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2,516 results for “Seri”
Science Communication Webinar Series: Designing Infographics Presentation
<p>Blue-Action coordinated a series of webinars on climate science communication in 2020. These were aimed at early-career researchers, but anyone who wishes to engage people with their research at any stage will find them valuable.</p> <p>This webinar was delivered on 17th July 2020 by <a href="https://www.sams.ac.uk/people/professional-services/harvey-will/#:~:text=Will%20Harvey&text=As%20a%20member%20of%20SAMS,intranet%20and%20asset%20management%20tools.&text=will.harvey%40sams.ac,%2B44%20(0)1631%20559327">Will Harvey</a>, who is a web and graphic designer at the <a href="https://www.sams.ac.uk/">Scottish Association for Marine Science.</a> Will spent over a decade as a graphic designer in industry, before moving to academia. Here he shares insights into the process of designing infographics and key principles to create a design with impact. </p>
Analysis data for ""Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance""
<p>Analysis data for the manuscript: "Integration of meta-omics data reveals how microbial ecosystems respond to disturbance"</p> <p>Files used with the repository: https://git-r3lab.uni.lu/malte.herold/laots_niche_ecology_analysis/</p> <p>The archive was split into multiple parts for uploading to zenodo which need to be joined in order to extract the files:</p> <pre><code class="language-bash">cat resultsdir_laots.tar.gz.part_* > resultsdir_laots.tar.gz tar xvfz resultsdir_laots.tar.gz</code></pre> <p>Version 2 contains additional files generated in the revision.</p> <p> </p>
Data from: Dynamics of deep soil carbon - insights from 14C time series across a climatic gradient
Quantitative constraints on soil organic matter (SOM) dynamics are essential for comprehensive understanding of the terrestrial carbon cycle. Deep soil carbon is of particular interest, as it represents large stocks and its turnover times remain highly uncertain. In this study, SOM dynamics in both the top and deep soil across a climatic (average temperature ~1-9 °C) gradient are determined using time-series (~20 years) 14C data from bulk soil and water-extractable organic carbon (WEOC). Analytical measurements reveal enrichment of bomb-derived radiocarbon in the deep soil layers on the bulk level during the last two decades. The WEOC pool is strongly enriched in bomb-derived carbon, indicating that it is a dynamic pool. Turnover time estimates of both the bulk and WEOC pool show that the latter cycles up to a magnitude faster than the former. The presence of bomb-derived carbon in the deep soil, as well as the rapidly turning WEOC pool across the climatic gradient implies that there likely is a dynamic component of carbon in the deep soil. Precipitation and bedrock type appear to exert a stronger influence on soil C turnover time and stocks as compared to temperature.
Science Communication Webinar Series: The Art of Pitching Presentation
<p>Blue-Action are coordinating a series of webinars on climate science communication in 2020. These are aimed at early-career researchers, but anyone who wishes to engage people with their research at any stage will find them valuable.</p> <p>This webinar was delivered on 21st August 2020 by <a href="https://nordic.climate-kic.org/what-we-offer/entrepreneurship/our-offering-for-start-ups/">Thomas Simon Oleson</a>, who is an Entrepreneurship Manager at <a href="https://nordic.climate-kic.org/">EIT Climate-KIC</a>. Thomas has worked with businesses and start-ups for over 8 years. Here he describes how to pitch your work to stakeholders with visual and verbal style.</p> <p> </p>
Insect Galls-Host Plants in Biomes Series (Cerrado) v1.0.1
<p>Insect Galls-Host Plants in Biomes Series (Cerrado). Dataset v1.0.1</p>
Data from: The value of time-series data for conservation planning
<ol> <li>Protected areas (PAs) are increasingly being used worldwide for the conservation and management of wildlife. Systematic conservation planning (SCP) aims at ensuring biodiversity persistence while minimizing the threats faced by the species and/or the economic costs related to protection. To account for spatio-temporal interactions between species and human threats, conservation planning for mobile wildlife requires time-series data derived from monitoring of species and human threats, a process that is costly and technically challenging. Therefore, assessments of the monitoring period needed to ensure sufficient data input in the design of efficient, adequate and representative networks of PAs are crucial.