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Data from: The roles of non-production vegetation in agroecosystems: a research framework for filling process knowledge gaps in a social-ecological context
<p>1. An ever-expanding human population, climatic changes, and the spread of intensive farming practices is putting increasing pressure on agroecosystems and their inherent biodiversity. Non-production vegetation elements, such as woody patches, riparian margins, and restoration plantings, are vital for conserving agroecosystem biodiversity. Further, such elements are key building blocks that are manipulated via land management, thereby influencing the biotic and abiotic processes that underpin functioning agroecosystems.</p> <p>2. Despite this critical role, there has been a lack of synthesis on which types of vegetation elements drive and/or support ecological processes, and the mechanisms by which this occurs. Using a systematic, quantitative literature review of 342 articles, we asked: what are the effects of non-production vegetation on agroecosystem processes and how are these processes measured within global agroecosystems?</p> <p>3. Woody patches, hedgerows and borders, riparian margins, and shelterbelts were the most studied types of non-production vegetation. The majority (61%) of studies showed positive effects of non-production vegetation on ecological processes, where the presence, level or rate of the studied process was increased or enhanced.</p> <p>4. However, four key research gaps were revealed: (1) most studies (83%) used proxies for, instead of direct measurements of, ecosystem processes related to non-production vegetation; (2) study designs used to investigate non-production vegetation effects on ecosystem processes directly were largely limited to observational comparisons of non-production vegetation types, farm-scale vegetation configurations, and different proximities to vegetation in terms of the effect on ecological processes; relatively few studies used manipulative experiments (3) the relatively few studies directly measuring ecosystem processes were dominated by four process categories: invertebrate biocontrol, predator and natural enemy spillover, animal movement, and ecosystem cycling, and (4) the methods used to directly measure non-production vegetation effects comprised a surprisingly limited set of approaches.</p> <p>5. To fill key research gaps that will inform the use of non-production vegetation to enhance agroecosystem processes, we present a framework for future research that emphasises the need to combine an understanding of human decision making with carefully-designed and targeted investigations into the roles of taxa, ecosystem processes, and landscape heterogeneity related to non-production vegetation, at multiple spatial scales within agroecosystems.</p>
Appendix II for: Social context modulates scale-free walks in a social insect
<p>Plots from the MLE (Maximum likelihood estimation) analysis for the step-lengths of the focal termite workers. Two competing models were tested: Truncated Pareto Lévy (TP - red line) vs exponential (EX - blue dashed line) for both (X and Y) axis. Data series are identified with "S" plus a number from 1 to 75). The Lévy exponent ($1 < \mu \leq 3.0$) and the Akaike weights (wAIC) for the competing models (1 for full support, 0 for not support) are shown in the plots. </p>
Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context
<p>The cold-tolerant leaf beetle <em>Gonioctena quinquepunctata</em> displays a large but fragmented European distribution and is restricted to mountain regions in the southern part of its range. Using a RAD-seq-generated large SNP data set (> 10,000 loci), we investigated the geographic distribution of genetic variation within the Vosges mountains, where the species is common. To translate this pattern of variation in an estimate of its capacity to disperse, we simulated SNP data under a spatially explicit model of population evolution and compared the simulated and real data with an approximate Bayesian computation (ABC) approach. For this purpose, we propose a new SNP statistic summarizing genetic variation in a spatially explicit context. The estimated number of effective migrants inferred with this statistic was compared to that derived from a combination of standard population genetic statistics often used in population genetic analyses. We conducted this ABC analysis with a relatively low number of data points compared to traditional ABC analyses, because spatially explicit models require long simulation times. A test of our overall strategy was conducted with simulated data and showed that it could provide a good estimate of the level of dispersal of an organism over its continuous geographic range. We suggest that the lower number of explored data points were at least partially compensated by the much larger number of simulations per data point associated with a large SNP data set. The results of our analyses suggested that this insect disperses well within the Vosges mountains, much more than was initially expected given the current and probably past fragmentation of its habitat and given the results of previous studies on genetic variation in other mountain leaf beetles.</p>
