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9,882 results for “Scale”
Input Data for "Assembly and Analysis of Cell-Scale Membrane Envelopes"
<p>Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`, which intentionally excludes large files. The full 4.8TB dataset that includes trajectories is available upon request.</p> <p>The data is split into multiple subdirectories and largely undocumented, however here are the highlights:</p> <ul> <li>The <strong>Analysis</strong> subdirectory is where the analysis in the paper lives. All other directories are related to building or running systems.</li> <li><strong>getsources.py</strong> in the main directory is the script that downloads the initial structure from MemProtMD.</li> <li><strong>transform.py</strong> builds the initial protein models from MemProtMD.</li> <li><strong>vesiclebuilder.py</strong> builds the lipid ball.</li> <li><strong>protpatchplacer.py</strong> sets up the ultra-coarse grained simulation, which is in the <strong>supercg</strong> directory.</li> <li><strong>movepatches.py</strong> takes the results from the ultra-coarse grained simulation, and builds the protein ball.</li> <li><strong>gendx.tcl</strong> generates the density maps from the protein ball.</li> <li>This is used in <strong>lipids/picklipids.py</strong>, which cuts out the pieces of the lipid that need to be removed.</li> <li>The water is added to the system with <strong>addwater/quicksolvate.sh</strong></li> <li>The system is ionized by <strong>ionize.py</strong></li> <li>And a topology is written by <strong>writetop.py</strong></li> </ul>
Replication package for: The real effects of monetary expansions: evidence from a large-scale historical experiment
<p>The replication materials contain a README file, STATA datasets and do-files. This replication package for Palma (2021) constructs the entire analysis from the data sources described in the published paper, using STATA. The replicator should expect the code to run for less than 10 minutes.</p> <p>Palma, N. (2021). The real effects of monetary expansions: evidence from a large-scale historical experiment. Review of Economic Studies, forthcoming</p> <p> </p>
Fig. 30. A scale model for the 1927 in A History Of Herpetology At The American Museum Of Natural History
Fig. 30. A scale model for the 1927 New Hall of Reptile and Amphibian Life. Compare with figures
Supplemental data for "Large-scale quantum machine learning"
<p>This data supports "Large-scale quantum machine learning" by Tobias Haug, Chris N. Self, M. S. Kim (arxiv:2108.01039) https://arxiv.org/abs/2108.01039</p> <p>Related code can be found in the GitHub repository: (https://github.com/chris-n-self/large-scale-qml). The 'studies' folder here can be dropped inside the code repository in order to run the analysis scripts.</p> <p>Both 'processed' and 'unprocessed' data is provided. Unprocessed data is the qiskit measurement results for each case study, executed on the IBM Quantum device <em>ibmq_guadalupe</em> and <em>ibmq_toronto</em>. Processed is the Gram matrix evaluated from the measurements and the data vectors needed to fit support vector machine classifiers.</p>
Fig. 2 in Acropyga and Azteca Ants (Hymenoptera: Formicidae) with Scale Insects (Sternorrhyncha: Coccoidea): 20 Million Years of Intimate Symbiosis
Fig. 2. Acropyga from Saül, French Guiana. An alate gyne carrying a mealybug while in copula.
Text-fig. 5. Fragment of the musk-ox skull from Herne-Crange. GMM A5.53. Scale bar 5 cm. in Everything Is A Question Of Time - Age Of Important Quaternary Palaeontological Finds From Westphalia
Text-fig. 5. Fragment of the musk-ox skull from Herne-Crange. GMM A5.53. Scale bar 5 cm.
Text-fig. 3. Third definite molar of the Ahlen mammoth. GMM A5N.412. Scale bar 5 cm. in Everything Is A Question Of Time - Age Of Important Quaternary Palaeontological Finds From Westphalia
Text-fig. 3. Third definite molar of the Ahlen mammoth. GMM A5N.412. Scale bar 5 cm.
An Assessment of Nonhydrostatic and Hydrostatic Dynamical Cores at Seasonal Time Scales in the Energy Exascale Earth System Model (E3SMv1)
<p>This is the companion data for the manuscript of the same title, submitted to Journal of Advances in Modeling Earth Systems on 09/03/2021. </p> <p><strong>summer: </strong>this folder contains part of the model outputs I ran on NERSC Cori in 2020-2021 corresponding to the summer simulations in the manuscript.</p> <p><strong>winter: </strong>this folder contains part of the outputs I ran on NERSC Cori in 2020-2021 corresponding to the winter simulations in the manuscript.</p> <p><strong>ne256: </strong>this folder contains part of the outputs I ran on NERSC Cori in 2021 corresponding to the ne256 simulations in the manuscript.</p> <p><strong>bubble</strong>: this folder includes the namelists used in the rising bubble experiments.</p> <p><strong>script: </strong>this folder includes an example of a script to generate the realistic SCREAM simulation </p> <p> </p> <p>Unfortunately, model outputs are too large (~ 30 TB). Therefore, I only provide mean data, used directly to generate figures, in this repository. All model output are archived on tape at NERSC. </p> <p>For more details, refer to the manuscript, or contact me (wrliu@ucdavis.edu). </p>
Fig. 6 in Identification of the stages of ovarian maturation of the Argentine hake Merluccius hubbsi Marini, 1933 (Teleostei: Merlucciidae): advantages and disadvantages of the use of the macroscopic and microscopic scales
Fig. 6. Merluccius hubbsi: oocyte with complete vitellogenesis (1.5mm length field).
