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FIGURE 1. Korean Micropezidae species, live individuals. A in New records of Micropezidae (Diptera, Acalyptratae) from South Korea, with description of a new species of Rainieria Rondani
FIGURE 1. Korean Micropezidae species, live individuals. A, Micropeza soosi, female, on a forest edge; B, ditto, male, on a plastic surface; C, Rainieria triseta, female; D, Mimegralla suzukiana, female [Figures C–D provided by Sangsu Kim]
Drivers of within- and among-individual variation in risk-taking behaviour during reproduction in a long-lived bird
Plastic and selective mechanisms govern parental investment adjustments to predation threat. We investigated the relative importance of plasticity and selection in risk-taking propensity of incubating female common eiders <i>Somateria mollissima</i> facing unprecedented predation in SW Finland, Baltic Sea. Using a 12-year individual-based dataset, we examined within- and among-individual variation in flight initiation distance (FID), in relation to predation risk, nest detectability, individual traits and reproductive investment (N<sub>FID</sub> = 1009; N<sub>individual</sub> = 559). We expected females nesting in riskier environments (higher predation risk, lower nest concealment) to mitigate environmentally-imposed risk by exhibiting longer FIDs, and females investing more in current reproduction (older, in better condition or laying large clutches) to display shorter FIDs. The target of predation - adult or offspring - affected the mechanisms adapting risk-taking propensity; females plastically increased their FID under higher adult predation risk, while risk-avoiding breeders were predominant on islands with higher nest predation risk. Risk-taking females selected thicker nest cover, consistent with personality-matching habitat choice. Females plastically attenuated their antipredator response (shorter FIDs) with advancing age, and females in better body condition were more risk-taking, a result explained by selection processes. Future research should consider predator type when investigating the fitness consequences of risk-taking strategies.
Individual-level leaf trait variation and correlation across biological and spatial scales
<p>Even with increasing interest in the ecological importance of intraspecific trait variation (ITV) for better understanding ecological processes, few studies have quantified ITV in seedlings and assessed constraints imposed by trade-offs and correlations among individual-level leaf traits. Estimating the amount and role of ITV in seedlings is important to understand tree recruitment and long-term forest dynamics. We measured ten different size, economic, and whole leaf traits (lamina and petiole) for more than 2800 seedlings (height ≥ 10 cm and diameter at breast height < 1 cm) in 283 seedling plots, and then quantified the amount of ITV and trait correlations across two biological (intraspecific and interspecific) and spatial (within and among plots) scales. Finally, we explored the effects of trait variance and sample size on the strength of trait correlations. We found about 40% (6~63%) variation in leaf-level traits was explained by ITV across all traits. Lamina and petiole traits were correlated across biological and spatial scales, whereas leaf size traits (e.g., lamina area) were weakly correlated with economics traits (e.g., specific lamina area); <a name="_Hlk61031779">lamina mass ratio was strongly related to the petiole length</a>. Trait correlations varied among species, plots, and different scales but there was no evidence that the strength of trait relationships was stronger at broader than finer biological and spatial scales. While larger trait variance increased the strength of correlations, the sample size was the most important factor that was negatively related to the strength of trait correlations. Our results showed that a large amount of trait variation was explained by ITV, which highlighted the importance of considering ITV when using trait-based approaches in seedling ecology. In addition, sample size was an important factor that influenced the strength of trait correlations, which suggests that comparing trait correlations across studies should consider the differences in sample size.</p>
Data for: Effects of nutrient heterogeneity on root foraging and plant growth at the individual and community level
<p>Plants can respond to heterogeneous nutrient distribution through selective root placement to enhance nutrient uptake. It is believed that nutrient heterogeneity can better promote plant growth than homogeneous nutrient distribution, but comprehensive analyses are relatively few. We meta-analyzed the data from 131 comparative studies and synthesized the effects of nutrient heterogeneity on root foraging and plant growth, and examined the roles of patch scale and contrast. Plant responses to nutrient heterogeneity was phylogenetically conserved, and the response in shoot biomass was more correlated with the response in root biomass than with root foraging precision. Root precision depended on competition status, and plants in interspecific competition had lower precision. Community-level responses to nutrient heterogeneity were more significant than individual-level responses. With increasing patch scale, root foraging precision declined, while overall shoot and root responses of individuals increased. Moderate patch contrast significantly increased root responses compared to low and high patch contrast. Our results indicate that plants optimize nutrient acquisition from heterogeneous patches mainly through increasing root growth rate and exploit nutrients more effectively at the community than individual level. Patch attribute mediation of nutrient heterogeneity effects on plants may help design fertilization practices to promote productivity and conserve biodiversity. </p>
