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1,079 results for “source data”
Data from: Sources of (co)variation in alternative siring routes available to male great tits (Parus major)
Males of socially monogamous species can increase their siring success via within-pair and extra-pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five-year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as "interactive phenotypes" arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra-pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra-pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multi-level structure of male fertilization routes when studying the evolution of male mating strategies.
Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck
Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from panmixia to deep, reciprocally monophyletic lineages. Yet these studies generally found weak or no nuclear (nu) DNA structure which was often attributed to sex-biased gene flow (i.e., male dispersal and female philopatry), a common behavior within this family. An alternative explanation for this "conflict" is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA leads to different signals of population structure. To test these alternatives, we simulated expected nuDNA differentiation based on mtDNA patterns of effective population sizes, gene flow, and divergence times in a Holarctic pair of waterfowl subspecies, the goosander (Mergus merganser merganser) and common merganser (M. m. americanus). We compared simulated results to empirical data from 12 nuDNA introns sampled from the species' global range. Between Europe and North America, nuDNA ФST was 3.4-fold lower than mtDNA ФST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA ФST values were generally < 0 and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by non-molecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.
Data from: Modelling of ships as a source of underwater noise
In this paper, a methodology is presented for modelling underwater noise emissions from ships based on realistic vessel activity in the Baltic Sea region. This paper combines the Wittekind noise source model with the Ship Traffic Emission Assessment Model (STEAM) in order to produce regular updates for underwater noise from ships. This approach allows the construction of noise source maps, but requires parameters which are not commonly available from commercial ship technical databases. For this reason, alternative methods were necessary to fill in the required information. Most of the parameters needed contain information that is available during the STEAM model runs, but features describing propeller cavitation are not easily recovered for the world fleet. Baltic Sea ship activity data were used to generate noise source maps for commercial shipping. Container ships were recognized as the most significant source of underwater noise, and the significant potential for an increase in their contribution to future noise emissions was identified.
Data from: Mangrove outwelling is a significant source of oceanic exchangeable organic carbon
Exchangeable dissolved organic carbon (EDOC) makes up a significant proportion of the oceanic dissolved organic carbon (DOC) pool, yet EDOC sources to the coastal ocean are poorly constrained. We measured the exchange of EDOC and concentrations of EDOC and DOC in mangrove waters over a 26° latitudinal gradient. A clear latitudinal trend was observed, with the highest EDOC concentrations in the tropics. EDOC exports to the coastal ocean were 4.7 ± 1.9 mmol m−2 d−1, equivalent to 11% of DOC exports (42.1 ± 6.7 mmol m−2 d−1). Pore-water and groundwater exchange were minor sources of EDOC. EDOC concentrations were equal to 13% ± 4% of DOC concentrations. Based on previous global DOC export estimates, and our EDOC : DOC ratios, mangroves outwell 3.1 Tg C yr−1 as EDOC, equivalent to ∼ 60% of the global EDOC flux from the ocean to the atmosphere. However, seasonality of mangrove EDOC cycling requires further research.
Data from: Can the source-sink hypothesis explain macrofaunal abundance patterns in the abyss? A modeling test
Low food availability is a major structuring force in deep-sea benthic communities, sustaining only very low densities of organisms in parts of the abyss. These low population densities may result in an Allee effect, whereby local reproductive success is inhibited, and populations are maintained by larval dispersal from bathyal slopes. This slope–abyss source–sink (SASS) hypothesis suggests that the abyssal seafloor constitutes a vast sink habitat with macrofaunal populations sustained only by an influx of larval 'refugees' from source areas on continental slopes, where higher productivity sustains greater population densities. Abyssal macrofaunal population densities would thus be directly related to larval inputs from bathyal source populations. We evaluate three predictions derived from the SASS hypothesis: (i) slope-derived larvae can be passively transported to central abyssal regions within a single larval period, (ii) projected larval export from slopes to the abyss reproduces global patterns of macrofaunal abundance and (iii) macrofaunal abundance decreases with distance from the continental slope. We find that abyssal macrofaunal populations are unlikely to be sustained solely through influx of larvae from slope sources. Rather, local reproduction probably sustains macrofaunal populations in relatively high-productivity abyssal areas, which must also be considered as potential larval source areas for more food-poor abyssal regions.