Fig. 4 in Identification of the stages of ovarian maturation of the Argentine hake Merluccius hubbsi Marini, 1933 (Teleostei: Merlucciidae): advantages and disadvantages of the use of the macroscopic and microscopic scales
Fig. 4. Merluccius hubbsi: oocyte in cortical alveolar stage (arrow) (1.5mm length field).
Fig. 3 in Identification of the stages of ovarian maturation of the Argentine hake Merluccius hubbsi Marini, 1933 (Teleostei: Merlucciidae): advantages and disadvantages of the use of the macroscopic and microscopic scales
Fig. 3. Merluccius hubbsi: oocyte in perinucleolar stage (center) (0.16mm length field).
Fig. 8 in Identification of the stages of ovarian maturation of the Argentine hake Merluccius hubbsi Marini, 1933 (Teleostei: Merlucciidae): advantages and disadvantages of the use of the macroscopic and microscopic scales
Fig. 8. Merluccius hubbsi: postovulatory follicle (arrow) (1.5mm length field).
Fig. 7 in Identification of the stages of ovarian maturation of the Argentine hake Merluccius hubbsi Marini, 1933 (Teleostei: Merlucciidae): advantages and disadvantages of the use of the macroscopic and microscopic scales
Fig. 7. Merluccius hubbsi: oocyte with nuclear migration (1.5mm length field).
Perl et al 2022 Substantial variability in morphological scaling among bumblebee colonies
<p>Data and R code for the submitted manuscript Perl et al 2021 Substantial variability in morphological scaling among bumblebee colonies</p>
Figure 2 in Variation in elasmoid fish scale patterns is informative with regard to taxon and swimming mode
Figure 2. Landmark definitions.
Data and code for the manuscript: "An ecological explanation for hyperallometric scaling of reproduction"
<p>Code, data, and data objects underlying the analyses presented in the manuscript "An ecological explanation for hyperallometric scaling of reproduction".</p> <p>A version of the manuscript is available on bioRxiv: https://doi.org/10.1101/2021.03.12.435090</p> <p>Abstract for the manuscript:</p> <p>"In wild populations, large individuals have disproportionately higher reproductive output than smaller individuals. Some theoretical models explain this pattern – termed reproductive hyperallometry – by individuals allocating a greater fraction of available energy towards reproductive effort as they grow. Here, we propose an ecological explanation for this observation: differences between individuals in rates of resource assimilation, where greater assimilation causes both increased reproduction and body size, resulting in reproductive hyperallometry at the level of the population. We illustrate this effect by determining the relationship between size and reproduction in wild and lab-reared Trinidadian guppies. We show that (i) reproduction increased disproportionately with body size in the wild but not in the lab, where resource competition was eliminated; (ii) in the wild, hyperallometry was greatest during the wet season, when resource competition is strongest; and (iii) detection of hyperallometric scaling of reproduction at the population level was inevitable if individual differences in assimilation were ignored. We propose that ecologically-driven variation in assimilation – caused by size-dependent resource competition, niche expansion, and chance – contributes substantially to hyperallometric scaling of reproduction in natural populations. We recommend that mechanistic models incorporate such ecologically-caused variation when seeking to explain reproductive hyperallometry.'</p> <p>The zip file contains:</p> <p>1. A single R script for running the analyses, generating the results, and producing the figures given in the manuscript </p> <p>- size_reproduction_scaling_lab_wild.R </p> <p>2. Two .csv files containing the wild and lab datasets used in the study:</p> <p>- wild_guppy_data_81-87.csv (the wild dataset)<br> - senecence_long_data.csv (the lab dataset)</p> <p>3. A folder containing 14 model objects. These are the models produced by running the R script. These are provided to save the user time. The model object names correspond to the models described in Table 1 of the manuscript.</p> <p>4. A READ_ME.txt file.</p>
Data and codes to replicate the analysis in: The spatial ecology of conflicts: Unravelling patterns of wildlife damage at multiple scales
<p><span><span>Human encroachment into natural habitats is typically followed by conflicts derived from wildlife damages to agriculture and livestock. Spatial risk modelling is a useful tool to gain understanding of wildlife damage and mitigate conflicts. Although resource selection is a hierarchical process operating at multiple scales, risk models usually fail to address more than one scale, which can result in the misidentification of the underlying processes. Here, we addressed the multi-scale nature of wildlife damage occurrence by considering ecological and management correlates interacting from household to landscape scales. We studied brown bear (<i>Ursus arctos</i>) damage to apiaries in the North-eastern Carpathians as our model system. Using generalized additive models, we found that brown bear tendency to avoid humans and the habitat preferences of bears and beekeepers determine the risk of bear damage at multiple scales. Damage risk at fine scales increased when the broad landscape context also favoured damages. Furthermore, integrated-scale risk maps resulted in more accurate predictions than single-scale models. Our results suggest that principles of resource selection by animals can be used to understand the occurrence of damages and help mitigate conflicts in a proactive and preventive manner. </span></span></p>
