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2,967 results for “secondary”
Ipsilateral stimulus encoding in primary and secondary somatosensory cortex of awake mice
<p>Data and code to accompany "Ipsilateral stimulus encoding in primary and secondary somatosensory cortex of awake mice" by Pala and Stanley, in press, Journal of Neuroscience, 2022.</p>
Individual glass and secondary standard analyses for tephra described in sediment cores from Skilak Lake, Alaska
<p>This dataset comprises individual glass shard and secondary standard analyses for tephra collected in sediment cores from Skilak Lake, Alaska. These geochemical analyses were used in the research article in Sedimentology titled “Unravelling a 2300 year long sedimentary record of megathrust and intraslab earthquakes in proglacial Skilak Lake, south-central Alaska” by Praet et al. (2022). DOI: <a href="https://doi.org/10.1111/sed.12986">10.1111/sed.12986</a></p>
Secondary Steenrod algebra calculations
<p>This repository contains data files generated by <a href="https://zenodo.org/record/6329789">ext-rs</a> pertaining to the secondary Steenrod algebra algorithm. This supersedes <a href="https://zenodo.org/record/4766457">https://zenodo.org/record/4766457</a> but is not a strict superset of the data.</p> <p>This repository contains three files.</p> <ul> <li> <p><code>d2-data.zip</code> is a zip file containing the generated data, which are as follows:</p> <ul> <li><code>d2</code>: The d₂ differentials. If the target bidegree is empty, the differentials are omitted.</li> <li> <p><code>product_a</code>: The secondary product of all elements with <code>[a]</code>.</p> </li> <li> <p><code>massey_a_b</code>: The secondary Massey product <code><[a], [b], -></code>. The only exception is <code>massey_P</code> which contains the Adams periodicity operator <code><[h_3], [h_0^4], -></code>.</p> </li> <li> <p><code>filtration_one</code>: A list of all filtration one products.</p> </li> <li> <p><code>charts.pdf</code>: The Adams charts showing the d₂'s and the E₃ page, drawn by TikZ.</p> </li> <li> <p><code>clean_charts.pdf</code>: The same charts but without showing h₂ products.</p> </li> <li> <p><code>differentials.gz</code>: The differentials in our minimal resolution, in a human-readable plain text format.</p> </li> <li> <p><code>change_of_basis</code>: The correspondence between our basis and Bruner's basis in <a href="https://arxiv.org/abs/2109.13117">arXiv:2109.13117</a>. Each row expresses one of our basis element in terms of Bruner's basis.</p> </li> </ul> <p>Unless otherwise suggested by the file extension, all files are plain text (utf-8) files. The script and the save file are known to be compatible with the version of the code in <a href="https://zenodo.org/record/5898397">https://zenodo.org/record/5898397</a></p> </li> <li> <p><code>script.sh</code> is a script that generates the files above, except for <code>change_of_basis</code> and the charts. This is to be run in the `ext/` directory of <a href="https://zenodo.org/record/6329789">sseq</a>. If the execution of the script is interrupted halfway through, it is safe to simply run the script again with the safe parameters to resume computation; the vast majority of the computation would have been saved in the save directory and need not be recomputed (If a save file was corrupted due to the interruption, the program will panic instead of silently propagate errors). Similarly, the script can be run with a larger/different range and previous computations would be reused.</p> </li> <li> <p><code>S_2_milnor.tar</code> is an archive containing the algorithm's save file for the above computation, up to <code>(n, s) = (140, 72)</code>.</p> </li> </ul>
Data from: Woody plant secondary chemicals increase in response to abundant deer and arrival of invasive plants in suburban forests
