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4,010 results for “Stabilization”
Dataset of the paper "Improving the Stability of Photodoped Metal Oxide Nanocrystals with Electron Donating Graphene Quantum Dots"
<p>The dataset provides the data for the publication: "Improving the Stability of Photodoped Metal Oxide Nanocrystals with Electron Donating Graphene Quantum Dots"</p>
High-frequency water temperature and dissolved oxygen data and derived stability and metabolism metrics for nine lakes in northeastern North America for months before and after Tropical Cyclone Irene, Fall 2011
This dataset is used in the analysis published in the following manuscript: Klug, J.L., D.C. Richardson, H.A. Ewing, B.R.Hargreaves, N. R. Samal, D. Vachon, D.C. Pierson, A. E. Lindsey, D. O'Donnell, S.W. Effler, and K.C. Weathers. 2012. Ecosystem effects of a tropical cyclone on a network of lakes in northeastern North America. Environmental Science and Technology 46(21): 11693–11701. We include Quality Assurance Quality Controlled (QAQC) high-frequency dissolved oxygen, wind speed, and water temperature data from nine lakes and reservoirs in northeastern North America which were near the track of Tropical Cyclone Irene in August 2011. These data were collected using a set of in situ, automated monitoring systems associated with the Global Lake Ecological Observatory Network (GLEON) that record data at high frequency (10 min to 6 h). These sensor data were the basis for the derived measures of Schmidt stability, net ecosystem production, respiration, and gross primary production included in the dataset. We also include daily rainfall data collected at on-site or nearby weather stations. All data cover the period from 01 August through 15 October 2011.
Flume experiments on the effects of sediment feed rates on step formation, evolution and stability
<p>The dataset contains:</p> <p>- Digital Elevation Models of the experiments collected every hour</p> <p>- Pics of the Bed topography collected every hour</p> <p>- Step number, location, evolution (as described in the paper submitted to Earth Surface Dynamics)</p> <p>- Bed grain-size distribution, sediment and sediment concentration.</p>
Morphodynamic stability of river and tidal bifurcations around bars tested in the Fast Flow Facility
<p>Multithread rivers such as the Jamuna and Mekong have networks of channels and bars that change with every flood. Tidal systems such as the Scheldt, Humber and Columbia estuaries and short tidal basins in the Wadden Sea and in Florida, have perpetually changing and interacting channels and shoals formed by ebb and flood currents. Current models fail to forecast these natural dynamics, yet main channels are economically important shipping fairways, whilst shoal areas that emerge and submerge daily are ecologically valuable habitats. Human interference, changing river discharge and sealevel rise threaten all functions. Furthermore, there are strong indications that fairway deepening leads to reduced urban safety due to enhanced flow resistance by groynes in rivers and enhanced tidal range in estuaries (e.g. Bolla Pittaluga et al. 2015 in AWR, Seminara et al., in EH 2011). This enhances dike failure risk during low water level and flooding during high water level. We urgently need dynamic forecasting models to optimise management strategies for these multiple functions (Wang et al. 2012 in Ocean Coastal Manage., Coco et al. 2013 in Mar. Geol.).</p> <p>Here we target firstly river bifurcations and secondly the mutually evasive ebb- or flood-dominated channels that form around bars and are found in all sandy tidal systems in the world (van Veen 1950/2002 in J. R. Dutch Geograph. Soc.). The cause for the mutual evasion is still incompletely understood despite the fact that they also appear in our numerical model results and experiments (Canestrelli et al., in JGR 2010; Kleinhans et al. 2015 in JGR). The nodes where ebb and flood channels connect can be seen as asymmetric bifurcations where one channel is preferred during ebb and the other during flood. Such bifurcations are critical elements that partition flow and sediment through the channel network, govern bar merging and splitting and are locations where bed steps form in shipping lanes, as in river bifurcations. Stability and equilibrium configurations are mostly unknown for tidal bifurcations except for one recent theory (Wang et al in prep.). In particular, we have a fair understanding of the tidal dynamics, but this is incomplete for the morphodynamics, especially related to understanding the sediment division at the bifurcation.