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4,684 results for “Criticality”
Overshooting the critical threshold for the Greenland ice sheet
<p>Model output of PISM-dEBM-simple and Yelmo-REMBO used in the paper <a href="https://doi.org/10.1038/s41586-023-06503-9"><strong>Overshooting the critical threshold for the Greenland ice sheet</strong></a>. Code for analysis/recreating the main figures of the paper is provided as well as an example script of how to run PISM-dEBM-simple.</p><p>The models, methods and the used parameters are described in the paper.</p><p>Contact: nils.bochow@uit.no</p>
Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis - Data and Code
<p>Data, code, and supplementary materials for "Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis" by Burke et al., published in Ecological Solutions and Evidence.</p>
Ecological Forestry in Western Oregon: A Critical Analysis from Andrews Forest LTER Research, 2014-2015
This work highlights the normative dimensions of “ecological forestry,” a strategy of forest management that uses silviculture to mimic the effects of non-anthropogenic processes of disturbance and succession in order to meet multiple objectives on a single piece of land. An analysis of the arguments made about ecological forestry, both broadly theoretical and pertaining specifically to western Oregon, shows that empirical uncertainties and normative gaps need to be addressed before we can make a clear, well-reasoned decision about whether ecological forestry is a viable and appropriate strategy for forest management and conservation.
Luquillo Critical Zone Observatory (LCZO) Data repository on HydroShare
Data archive for the Luquillo Critical Zone Observatory (LCZO), Puerto Rico. Active from 2009 to 2020. The archive is here: https://www.hydroshare.org/group/144 LCZO focuses on how Critical Zone processes and water balances differ in tropical landscapes with contrasting bedrock but similar climatic and environmental histories. Our infrastructure, sampling strategy, and data management system include watersheds underlain by granodiorite (GD) and volcaniclastic (VC) bedrock in the natural laboratory of the Luquillo Mountains, Puerto Rico. LCZO is one of ten NSF-supported critical zone observatories. The archive is here: https://www.hydroshare.org/group/144 An additional dataset on Forest and Ground Cover classification, DEM, and Beryllium-10 data for the Luquillo Experimental Forest has been published here: https://doi.org/10.4211/hs.0181f4621d184a89a625ee16dd9858a6 An additional datasets for LCZO -- Stream Water Chemistry, Meteorology -- Environmental Monitoring -- Luquillo Mountains -- (2014-Ongoing) https://www.hydroshare.org/resource/b05e1645887f4122a284719bb6cb70dc/ Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Figure 1 in Conservation in a changing landscape: habitat occupancy of the critically endangered Tennent's leaf-nosed lizard (Ceratophora tennentii) in Sri Lanka
Figure 1. Location of Knuckles forest reserve within Kandy and Matale Districts (left) and the four study sites [two at Riverston (1 and 2), Hunasgiriya (3) and Deanston (4)] within the reserve (right).
Figure 3 in Conservation in a changing landscape: habitat occupancy of the critically endangered Tennent's leaf-nosed lizard (Ceratophora tennentii) in Sri Lanka
Figure 3. Comparison of climatic and structural parameters among the four habitat types during the dry (dashed line) and wet (solid line) seasons. Data from both locations with lizards and random locations are considered in combination. (C = Cardamom plantations, M = Mixed cardamom forests, N = Natural forests, P = Pine plantations.)
Figure 2 in Conservation in a changing landscape: habitat occupancy of the critically endangered Tennent's leaf-nosed lizard (Ceratophora tennentii) in Sri Lanka
Figure 2. Mean number of sightings of Ceratophora tennentii within three habitat types at Knuckles Range, Sri Lanka.