Genome-wide study on 72,298 individuals in Korean biobank data for 76 traits
<p>Summary statistics relevant to Nam et al. "Genome-wide study on 72,298 individuals in Korean biobank data for 76 traits".</p> <p>See README.txt for details.</p>
RAD-seq of Ash individuals
<p>Ash (<i>Fraxinus </i>spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest <i>Agrilus planipennis </i>(Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by <i>A. planipennis</i>, but some trees have been found to be tolerant to infestation despite years of exposure.</p> <p>Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to <i>A. planipennis </i>attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines.</p> <p>Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand <i>A. planipennis</i> infestation. We were successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of <i>A. planipennis</i>. This was a first step toward uncovering the genetic basis for host tolerance to <i>A. planipennis</i>.</p>
Mechanisms of individual variation in large herbivore diets: Roles of spatial heterogeneity and state-dependent foraging
<p>Many populations of consumers consist of relatively specialized individuals that eat only a subset of the foods consumed by the population at large. Although the ecological significance of individual specialization is recognized, it is difficult to document and its underlying mechanisms are poorly understood. Optimal foraging theory provides a useful framework for predicting how individuals might select different diets, positing that animals balance the 'opportunity cost' of stopping to eat an available food item against the cost of searching for something more nutritious; diet composition should be contingent on the distribution of food, and foragers should be more specialized when individuals have high energy reserves to spend searching for high-quality foods. We tested these predicted mechanisms of individual niche differences by quantifying environmental (resource heterogeneity) and organismal (nutritional condition) determinants of diet in a widespread browsing antelope (bushbuck, <em>Tragelaphus sylvaticus</em>) in an African floodplain-savanna ecosystem. We quantified individual diet breadth and composition using DNA metabarcoding of fecal samples collected repeatedly from 15 GPS-collared animals (6–14 samples per individual, median 12). Bushbuck diets were structured by spatial heterogeneity and constrained by individual conditions. We observed significant individual-level partitioning of food plants by bushbuck both within and between two adjacent habitat types (floodplain and woodland). Individuals with home ranges that were closer together and/or had similar vegetation structures (measured using LiDAR) ate more similar diets, supporting the prediction that heterogeneous resource distribution promotes individual differentiation. Individuals in good nutritional condition had significantly narrower diets (fewer plant taxa), searched their home ranges more intensively (intensity-of-use index), and had higher-quality diets (percent digestible protein) than those in poor condition, supporting the prediction that animals with greater endogenous reserves are more specialized because they can invest time in searching for nutritious foods. Our results support predictions from optimal foraging theory about the energetic basis of individual specialization and provide a potentially generalizable framework for understanding how individual niche width is governed by animal behavior and physiology in heterogeneous landscapes.</p>
Genetically predicted lipid traits, diabetes mellitus liability and carotid intima-media thickness in African ancestry individuals: a Mendelian randomization study
<p>Genetic variants used for the analysis of 'Genetically predicted lipid traits, diabetes mellitus liability and carotid intima-media thickness in African ancestry individuals: a Mendelian randomization study'.</p>
Fig. 1 in Multiple Visual Hallucinations and Pseudohallucinations in One Individual Patient: When the World Is Turning Upside Down and the Television Keeps Falling to the Ground while Dwarfs Are Parading on the Ceiling
<p>Fig. 1. coronary (c) T 2 - weighted magnetic resonance images clearly demonstrating predominantly small-vessel disease with lacunar lesions in the right pons (arrows in a and c) and bilaterally in the subcortical insular cortex and to a lesser extent in the periventricular white matter. The size of the ventricles and the extent of atrophy do not exceed age-related normal values.</p>
Fig. 1 in Multiple Visual Hallucinations and Pseudohallucinations in One Individual Patient: When the World Is Turning Upside Down and the Television Keeps Falling to the Ground while Dwarfs Are Parading on the Ceiling
<p>Fig. 1. Axial (a, b) T 2 - weighted magnetic resonance images clearly demonstrating predominantly small-vessel disease with lacunar lesions in the right pons (arrows in a and c) and bilaterally in the subcortical insular cortex and to a lesser extent in the periventricular white matter. The size of the ventricles and the extent of atrophy do not exceed age-related normal values.</p>
FIGURE 7. Egg sizes and frequencies from four individuals. Binned into 0.5 in Pseudoliparis swirei sp. nov.: A newly-discovered hadal snailfish (Scorpaeniformes: Liparidae) from the Mariana Trench
FIGURE 7. Egg sizes and frequencies from four individuals. Binned into 0.5 mm increments. Small peaks show 22, 23, 7, 14 large eggs for specimens USNM 438994/HADES 200027, SIO 16-81/HADES 200039, SIO 16-87/HADES 200025, USNM 438995/HADES 200085.
