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13,864 results for “staging”
Herbivory selects for tolerance and constitutive defence across stages of community succession
<p>Plants defend themselves from herbivory by either reducing damage (resistance) or minimizing its negative fitness effects with compensatory growth (tolerance). Factors mediating the selection for defenses such as herbivory and competition are in constant flux in an early secondary successional community, which can create temporal variation in selection for these traits. We manipulated successional age of the community and insect herbivory in a genotypic selection experiment with the perennial herb Solidago altissima. We found selection for investment in aboveground biomass in early succession but not in mid-succession, suggesting that the importance of competition is highest in the very first years of succession. Herbivory selected for smaller and better defended plants in both successional ages but decreased plant survival and probability of flowering only in mid-succession. Despite dramatic differences in herbivory between early and mid-succession, selection on defense traits did not change. These results demonstrate that changes in the community that affect key life-history traits in an individual species can occur over very short timescales in a dynamic secondary successional environment. Such temporal variation may be an important, yet overlooked, contributor to adaptive mosaics across populations.</p>
Cowpea drought stress application at early vegetative stage 2022 - screen 03 - day 06 - raw image data
<p>Cowpea (<em>Vigna unguiculata</em>) miniCore accessions were screened for responses to drought stress at early vegetative stress. The cowpea seedlings were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. </p> <p>This dataset represents the images collected for Screen number 03 and day 06 after drought stress application.</p>
Cowpea drought stress application at early vegetative stage 2022 - screen 03 - day 04 - raw image data
<p>Cowpea (<em>Vigna unguiculata</em>) miniCore accessions were screened for responses to drought stress at early vegetative stress. The cowpea seedlings were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. </p> <p>This dataset represents the images collected for Screen number 03 and day 04 after drought stress application.</p>
Frozen feather and motif files for Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue.
<p>Frozen feather and motif files for manuscript "Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue" by Espinoza DA, et al. Data was downloaded from cisTarget database from aertslab.org.</p>
Single-cell RNA sequencing of mouse embryonic cells from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages
<p>STRT-N is a newly optimized single-cell RNA sequencing method for studies of early genome activation in mammalian preimplantation development. Single embryos from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages were sampled for experiments and were sequenced using STRT-N method. Here is the raw data from STRTN-seq. FASTQ files are available in <a href="https://www.ebi.ac.uk/biostudies/studies/S-BSST976">BioStudies database</a>.</p>
Built to change: dominance strategy changes with life stage in a primitively eusocial bee
<p>Access to reproduction is determined by an individual's dominance rank in many species and is achieved through aggression and/or dominance signalling. In eusocial insects one or several dominant females (queens) monopolize reproduction but to what extent queens rely on aggression and signalling remains obscure. Aggression is costly and its efficiency depends on the group size, whereas signalling may reduce the risks and costs of aggression. Both strategies are used to regulate reproduction in social taxa, with aggression being more common in small social groups, compared to signalling in larger societies. Here, we examine the use of aggression and chemical signalling in a social species (Bombus impatiens) where the dominant queen interacts with increasing numbers of workers as she ages. We found that the queen's strategy to monopolize reproduction changes with life stage, shifting from overt aggression to chemical signalling as the queen gets older. Particularly, old queens exhibited a higher ratio of short to long cuticular hydrocarbons compared to young queens, an endogenous shift that was attributed to age, as all egg-laying queens were fecund and kept with the same number of workers. Our findings contribute to the understanding of reproductive dominance in the context of an individual's life history.</p>
Fig. 3 in New data on the early stages and behaviour of the endangered species Callophrys mystaphia (Lepidoptera: Lycaenidae) and its first larval parasitoid, Cotesia sp. (Hymenoptera: Braconidae)
Fig. 3. Larvae of Callophrys mystaphia Miller, 1913 on host plant from various perspectives.