</p> <p>We take advantage of the better but yet incomplete understanding of river bifurcations. The stability of river bifurcations has been studied for two decades in fieldwork, experimentation, linear stability theory and numerical modelling (e.g. Wang et al. 1995, JHR, see review in Kleinhans et al. 2013, ESPL) and our recent theory (Bolla Pittaluga et al. 2015 in GRL) synthesises many of the earlier results as follows: In bedload-dominated rivers, symmetrical bifurcations are unstable and develop towards a highly asymmetrical division of discharge and sediment. The same is the case for suspended sediment-dominated rivers, but the theory predicts stable bifurcations for intermediate sediment mobility. However, there is very little data for conditions intermediate between low and high mobility rivers. Moreover, we have no idea whether bifurcations in reversing tidal flow are unstable for similar configurations and conditions as in rivers. Here we mean configurations that are entirely free of topographic forcings on the flow: straight channels split into two channels over some length and depth.</p> <p>Our objective was therefore to experimentally investigate bifurcation stability in a range of sediment mobilities in unidirectional flow and reversing tidal flow ceteris paribus.</p>
Impact of processing and storage conditions on color stability of strawberry puree: the role of PPO reactions revisited
<p>The effect of pre-heating fresh strawberries (hot break) and the use of refrigerated temperatures prior to pasteurization on the stability of anthocyanins, vitamin C, color and polyphenol oxidase (PPO) activity during storage (42 days at 35 ºC) of strawberry puree was studied. Hot break resulted in 20% residual PPO activity and caused 10% anthocyanin degradation, whereas vitamin C was unaffected. After mashing, purees were stored at 4 ºC and 25 ºC for 3 hours. During this period, anthocyanins and PPO activity remained constant independently of the processing history but ascorbic acid was oxidized faster at 25 ºC. Pasteurization caused complete inactivation of PPO, reduction of anthocyanins (25%), of <em>a*</em> value (6%) and of vitamin C (50%). Neither partial inactivation of PPO early in the processing (hot break) nor the use of refrigeration prior to pasteurization had a positive effect on color and anthocyanin stability of strawberry puree during subsequent storage, suggesting that PPO-derived reaction products formed during processing have a very limited impact on color degradation during shelf-life.</p>
Unravelling the modus operandi of phytosiderophores during zinc uptake in rice: the importance of geochemical gradients and accurate stability constants
<p>Dataset for figures in the article 'Unravelling the modus operandi of phytosiderophores during zinc uptake in rice: the importance of geochemical gradients and accurate stability constants'.</p>
Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits
Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and 17 ecological factors (including tree tissue chemistry, magnitude of organic matter inputs and their turnover, microbial community descriptors, and soil physico‐chemical properties). We measured five SOM stability indices, including heterotrophic respiration, C in aggregate‐occluded particulate organic matter (POM) and mineral‐associated SOM, and bulk SOM δ15N and ∆14C. The stability of SOM varied substantially among tree species and this variability was independent of the amount of organic C in soils. Thus, when considering forest soils as C sinks, the stability of C stocks must be considered in addition to their size. Further, our results suggest tree species regulate soil C stability via the composition of their tissues, especially roots. Stability of SOM appeared to be greater (as indicated by higher δ15N and reduced respiration) beneath species with higher concentrations of nitrogen and lower amounts of acid‐insoluble compounds in their roots, while SOM stability appeared to be lower (as indicated by higher respiration and lower proportions of C in aggregate‐occluded POM) beneath species with higher tissue calcium contents. The proportion of C in mineral‐associated SOM and bulk soil ∆14C, though, were negligibly dependent on tree species traits, likely reflecting an insensitivity of some SOM pools to decadal‐scale shifts in ecological factors. Strategies aiming to increase soil C stocks may thus focus on particulate C pools, which can more easily be manipulated and are most sensitive to climate change.
Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption (increasing trait variation and potentially generating new traits) or stabilization (decreasing trait variation). In the short term, stabilization is more economical, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalization is deleterious in the face of persistently increasing stress, because it reduces variability and thus decreases the ability to react to further changes. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptation of populations facing extinction are rare. Here, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variation in two species across a salinity rise leading to their local extinction. One species reacted by stabilization in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remained stable or reacted by further stabilization. These observations indicate that the default reaction of the studied Foraminifera is canalization, and that stress escalation did not lead to the emergence of adapted forms. An inherent inability to breach the global adaptive threshold would explain why communities of Foraminifera and other marine protists reacted to Quaternary climate change by tracking their zonally shifting environments. It also means that populations of marine plankton species adapted to response by migration will be at risk of extinction when exposed to stress outside of the adaptive range.
Introduced-stability: First release of introduced stability model
<p>First release for the model associated with the "Introduced omnivores can increase stability in a tri-trophic model" manuscript.</p>
An Empirical Study of Activity, Popularity, Size, Testing, and Stability in Continuous Integration
<p>A good understanding of the practices followed by software development projects can positively impact their success --- particularly for attracting talent and on-boarding new members. In this paper, we perform a cluster analysis to classify software projects that follow continuous integration in terms of their activity, popularity, size, testing, and stability. Based on this analysis, we identify and discuss four different groups of repositories that have distinct characteristics that separates them from the other groups. With this new understanding, we encourage open source projects to acknowledge and advertise their preferences according to these defining characteristics, so that they can recruit developers who share similar values.</p>
Plant community compositional stability over 40 years in a Fraser River Estuary tidal freshwater marsh
<p class="MsoNormal"><span>Long-term data sets documenting temporal changes in vegetation communities are uncommon, yet imperative for understanding trends and triggering potential conservation management interventions. For example, decreasing species diversity and increasing non-native species abundance may be indicative of decreasing community stability. We explored long-term plant community change over a 40-year period through the contribution of data collected in 2019 to two historical datasets collected in 1979 and 1999 to evaluate decadal changes in plant community biodiversity in a tidal freshwater marsh in the Fraser River Estuary in British Columbia, Canada. We found that plant assemblages were characterized by similar indicator species, but most other indicator species changed, and that overall </span><span>α-diversity</span><span> decreased while </span><span>β</span><span>-diversity increased. Further, we found evidence for plant assemblage homogenization through the increased abundance of invasive species such as yellow flag iris (<em>Iris pseudacorus</em>), and reed canary grass (<em>Phalaris arundinacea</em>). These observations may inform concepts of habitat stability in the absence of direct anthropogenic disturbance and corroborate globally observed trends of native species loss and non-native species encroachment. Our results indicate that within the Fraser River Estuary, active threat management may be necessary in areas of conservation concern in order to prevent further native species biodiversity loss. </span></p>
Data and code: Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish
<p>Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (<em>Salvelinus fontinalis</em>), understanding drivers of asynchrony in population dynamics can improve predictions of range-wide climate impacts. We analyzed demographic time-series from mark-recapture surveys of eleven natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km<sup>2</sup>) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables, and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrate that population demographic and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.</p>
Supplementary Data for Stabilizing the Proteomes of Acute Myeloid Leukemia Cells: Implications for Cancer Proteomics
