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6,467 results for “process”
Data from: An indexed, mapped mutant library enables reverse genetics studies of biological processes in Chlamydomonas reinhardtii
The green alga Chlamydomonas reinhardtii is a leading single-celled model for dissecting biological processes in photosynthetic eukaryotes. However, its usefulness has been limited by difficulties in obtaining mutants in genes of interest. To allow generation of large numbers of mapped mutants, we developed high-throughput methods which: (1) Enable easy propagation on agar and cryogenic maintenance of tens of thousands of C. reinhardtii strains; (2) Identify mutant insertion sites and physical coordinates in such collections; (3) Validate the insertion sites in pools of mutants by obtaining >500 bp of flanking genomic sequences. We used these approaches to construct a stably maintained library of 1,935 mapped mutants, representing disruptions in 1,562 genes. We further characterized randomly selected mutants, and found that 33 out of 44 insertion sites (75%) could be confirmed by PCR, and 17 out of 23 mutants (74%) contained a single insertion. To demonstrate the power of this library for elucidating biological processes, we analyzed the lipid content of mutants disrupted in genes encoding proteins of the algal lipid droplet proteome. This study revealed a central role of the long-chain acyl-CoA synthetase LCS2 in the production of triacylglycerol from de novo synthesized fatty acids.
Data from: Meaningful call combinations and compositional processing in the southern pied babbler
Language's expressive power is largely attributable to its compositionality: meaningful words are combined into larger/higher-order structures with derived meaning. Despite its importance, little is known regarding the evolutionary origins and emergence of this syntactic ability. Although previous research has shown a rudimentary capability to combine meaningful calls in primates, because of a scarcity of comparative data, it is unclear to what extent analog forms might also exist outside of primates. Here, we address this ambiguity and provide evidence for rudimentary compositionality in the discrete vocal system of a social passerine, the pied babbler (Turdoides bicolor). Natural observations and predator presentations revealed that babblers produce acoustically distinct alert calls in response to close, low-urgency threats and recruitment calls when recruiting group members during locomotion. On encountering terrestrial predators, both vocalizations are combined into a "mobbing sequence," potentially to recruit group members in a dangerous situation. To investigate whether babblers process the sequence in a compositional way, we conducted systematic experiments, playing back the individual calls in isolation as well as naturally occurring and artificial sequences. Babblers reacted most strongly to mobbing sequence playbacks, showing a greater attentiveness and a quicker approach to the loudspeaker, compared with individual calls or control sequences. We conclude that the sequence constitutes a compositional structure, communicating information on both the context and the requested action. Our work supports previous research suggesting combinatoriality as a viable mechanism to increase communicative output and indicates that the ability to combine and process meaningful vocal structures, a basic syntax, may be more widespread than previously thought.
Data from: Novel forests maintain ecosystem processes after the decline of native tree species
The positive relationship between species diversity (richness and evenness) and critical ecosystem functions, such as productivity, carbon storage, and nutrient cycling, is often used to predict the consequences of extinction. At regional scales, however, plant species richness is mostly increasing rather than decreasing because successful plant species introductions far outnumber extinctions. If these regional increases in richness lead to local increases in diversity, a reasonable prediction is that productivity, carbon storage, and nutrient cycling will increase following invasion, yet this prediction has rarely been tested empirically. We tested this prediction in novel forest communities dominated by introduced species (~ 90% basal area) in lowland Hawaiian rainforests by comparing their functionality to that of native forests. We conducted our comparison along a natural gradient of increasing nitrogen availability, allowing for a more detailed examination of the role of plant functional trait differences (specifically, N2-fixation) in driving possible changes to ecosystem function. Hawai'i is emblematic of regional patterns of species change; it has much higher regional plant richness than it did historically, due to > 1000 plant species introductions and only ~ 71 known plant extinctions--resulting in an approximately 100% increase in richness. At local scales, we found that novel forests had significantly higher tree species richness and higher diversity of dominant tree species. We further found that aboveground biomass, productivity, nutrient turnover (as measured by soil-available and litter-cycled nitrogen and phosphorus), and belowground carbon storage either did not differ significantly or were significantly greater in novel relative to native forests. We found that the addition of introduced N2-fixing tree species on N-limited substrates had the strongest effect on ecosystem function--a pattern found by previous empirical tests. Our results support empirical predictions of the functional effects of diversity, but they also suggest basic ecosystem processes will continue even after dramatic losses of native species diversity if simple functional roles are provided by introduced species. Because large portions of the Earth's surface are undergoing similar transitions from native to novel ecosystems, our results are likely to be broadly applicable.