Context-dependent effects of Trichoderma seed inoculation on anthracnose disease and seed yield of bean (Phaseolus vulgaris): ambient conditions override cultivar-specific differences
<p>Root colonizing <i>Trichoderma </i>fungi can stimulate plant immunity, but net effects are strain × cultivar-specific and changing ambient conditions further contribute to variable outcomes. Here, we used four <i>Trichoderma</i> spp. to inoculate seeds of four common bean (<i>Phaseolus vulgaris</i>) cultivars and explored in three different experimental setups the effects on fungal anthracnose after leaf inoculation with <i>Colletotrichum lindemuthianum</i>. Plants growing in pots with field soil under greenhouse conditions exhibited the highest and those in the open field the lowest overall levels of disease. Among 48 <i>Trichoderma</i> strain × bean cultivar × setup combinations, <i>Trichoderma</i>-inoculation enhanced disease in six and decreased disease in ten cases, but with the exception of <i>T. asperellum</i> B6-inoculated Negro San Luis beans, the strain × cultivar-specific effects on anthracnose severity differed among the setups, and anthracnose severity did not predict seed yield in the open field. In the case of Flor de Mayo beans, <i>Trichoderma</i> even reduced yield in anthracnose-free field plots, although this effect was counterbalanced in anthracnose-infected plots. We consider our work as a case study that calls for stronger emphasis on field experiments in the early phases of screenings of <i>Trichoderma</i> inoculants as plant biostimulants.</p>
FIG. 2 in Le site paléontologique du Grand Morier (Pont-Boutard, Indre-et-Loire, France): contexte géologique et détail biostratigraphique des formations cénozoïques à partir des assemblages de vertébrés fossiles
FIG. 2. — Carte géologique de Pont-Boutard (Indre-et-Loire, France).
Barbier et al., 2021_Diagnosis of the structure of the social representations of organ donation (test of context independance)
<p>Abstract</p> <p><em>Introduction.</em> – On 1<sup>st</sup> January 2017, the updated presumed consent for organ donation was widely communicated in France. From a social psychological point of view, this may have changed the shared meanings people associate with organ donation.</p> <p><em>Objective</em>. –First, this study aimed to identify the content and structure of the social representation of organ donation. Second, it aimed to account for social anchoring and see how the processes of social anchoring participate in the arrangement of structured sets of the social representation of organ donation.</p> <p><em>Method. –</em> The study consisted of filling in a self-reported online survey disseminated through Facebook. In total, 778 French people participated (393 women, 381 men, <em>M</em>age = 37.02 yrs, <em>SD</em> = 12.60). A two-step methodology from exploratory to confirmatory analysis was applied.</p> <p><em>Results. –</em> In line with our assumptions, findings showed: changes in the content of representation that may have occurred in response to the legislative update, in particular; a dichotomy that structures the social representations of organ donation, intrinsically linked to the donor/non-donor variable; effects of gender and age on content of the social representations of organ donation. Contrary to our preliminary expectations, findings showed: no effects of gender and age on structure of the social representations of organ donation; no effect of religious affiliation on content nor on structure, suggesting that the role of religion is not orientating social thinking about organ donation, but rather, legitimising social practices related to organ donation.</p> <p><em>Conclusion. –</em> These results are discussed in relation to the identity issues facing organ donation, in the sense that the shared meaning associated with organ donation reveal ideological positions. We suggest avenues for future research likely to find interesting applications in the organ donation field.</p>
FIG. 1 in Les restes animaux en contexte funéraire dans l'Alsace du premier Moyen Âge et ses marges géographiques
FIG. 1. – Villey-Saint-Etienne, Musée Salin. Ossements des tombes 14 et 60 (Cliché Putelat).
Figure 3 in Genus Baseodiscus (Nemertea: Heteronemertea): Molecular identification of a new species in a phylogenetic context
Figure 3. External view of Baseodiscus jonasii sp. nov. Drawing made by Ray Gibson.
