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885 results for “data strategy”
PP-recyclates characterization after different sampling and recycling strategies-Parallel Plate Rheology data
<p>The purpose of this analysis is to evaluate the efficiency of different recycling procedures and the quality of the resulting recyclates.</p> <p>This dataset contains raw parallel plate rheology data of PP-recyclates from different recycling strategies. The content is:</p> <ul> <li>One Excel file containing parallel plate rheology data of PP recyclates after scCO2 recycling, reference samples and measurement protocol</li> <li>One Excel file containing parallel plate rheology of PP recyclates after solvent-based recycling, reference samples and measurement protocol</li> <li>One Excel file containing parallel plate rheology data of PP recyclates after upcycling, reference samples and measurement protocol</li> <li>One Readme file containing further information about the methodology and nomenclature</li> </ul> <p>This dataset was generated in the framework of PRecycling Horizon Europe project (101058670)</p>
Data from: Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (edgeR vs. baySeq software) works well even in the absence of a reference genome, and is robust across a broad range of parameters. We advise against library normalization, and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, SOAPdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies, and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications, and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.
Data from: Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure
Ecological data often show temporal, spatial, hierarchical (random effects), or phylogenetic structure. Modern statistical approaches are increasingly accounting for such dependencies. However, when performing cross-validation, these structures are regularly ignored, resulting in serious underestimation of predictive error. One cause for the poor performance of uncorrected (random) cross-validation, noted often by modellers, are dependence structures in the data that persist as dependence structures in model residuals, violating the assumption of independence. Even more concerning, because often overlooked, is that structured data also provides ample opportunity for overfitting with non-causal predictors. This problem can persist even if remedies such as autoregressive models, generalized least squares, or mixed models are used. Block cross-validation, where data are split strategically rather than randomly, can address these issues. However, the blocking strategy must be carefully considered. Blocking in space, time, random effects or phylogenetic distance, while accounting for dependencies in the data, may also unwittingly induce extrapolations by restricting the ranges or combinations of predictor variables available for model training, thus overestimating interpolation errors. On the other hand, deliberate blocking in predictor space may also improve error estimates when extrapolation is the modelling goal. Here, we review the ecological literature on non-random and blocked cross-validation approaches. We also provide a series of simulations and case studies, in which we show that, for all instances tested, block cross-validation is nearly universally more appropriate than random cross-validation if the goal is predicting to new data or predictor space, or for selecting causal predictors. We recommend that block cross-validation be used wherever dependence structures exist in a dataset, even if no correlation structure is visible in the fitted model residuals, or if the fitted models account for such correlations.
Data from: Two different strategies of host manipulation allow parasites to persist in intermediate-definitive host systems
Trophically-transmitted parasites start their development in an intermediate host, before they finish the development in their definitive host when the definitive host preys on the intermediate host. In intermediate-definitive host systems, two strategies of host manipulation have been evolved: increasing the rate of transmission to the definitive host by increasing the chance that the definitive host will prey on the intermediate host, or increasing the lifespan of the parasite in the intermediate host by decreasing the predation chance when the intermediate host is not yet infectious. As the second strategy is less well studied than the first, it is unknown under what conditions each of these strategies are prevailed and evolved. We analysed the effect of both strategies on the presence of parasites in intermediate-definitive host systems with a structured population model. We show that the parasite can increase the parameter space where it can persist in the intermediate-definitive host system by using one of these two strategies of host manipulation. We found that when the intermediate host or the definitive host have life-history traits that allow the definitive host to reach large population densities, i.e. high reproduction rate of the intermediate host or high conversion efficiency of the definitive host (efficiency at which the uninfected definitive host converts caught intermediate hosts into offspring) respectively, evolving manipulation to decrease the predation chance of the intermediate host will be more beneficial than manipulation to increase the predation chance to enhance transmission. Furthermore, manipulation to decrease the predation chance of the intermediate host results in higher population densities of infected intermediate hosts than manipulation that increases the predation chance to enhance transmission. Our study shows that host manipulation in early stages of the parasite development to decrease predation might be a more frequently evolved way of host manipulation than is currently assumed.
