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12,346 results for “derivatives”
Sinking efficiency of cyanobacteria-derived particulate organic carbon from one eutrophic lake and global perspectives on carbon burial flux in subtropical shallow lakes
<p>It is the data that support the findings entitled "Sinking efficiency of cyanobacteria-derived particulate organic carbon from one eutrophic lake and global perspectives on carbon burial flux in subtropical shallow lakes” </p>
Greenheugh capping unit ChemCam derived data products
<p>The ChemCam derived data products used in Bedford et al. (2022) "An insight into ancient aeolian processes and post-Noachian aqueous alteration in Gale crater; Mars, using ChemCam geochemical data from the Greenheugh capping unit."</p>
CLDF dataset derived from Streitberg's 'Die Gotische Bibel [The Gothic bible]' from 1910
<p>Cite the source of the dataset as:</p> <blockquote> <p>Streitberg 1910, Van Loon 2004</p> </blockquote>
Derived products from "Beyond glacier wide mass balances: parsing seasonal elevation change into spatially-resolved patterns of accumulation and ablation at Wolverine Glacier, Alaska"
<p>Distributed mass balances, emergence velocities, firn compaction rates, and co-registered 10 m resolution DEMs from "Beyond glacier wide mass balances: parsing seasonal elevation change into spatially-resolved patterns of accumulation and ablation at Wolverine Glacier, Alaska" (in review) (Zeller et al., 2022).</p>
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
Data from: Ocean acidification alters sperm responses to egg-derived chemicals in a broadcast spawning mussel
<p>The continued and unprecedented emissions of anthropogenic carbon dioxide (CO<sub>2</sub>) are causing progressive ocean acidification (OA). While deleterious effects of OA on biological systems are well documented in the growth of calcifying organisms, lesser studied impacts of OA include potential effects on gamete interactions that determine fertilisation, which are likely to influence the many marine species that spawn gametes externally. Here, we explore the effects of OA on the signalling mechanisms that enable sperm to track egg-derived chemicals (sperm chemotaxis). We focus on the mussel <i>Mytilus galloprovincialis</i>, where sperm chemotaxis enables eggs to selectively bias fertilisation in favour of genetically compatible males. Using a factorial experimental design, we test whether the experimental manipulation of seawater pH (comparing ambient conditions to predicted end-of-century scenarios) alters these patterns of differential sperm chemotaxis. While we find no evidence that patterns of male-female gametic compatibility are impacted by OA, we do find that individual males exhibit consistent variation in how their sperm perform in lowered pH levels. This finding of individual variability in the capacity of ejaculates to respond to chemoattractants under acidified conditions suggests that climate change will exert considerable pressure on male genotypes that can withstand an increasingly hostile fertilisation environment.</p>
10Be concentrations constraining surface age and valley growth rate in a seepage-derived drainage network in the Apalachicola River basin, Florida
<p class="Head1"><span><span>Measuring rates of valley head migration and determining the timing of canyon-opening are insightful quantifications for the history and evolution of planetary surfaces. Horizontal spatial gradients of <em>in situ-</em>produced cosmogenic nuclide concentrations provide a framework for assessing the migration of these and similar topographic features. We developed a theoretical model for the concentration of <em>in situ</em> produced cosmogenic radionuclides in valley walls during retreat of a valley head. The retreat rate is inversely proportional to the magnitude of the spatial concentration gradient and proportional to local nuclide accumulation rates. By solving for a spatial gradient in concentration along a valley parallel transect, we created an expression for the explicit determination of valley head retreat, termed unzipping. We applied this theory to a developing seepage-derived drainage network along the Apalachicola River, Florida, USA. Sample concentrations along a valley margin transect vary systematically from 2.9 x 10<sup>5</sup> atoms/g to 3.5 x 10<sup>5</sup> atoms/g resulting in a gradient of 160 atoms/g/m, and from this value a valley head retreat rate of 0.025 m/y is found. The discrepancy between overall network age and current rates of valley head migration suggests intermittent network growth which is consistent with glacial-interglacial precipitation variations during the Pleistocene. This method can be applied to a wide range of Earth-surface environments. For the <sup>10</sup>Be system, this method should be sensitive to unzipping rates bounded between 10<sup>-6</sup> m/y and 10<sup>0</sup> m/y.</span></span></p>
