Find research datasets worth reusing

opencc-by-4.0Mar 2017View details →

A dataset for high-level activity recognition based on low level audio events

The high level activities are: - kitchencleanup - music - no activity - other activity - talk - tv Each recording of low-level audio events is stored in a separate file. Files are organized in 6 folders, each folder corresponding to a separate file. The format of is file is json-like. In particular, each row has the following format: {"prob": 0.88557562121157585, "energy": 0.024511212402412885, "t": 1485110417, "event": "speech"} This dataset can be evaluated with the python code metaClassifier/evaluate.py of the AUOR repository: https://github.com/tyiannak/AUROS

opencc-by-4.0Mar 2024View details →

STORM Data: Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters

The dataset underlying the SMLM STORM super-resolution images of 'Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters'. See Biorxiv paper for details on sample preparation: <a href="https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf">https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf</a>, Pyranose Oxidase STORM buffer on Elyra 7 Zeiss Microscope, processed with Zen Black. Samples are named according to which figures they occur in the above paper.

opencc-zeroMar 2024View details →

Blood lead levels in an endangered vulture decline following changes in hunting activity

Lead ammunition stands out as one of the most pervasive pollutants affecting wildlife. Its impact on bird populations has spurred efforts for the phase-out of leaded gunshots in several countries, although with varying scopes and applications. Ongoing and future policy changes require data to assess the effectiveness of adopted measures, particularly in the current context of biodiversity loss. Here, we assessed the long-term changes in blood lead (Pb) levels of Egyptian vultures from the Canary Islands, Spain, which have been severely affected by Pb poisoning over the past two decades. During this period, the reduction in hunting pressure and changes in legislation regarding firearms usage for small game hunting likely contributed to a decrease in environmental Pb availability. As anticipated, our results show a reduction in Pb levels, especially after the ban on wild rabbit hunting with shotguns since 2010. This effect was stronger in the preadult fraction of the vulture population. However, we still observed elevated blood Pb levels above the background and clinical thresholds in 5.6% and 1.5% of individuals, respectively. Our results highlight the positive impact of reducing the availability of Pb from ammunition sources on individual health. Nonetheless, the continued use of Pb gunshot remains an important source of poisoning, even lethal, mainly affecting adult individuals. This poses particular concerns for long-lived birds, compounding by potential chronic effects associated with Pb bioaccumulation. Our findings align with recent studies indicating insufficient reductions in Pb levels among European birds of prey, attributed to limited policy changes and their uneven implementation. We anticipated further reductions in Pb levels among Egyptian vultures with expanded restrictions on hunting practices, including a blanket ban on Pb shot usage across all small game species.

opencc-by-4.0Aug 2024View details →

The yin and yang of hsa-miR-1244 expression levels during activation of the UPR control cell fate - Raw data for label-free holographic microscopy

