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10,735 results for “dependence”
The effects of visual distractors on serial dependence
<p>Datasets and analysis script for two experiments on behavioral serial dependence, using discrimination & orientation adjustment tasks.<br> The datasets are used and described in:<br> Title: "The effects of visual distractors on serial dependence"<br> Authors: Christian Houborg, David Pascucci, Ömer Daglar Tanrikulu & Árni Kristjánsson<br> Year: 2023<br> Journal: Journal of Vision<br> The link and DOI to the related paper will be available soon.</p>
Dependency networks of PyPI, npm, CRAN and Bioconductor repositories
<p>A set of datasets with a list of dependencies from the software repositories PyPI, npm, CRAN and Bioconductor.</p>
Mu-opioid receptor-dependent changes in social reward across adolescence in mice
<p>Datasets used in publication "Mu-opioid receptor-dependent changes in social reward across adolescence in mice" (in preparation). The social conditioned place preference data were pre-processed before statistical analysis. Three diffrent datatables with the same dataset reflect the steps of the pre-processing:</p> <p>1. Animals that spent more than 70% of the pretest time in one of the contexts were excluded (datable "30_70%")</p> <p>2. Outliers were identified using Grubbs test, and removed (datatable "no_outlier")</p> <p>3. In cases where the final number of animals conditioned in each context was not equal (due to an unequal number of animals passing the 70% criterion or unequal number of animals in the litter), we pseudorandomly trimmed the larger group using a Python script (file number 10). The exception from completely random selection was introduced to preserve a mean 50% initial context preference during the pretest</p>
A Complement Atlas identifies interleukin 6 dependent alternative pathway dysregulation as a key druggable feature of COVID-19.
<p>Improvements in COVID-19 treatments, especially for the critically ill, require deeper understanding of the mechanisms driving disease pathology. The complement system is a crucial component of innate host defense, but can also contribute to tissue injury. Although all complement pathways have been implicated in COVID-19 pathogenesis, the upstream drivers and downstream effects on tissue injury remain poorly defined. We demonstrate that complement activation is primarily mediated by the alternative pathway, and we provide a comprehensive atlas of the complement alterations around the time of respiratory deterioration. Proteomic and single-cell sequencing mapping across cell types and tissues reveals a division of labor between lung epithelial, stromal, and myeloid cells in complement production, in addition to liver-derived factors. We identify IL-6 and STAT1/3 signaling as an upstream driver of complement responses, linking complement dysregulation to approved COVID-19 therapies. Furthermore, an exploratory proteomic study indicates that inhibition of complement C5 decreases epithelial damage and markers of disease severity. Collectively, these results support complement dysregulation as a key druggable feature of COVID-19.</p>
Supplementary data for the article "Head and dependent marking and dependency length in possessive noun phrases: a typological study of morphological and syntactic complexity"
<p>This material contains the Supplementary material (including the R-scripts) of the following article. Please cite the article when using the data.</p> <p>Sinnemäki, Kaius and Haakana, Viljami. 2023. Head and dependent marking and dependency length in possessive noun phrases: a typological study of morphological and syntactic complexity. <em>Linguistics Vanguard</em> 9(s1). 45-57. <a href="https://doi.org/10.1515/lingvan-2021-0074">https://doi.org/10.1515/lingvan-2021-0074</a></p>
Diversity loss from multiple interacting disturbances is regime-dependent
<p>Data and R code for 'Diversity loss from multiple interacting disturbances is regime-dependent'.</p> <p>Information about the files can be found in the ._README.txt file.</p>
Supplementary files for the manuscript "Elevation-dependent periglacial and paraglacial processes modulate tectonically-controlled erosion of the Western Southern Alps, New Zealand", submitted to JGR Earth Surface
<p>This repository contains supplementary files to the manuscript ""Elevation-dependent periglacial and paraglacial processes modulate tectonically-controlled erosion of the Western Southern Alps, New Zealand" submitted to JGR: Earth Surface. It contains: </p> <p>- The Matlab script used to find the optimal distance-from-fault and elevation windows ("elevation_distance_window_optimization"), and 3 text files used for input in this script ("data_erates" contains the erosion rates, "data_elev" the number of pixels in each elevation bin, "data_distAF" the number of pixels in each distance-from-fault bin). </p> <p>- An Excel spreadsheet with the same information that the input text files contain, but specifiying the elevation or distance from fault bin values ("elevation and distance from fault with bins")</p> <p>- A shapefile of catchment outlines ("WSAcatch") for the catchments sampled for CRN denudation rates</p> <p>- Raw CRN data ("Table 2_new_CRN_data")</p> <p>- Excel spreadsheet with the compilation of themochronometric cooling ages used in the age2exhume code (van der Beek & Schildgen, 2023; <a href="https://doi.org/10.5281/zenodo.7341603">https://doi.org/10.5281/zenodo.7341603</a>).</p> <p>CRN data and catchment outlines will also be uploaded to the OCTOPUS database (<a href="https://octopusdata.org/">https://octopusdata.org/</a>) after manuscript acceptance.</p>
Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity
<p>The dataset contains bulk RNA-seq read count matrices of NK cells from healthy donors after 48 h of co-culture with hepatitis D virus infected and non-infected HepG2-hNTCP cells. The samples are described in the table RNA-seq_samples.xls that is included with the count matrices. Further details are given in the publication associated with this dataset (Groth et al., <i>Front Immunol</i>, 2023, https://doi.org/10.3389/fimmu.2023.1287367).</p>
Data for “Herbivory damage but not plant disease under experimental warming is dependent on weather for three subalpine grass species”, Rocky Mountain Biological Laboratory, Gothic, Colorado, 2015-2017.