Incucyte data for progeny virus derived from insect cells with or without methyltransferase inhibitor
<p>Arthropod endosymbiont <em>Wolbachia pipientis </em>is part of a global biocontrol strategy aimed at reducing the spread of mosquito-borne RNA viruses such as alphaviruses. Our prior work examining <em>Wolbachia-</em>mediated pathogen blocking has demonstrated (i) the importance of a host cytosine methyltransferase, DNMT2, in <em>Drosophila</em>, and (ii) viral RNA as a target through which pathogen-blocking is mediated<em>.</em> Here we report on the role of DNMT2 in <em>Wolbachia</em> induced virus inhibition of alphaviruses in <em>Aedes sp..</em> Mosquito DNMT2 levels were altered in the presence of both viruses and <em>Wolbachia, </em>albeit in opposite directions. Elevated levels of DNMT2 in mosquito salivary glands induced by virus infection were suppressed in <em>Wolbachia </em>colonized animals coincident with a reduction of virus replication, and decreased infectivity of progeny virus. Ectopic expression of DNMT2 in cultured <em>Aedes </em>cells was proviral increasing progeny virus infectivity, and this effect of DNMT2 on virus replication and infectivity was dependent on its methyltransferase activity. Finally, examination of the effects of <em>Wolbachia</em> on modifications of viral RNA by LC-MS showed a decrease in the amount of 5-methylcytosine modification consistent with the down-regulation of DNMT2 in <em>Wolbachia </em>colonized mosquito cells and animals. Collectively, our findings support the conclusion that disruption of 5-methylcytosine modification of viral RNA is an important mechanism operative in pathogen blocking. These data also emphasize the essential role of epitranscriptomic modifications in regulating fundamental processes of virus replication and transmission.</p>
Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions
<p>Marker genotypes, linkage map and phenotypic data used for QTL analysis included in the manuscript by Gonzalo et al. <em>in press "</em>Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between <em>S. pimpinellifolium</em> and <em>S. lycopersicum</em> Accessions".</p>
Subspecies and Distribution. A.l.lerviaPallas,1777—Morocco,NA.l.,andNTunisia. A.l.angusiRothschild,1921—NWNiger(Air&TermitMassifs). A.l.blaineiRothschild,1913—SELybia,NEChad,andNW&NESudan(probablynowrestrictedtoRedSeahills). A.l.fassiniLepri,1930—NWLibya,extremeSTunisia. A.l.ornatus1.GeoffroySaint-Hilaire,1827—SE&SWEgypt. A. l. sahariensis Rothschild, 1913 — S Morocco, Western Sahara, NW Mauritania, S A.l ria, extreme S Libya, NE Mali, SE Niger, and NW Chad. Introduced, free-ranging populations occur in S Spain, the Canary Is, USA (California, New Mexico, and Texas), and NE Mexico. Subspecies of free-ranging introduced populations are unknown because they originate from zoo animals of uncertain origin or from hybrids. Most introduced populations are probably from subspecies lervia, derived from European zoos. The Aoudad has become a widespread invasive species. in Bovidae
Subspecies and Distribution. A.l.lerviaPallas,1777—Morocco,NA.l.,andNTunisia. A.l.angusiRothschild,1921—NWNiger(Air&TermitMassifs). A.l.blaineiRothschild,1913—SELybia,NEChad,andNW&NESudan(probablynowrestrictedtoRedSeahills). A.l.fassiniLepri,1930—NWLibya,extremeSTunisia. A.l.ornatus1.GeoffroySaint-Hilaire,1827—SE&SWEgypt. A. l. sahariensis Rothschild, 1913 — S Morocco, Western Sahara, NW Mauritania, S A.l ria, extreme S Libya, NE Mali, SE Niger, and NW Chad. Introduced, free-ranging populations occur in S Spain, the Canary Is, USA (California, New Mexico, and Texas), and NE Mexico. Subspecies of free-ranging introduced populations are unknown because they originate from zoo animals of uncertain origin or from hybrids. Most introduced populations are probably from subspecies lervia, derived from European zoos. The Aoudad has become a widespread invasive species.