Extreme power shortage events of wind-solar supply systems for individual countries
<p><span>Raw data of extreme power shortage events in wind-solar supply system in the paper entitled “Climate change impacts on the power shortage events of wind-solar supply systems worldwide during 1980–2022” on Nature Communications.</span></p>
Data for Individual and combined impacts of carbon dioxide enrichment, heatwaves, flow velocity variability and fine sediment deposition on stream invertebrate communities
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Exploring the Interaction Between Proprioceptive Sensitivity in the Hip, Knee, and Ankle Joints, Alongside Stability Limits Evaluated Through Computerized Posturography, in Elderly Individuals Afflicted with Fibromyalgia Syndrome.
<p><strong><span>Objectives: </span></strong><span>This study investigates proprioceptive sensitivity and stability limits in patients with Fibromyalgia syndrome (FMS) compared to healthy controls, focusing on joint reposition sense (JRS) and limits of stability (LOS). By delineating differences between the groups, it aims to uncover the proprioceptive deficits that contribute to balance impairments in FM sufferers. Additionally, the study explores correlations between JRS and LOS within the FM group, potentially informing targeted therapeutic strategies to enhance patient outcomes.</span></p> <p><span> </span></p> <p><strong><span>Methods: </span></strong><span>Fifty-four individuals with FM and 54 healthy controls participated in this research. Using precise digital inclinometers, JRS was evaluated at the hip, knee, and ankle joints. LOS was assessed using dynamic posturography with advanced iso-free technology. Various parameters were measured, including reaction time, maximum excursion, and directional control. </span></p> <p><span> </span></p> <p><strong><span>Results:</span></strong><span> Individuals with FM exhibited significant differences in JRS and LOS compared to healthy controls. For JRS errors in the hip, knee, and ankle joints (mean ± SD), the FM group showed 3.2° ± 0.6°, 2.9° ± 0.5°, and 3.5° ± 0.7°, respectively, while the control group exhibited 1.1° ± 0.4°, 1.0° ± 0.3°, and 1.2° ± 0.4°, respectively. In LOS, FM individuals had a reaction time of 1.8 ± 0.3 seconds, maximum excursion of 54.6% ± 6.2%, and directional control of 65.2% ± 5.8%, while healthy controls showed 0.9 ± 0.2 seconds, 72.4% ± 7.1%, and 77.8% ± 6.9%, respectively. </span></p> <p><span> </span></p> <p><strong><span>Conclusions:</span></strong><span> Correlation analysis revealed significant associations between JRS parameters and LOS outcomes within the FMS group, indicating that better proprioception was linked to improved postural stability. These findings have clinical implications for assessing and managing balance impairments in individuals with FMS, potentially contributing to the development of targeted interventions to improve their quality of life.</span></p>
Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix
<p><span>Data on studied willows, their traits, associated arthropod herbivore species, and script to perform analyses for the manuscript: "Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European <em>Salix</em>".</span></p>
Paired datasets to study alternative splicing regulation by individual RNA-binding proteins
<p>This project stores datasets generated to study the regulation of alternative splicing using deep learning models (e.g., SpliceAI). In particular, these datasets were used to perform ablation studies (sequence perturbations at motif locations) to evaluate their effects on the deep learning model.</p> <p><span>I </span><span>used public RNA-Seq data from the ENCODE consortium to identify exons sensitive to the knockdown of RNA-binding proteins (RBPs). The idea is that exons sensitive to RBP knockdowns are more likely to be directly or indirectly regulated by such RBPs, hence providing hints on their regulation mechanisms. Importantly,</span><span> I </span><span>also generated paired control exons, which were not alternatively spliced upon RBP knockdown but have similar GC composition and length compared to the knockdown-sensitive exons (target exon and surrounding introns). These control sets were generated to account for potential confounding factors of gene architecture features and, therefore, focus only on RBP binding motifs and their regulatory logic.</span></p> <p><strong>Information about the files</strong></p> <p>After uncompressing the 'paired_dataset.tar.gz' file, a directory with multiple files will be created with the following structure:</p> <ul> <li><em>0_rMATS_ES_events.tsv.gz</em><em>: </em>Summary tables of differential splicing analysis, with deltaPSI estimates referring to Ctrl - Knockdown groups. Important columns: 'target_coordinates' refers to the 1-based coordinates of the alternatively spliced exon, and 'group' indicates the individual knockdown experiments where the exon was observed to be alternatively spliced.</li> <li><em>0_rMATs_ES_non_changing_events.tsv.gz:</em> Summary tables of differential splicing analysis, but in this case, contains all non-changing events (dPSI < |0.025|).</li> <li> <p><em>1_KD_exons_dPSI0.1.tsv.gz:</em> Table with knockdown-sensitive exons along with values for gene architecture features along the exon triplet (exon upstream, intron upstream, cassette exon, intron downstream exon downstream).</p> </li> <li> <p><em>1_Ctrl_exons_dPSI0.025.tsv.gz:</em> Same as '1_KD_exons_dPSI0.1.tsv.gz', but for all non-changing events.