To Fix or Not to Fix: A Critical Study of CryptoAPI Misuses Found in the Wild
<p>Data used for the paper: "To Fix or Not to Fix: A Critical Study of CryptoAPI Misuses Found in the Wild".<br> - **BA.zip** - contains the BA data set presented in the paper.<br> - **Data.zip** - contains the identified misuses for both sets discussed in the paper (_50K -> results for 50K data set and _business -> results for the BA data set) and the R Markdown files used for the paper.<br> - **issue-[1,2,3].png*** - are three anonymized GitHub issues we opened during our study to improve current analyses for crypto misuses.</p>
Revealing, examining, and critical understanding in the digital age
<p>During the second Project Presentation Session on <strong>Friday</strong> 20.07.2018 the following 3 projects were presented:</p> <ul> <li><strong>Rasa Kasperienė</strong> (Vytautas Magnus University, Kaunas, Lithuania): "Application of Social Network & Content Analysis Methods for Facebook Groups Dynamics"</li> <li><strong>Jeffrey Allan Kelly Lowenstein</strong> (Grand Valley State University, USA): "Gaming the Lottery: Anatomy of a Global Investigation"</li> <li><strong>Erik Radisch</strong>, Gernot Howanitz, Bernhard Bermeitinger (University of Passau, Germany): "Contextualizing Bandera: A Distant Watching Approach"</li> </ul>
FIG. 1. — A-C, Spiradiclis purpureocaerulea H. S in Critical notes on Spiradiclis purpureocaerulea H. S. Lo (Rubiaceae) from Vietnam
FIG. 1. — A-C, Spiradiclis purpureocaerulea H. S. Lo: A, habit; B, brevistylous flower, top view; C, flower, lateral view; D-F, S. coccinea H. S. Lo: D, flower, lateral view; E, longistylous flowers, top view; F, habit
A quantum magnetic analogue to the critical point of water
<p>Specific heat data for SrCu2(BO3)2 with pressure and magnetic fields and iPEPS results for specific heat, correlation length and dimer correlations</p>
Wildfires and climate change push low-elevation forests across a critical climate threshold for tree regeneration
Climate change is increasing fire activity in the western United States, which has the potential to accelerate climate-induced shifts in vegetation communities. Wildfire can catalyze vegetation change by killing adult trees that could otherwise persist in climate conditions no longer suitable for seedling establishment and survival. Recently documented declines in postfire conifer recruitment in the western United States may be an example of this phenomenon. However, the role of annual climate variation and its interaction with long-term climate trends in driving these changes is poorly resolved. Here we examine the relationship between annual climate and postfire tree regeneration of two dominant, low-elevation conifers (ponderosa pine and Douglas-fir) using annually resolved establishment dates from 2,935 destructively sampled trees from 33 wildfires across four regions in the western United States. We show that regeneration had a nonlinear response to annual climate conditions, with distinct thresholds for recruitment based on vapor pressure deficit, soil moisture, and maximum surface temperature. At dry sites across our study region, seasonal to annual climate conditions over the past 20 years have crossed these thresholds, such that conditions have become increasingly unsuitable for regeneration. High fire severity and low seed availability further reduced the probability of postfire regeneration. Together, our results demonstrate that climate change combined with high severity fire is leading to increasingly fewer opportunities for seedlings to establish after wildfires and may lead to ecosystem transitions in low-elevation ponderosa pine and Douglas-fir forests across the western United States.
Data related to the manuscript "Functional relationships between critical erosion thresholds of fine reservoir sediments and their sedimentological characteristics"
<p>-----------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p>Data used in the publication "Functional relationships between critical erosion thresholds of fine reservoir sediments and their sedimentological characteristics", which is accepted by the Journal of Hydraulic Engineering and will be published in a forthcoming issue.</p> <p>Beckers, F., K. Koca, S. Haun, M. Noack, S. U. Gerbersdorf, and S. Wieprecht. Forthcoming. „Functional relationships between critical erosion thresholds of fine reservoir sediments and their sedimentological characteristics.” J. Hydraul. Eng. <a href="https://doi.org/10.1061/(ASCE)HY.1943-7900.00019864">https://doi.org/10.1061/(ASCE)HY.1943-7900.0001984</a></p> <p> </p> <p>The data consists of two files:</p> <ul> <li>GBS.txt contains the sediment data of the reservoir <em>Großer Brombachsee</em></li> <li>SBT.txt contains the sediment data of the reservoir <em>Schwarzenbachtalsperre</em></li> </ul> <p>Both files contain information on the sediment depth and erosion stability separated into τ<sub>c,0</sub> and τ<sub>c,S</sub>.</p> <p>Furthermore, both files contain a collection of physico-chemical sediment parameters, including bulk density, sediment composition (Clay, Silt, Sand), percentiles (d<sub>10</sub>, d<sub>50</sub>, d<sub>90</sub>),cation exchange capacity (CEC), and organic content (TOC).</p> <p>Additionally, the SBT data contains biological sediment parameters, including chlorophyll-a (CHL-a), and extracellular polymeric substances separated into proteins (EPS-p) and carbohydrates (EPS-c).<br> -----------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p>The data was collected within the transdisciplinary research project "CHARM - Challenges of Reservoir Management".</p> <p>-----------------------------------------------------------------------------------------------------------------------------------------------------------------</p>
Data from: Spatial processes and evolutionary models: a critical review
Evolution is a fundamentally population level process in which variation, drift, and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time, using models like Brownian motion, stabilizing selection (Ornstein-Uhlenbeck), and directional selection on traits measured from stratigraphic sequences or on phylogenetic trees. But these models assume that the traits possessed by a species are homogeneous. Spatial processes such as dispersal, gene flow, and geographic range changes can produce patterns of trait evolution that do not fit the expectations of standard models, even when evolution at the local-population level is governed by drift or a typical OU model of selection. The basic properties of population level processes (variation, drift, selection, and population size) are reviewed and the relationship between their spatial and temporal dynamics is discussed. Typical evolutionary models used in palaeontology incorporate the temporal component of these dynamics, but not the spatial. Range expansions and contractions introduce rate variability into drift processes, range expansion under a drift model can drive directional change in trait evolution, and spatial selection gradients can create spatial variation in traits that can produce long-term directional trends and punctuation events depending on the balance between selection strength, gene flow, extirpation probability, and model of speciation. Using computational modelling that spatial processes can create evolutionary outcomes that depart from basic population-level notions from these standard macroevolutionary models.