Peakhood: individual site context extraction for CLIP-seq peak regions
<p>Peakhood Supplementary Data Archive, see content.txt for file content descriptions.</p>
Supplementary Material for "TITANIA Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds"
<p>Simulation input (RDC data, input geometries, keywords) and output files (simulation / geometry trajectories, alignment data, SECONDA analysis) for isopinocampheol, tubocurarine and strychnine runs with the TITANIA software.</p>
Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
<p>A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiont <em>Sinorhizobium meliloti</em> paired with two genotypes of the host <em>Medicago truncatula</em> in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype – partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments.</p> <p><span>IMPORTANCE:</span><strong> </strong>Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.</p>
Data from: Ecological requirements drive the variable responses of wheat pests and natural enemies to the landscape context
<p>1. Semi-natural habitats (SNH) are considered essential for pest suppressive landscapes, but their influence on crop pests and natural enemies can be highly variable. Instead of SNH per se, the availability of resources, such as pollen and nectar, may be more relevant for supporting pest control.</p> <p>2. Here, we assessed the spatio-temporal variation of multiple insect pests (cereal leaf beetles and aphids) and natural enemies (predators and aphid parasitoids) in wheat fields and their responses to landscape context and flower availability. We combined detailed information on pollen use by natural enemies with the specific distribution of pollen-providing plants across a gradient of landscape composition and configuration.</p> <p>3. The abundance of wheat pests was tightly linked to wheat development stage. Syrphids colonised the fields early in the season, while the abundance of other enemies increased later in the season. The responses of pests to landscape structure were variable and, while some pests had low abundances in landscapes with high edge density and SNH cover, <em>Sitobion avenae</em> abundance was positively associated with SNH cover. Lacewings, syrphids and cereal leaf beetles were abundant in landscapes with diverse and abundant flower resources, whereas the abundance of parasitoids and Nabis sp. was driven by aphid abundance. We detected no significant indirect effects of landscape on pests via natural enemies.</p> <p>4. Synthesis and applications. Our findings highlight the need for conservation biological control to go beyond "one size fits all" and consider the specific ecology of the involved organisms. Landscapes with high edge density and flowering woody plants may support natural enemies, in particular syrphids, which colonised the fields early in the season. Incentives for pest-suppressive landscapes should focus on tailored strategies that disfavour pests and simultaneously enhance natural enemies according to their ecological requirements.</p>
Raw Data supporting Promoters adopt distinct dynamic manifestations depending on transcription factor context
<p>All source data is provided as MAT-files, which can be opened in Matlab. In total, the source data contain 270 core data files and 540 processed data files. The data for each individual promoter is stored in a different directory and the 9 promoters are:</p> <ul> <li> <p><em>ALD3 </em></p> </li> <li> <p><em>DCS2 </em></p> </li> <li> <p><em>DDR2 </em></p> </li> <li> <p><em>HXK1 </em></p> </li> <li> <p><em>RTN2 </em></p> </li> <li> <p><em>TKL2 </em></p> </li> <li> <p><em>SIP18 </em></p> </li> <li> <p><em>pSIP18_mut6</em> (also referred to as mutant A4)</p> </li> <li> <p><em>pSIP18_mut21</em> (also referred to as mutant D6)</p> </li> </ul> <p>The data for the first 7 promoters was previously reported in (Hansen and O’Shea, 2013), though in an unnormalized form. That is, it was previously reported as a concentration per cell in arbitrary fluorescence units (AU). In the present manuscript, we have calibrated the data to obtain absolute abundances, such that the MAT-files now contain both the old AU concentration as well as absolute abundances, i.e. number of YFP molecules per cell. The calibration was performed as described in (Huang et al., 2016). Similarly, the data for the last 2 promoters (A4 and D6) was previously reported in its unnormalized form in (Hansen and O’Shea, 2015) and it is here also reported in the form of absolute abundances.