<p>Plants in suburban forests of eastern North America face the dual stressors of high white-tailed deer density and invasion by nonindigenous plants. The combination of chronic deer herbivory and strong competition from invasive plants could alter a plant's stress- and defense-related secondary chemistry, especially for long-lived juvenile trees in the understory, but this has not been studied. We measured foliar total antioxidants, phenolics, and flavonoids in juveniles of two native trees, <em>Fraxinus pennsylvanica</em> (green ash) and <em>Fagus grandifolia </em>(American beech), growing in six forests in the suburban landscape of central New Jersey, USA. The trees grew in experimental plots that had been subject for 2.5 years to factorial treatments of deer access/exclosure X addition/no addition of the nonindigenous invasive grass <em>Microstegium vimineum </em>(Japanese stiltgrass). As other hypothesized drivers of plant secondary chemistry, we also measured non-stiltgrass herb layer cover, light levels, and water availability. Univariate mixed model analysis of the deer and stiltgrass effects and multivariate structural equation modeling (SEM) of all variables showed that both greater stiltgrass cover and greater deer pressure induced antioxidants, phenolics, and flavonoids, with some variation between species. Deer were generally the stronger factor, and stiltgrass effects were most apparent at high stiltgrass density. SEM also revealed that soil dryness directly increased the chemicals; deer had additional positive, but indirect, effects via influence on the soil; in beech PAR positively affected flavonoids; and herb layer cover had no effect. Juvenile trees' chemical defense/stress responses to deer and invasive plants can be protective, but also could have a physiological cost, with negative consequences for recruitment to the canopy. Ecological implications for species and their communities will depend on costs and benefits of stress/defense chemistry in the specific environmental context, particularly with respect to invasive plant competitiveness, extent of invasion, local deer density, and deer browse preferences.</p>
Data tables for primary and secondary datasets
<p>These tables contain select information used to create Fig. 1 in arxiv: <a href="https://arxiv.org/abs/2102.01079">2102.01079</a>.</p> <p>PRIMARY.csv contains information for pairs of stars in the primary data set. SECONDARY.csv contains information for pairs of stars in the secondary data set.</p>
Low-intensity cattle grazing is better than cattle exclusion to drive secondary savannas towards the features of native Cerrado vegetation
<p><span>Although livestock have been historically associated with land conversion and biodiversity loss, well-managed cattle grazing has been reported to contribute to conservation of open ecosystems. Knowing the balance between positive and negative effects of livestock (presence or exclusion) on different ecosystems is, therefore, crucial to support management decisions. </span><span>We conducted an experiment </span><span>in a secondary savanna with exotic grasses, used as pasture, to assess the effect of cattle presence in low density and cattle exclusion (in paired plots) on the trajectory of these ecosystems. Richness, composition and structure of the woody community, and exotic grass cover and biomass were compared between treatments in the beginning of the experiment and after seven years. At the end of the experiment, we also compared composition, richness, and density of the native ground layer. We verified that (a) cattle exclusion accelerates the undesirable woody encroachment, changes the species composition and leads to huge grass fuel accumulation, while (b) cattle grazing/browsing hinders changes in savanna structure and composition and reduces the exotic grass cover and biomass, thus favoring native herbaceous plants. By decreasing the grass biomass, cattle grazing also reduces the system flammability and, therefore, the risk and intensity of wildfires. Together, the positive effects of cattle presence and the negative effects of cattle exclusion lead to the conclusion that cattle should be maintained in these systems. Low-intensity cattle grazing limits woody and exotic grass invasion, improves native forb biodiversity, and help maintain </span><span>composition and structural features of secondary savannas of the Cerrado.</span></p>
Umbilicaria phaea var. coccinea: conservation status, variety rank, and secondary chemistry
