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Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations
<p>Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations. Integrating experimental observations into single-neuron and network-level computational models shows how a non-linear dependence of T-type calcium channel opening on GABA<sub>B</sub> receptor activity regulates network oscillations. Receptor activity that is either too brief or too protracted fails to sufficiently open T-type channels necessary for sustaining oscillations. Only within a narrow range does prolonging GABA<sub>B</sub> receptor activity promote channel opening and intensify oscillations. These results have implications for therapeutics that modulate GABA transporters.</p>
Dataset for: Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs
<p>Niemann-Pick disease type C is a rare, fatal neurodegenerative disorder characterized by massive intracellular accumulation of cholesterol. In most cases, loss-of-function mutations in NPC1 gene that encodes for a lysosomal cholesterol transporter NPC1 are responsible for the disease, and more than half of the mutations are considered to interfere with biogenesis or folding of the protein. Previously we have identified a series of oxysterol derivatives and phenanthridine-6-one derivatives as pharmacological chaperones, small molecules that rescue folding defective phenotypes of a mutated NPC1, and opened an avenue to develop chaperone therapy for Niemann-Pick disease type C. Here, we established an improved image-based screen for NPC1 chaperones and performed drug-repurposing screening to identify some azole antifungals, including itraconazole and posaconazole, and a kinase inhibitor lapatinib as probable pharmacological chaperones. Photo-crosslinking probes of the compounds allowed us to detect direct binding of itraconazole to a representative folding-defective mutant, NPC1-I1061T. Competitive photo-crosslinking experiments suggested that oxysterol-based chaperones and itraconazole share the same or nearby binding site(s), and sensitivity of the crosslinking to P691S mutation on the sterol-sensing domain supported currently proposed hypothesis that their binding sites are located near the domain. Although the azoles were less effective in reducing cholesterol accumulation than the oxysterol-derived chaperone or an HDAC inhibitor LBH-589, our findings should offer new starting points for developing better pharmacological chaperones for NPC1 through medicinal chemistry efforts.</p>
Data from: Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi
Aim: Plant community assembly in tropical rainforest has been shown to be largely governed by stochastic processes, but as arbuscular mycorrhizal (AM) fungi display limited host preference, they may not follow the same stochastic assembly pattern. Here, we determined the relative importance of environmental and spatial drivers responsible for the community assembly process of AM fungi in two types of tropical rainforest (semideciduous rainforest and dense ombrophilous forests). Location: Atlantic rainforest in northeastern Brazil, South America. Taxon: Arbuscular mycorrhizal fungi (Glomeromycota). Methods: We collected root samples from eight protected areas of Atlantic forest along a 700 km transect in northeastern Brazil. We measured the relative importance of deterministic and stochastic processes by redundancy analysis (RDA) and variation partitioning in comparison with null expectations using ad hoc generated neutral communities. Furthermore, we accessed species associations from co-occurrence data, at different scales using a Bayesian approach of Hierarchical Modelling of Species Communities (HMSC). Results: Overall, the extent to which stochastic and deterministic processes affected community assembly depended on the forest type and the spatial scale. Specifically, we found that abiotic and biotic predictors of AM fungal community assemblages are related to environmental homogeneity in tropical rainforests. Main conclusions: The results of the study show that dynamics in community assembly was clearly different between the two forest types, and that the difference most likely is due to differences in responses to environmental variables.