</p> <p> </p> <p>The MAT-files containing the raw data have the suffix “_size.mat”. The name of the MAT files describes the experiment. If the file name contains “DM”, then it is a single pulse. Thus, “SIP18_DM_40min_275nM_size.mat” refers to a single 40 min pulse with 275 nM 1-NM-PP1 for the <em>SIP18</em> promoter. Similarly if the file name contains “FM”, e.g. “RTN2_FM_8_5min_690nM_size.mat” then it refers to eight 5 min pulses separated by 5 min intervals at 690 nM for the <em>RTN2</em> promoter. Finally, if the file name contains “FM4”, e.g. “TKL2_FM4_15minINT_690nM_size.mat” then the experiment was four 5 min pulses separated by 15 min intervals at 690 nM for the <em>TKL2</em> promoter. The concentration is the concentration of 1-NM-PP1 that was used and 100 nM, 275 nM, 690 nM and 3mM refers to approximately, 25%, 50%, 75% and 100% Msn2 activation. For full experimental details please see (Hansen and O’Shea, 2013; Hansen et al., 2015).</p> <p> </p> <p>The “_size.mat” MAT-files contain the following variables:</p> <ul> <li> cell_size_pixels</li> <li> CFP</li> <li> CFP_molecules</li> <li> CFP_raw</li> <li> inhibitor_conc</li> <li> MSN2_raw</li> <li> MSN2_RFP</li> <li> pulse_parameters • time</li> <li> YFP</li> <li> YFP_molecules</li> <li> YFP_raw</li> </ul> <p>CFP, CFP_molecules, CFP_raw and YFP, YFP_molecules, YFP_raw are Nx64 matrices, where each row N correspond to a different cell and the 64 columns correspond to the 64 experimentally measured timepoints corresponding to the “time” vector running from -5 min to 152.5 min in increments of 2.5 min and the 1NM-PP1 inhibitor was added at time 0. “CFP_raw” and “YFP_raw” contains raw, uncorrected data, so without photobleaching correction and background subtraction. “CFP” and “YFP” contain corrected data in arbitrary fluorescence units (AU) and report on the concentration (i.e. size normalized). Finally, “CFP_molecules” and “YFP_molecules” contains the total number of CFP and YFP molecules per cell (i.e. this is not a concentration, but the absolute abundance). The area of each cell at each timepoint can be found in the matrix “cell_size_pixels”. Since the cells are live and growing, this will tend to increase during the experiments. Occasionally large fluctuations can occur due to errors in cell segmentation or due to division. For full details on the image analysis and cell segmentation, please see (Hansen and O’Shea, 2013; Hansen et al., 2015).</p> <p> </p> <p>The variables “inhibitor_conc” and “pulse_parameters” refer to the type of experiment and is also given by the name. “inhibitor_conc” gives the 1NMPP1 concentration: 100 nM, 275 nM, 690 nM or 3000 nM. “pulse_parameters” contains either 2 or 3 elements and given the dynamical pulse sequence parameters. Column 1 contains the number of pulses and column 2 the duration of the pulses. Column 3 gives the interval between the pulses if more than one pulse is used – otherwise column 3 is zero.</p> <p> </p> <p>Moreover, on a more technical note it should be noted that the signal-to-noise of the CFP reporter is worse than the YFP reporter. Therefore, we always use the YFP reporter for quantitative analysis. Furthermore, the two other MAT-files “…MSN2.mat” and “…YFP.mat” contain processed data. Please see the ReadMe file on the code for a full description and how these were derived.</p> <p> </p> <p>Finally, Supplementary Table 1 contains the model-inferred parameters for each promoter and condition.</p> <p> </p> <p> </p> <p><strong>References</strong></p> <p>Hansen, A.S., and O’Shea, E.K. (2013). Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol.</p> <p>Hansen, A.S., and O’Shea, E.K. (2015). Cis Determinants of Promoter Threshold and Activation Timescale. Cell Rep.</p> <p>Hansen, A.S., Hao, N., and OShea, E.K. (2015). High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nat. Protoc.</p> <p>Huang, L., Pauleve, L., Zechner, C., Unger, M., Hansen, A.S., and Koeppl, H. (2016). Reconstructing dynamic molecular states from single-cell time series. J. R. Soc. Interface.</p>
Data from: Environmental context determines pollution impacts on ecosystem functioning
<p><span>Global change assessments have typically ignored synthetic chemical pollution, despite the rapid increase of </span><span>pharmaceuticals, pesticides, and industrial chemicals in the environment.