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2,031 results for “Transformation”
Data from: Adaptation services of floodplains and wetlands under transformational climate change
Adaptation services are the ecosystem processes and services that benefit people by increasing their ability to adapt to change. Benefits may accrue from existing but newly-used services where ecosystems persist, or from novel services supplied following ecosystem transformation. Ecosystem properties that enable persistence or transformation are important adaptation services because they support future options. The adaptation services approach can be applied to decisions on trade-offs between currently valued services and benefits from maintaining future options. For example, ecosystem functions and services of floodplains depend on river flows. In those regions of the world where climate change projections are for hotter, drier conditions, floods will be less frequent and floodplains will either persist, though with modified structure and function, or transform to terrestrial (flood-independent) ecosystems. Many currently valued ecosystem services will reduce in supply or become unavailable, but new options are provided by adaptation services. We present a case study from the Murray-Darling Basin, Australia, for operationalizing the adaptation services concept for floodplains and wetlands. We found large changes in flow and flood regimes are likely under a scenario of +1.6°C by 2030, even with additional water restored to rivers under the proposed Murray-Darling Basin Plan. We predict major changes to floodplain ecosystems, including contraction of riparian forests and woodlands and expansion of terrestrial, drought-tolerant vegetation communities. Examples of adaptation services under this scenario include substitution of irrigated agriculture with dryland cropping and floodplain grazing; mitigation of damage from rarer, extreme floods; and increased tourism, recreational and cultural values derived from fewer, smaller wetlands that can be maintained with environmental flows. Management for adaptation services will require decisions on where intervention can enable ecosystem persistence and where transformation is inevitable. New ways of managing water that includes consideration of the increasing importance of adaptation services requires major changes to decision-making that better account for landscape heterogeneity and large-scale change, rather than attempting to maintain ecosystems in fixed states.
Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state
The concept of lakes "evolving" phosphorus (P) limitation has persisted in limnology despite limited direct evidence. Here, we developed a simple model to broadly characterize nitrogen (N) surpluses and deficits relative to P in lakes, and compared the magnitude of this imbalance to estimates of N gains and losses through biological N transformations. The model suggested that approximately half of oligotrophic lakes in the US had a stoichiometric N deficit, but almost 90% of the most productive lakes had a similar N deficit. Although reactive N appeared to accumulate in the most oligotrophic lakes, net denitrification perpetuated the N deficit in more productive lakes. Productive lakes tended to export reactive N via biological N transformations regardless of their N deficit. The lack of N accumulation through N fixation has important implications for our understanding of lake biogeochemistry, ecology, and eutrophication management.
Data from: Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest
Community-based tropical forest restoration projects, often promoted as a win-win solution for local communities and the environment, have increased dramatically in number in the past decade. Many such projects are underway in Andean cloud forests, which, given their extremely high biodiversity and history of extensive clearing, are understudied. This study investigates the efficacy of community-based tree-planting projects to accelerate cloud forest recovery, as compared to unassisted natural regeneration. This study takes place in northwest Andean Ecuador, where the majority of the original, highly diverse cloud forests have been cleared, in five communities that initiated tree-planting projects to restore forests in 2003. In 2011, we identified tree species along transects in planted forests (n = 5), naturally regenerating forests (n = 5), and primary forests (n = 5). We also surveyed 120 households about their restoration methods, tree preferences, and forest uses. We found that tree diversity was higher in planted than in unplanted secondary forest, but both were less diverse than primary forests. Ordination analysis showed that all three forests had distinct species compositions, although planted forests shared more species with primary forests than did unplanted forests. Planted forests also contained more animal-dispersed species in both the planted canopy and in the unplanted, regenerating understory than unplanted forests, and contained the highest proportion of species with use value for local people. While restoring forest increased biodiversity and accelerated forest recovery, restored forests may also represent novel ecosystems that are distinct from the region's previous ecosystems and, given their usefulness to people, are likely to be more common in the future.