Both theory and prior studies predict that climate warming should increase attack rates by herbivores and pathogens on plants. However, past work has often assumed that variation in abiotic conditions other than temperature (e.g., precipitation) do not alter warming responses of plant damage by natural enemies. Studies over short time periods span low variation in weather, and studies over long-time scales often neglect to account for fine-scale weather conditions. Here, we used a 20+ year field warming experiment to investigate if warming affects herbivory and disease are dependent on variation in ambient weather observed over three years. We studied three common grass species in a subalpine meadow in the Colorado Rocky Mountains, USA. We visually estimated herbivory and disease every two-weeks during the growing season and evaluated weather conditions during the previous two- or four-week time interval (two-week average air temperature, two- and four-week cumulative precipitation) as predictors of the probability and amount of damage. Herbivore attack was 13% more likely and amount of damage was 29% greater in warmed plots than controls across the focal species, but warming treatment had little affect on plant disease. Herbivory presence and damage increased the most with experimental warming when preceded by wetter, rather than drier, fine-scale weather, but preceding ambient temperature did not strongly interact with elevated warming to influence herbivory. Disease presence and damage increased, on average, with warmer weather and more precipitation regardless of warming. The effect of warming over reference climate on herbivore damage is dependent on and amplified by fine-scale weather variation, suggesting more boom-and-bust damage dynamics with increasing climate variability. However, the mean effect of regional climate change is likely reduced monsoon rainfall, for which we predict a reduction in insect herbivore damage. Plant disease was generally unrelated
Carbon quality regulates the temperature dependence of aquatic ecosystem respiration
Lakes are undergoing a variety of changes that may alter their role in the global carbon cycle. Lake temperatures are increasing at the same time that lakes in many regions are experiencing long-term increases in dissolved organic carbon (DOC) concentrations. The balance between rates of ecosystem respiration (ER) and gross primary production (GPP) is an important determinant of CO2 outgassing from lakes and thus it is important to understand factors regulating ER rates in these systems. Temperature is known to regulate rates of ER, but other factors have the potential to modulate this relationship. One such regulator may be the quality of the dissolved organic matter (DOM) in the system. Theory suggests that ER may increase more with temperature in lakes dominated by allochthonous, refractory material than in systems dominated by more autochthonous DOM. To test this theory, we conducted a mesocosm study where half of the mesocosms received water from a naturally occurring autochthonous DOM source and the other half from an allochthonous DOM source. We monitored water temperature and dissolved oxygen concentrations in each mesocosm using in-situ high frequency DO sensors. After 27 days we used this data to calculate daily ER for each mesocosm. We then related daily ER to mean nighttime temperature and tested whether the relationship was different in the two DOM treatments. Treatments dominated by allochthonous DOM had a greater temperature dependence of respiration than those dominated by autochthonous DOM. These results suggest that as lake temperatures continue to increase, ER will increase more in lakes dominated by allochthonous DOM than those dominated by autochthonous DOM.