<p><span>Originally described from a single collection in northern California, <em>Umbilicaria phaea</em> var. <em>coccinea</em> has since been reported from additional sites in California, Oregon, and Washington. Although relatively rare in all three states, there is currently no conservation status for <em>U. phaea</em> var. coccinea in California. Developing conservation strategies and status ranks requires a sound understanding of distribution, frequency, habitat requirements, and taxonomic placement. Therefore, we evaluated distributions and constructed climate envelope models for both varieties of <em>U. phaea</em>. <em>Umbilicaria phaea</em> var. <em>coccinea</em> appears to be restricted to relatively small habitats within the range of <em>U. phaea</em> var. <em>phaea</em> and is only locally common in portions of the Klamath River watershed. To assess evolutionary relationships between the varieties, we evaluated four molecular loci: ITS2, LSU, Mcm7, and mtSSU. A combined phylogeny using maximum-likelihood and Bayesian inference indicated that <em>U. phaea</em> is monophyletic. Within the <em>U. phaea</em> clade, var. coccinea and var. phaea do not form mutually exclusive, monophyletic clades; instead, individuals are intermixed. Based on variation in pigment production, morphology, and geographic distribution, we recommend continued designation of <em>U. phaea</em> var. <em>coccinea</em> as a variety. To better understand the chemical diversity within <em>U. phaea</em>, we compared </span><span>qualitative differences between secondary metabolite profiles of </span><em><span>U. phaea</span></em><span> var. phaea and <em>U. phaea</em> var. <em>coccinea</em></span><span> acetone </span><span>extracts using </span><span>ultraperformance-liquid chromatography high resolution tandem mass spectrometry</span><span> in negative ion mode. UV spectroscopy, thin-layer chromatography and chemical spot testing were used to further characterize the compounds present. </span><span>Overall, </span><span>ten compounds were detected in extracts of <em>U. phaea</em> var. <em>phaea</em> and <em>U. phaea</em> var. <em>coccinea</em>. </span><span>Five previously known chemical substances were identified in both </span><span><em>U. phaea</em> </span><span>varieties including</span><span>: orsellinic acid, lecanoric acid, hiascic acid, gyrophoric acid, and </span><span>orsellinylgyrophorate</span><span>, along with four unknown metabolites. One additional unknown substance whose chemical properties are consistent with a polyhydroxylated anthraquinone pigment was detected only in </span><span><em>U. phaea</em> </span><span>var. </span><em><span>coccinea</span></em><span>. Given its rarity, chemical uniqueness, and distinct ecological association, </span><em><span>U. phaea</span></em><span> var. <em>coccinea</em> warrants a protected status throughout its range.</span></p>
Data from: Resource supply and organismal dominance are associated with high secondary production in temperate agricultural streams
<p><span>Agricultural land use affects the environmental and biological characteristics of stream </span><span>ecosystems through multiple pathways including nutrient and pesticide contamination, riparian clear-cutting, and hydromorphological degradation. These changes in the abiotic environment can have a direct effect on the productivity of macroinvertebrate communities through environmental filtering and via altered resource conditions encompassing a shift from allochthonous to autochthonous primary production and changes in elemental stoichiometry and food quality. Additionally, macroinvertebrate productivity can be affected indirectly via biological mechanisms, such as changes in species interactions, richness, competition, and predation. We studied the effects of agriculture on structural and functional descriptors of macroinvertebrate communities by assessing environmental characteristics and macroinvertebrate secondary production (MSP), biomass, and density in two forested and two agricultural streams and investigated underlying biotic mechanisms. On average, MSP was 1.6–3.6, biomass 2.8–6.2, and density 5–13 times higher in agricultural than in forested streams. This pattern was associated with higher nutrient concentrations, standing crops of riparian herbaceous vegetation, suspended particulate organic carbon, quantity and quality of epilithic biofilms, and chlorophyll-a concentrations in seston and biofilm of the agricultural streams. Species richness and evenness were significantly lower in agricultural than in forested streams. A negative relationship between MSP and species richness and evenness