<p>Supplementary data for: <br>Stabilizing the Proteomes of Acute Myeloid Leukemia Cells: Implications for Cancer Proteomics<br>Authors: Robert Sprung, Qiang Zhang, Michael H. Kramer, Matthew C. Christopher, Petra Erdmann-Gilmore, Yiling Mi, James P. Malone, Timothy J. Ley, and R. Reid Townsend.</p><p>Table S1 - AML Case descriptors and LC-MS data files<br>Table S2 - All Peptides by Case -LFQ<br>Table S3 - Identification of tryptic and non-tryptic peptides from five AML cases with high and low expression of ELANE<br>Table S4 - Number of proteins identified by LFQ proteomics with a minimum of 2 tryptic peptides<br>Table S5 - DFP Adduct Database Search Tryptic Peptides<br>Table S6 - Protein quantification from TMT 11-plex tryptic peptides with and without DFP<br>Table S7 - Tryptic peptides used for protein quantification from TMT 11-plex with and without DFP<br>Table S8 - Changes in TMT relative abund. with DFP treatment<br>Table S9 - Protein quantification from LFQ tryptic peptides with and without DFP<br>Table S10 - Proteins with significant change in abundance with DFP treatment using Label-Free Quantitation</p>
Data from: Wildlife fecal microbiota exhibit community stability across a semi-controlled longitudinal non-invasive sampling experiment
<p>Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (<em>Cervus canadensis</em>) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared microbiomes of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (<em>Bacteroides</em> and <em>Sporobacter</em>) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize microbiome composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiome diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.</p>
Stable Vowel Corpus (SVC): a benchmark for spectral stability analyses
<p>This dataset comprises 4,860 synthesized CVC-like sequences generated using Praat's articulatory synthesizer (Boersma, 1998; Boersma & Weenink, 2021). The duration and location of the spectrally stable portion of the vowel within these CVC-like sequences were randomly varied.</p><p>Each corresponding .wav file is labeled with the following format:</p><ul><li><strong>Stimulus</strong> <i>ID_TsV_TeV_C1_V_C2_speaker.wav</i></li><li><strong>e.g.</strong> <i>1000_0.2197529077064245_0.2906336685046843p_a_d_female.wav</i></li></ul><p>Here's the breakdown of the naming convention:</p><ul><li><strong>Stimulus ID</strong>: A unique identifier for each stimulus.</li><li><strong>TsV</strong>: The timecode of the start of the stable portion of the vowel.</li><li><strong>TeV</strong>: The timecode of the end of the stable portion of the vowel.</li><li><strong>C1</strong>: The first consonant category.</li><li><strong>V</strong>: The vowel category.</li><li><strong>C2</strong>: The second consonant category.</li><li><strong>Speaker</strong>: The type of artificial speaker used for the synthesis.</li></ul><p>Further details about the design and synthesis of the corpus have been published in:</p><ul><li>Genette, J., Rivera Espejo, J. M., Gillis, S., & Verhoeven, J. (2023). Determining spectral stability in vowels: A comparison and assessment of different metrics. <i>Speech Communication</i>, <i>154</i>, 102984. <a href="https://doi.org/10.1016/j.specom.2023.102984">https://doi.org/10.1016/j.specom.2023.102984</a></li></ul><h4><strong>References</strong></h4><p>Boersma, P. (1998). <i>Functional Phonology: Formalizing the Interactions between Articulatory and Perceptual Drives</i> [PhD Thesis]. University of Amsterdam.</p><p>Boersma, P., & Weenink, D. (2021).<i> Praat: doing phonetics by computer</i> [Computer program. Version 6].</p>
Data from: Opposing responses of temporal stability of aboveground and belowground net primary productivity to water and nitrogen enrichment in a temperate grassland
<p><span>Changes in water and nitrogen availability, as important elements of global environmental change, are known to affect the temporal stability of aboveground net primary productivity (ANPP). However, evidences for their effects on the temporal stability of belowground net primary productivity (BNPP), and whether such effects are consistent between belowground and aboveground, are rather scarce. Here, we investigated the responses of temporal stability of both ANPP and BNPP to water and nitrogen addition based on a 9-year manipulative experiment in a temperate grassland in northern China. The results showed that the temporal stability of ANPP increased with water addition but decreased with nitrogen addition. By contrast, the temporal stability of BNPP decreased with water addition but increased with nitrogen enrichment. The temporal stability of ANPP was mainly determined by the soil moisture and inorganic nitrogen, which modulated species asynchrony, as well as by the stability of dominant species. On the other hand, the temporal stability of BNPP was mainly driven by the soil moisture and inorganic nitrogen that modulated ANPP of grasses, and by the direct effect of soil water availability. Our study provides the first evidence on the opposite responses of aboveground and belowground grassland temporal stability to increased water and nitrogen availability, highlighting the importance of considering both aboveground and belowground components of ecosystems for a more comprehensive understanding of their dynamics.</span></p>
Dataset from : Effects of inlet guide vanes on the performance and stability of an aeronautical centrifugal compressor
<p>This dataset pertains to the publication 'Effects of inlet guide vanes on the performance and stability of an aeronautical centrifugal compressor', N. Poujol, P. Duquesne, I. Trébinjac. Journal of turbomachinery. ASME (2021)</p><p>These data were obtained from the figures in the article.</p><p>Where possible, each figure is provided in CSV format.</p>
Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"
<p><strong>Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar'</strong></p> <p>An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh</p> <p> </p> <p>Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. <em>et al.<strong> Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar</strong></em>. <em>BMC Biol</em> <strong>22</strong>, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1</p> <ul> <li>* These authors contributed equally.</li> </ul> <p>--------------------------------------------------</p> <p><strong>Background: </strong>Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (<em>Populus nigra</em> cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome.</p> <p><strong>Results: </strong>We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment.</p> <p><strong>Conclusions: </strong>Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.</p> <p> </p> <p><strong>ADDITIONAL FILES</strong></p> <p><strong>Additional file 1.</strong> CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (<em>metadata</em>). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission GSE225596).</p> <p><strong>Additional file 2.</strong> CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (<em>processed data</em>).</p> <p><strong>Additional file 3</strong>. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Additional file 4. </strong>POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1, E. SPC1 versus UKD2</p> <p><strong>Additional file 5. </strong>CSV-file with the raw data of the bud set observations in the common garden experiment (<em>raw data</em>).</p> <p><strong>Additional file 6. </strong>HTML-file with the R source codes to reproduce the results of the bud set analysis (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 7. </strong>A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (<em>code, Snakefile</em>).</p> <p><strong>Additional file 8. </strong>RMD-file<strong> </strong>with the code to reproduce the analyses to identify differential methylated predefined regions (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 9. </strong>R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (<em>code,</em> <em>R script</em>).</p> <p><strong>Supporting files 1</strong>. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Supporting files 2</strong>. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (<em>processed data</em>).</p> <p>---------------------------------------------------------</p> <p>Version 3:</p> <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>
Dataset for manuscript entitled "Insights into the LiMn2O4 Cathode Stability in Aqueous Electrolyte"
<p>Dataset for manuscript entitled <em>Insights into the LiMn2O4 Cathode Stability in Aqueous Electrolyte</em>. This dataset includes:</p> <p>-XRD of as-deposited films and bare substrate</p> <p>-TERS average spectra and maps of the as-deposited and cycled samples</p> <p>-Macro-Raman spectra of the as-deposited and cycled samples.</p> <p>-PALS data of the as-deposited and cycled films, as a function of depth and extracted for 2 keV</p> <p> </p> <p> </p>
Preferential cannibalism as a key stabilizing mechanism of intraguild predation systems with trophic polymorphic predators
<p><span>Theory predicts intraguild predation (IGP) to be unstable despite its ubiquity in nature, prompting exploration of stabilizing mechanisms of IGP. One of the many ways IGP manifests is through inducible trophic polymorphisms in the intraguild (IG) predator, where a resource-eating predator morph competes with the intraguild (IG) prey for the shared resource while a top predator morph consumes the IG prey. Cannibalism is common in this type of system due to the top predator morph's specialization on the trophic level below it, which includes the resource-eating predator morph. Here, we explore the consequences of inducible trophic polymorphisms in cannibal predators for IGP stability using an IGP model with and without cannibalism. We employ linear stability analysis and identify regions of coexistence based on the top predator morph's preference for conspecifics vs. heterospecifics and the IG prey's competitive ability relative to the resource-eating morph. Our findings reveal preferential cannibalism (i.e. the preferential consumption of conspecifics) stabilizes the system when the IG prey and resource-eating morph have similar competitive abilities for the shared resource. Though original IGP theory finds the IG prey must be a superior resource competitor as a general criterion for coexistence, this is not typically the case when the predator has an inducible trophic polymorphism and the resource-eating morph is specialized in resource acquisition. Preferential cannibalism may therefore be a key stabilizing mechanism in IGP systems with a cannibalistic, trophic polymorphic IG predators, providing further insight into what general mechanisms stabilize the pervasive IGP interaction.</span></p>
ScienceDex guides
Understand access before you commit
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.