Scale-dependent interactions between tree canopy cover and impervious surfaces reduce daytime urban heat during summer
As cities warm and the need for climate adaptation strategies increases, a more detailed understanding of the cooling effects of land-cover across a continuum of spatial scales will be necessary to guide management decisions. We asked how tree canopy cover and impervious surface cover interact to influence daytime and nighttime summer air temperature, and how effects vary with the spatial scale at which land-cover data are analyzed (10, 30, 60 and 90-m radii). A bicycle-mounted measurement system was used to sample air temperature every 5 m along 10 transects (about 7 km length, sampled 3-12 times each) spanning a range of impervious and tree canopy cover (0 to 100%, each) in a mid-sized city in the Upper Midwest, USA. Variability in daytime air temperature within the urban landscape averaged 3.5 degreeC (range 1.1 to 5.7 degreeC). Temperature decreased nonlinearly with increasing canopy cover, with the greatest cooling when canopy cover exceeded 40%. The magnitude of daytime cooling also increased with spatial scale, and was greatest at the size of a typical city block (60-90 m). Daytime air temperature increased linearly with increasing impervious cover, but the magnitude of warming was less than the cooling associated with increased canopy cover. Variation in nighttime air temperature averaged 2.1C (range 1.2 to 3.0 degreeC), and temperature increased with impervious surface. Effects of canopy were limited at night; thus, reduction of impervious surfaces remains critical for reducing nighttime urban heat. Results suggest strategies for managing urban land-cover patterns to enhance resilience of cities to climate warming.
Groundwater dependence of riparian woodlands and the disrupting effect of anthropogenically altered streamflow
This dataset includes data inputs from public sources, scripts and outputs to evaluate riparian vegetation reliance on groundwater across California from 2015 to 2020. This dataset accompanies the Rohde et al. paper titled, Groundwater dependence of riparian woodlands and the disrupting effect of anthropogenically altered streamflow. The provided scripts process groundwater, vegetation, climate, and streamflow input data from various sources. Further, all output data and statistical analyses are included.
MCR LTER: Coral Reef: Density-dependence data for Edmunds, et al., Ecology 2018
This dataset contains coral cover data describing the context within which denisty-dependence (DD) was measured on the island of Moorea, French Polynesia, including data describing the benthic community, diameters of Pocillopora spp. measured in photoquadrats, surveys of corals and recruits. These data correspond to figures 1 through 3 in the manuscript by PJ Edmunds, L. Bramanti, and H.R. Nelson, 'Density-dependence mediates coral community structure', Ecology, 99(11), 2018, pp. 2605-2613. This ata set was revised on 27 November 2018. The data managed for Fig. 3 were missing values for two quadrats used in the analysis (quadrats 24 and 9). In this data revision, the values from the missing quadrats have been included. The reefs of Mo’orea, French Polynesia, provide the opportunity to study DD of coral population growth, because coral assemblages in this location responded to declines in abundance with high recruitment and an increase in cover during which recruitment of pocilloporid corals was inversely associated with density. This study tests for DD in this system, first, by describing the context within which it operates: coral cover changed from 46% in 2005, to less than 1% in 2010 following an outbreak of a corallivorous sea star and a cyclone, and then increased to 74% by 2017, in large part through inverse density- associated pocilloporid recruitment. Second, a test for DD of recruitment was conducted by decreasing Pocillopora spp. cover from 33% to 19%: one year later, the density of Pocillopora spp. recruits was 1.65-fold higher in the low versus high cover treatment. Finally, the effects of DD were investigated by comparing simulated and empirical distributions of pocilloporid colonies: as predicted by DD, small colonies were randomly distributed, while large colonies were uniformly distributed. Together these results demonstrate DD of population regulation for Pocillopora spp. corals, thus revealing the potential importance of this ecological principle i
SBC LTER: Reef: The size-dependent functional response of lobster foraging on purple urchin
These data summarize the results of a size-dependent functional response experiment in which California spiny lobster (Panulirus interruptus) foraged on purple urchins (Strongylocentrotus purpuratus). Lobster of different sizes foraged on one of three different size classes of urchins at 4-6 different densities of urchin. Data is used to support manuscript: DiFiore, B.P. and A.C. Stier. 2023. Variation in body size drives spatial and temporal variation in lobster-urchin interaction strength. Journal of Animal Ecology
Cataloging Dependency Injection Anti-Patterns in Software Systems