Data from: Novel bird responses to successive large-scale, landscape transformations
Transformation of intact vegetation into new kinds and configurations of human-modified habitats is a well established driver of biodiversity loss. Following initial conversion, many human-dominated landscapes are then subject to further large-scale changes in land use. The impacts on biodiversity of repeated changes in land use remain poorly known, particularly how changes in the matrix interact with initial patterns of vegetation clearing. We used an 18-year study of birds in remnant patches of endangered temperate woodland in south-eastern Australia to quantify the spatial and temporal effects of successive land use transformation in the surrounding landscape. We examined bird response to: (1) initial patterns of landscape modification (creating semi-cleared grazing land dominated by pastures that surrounded remnant woodland patches), (2) subsequent establishment and maturation of exotic tree plantations on the pastures surrounding woodland patches, and (3) additive and interactive effects of both types of landscape transformation. The majority of the 57 bird species modelled responded to conversion of grazing land to exotic plantations, either independently from initial patterns of landscape transformation (20 species), or interactively (18 species) or additively (15 species) with initial landscape transformation. The occurrence of only one species (the Common Bronzewing) was related to patterns of initial transformation but not subsequent transformation due to plantation establishment. Thus, despite many characteristics of the woodland patches within the plantation remaining largely unaltered throughout our 18 year investigation, the matrix had a profound effect on the kinds of species inhabiting them, with such impacts often magnified over time as the matrix continued to change. Plantation establishment triggered new regional-level spatial processes with effects on birds detected in woodland patches up to 2 km away from the plantation. Matrix conversion selected for species with different traits (size, diet and movement patterns) compared to the initial transformation, suggesting it is acting as a different filter on the bird community. New kinds of landscape transformation (such as plantation establishment on previously cleared land) can radically affect the species that have persisted for many decades in previously modified landscapes. This highlights the challenges, but also opportunities, for conserving taxa in ever changing human-dominated environments.
Data from: Invasive seaweeds transform habitat structure and increase biodiversity of associated species
The visual landscape of marine and terrestrial systems is changing as a result of anthropogenic factors. Often these shifts involve introduced species that are morphologically dissimilar to native species, creating a unique biogenic structure and habitat for associated species within the landscape. While community level changes as a result of introduced species have been documented in both terrestrial and marine systems, it is still unclear how long-term shifts in species composition will affect habitat complexity or its potential to influence the biodiversity of species that occur at the base of the food web. We analysed quadrat photos collected at several subtidal sites in the Gulf of Maine over a 30+ year period, and collected individual seaweed species to determine their complexity and the biodiversity of meso-invertebrates associated with each species. By coupling the relationship of 30+ years of shifts in seaweed assemblages, morphological structure of the seaweed assemblage, and their meso-invertebrates, we determined introduced seaweeds have increased by up to 90%, corresponding to a rise in two-dimensional (2D) structure, and a decline in canopy height of subtidal rocky habitats. The highly complex two-dimensional habitat provided by introduced filamentous red seaweeds supports 2 to 3 times more meso-invertebrate individuals and species that form the base of the food web than simpler forms of morphological habitat. Synthesis: The present study demonstrates a long-term shift in foundation species towards a dominance of invasive seaweeds that directly reduce canopy height and increase the 2D biogenic structure of the habitat. These introduced seaweeds harbour greater biodiversity of species found at the base of the food web than seaweeds with simpler forms such as the native kelp species. Such shifts in habitat structure will propagate to food-webs by influencing the structure of lower trophic level meso-invertebrates and indirectly upper trophic level species that feed on these invertebrates and use the seaweed structure as refuge.
