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9,882 results for “Scale”
Figure 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 1 Examples of lichen herbarium specimens used for this study AParmotrema perlatum, specimen J.A. Elix 43686 (CANB790817) BEndocarpon pusillum, specimen H. Streiman 45100 (CBG9011273) CBuellia albula, specimen J.A. Elix 45138 (CANB810791) DCatillaria sp., specimen J.A Elix 37142 (CANB872684). Scale bar: 1 cm. Photos C. Gueidan.
Figure 2 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 2 Sequencing success for different morphological groups of taxa included in this study. Specimens were grouped into three main morphological categories: 1Buellia, Catillaria and other crustose saxicolous taxa 2Endocarpon and other squamulose terricolous taxa 3 the foliose corticolous genus Parmotrema. In the graph, stalked columns show successful samples (sequence generated for the target species) in dark grey and unsuccessful samples (no sequence generated or generated sequences not from the target species) in light grey. The total number of samples (N) is indicated below each corresponding column.
Figure 3 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 3 Sequencing success for different ages of specimens included in this study. Specimens were grouped in five categories: 1966–1980, 1981–1990, 1991–2000, 2001–2010, 2011–2020. In the graph, stalked columns show successful samples (sequence generated for the target species) in dark grey and unsuccessful samples (no sequence generated or generated sequences not from the target species) in light grey. The total number of samples (N) is indicated below each corresponding column.
Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
<p>Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population histories and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism (SNP) genotypic data from archival scale samples, and demonstrate its application to a study of kokanee salmon (<i>Oncorhynchus nerka</i>) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.</p>
Identification of Plant Pests Using Multi-scale SE-Xception Model
<p>The pest dataset of plant pest recognition.</p>
FIGURE 4 in Towards identification of the scale insects (Hemiptera: Coccomorpha) of continental Africa: 2. Checklists and keys to six archaeococcoid families
FIGURE 4. Neomargarodes trabuti Marchal, adult female, developed from Morrison (1928: 79, Fig. 28).
Figure 1 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies
Figure 1. Boxplot of length of each protein-coding gene.
Supplementary material 1 from: D'Cruze N, Assou D, Coulthard E, Norrey J, Megson D, Macdonald DW, Harrington LA, Ronfot D, Segniagbeto GH, Auliya M (2020) Snake oil and pangolin scales: insights into wild animal use at "Marché des Fétiches" traditional medicine market, Togo. Nature Conservation 39: 45-71. https://doi.org/10.3897/natureconservation.39.47879
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Climate oscillations drive millennial-scale changes in seabird colony size
<p>Seabird population size is intimately linked to the physical, chemical, and biological processes of the oceans. Yet, the overall effects of long-term changes in ocean dynamics on seabird colonies are difficult to quantify. Here, we used dated lake sediments to reconstruct ~10,000-years of seabird dynamics in the Northwest Atlantic to determine the influences of Holocene-scale climatic oscillations on colony size. On Baccalieu Island (Newfoundland and Labrador, Canada) – where the world's largest colony of Leach's storm-petrel (<em>Hydrobates leucorhous</em> Vieillot 1818) currently breeds – our data track seabird colony growth in response to warming during the Holocene Thermal Maximum (ca. 9,000 to 6,000 BP). From ca. 5,200 BP to the onset of the Little Ice Age (ca. 550 BP), changes in colony size were correlated to variations in the North Atlantic Oscillation (NAO). By contrasting the seabird trends from Baccalieu Island to millennial-scale changes of storm-petrel populations from Grand Colombier Island (an island in the Northwest Atlantic that is subjected to different ocean climate), we infer that changes in NAO influenced the ocean circulation, which translated into, among many things, changes in pycnocline depth across the Northwest Atlantic basin where the storm-petrels feed. We hypothesize that the depth of the pycnocline is likely a strong bottom-up control on surface-feeding storm-petrels through its influence on prey accessibility. Since the Little Ice Age, the effects of ocean dynamics on seabird colony size have been altered by anthropogenic impacts. Subsequently, the colony on Baccalieu Island grew at an unprecedented rate to become the world's largest resulting from favourable conditions linked to climate warming, increased vegetation (thereby nesting habitat), and attraction of recruits from other colonies that are now in decline. We show that although ocean dynamics were an important driver of seabird colony dynamics, its recent influence has been modified by human interference.</p>
FIGURE 1 in A new coccoid family (Hemiptera: Coccomorpha) for an unusual species of scale insect on Podocarpus macrophyllus (Podocarpaceae) from southern China
FIGURE 1. Podocarpus macrophyllus infested by Qinococcus podocarpus Wu, sp. n.