</li> <li>We demonstrated the value of time-series data in conservation planning by implementing SCP and data from different monitoring periods to identify priority conservation areas for highly mobile marine megafauna accounting for their main threat: commercial fishing. Two analyses of ten reserve-design scenarios each, replicated as many times as the data composing each scenario permitted were run in Marxan. The best solutions of the planning scenarios were statistically compared using the Cohen`s Kappa test. We also assessed differences in spatial similarity among and within scenarios using the Wilcoxon non-parametric test and a non-metric multidimensional scaling analysis. Finally, we compared the necessary cost and the area selected for each scenario.</li> <li>Our study highlights the importance of time-series ecological and socioeconomic data for the robust selection of priority conservation areas. The results revealed different thresholds of the minimum temporal data required to design efficient networks of PAs for highly mobile species, demonstrating that the incorporation of data covering longer periods to the scenarios produce a more robust selection of priority conservation areas. Conservation plans using data covering less than three years were missing important priority areas.</li> <li> <i>Synthesis and applications. </i>We provide a method for estimating the minimum number of years of monitoring required to design efficient networks of protected areas that ensure the persistence of highly mobile species such as cetaceans and seabirds. This method can be used within an adaptive management framework to evaluate whether a network of PAs performs as planned, and to test whether management strategies should be altered or adjusted in response to local and global changes.</li> </ol>
Data from: Soil solution in Swiss forest stands: a 20 year's time series
<p>Soil solution chemistry is influenced by atmospheric deposition of air pollutants, exchange processes with the soil matrix and soil-rhizosphere-plant interactions. In this study we present the results of the long-term Intercantonal Forest Observation Program in Switzerland with soil solution measurements since 1998 on a current total of 47 plots. The forest sites comprise two major forest types of Switzerland including a wide range of ecological gradients such as different nitrogen (N) deposition and soil conditions. The long-term data set of 20 years of soil solution measurements revealed an ongoing, but site-specific soil acidification. In strongly acidified soils (soil pH below 4.2), acidification indicators changed only slowly over the measured period, possibly due to high buffering capacity of the aluminum buffer (pH 4.2 – 3.8). In contrast, in less acidified sites we observed an increasing acidification rate over time, reflected, for example, by the continuous decrease in the ratio of base cations to aluminum (BC/Al ratio). Nowadays, the main driver of soil acidification is the high rate of N deposition, causing cation losses and hampering sustainable nutrient balances for tree nutrition. Mean nitrate leaching rates for the years 2005-2017 were 9.4 kg N ha<sup>‑1</sup> yr<sup>‑1</sup>, ranging from 0.04 to 53 kg N ha<sup>‑1</sup> yr<sup>‑1</sup>. Three plots with high N input had a remarkable low nitrate leaching. Both N deposition and nitrate leaching have decreased since 2000. However, the latter trend may be partly explained due to increased drought in recent years. Nonetheless, those high N depositions are still affecting the majority of the forest sites. Taken together, this study gives evidence of anthropogenic soil acidification in Swiss forest stands. The underlying long-term measurements of soil solution provides important information on nutrient leaching losses and the impact climate change effects such as droughts.. Furthermore, this study improves the understanding of forest management and tree mortality regarding varying nitrate leaching rates.</p>
Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"
<p>Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"</p> <p> </p> <p>Missing values in the blood glucose datasets are represented with -2.</p>
Analysis and Figures from "Causal network inference from gene transcriptional time-series response to glucocorticoids"