Data from: Collective strategy for obstacle navigation during cooperative transport by ants
Group cohesion and consensus have primarily been studied in the context of discrete decisions, but some group tasks require making serial decisions that build on one another. We examine such collective problem solving by studying obstacle navigation during cooperative transport in ants. In cooperative transport, ants work together to move a large object back to their nest. We blocked cooperative transport groups of Paratrechina longicornis with obstacles of varying complexity, analyzing groups' trajectories to infer what kind of strategy the ants employed. Simple strategies require little information, but more challenging, robust strategies succeed with a wider range of obstacles. We found that transport groups use a stochastic strategy that leads to efficient navigation around simple obstacles, and still succeeds at difficult obstacles. While groups navigating obstacles preferentially move directly toward the nest, they change their behavior over time; the longer the ants are obstructed, the more likely they are to move away from the nest. This increases the chance of finding a path around the obstacle. Groups rapidly changed directions and rarely stalled during navigation, indicating that these ants maintain consensus even when the nest direction is blocked. Although some decisions were aided by the arrival of new ants, at many key points, direction changes were initiated within the group, with no apparent external cause. This ant species is highly effective at navigating complex environments, and implements a flexible strategy that works for both simple and more complex obstacles.
Data from: Correlates of alternative migratory strategies in western bluebirds
Partial migration occurs when only some animals in a population migrate. While evidence suggests that migratory strategies are partially controlled by genes, individual and environmental conditions which alter the cost‐benefit trade‐off of migration among individuals are also likely to play a role. Three hypotheses have been advanced to explain condition‐dependent partial migration: the arrival time, dominance, and body size hypotheses. In this study, we asked whether these hypotheses explained differences in migratory strategy among individuals in a partially migratory population of western bluebirds (Sialia mexicana) breeding in southern British Columbia, Canada. We used stable hydrogen isotope signatures in claw tissue to determine migratory strategy of individual bluebirds, and examined patterns of migration at both individual and population levels. The proportion of resident bluebirds varied significantly over the three years of the study, and across study sites. Several migrants switched to the resident strategy between years; however, we found no evidence of strategy switching in the opposite direction. Young birds were significantly more likely to be resident than older birds, a pattern which could arise if early arrival is particularly important for birds obtaining a territory for the first time. Furthermore, young females were the most likely of all sex‐age classes to be resident, which may reflect a survival advantage of residency for young females. Finally, birds mated assortatively by migratory strategy and isotopic evidence suggests that members of a pair often wintered in the same place. Our results provided no support for the dominance or body size hypotheses, and only limited support for the arrival time hypothesis in bluebirds. However, taken together, we suggest that our findings indicate that social factors may influence migratory strategies in this system.
Data from: Unpredictable movement as an anti-predator strategy
Prey animals have evolved a wide variety of behaviours to combat the threat of predation, and these have been generally well studied. However, one of the most common and taxonomically widespread antipredator behaviours of all has, remarkably, received almost no experimental attention: so-called 'protean' behaviour. This is behaviour which is sufficiently unpredictable to prevent a predator anticipating in detail the future position or actions of its prey. In this study, we used human 'predators' participating in 3D virtual reality simulations to test how protean (i.e. unpredictable) variation in prey movement affects participants' ability to visually target them as they move (a key determinant of successful predation). We found that targeting accuracy was significantly predicted by prey movement path complexity, although, surprisingly, there was little evidence that high levels of unpredictability in the underlying movement rules equated directly to decreased predator performance. Instead, the specific movement rules differed in how they impacted on targeting accuracy, with the efficacy of protean variation in one element depending on the values of the remaining elements. These findings provide important insights into the understudied phenomenon of protean antipredator behaviour, which are directly applicable to predator-prey dynamics within a broad range of taxa.
Data from: Life-history strategy and behavioral type: risk-tolerance reflects growth rate and energy allocation in ant colonies
Despite the recent interest in animal personality and behavioral syndromes, there is a paucity of explanations for why distinct behavioral traits should evolve to correlate. We investigate whether such correlations across apparently distinct behavioral traits may be explained by variation in life history strategy among individual ant colonies. Life history theory predicts that the way in which individuals allocate energy towards somatic maintenance or reproduction drives several distinct traits in physiology, morphology, and energy use; it also predicts that an individual's willingness to engage in risky behaviors should depend on reproductive strategy. We use Temnothorax ants, which have been shown to exhibit 'personalities' and a syndrome that may reflect risk tolerance at the colony level. We measure colonies' relative investment in growth rate (new workers produced) compared to reproductive effort (males and queens produced). Comparing sterile worker production to reproductive alate production provides a direct measure of how colonies are investing their energy, analogous to investment in growth versus reproduction in a unitary organism. Consistently with this idea, we found that behavioral type of ant colonies was associated with their life history strategy: risk-tolerant colonies grew faster and invested more in reproduction, whereas risk-averse colonies had lower growth rate but invested relatively more in workers. This provides evidence that behavioral syndromes can be a consequence of life-history strategy variation, linking the two fields and supporting the use of an integrative approach.