indicated that density compensation and trait dominance were the prevalent mechanisms facilitating higher MSP in agricultural streams. </span></p> <p><span>Our findings suggest that the loss of riparian canopy and excess nutrient conditions are the major environmental drivers contributing to homogenization of ecological niches </span><span>and dominance of highly productive non-insect generalist species. This study highlights the importance of an ecosystem approach to understanding how complex aggregate stressors affect the regulation of consumer-resource interactions. There is an urgent need to preserve or restore natural riparian vegetation, fostering habitat and resource diversity and limiting nutrient contamination to stream ecosystems. </span></p>
The role of a synanthropic bird in the nest niche expansion of a secondary cavity-nester to man-made structures
<p><span>Species with similar ecological characters often compete with each other; however, a species may also facilitate the survival or reproduction of another ecologically similar species although such interaction is rarely documented in birds. Here we reported a facilitative species interaction between Asian house martins (<em>Delichon dasypus</em>) and russet sparrows (<em>Passer cinnamomeus</em>), both passerines using closed nests, in a montane farming area of Taiwan. We found that Asian house martins constructed dome-shaped nests in human houses that provided additional nest sites for russet sparrows, secondary cavity-nesters with greatly declining populations in Taiwan. Russet sparrows that used house martin nests had reproductive success comparable to those that used artificial nest boxes. However, Asian house martins avoided reclaiming sparrow-used nests, which reduced their available nest sites. Interestingly, our results imply that man-made structures may be used as a conservation tool to improve the breeding of the endangered russet sparrows via this facilitative interaction.</span></p>
Results of Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund
<p>These files contain the figures and modelled dataset used in the article "Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund".</p>
Particle number size distributions associated with secondary organics
<p>We provide the model data used to reproduce the figures in our manuscript titled "secondary organic aerosol formation regulates cloud condensation nuclei in the global remote troposphere". </p>
Genomic data, part 1, of "Secondary contact rather than co-existence – Erebia butterflies in the Alps"
<p>Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. While such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species <em>Erebia</em> <em>cassioides </em>and <em>E.</em> <em>tyndarus</em> in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology in order to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past. Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why co-existence between these butterflies may currently not be possible.</p>
Genomic data, part 2, of "Secondary contact rather than co-existence – Erebia butterflies in the Alps"
<p>Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. While such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species <em>Erebia</em> <em>cassioides </em>and <em>E.</em> <em>tyndarus</em> in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology in order to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past.<strong> </strong>Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why co-existence between these butterflies may currently not be possible.</p>
Data used in "Observation of secondary ice production in clouds at low temperatures"
<p>To support open research, the data used in Korolev et al 2022 "Observation of secondary ice production in clouds at low temperatures" submitted to Atmospheric Chemistry and Physics has been provided here. <br> This in-situ data was collected by Environment and Climate Change Canada (ECCC) in collaboration with the National Research Council (NRC) on the NRC Convair-580 research aircraft on March 25 2017 between 11:00 and 12:00 UTC.<br> Radar data included was collected and processed by N. Cuong and M. Wolde of NRC Canada. <br> </p>
Supplementary Material to: A secondary zone of uplift measured after megathrust earthquakes: caused by early downdip afterslip?
