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Raw data to "Continuously varying critical exponents in long-range quantum spin ladders"
<p>This directory contains the data used to generate the numerical results in the work "Continuously varying critical exponents in long-range quantum spin ladders [1]".</p> <p>To get an overview of the organization of the directory and a description of the data we recommend the README.md file.</p> <p>[1]: P. Adelhardt and K. P. Schmidt, Continuously varying critical exponents in long-range quantum spin ladders, <a href="https://www.scipost.org/SciPostPhys.15.3.087">SciPost Phys. 15, 087 (2023)</a></p>
Fig. 7 in Meuffelsia, a new genus of long-legged flies from South Africa, with a key to Afrotropical peloropeodine and allied genera (Diptera: Dolichopodidae)
Fig. 7. Habitat at Sanyati Farm where the holotype and one of the paratypes of M. erasmusorum sp. n. were collected. (Photo courtesy Th. & C. Erasmus.)
Data from: Extensive, transient, and long-lasting gene regulation in a song-controlling brain area during testosterone-induced song development in adult female canaries
<p>Like other canary reproductive behaviors, song production occurs seasonally and can be triggered by gonadal hormones. Adult female canaries treated with testosterone sing first songs after four days and progressively develop towards typical canary song structure over several weeks, a behavior that females otherwise rarely or never show. We compared gene regulatory networks in the song-controlling brain area HVC after 1 hour (h), 3 h, 8 h, 3 days (d), 7d, and 14d testosterone treatment with placebo-treated control females, paralleling HVC and song development. Rapid onset (1 h or less) of extensive transcriptional changes (2,700 genes) preceded the onset of song production by four days. The highest level of differential gene expression occurred at 14 days when song structure was most elaborate, and song activity was highest. The transcriptomes changed massively several times during the two-week of song production. A total of 9,710 genes were differentially expressed, corresponding to about 60% of the known protein-coding genes of the canary genome. Most (99%) of the differentially expressed genes were regulated only at specific stages. The differentially expressed genes were associated with diverse biological functions, of which cellular level occurring early and nervous system level occurring primarily after prolonged testosterone treatment. Thus, the development of adult songs requires restructuring the entire HVC, including most HVC cell types, rather than altering only neuronal subpopulations or cellular components. Parallel regulation directly by androgen and estrogen receptors and by other hub genes such as the transcription factor SP8, which are under steroidogenic control, lead to massive transcriptomic and neural changes in the specific behavior-controlling brain areas and gradual seasonal occurrence of singing behavior.</p>
Figure 4. Bayesian Inference phylogenetic tree inferred from 1039 in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 4. Bayesian Inference phylogenetic tree inferred from 1039 bp of concatenated CO1 and ND2 mitochondrial DNA sequence data. Posterior probabilities for major lineages are shown. A similar tree topology was also inferred from Maximum Likelihood.
Figure 3. Maximum Likelihood phylogenetic tree inferred from 695 in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 3. Maximum Likelihood phylogenetic tree inferred from 695 bp of CO1 mtDNA sequence, including data from the Potorous tridactylus benormi Holotype (AM M.8319) and Paratype (AM M.8373). Bootstrap values for major lineages are shown. A similar tree topology was inferred from Bayesian inference.
Figure 2 in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 2. Holotype of Potorous tridactylus benormi AM M.8319 dorsal view (top) and lateral view (bottom). Photography by Sally Cowan.
Figure 5 in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 5 The age-stage specific consumption rate (Cxj) of Neoseiulus cucumeris when fed on saffron pollen for 10 and 20 generations (G10, G20) then switched toTetranychus urticae.
Figure 6 The age-specific predation rate k in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 6 The age-specific predation rate k (x), and age-specific net predation rateqx() of Neoseiulus cucumeris when fed on saffron pollen for 10 and 20 generations (G10, G20) then switched toTetrany-
Figure 2 in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 2 Age-specific survivorship (lx), age-specific fecundity (mx), and age-stage specific fecundityfxj() of Neoseiulus cucumeris fed on saffron pollen for 20 consecutive generations (G1-G20).
Figure 1 in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 1 Age-stage-specific survival rate (sxj) of Neoseiulus cucumeris fed on saffron pollen for 20 consecutive generations (G1-G20).
Figure 4 in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 4 Age-specific survivorship (lx), age-specific fecundity (mx), and age-stage specific fecundity (fxj) of Neoseiulus cucumeris when fed on saffron pollen for 10 and 20 generations (G10, G20) then switched toTetranychus urticae.
Figure 3 in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 3 Age-stage-specific survival rate (sxj) of Neoseiulus cucumeris when fed on saffron pollen for 10 and 20 generations (G10, G20) then switched toTetranychus urticae.
Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.