<p><strong>Background</strong> Dependency Injection (DI) is a commonly applied mechanism to decouple classes from their dependencies in order to provide better modularization of software. In the context of Java, the availability of a DI specification and popular frameworks, such as Spring, facilitate DI usage in software projects. However, bad DI implementation practices can have negative consequences, such as increasing coupling, hindering the achievement of DI's main goal. Even though the literature suggests the existence of DI anti-patterns, there is no detailed documentation of such bad practices. Moreover, there is no evidence on their occurrence and perceived usefulness from the developer's point of view. </p> <p><strong>Aims</strong> Our goal is to review the reported DI anti-patterns in order to analyze their completeness and to propose and evaluate a novel catalog of Java DI anti-patterns. </p> <p><strong>Method</strong> We propose a catalog containing twelve Java DI anti-patterns. We selected four open-source and two closed-source software projects that adopt a DI framework and developed a tool to statically analyze the occurrence of the candidate DI anti-patterns within their source code. Also, we conducted a survey through face to face interviews with three experienced developers that regularly apply DI. We extended the survey in order to gather the perception of a set of fifteen expert and novice developers through an online questionnaire. </p> <p><strong>Results</strong> At least nine different DI anti-patterns appeared frequently in the analyzed projects. In addition, the feedback received from the developers confirmed the relevance of the catalog. Besides, the respondents expressed their willingness to refactor instances of anti-patterns from source code.</p> <p><strong>Conclusions</strong> The catalog contains Java DI anti-patterns that occur in practice and are useful. Sharing it with practitioners may help them to avoid such anti-patterns.</p>
The Updated Maven Central Dependency Graph
<p><strong>Maven Central Dependency Graph</strong></p> <p>This is an updated version of the artifact at https://zenodo.org/record/1489120</p> <p>The Maven dependency graph is an open dataset of Maven Central artifacts, their dependencies, as well as other relationships. Its main intent is to domesticate the wild within and around the Maven central ecosystem, in particular, and JVM-based libraries at large, making it more harnessable to both academics and industry. It is intended to answer high-level research questions concerning artifacts releases, evolution, and usage trends over time. It can also be used to assist researchers in selecting relevant datasets, among the mass of existing software artifact, for assessing particular empirical software engineering challenges. The complexity of these questions can range from simple pattern matching to advanced big data analysis and machine learning techniques.</p> <p>The accompanying paper to this dataset is has been accepted for publication in the proceedings of the International Conference on Mining Software Repositories 2019 and has received the MSR 2019 Data Showcase Award. This paper is available for download on <a href="https://arxiv.org/abs/1901.05392">arXiv</a>.</p> <p><strong>What is new?</strong></p> <p>The previous version included artifacts until September 6, 2018.<br> This version includes artifacts until September 10, 2019.</p> <p>This version includes license information as well as information about associated code repository.</p> <p>This version contains 4 201 392 artifacts (version) of 308116 distinct libraries from 47481 distinct group IDs.</p> <p>Note 33 638 artifacts represents version ranges and note actual versions. They can be filtered out by excluding version containing ','.</p> <p><br> <strong>Usage</strong></p> <p>Usage:</p> <ul> <li> Download the archive from zenodo</li> <li> Decompress the archive</li> </ul> <pre><code class="language-bash"># Pull the image and start the container docker run -d --name mm-neo4j -p 7474:7474 -p 7687:7687 -v /path/to/neo4j-data:/data --env=NEO4J_dbms_memory_heap_max__size=8g lyadis/mm-neo4j:latest</code></pre> <ul> <li> Open http://127.0.0.1:7474/browser/ in your browser</li> </ul>
Granulosa cell transcriptome data from four different time points before and up to 48 hours after PMSG induction to GTH-depend phase in mice
<p>GTH-dependent follicle development begins with small antrum follicles and ends with preovulatory follicles. GTH-dependent follicle development is mainly controlled by gonadotropins, and the development time is 48h. The purpose of this study is to monitor the changes in gene expression of granulosa cells at four different time points during the GTH-dependent phase to increase our understanding of human GTH-dependent follicle development.Granulosa cell mRNA profiles of GTH-depend phase in mice.There are 12 samples represented four time points 0h (n=3), 12h (n=3), 24h (n=3) and 48h (n=3)</p>
Structural dynamics of DNA depending on methylation pattern: Simulation dataset
<p>Dataset of molecular dynamics simulations of double-stranded DNA<br> (repeats of CpG dinucleotides with regular patterns of methylation).</p> <p>- Input: Parameters and initial structures<br> - Output: Trajectories</p> <p>NAMD 2.13 (multi-core with CUDA) was used for the simulations.</p>
Data for "First Principle Calculation on Pressure Dependent Yielding in Solute Strengthened Aluminium Alloys"
<p>The dataset contains the DFT results which is the basis for the results and discussions in the related article, "First principle calculations of pressure dependent yielding in solute strengthened aluminium alloys". The details of the DFT calculations are written in the article.</p> <p>The two different file-name conventions are explained below.</p> <p>OUTCAR_Al_R1_HSP<br> OUTCAR_X_HSP_POS</p> <p>Al-files represent the pure aluminium models, showing the dislocation energies at various hydrostatic pressures. X (Cu, Si, Mg) represents the solute specie in the full model showing the configurational energy. R1 is the radius of the relaxed region. HSP represents the superimposed hydrostatic pressure, which is given by (-560+HSP*80) MPa. POS is the atomic index in the OUTCAR files, where the solute is substituted.</p>
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
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.