Find research datasets worth reusing

opencc-zeroAug 2015View details →

Data from: Evolutionary processes driving spatial patterns of intra-specific genetic diversity in river ecosystems

Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.

Data from: Diel activity, frequency and visit duration of pollinators in focal plants: in situ automatic camera monitoring and data processing

Data collection on interactions between organisms and their environment has traditionally been conducted by on-site human observations, a time-consuming enterprise that could explain the shortage of around-the-clock observations of free-ranging wild animals. In this paper, I outline a time-efficient procedure to collect data on flower-visiting animals. The objectives were, first, to model diel activity rhythms by using cosine-based mixed-effects regression models (cosinor method) on data from an established automatic video monitoring system and, secondly, to test the use of a cheap off-the-shelf digital camera modified for automated monitoring of flower visitors. Two different model systems were studied: foraging bumblebees visiting focal white clovers, monitored around-the-clock (193 h) to model diel activity; and honeybees visiting thistles, monitored over a shorter period (5 h) to test the applicability and reliability of a new method for monitoring pollinators. The data were automatically entered and processed using R-scripts after manual filtering of the images, obviating the need for manual data entry prior to analysis. For diel activity in bumblebees, the model that gave the best fit included the 24-h fundamental period and one harmonic, a 12-h period to modulate the signal, together with temperature. The bumblebees were exclusive diurnal, with activity starting about 5 h after sunrise, peaking sharply in the afternoon and ending about 1 h before sunset. In addition to time of day, activity also increased with temperature. The off-the-shelf digital camera, Canon PowerShot®, with motion detection script, was triggered by every flower-visiting honeybee. In addition to recorded visitor frequency and visitor duration, it enabled high-resolution images, which could be important for species identification. Automatic camera recording is advantageous for close-up monitoring, compared with continuous video recording, because the latter demands more time and effort in reviewing the material. It could be used to study a range of different species such as pollinators, on-plant behaviour of herbivorous animals, cavity dwellers or cavity breeders. Moreover, the procedures for automatic data entry, data processing and statistical analysis for modelling diel activity rhythms could have great relevance for researchers using other types of camera monitoring systems operating 24 h per day.

Data from: Disentangling relationships between plant diversity and decomposition processes under forest restoration

Biodiversity has been elucidated to be one of the major factors sustaining ecosystem functioning. The vast majority of studies showing a relationship between biodiversity and ecosystem functioning have come from experiments, and this knowledge has not yet been applied to most real-world cases of conservation and management. This is especially true in forest ecosystems, characterized by the dominance of long-lived organisms (trees) and high levels of structural complexity and environmental heterogeneity. To apply biodiversity–function relationships to actual forest management, there are several issues to be considered. These include employing a cross-taxon perspective, as some functions (e.g. soil biogeochemical processes) cannot be maintained by a narrow set of organisms, as is usually the case with experimental systems. More specifically, although the interaction between above- and below-ground diversity is important for many functions in forests, there are few studies that evaluated the roles of diversity in both subsystems in a manner that could be informative in practice. To evaluate the roles of above- and below-ground diversity to support natural soil ecosystem functions, we conducted a decomposition experiment in the northern forests of Japan, which are currently under restoration management. The restoration area consists of mosaics of different vegetation types by various revegetation activities and establishment of ungulate exclosures. Using structural equation modelling and linear mixed-effects models, we assessed direct and indirect pathways from diversity to functions by focusing on both of taxonomic and functional diversity indices. To put our findings into practice, we utilized a trait-based approach, which provides a link between the functional consequences of human influences and ecosystem structure. We found little direct effects of tree diversity on below-ground functions such as decomposition rate and litter stabilization. However, once the diversities of understorey herbaceous plants and soil fungi were considered as a possible mediating explanatory factor, we found a significant effect of tree diversity to indirectly support these functions by supporting these other types of biodiversity. Particularly, we found that the models based on functional trait diversity, rather than on taxonomic species richness, best explained the variation in below-ground processes. Synthesis and applications. Forest restoration in the northern forests of Japan has had no explicit objective to restore soil functions. Nevertheless, afforestation, and the associated increase in tree diversity as a measure of forest restoration, was, although often unintentionally, proven effective for the maintenance of multiple ecosystem functions, such as soil biogeochemical processes. This finding suggests a great potential for management to make local tree assemblages functionally dissimilar and diverse for the sake of supporting and enhancing fundamental ecosystem functions in forests.