Derivation and analysis of a phase field crystal model for a mixture of active and passive particles
<p>Supplementary data for the following manuscript: Michael te Vrugt, Max Philipp Holl, Aron Koch, Raphael Wittkowski, Uwe Thiele, "Derivation and analysis of a phase field crystal model for a mixture of active and passive particles"</p>
Tracer and Observationally Derived Constraints on Diapycnal Diffusivities in an Ocean State Estimate
<p>Data used to generate figures in Trossman et al. (2022) in Ocean Science</p>
Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
<p>Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".</p>
A method for determining the origin of crude drugs derived from animals using MinION, a compact next-generation sequencer
<p><span>We evaluated whether MinION, an inexpensive, portable sequencer, can be applied for identifying the origin of crude drugs</span> <span>derived from animals</span><span>.</span><span> Standard and nonstandard crude drugs with different species of origin were examined. In addition, the standards mixed with nonstandard samples </span><span>were used</span><span>.</span><span> As a target gene, cytochrome c oxidase I was amplified and sequenced. The Fast mode results had a slightly lower match ratio than High-accuracy mode, but the animals of origin were correctly determined by BLAST for all samples. For antler velvet derived from <em>Rangifer tarandus</em>, even the sequences were aligned based on <em>Cervus elaphus</em>, the animal of origin was determined correctly. Minor contents could be detected from mixtures of two animals, if the mixtures contained at least 19:1 mtDNA when the coverage allele-fraction threshold was 0.05. By contrast, in Fast mode, two sequences could not be separated due to the low accuracy of the base-calling in each read. For field work, the species of origin of crude drugs could be identified, by only simple DNA extraction and library preparation. Therefore, MinION appears to be a convenient tool for identifying the origin of crude drugs derived from animals.</span></p>
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold. in Four new species of Entoloma (Entolomataceae, Agaricomycetes) subgenera Cyanula and Claudopus from Vietnam and their phylogenetic position
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold.
Data from: Polymicrobial Lysis-Hi-C experiments of three bacteria and plasmids derived from HiC-Pro
<p>Microbes interact in biofilms and polymicrobial infections in a spatially structured manner, yet next-generation sequencing approaches generally fail to recover <em>in situ</em> spatial proximity between distinct genotypes in the interactome or eDNA matrix. This study explored a modified Hi-C approach involving an initial lysis phase prior to DNA cross-linking, to test whether adjacent cell chromatin can be cross-linked, anticipating that this could provide a new avenue for the study of spatial-mutational dynamics in structured microbial communities. An artificial polymicrobial mixture of <em>Pseudomonas aeruginosa</em>, <em>Staphylococcus aureus</em>, and <em>Escherichia coli</em> was lysed for 1 to 18 hours, then prepared for Hi-C. A murine biofilm infection model was treated with sonication, mechanical lysis, or chemical lysis before Hi-C. Bioinformatic analyses of resulting Hi-C interspecies chromatin links showed that while microbial species differed from one another, generally lysis significantly increased links between species and increased the distance of Hi-C links within species, while also increasing novel plasmid-chromosome links. The success of this modified lysis-Hi-C protocol in creating extracellular DNA links is a promising first step toward a new lysis-Hi-C-based method to recover genotypic microgeography in polymicrobial communities, with potential future applications in diseases with localized resistance, such as cystic fibrosis lung infections and chronic diabetic ulcers.</p>
Data for "Derivatives use and the risk-taking behaviour of African banks"
<p>This file contains the data supporting the findings of our study, Derivatives use and the risk-taking behaviour of African banks, including that generated by transforming original variables before performing relevant data analyses, which was submitted for publication in the Journal of International Development.</p>
RNA sequencing analysis of CAF treated by colon cancer cell-derived exosomes
