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342 results for “Proxies”
PhanSST - A global database of Phanerozoic sea surface temperature proxy data
<p>Beta pre-publication release of the PhanSST database of globally distributed Phanerozoic paleo-sea surface temperature proxy data. The database is currently accepted at Scientific Data.</p>
Different proxies, different stories? Imperfect correlations and different determinants of fitness in bighorn sheep
<p>Measuring individual fitness empirically is required to assess selective pressures and predict evolutionary changes in nature. There is, however, little consensus on how fitness should be empirically estimated. As fitness proxies vary in their underlying assumptions, their relative sensitivity to individual, environmental, and demographic factors may also vary. Here, using a long-term study, we aimed at identifying the determinants of individual fitness in bighorn sheep (<em>Ovis</em> <em>canadensis</em>) using seven fitness proxies. Specifically, we compared four-lifetime fitness proxies: lifetime breeding success, lifetime reproductive success, individual growth rate, and individual contribution to population growth, and three multi-generational proxies: number of granddaughters, individual descendance in the next generation, and relative genetic contribution to the next generation. We found that all proxies were positively correlated, but the magnitude of the correlations varied substantially. Longevity was the main determinant of most fitness proxies. Individual fitness calculated over more than one generation was also affected by population density and growth rate. Because they are affected by contrasting factors, our study suggests that different fitness proxies should not be used interchangeably as they may convey different information about selective pressures and lead to divergent evolutionary predictions. Uncovering the mechanisms underlying variation in individual fitness and improving our ability to predict evolutionary change might require the use of several, rather than one, proxy of individual fitness.</p>
Second-line drug resistance markers as proxy indicators of sputum culture conversion for samples tested in Uganda
<p>Increased TB disease burden arises as a result of low treatment success rates stemming from the emergence of second-line drug (SLD) resistance. We aimed at determining the usefulness of SLD resistance markers as proxy indicators of time to sputum culture conversion; a renowned predictor of Tuberculosis (TB) treatment outcome, among SLD-resistant TB patients tested at the Uganda National TB Reference Laboratory (NTRL). A cross-sectional study was conducted on 72 bacteriologically confirmed SLDR TB patients with datasets including culture conversion time and second-line probe assay mutation profiles between 01/06/2017 and 31/12/2019. The data were then imported into STATA v15 for descriptive statistical analysis, Univariate cox proportional hazard model analysis and Kaplan-Meier survival curves at a 5% level of significance; p-value ≤ 0.05. Results indicate the median time was achieved at 3 (0–12) months across the studied patients. The <em>rrs</em> G1484T mutation associated with conferring drug resistance to aminoglycosides was observed to have the shortest median conversion time of 1.5 months and the longest by the <em>gryB</em> E540D at 5 months. A single mutation in the <em>gryA</em> gene locus showed higher converted proportions 70.8% (58.9–81.0) than those that had two 8.3% (3.1–17.3) or three 2.7% (0.3–10.0) mutations. We conclude that the studied second-line drug resistance markers had no statistically significant association with the time to sputum culture conversion, although increased drug resistance levels reduced the converted proportions and stressed the need to utilize molecular diagnostics data to better comprehend proxy indicators of SLD-resistant tuberculosis management.</p>
Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death
<p>This dataset accompanies the article entitled <em>Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death</em>, published in ACS Cent. Sci. (<a href="https://doi.org/10.1021/acscentsci.2c01078">https://doi.org/10.1021/acscentsci.2c01078</a>).</p> <p><strong>subboxes_overview.xlsx: </strong>This spreadsheet contains information about the protein composition of each sub-box.</p> <p><strong>BOX_GEOMETRIES.zip: </strong>Starting structures (saved in Gromos87 .gro format) used for the production runs of the all-atom sub-boxes.</p> <p><strong>PROTEIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual proteins, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the protein numbering corresponds to the subboxes_overview.xlsx spreadsheet.</p> <p><strong>CHAIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet.</p> <p><strong>CHAIN_ROTACF.zip: </strong>Text files containing the rotational autocorrelation functions for individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds; the autocorrelation functions were calculated using a second-order Legendre polynomial. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet.</p>
Traumatic events, post-traumatic stress disorder, and proxy measures for central sensitization in chronic pain patients of a German university outpatient pain clinic