Supplementary material to `Accelerating Lagrangian transport simulations on graphics processing units: performance optimizations of MPTRAC v2.5'
<p>This repository contains the supplementary material to the following paper: Hoffmann, L., Haghighi Mood, K., Herten, A., Hrywniak, M., Kraus, J., Clemens, J., and Liu, M., Accelerating Lagrangian transport simulations on graphics processing units: performance optimizations of MPTRAC v2.5, Geoscientific Model Development, submitted, 2023.</p><p> </p>
Applying Process Dissociation to Self-Sacrificial Moral Dilemmas: Extending the Dual-Process Model (Analysis Syntax Included)
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Pulsed 193 nm Excimer laser processing of 4H-SiC(0001) wafers with radiant exposure dependent "in situ" reflectivity studies for process optimization.
<p>Conference paper</p>
SOIL STRUCTURE AND CHANGES IN THEIR PHYSICAL PROPERTIES UNDER THE INFLUENCE OF EROSION PROCESSES
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HARMFUL FACTORS IN PRODUCTION PROCESSES AND MEASURES FOR PROTECTION AGAINST THEM
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OCCUPATIONAL DISEASES IN OIL PROCESSING
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Supplementary material for "The comparative role of physical system processes in Hudson Strait ice stream cycling: a comprehensive model-based test of Heinrich event hypotheses"
<p>This supplementary material for "The comparative role of physical system processes in Hudson Strait ice stream cycling: a comprehensive model-based test of Heinrich event hypotheses" includes two animations showing a full Hudson Strait surge cycle with the default GSM heat flux.</p>
Exploring the Molecular Pathways of the Activation Process on PPARγ Recurrent Bladder Cancer Mutants
<p><span>The intricate involvement of Peroxisome Proliferator-Activated Receptor Gamma </span><span>(PPAR</span><span>γ</span><span>) in vital processes such as glucose homeostasis and adipogenesis is well </span><span>established. However, its multifaceted role in cancer, particularly in luminal bladder </span><span>cancer, remains a subject of intense debate. In this context, PPAR</span><span>γ</span><span>’s overexpression </span><span>and activation have been implicated in tumorigenesis. Notably, specific gain-of-function </span><span>mutations (M280I, I290M, and T475M) within PPAR</span><span>γ</span><span>’s ligand-binding domain have </span><span>been pinpointed in bladder cancer, correlating with receptor activation.</span><span> </span><span>Nonethe</span><span>less, the underlying molecular pathways prompted by these mutations remain obscure. <span>Here, we employed a dual-basin structure-based model (db SBM) to unveil the intricate </span><span>conformational dynamics that underlie the transition between PPAR</span><span>γ</span><span>’s inactive and </span><span>active states. Additionally, we explored the effects of the M280I, I290M, and T475M </span><span>mutations on this pivotal process. Our findings concur with existing literature, reveal</span><span>ing heightened ligand-independent transcriptional activity in the I290M and T475M </span><span>mutants compared to other variants.</span><span> </span><span>Importantly, both mutants displayed enhanced </span><span>stabilization of the active state relative to the wild-type receptor, and the I290M mu</span><span>tation promoted a remarkably specific transition route, rendering it a prime candidate </span><span>for further investigation. Electrostatic analysis pinpointed the pivotal role of residues </span><span>K303 and E488 in the activation cascade of I290M. This insight was substantiated by </span><span>biophysical assays, as disruption of the K303-E488 interaction curtailed the thermal </span><span>stabilization characteristic of the I290M mutation. These findings designate K303 and </span><span>E488 as potential targets for inhibitors aimed at modulating PPAR</span><span>γ</span><span> </span><span>activation, with </span><span>promising implications for refining bladder cancer prognosis. In sum, our study high</span><span>lights the remarkable predictive capabilities achieved through the integration of sim</span><span>ulation and cheminformatics methods, validated by biochemical experiments, to gain </span><span>deeper insights into molecular mechanisms of activation and identify target residues </span><span>for protein modulation.</span><br></span></p>