Fig. 5 in New data on the early stages and behaviour of the endangered species Callophrys mystaphia (Lepidoptera: Lycaenidae) and its first larval parasitoid, Cotesia sp. (Hymenoptera: Braconidae)
Fig. 5. Larvae of Callophrys mystaphia Miller, 1913 forming 'feeding windows' on the host plant.
Data for: Deep brain stimulation in early-stage Parkinson disease
<p><strong>Objective</strong>: To report 5-year outcomes from the subthalamic nucleus (STN) deep brain stimulation (DBS) in early-stage Parkinson disease (PD) pilot clinical trial.</p> <p><strong>Methods</strong>: The pilot was a prospective, single-blind clinical trial that randomized patients with early-stage PD (Hoehn & Yahr II off medications) to receive bilateral STN DBS plus optimal drug therapy (ODT) vs ODT alone (IDEG050016, NCT0282152, IRB040797). Participants who completed the 2-year trial participated in this observational follow-up study, which included annual outpatient visits through 5 years. This analysis includes 28 patients who were taking PD medications for 6 months to 4 years at enrollment. Outcomes were analyzed using both proportional odds logistic regression and linear mixed effects models.ResultsEarly STN DBS + ODT participants required lower levodopa equivalent daily doses (p = 0.04, β = −240 mg, 95% confidence interval [CI] −471 to −8) and had 0.06 times the odds of requiring polypharmacy at 5 years compared to early ODT participants (p = 0.01, odds ratio [OR] 0.06, 95% CI 0.00 to 0.65). The odds of having worse rest tremor for early STN DBS + ODT participants were 0.21 times those of early ODT participants (p < 0.001, OR 0.21, 95% CI 0.09 to 0.45). The safety profile was similar between groups.</p> <p><strong>Conclusions</strong>: These results suggest that early DBS reduces the need for and complexity of PD medications while providing long-term motor benefit over standard medical therapy. Further investigation is warranted, and the Food and Drug Administration has approved the conduct of a prospective, multicenter, pivotal clinical trial of DBS in early-stage PD (IDEG050016).</p> <p><strong>Classification of evidence</strong>: This study provides Class II evidence that DBS implanted in early-stage PD decreases the risk of disease progression and polypharmacy compared to optimal medical therapy alone.</p>
Single stage exchange for PJI of the hip
<p>This video illustrates our surgical technique for single stage exchange for periprosthetic joint infection of the hip.</p>
Supplementary code and data for the paper `From stage to page: language independent bootstrap measures of distinctiveness in fictional speech`
<p>The repository provides full data and processing / analysis pipeline for the paper <strong>'From stage to page: language independent bootstrap measures of distinctiveness in fictional speech</strong>'<br> <br> Rendered notebooks are also available through Github:</p> <p>1) <a href="https://github.com/perechen/difs-character-voices/blob/master/data/all_stars_clean.ipynb">Preparation, energy distance and exploration</a> (main)</p> <p>2) <a href="https://github.com/perechen/difs-character-voices/blob/master/03_analysis.md">Keyword curves & formal modeling</a></p> <p> </p> <p>- `00_dracor_get_data.R`. Script uses <a href="https://dracor.org/">DraCor</a> dedicated API to get texts spoken by characters</p> <p>- `01_distinctiveness_energy.ipynb` does the heavy lifting of data wrangling, cleaning and preprocessing, plus implements energy distance bootstrapping and does exploratory analysis</p> <p>- `02_logodds_curves.R` calculates keyword curves for characters<br> <br> - `03_analysis_and_models.R` explores keyword curves and does Bayesian models</p>
Ex vivo 100 μm isotropic diffusion MRI‐based tractography of connectivity changes in the end‐stage R6/2 mouse model of Huntington's disease
<div> <div> <div> <div> <p><strong>Background</strong>: Huntington's disease is a progressive neurodegenerative disorder. Brain atrophy, as measured by volumetric magnetic resonance imaging (MRI), is a downstream consequence of neurodegeneration, but microstructural changes within brain tissue are expected to precede this volumetric decline. The tissue microstructure can be assayed non-invasively using diffusion MRI, which also allows a tractographic analysis of brain connectivity.</p> <p><strong>Methods</strong>: We here used ex vivo diffusion MRI (11.7T) to measure microstructural changes in different brain regions of end‐stage (14 weeks of age) wild type and R6/2 mice (male and female) modeling Huntington's disease. To probe the microstructure of different brain regions, reduce partial volume effects and measure connectivity between different regions, a 100 μm isotropic voxel resolution was acquired.