Data from: The alternative regenerative strategy of bearded dragon unveils the key processes underlying vertebrate tooth renewal
Deep understanding of lifelong tooth replacement is hampered by the lack of polyphyodonty or oral dentition in conventional models. Here, we show that the bearded dragon, one of the rare vertebrate species with both polyphyodont and monophyodont teeth, constitutes a key model for filling this gap, allowing direct comparison of extreme dentition types. Our developmental and high-throughput transcriptomic data of microdissected dental cells unveils the critical importance of successional dental lamina patterning, in addition to maintenance, for vertebrate tooth renewal. This patterning process happens at various levels, including directional growth but also gene expression levels, dynamics, and regionalization, and involves a large number of yet uncharacterized dental genes. Furthermore, the alternative renewal mechanism of bearded dragon dentition, with dual location of slow-cycling cells, demonstrates the importance of cell migration and functional specialization of putative epithelial stem/progenitor niches in tissue regeneration, while expanding the diversity of dental replacement strategies in vertebrates.
Data and Material for the master's thesis: Cost of code review goals and code review strategies
<p>Data and Material for the master's thesis: Cost of review goals and review strategies</p>
Data from: Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat
<p>Like many carnivore species, European wildcats (<em>Felis silvestris</em>) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck in the beginning of the 20th century. In Germany, the species has managed to survive its near-extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP genotyped and mtDNA sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, e.g., regarding population structure and the delineation of appropriate conservation units, potentially informing todays' species conservation.</p>
PDBscreen with multiple data augmentation strategies suitable for training protein-ligand interaction prediction methods
<p>PDBscreen with multiple data augmentation strategies suitable for training protein-ligand interaction prediction methods.</p> <p>PDBscreen is the training dataset for EquiScore.</p>
Data from: Trade-offs in Coordination Strategies for Networked Jazz Performances (anonymized for peer review)
<p>This dataset is associated with the paper “Trade-offs in Coordination Strategies for Networked Jazz Performances” and includes recordings of improvisations by jazz duos over a network.</p> <p><strong>Introduction:</strong></p> <p>This dataset includes data from approximately four hours of live, improvised musical duo performances over a simulated network environment collected in LOCATION REMOVED FOR PEER REVIEW. Data includes audio and video recordings of 130 individual performances, biometric data, and subjective evaluations and comments from the musicians. The primary aim of the project was to collect data via a novel performance capture and manipulation system for use in the empirical modelling of ensemble coordination strategies during networked music-making. This analysis is reported in ANONYMIZED FOR PEER REVIEW. Please refer to this publication for full details on the data collection procedure.</p> <p>The ten musicians shown in these recordings were recruited for their expertise in jazz improvisation. They were grouped into five duos consisting each of one pianist and drummer, with no musician performing in more than one duo. Participants were instructed to improvise together over a standard twelve-bar blues musical structure, but following a formula which required them to provide a clear and unambiguous pulse of continuous quarter notes. Varying amounts of network latency and jitter were simulated for each performance, consisting respectively of the minimum amount of delay applied to the live feedback a musician heard from their partner and the degree that this delay varied. The amount of latency and jitter applied to the performance is summarised in the file or directory name for each performance and is described in detail in the above publication. Note that latency and jitter conditions were presented in a random order for each duo.</p> <p><strong>Data collected includes:</strong></p> <ul> <li>audio recordings for each performance, with and without delay, collected via direct line-in (MIDI, WAV).</li> <li>video recordings, collected via high-quality webcams (MKV, AVI).</li> <li>streams of the quarter note pulse provided by each musician in a performance (MIDI).</li> <li>muxed audio-visual recordings of both participants in each performance (MP4)</li> <li>accelerometer and photoplethysmography streams, collected from arm-worn devices (TXT, duos 3-5 only)</li> <li>questionnaire responses from performers, evaluating each condition (XLSX)</li> <li>ratings of performance quality from an unbiased sample of listeners, collected during an online perceptual study (CSV)</li> </ul> <p><strong>Repository structure:</strong></p> <p><strong><em>NB: please see this section of the code documentation website (LINK REMOVED FOR PEER REVIEW) for a full description of how to recreate the analyses and models created in the paper.