Regulation of endoplasmic reticulum (ER) homeostasis plays a critical role in maintaining cell survival. When ER stress occurs, a network of three pathways called the unfolded protein response (UPR) is activated to reestablish homeostasis. While it is known that there is cross-talk between these pathways, how this complex network is regulated is not entirely clear. Using human cancer and non-cancer cell lines, two different genome-wide approaches, and two different ER stress models, we searched for miRNAs that were decreased during the UPR and surprisingly found only one, miR-1244, that was found in all these conditions. The activation of both UPR adaptive and apoptotic signaling pathway was confirmed by parallel genome-wide mRNA expression arrays for Calu 3 cells and next generation sequencing for 16HBE14o- cells. We also verified that ER-stress related downregulation of miR-1244 expression occurred with 5 different ER stressors and was confirmed in another human cell line (HeLa S3). These analyses demonstrated that the outcome of this reduction during ER stress supported both IRE1 signaling and elevated BIP expression. Further analysis also revealed that this novel miRNA impacted all three pathways of the UPR using inhibitors specific for IRE1, ATF6, and PERK. This is the first example of a complex mechanism by which this miRNA serves as a regulatory check point for all 3 pathways that is switched off after UPR activation. In summary, the results indicate that ER stress reduction of miR-1244 expression contributes to the pro-survival arm of UPR. For real-time monitoring of cell viability, we applied real-time and label-free holographic microscopy-based monitoring of cell death and viability using HoloMonitor M4® time-lapse cytometer (Phase Holographic Imaging PHI AB, Lund, Sweden). Holographic microscopy was used to follow the optical thickness and irregularity of cells exposed for up to 24 h to Tm or Tg in the presence or absence of miR-1244 mimic or antagomiR. The images from up to 8 independent optical fields were collected and analyzed according to manufacture instructions with HoloMonitor® App Suite software. Healthy cells are irregular in shape and thin, whereas dying cells are round and thick . For all analysis, the same cells parameters qualification was applied.     Figure 4. Overexpression of miR-1244 promotes cell death. The results of real-time monitoring of cell viability are shown with the real time and label free holographic microscopy using a HoloMonitor M4® time-lapse cytometer of HeLa cells transfected with miR-1244 mimic or inhibitor or the scramble control and 48 h later monitored up to 24 h. Images were collected every 15 min (from 8 independent optical fields), and the distribution of live (blue) and dying cells (red) based on their optical thickness (Y-axes) and irregularity (X-axes) is presented at the 0, 8, 16 and 24 h time points. The images from up to 5 independent optical fields were collected and analyzed according to manufacturer’s instructions with HoloMonitor® App Suite software. Representative samples are shown (A). For all analyses, the same cell parameter qualifications were applied. Experiments were performed in triplicate. Based on the cells irregularity and average optical thickness the percentages of healthy cells (B) and of dying cells (C) were calculated. Data represents the mean ± SE of three independent experiments. *P< 0.05, **P< 0.001, ***P< 0.0001 were considered significant. Figure 5. miR-1244 influences the fate of cells challenged with Tm induced ER stress. The results of real-time monitoring of cell viability with the real time and label free holographic microscopy are shown using a HoloMonitor M4® time-lapse cytometer of HeLa cells transfected with miR-1244 mimic or inhibitor or the scramble control and 48 h later treated with Tm (2.5 µg/ml) up to 24 h. Images were collected every 15 min (from 5 independent optical fields), and the distribution of live (blue) and dying cells (red) based on their optical thickness (Y-axes) and irregularity (X-axes) is presented at the 0, 8, 16 and 24 h time points. The images from up to 5 independent optical fields were collected and analyzed according to manufacturer’s instructions with HoloMonitor® App Suite software. Representative samples are shown (A). For all analyses, the same cell parameter qualifications were applied. Experiments were performed in triplicate. Based on the cells irregularity and average optical thickness the percentages of healthy cells (B) and of dying cells (C) were calculated. <a name="OLE_LINK3"></a>Data represents the mean ± SE of three independent experiments. *P< 0.05, **P< 0.001, ***P< 0.0001 were considered significant. Figure 6. Exogenous miR-1244 influences the fate of cells challenged with Tg induced ER stress. The results of real-time monitoring of cell viability with the real time and label free holographic microscopy are shown using a HoloMonitor M4® time-lapse cytometer of HeLa cells transfected with miR-1244 mimic or inhibitor or the scramble control and 48 h later treated with Tg (500 nM) up to 24 h. Images were collected every 15 min (from 5 independent optical fields), and the distribution of live (blue) and dying cells (red) based on their optical thickness (Y-axes) and irregularity (X-axes) is presented at the 0, 8, 16 and 24 h time points. The images from up to 5 independent optical fields were collected and analyzed according to manufacturer’s instructions with HoloMonitor® App Suite software. Representative samples are shown (A). For all analyses, the same cell parameter qualifications were applied. Experiments were performed in triplicate. Based on the cells irregularity and average optical thickness the percentages of healthy cells (B) and of dying cells (C) were calculated. Data represents the mean ± SE of three independent experiments. *P< 0.05, **P< 0.001, ***P< 0.0001 were considered significant.

opencc-by-4.0Feb 2022View details →

Differences in gut microbiome abundances and diversity by physical activity levels and BMI among patients with colorectal cancer

We investigated associations of physical activity, BMI, and combinations of physical activity levels/BMI with gut microbiome diversity and differential abundances among colorectal cancer patients. Pre-surgery stool samples from 179 colorectal cancer patients were used to perform 16S rRNA gene sequencing.

opencc-by-4.0Apr 2022View details →

Data from: Even low light pollution levels affect the spatial distribution and timing of activity of a "light tolerant" bat species

Abstract of the related publication : By disrupting nocturnal landscapes worldwide, light pollution caused by Artificial Light At Night (ALAN) is recognised as a major threat to biodiversity. As even low light intensities might affect some taxa, concerns are arising about biological responses to widespread low light levels. We used data from a French citizen science bat monitoring program (1,894 full-nights monitored on 1,055 sites) to explore the landscape-scale effects of light on an open-space-foraging bat species, the Serotine bat (Eptesicus serotinus). We assessed this species' abundance and timing of night-time activity (median time of activity) at foraging sites. ALAN, and to a lesser extent moonlight, reduced E. serotinus abundance. ALAN delayed activity, and this delay was amplified during overcast nights. On the contrary, where there was no ALAN, the higher the cloud cover, the earlier the activity occurred. Cloud cover likely darkened the night sky in rural locations, whereas it amplified skyglow in light-polluted places, increasing ALAN effects on bats. Interestingly, moonlight also delayed activity but this effect was weakened where there was ALAN. Our study shows that even fine variations of light levels could affect the spatiotemporal distribution of a common species usually considered to be “light tolerant”, with potential cascading effects on individual fitness and population dynamics. It stresses how urgent it is to preserve and restore dark areas to protect biodiversity from light pollution while working on light intensity and directivity where ALAN is needed.