The dataset of article "Analysis of Uncertainties and Associated Convective Processes in Simulations of Extreme Precipitation over Cities with a Regional Earth System Model: A Case Study"
<p>The "out<i>EXP02.nc" and "out</i>EXP11.rar" are two examples of 11 simulations' output file in the article, in each of the file, 9 variables (horizontal wind u, horizontal wind v, vertical speed, height, temperature, pressure, precipitation, longitude and latitude) from outputs of simulation are included, the time interval is 2 hours.</p><p>The MERRA-2 dataset provides the initial and boundary conditions of chemical fields in simulations.</p><p>The era5 dataset provides the meteorological initial and boundary conditions in simulations.</p><p> </p>
Temperate forest elevational gradient: spatial variation and deterministic processes in soil oribatid mite community assembly
<p>The data sets were analyzed during the current study. Data from: Temperate forest elevational gradient: spatial variation and deterministic processes in soil oribatid mite community assembly.</p>
"Learning the intrinsic dynamics of spatio-temporal processes through Latent Dynamics Networks": Dataset
<p>This repository contains the data accompanying the paper "<em>Learning the intrinsic dynamics of spatio-temporal processes through Latent Dynamics Networks</em>", by Francesco Regazzoni, Stefano Pagani, Matteo Salvador, Luca Dedè and Alfio Quarteroni.</p> <p> </p> <p>The associated codes are available in the Github repository <a href="https://github.com/FrancescoRegazzoni/LDNets">https://github.com/FrancescoRegazzoni/LDNets</a></p>
SARS CoV 2 Evolution, Processed Illumina VCF Files
<p>Processed (vcf) files for Communications Biology manuscript "SARS-CoV-2 evolution in the absence of selective immune pressures, results in antibody resistance, interferon suppression and phenotypic differences by lineage". VCFs have already had variants overlapping with primers removed and represent the output when aligning merged fastq files, which are in a linked Zenodo repository.</p>
Attentional Processing Differentiate Individual Capacity in Associative Learning
<p>This repository contains:</p> <p> </p> <p>- the behavioral raw data and the behavioral data coded according to the confusion matrix</p> <p>- workflow for preprocessing (History file from BrainVision Analyzer version 2.2)</p> <p>- the list of removed segments (per participant) after artifact rejection</p> <p>- preprocessed EEG data (average by participant)</p> <p> </p>
Processed tracking data of Southern Giant Petrels during breeding activity in Harmony Point, Nelson Island, between 2021 and 2023
<p>Processed GPS data for 36 Southern Giant Petrels (Macronectes giganteus) in December and January of 2021/22 and 2022/23 breeding season in Harmony Point (<span>62°17′60″ S, 59°10′60″ W</span>), Nelson Island, Maritime Antarctic Peninusula. All individuals had active nests. Bill size and tarsus length for 50 southern giant petrels ringed in the area.</p> <p>Between 2021 and 2023 50 breeding individuals were captured on the nest, following methods and protocols previously approved (https://zenodo.org/doi/10.5281/zenodo.10640094). For capture, one researcher approached the colony, while the others remained at a distance, preferentially out of sight of the birds. Response behavior to the approaching researcher was used as a proxy for capture selection, for instance, animals that regurgitate or stand on the nest exposing the eggs when the researcher approaches are more likely to leave the nest or might take longer to return to the nest after releasing, increasing the risk of breeding failure (Krüger et al. in prep). Therefore, animals displaying those behaviors were not captured. Before capture, the egg was gently removed from below the bird, covered in thermal tissue and put inside a box, for protection from cold and predation. Then the bird was captured by hand and taken to the site where other two researchers were waiting. Animals had their eyes covered with a head hood. All captured animals were ringed with stainless steel bands (rings), preferentially both animals from the same nest each season. All captured animals had bill and tarsus measured with calipers. Bill was used to determine sex, since males have larger bills with no overlap of measures with females. After release back to the nest, behavioral status of the animal was observed, and after the animal remained sat at the nest, the egg was placed back.