</span> <span>Part of the problem reflects the multifarious origins of these micropollutants, which can derive from urban and agricultural sources. Understanding how micropollutants harm ecosystems is a major scientific challenge due to asymmetries of stress across trophic levels and </span><span>ecological surprises generated by multiple</span><span> drivers interacting in human-impacted landscapes. We used field assays above and below municipal wastewater treatment plants (WWTPs) in 60 sampling locations across 20 Swiss streams to test how micropollutants and nutrients originating from WWTPs affect two trophic levels (microbes and detritivores) and their role in leaf litter processing. Wastewater impacts were asymmetric across trophic levels, with the detritivore contribution declining relative to microbial-driven decomposition. The strength of negative impacts was context-dependent, peaking at sites with the highest upstream abundances of detritivorous invertebrates. Diffuse pollution from intensive agriculture and wastewater-born micropollutants contributed to reduced litter processing rates, including indirect effects apparently mediated through negative influences of insecticides on detritivores. Asymmetries in stress responses across trophic levels can introduce quantitative changes in consumer-resource dynamics and leaf litter processing. </span><span>This means functional redundancies at different trophic levels are insufficient to compensate for biodiversity losses, causing environmental stressors such as chemical pollutants to have pervasive ecosystem-level impacts. </span></p>
Fitness landscapes reveal context-dependent benefits of oviposition behaviour
<p><span>Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Do such context-dependent behaviours reflect maladaptive variation, or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behaviour reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating female egg allocation across patches, which allowed us to assess behaviours not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower-developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts. </span></p>
What's in a name? Role of verbal context in touch
<p>Can a name (i.e., verbal context) change how we react to and perceive an object? This question has been addressed several times for chemosensory objects, but never for touch. To address this, two studies were run. In each, we allocated participants to a Positive, Neutral or Negative Group, and asked them to touch the same four objects, twice – first, named by the experimenter according to their Group-name, and second, named by the participant. Participants were timed as they touched and rated the objects on pleasantness and disgust. Negative-named objects were touched for shorter durations, and rated more negatively, than neutral-named objects, and positive-named objects were touched for the longest and rated most positively. In the second presentation, most objects (>90%) were named by participants in accord with their assigned Group-names. The similarity of these findings to chemosensory verbal context effects and their mechanistic basis is discussed.</p>
Data for: Context dependency in interference competition among birds in an endangered woodland ecosystem
<p><strong>Aim</strong></p> <p>Much research has quantified species responses to human-modified ecosystems. However, there has been relatively limited work on how human-modified ecosystems may reshape competitive interactions between species. Using extensive data gathered over 19 years across an area exceeding three million ha, we asked: <em>Are levels of interference competition between bird species context-dependent and influenced by habitat structure and productivity</em>? We focussed on the hyper-aggressive behaviour of the Noisy Miner, which has been recognised as a Key Threatening Process for other woodland bird species.</p> <p><strong>Location</strong></p> <p>Temperate woodlands of south-eastern Australia</p> <p><strong>Methods </strong></p> <p>We constructed Bayesian multi-species occupancy/detection models of bird species in woodland patches and tested the fixed and interactive effects of Noisy Miner presence, the amount of tree cover, net primary productivity, and time. We quantified the responses of 31 species, many with known interactions with the Noisy Miner documented in previous studies at fine spatial scales. However, whether environmental conditions such as amount of forest cover and net primary productivity mediate the impact of Noisy Miners remains untested at large spatial scales and over decadal time scales.</p> <p><strong>Results</strong></p> <p>We identified negative associations between the Noisy Miner and 18 bird species, including, unexpectedly, both small- and large-bodied taxa. Site occupancy in some species was influenced by interactions between Noisy Miner presence and increasing amounts of tree cover or productivity. Our results suggest that for some species, interference competition by the Noisy Miner is context-dependent and mitigated by increasing tree cover and/or increasing net primary productivity</p> <p><strong>Main</strong> <strong>conclusions</strong></p> <p>Areas of high productivity or tree cover may be important refugia for some species of woodland birds. Vegetation clearing that reduces tree cover could likely strengthen interference competition by the Noisy Miner on parts of the remaining woodland bird community, including species of conservation concern.</p>