OpenABC-D: A Large-Scale Dataset For Machine Learning Guided Integrated Circuit Synthesis
<p>Logic synthesis is a challenging and widely-researched combinatorial optimization problem during integrated circuit (IC) design. It transforms a high-level description of hardware in a programming language like Verilog into an optimized digital circuit netlist, a network of interconnected Boolean logic gates, that implements the function. Spurred by the success of ML in solving combinatorial and graph problems in other domains, there is growing interest in the design of ML-guided logic synthesis tools. Yet, there are no standard datasets or prototypical learning tasks defined for this problem domain. Here, we describe OpenABC-D,a large-scale, labeled dataset produced by synthesizing open source designs with a leading open-source logic synthesis tool and illustrate its use in developing, evaluating and benchmarking ML-guided logic synthesis. OpenABC-D has intermediate and final outputs in the form of 870,000 And-Inverter-Graphs (AIGs) produced from 1500 synthesis runs plus labels such as the optimized node counts, and de-lay. We define a generic learning problem on this dataset and benchmark existing solutions for it. The codes related to dataset creation and benchmark models are available athttps://github.com/NYU-MLDA/OpenABC.git.</p>
Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction events
<ol> <li class="Body">Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction – a process known as the 'extinction vortex.' However, empirical studies investigating extinction dynamics in relation to species' traits have been lacking.</li> <li class="Body">We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals and two reptiles. We supplemented these population time series with species-specific mean adult body size to investigate whether this key intrinsic trait affects the dynamics of populations declining towards extinction.</li> <li class="Body">We performed three analyses to quantify the effects of adult body size on three characteristics of population dynamics: time to extinction, population growth rate, and residual variability in population growth rate.</li> <li class="Body">Our results provide support for the existence of extinction vortex dynamics in extirpated populations. We show that populations typically decline non-linearly to extinction, while both the rate of population decline, and variability in population growth rate increase as extinction is approached. Our results also suggest that smaller-bodied species are particularly prone to the extinction vortex, with larger increases in rates of population decline and population growth rate variability when compared to larger-bodied species.</li> <li class="Body">Our results reaffirm and extend our understanding of extinction dynamics in real-life extirpated populations. In particular, we suggest that smaller-bodied species may be at greater risk of rapid collapse to extinction than larger-bodied species, and thus management of smaller-bodied species should focus on maintaining higher population abundances as a priority. </li> </ol>
Household Survey - Impacts of large-scale land acquisitions on smallholder agriculture and livelihoods in Tanzania
<p><strong>** Article & Dataset Currently Under Review **</strong></p> <p><strong>Dataset Overview</strong></p> <p>Our household dataset is associated with a pre-print article "Impacts of large-scale land acquisitions on smallholder agriculture and livelihoods in Tanzania". The household survey is designed for the purposes of policy evaluation with selection of households based on proximity to large-scale land acquisitions (treatment) and a set of households in similar socio-ecological contexts with no association to large-scale land acquisitions (control). Households were selected as a random sample in 35 villages surrounding LSLAs who provided responses to a questionnaire covering household income, assets, farming practices, health, food-security, and energy-use. </p> <p>Two datasets are provided. First, the "hh_dataset_rep.csv" providing household responses for variables used in this study. Second, the "hh_crops_rep.csv" provides detail on crops cultivated by each household, self-reported yields and farm-gate prices. Each variable is described in the "variable_descriptoin.xlsx". In addition to the datasets, we provide replication code for this study "lsla_mechanisms_rep.Rmd" as an R-Markdown file.</p> <p><strong>Article Abstract</strong></p> <p>Improving agricultural productivity is a major sustainability challenge of the 21<sup>st</sup> century. Large-scale land acquisitions (LSLAs) have important effects on both well-being and the environment in the Global South, but their impacts on agricultural productivity and subsequent effects on farm incomes or food-security are under-investigated. Prior studies lack data or methods to investigate the mechanistic nature of household change in agricultural practices that may vary due to LSLA conditions. To overcome this challenge, we use a novel household dataset and a quasi-experimental design to estimate household level changes in agricultural value driven by LSLAs in Tanzania. In addition, we use a causal mediation analysis to assess how contract farming arrangements, land loss, and adoption of new farming technologies around LSLAs influence agricultural productivity. We find that households near LSLAs produced 19.2% (95% CI: 3.5 – 37.2%) higher agricultural value, primarily due to increased crop prices and farmer selection of high-value crops. Importantly, effect sizes are positively and negatively mediated by different mechanisms. The presence of contract farming explains 18.1% (95% CI: 0.56%, 47%) of the effect size in agricultural value, whereas land loss reduces agricultural value by 26.8% (95% CI: -71.3%, -4.0%). We also estimate whether improvements in food-security and household incomes occur in proximity to LSLAs, as anticipated with higher agricultural value. However, we do not find increases in agricultural income and food security, which may be due to higher crop prices in proximity to LSLAs. Our results stand in contrast to assumptions that technological spillovers occur through LSLAs and are principal drivers of agrarian change, holding important implications for agricultural transformations. Instead access to output markets through contract farming enables greater agricultural value whereas land loss negatively affects the agricultural value of households. Governance strategies should focus on limiting negative impacts related to the loss of smallholder land rights enabling greater access to contract farming.</p> <p> </p>
FIGURE 63 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 63. Adult female of Vryburgia succulentarum Williams.
FIGURE 62 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 62. Adult female of Vryburgia amaryllidis (Bouché).
FIGURE 60 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 60. Adult female of Trabutina mannipara (Hemprich & Ehrenberg).
FIGURE 55 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 55. Adult female of Saccharicoccus sacchari (Cockerell).
FIGURE 58 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 58. Adult female of Spilococcus williamsi Moghaddam & Watson sp. n.
FIGURE 53 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 53. Adult female of Pseudococcus viburni (Signoret).
FIGURE 51 in The Scale Insects Of Iran (Hemiptera: Coccomorpha) Part 2 The Mealybugs (Pseudococcidae And Rhizoecidae) And Putoidae
FIGURE 51. Adult female of Pseudococcus comstocki (Kuwana).
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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.