<p>This dataset was acquired at Hannover Medical School, Hannover, Germany. The study complied with the Declaration of Helsinki, and was approved by the local ethics committee. All subjects gave written informed consent, and consent to use their data anonymously for research purposes. The study was registered at ClinicalTrials.gov (NCT05190367).</p> <p>Between February 2019 and July 2020, 914 patients who visited our outpatient pain department gave written consent to use their routinely collected data anonymously for research purposes. Participants were divided into four groups depending on their trauma severity: (1) no trauma; (2) accidental trauma (e.g. illness, accident, natural disaster); (3) interpersonal trauma (e.g. assault, rape, war); (4) PTSD (diagnosed according to ICD-10). Patients fulfilling two or more categories were assigned to the highest group.</p> <p>Data were collected using the SymptomMapper application [1]. Participants provided information about their traumas, current pain intensity (visual analogue scale, VAS (0-100) [2]), mean and maximal pain in the last 4 weeks (VAS (0-100)), sleep impairment (VAS (0-100)), acceptable pain (VAS (0-100)), pain disability index (PDI [3]), pain area (digital drawings), pain widespreadness (widespread pain index, WPI [4], derived from drawings), stress (patient health questionnaire, German version, PHQ-D [5]), anxiety (PHQ-D), depression (PHQ-D), and somatization symptoms (PHQ-D).</p> <p>This dataset contains the raw data as well as necessary scripts for reproducing the results of this study.</p> <p> </p> <p>References<br> ##########</p> <p>[1] Neubert TA, Dusch M, Karst M, Beissner F. Designing a Tablet-Based Software App for Mapping Bodily Symptoms: Usability Evaluation and Reproducibility Analysis. JMIR Mhealth Uhealth 2018;6(5):e127.<br> [2] Dworkin RH, Turk DC, Farrar JT et al. Core outcome measures for chronic pain clinical trials: IMMPACT recommendations. Pain 2005;113(1):9-19.<br> [3] Pollard CA. Preliminary Validity Study of the Pain Disability Index. Percept Mot Skills 1984;59(3): 974.<br> [4] Wolfe F, Clauw DJ, Fitzcharles MA et al. The American College of Rheumatology Preliminary Diagnostic Criteria for Fibromyalgia and Measurement of Symptom Severity. Arthritis Care Res 2010;62(5):600-10.<br> [5] Löwe B, Spitzer RL, Zipfel S, Herzog W. Gesundheitsfragebogen für Patienten (PHQ-D). Manual und Testunterlagen (second edition). Pfizer 2002.</p>
EMIC-driven precipitation events observed by ELFIN, using proton precipitation as a proxy for EMIC waves
<p>This dataset lists the time intervals of the precipitation events observed by ELFIN nearby proton precipitation (a proxy for EMIC waves). This dataset is analyzed in the paper "Electron Precipitation Observed by ELFIN Using Proton Precipitation as a Proxy for Electromagnetic Ion Cyclotron (EMIC) Waves", currently under review in Geophysical Research Letters.</p>
A novel proxy to examine interspecific phosphorus facilitation between plant species
<p>Resource complementarity can contribute to enhanced ecosystem functioning in diverse plant communities, but the role of facilitation in the enhanced complementarity is poorly understood.</p> <p>Here, we use leaf manganese concentration ([Mn]) as a proxy for rhizosheath carboxylate concentration to explore novel mechanisms of complementarity mediated by phosphorus (P) facilitation.</p> <p>In pot experiments, we showed that mixtures involving <em>Carex korshinskyi</em>, an efficient P-mobilizing species, exhibited greater biomass and relative complementarity effect than combinations without <em>C. korshinskyi </em>on P-deficient soils. Compared with monocultures, leaf [Mn] and [P] of species that are inefficient at P mobilization increased by 27 and 21% when grown with <em>C. korshinskyi</em> (i.e. interspecific P facilitation via carboxylates) rather than next to another inefficient P-mobilizing species. This experimental result was supported by a meta-analysis including a range of efficient P-mobilizing species. Phosphorus facilitation enhanced the relative complementarity effect in low-P environments, related to a greater change in several facilitated species of their root morphological traits relative to those in monoculture.</p> <p>Using leaf [Mn] as a proxy, we highlight a vital mechanism of interspecific P facilitation via belowground processes and provide evidence for the pivotal role of P facilitation mediated by the plasticity of root traits in biodiversity research.</p>
20th century winds, pressure, and temperature around Antarctica from single-proxy data assimilation
<p>Please cite <a href="https://doi.org/10.5194/tc-2023-16">O'Connor et al., 2023</a> (preprint available in The Cryosphere Discussions) when using these single-proxy reconstruction datasets. The reconstructions generated using all proxy data (O'Connor et al., 2021) are archived <a href="https://zenodo.org/record/5507607">here</a>.</p> <p>This dataset contains four sets of single-proxy reconstructions of annually resolved zonal surface wind (us), sea level pressure (psl), and surface temperature (tas) anomalies around Antarctica over the period 1900 to 2005 CE. The reconstructions were generated using the Last Millennium Reanalysis data assimilation framework (<a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2016JD024751">Hakim et al., 2016</a>), adapted for Antarctic atmospheric reconstructions following the methods from <a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GL095999">O'Connor et al., 2021</a>. The reconstructions were generated using the same proxy databases and methods as outlined in O'Connor et al., 2021, but we only assimilate proxies from ice cores or coral records in each reconstruction.