Effects of a Vibro-Tactile P300 Based Brain-Computer Interface on the Coma Recovery Scale-Revised in Patients With Disorders of Consciousness
<p>Persons diagnosed with disorders of consciousness (DOC) typically suffer from motor and cognitive disabilities. Recent research has shown that non-invasive brain-computer interface (BCI) technology could help assess these patients’ cognitive functions and command following abilities. 20 DOC patients participated in the study and performed 10 vibro-tactile P300 BCI sessions over 10 days with 8–12 runs each day. Vibrotactile tactors were placed on the each patient’s left and right wrists and one foot. Patients were instructed, via earbuds, to concentrate and silently count vibrotactile pulses on either their left or right wrist that presented a target stimulus and to ignore the others. Changes of the BCI classification accuracy were investigated over the 10 days. In addition, the Coma Recovery Scale-Revised (CRS-R) score was measured before and after the 10 vibro-tactile P300 sessions. In the first run, 10 patients had a classification accuracy above chance level (>12.5%). In the best run, every patient reached an accuracy ≥60%. The grand average accuracy in the first session for all patients was 40%. In the best session, the grand average accuracy was 88% and the median accuracy across all sessions was 21%. The CRS-R scores compared before and after 10 VT3 sessions for all 20 patients, are showing significant improvement (<em>p</em> = 0.024). Twelve of the twenty patients showed an improvement of 1 to 7 points in the CRS-R score after the VT3 BCI sessions (mean: 2.6). Six patients did not show a change of the CRS-R and two patients showed a decline in the score by 1 point. Every patient achieved at least 60% accuracy at least once, which indicates successful command following. This shows the importance of repeated measures when DOC patients are assessed. The improvement of the CRS-R score after the 10 VT3 sessions is an important issue for future experiments to test the possible therapeutic applications of vibro-tactile and related BCIs with a larger patient group.</p>
Dataset (n=1671) of the publication "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes"
<p>The excel file contains the replies of small-scale private forest owners in Lower Saxony, Germany, to certain questions of a survey analyzed within the following publication: "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes”.<br> <br> The questions included in this dataset cover their objectives, management activities, attitudes and forest stand structures. Further details can be found in the second sheet of the file called “Code explanation”.<br> <br> More information about the methods of data collection can be found in the before-mentioned publication.</p>
Large-scale drivers of relationships between soil microbial properties and organic carbon across Europe
<p>The aim of this study was to quantify direct and indirect relationships between soil microbial community properties (potential basal respiration, microbial biomass) and abiotic factors (soil, climate) in three major land-cover types.</p> <p>Location: Europe</p> <p>Time period: 2018</p> <p>Major taxa studied: Microbial community (fungi and bacteria)</p> <p>We collected 881 soil samples from across Europe in the framework of the Land Use/Land Cover Area Frame Survey (LUCAS). We measured potential soil basal respiration at 20ºC and microbial biomass (substrate-induced respiration) using an O2-microcompensation apparatus. Climate and soil data were obtained from previous LUCAS surveys and online databases. Structural equation modeling (SEM) was used to quantify relationships between variables, and equations extracted from SEMs were used to create predictive maps. Fatty acid methyl esters were measured in a subset of samples to distinguish fungal from bacterial biomass. Soil microbial properties in croplands were more heavily affected by climate variables than those in forests. Potential soil basal respiration and microbial biomass were correlated in forests but decoupled in grasslands and croplands, where microbial biomass depended on soil carbon. Forests had a higher ratio of fungi to bacteria than grasslands or croplands. Soil microbial communities in grasslands and croplands are likely carbon-limited in comparison with those in forests, and forests have a higher dominance of fungi indicating differences in microbial community composition. Notably, the often already-degraded soils of croplands could be more vulnerable to climate change than more natural soils. The provided maps show potentially vulnerable areas that should be explicitly accounted for in coming management plans to protect soil carbon and slow the increasing vulnerability of European soils to climate change.</p>
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.