (download the .m files here: https://github.com/jean-remyGloaguen/article2017EstimationAmbiance) dedicated to the estimation of the traffic sound level on urban sound mixtures.</p> <p>This sound database includes two subfolders: <em>ambiance</em> and <em>dictionary</em></p> <p><em>- ambiance </em>folder includes 6 sub-corpus (<em>alert</em>, <em>animals, climate, human, mechanics</em> and <em>transportation</em>). In each sub-corpus, 50 sound mixtures are available and divided into two files: one dedicated to the traffic signal, the other to the interfering signal.</p> <p><em>- dictionary </em>folder includes the isolated sounds dedicated to the dictionary learning for NMF</p>
Fig. 3. The genetic relatedness matrix summarising similarities and differences among the 90 in Morphological and molecular evidence refute a broad circumscription for Pultenaea glabra (Fabaceae: Mirbelieae), with implications for taxonomy, biogeography, and conservation
Fig. 3. The genetic relatedness matrix summarising similarities and differences among the 90 individuals included in the final, filtered dataset containing 2452 SNPs.
Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix
<p>Monotropoideae (Ericaceae) is a wholly leafless and holomycotrophic group of primarily temperate herbs with centers of diversity in western North America and east Asia. The eleven genera are structurally diverse and also vegetatively reduced, making relationships difficult to assess based on morphology. Previous molecular analyses have focused primarily on segments of the ribosomal RNA repeat and yielded sometimes conflicting topologies. We employed a genomic sampling approach to obtain 102 nuclear loci and plastid coding loci for nine of the genera, as well as sampling ITS-26S and plastid <em>rps2</em> for a broader set of accessions via PCR and Sanger sequencing Data filtering for character completeness had a clear effect on relationships and branch support. Nuclear and plastid loci agree on a topology that resolves <em>Allotropa</em> and <em>Hemitomes</em> as sisters and <em>Monotropsis</em> sister to <em>Eremotropa</em>+<em>Monotropa</em>+<em>Monotropastrum</em>, relationships that were unclear from previous analyses. <em>Hypopitys</em> should be recognized as distinct from <em>Monotropa</em>, with previous ambiguity in <em>rps2</em> relationships here explained by the existence of plastid and mitochondrial paralogs. Comparison of branch lengths between nuclear and plastid loci reveals increased rates of change in plastid sequences in most cases, especially in <em>Monotropsis</em> and <em>Monotropa</em>, but the reverse situation in <em>Pityopus</em>, with nuclear branches being unusually long, possibly indicating cryptic diversity. Parallel shifts in plant form to a ground-level floral display correlate with shifts from capsular to berry fruits and reduction in species ranges. The optimal tree from molecular data requires significant parallelism and/or reversal in morphological features due to the placement of <em>Allotropa</em> and <em>Hemitomes</em>.</p>
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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.
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.