</p> <p>This dataset contains four sets of reconstructions, based on two different climate model simulation priors and either ice cores or coral assimilated:</p> <ol> <li>CESM LM prior, ice cores only</li> <li>CESM LM prior, corals only</li> <li>PACE prior, ice cores only</li> <li>PACE prior, corals only</li> </ol> <p>The CESM LM prior is drawn from the iCESM Last Millennium Ensemble (<a href="https://doi.org/10.1029/2019PA003625">Stevenson et al., 2019</a>) and includes only natural forcings. The PACE prior is drawn from the CESM1 Pacific Pacemaker Ensemble (“PACE”; <a href="https://doi.org/10.1175/JCLI-D-16-0844.1">Deser et al., 2017</a>) and includes historical anthropogenic forcings. For each reconstruction, there are three netCDF files containing the ensemble mean (mean of 100 ensemble members) for each climate field. The anomaly reference period is 1961-1990.</p>
Proxy SIT Canadian Arctic - dataset
<p>Dataset of proxy sea ice thickness for Canadian Arctic 1996-2020. A discussion of how the proxy sea ice thickness dataset was created is available as a preprint (Glissenaar et al., accepted) at <a href="https://doi.org/10.5194/egusphere-2023-269">https://doi.org/10.5194/egusphere-2023-269</a>. Code used to generate and analyse proxy SIT is available on <a href="https://github.com/IsoldeGlissenaar/seaiceproxy">https://github.com/IsoldeGlissenaar/seaiceproxy</a>.</p> <p>There is a different file for each month in November-April. Files contain the proxy sea ice thickness using the mean of the Ku band and the C band models and a corrected proxy sea ice thickness version. Dataset is now gridded.</p>
Supplementary material – Sedimentary organic matter accumulation provinces in the Santos Basin, SW Atlantic: insights from multiple bulk proxies and machine learning analysis
<p>Table S1 - Supplementary material: a complete dataset of the bulk and isotopic composition of organic matter, pigments, biopolymers, and related indices obtained in surface sediments from the Santos Basin. </p>
Data from: In situ correlation between microplastic and suspended particulate matter concentrations in river-estuary systems support proxies for satellite-derived estimates of microplastic flux
<p>Data from Sullivan et al., (in press) In situ correlation between microplastic and suspended particulate matter concentrations in river-estuary systems support proxies for satellite-derived estimates of microplastic flux, <em>Marine Pollution Bulletin. </em></p> <p>It contains the summary of the in situ measurements of TSM and microplastic counts and concentrations for each site. For more detail on the methods, users are directed to the methods section 2.2 of the open access paper. </p>
Dataset for Paul et al., "Revisiting the applicability and constraints of molybdenum and uranium-based paleo redox proxies: comparing two contrasting sill fjords", Biogeosciences, 2023
<p>The datafile contains the solid phase data for Gullmar Fjord (GF-117) and Koljö Fjord (KF-43), presented in Figures 3, 4 and 6 in the publication:</p> <ol> <li>pore water data (SO<sub>4</sub><sup>2-</sup>, ΣH<sub>2</sub>S, Fe, Mn, Mo, and U)</li> <li>solid-phase carbon and nitrogen data (TOC, TN, C/N, OC<sub>terr</sub> and OC<sub>phyt</sub>)</li> <li>solid-phase sequential extraction data (Mo, U, Fe, Mn, Al, Ca, and S)</li> <li>Mo and U-Enrichment Factors (EF)</li> </ol>
Wooden Comb [3D Printable Proxy]
"Wooden comb with a single row of teeth." ~ http://twoway.st/things/YCA51340 Used as a 3D proxy in a demo Musueum in a Box http://museuminabox.org  "We made a demonstration box that's a blend of 3D and 2D objects about daily life in ancient Egypt. We're finding that a demo box speaks volumes about potential, and it was great to be able to show the box to families at the museum." ~ http://museuminabox.org/boxes Because of a super fast turnaround to produce this box we were unable to get access to 3D scan the objects we wanted to include - so we quickly bashed out some proxy replicas in Blender! Source: Objaverse 1.0 / Sketchfab
Different proxies, different stories? Imperfect correlations and different determinants of fitness in bighorn sheep
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Data from: Delusions of grandeur: seed count is not a good fitness proxy under individual variation in phenology
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Second-line drug resistance markers as proxy indicators of sputum culture conversion for samples tested in Uganda
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Data from: Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards
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Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
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Shorter CWR cycling tests as proxies for longer tests in highly trained cyclists
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Multi-proxy paleolimnological records provide evidence for a shift to a new ecosystem state in the Northern Great Plains, USA
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.