Raw data for the publication "Effect of graphene substrate type on formation of Bi2Se3 nanoplates", Sci. Rep. 9, 4791, 2019. https://doi.org/10.1038/s41598-019-41178-1
<p>This dataset contains the raw AFM and SEM measurement data used for the study of stages of formation of Bi2Se3 nanoplates on different substrates and for the statistical analysis of sizes and thicknesses of the nanoplates. The results are published in Sci. Rep. 9, 4791, 2019. https://doi.org/10.1038/s41598-019-41178-1</p>
Data for GMD article: "Towards an improved treatment of cloud-radiation interaction in weather and climate models: exploring the potential of the Tripleclouds method for various cloud types using libRadtran 2.0.4"
<p>Dataset for the publication by Nina Črnivec and Bernhard Mayer: "Towards an improved treatment of cloud-radiation interaction in weather and climate models: exploring the potential of the Tripleclouds method for various cloud types using libRadtran 2.0.4" submitted to Geoscientific Model Development in 2020.</p> <p>The repository contains data for stratocumulus, cirrus and cumulonimbus cloud case studies. It also contains MYSTIC benchmark radiation data (including atmosphering heating rate and net surface flux) for the aforementioned cloud cases. See README for additional information and description of data files.</p>
Modified version of intronIC for classifying U12-type introns in Physarum polycephalum
<p>A modified version of <a href="https://github.com/glarue/intronIC">intronIC</a> with position-specific BPS score weighting to reflect the unique U12-type BPS motif found in <em>Physarum</em>. See the README inside the included directory for instructions on recreating the intron classifications present in the manuscript.</p> <p> </p> <p>IMPORTANT UPDATE (08/2021): There is a typo in the README file within the archive—in order to run the program correctly, the argument flags "-r12" and "-r2" need to be inverted from how they are listed in the example command. In other words, the "-r12" flag needs to be placed where the "-r2" flag is, and vice-versa. Apologies for the error!</p>
Data from: Trait-based formal definition of plant functional types and functional communities in the multi-species and multi-traits context
<p>The concepts of traits, plant functional types (PFT), and functional communities are effective tools for the study of complex phenomena such as plant community assembly. Here, we (1) suggest a procedure formalising the classification of response traits to construct a PFT system; (2) integrate the PFT, and species compositional data to formally define functional communities; and, (3) identify environmental drivers that underpin the functional-community patterns.A species–trait data set featuring species pooled from two study sites (Eneabba and Cooljarloo, Western Australia), both supporting kwongan vegetation (sclerophyllous scrub and woodland communities), was subjected to classification to define PFTs. Species of both study sites were replaced with the newly derived PFTs and projected cover abundance-weighted means calculated for every plot. Functional communities were defined by classifications of the abundance-weighted PFT data in the respective sites. Distance-based redundancy analysis (using the abundance-weighted community and environmental data) was used to infer drivers of the functional community patterns for each site.A classification based on trait data assisted in reducing trait-space complexity in the studied vegetation and revealed 26 PFTs shared across the study sites. In total, seven functional communities were identified. We demonstrate a putative functional-community pattern-driving effect of soil-texture (clay—sand) gradients at Eneabba (42% of the total inertia explained) and that of water repellence at Cooljarloo (36%). Synthesis. This paper presents a procedure formalising the classification of multiple response traits leading to the delineation of PFTs and functional communities. This step captures plant responses to stresses and disturbance characteristic of kwongan vegetation, including low nutrient status, water stress, and fire (a landscape-level disturbance factor). Our study is the first to introduce a formal procedure assisting their formal recognition. Our results support the role of short-term abiotic drivers structuring the formation of fine-scale functional community patterns in a complex, species-rich vegetation of Western Australia.</p>
Comparison of different types of restitution in groundwater for open-loop shallow geothermal systems
<p>Comparison of different types of restitution in groundwater of the thermally modified water, exploited by open-loop shallow geothermal systems. The comparison shows that the restitution in the vadose zone in more thermally sustainable, since the produced thermal alteration is lower when reinstating the aquifer by trenches or infiltration wells rather than using a reinjection well directly in groundwater. These would be wiser solutions to avoid an overheating/overcooling of the aquifer at higher depths, especially in urban areas where the density of shallow geothermal systems is constantly increasing. The white line represents the elevation of the groundwater table calculated by the model for each simulated day.</p>
Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer's disease
<p>Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sleep in males more so than in females. Diffuse TBI was induced in C57BL/6J mice and serial blood samples were collected (baseline, 1, 5, 7 days post‐injury [DPI]) to quantify peripheral immune cell populations and sleep regulatory cytokines. Brains and spleens were harvested at 7DPI to quantify central and peripheral immune cells, respectively. Mixed‐effects regression models were used for data analysis. Female TBI mice had 77%–124% higher IL‐6 levels than male TBI mice at 1 and 5DPI, whereas IL‐1β and TNF‐α levels were similar between sexes at all timepoints. Despite baseline sex differences in blood‐measured Ly6Chigh monocytes (females had 40% more than males), TBI reduced monocytes by 67% in TBI mice at 1DPI. Male TBI mice had 31%–33% more blood‐measured and 31% more spleen‐measured Ly6G+ neutrophils than female TBI mice at 1 and 5DPI, and 7DPI, respectively. Compared with sham, TBI increased sleep in both sexes during the first light and dark cycles. Male TBI mice slept 11%–17% more than female TBI mice, depending on the cycle. Thus, sex and TBI interactions may alter the peripheral inflammation profile and sleep patterns, which might explain discrepancies in disease progression based on sex.</p>
Size-selective exclusion of mammals and invertebrates differently affects grassland plant communities depending on vegetation type
<p>Human-caused loss of vertebrate and invertebrate animals, defaunation, is increasing, and potentially affects plant community structure of diverse grassland ecosystems worldwide. We experimentally simulated defaunation using size-selective fences to progressively exclude large-, medium- and small-sized mammals, and invertebrates from two subalpine vegetation types in the Swiss National Park (SNP): intensively grazed short-grass and moderately grazed tall-grass vegetation. We assessed plant community properties yearly from 2009 to 2013, and examined treatment effects on plant community structure in the two grassland types. In the short-grass vegetation, the exclusion of large mammals increased total plant biomass, while the exclusion of large and medium-sized mammals increased total, grass and forb biomass compared to when all animals had access. These increases became stronger when also invertebrates were excluded. The exclusion of all mammals and invertebrates increased biomass of grasses by 205%, forbs by 100% and total plant biomass by 118% compared to when all animals had access, hence enhancing relative biomass of grasses from 43.6% to 60%, changing plant species composition and lowering richness of forbs by 16%, the number of plant families by 13% and family-level Shannon diversity by 23%. In contrast to these significant community-level responses found in the short-grass vegetation, there was no evidence that the size-selective exclusion of animals altered the plant community structure of the tall-grass vegetation. The contrasting results were due to the difference in plant community composition prior to our experiment, which were related to differences in quantity and quality of forage and in grazing intensities of herbivores between the two grassland types. Synthesis. Our results showed that different-sized animals, in particular large mammals and invertebrates, contributed to maintain the plant community structure in the short-grass vegetation, highlighting the importance of multiple, functionally different animal groups for ecosystem functioning and stability. In contrast to the short-grass vegetation, we could not detect such a top-down control by animals in the tall-grass vegetation. Our results suggest that potential defaunation effects on grassland plant community structure depend on the degree of grazing pressure release and grassland vegetation type.</p>
Different types of kinase inhibitors with experimentally confirmed mechanism of action
<p>A data set of ATP-competitive and allosteric inhibitors of human protein kinases with mechanisms of action confirmed by X-ray crystallography is provided. Data were acquired from the Protein Data Bank (PDB) and the KLIFS, ProfKin, ASD, and ChEMBL databases, curated, and organized. The composition of the data set is detailed in the accompanying readme.txt file.</p> <p> </p> <p> </p>
Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study
<p><span><span>Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic and lifestyle behavioural factors on the risk of T2D, a total of 12,403 individuals were identified as incident T2D cases and a representative sub-cohort of 16,154 individuals was selected from a larger cohort of 340,234 participants with a follow-up time of 3.99 million person-years. We describe the results from a genome-wide association analysis between more than 8.9 million SNPs and T2D risk among 22,326 individuals (9,978 cases and 12,348 non-cases) from the EPIC-InterAct study. The summary statistics to be shared provide a valuable resource to facilitate further investigations into the genetics of T2D. </span></span></p>
Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
<p>Processed and analysis-ready input data discussed in our Augur procedures.</p>