<p>This archive contains supplementary material to the publication "A secondary zone of uplift measured after megathrust earthquakes: caused by early downdip afterslip?"</p> <p>This archive is divided into two folders. One contains scripts and parameterization used for our subduction zone toy models, input files for use with the Pylith software, and slip optimization utilities. A second folder contains scripts and parameterization for our study of the 2010 Mw8.8 Maule (Chile) earthquake. Note that slip optimization utilities rely on the use of the Classic Slip Inversion python library (https://github.com/jolivetr/csi).</p>
Recent HIV infections among newly diagnosed individuals living with HIV in rural Lesotho: Secondary data from the VIBRA cluster-randomized trial
<p>These are pseudo-anonymised data from a secondary analysis of the VIBRA randomised trial.</p> <p>HIV recency assays are used to distinguish recently acquired infection from long-term infection among individuals newly diagnosed with HIV. Since 2015, the World Health Organisation recommends the use of an algorithm to assess recency of infections which is based on an HIV recency assay and viral load (VL) quantification. We determined the proportion of recent HIV infections among participants of the VIBRA (Village-Based Refill of Antiretroviral therapy) cluster-randomized trial in Lesotho and assessed risk factors for these recent infections.</p> <p>The VIBRA trial recruited individuals living with HIV and not taking antiretroviral therapy during a door-to-door HIV testing campaign in two rural districts (Butha-Buthe and Mokhotlong). Samples were collected from participants newly diagnosed and tested for HIV recency using the Asanté HIV-1 Rapid Recency Assay and VL using the Roche Cobas System. Clinical and socio-demographic data were extracted from the trial database. Univariate analysis was conducted to determine factors associated with recent compared to long-term infection.</p> <p>There is one dataset containing all data presented in this dtuy. The data codebook explains the data available in the dataset.</p>
Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants
<p><span>Plant secondary metabolites (SMs) play crucial roles in plant-environment interactions and contribute greatly to human health. Global climate changes are expected to dramatically affect plant secondary metabolism, yet a systematic understanding of such influences is still lacking. Here, we employed medicinal and aromatic plants (MAAPs) as model plant taxa and performed a meta-analysis from 360 publications using 1828 paired observations to assess the responses of different SMs levels and the accompanying plant traits to elevated carbon dioxide (eCO<sub>2</sub>), elevated temperature (eT), elevated nitrogen deposition (eN), and decreased precipitation (dP). The overall results showed that phenolic and terpenoid levels generally respond positively to eCO<sub>2</sub> but negatively to eN, while the total alkaloid concentration was increased remarkably by eN. By contrast, dP promotes the levels of all SMs, while eT exclusively exerts a positive influence on the levels of phenolic compounds. Further analysis highlighted the dependence of SM responses on different moderators such as plant functional types, climate change levels or exposure durations, mean annual temperature and mean annual precipitation. Moreover, plant phenolic and terpenoid responses to climate changes could be attributed to the variations in C/N ratio and total soluble sugar levels, while the <em>trade-off</em> supposition contributed to SM responses to climate changes other than eCO<sub>2</sub>. Taken together, our results predicted the distinctive SM responses to diverse climate changes in MAAPs, and allowed us to define potential moderators responsible for these variations. Further, linking SM responses to C-N metabolism and growth-defence balance provided biological understandings in terms of plant secondary metabolic regulation.</span></p>
Secondary door - Westminster Abbey
18 shots - Panasonic GF7 Westminster Abbey - London One door of the Westminster Abbey, just this part was worth sharing.. didn't took enough pics unfortunatly. I just put it here to share. Feel free to post any comments or tips in order to improve it.. I'm really willing to improve. Source: Objaverse 1.0 / Sketchfab
Data and scripts for "Unraveling secondary ice production in winter orographic clouds through a synergy of in-situ observations, remote sensing and modeling"
<div> <div> <div>This repository contains field observations and processed data from the Weather Research and Forecasting (WRF) model simulations and the Cloud Resolving Model Radar Simulator (CR-SIM), alongside scripts designed to reproduce the figures presented in the paper titled "Unraveling Secondary Ice Production in Winter Orographic Clouds through a Synergy of In-Situ Observations, Remote Sensing, and Modeling." The in-situ and remote sensing measurements were conducted at Mount Helmos in Peloponnese as part of the CALISHTO campaign (https://calishto.panacea-ri.gr/).</div> </div> </div> <div>Preprint accessible at: https://doi.org/10.21203/rs.3.rs-3502790/v1</div>
The effects of primary or secondary prevention with vitamin A supplementation on clinically important outcomes. A systematic review of randomised clinical trials with meta-analysis and Trial Sequential Analysis
<p>Meta data for the review entitled "The effects of primary or secondary prevention with vitamin A supplementation on clinically important outcomes. A systematic review of randomised clinical trials with meta-analysis and Trial Sequential Analysis<strong>"</strong></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)
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.