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165 results for “conversational data”
Supporting data for increasing fire activity reinforces shrub conversion in Southwestern US forests
<p>Fire-exclusion in historically frequent-fire forests of the southwestern United States has altered forest structure and increased the probability of high-severity fire. Warmer and drier conditions, coupled with dispersal distance limitations are limiting tree seedling establishment and survival following high-severity fire. Post-fire conversion to non-forest vegetation can be reinforced by subsequent fire events. We sought to determine the influence of fire probability on post-fire vegetation development in a severely burned landscape in New Mexico, USA. We used LANDIS-II to simulate three fire probability scenarios—contemporary mean fire return interval (CMFRI), and 1.5 times and 2 times CMFRI—with contemporary climate. As fire probability increased, the mean size of the largest fires and the mean landscape fire severity increased. These changes in fire characteristics resulted in a net decrease in total above ground biomass and photosynthetic capacity on the landscape. Additionally, the distribution of individual species biomass shifted, with early successional species, especially those that resprout after fire, increasing as a fraction of total biomass with increasing fire occurrence. Continued increases in fire frequency are likely to favor resprouting species and result in a loss of forest biomass and ecosystem productivity in this southwestern forest landscape.</p>
Raw data for manuscript Semantic context can mask intelligibility declines at above-conversational speech levels in normal-hearing listeners
<p>Raw data for the manuscript in doc file. <br> Copied from the Matlab .m file. used for the analysis.</p> <p>To be updated.</p> <p>For details, contact me at mfer@health.sdu.dk</p>
GRAND-SLAM analysis of simulated nucleotide conversion in Illumina TruSeq data sets for grandRescue
<p>These are processed data sets from the simulation of nucleotide conversions (T>C) in single-end and paired-end Illumina TruSeq reads for the purpose of investigating 4sU-induced mapping impairment by read lengths and library preparation methods and the potential of grandRescue to alleviate these effects.</p> <p>The original data set is from: Sarantopoulou, D. <em>et al. </em>(https://doi.org/10.1038/s41598-019-49889-1)</p> <p>GEO Accession:GSE124167 (samples: GSM3523316 - GSM3523318)</p> <p> </p> <p>The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output) for single-end (R1) and paired-end before and after rescue. The *.tsv.gz files are the GRAND-SLAM output tables.</p> <p><br> To generate the GRAND-SLAM output yourself, first prepare the mouse genomes. Then run the following command with the respective cit-files, prefixes (*.cit) and genome:</p> <p>gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -prefix grandslam_t15/* -plot -D -modelall</p> <p>To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.</p> <p> </p> <p>Software versions:</p> <p> gedi toolkit 1.0.5<br> GRAND-SLAM 2.0.7<br> STAR version 2.7.10b</p>
GRAND-SLAM analysis of simulated nucleotide conversion in QuantSeq data sets for grandRescue
<p>These are processed data sets from the simulation of nucleotide conversions (T>C) in QuantSeq reads for the purpose of investigating 4sU-induced mapping impairment by read lengths and library preparation methods and the potential of grandRescue to alleviate these effects.</p> <p>The original data set is from: Lee, J. W. <em>et al. </em>(https://doi.org/10.1038/s41586-019-1004-y)</p> <p>GEO Accession: GSE109480 (Samples: GSM2944116 – GSM2944120)</p> <p> </p> <p>The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output) before and after rescue. The *.tsv.gz files are the GRAND-SLAM output tables.</p> <p><br> To generate the GRAND-SLAM output yourself, first prepare the mouse genome. Then run the following command with the respective cit-files, prefixes (*.cit) and genome:</p> <p>gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -prefix grandslam_t15/* -plot -D -modelall</p> <p>To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.</p> <p> </p> <p>Software versions:</p> <p> gedi toolkit 1.0.5<br> GRAND-SLAM 2.0.7<br> STAR version 2.7.10b</p>
Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
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Data from: Ultra-wideband and polarization-independent RCS reduction based on polarization conversion metasurface
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Data from: Interactive bioacoustic playback as a tool for detecting and exploring nonhuman intelligence: “Conversing” with an Alaskan humpback whale
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Supporting data for increasing fire activity reinforces shrub conversion in Southwestern US forests
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Code and data for: Wlodarczak and Heldner. (2020). Breathing in conversation.