</p> <p><strong>Results</strong>: Although fractional anisotropy did not reveal any difference between wild‐type controls and R6/2 mice, mean, axial, and radial diffusivity were increased in female R6/2 mice and decreased in male R6/2 mice. Whole brain streamlines were only reduced in male R6/2 mice, but streamline density was increased. Region‐to‐region tractography indicated reductions in connectivity between the cortex, hippocampus, and thalamus with the striatum, as well as within the basal ganglia (striatum—globus pallidus—subthalamic nucleus—substantia nigra—thalamus).</p> <p><strong>Conclusions</strong>: Biological sex and left/right hemisphere affected tractographic results, potentially reflecting different stages of disease progression. This proof‐of‐principle study indicates that diffusion MRI and tractography potentially provide novel biomarkers that connect volumetric changes across different brain regions. In a translation setting, these measurements constitute a novel tool to assess the therapeutic impact of interventions such as neuroprotective agents in transgenic models, as well as patients with Huntington's disease.</p> </div> </div> </div> </div>
A decade of diversity and forest structure: Post-logging patterns across life stages in an Afrotropical forest
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Tropical forests are under threat of increasing pressure from income-generating land uses. Selective logging is a compromise that allows the use of the land while leaving much of the forest canopy intact across a landscape. However, the ecological impacts of selective logging are unclear, with evidence of positive, negative, and negligible effects on forest structure and diversity. We examined the impact of selective logging on the structure and diversity of evergreen tropical forests in the Monts de Cristal region, a chain of mid-elevation hills in northwestern Gabon. For three size classes (seedling, sapling, and adult) of woody plant species, we tested whether forest structure (canopy openness, stem density, basal area, and relative liana abundances) and diversity were altered in forests that had been logged one year and ten years prior, compared to unlogged forest. In general, we found no large impact of selective logging treatment on the structure and diversity of adult woody plant communities, but the seedling and sapling communities were affected. Compared to unlogged forest, one-year post-logging forest had greater variation in canopy openness and lower sapling stem density. Ten-year post-logging forest had higher seedling and sapling species evenness, higher sapling species diversity, and higher relative abundance of sapling-sized lianas compared to unlogged forest. Our results show that key differences between intact and selectively logged forests persist in the understory at least a decade after logging. Overall, these results contribute an additional data point in the literature on selective logging, specifically representing the impacts of very low impact selective logging in Central African forests. Our study highlights the value of exploring selective logging impacts at multiple time periods of recovery, and makes an important contribution to the knowledge of Central African managed forests.</p> </div> </div> </div>
Data for: The relationships of breeding stage to daytime singing behaviour and song perch height in Bermuda White-eyed Vireos (Vireo griseus bermudianus)
<p><span>Bird song is crucial for attracting mates and defending territories, but different types of song or different singing behaviours may be involved in acquiring or maintaining each resource. Furthermore, male songbirds may adjust when and where they sing throughout the breeding season, depending on their breeding stage. However, such relationships remain untested in several avian taxa. Here, we studied male Bermuda White-eyed Vireos (<em>Vireo griseus bermudianus</em>), a passerine with two distinct song types (discrete and rambling), to test the mate attraction and territory defence hypotheses. We compare song production and song perch height among different stages of the breeding season and during the non-breeding season. We show that male vireos produce both song types during the breeding and non-breeding seasons, suggesting dual roles in mate choice and territorial defence. Song production did not differ significantly between the breeding and non-breeding seasons, but, within the breeding season, males without nesting duties sang significantly more songs than males with nesting duties. Song perch height was higher during the breeding season versus non-breeding season, among males without nesting duties compared to males with nesting duties, and when males produced discrete versus rambling songs. Our findings suggest that male vireos increase their conspicuousness to prospecting females by increasing song production and song perch height, and that they sing during the breeding and non-breeding seasons to defend year-round territories. Collectively, our study supports the mate attraction and territory defence hypotheses of bird song.</span></p>