opencc-by-4.0Dec 2017View details →

Active thermography to estimate leaf heat transfer - leaf level data to manuscript

Active thermography is an informative methodology to measure that we adopted to plant sciences to measure leaf heat transfer and derive spatial maps of thermal responsiveness of leaves. This method and its usability is described in a publication in 'Frontiers of Plant Sciences'. Here we publish the data-set of active thermography measurements that were used in this publication. The Mat-lab code that was developed with this publication is also published at Zenodo under the doi 10.5281/zenodo.1195869

opencc-by-4.0Oct 2024View details →

Linking 23 physical activity intensity levels to health-related quality of life in 10-year-old children

This anonymized data is a subset of the ASK study:   Resaland, G.K., Moe, V.F., Aadland, E., et al. Active Smarter Kids (ASK): Rationale and design of a cluster-randomized controlled trial investigating the effects of daily physical activity on children’s academic performance and risk factors for non-communicable diseases.BMC Public Health 15, 709 (2015). https://doi.org/10.1186/s12889-015-2049-y The ASK study was approved by the Regional Committees for Medical and Health Research Ethics in Norway (reference number: 2013/1893) and registered at www.Clinicaltrials.gov with ID NCT02132494.  The selected cross-sectional baseline data in this file are used in the following unpublished paper:  Stai, M., Aadland, E., Andersen, J.R. (Year). *Linking 23 physical activity intensity levels to health-related quality of life in 10-year-old children. The data is stored in Excel. Explanations:   - #NULL! = missing data - Sex (0 = Girl, 1= Boy)   - Overweight or obesity (0 = No, 1 = Yes) - All other data has labeling that is self-explanatory.  Corresponding Author:   John Roger Andersen, johnra@hvl.no

opencc-zeroAug 2021View details →

Integrating light-level geolocation with activity tracking reveals unexpected nocturnal migration patterns of the tawny pipit

Migratory birds complete their seasonal journeys between breeding and non-breeding sites with a series of migratory flights that are separated by prolonged stopovers. While songbirds are the most common taxa among migratory birds, empirical data on flight and stopover behaviour along their entire migratory journeys are still rare. Here, we integrate activity and barometric pressure tracking with classical light-level geolocation to describe migration behaviour of tawny pipits Anthus campestris breeding in Central Europe. Surprisingly, tracked pipits used, on average, as many as 10 stopover sites during their six week, >5000 km long autumn migration. This conforms to a typical hop-type pattern of migration. In contrast to common knowledge which considers the tawny pipit as a typical diurnal migrant, our data revealed that more than 2/3 of all migratory movements were carried out at night. Nocturnal departure times were highly variable within individuals and spread across the entire night while landing most often took place within the first few hours after sunrise. Consequently, there was a negative relationship between departure timing relative to sunset and flight duration. Short flights of up to 2 h were most common and median flight duration was 4.5 h. There was a hyperbolic relationship between flight duration and maximum flight altitude and flight altitudes during night were two times higher compared to daytime. The overall ratio of flight vs stopover duration during migration was on average 1:6.5. This closely matches predictions from theoretical models. We show that multi-sensor tracking has the potential to provide unprecedented details on migratory behaviour of individual birds along their entire migratory journeys, and it also improves the precision of geographical locations derived from light-level geolocators.

opencc-zeroSep 2021View details →

Expression levels and activities of energy-yielding ATPases in the oligohaline neritid snail Theodoxus fluviatilis under changing environmental salinities

The aquatic gastropod Theodoxus fluviatilis occurs in Europe and adjacent areas of Asia. The snail species has formed two genetically closely related subgroups, the freshwater ecotype (FW) and the brackish water ecotype (BW). Other than individuals of the FW ecotype, those of the BW ecotype survive in salinities of up to 28‰. Coastal aquatic ecosystems may be affected by climate change due to salinization. Thus, we investigated how the two Theodoxus ecotypes adjust to changes in environmental salinity focussing on the question whether Na+ /K+ -ATPase or V-ATPase are regulated on the transcriptional, the translational or at the activity level under changing external salinities. Animals were gradually adjusted to extreme salinities in containers under long-day conditions and constant temperature. Whole body RNA- or protein extracts were prepared. Semi-quantitative PCR and Western Blot-analyses did not reveal major changes in transcript or protein abundances for the two transporters under low or high salinity conditions. No significant changes in ATPase activities in whole body extracts of animals adjusted to high or low salinity conditions were detected. We conclude that constitutive expression of ATPases is sufficient to support osmotic and ion regulation in this species under changing salinities given the high level of tolerance with respect to changes in body fluid volume.