</p> </li> <li> <p><em><strong>2_paired_datasets.tsv.gz:</strong></em> Paired datasets in tidy format, where Knockdown-sensitive exons and their Control pairs come in consecutive lines. The 'rbp_name' column refers to the individual knockdown experiment where that exon was observed.</p> </li> <li><em>2_paired_datasets_negative_dPSI.tsv.gz, 2_paired_datasets_positive_dPSI.tsv.gz:</em> Same as '2_paired_datasets.tsv.gz', but knockdown-sensitive exons are split according to the direction of dPSI observed in the RNA-Seq data (along with the respective control pair).</li> <li><em>2_paired_datasets_individualRBPs</em>: This folder contains the paired datasets in wide format, where a single line contains both the knockdown-sensitive and control pair. In addition, each paired dataset (knockdown of individual RBP) is written in a separate file.</li> </ul> <div><strong>Details of the sh knockdown RNA-Seq analysis</strong></div> <div>Because in the ENCODE study (Van Nostrand E.L. et al., 2020), authors analyzed knockdown RNA Seq data using an older version of the human genome (hg19) along with old genome annotations (GENCODE v19), I reanalyzed ENCODE data aligned to the hg38 genome build. I used rMATS v4.1.2 on each RBP knockdown experiment to detect differentially spliced events between the two knockdown replicates vs the two control replicates. rMATS was run with GENCODE annotations v44 and specifically tweaked with <em>--cstat 0.05</em>. <div> </div> <div>Significant knockdown-sensitive events were identified with a deltaPSI > |0.1|, using a False Discovery Rate cutoff of 0.05. Non-changing events, assumed as knockdown-agnostic controls, were defined as those exhibiting negligible deltaPSI variation (< |0.025|). To ensure the high quality of the exon sets, further analytical steps were performed. First, I applied a read coverage filter, by retaining events where the median coverage across replicates per condition for the isoform with more read counts was higher than 7. Then, I exclusively focused on exon skipping events in protein-coding genes, and filtered out unannotated exons (pseudoexons) as well as first or last exons of genes. In addition, I excluded duplicate exon skipping events by picking the transcript with the highest biological importance (based on the presence of transcript flags such as MANE selected, CCDS, or APPRIS). A total of 15,235 events were detected across all RBP knockdown experiments (N=72, splicing-associated RBPs with data available for the HepG2 cell line), covering 6,659 unique exons.</div> </div> <div> <div> </div> </div>
Biomechanical Analysis of Limits of Stability Using Computerized Posturography: Correlations with Functional Mobility in Elderly Individuals with Hip Osteoarthritis – A Cross-Sectional Study
<p>The study titled "Biomechanical Analysis of Limits of Stability Using Computerized Posturography: Correlations with Functional Mobility in Elderly Individuals with Hip Osteoarthritis – A Cross-Sectional Study" delves into the intricate relationship between postural stability and functional mobility in elderly patients suffering from hip osteoarthritis (OA). Utilizing advanced computerized posturography, the research quantitatively assesses the limits of stability (LOS) in various directional planes, providing a comprehensive biomechanical profile of the participants. The findings reveal significant discrepancies in LOS between hip OA patients and age-matched asymptomatic controls, underscoring the profound impact of hip OA on balance and stability. Additionally, the study examines the correlation between LOS measurements and functional mobility, as assessed by the Timed Up and Go (TUG) test. The results indicate a strong association, suggesting that diminished postural stability in hip OA patients contributes to impaired functional mobility. This cross-sectional analysis highlights the importance of targeted interventions to enhance stability and mobility in this population, aiming to mitigate the risk of falls and improve overall quality of life.</p>
Supporting data for "Collisional alignment and molecular rotation control the chemi-ionization of individual conformers of hydroquinone with metastable neon"
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Generative AI enhances individual creativity but reduces the collective diversity of novel content
<p>Creativity is core to being human. Generative AI—made readily available by powerful large language models (LLMs)—holds promise for humans to be more creative by offering new ideas, or less creative by anchoring on generative AI ideas. We study the causal impact of generative AI ideas on the production of short stories in an online experiment where some writers obtained story ideas from an LLM. We find that access to generative AI ideas causes stories to be evaluated as more creative, better written, and more enjoyable, especially among less creative writers. However, generative AI-enabled stories are more similar to each other than stories by humans alone. These results point to an increase in individual creativity at the risk of losing collective novelty. This dynamic resembles a social dilemma: with generative AI, writers are individually better off, but collectively a narrower scope of novel content is produced. Our results have implications for researchers, policy-makers, and practitioners interested in bolstering creativity.</p>
Summary Statistics for Genetic determinants and phenotypic consequences of blood T-cell proportions in 207,000 diverse individuals
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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.