Data from: Using risk of bias domains to identify opportunities for improvement in food- and nutrition-related research: an evaluation of research type and design, year of publication, and source of funding
Purpose: This retrospective cross-sectional study aimed to identify opportunities for improvement in food and nutrition research by examining risk of bias (ROB) domains. Methods: Rating were extracted from critical appraisal records for 5675 studies used in systematic reviews conducted by three organizations. Variables were as follows: ROB domains defined by the Cochrane Collaboration (Selection, Performance, Detection, Attrition, and Reporting), publication year, research type (intervention or observation) and specific design, funder, and overall quality rating (positive, neutral, or negative). Appraisal instrument questions were mapped to ROB domains. The kappa statistic was used to determine consistency when multiple ROB ratings were available. Binary logistic regression and multinomial logistic regression were used to predict overall quality and ROB domains. Findings: Studies represented a wide variety of research topics (clinical nutrition, food safety, dietary patterns, and dietary supplements) among 15 different research designs with a balance of intervention (49%) and observation (51%) types, published between 1930 and 2015 (64% between 2000-2009). Duplicate ratings (10%) were consistent (k=0.86-0.94). Selection and Performance domain criteria were least likely to be met (57.9% to 60.1%). Selection, Detection, and Performance ROB ratings predicted neutral or negative quality compared to positive quality (p<0.001). Funder, year, and research design were significant predictors of ROB. Some sources of funding predicted increased ROB (p<0.001) for Selection (Interventional: industry only and none/not reported; Observational: other only and none/not reported) and Reporting (Observational: university only and other only). Reduced ROB was predicted by combined and other-only funding for intervention research (p<0.005). Performance ROB domain ratings started significantly improving in 2000; others improved after 1990 (p<0.001). Research designs with higher ROB were nonrandomized intervention and time series designs compared to RCT and prospective cohort designs respectively (p<0.001). Conclusions: Opportunities for improvement in food and nutrition research are in the Selection, Performance, and Detection ROB domains.
Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
CMIP5 P50 Analysis v1.0 for Tuna Species: Source Data
<p><strong>Model results and data used to make future projections of the effects of climate change on the physiology of tuna in the global ocean</strong></p> <p>-------------------------------------------------</p> <p><strong>Description:</strong></p> <p>Coupled Model Intercomparison Project Phase 5 (CMIP5) model results were downloaded from here:<br> https://esgf-node.llnl.gov/search/cmip5/</p> <p>World Ocean Atlas (WOA) 2009 data were downloaded from here:<br> https://www.nodc.noaa.gov/OC5/WOA09/netcdf_data.html</p> <p>The model results and data should only be used to reproduce the analysis described in this publication:</p> <p>Mislan, K. A. S., C. A. Deutsch, R. W. Brill, J. P. Dunne, and J. L. Sarmiento. (2017) Projections of climate driven changes in tuna vertical habitat based on species-specific differences in blood oxygen affinity. Global Change Biology.</p> <p><strong>The Zenodo archive of the code is here:<br> https://doi.org/10.5281/zenodo.808742</strong></p> <p> </p> <p>-------------------------------------------------</p> <p><strong>Instructions:</strong></p> <p>Download the tar.gz file, unzip, and put the folders in the data folder of the CMIP5_p50_tuna code.</p>
Supporting data and source code for Hnilica et al. (submitted to HESS)
<p>Data and code to reproduce the results and plots presented in Technical note: Changes of cross- and auto-dependence structures in climate projections of daily precipitation and their sensitivity to outliers (submitted to Hydrology and Earth System Sciences)</p>
adx1135_source data
Open the record for dataset details and reuse information.
Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids (Source Data)
<p>Source data for Chemical Science paper "Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids" DOI: 10.1039/D3SC02761A</p>
Data for PASP paper: Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation
<p>High-resolution figures for paper "Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation", accepted for publication in The Publications of the Astronomical Society of the Pacific (PASP).</p>
Data from: Biofertilizers from wastewater treatment as a potential source of mineral nutrients for growth of amaranth plants
<p>Exploring alternative fertilizers is crucial in agriculture due to the cost and environmental impact of inorganic options. This study investigated the potential of biofertilizers derived from sewage treatment on the growth and physiology of <em>Amaranthus cruentus</em> plants. Various treatments were compared, including control treatments with inorganic fertilizer and treatments with biofertilizers composed of microalgae, biosolids and reclaimed water. The following traits were investigated: photosynthetic pigments, gas exchange, growth, and leaf nutrient concentrations. Results show that the concentrations of N, P, Cu, Fe Zn and Na nutrients, in the dry microalgae and biosolids, were quite high for the needs of the plants. The wet microalgae presented high concentration of Cu, Fe and Zn nutrients while reclaimed water contained high concentration of N, K, Ca and S. Na and Zn nutrients increased in the leaf of plants treated with dry microalgae and biosolid, respectively. At the beginning of the flowering phase, total chlorophyll and carotenoids contents were lower for plants grown with wet microalgae while for plants grown with higher doses of biosolid or reclaimed water total chlorophyll was increased, and carotenoids were not affected. Lower photosynthetic pigments under wet microalgae resulted in lower photosynthetic rates. On the other hand, amendments with dry microalgae and biosolid increased photosynthetic rates with the biosolid being the most effective. Higher applications of biosolid, wet and dry microalgae produced a considerable increase in shoot biomass of amaranth, with the dry microalgae being the most effective. Additionally, reclaimed water obtained after tertiary treatment of sewage with microalgae and biosolids applied alone showed promising effects on plant growth. Overall, these findings suggest that organic fertilizers derived from sewage treatment have the potential to enhance plant growth and contribute to sustainable agricultural practices.</p>
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Source Data for the paper: "The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants"
<p>This dataset contains the raw data for the results shown in the paper.</p>
[data]Pollution source detection with low-cost low-accuracy sensors through coupling forward data assimilation and inverse optimization
<p>The data used in the case study(Cases-S1,S2,S3)in manuscript "Pollution source detection with low-cost low-accuracy sensors through coupling forward data assimilation and inverse optimization"</p>
Information sources of recreationists - survey data and script
Open the record for dataset details and reuse information.
SOURCE_DATA_NCOMMS-23-38557B_part9
<p>Source dataset of histopathology (H&E) and immunofluorescence figures for nature communications article: <strong><span>Human coronavirus OC43-elicited CD4<sup>+</sup> T cells protect against SARS-CoV-2 in HLA transgenic mice (under review).</span></strong></p>
The evaluation data and source codes of a new conceptual coupled Earth system model and the MOC box model.
<p>The dataset contains the results of a conceptual Atmosphere-Ocean-Ice-Land coupled Earth system model and a MOC box model and the evaluation data of their.</p>
MGP: a new 1-hourly 0.25° global precipitation product (2000-2020) based on multi-source precipitation data fusion
<p>The multi-source merged global precipitation product (MGP; 0.25°/ hourly; 2000-2020; 60°N/S), which takes advantage of the complementary strengths of satellite, reanalysis, and gauge data to obtain reliable precipitation estimates over the global land surface, provides a new higher-quality precipitation dataset for data users to realize their respective research purposes and the social and economic activities. The data developers hope that MGP will play an important role in a variety of science communities (e.g., hydrology, meteorology, climatology, ecology, and agriculture).</p>
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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)
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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.