</em></strong></p> <p>The files <em>data.zip </em>and <em>data.z0*</em> contain all data collected from the study, APART from the perceptual study stimuli & results. To open these files, download the <em>data.zip</em> file and <em><strong>all the corresponding volumes ending in .z0 </strong></em>and open the <em>data.zip</em> file using a tool for opening multi-part zip files, such as WinRAR. <em>Do not try to open the files ending in .z0</em>, otherwise you may get a message about the data being corrupted. Inside <em>data.zip</em>, you'll see the following folders and files:</p> <ul> <li><em>avmanip_output</em>: the raw MIDI, audio, and video output from each performance <ul> <li>the subfolders are organised with a single folder per participant duo, experimental block, and condition.</li> <li>avmanip_output\trial_1\Block 1\Condition 1 - 23 05 relates to the performance of the first duo of participants in the first session of the experiment, in the first condition they encountered, with 23ms of latency and 0.5x jitter.</li> </ul> </li> <li><em>midi_bpm_cleaning</em>: the cleaned MIDI files (quarter note onset positions) <ul> <li>the subfolders are organised similarly to the <em>avmanip_output</em> folder, using the same conventions.</li> </ul> </li> <li><em>muxed_performances</em>: the combined audio-video .mp4 files from each performance <ul> <li>these files are labelled in the format: duo_session_latency_jitter_keysfmt_drumsfmt.</li> <li>muxed_performances\kdelay_ddelay\d1_s1_l23_j00_kdelay_ddelay.mp4 relates to the performance of the first duo of participants in the first session of the experiment, in the first condition they encountered, with 23ms of latency and 0.5x jitter, and with latency and jitter applied to both keys and drummer.</li> <li>for more information on recreating these videos, see the linked section of the code documentation website (LINK REMOVED FOR PEER REVIEW).</li> </ul> </li> <li><em>questionnaire_anonymized</em>: the anonymized questionnaire responses given by participants, also contained in the supplementary material of the associated paper (see preprint).</li> </ul> <p>Alongside <em>data.zip </em>and the <em>data.z0*</em> archives, there are two further loose files, <em>Database View Participant - Dashboard.csv, Database View SuccessTrial - Dashboard.csv, </em>which are the anonymized demographic and response data from the perceptual experiment, and one loose archive folder <em>perceptual_study_videos.rar</em>, which contains the stimuli used in the perceptual experiment.</p> <p><strong>Usage:</strong></p> <p>To reproduce the analysis, models, and graphs from the paper, download the code in code-analysis-modeling.rar and extract it to a new folder, then extract all the files inside <em>data.zip</em> and the two perceptual study CSV files into \data\raw. Install Python 3.10 if you don't have it already, and then open a command prompt in the root directory of the analysis code and execute the command <em>run.cmd</em><em>.</em></p> <p>The remaining code files (<em>code-perceptual-study.rar</em> and <em>code-testbed-software.rar</em>) contain the code used in the perceptual and laboratory experiments. Documentation and installation instructions are provided within each archive.</p> <p>These recordings of live, improvised duo performances are unattributed and anonymized as agreed with participants at the point of data collection. The musicians involved received a one-off, fixed payment for their time and had their travel expenses reimbursed, with funding provided by ANONYMIZED FOR PEER REVIEW. All participants consented to the use of their recordings for projects by the current authors and for these recordings to be shared with interested members of the music psychology community, with the intention of furthering academic research. The musicians did not intend that the recordings be used for commercial, artistic, or entertainment purposes, and such use is not permitted.</p> <p><strong>Citation:</strong></p> <p>If you use this dataset in your research, please follow the citation format posted on GitHub (LINK REMOVED FOR PEER REVIEW).</p> <p><strong>Contact:</strong></p> <p>ANONYMIZED FOR PEER REVIEW</p>
Implementation a Data-to-Care Strategy to Improve HIV Continuum Outcomes for Out of Care People Living With HIV (PLWH) in Ukraine
ClinicalTrials.gov study NCT05821413. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Life-history strategy and behavioral type: risk-tolerance reflects growth rate and energy allocation in ant colonies
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Data from: Are extraversion and openness indicators of a slow life history strategy?
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Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies
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Data from: Ornament size and colour as alternative strategies for effective communication in gliding lizards
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Data from: Development of sound localization strategies in children with bilateral cochlear implants
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Data from: Predator prey games in multiple habitats reveal mixed strategies in diel vertical migration
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ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.