<p>In this study, we analyzed differentially expressed genes by obtaining gene expression values through transcriptome sequencing of Homo sapiens, and performed functional classification and gene annotation for significant genes based on gene ontology and pathway information. After the pre-processed trimmed reads were mapped to a known reference genome using the HISAT2 program, transcript assembly was performed through the StringTie program. As a result, expression profile values were obtained for each sample for the known transcript, and read count, based on transcript/gene Fragment per Kilobase of transcript per Million mapped reads (FPKM), Transcripts per Kilobase (TPM) Million) values have been summarized. This value was subjected to DEG (Differentially Expressed Genes) analysis using edgeR for comparison combinations (HT-29_Exo-CAF vs. CTL_PBS-CAF, LoVo_Exo-CAF vs. CTL_PBS-CAF, and SW480_Exo-CAF vs. CTL_PBS-CAF), and genes that satisfies the condition |fc|>=2 & exactTest raw p-value<0.05 in at least one comparison combination Dogs were extracted. Transcriptome resequencing data was used to compare expression profiles between comparable samples. Gene Ontology Enrichment analysis was performed using the g:Profiler tool (https://biit.cs.ut.ee/gprofiler/) for a list of genes with significant expression level differences. GO_stat is the result of organizing the associated gene and test stat based on term_id. GO_genes is the result of arranging the associated term_id and DEG analysis result stat based on the gene.</p>
Data derived state probabilities for Z. noltei monitoring study. Observed variables were shoot density at four sites in this study
<p>1. In general, it is not feasible to collect enough empirical data to capture the entire range of processes that define a complex system, either intrinsically or when viewing the system from a different geographical or temporal perspective. In this context, an alternative approach is to consider model transferability, which is the act of translating a model built for one environment to another less well-known situation. Model transferability and adaptability may be extremely beneficial - approaches that aid in the reuse and adaption of models, particularly for sites with limited data, would benefit from widespread model uptake. Besides the reduced effort required to develop a model, data collection can be simplified when transferring a model to a different application context.</p> <p>2. The research presented in this paper focused on a case study to identify and implement guidelines for model adaptation. Our study adapted a general Dynamic Bayesian Networks (DBN) of a seagrass ecosystem to a new location where nodes were similar, but the conditional probability tables varied. We focused on two species of seagrass (Zostera noltei and Zostera marina) located in Arcachon Bay, France. Expert knowledge was used to complement peer-reviewed literature to identify which components needed adjustment including parameterisation and quantification of the model, and desired outcomes. We adopted both linguistic labels and scenario-based elicitation to elicit from experts the conditional probabilities used to quantify the DBN.</p> <p>3. Following the proposed guidelines, the model structure of the general DBN was retained, but the conditional probability tables were adapted for nodes that characterised the growth dynamics in Zostera spp. population located in Arcachon Bay, as well as the seasonal variation on their reproduction. Particular attention was paid to the light variable as it is a crucial driver of growth and physiology for seagrasses.</p> <p>4. Our guidelines provide a way to adapt a general DBN to specific ecosystems to maximise model reuse and minimise re-development effort. Especially important from a transferability perspective are guidelines for ecosystems with limited data, and how simulation and prior predictive approaches can be used in these contexts.</p>
Distribution. SE Nigeria, in a few small, scattered populations in forest and derived savanna between the lower Niger and Cross rivers, including the Niger Delta (specifically, from W of Oguta at 5° 42° N, just E of the Niger); it occurs N as far as the Eastern Aboine River in Ebonyi State. in Cercopithecidae
Distribution. SE Nigeria, in a few small, scattered populations in forest and derived savanna between the lower Niger and Cross rivers, including the Niger Delta (specifically, from W of Oguta at 5° 42° N, just E of the Niger); it occurs N as far as the Eastern Aboine River in Ebonyi State.
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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)
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.