<p>This is code and data accompanying the paper Wlodarczak and Heldner (2020). Breathing in conversation. Frontiers in Psychology.</p> <p>To reproduce the results, run the following commands in the terminal:</p> <pre><code class="language-bash">cd code make all </code></pre> <p>The code is released the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</p>
Data from: Litter conversion into detritivore faeces reshuffles the quality control over C and N dynamics during decomposition
1. In many terrestrial ecosystems, detritivorous soil organisms ingest large amounts of leaf litter returning most of it to the soil as faeces. Such conversion of leaf litter into faeces may stimulate decomposition by increasing the surface area available for microbial colonization. Yet, experimental support for either the outcome or the mechanism of these conversion effects is lacking. 2. Based on the hypothesis that the identity of plant species from which leaf litter is transformed into faeces has a critical role in how faeces decomposition proceeds, we collected faeces of the widely abundant millipede Glomeris marginata fed with leaf litter from seven distinct tree species. We compared the physical and chemical characteristics and the rates of carbon (C) and nitrogen (N) loss between litter and faeces. 3. We found that after 100 days of exposure under controlled conditions, C loss was on average higher in faeces (40%) than in litter (26.6%), with a significant increase for six out of the seven species. Concurrently, N dynamics switched from a net immobilisation (7.7%) in litter to a net release (14.6%) in faeces, with a significant increase for five out of the seven species. 4. Litter conversion into faeces generally homogenised differences in physical and chemical characteristics among species. Despite such homogenisation, variability in rates of faeces C and N loss among species was similar compared to leaf litter, but correlated with a different set of traits. Specifically, faecal pellet C loss was positively related to compaction (decreased specific area and increased density of faecal pellets), and both C and N loss from faecal pellets were positively related to fragmentation (increased specific area and perimeter of particles within faecal pellets). 5. We conclude that litter fragmentation and compaction into detritivore faecal pellets leads to substantially enhanced decomposition, with a particularly strong impact on N dynamics that changed from immobilisation to net release depending on litter species. Moreover, litter quality control on decomposition is reshuffled by litter conversion into faeces. In ecosystems with high detritivore abundance, this so far largely overlooked pathway of organic matter turnover may strongly affect ecosystem C and N cycling.
Data from: A pantropical analysis of the impacts of forest degradation and conversion on local temperature
Temperature is a core component of a species' fundamental niche. At the fine scale over which most organisms experience climate (mm to ha), temperature depends upon the amount of radiation reaching the Earth's surface, which is principally governed by vegetation. Tropical regions have undergone widespread and extreme changes to vegetation, particularly through the degradation and conversion of rainforests. Since most terrestrial biodiversity is in the tropics, and many of these species possess narrow thermal limits, it is important to identify local thermal impacts of rainforest degradation and conversion. We collected pan-tropical, site-level (< 1 ha) temperature data from the literature to quantify impacts of land-use change on local temperatures, and to examine whether this relationship differed above-ground relative to below-ground and between wet and dry seasons. We found that local temperature in our sample sites was higher than primary forest in all human-impacted land-use types (N = 113,894 day-time temperature measurements from 25 studies). Warming was pronounced following conversion of forest to agricultural land (minimum +1.6°C, maximum +13.6°C), but minimal and non-significant when compared to forest degradation (e.g. by selective logging; minimum +1°C, maximum +1.1°C). The effect was buffered below-ground (minimum buffering 0°C, maximum buffering 11.4°C), whereas seasonality had minimal impact (maximum buffering 1.9°C). We conclude that forest-dependent species that persist following conversion of rainforest have experienced substantial local warming. Deforestation pushes these species closer to their thermal limits, making it more likely that compounding effects of future perturbations, such as severe droughts and global warming, will exceed species' tolerances. By contrast, degraded forests and below-ground habitats may provide important refugia for thermally-restricted species in landscapes dominated by agricultural land.
Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata L'Hér. (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ~22% of the plastome nucleotide content. Among the largest repeats (>2 kb) we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome, and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Data from: Tropical rainforest conversion and land-use intensification reduce understory plant phylogenetic diversity
1. Conversion of rainforest into agricultural land affects multiple facets of tropical plant diversity. While the effects of tropical land use change and intensification on species diversity are comparatively well studied, the effects on phylogenetic diversity and structure of plant communities are largely unknown. Furthermore, it is not clear how the loss of native species and addition of alien species collectively affect phylogenetic diversity and structure. 2. We investigated the phylogenetic diversity and structure of understorey plants; a diverse and ecologically important, yet poorly studied group. We studied four prominent land use systems (tropical lowland rainforest, jungle rubber agroforest, rubber plantations and oil palm plantations) in the lowlands of Sumatra (Indonesia), a region experiencing dramatic land use changes. 3. Across the four systems, we investigated differences in four metrics of phylogenetic community structure (phylogenetic diversity, mean pairwise distance, mean nearest taxon distance and their abundance-weighted variants). Our analyses were based on a comprehensive vegetation survey consisting of 32 plots, 1,197 species of vascular plants, and 146,599 plant individuals. 4. Our results showed that forest conversion into agricultural systems leads to a pronounced loss of phylogenetic diversity. Furthermore, the standard effect size of mean pairwise distance indicated a gradual change from clustered to overdispersed phylogenetic community structure with increasing land use intensity from forest over jungle rubber to the monoculture plantations. In most land use systems, the presence or absence of alien plant species did not affect phylogenetic structure. Only in oil palm plantations, removing alien species from the data led to a more overdispersed structure. In conclusion, conserving the phylogenetic diversity and structure requires efficient protection of the last remaining rainforests. 5. Synthesis and applications. Forest conversion into agricultural areas negatively affects phylogenetic understorey plant diversity and leads to a shift from clustered to overdispersed phylogenetic community structure. These trends are partly driven by alien species particularly in oil palm plantations. Protecting the remaining rainforests, and considering multi-species agroforestry systems in favour of intensive monoculture plantations are thus imperative to conserve phylogenetic plant diversity and community structure.