</p> <p>GPSs were deployed on the back of the birds using 3M Extreme Hold Duct Tape 2835-B (1.88 inches) and Loctite glue. In 2021/22 and 2022/2023 seasons 30 and 20 birds were tagged with GPSs, respectively. In 2021/22, 4 females lost the GPS, and in 2022/23 one male and one female lost the GPS. Therefore there was tracking data for 26 and 18 animals, respectively. Eight animals were repeated in both seasons, totalizing 36 animals tracked in the two seasons. CatLog-P Gen 2 epoxy cased GPSs loggers (Perthold Technology, 50g) and Sputnik XAIS GPSs (Sextant technology, 70g) were used. Southern Giant Petrel weight varies between 4 kg and 6 kg, therefore the heavier instrumentation on the lighter birds would represent less than 2% of body weight, percentage which is accepted to have no significant effect on large procellariforms . Loggers were configurated to record one geographical fix each 5 minutes, and were recovered from the birds after 2 to 4 weeks.</p> <p>See https://github.com/drlucaskruger/SouthernGiantPetrel_Movements_and_Individual_Size for codes.</p> <p>This study was funded by INACH (Programa Áreas Marinas Protegidas 24 03 052) and ANID – Programa Iniciativa Milenio – ICN2021_002 (BASE).</p>
DeepCube: Post-processing and annotated datasets of social media data
<p>Researcher(s): Alexandros Mokas, Eleni Kamateri</p> <p>Supervisor: Ioannis Tsampoulatidis</p> <p>This repository contains 3 social media datasets:</p> <p><strong>2 Post-processing datasets:</strong> These datasets contain post-processing data extracted from the analysis of social media posts collected for two different use cases during the first two years of the <a href="https://deepcube-h2020.eu/">Deepcube </a>project. More specifically, these include:</p> <ul> <li>The UC2 dataset containing the post-processing analysis of the Twitter data collected for the <a href="https://deepcube-h2020.eu/">DeepCube</a> use case (UC2) dealing with the climate induced migration in Africa. This dataset contains in total 5,695,253 social media posts collected from the Twitter platform, based on the initial version of search criteria relevant to UC2 defined by Universitat De Valencia, focused on the regions of Ethiopia and Somalia and started from 26 June, 2021 till March, 2023.</li> <li>The UC5 dataset containing the post-processing analysis of the Twitter and Instagram data collected for the <a href="https://deepcube-h2020.eu/">DeepCube</a> use case (UC5) related to the sustainable and environmentally-friendly tourism. This dataset contains in total 58,143 social media posts collected from the Twitter and Instagram platform (12,881 collected from Twitter and 45,262 collected from Instagram), based on the initial version of search criteria relevant to UC5 defined by MURMURATION SAS, focused on the regions of Brasil and started from 26 June, 2021 till March, 2023.</li> </ul> <p><strong>1 Annotated dataset: </strong>An additional anottated dataset was created that contains post-processing data along with annotations of Twitter posts collected for UC2 for the years 2010-2022. More specifically, it includes:</p> <ul> <li>The UC2 dataset contain the post-processing of the Twitter data collected for the <a href="https://deepcube-h2020.eu/">DeepCube</a> use case (UC2) dealing with the climate induced migration in Africa. This dataset contains in total 1721 annotated (412 relevant and 1309 irrelevant) by social media posts collected from the Twitter platform, focused on the region of Somalia and started from 1 January, 2010 till 31 December, 2022.