<p>Gene regulatory network inference is essential to uncover complex relationships among gene pathways and inform downstream experiments, ultimately enabling regulatory network re-engineering. Network inference from transcriptional time-series data requires accurate, interpretable, and efficient determination of causal relationships among thousands of genes. Here, we develop Bootstrap Elastic net regression from Time Series (BETS), a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets. We show competitive accuracy on a community benchmark, the DREAM4 100-gene network inference challenge, where BETS is one of the fastest among methods of similar performance and additionally infers whether the causal effects are activating or inhibitory. We apply BETS to transcriptional time-series data of 2,768 differentially-expressed genes from A549 cells exposed to glucocorticoids over a period of 12 hours. We identify a network of 2,768 genes and 31,945 directed edges (FDR <= 0.2). We validate inferred causal network edges using two external data sources: overexpression experiments on the same glucocorticoid system, and genetic variants associated with inferred edges in primary lung tissue in the Genotype-Tissue Expression (GTEx) v6 project. BETS is available as an open source software package at https://github.com/lujonathanh/BETS</p> <p>This upload documents the analysis and figure files that support each numerical claim of the manuscript. Full Progeny.xlsx lists out the relevant code and files for each numerical claim of the manuscript, assuming the home folder of port-from-della</p>
Micro X-ray CT time-series (4D dataset)
<p>The CGLS reconstruction from a time-series with 21 tomograms each collected with 91 projections. For the reconstruction the Savu Python package was used (https://doi.org/10.5281/zenodo.32840). We acknowledge Diamond Light Source for the time on I13-2 under proposal mt9396.</p>
Data from: Using time series analysis to characterize evolutionary and plastic responses to environmental change: a case study of a shift toward earlier migration date in sockeye salmon
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change.
Data from: Spatiotemporal dynamic of surface water bodies using Landsat time-series data from 1999 to 2011
Detailed information on the spatiotemporal dynamic in surface water bodies is important for quantifying the effects of a drying climate, increased water abstraction and rapid urbanization on wetlands. The Swan Coastal Plain (SCP) with over 1500 wetlands is a global biodiversity hotspot located in the southwest of Western Australia, where more than 70% of the wetlands have been lost since European settlement. SCP is located in an area affected by recent climate change that also experiences rapid urban development and ground water abstraction. Landsat TM and ETM+ imagery from 1999 to 2011 has been used to automatically derive a spatially and temporally explicit time-series of surface water body extent on the SCP. A mapping method based on the Landsat data and a decision tree classification algorithm is described. Two generic classifiers were derived for the Landsat 5 and Landsat 7 data. Several landscape metrics were computed to summarize the intra and interannual patterns of surface water dynamic. Top of the atmosphere (TOA) reflectance of band 5 followed by TOA reflectance of bands 4 and 3 were the explanatory variables most important for mapping surface water bodies. Accuracy assessment yielded an overall classification accuracy of 96%, with 89% producer's accuracy and 93% user's accuracy of surface water bodies. The number, mean size, and total area of water bodies showed high seasonal variability with highest numbers in winter and lowest numbers in summer. The number of water bodies in winter increased until 2005 after which a decline can be noted. The lowest numbers occurred in 2010 which coincided with one of the years with the lowest rainfall in the area. Understanding the spatiotemporal dynamic of surface water bodies on the SCP constitutes the basis for understanding the effect of rainfall, water abstraction and urban development on water bodies in a spatially explicit way.
Data from: Discrimination of fast click series produced by tagged Risso's dolphins (Grampus griseus) for echolocation or communication
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two types of rapid click-series pulsed sounds, buzzes and burst pulses, were identified as produced by the tagged dolphins and classified using a Gaussian mixture model based on their duration, association with jerk (i.e., rapid change of acceleration), and temporal association with click trains. Buzzes followed regular echolocation clicks and coincided with a strong jerk signal from accelerometers on the tag. They consisted of series averaging 359 ± 210 (mean ± SD) clicks with an increasing repetition rate and relatively low amplitude. Burst pulses consisted of relatively short click series averaging 45 ± 54 clicks with decreasing repetition rate and longer inter-click interval that were less likely to be associated with regular echolocation and the jerk signal. These results suggest that the longer, relatively lower amplitude, jerk-associated buzzes are used in this species to capture prey, mostly during the bottom phase of foraging dives, as seen in other odontocetes. In contrast, the shorter, isolated burst pulses that are generally emitted by the dolphins while at or near the surface are used outside of a direct, known foraging context.
Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales compared with modern observational studies. We also demonstrate with palaeoecological time-series data that a larger species pool does not enhance ecosystem stability through time, whereas abundance, as an indicator of higher ecosystem functioning, may enhance ecosystem stability. These results suggest that BEF relationships are potentially timescale-dependent. Environmental impacts on biodiversity and ecosystem functioning may be much stronger than biodiversity impacts on ecosystem functioning at long, decadal–millennial, time scales. Longer time-scale perspectives, including palaeoecological and ecosystem monitoring data, are critical for predicting future BEF relationships on a rapidly changing planet.
Data from: Cambrian series 3 agnostoid trilobites Ptychagnostus sinicus and Ptychagnostus atavus from the Machari Formation, Yeongwol Group, Taebaeksan Basin, Korea
This paper reports the successive occurrence of Ptychagnostus sinicus Lu, 1957 and Ptychagnostus atavus (Tullberg, 1880) from the lower part of the Machari Formation, Yeongwol Group, Korea. Morphometric approaches of using the landmark and principal component analyses make it possible to differentiate P. sinicus from P. atavus with clarity: pygidia of P. sinicus have a relatively narrow M1, a transverse F2, and a weakly developed M2 tubercle, whereas those of P. atavus are characterized by a broadly arching M1, a chevron-shaped F2, and a prominent M2 tubercle. Recognition of P. atavus, for the first time in Korea, allows the determination of the base of the Drumian Stage in Korea and aids correlation with other parts of the world.
Data from: Hurdiid radiodontans from the middle Cambrian (Series 3) of Utah
Radiodontan body elements, some belonging to Peytoia and Hurdia and some unassigned, have been reported from the Langston Formation (Spence Shale Member), Wheeler Formation, and Marjum Formation of the middle Cambrian (Series 3) of Utah. These identifications are reassessed in light of recent work on the morphology of the radiodontan Hurdia. New specimens of Hurdia are identified from the Spence Shale, representing mouthparts (oral cones), cephalic carapace H-elements, frontal appendages, and a single isolated swimming flap. The shape of the H-elements allows H. victoria Walcott, 1912 to be identified from the Spence Shale for the first time. The flap is larger and more complete than any reported from the Burgess Shale and allows for a better understanding of the morphology of Hurdia swimming flaps. A 3D model of a Hurdia frontal appendage indicates that there is only one morph of Hurdia frontal appendage found in both species, and apparent morphological differences between disarticulated appendages reflect a preservational continuum caused by varying oblique angles relative to the seafloor. Peytoia should no longer be reported from the Spence Shale, but its presence is confirmed in the Wheeler and Marjum formations. New mouthparts (oral cones) of Hurdia from the Spence Shale and Peytoia from the Marjum Formation with surface textures of submillimeter-diameter raised nodes are described. These new features have not been observed in material from the Burgess Shale and suggest slight differences in preservation.
Data from: Ontogeny of the articulated yiliangellinine trilobite Zhangshania typica from the lower Cambrian (Series 2, Stage 3) of southern China
New discoveries of the early Cambrian yiliangellinine trilobite Zhangshania typica Li and Zhang in Kunming preserve almost all instars from early postembryonic (protaspid) to mature (holaspid) phases in articulated state, in addition to mature specimens with antennae bearing paired spines on the basal articles. The ontogenetic series shows protarthrous development with some, but likely not all, early holaspid instars expressing additional pygidial segments, gradual rearward migration of the location of the longest pleural spines on the trunk segments, and striking positive allometry of the genal spines. It also reveals Parazhangshania sichuanensis Li and Zhang, 1990 to be the holaspid stage 3 of Z. typica, and therefore its junior synonym. This new find in the Hongjingshao Formation provides species-based regional correlation across the South China block and Z. typica may provide an important biostratigraphic marker for the base of the traditional Tsanglangpuan Stage.