Data from: Scale-dependent responses of pollination and seed dispersal mutualisms in a habitat transformation scenario
Transformed habitats are the result of deliberate replacement of native species by an exotic monoculture, involving changes in biotic and abiotic conditions. Despite this, transformed habitats are becoming more common and constitute a major biodiversity change driver, little is known about the scale-dependent responses of plant-animal mutualisms. Aiming to test the multi-scale responses of pollination and seed dispersal in a habitat transformation scenario, we examined a gradient of native and transformed habitats at three spatial scales (0-50, 50-100, and 100-250 m), focused on a highly-specialized mutualistic system composed of a hemiparasitic mistletoe (Tristerix corymbosus) that is almost exclusively pollinated by a hummingbird (Sephanoides sephaniodes) and dispersed by an arboreal marsupial (Dromiciops gliroides). Even though mistletoes were found along the gradient, they were more abundant and more densely aggregated when the transformed habitat was dominant. Disperser and pollinator activity also increased as the transformed habitat become dominant, at the scale of 0-50 m and 50-100 m, respectively. Furthermore, crop size and disperser activity co-varied at broad and intermediate scales, whereas recruitment co-varied at intermediate and fine scales. Moreover, disperser activity and the number of seedlings were spatially associated, stressing D. gliroides' role in the recruitment of the mistletoe. Synthesis: This highly specialized mutualistic system seems to be responding positively to the habitat structure modifications associated with Eucalyptus plantations. However, the actual costs (e.g., reduced gene flow, increased herbivory) in these transformed habitats are yet to be assessed.
Data from: Reinvestigation of Protelytron permianum (Insecta; Early Permian; USA) as an example for applying reflectance transformation imaging to insect imprint fossils
We reinvestigated the holotype of Protelytron permianum, one of the earliest putative stem-dermapteran (i.e. stem-earwig). We recurred to reflectance transformation imaging (RTI) to deliver exhaustive and interactive photographic data. We were able to ascertain the occurrence of broadenings located along veins of the hind wing vannus and forming an arc, as well as a series of radiating folds, alternatively concave and convex. Such an organization is diagnostic of Dermaptera, in which it is indicative of hind wing folding mechanisms, particularly elaborated in these insects. We provide a foldable, paper model of the hind wing. Based on the case presented herein we anticipate that RTI process will be a major upheaval in the documentation of fossil insects preserved as imprints.
Data from: Transformational mimicry in a myrmecomorphic spider
Species which are Batesian mimics during post-embryonic development shift between mimetic models as they grow in size. However, it has not yet been tested whether these successive mimetic phenotypes are similarly protected from predators. Early instar phenotypes could represent an inaccurate phenotype or an accurate phenotype because of selection from different predators. Here, we tested the hypotheses of transformational Batesian mimicry in the ant-mimicking jumping spider Leptochestes berolinensis . We quantified the mimetic accuracy of different ontogenetic stages to potential ant models by using an multi-trait approach. We measured movement, body profile, body size, and colouration. Analysis revealed adults to be more accurate mimics than juveniles. Adults were similar to smaller morphs of Camponotus or Lasius ants, whereas juveniles were more similar to Lasius and Colobopsis ants. We tested whether predators, mantises and Pisaura spiders, were deceived by mimics after having experience with ant models. These predators never captured any ant or a mimic, but always captured the non-myrmecomorphic spider. We conclude that Leptorchestes berolinensis is a Batesian mimic of ants undergoing transformational mimicry with all stages being accurate mimics.