Prosocial Behavior and the Individual Normative Standard of Fairness within a Dynamic Context: Experimental Evidence
<p>The data is of the economic experiment conducted in Georgia in summer 2022. The experiment was conducted online via LIONESS web-based software. The experiment was conducted in Georgian Language. The instructions and PC screen information translated from Georgian language into English language. The participants were mostly students of different major, average age of 20, about 16% were non-students. 63% was female. The data consist of two treatments: (1) Control treatment - two round standard double blind dictator game, dictators' roles were kept constant in both rounds (2) Treatment T1 - consisted from three parts, in part 1 subjects play standard double blind Dictator Game, in part 2 subjects play tend rounds of Public Goods Game with peer punishment, and in part 3 subjects play same standard double blind Dictator Game; dictators' stay in same role in part 1 and part 3. In part 2 , in Public Goods Game was partner treatment with constant group composition. </p>
Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"
<p>Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available <a href="https://doi.org/10.1101/2022.08.15.503960">here</a>)</p> <p><strong>Analysis of AP-MS data</strong>: analysis.zip</p> <p>Contains the following scripts as well as their outputs:</p> <ul> <li>01_preparation.R R script for filtering and processing our mass spec data.</li> <li>02_diffbinding.R R script for differential analysis followed by gene set enrichment.</li> <li>03_funcstats.R R script for statistical analysis over different ontology terms.</li> <li>04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03.</li> <li>05_1_random_walks.py Python script for performing random walks for specific functional terms.</li> <li>05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1.</li> </ul> <p>The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD035399">entry</a>.</p> <p>Interactive visualization of the results of most of this analysis is available on <a href="https://github.com/PhilippJunk/kras_apms_vis">GitHub </a>as a Shiny app.</p> <p> </p> <p><strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip</p> <p>Contains the following script, as well as its output:</p> <ul> <li>01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances.</li> </ul> <p>The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD039404">entry</a>.</p>
Pollen limitation and context-dependent alleviating mechanisms in a co-flowering alpine grassland community
<p>1. The consequences of community metrics (e.g., co-flowering diversity and floral density) and plant traits (e.g., pollinator dependency and trait similarity) on pollen limitation may depend on pollinator-mediated competitive or facilitative interactions among plants in co-flowering communities, which could vary with community contexts (i.e. different altitude communities) and under human disturbances (e.g., livestock grazing). However, the mechanisms to alleviate pollen limitation under the different contexts, considering pollinator-mediated interactions among neighbor plants are unclear.</p> <p>2. We investigated pollen limitation under grazing versus ungrazing conditions in low versus high altitude alpine meadows on the Tibetan Plateau to uncover the underlying mechanisms mediating pollen limitation associated with livestock grazing.</p> <p>3. Pollen limitation is prevalent in alpine grasslands, irrespective of community contexts. Grazing exclusion decreased pollen limitation in the two sites but in different ways. In the high-altitude site, pollen limitation was reduced by the exclusion of grazers through increased trait similarity (suggesting facilitation). While pollen limitation was reduced by decreased trait similarity (suggesting competition avoidance) under grazing exclusion in the low-altitude site.</p> <p>4. Synthesis and Applications: This study suggests that flower trait distribution patterns (i.e. trait similarity) influence pollen limitation through reducing competition in the low-altitude site or enhancing facilitation in the high-altitude site under grazing exclusion in alpine grasslands. Our results provide a mechanistic understanding of pollen limitation in co-flowering alpine grassland communities under distinct human disturbances at different altitudes, emphasizing the role of pollinator-mediated interactions among plants on plant reproductive success.</p>
ScienceDex guides
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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.