<p>We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We are awaiting release of the genome through NCBI, so we have made the assembly and annotations available here.</p>
Data for "Symbiotic nutrient cycling enables the long-term survival of Aiptasia in the absence of heterotrophic food sources"
<p>Supplementary figures and raw data associated with the publication "Symbiotic nutrient cycling enables the long-term survival of Aiptasia in the absence of heterotrophic food sources". Data for physiological and NanoSIMS measurements are uploaded as individual sheets/tabs in the .xslx file. </p> <p>"Fig. 1" contains data for physiological measurements (biomass, protein content, and symbiont density) of fed and starved Aiptasia. </p> <p>"Fig. 2" contains data for NanoSIMS measurements for regions of interest from the tissue of fed and starved Aiptasia as well as unlabelled control Aiptasia. </p> <p>The R script contains all code required to repeat the data analysis and plotting.</p> <p> </p>
The adaptive significance of off-lek sociality in birds: A synthetic review, with evidence for the reproductive benefits hypothesis in Long-wattled umbrellabirds
<p>Anecdotal evidence suggests that lekking birds exhibit considerable variation in form and degree of sociality away from the lek, yet this phenomenon has received very little theoretical or empirical research attention. Here, we provide the first synthetic literature review of off-lek sociality in birds and develop a conceptual framework for the potential adaptive function of off-lek sociality across lekking taxa. We then present a case study of the Long-wattled Umbrellabird (<em>Cephalopterus penduliger</em>), where we find support for the hypothesis that off-lek sociality is primarily driven by male reproductive incentives for coordinating lek attendance during the breeding season. During periods of high lekking activity, male umbrellabirds depart the lek in highly coordinated groups and maintain larger off-lek social groups relative to periods of low lekking activity. These seasonal differences in off-lek sociality do not occur in females, are not explained by patterns of foraging behavior, and are expected to confer individual-level benefits for participating males. Both the literature review and empirical study of umbrellabirds suggest that off-lek interactions and behavioral strategies may shape sexual selection processes at leks in important ways. Further research into this historically understudied area of lekking species' behavioral ecology will likely deepen our understanding of the evolutionary dynamics of lek mating.</p>
Long-term spatial memory, across large spatial scales, in Heliconius butterflies
<p>Data accompanying "Long-term spatial memory, across large spatial scales, in <em>Heliconius </em>butterflies", <em>Current Biology </em>2023:</p> <p> </p> <p>exp1.csv. Behavioural data from experiment 1.</p> <p>exp2.csv. Behavioural data from experiment 2.</p> <p>exp3.csv. Behavioural data from experiment 3.</p> <p>Exp1&2.csv. Behavioural data comparing experiment 1 and 2.</p> <p>Exp1byDay.csv. Behavioural data for experiment 1 split by day.</p> <p>Exp2byDay.csv. Behavioural data for experiment 2 split by day.</p> <p>Exp3byDay.csv. Behavioural data for experiment 3 split by day.</p> <p>exp1.R. R code for experiment 1 analysis.</p> <p>exp2.R. R code for experiment 2 analysis.</p> <p>exp3.R. R code for experiment 3 analysis.</p> <p>exp1vsExp2.R. R code for comparing experiment 1 and 2.</p>
Dataset for Modelling the long-term carbon storage potential from recalcitrant matter inputs in tropical arable croplands
<p>Soil organic carbon dynamics for Ecuadorian croplands on the period 2020-2070, under RCP4.5, for various carbon sequestration alternatives, relative to a business as usual situation. Results obtained from adapted version of RothC for carbon sequestration technologies.</p>
Evolution of reproductive isolation in a long-term evolution experiment with Drosophila melanogaster: 30 years of divergent life history selection
<p>We ask if three decades and over 1,500 generations of divergent life history selection on age at reproduction has resulted in the evolution of reproductive isolation (RI) between laboratory populations of <em>Drosophila</em> <em>melanogaster</em>. We tested for premating, postmating-prezygotic and postzygotic reproductive isolation between 3 replicate population pairs. Large evolved differences in body size between selection treatments suggested the potential for prezygotic barriers driven by sexual selection or physical incompatibilities between the sexes. Although a simple prediction would be preference for larger size, creating directional isolation, our results from individual mate choice trials indicate that populations from both selection treatments show a marked bias towards homotypic mate choice; indicative of prezygotic RI driven by sexual selection or sexual conflict. Hybridization between the focal populations resulted in the production of viable adult flies with intermediate size and developmental traits. We observed a suggestive but statistically non-significant trend of fitness decline in the F2 generation of hybrids, but no significant evidence suggesting the evolution of postmating-prezygotic or postzygotic RI. Our findings are in accord with extant literature that posits that premating RI evolves before postmating forms of RI.</p>
Dataset for the intervention effects and long-term changes in physical activity and cardiometabolic outcomes among children at risk of noncommunicable diseases in South Africa
<p>Dataset used to evaluate the short-term effects of the physical and health <em>KaziKidz</em> intervention on cardiometabolic risk factors and the long-term changes thereof among school-aged children at risk of NCDs from disadvantaged communities in South Africa.</p> <p>It encompasses anonymized, unique, identification numbers, anthropometric and clinical measures, such as blood pressure, blood sugar and blood lipids, and Actigraphy-measured physical activity levels. Assigned categories to each cardiovascular risk factor and the overall classification as at risk or not is available too.</p>
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
<p>In the paper associated with this dataset, a workflow is presented which enables the identification of single-/low-copy nuclear molecular markers for a plant group of interest, by mining data from a small representative target capture experiment done using a commercial probe kit and Oxford Nanopore long-read sequencing. The proposed pipeline first assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low-copy. The approach can be applied to any probe set. As it relies on long reads, the contribution also provides template workflows for processing Nanopore-based target capture data. Identified loci can be used for NGS amplicon sequencing. For detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, the long-read assembly tool CANU is employed. The presented workflow can be useful for researchers dealing with reticulate or polyploidization phylogenetic histories in plants.</p> <p>The present dataset contains several documents supplementing the original paper. Its most important elements are a detailed description (alongside two graphical workflow figures) of all methods employed in the study, suitable for reproducing the steps of the workflow and also the wet-lab work. The workflow employs a collection of BASH, Python and R scripts which is available here, together with a detailed account on command line use in Linux. Also, reference sequences for the identified markers can be found as well as sequence alignments derived from the amplicon sequencing.</p>
ScienceDex guides
Understand access before you commit
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.