Comparing thermal regime stages along a small Yakutian fluvial valley with point scale measurements, thermal modeling and near surface geophysics
<ul> <li>Dataset associated with the paper :</li> </ul> <p>"<em>Comparing thermal regime stages along a small Yakutian fluvial valley with point scale measurements, thermal modeling and near surface geophysics</em>"</p> <p>Emmanuel Léger 1 , Albane Saintenoy 1 ,Christophe Grenier 2,† , Antoine Séjourné1 , Eric<br> Pohl2,3 , Frédéric Bouchard4, Marc Pessel1 , Kirill Bazhin5 , Kencheeri Danilov5, François<br> Costard1 , Claude Mugler2 , Alexander Fedorov5 , and Ivan Khristoforov5 and Pavel<br> Konstantinov5<br> 1 Laboratoire Geosciences Paris-Saclay, Université Paris-Saclay, CNRS, GEOPS, 91405, Orsay, France.<br> 2 Laboratoire des Sciences du Climat et de L’Environnement (LSCE), CEA CNRS UVSQ, Université<br> Paris-Saclay, Gif-sur-Yvette, France<br> 3 Department of Geosciences, University of Fribourg, Fribourg, Switzerland<br> 4 Universite de Sherbrooke Département de géomatique appliquée, Sherbrooke, QC, CA<br> 5 Melnikov Permafrost Institute, Yakutsk, Yakutia.</p>
Ornamented species incur higher male mortality in the larval stage
<p>Life-cycle stages are not always capable of evolving independently from each other, but it remains unclear if evolving to meet the demands of one stage actually imposes costs on other stages. Male ornamentation is a useful trait in which to test this potential evolutionary constraint because ornaments improve reproduction in the adult stage but can require the expression of risky traits in the juvenile stage. Here, I compared larval mortality between populations of ornamented and non-ornamented dragonfly species. Since males produce more exaggerated melanin wing ornaments than females, I tested if larval mortality of males is higher in populations of species that have evolved adult male wing ornamentation. My analyses reveal larval mortality is more male-biased in species that have evolved male ornamentation. These findings indicate that evolving to optimize mating for the adult stage imposes a cost to survival in the larval stage. Thus, this study reveals that evolution in one life-cycle stage can shape fitness differences in other stages over macroevolutionary timescales.</p>
SlumberNet: Deep learning classification of sleep stages using residual neural networks
<p>Sleep research is fundamental to understanding health and well-being, as proper sleep is essential for maintaining optimal physiological function. Here we present SlumberNet, a novel deep learning model based on residual network (ResNet) architecture, designed to classify sleep states in mice using electroencephalogram (EEG) and electromyogram (EMG) signals. Our model was trained and tested on data from mice undergoing baseline sleep, sleep deprivation, and recovery sleep, enabling it to handle a wide range of sleep conditions. Employing k-fold cross-validation and data augmentation techniques, SlumberNet achieved high levels of accuracy (~98%) in predicting sleep stages and showed robust performance even with a small and diverse training dataset. Comparison of SlumberNet's performance to manual sleep stage classification revealed a significant reduction in analysis time (~50x faster), without sacrificing accuracy. Our study showcases the potential of deep learning to facilitate sleep research by providing a more efficient, accurate, and scalable method for sleep stage classification. Our work with SlumberNet demonstrates the power of deep learning in sleep research, and looking forward, SlumberNet could be adapted to human EEG analysis and sleep stage classification. Thus, SlumberNet could be a valuable tool in understanding both sleep physiology and disorders in mammals.</p>
Figure 3 in DESCRIPTION OF THE LARVAE OF CRICOTOPUS FESTIVELLUS (KIEFFER 1906) AND CRICOTOPUS DIVERSUS (BOESEL 1983) WITH KEYS TO DISCRIMINATION OF LARVAL, PUPAL AND ADULT STAGES (DIPTERA: CHIRONOMIDAE) Abstract
Figure 3. Cricotopus festivellus; lateral tufts on segment 6 and 7. Veluwerandmeer, 5 October 2016.