</li> </ul> <p>For every social media post retrieved from Twitter and Instagram, a preprocessing step was performed. This involved a three-step analysis of each post using the appropriate web service. First, the location of the post was automatically extracted from the text using a location extraction service. Second, the images included in the post were analyzed using a concept extraction service, which identified and provided the top ten concepts that best described the image. These concepts included items such as "person," "building," "drought," "sun," and so on. Finally, the sentiment expressed in the post's text was determined by using a sentiment analysis service. The sentiment was classified as either positive, negative, or neutral.</p> <p>After the social media posts were preprocessed, they were visualized using the <a href="https://deepcube.infalia.com/">Social Media Web Application</a>. This intuitive, user-friendly online application was designed for both expert and non-expert users and offers a web-based user interface for filtering and visualizing the collected social media data. The application provides various filtering options, an interactive map, a timeline, and a collection of graphs to help users analyze the data. Moreover, this application provides users with the option to download aggregated data for specific periods by applying filters and clicking the "Download Posts" button. This feature allows users to easily extract and analyze social media data outside of the web application, providing greater flexibility and control over data analysis.</p> <p>The dataset is provided by <a href="https://infalia.eu/">INFALIA</a>. <br><br><a href="https://infalia.eu/">INFALIA</a>, being a spin-off of the <a href="https://www.certh.gr/root.en.aspx">CERTH</a> institute and a partner of a research EU project, releases this dataset containing Tweets IDs and post pre-processing data for the sole purpose of enabling the validation of the research conducted within the <a href="https://deepcube-h2020.eu/">DeepCube</a>. Moreover, Twitter Content provided in this dataset to third parties remains subject to the Twitter Policy, and those third parties must agree to the Twitter Terms of Service, Privacy Policy, Developer Agreement, and Developer Policy (<a href="https://developer.twitter.com/en/developer-terms">https://developer.twitter.com/en/developer-terms</a>) before receiving this download.</p>
urbisphere_gb-london_UR-1: Processing and modelling grid of 500-m horizontal resolution for London, UK
<h2>Files in this archive </h2> <ul> <li>London_500m_grid.zip <ul> <li>Grid with ~500 m horizontal resolution, covering Greater London, UK </li> <li>Polygons, ESRI shapefile format (*.shp, *.shx, *.cpg, *.dbf, *.prj)</li> </ul> </li> <li>code.zip <ul> <li>Code to produce the dataset (Python3)</li> </ul> </li> <li>urbisphere_gb-london_UR-1.pdf <ul> <li>Documentation</li> </ul> </li> </ul> <h2>Data purpose </h2> <p>This dataset includes a grid with ~500 m horizontal resolution covering Greater London, UK. It is used to support <em>urbisphere</em>–London, APex and ASSURE modelling activities and analyses of socio-economic data. </p> <h3>Linked with</h3> <ul> <li>Hertwig et al. 2024a. urbisphere_presentations_UR-1: Modelling anthropogenic heat emissions from residential buildings-comparison between Berlin and London. EMS Annual Meeting 2023 [Poster]. Zenodo. https://doi.org/10.5281/zenodo.10889863</li> <li>Hertwig et al. 2024b. urbisphere_presentations_UR-2: Connecting physical and socio-economic spaces for urban agent-based modelling, EMS Annual Meeting 2023 [Poster]. Zenodo. https://doi.org/10.5281/zenodo.10889885</li> <li>McGrory et al. 2024. urbisphere_presentations_UR-3: Dynamic Anthropogenic actiVities and feedback to Emissions (DAVE): An agent-based model for heat and exposure to other anthropogenic emissions. EMS Annual Meeting 2023 [Presentation]. Zenodo. https://doi.org/10.5281/zenodo.10889900</li> </ul>
Development of an IoT based smart potato leaf diseases monitoring and controlling system with image processing
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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.