Data from: Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus
Background: Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages. Results: In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations. Conclusions: The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.
Data from: Disparity in preemptive end-of-life conversation experience caused by subjective economic status among general Japanese elderly people: a cross-sectional study with stratified random sampling
Objectives: Preemptive conversations (PCs) about end-of-life (EOL) preferences are beneficial for both elderly people and their families to understand and share the preferences. However, the factors which promote/inhibit PCs have yet to be clarified. We therefore aimed to determine the factors related to having PCs with hypothesis that age, subjective economic status and subjective health status are associated with having PC experience. Design: A cross-sectional study administering a questionnaire and using stratified random sampling by gender and region. Setting: Residents aged 65 years or older who were not receiving nursing care as of November 1, 2016, were extracted from the Japanese long-term care insurance system registry in Koriyama City, Fukushima Prefecture, Japan. Participants: 1,575 participants (717 males and 858 females). Outcome: Presence or absence of PC experience with family or friends (yes/no). Results: The mean age of the participants was 74.0 years. A multivariable logistic-regression analysis revealed that having PC experience was significantly associated with gender (OR = 1.907; 95% CI = 1.556, 2.337; p < 0.001), subjective economic status (OR = 0.832; 95% CI = 0.716, 0.966; p=0.016), and subjective happiness (OR = 0.926; 95% CI = 0.880, 0.973; p=0.003). Conclusions: Poor subjective economic status of elderly people may result in absence of EOL conversation experience with their families and friends, hindering the elderly from sharing and understanding the EOL preferences. To promote PCs about EOL, gerontology and public health professionals should give special consideration to the subjective economic status of elderly people.
Data set: Native forest conversion alters soil macroinvertabrate diversity and soil quality in tropical mountain landscapes of northern Ecuador
<p>Data set an related material of the article entitled: Native forest conversion alters soil macroinvertabrate diversity and soil quality in tropical mountain landscapes of northern Ecuador</p>
Source data for figures in the main text of the publication: "Iron-catalyzed cooperative red-ox mechanism for the simultaneous conversion of nitrous oxide and nitric oxide"
<p>Source data for figures 2, 4, 5 and 6 present in the main text of the manuscript titled: "Iron-catalyzed cooperative red-ox mechanism for the simultaneous conversion of nitrous oxide and nitric oxide"</p>
SST data from JAXA for "Importance of Strains in Kinetic Energy Conversion for Submesoscale Processes from an Anisotropic Perspective"
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Data from: Soil nitrogen-cycling responses to conversion of lowland forests to oil palm and rubber plantations in Sumatra, Indonesia
Rapid deforestation in Sumatra, Indonesia is presently occurring due to the expansion of palm oil and rubber production, fueled by an increasing global demand. Our study aimed to assess changes in soil-N cycling rates with conversion of forest to oil palm (Elaeis guineensis) and rubber (Hevea brasiliensis) plantations. In Jambi Province, Sumatra, Indonesia, we selected two soil landscapes – loam and clay Acrisol soils – each with four land-use types: lowland forest and forest with regenerating rubber (hereafter, "jungle rubber") as reference land uses, and rubber and oil palm as converted land uses. Gross soil-N cycling rates were measured using the 15N pool dilution technique with in-situ incubation of soil cores. In the loam Acrisol soil, where fertility was low, microbial biomass, gross N mineralization and NH4+ immobilization were also low and no significant changes were detected with land-use conversion. The clay Acrisol soil which had higher initial fertility based on the reference land uses (i.e. higher pH, organic C, total N, effective cation exchange capacity (ECEC) and base saturation) (P≤0.05–0.09) had larger microbial biomass and NH4+ transformation rates (P≤0.05) compared to the loam Acrisol soil. Conversion of forest and jungle rubber to rubber and oil palm in the clay Acrisol soil decreased soil fertility which, in turn, reduced microbial biomass and consequently decreased NH4+ transformation rates (P≤0.05–0.09). This was further attested by the correlation of gross N mineralization and microbial biomass N with ECEC, organic C, total N (R=0.51–0. 76; P≤0.05) and C:N ratio (R=-0.71 – -0.75, P≤0.05). Our findings suggest that the larger the initial soil fertility and N availability, the larger the reductions upon land-use conversion. Because soil N availability was dependent on microbial biomass, management practices in converted oil palm and rubber plantations should focus on enriching microbial biomass.
Data for the paper "A new mapping function for spaceborne TEC conversion based on the plasmaspheric scale height"
<p>This dataset works specifically for the paper Wu et al., (2021), "A new mapping function for spaceborne TEC conversion based on the plasmaspheric scale height"</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.