Data from: Root morphology and mycorrhizal type strongly influence root production in nutrient hot spots of mixed forests
1. Plants compete for nutrients using a range of strategies. We investigated nutrient foraging within nutrient hot-spots simultaneously available to plant species with diverse root traits. We hypothesized that there would be more root proliferation by thin-root species than by thick-root species, and that root proliferation by thin-root species would limit root proliferation by thick-root species. 2. We conducted a root ingrowth experiment in a temperate forest in eastern USA where root systems of different tree species could interact. Tree species varied in the thickness of their absorptive roots, and were associated with either ectomycorrhizal (EM) or arbuscular mycorrhizal (AM) fungi. Thus, there were thin- and thick-root AM and thin- and thick-root EM plant functional groups. Half the ingrowth cores were amended with organic nutrients (dried green leaves). Relative root length abundance, the proportion of total root length in a given soil volume occupied by a particular plant functional group, was calculated for the original root population and ingrowth roots after 6 months. 3. The shift in relative root length abundance from original to ingrowth roots was positive in thin-root species but negative in thick-root species (P < 0.001), especially in unamended patches (AM: +6% vs. -7%; EM: +8% vs. -9%). Being thin-rooted may thus allow a species to more rapidly recolonize soil after a disturbance, which may influence competition for nutrients. Moreover, we observed that nutrient additions amplified the shift in root length abundance of thin over thick roots in AM trees (+13% vs. -14%), but not in EM trees (+1% vs -3%). In contrast, phospholipid fatty acid biomarkers suggested that EM fungal hyphae strongly proliferated in nutrient hot-spots whereas AM fungal hyphae exhibited only modest proliferation. 4. We found no evidence that when growing in the shared patch, the proliferation of thin roots inhibited the growth of thick roots. 5. Synthesis. Knowledge of root morphology and mycorrhizal type of co-existing tree species may improve prediction of patch exploitation and nutrient acquisition in heterogeneous soils.
Figure 2 in Cercopoidea types (Hemiptera-Cicadomorpha) housed at the Museo de la Plata entomological collection (Argentina)
Figure 2. Ischnorhininae. Deois (Deois) correntina (Berg), Holotype, male, dorsal (A) and lateral view (B). Scale = 1 mm.
Figure 8 in Cercopoidea types (Hemiptera-Cicadomorpha) housed at the Museo de la Plata entomological collection (Argentina)
Figure 8. Ischnorhininae. Notozulia entreriana (Berg), Holotype, female, dorsal (A) and lateral view (B). Scale = 1 mm.
Figure 5 in Cercopoidea types (Hemiptera-Cicadomorpha) housed at the Museo de la Plata entomological collection (Argentina)
Figure 5. Ischnorhininae. Tomaspis perezii Berg, Lectotype, female, dorsal (A) and lateral view (B). Scale = 1 mm.
Data from: Divergent rates of change between tree cover types in a tropical pastoral region
Context: Forest cover change analyses have revealed net forest gain in many tropical regions. While most analyses have focused solely on forest cover, trees outside forests are vital components of landscape integrity. Quantifying regional-scale patterns of tree cover change, including non-forest trees, could benefit forest and landscape restoration (FLR) efforts. Objectives: We analyzed tree cover change in Southwestern Panama to quantify: 1) patterns of change from 1998-2014, 2) differences in rates of change between forest and non-forest classes, and 3) the relative importance of social-ecological predictors of tree cover change between classes. Methods: We digitized tree cover classes, including dispersed trees, live fences, riparian forest, and forest, in very high resolution images from 1998-2014. We then applied hurdle models to relate social-ecological predictors to the probability and amount of tree cover gain. Results: All tree cover classes increased in extent, but gains were highly variable between classes. Non-forest tree cover accounted for 21% of tree cover gains, while riparian trees constituted 31% of forest cover gains. Drivers of tree cover change varied widely between classes, with opposite impacts of some social-ecological predictors on non-forest and forest cover. Conclusions: We demonstrate that key drivers of forest cover change, including topography, road distance and historical forest cover, do not explain rates of non-forest tree cover change. Consequently, predictions from medium-resolution forest cover change analyses may not apply to finer-scale patterns of tree cover. We highlight the opportunity for FLR projects to target tree cover classes adapted to local social and ecological conditions.
Figure 4 in Cercopoidea types (Hemiptera-Cicadomorpha) housed at the Museo de la Plata entomological collection (Argentina)
Figure 4. Ischnorhininae. Tomaspis argentina Berg, Lectotype, male, dorsal (A) and lateral view (B). Scale = 2 mm.
Figure 9 in Cercopoidea types (Hemiptera-Cicadomorpha) housed at the Museo de la Plata entomological collection (Argentina)
Figure 9. Ischnorhininae. Tomaspis platensis Berg, Lectotype, male (A) and lateral view (B). Scale = 2 mm.
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.