Materials for Resource Abundance and the Critical Transition to Cooperation
<p>This repository contains data, configuration files, and analysis scripts related to <em>Resource Abundance and the Critical Transition to Cooperation</em> (doi:10.1111/jeb.13039). To ensure reproducibility, Avida version 2.12.4, which was used for this work, is also included. Protocols used for the microbial experiments are described in the paper.</p> <p>This archive should contain all of the materials related to the published version of the paper.</p>
Negative Differential Resistance, Instability, and Critical Transition in Lightning Leader
<p>There is a challenging issue of die out and restrike of leaders in a burst of lightning event, such as multiplicity of strokes in grounded flash or recoil leader in cloud flash, although the argument involves the effects of channel characteristic of negative differential resistance instability, there is internal consistency about the instability, the bi-stability of insulation and induction and their critical transition from the view of bifurcation theory of nonlinear dynamics. In this paper, we examined the differential resistance characteristics of the leader-streams lighting system, we associate the leader-streamer channel differential resistance characteristics and sign change with channel state and instability transitions. The critical current and potential difference conditions for the stable transition of the leader-streamer channel are investigated. It is found that the necessary current required for the stable development of the channel is increased with the length of the leader channel, while the internal channel electric field of the leader decreases accordingly.</p>
Supporting data for: Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought
<p>These data were used in the publication "Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought", currently in review. </p><p>The acoustic measurements provided in the file were input to the clustering analyses detailed in the paper. Each row corresponds to a single male song phrase. The columns include:</p><ul><li>GroupID - the name of the gibbon group, based on manual identification of the song phrase</li><li>MFCC[1-88] - Mel-frequency cepstral coefficients as detailed in the paper</li><li>Delta[89-176] - Delta-cepstral coefficients as detailed in the paper</li><li>Duration - the length of the song phrase (in seconds)</li><li>Freq 5% (Hz) and Freq 95% (Hz) - 5th and 95th percentile frequencies, respectively</li><li>Cao and Vit - the number of "cao" and "vit" components, respectively, present in the song phrase</li><li>CutFileName - the file name of the extracted song phrase (which also acts as a unique identifier)</li><li>Representative - whether the given song phrase was 'representative' ("Yes" or "No") of a typical phrase for that male (as defined by the modal number of 'cao' and 'vit' components for males)</li></ul><p>All columns (except GroupID, CutFileName and Representative) have been standardised (i.e. centred to the mean and scaled according to the standard deviation).</p>
Critical Assessment of RNA-Seq Differential Expression
<p><strong>Warden and Wu Preprint</strong>: <a href="https://www.biorxiv.org/content/10.1101/2024.02.10.579728v1">v1</a></p> <p>In general, this primarily focuses on the following types of comparisons:</p> <ol> <li>Cell line experiments with over-expression or knock-down to define a known causal gene, with processing starting with public reads.</li> <li>Processed TCGA (The Cancer Genome Atlas) data for breast cancer (BRCA) to compare gene expression by immunohistochemistry status (ER/ESR1, PR/PGR, or HER2/ERBB2).</li> </ol> <p>Differential expression methods include the following:</p> <ul> <li><em>edgeR (GLM)</em></li> <li><em>edgeR-robust (GLM)</em></li> <li><em>edgeR (QL)</em></li> <li><em>edgeR-robust (QL)</em></li> <li><em>DESeq1</em></li> <li><em>DESeq2</em></li> <li><em>limma-voom</em></li> <li><em>limma-trend (CPM)</em></li> <li><em>limma-trend (FPKM/RPKM)</em></li> <li><em>ANOVA (log2 FRPKM/RPKM)</em></li> </ul> <p>The most common preprocessing strategies include STAR, TopHat2, and Salmon. However, a limited amount of additional processing with HISAT2, kallisto, Bowtie2 (+eXpress), and Bowtie1 (+RSEM) is also provided.</p> <p>Most STAR and TopHat2 alignments use htseq-count for quantification, as well as running cuffdiff (for single variable 2-group comparisons). However, a limited amount of additional processing with featureCounts is also provided.</p> <p>Most STAR and TopHat2 alignments start with the public <strong>forward</strong> reads, even if paired-end data was available.</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.