Continuous Wavelet Transform and Short-Time Fourier Transform used to generate S1_Table2
<p>Continuous Wavelet Transform and Short-Time Fourier Transform true vs. false recognition accuracies: the t-test was used to compare CWT and STFT recognition accuracies with mean <em>f</em>NIRS classification accuracy. The result was used to generate S1_Table2.</p>
Data from "Transforming the Energy Landscape of a Coiled-coil Peptide via Point Mutations" in J. Chem. Theor. Comput., 2017
<p>Data set for the work presented in "Transforming the Energy Landscape of a Coiled-coil Peptide via Point Mutations"</p> <p>A README file gives instructions on each file. </p> <p>Due to the size of the databases and trajectories, only a representative sample is given here. </p> <p>For more information please contact the authors. (Prof. David Wales at dw34@cam.ac.uk)</p> <p>This work was funded by a PhD scholarship of the Engineering and Physical Sciences Research Council UK.</p> <p>When using this data, please reference it accordingly.</p>
Supporting data for: "Heritage of Tethyan oceanic transform faults within Alpine orogens: Paleomagnetic evidence from the Shkoder-Peja transverse zone (Northern Albania)"
<p>Paleomagnetic data from the Shkoder-Peja transverse zone, collected in the Krasta-Cukali and Albanian Alps tectonic units (Northern Albania).</p> <p>To open and navigate with Remasoft software (https://www.agico.com/text/software/remasoft/remasoft.php).</p>
Artifact: Quick Theory Exploration for Algebraic Data Types via Program Transformations
<p>This is the repeatability package, including the tool (called LemmaCalc) in the paper, the benchmark files, a TheSy binary, Z3 binaries for Linux, and scripts to repeat the experiments.</p> <p>Parts of the paper supported by this artifact: Main results in Fig 1, implementation of Algs 1--3.</p>
Organocatalytic Iminium-Assisted Asymmetric B(sp²)-to-B(sp³) Transformation
<p><span>The folder /DFT_optimized_structures/ contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</span></p> <p><span>"Asymmetric Organocatalytic Nucleophilic Addition to B(sp2) for Direct Construction of Stereogenic B(sp3) Center"</span></p> <p><span>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, .., etc.</span></p>
Pre-training and fine-tuning dataset for transformers consisting of basic blocks and their execution times (average, minimum, and maximum) along with the execution context of these blocks, for various Cortex processors M7, M4, A53, and A72.
<p>We are making public the dataset used for training CAWET, a tool for estimating the Worst-Case Execution Time (WCET) of basic blocks using the Transformer XL model. CAWET leverages the Transformer architecture for accurate WCET predictions, and its training involves two main phases: self-supervised pre-training and fine-tuning.</p><p>CAWET undergoes a pre-training process on a substantial corpus of basic blocks to enable the Transformer to grasp the intricacies of the assembly language in focus. For this, we utilized CodeNet \cite{codenet}, a comprehensive collection of publicly submitted solutions to competitive programming challenges, comprising roughly 900,000 C programs. These programs were cross-compiled to the target architecture and subsequently disassembled using GNU binary utilities with objdump. The textual output from objdump, post a series of basic parsing operations (e.g., address extraction, separation of basic blocks), serves as the foundation for an extensive pre-training dataset. We employed this dataset to develop a vocabulary model utilizing sentence piece \cite{sentencepiece}. Following the completion of the sentence piece model's training, it becomes ready for use in tokenizing any binary programs written in the target instruction set.</p><p>The fine-tuning phase of CAWET involves its adaptation to basic blocks along with their contextual information. Here, we used a varied and openly accessible collection of programs, namely, The Algorithms (accessible at: <a href="https://github.com/TheAlgorithms/C">https://github.com/TheAlgorithms/C</a>), MiBench \cite{mibench}, and Polybench \cite{polybench}.</p><p>The provided zip file encompasses the following directories:</p><p>Fine_Tuning: This includes four distinct files, each tailored for a specific processor: Cortex_M4, Cortex_M7, Cortex_A53, and Cortex_72. Each file encompasses the basic block under analysis (bbUA), the preceding 10 basic blocks executed prior to it, and timing information related to the bbUA (mean, min, max, normalization, etc.).