Multilevel modeling of time-series cross-sectional data reveals the dynamic interaction between ecological threats and democratic development
<p>What is the relationship between environment and democracy? The framework of cultural evolution suggests that societal development is an adaptation to ecological threats. Pertinent theories assume that democracy emerges as societies adapt to ecological factors such as higher economic wealth, lower pathogen threats, less demanding climates, and fewer natural disasters. However, previous research confused within-country processes with between-country processes and erroneously interpreted between-country findings as if they generalize to within-country mechanisms. In this article, we analyze a time-series cross-sectional dataset to study the dynamic relationship between environment and democracy (1949-2016), accounting for previous misconceptions in levels of analysis. By separating within-country processes from between-country processes, we find that the relationship between environment and democracy not only differs by countries but also depends on the level of analysis. Economic wealth predicts increasing levels of democracy in between-country comparisons, but within-country comparisons show that democracy declines as countries become wealthier over time. This relationship is only prevalent among historically wealthy countries but not among historically poor countries, whose wealth also increased over time. By contrast, pathogen prevalence predicts lower levels of democracy in both between-country and within-country comparisons. Our longitudinal analyses identifying temporal precedence reveal that not only reductions in pathogen prevalence drive future democracy, but also democracy reduces future pathogen prevalence and increases future wealth. These nuanced results contrast with previous analyses using narrow, cross-sectional data. As a whole, our findings illuminate the dynamic process by which environment and democracy shape each other.</p>
Data from: A Neognathodus-based biozonation of the Desmoinesian Series (Pennsylvanian) in the Illinois Basin, USA
The Neognathodus Index (NI) is developed as a primary biostratigraphic indicator for the Desmoinesian Series of the Illinois Basin in Indiana, Illinois and Kentucky. It is based on the gradual evolutionary morphotypic variations of P1 elements of named Neognathodus species. The NI analyses and zonations presented herein are constructed from 472 productive conodont samples from 105 different localities. NIs for the Illinois Basin show morphologic drift in Indiana from the Perth Limestone Member of the Staunton Formation (NI = 2.03) to the Velpen Limestone and Mecca Quarry Shale members of the Linton Formation (NI = 5.04) followed by stability through the Alum Cave (NI = 4.83). Further morphologic drift then occurred through the Providence Limestone Member of the Dugger Formation (NI = 5.43) and continued through the West Franklin Limestone Member of the Shelburn Formation (NI = 6.32) until the extinction of Neognathodus at the end of Desmoinesian. The patterns of drift and stability translate to Neognathodus biozones, and are supported by Kolmogorov–Smirnov tests of standardized Neognathodus morphotype distributions. Localized Neognathodus Index variations are due to morphologic shifts and differential evolution in response to localized environmental conditions. Examination of the NI differences in the states of Illinois, Kentucky, and Indiana reflect similar morphologic simplification of the P1 element from Perth to Velpen and Mecca Quarry in Indiana (NI values 2.03–5.04) and from Seville to Brereton in Illinois and Kentucky (NI values 2.80–5.00). Post-Brereton in Illinois and Kentucky (NI values 5.00–5.65) and post-Providence in Indiana (NI values 5.43–6.32) saw progressive P1 simplification, but it was much more pronounced in Indiana.
GNSS uplift time series and ice surface elevation changes
<p class="MsoNoSpacing">We use Global Navigation Satellite System (GNSS) stations attached to bedrock to measure elastic displacements of the solid Earth caused by dynamic thinning near the glacier terminus. When we compare our results with discharge, we find a time lag between glacier speedup/slowdown and onset of dynamic thinning/thickening. Our results show that dynamic thinning/thickening on Jakobshavn Isbræ occurs 0.87 ± 0.07 years before speedup/slowdown. This implies that using GNSS time series we are able to predict speedup/slowdown of Jakobshavn Isbræ by up to 10.4 months. For Kangerlussuaq Glacier the lag between thinning/thickening and speedup/slowdown is 0.37 ± 0.17 years (4.4 months).</p>
ScienceDex guides
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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.