Data from: EEG theta dynamics within frontal and parietal cortices for error processing during reaching movements in a prism adaptation study altering visuo-motor predictive planning

Modulation of frontal midline theta (fmθ) is observed during error commission, but little is known about the role of theta oscillations in correcting motor behaviours. We investigate EEG activity of healthy partipants executing a reaching task under variable degrees of prism-induced visuo-motor distortion and visual occlusion of the initial arm trajectory. This task introduces directional errors of different magnitudes. The discrepancy between predicted and actual movement directions (i.e. the error), at the time when visual feedback (hand appearance) became available, elicits a signal that triggers on-line movement correction. Analysis were performed on 25 EEG channels. For each participant, the median value of the angular error of all reaching trials was used to partition the EEG epochs into high- and low-error conditions. We computed event-related spectral perturbations (ERSP) time-locked either to visual feedback or to the onset of movement correction. ERSP time-locked to the onset of visual feedback showed that fmθ increased in the high- but not in the low-error condition with an approximate time lag of 200 ms. Moreover, when single epochs were sorted by the degree of motor error, fmθ started to increase when a certain level of error was exceeded and, then, scaled with error magnitude. When ERSP were time-locked to the onset of movement correction, the fmθ increase anticipated this event with an approximate time lead of 50 ms. During successive trials, an error reduction was observed which was associated with indices of adaptations (i.e., aftereffects) suggesting the need to explore if theta oscillations may facilitate learning. To our knowledge this is the first study where the EEG signal recorded during reaching movements was time-locked to the onset of the error visual feedback. This allowed us to conclude that theta oscillations putatively generated by anterior cingulate cortex activation are implicated in error processing in semi-naturalistic motor behaviours.

opencc-zeroDec 2014View details →

Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state space where such a tipping point might exist. We illustrate how a Bayesian non-parametric approach using a Gaussian process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a stochastic dynamic programming framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favours models without tipping points, leading to harvest policies that guarantee extinction. The Gaussian process dynamic programming (GPDP) performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, as it does not underestimate the uncertainty outside of the observed data.

opencc-zeroDec 2014View details →

Data from: In-vivo imaging of cell migration using contrast enhanced MRI and SVM based post-processing

The migration of cells within a living organism can be observed with magnetic resonance imaging (MRI) in combination with iron oxide nanoparticles as an intracellular contrast agent. This method, however, suffers from low sensitivity and specificty. Here, we developed a quantitative non-invasive in-vivo cell localization method using contrast enhanced multiparametric MRI and support vector machines (SVM) based post-processing. Imaging phantoms consisting of agarose with compartments containing different concentrations of cancer cells labeled with iron oxide nanoparticles were used to train and evaluate the SVM for cell localization. From the magnitude and phase data acquired with a series of -weighted gradient-echo scans at different echo-times, we extracted features that are characteristic for the presence of superparamagnetic nanoparticles, in particular hyper- and hypointensities, relaxation rates, short-range phase perturbations, and perturbation dynamics. High detection quality was achieved by SVM analysis of the multiparametric feature-space. The in-vivo applicability was validated in animal studies. The SVM detected the presence of iron oxide nanoparticles in the imaging phantoms with high specificity and sensitivity with a detection limit of 30 labeled cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept, we applied the method to follow the migration of labeled cancer cells injected in rats. The combination of iron oxide labeled cells, multiparametric MRI and a SVM based post processing provides high spatial resolution, specificity, and sensitivity, and is therefore suitable for non-invasive in-vivo cell detection and cell migration studies over prolonged time periods.

opencc-zeroDec 2016View details →

Data from: Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche-based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche-based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche-based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche-based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche-based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche-based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche-based or neutral-based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.

opencc-zeroDec 2017View details →

Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing

Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0.50 per specimen) through Next Generation Sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3290 of 4032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases, and yields precise abundance information.