</p><p>Pre_Training: This comprises two extensive files, dataset_CortexA and dataset_CortexM, utilized for pre-training the transformers for the Masked Language Modeling Task (MLM). Additionally, it includes the sentence piece model and the necessary code to facilitate accurate tokenization.</p><p>For additional information, please refer to the CAWET paper or contact us at <a href="mailto:ea_amalou@esi.dz">ea_amalou@esi.dz</a></p><p> </p><p>Citation:</p><p>@inproceedings{amalou2023cawet,</p><p> title={CAWET: Context-Aware Worst-Case Execution Time Estimation Using Transformers},</p><p> author={Amalou, Abderaouf N and Fromont, Elisa and Puaut, Isabelle},</p><p> booktitle={35th Euromicro Conference on Real-Time Systems (ECRTS 2023)},</p><p> year={2023},</p><p> organization={Schloss Dagstuhl-Leibniz-Zentrum f{\"u}r Informatik}</p><p>}</p><p> </p><p><strong>Bibliography</strong>:</p><p>codenet</p><p>@article{codenet2021,</p><p> title={CodeNet: A large-scale AI for code dataset for learning a diversity of coding tasks},</p><p> author={Puri, Ruchir and Kung, David S and Janssen, Geert and Zhang, Wei and Domeniconi, Giacomo and Zolotov, Vladimir and Dolby, Julian and Chen, Jie and Choudhury, Mihir and Decker, Lindsey and others},</p><p> journal={arXiv preprint arXiv:2105.12655},</p><p> year={2021}</p><p>}</p><p>sentencepiece</p><p>@article{sentencepiece2018,</p><p> title={Sentencepiece: A simple and language independent subword tokenizer and detokenizer for neural text processing},</p><p> author={Kudo, Taku and Richardson, John},</p><p> journal={arXiv preprint arXiv:1808.06226},</p><p> year={2018}</p><p>}</p><p>mibench</p><p>@inproceedings{polybench2014,</p><p> title={Understanding polybench/c 3.2 kernels},</p><p> author={Yuki, Tomofumi},</p><p> booktitle={International workshop on polyhedral compilation techniques (IMPACT)},</p><p> pages={1--5},</p><p> year={2014}</p><p>}</p><p>polybench: </p><p>@inproceedings{mibench,</p><p> title={MiBench: A free, commercially representative embedded benchmark suite},</p><p> author={Guthaus, Matthew R and Ringenberg, Jeffrey S and Ernst, Dan and Austin, Todd M and Mudge, Trevor and Brown, Richard B},</p><p> booktitle={4th IEEE international workshop on workload characterization},</p><p> year={2001}</p><p>}</p>
Atom-by-atom Imaging of Moiré Transformations in 2D Transition Metal Dichalcogenides
<p>This dataset contains the images used in the manuscript "Atom-by-atom Imaging of Moiré Transformations in 2D Transition Metal Dichalcogenides".</p>
Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents
<p>This repository is supplementary to the manuscript "Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents" (DOI: 10.1021/acs.est.3c05008). This repository contains scripts of TPs collection and QSRR model as well the generated data set.</p><p>We compiled a suspect list of antibiotics containing 663 compounds. Corresponding suspect TPs were collected in silico with BioTransformer 3.0 and through a library search from PubChem data, which were both performed in batch mode using the patRoon 2.0 package. After merging results and removing duplicates, 88,823 TPs remained for suspect screening. Quantitative-structure retention relationship (QSRR) models were developed for the suspect antibiotics and TPs using target compounds to predict their retention times with the Retip package.</p>
Figure 16 in An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family
Figure 16. One of the 54 minimum-length cladograms, showing transformation series for selected characters (see also Figs 13–15) that contribute to the non-monophyly of Polycirrus, Lysilla, and Amaeana.
Figure 7 in An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family
Figure 7. Polycirrus papillosus: A (holotype, MZUSP 1216), tips of notochaetae; B (paratype, MZUSP 1244), tips of notochaetae from the posterior row. Polycirrus bicrinalis (paratype, AM W199638): C, notochaetae from segment 13. Lysilla bilobata (AM W199514): D, E, notochaetae. Polycirrus breviuncinatus: F (paratype, MZUSP 1245), G (holotype, MZUSP 1220), notochaetae. Scale bars: A–C, E–G, 20 μm; D, 6 μm.
Figure 11 in An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family
Figure 11. Strict consensus tree of 54 minimum-length cladograms. Note that except for Hauchiella, non-monotypic ingroup genera are either para- or polyphyletic, i.e. Polycirrus, Amaeana, and Lysilla.
Figure 15 in An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family
Figure 15. One of the 54 minimum-length cladograms, showing transformation series for selected characters (see also Figs 13–14, 16) that contribute to the non-monophyly of Polycirrus, Lysilla, and Amaeana.
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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.