Data for: Behavioral evidence of olfactory imprinting during embryonic and larval stages in lake sturgeon
<p>Many migratory fishes are thought to navigate to natal streams using olfactory cues learned during early life stages. However, direct evidence for early-life olfactory imprinting is largely limited to Pacific salmon, and other species suspected to imprint show life history traits and reproductive strategies that raise uncertainty about the generality of the salmonid-based conceptual model of olfactory imprinting in fishes. Here, we studied early-life olfactory imprinting in lake sturgeon (<em>Acipenser fulvescens</em>), which have a life cycle notably different from Pacific salmon, but are nonetheless hypothesized to home via similar mechanisms. We tested one critical prediction of the hypothesis that early-life olfactory imprinting guides natal homing in lake sturgeon: that exposure to odorants during early-life stages results in increased activity when exposed to those odorants later in life. Lake sturgeon were exposed to artificial odorants (phenethyl alcohol and morpholine) during specific developmental windows and durations (limited to the egg, free-embryo, exogenous feeding larvae, and juvenile stages), and later tested as juveniles for behavioral responses to the odorants that were demonstrative of olfactory memory. Experiments revealed that lake sturgeon reared in stream water mixed with artificial odorants for as little as 7 days responded to the odorants in behavioral assays over 50 days after the initial exposure, specifically implicating the free-embryo and larval stages as critical imprinting periods. Our study provides evidence for olfactory imprinting in a non-salmonid fish species, and supports further consideration of conservation tactics such as stream-side rearing facilities that are designed to encourage olfactory imprinting to targeted streams during early life stages. Continued research on lake sturgeon can contribute to a model of olfactory imprinting that is more generalizable across diverse fish species and will inform conservation actions for one of the world's most imperiled fish taxonomic groups.</p>
Nutritional Value Formation of Silkworm Pupa at Different Growth Stages: Analysis from Multi-omics Perspective
<p>Silkworm pupa (Bombyx mori) is affinal drug and diet in China, which is rich in protein and human essential amino acids. However, it is unclear how the internal nutritional composition changes and the antioxidant situation throughout the transformation of a silkworm pupa into a silkworm moth. In this study, we investigated the samples from four growth stages during silkworm pupal emergence by integrating proteomics and metabolomics. The results of the systematic bioinformatics study revealed that the growth of silkworm pupae considerably altered the ribosome-related genetic expression, cuticle development, and folate metabolism. The partial redox-active amino acid levels and the level of peroxiredoxin 1 expression were consistent with the fact that the total antioxidant capacity was higher in 7- and 10-day-old silkworm pupae. As compared to silkworm pupae, the amounts of fatty acids rose while those of amino acids, peptides, and organic acids dropped. This research also discovered that the altered protein profiles of silkworm pupae were controlled by the differential expression of mTOR signaling proteins (V-ATPase, S6, eIF4E) and ubiquitin mediate proteins (RP-L40e, UBE2L3, UBE2N, SKP1, ELOC). This study provided a new scientific foundation for the development and utilization of edible insect silkworm pupa functional food products.</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.