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.

opencc-zeroDec 2011View details →

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.

restrictedcc-by-4.0Feb 2024View details →

Processed tracking data of Southern Giant Petrels during breeding activity in Harmony Point, Nelson Island, between 2021 and 2023

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 (62°17′60″ S, 59°10′60″ W), Nelson Island, Maritime Antarctic Peninusula. All individuals had active nests. Bill size and tarsus length for 50 southern giant petrels ringed in the area. 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. 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. See https://github.com/drlucaskruger/SouthernGiantPetrel_Movements_and_Individual_Size for codes. This study was funded by INACH (Programa Áreas Marinas Protegidas 24 03 052) and ANID – Programa Iniciativa Milenio – ICN2021_002 (BASE).

restrictedcc-by-sa-4.0Feb 2024View details →

DeepCube: Post-processing and annotated datasets of social media data

Researcher(s): Alexandros Mokas, Eleni Kamateri Supervisor: Ioannis Tsampoulatidis This repository contains 3 social media datasets: 2 Post-processing datasets: 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: <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> 1 Annotated dataset: 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: <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> 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. 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. The dataset is provided by <a href="https://infalia.eu/">INFALIA</a>.  <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.

opencc-by-4.0Nov 2024View details →

Universal Translation Process: Incorporating Inter-Personal and Other Memetic Semantic Data Translations within the GOD Framework

This document expands the universal translation process within the Gravitational Omnipotent Dimensionality (GOD) framework by integrating inter-personal communication and non-linguistic memetic semantic data. It explores how memetic gravity, semantic propagation, and spacetime contextualisation enable the translation of meaning across languages, cultural symbols, behaviours, and cognitive structures, providing a unified approach to understanding and propagating knowledge in diverse contexts.

opencc-by-4.0Mar 2022View details →

MD Analysis Pre-Processed Data Input Files: Towards a New Model for the TREX1 Exonuclease, Hemphill et al.

All atoms molecular dynamics simulations were performed for TREX1 apoenzyme, TREX1-ssDNA complex, and TREX1-dsDNA complex, with four replicate simulations per system. Trajectory and initial condition output files were pre-processed in VMD to generate time-step sampled mol2 files of the macromolecules in each simulation. The mol2 files were used to calculate phi/psi angles of the protein backbone, and to extract all-atoms coordinate information over time, and this information was organized into an RData file for each simulation system, including all simulation replicates. These RData files are provided, and they were analyzed with the scripts described in the affiliated manuscript.

opencc-by-4.0Jun 2022View details →

Data and code for: Conserved subcortical processing in visuo-vestibular gaze control (Nat. Comm).

Source data, code used for analysis and presentation of visuo-vestibular stimulation, and additional datasets of the manuscript published in Nature Communications entitled: Conserved subcortical processing in visuo-vestibular gaze control.

opencc-by-4.0Sep 2022View details →

Processed data for "Effects of Anthropogenic Forcings on Multidecadal Variability of the Sea Level around the Japanese Coast Simulated by MRI-ESM2.0 for CMIP6"

Processed data for "Effects of Anthropogenic Forcings on Multidecadal Variability of the Sea Level around the Japanese Coast Simulated by MRI-ESM2.0 for CMIP6" submitted to Geophysical Research Letters. Detailed information is described in README.txt in the zip file.

openMay 2024View details →

Supporting data for: Effects of type and content of dissolved salts on primary characteristics of porous sandstones during maturing process

This dataset includes experimental data used to generate the results detailed in the paper titled: Effects of type and content of dissolved salts on primary characteristics of porous sandstones during maturing process and submitted to Water Resources Research.

opencc-by-4.0Jul 2024View details →

[5G-IANA] UC1 - Data processed by the AI object detection algorithm

Bounding boxes of objects detected by the artificial intelligence algorithm for each video frame received.