opencc-by-4.0Oct 2021View details →

Activation level of 64 gene signatures in glioblastoma

This repository includes the XGBoost models and the R scripts to infer the activation status of 64 gene signatures in GBM, as published in this manuscript: Topographic mapping of the glioblastoma proteome reveals a triple axis model of intra-tumoral heterogeneity Lam KHB, Leon AJ, Hui W, Lee SCE, Batruch I, Faust K, Koritzinsky M, Richer M, Djuric U, Diamandis P (under review) The models take as input proteomics (LFQ) of rna (TPM) expression data. Execute the following command to analyze the sample data: <pre><code>Rscript predictXGB.R --data sample/sample_prot.rds \ --models data/list_xgb-gbm_64_signatures-prot-v01.RData \ --out_csv predictXGB_sample_rna.csv</code></pre>

opencc-zeroJan 2023View details →

Datasets for: Colony-nesting gulls restrict activity levels of native top carnivore during the breeding season

Although nesting in colonies can offer substantial reproductive benefits for many seabird species, increased visibility to predators remains a significant disadvantage for most colony-breeders. To counteract this, some seabird species have evolved aggressive nest defense strategies to protect vulnerable eggs and chicks. Here we used an experimental approach to test whether colony inhabitance by breeding gulls (Larus spp.) in western Norway impacts visitation rates of a native, mammalian predator, the Eurasian otter (Lutra lutra) during the breeding season. Camera traps were placed inside of and on the periphery of seabird colonies prior to the breeding season and left to run for one continuous year. Sighting frequency of otters on these cameras was compared to a control region free of gull nesting. We found that otter activity was significantly reduced on the colonies when gulls were incubating and rearing chicks, compared to time periods when gulls were building nests and absent from the colonies. Rhythmic activity patterns did not seem to be significantly impacted by the presence of gulls. This study provides clear evidence that certain colony-nesting species can have a direct, negative impact on visitation rates of a native carnivore. Seasonal carnivore activity patterns are likely to be highly dependent on differing nesting strategies and level of nest defense by seabirds.

opencc-by-4.0Mar 2023View details →

Data for: The Neonicotinoid Imidacloprid Impairs Sucrose Solution Consumption, Learning and Locomotor Activity Levels In Bumblebees (Bombus Terrestris)

# README The following files are for creating the figures from the paper:  ## `plot_flowervisits_nectar.ipynb` Jupyter notebook that creates the figures concerning flower visits, nectar consumption and the proportion of empty honeypots. ## `plot_activity.py` Python script that takes trajectory fragments from video analysis and computes the locomotor activity level through making histograms of bumblebee speeds. Makes two figures that are equivalent to the figure on locomotor activity in the paper. ## `statistical analysis.py` R markdown notebook that performs all the hypothesis testing for the paper. ## Data These files contain the data, and are located in the folder called `data`.  `activity/activityproportions.csv` contains the computed locomotor activity level for easy plotting. `boldata/boldata.csv` contains data about the nectar bag weight before and after experiment and the counted number of empty and full honeypots. Used by `plot_flowervisits_nectar.ipynb` `flower_data/flowerData.csv` contains the computed number of visits to blue and yellow flowers per hive for easy plotting. `humlevideo_production/*/traj*_trajectories*.csv` contains constructed trajectories from all experiments seen from both cameras. These are being used by the script `plot_activity`. `humlevideo_production/*/traj*.json` contains data about the occurence of bees on flowers in each frame in each experiment. `landinger_csv` contains data about landings, that have been extracted from the `humlevideo_production/*/traj*.json` files. Used by `plot_flowervisits_nectar.ipynb`.

opencc-zeroOct 2023View details →

Data from: Dynamic shifts in predator diel activity patterns across landscapes and threat levels

Understanding the constraints dominant predators impose on subordinate species is important for predicting ecosystem dynamics and anticipating outcomes of predator management. Subordinate predators may avoid dominant predators in time or space, making it difficult to quantify antipredator behaviours unless joint spatiotemporal analyses are used. Here, we tested whether an invasive dominant predator (red fox Vulpes vulpes) alters the spatiotemporal activity of an invasive subordinate predator (feral cat Felis catus). We collated records of both species from 3,667 camera-traps deployed experimentally across two regions of south-eastern Australia with simplified predator guilds. Foxes were poison-baited in some landscapes within each region. We used generalised additive models to quantify changes in predator spatiotemporal activity across geographic space, vegetation types, human footprint and (artificially manipulated) gradients of dominant predator activity. Foxes and cats had similar diel activity patterns when averaged across all sites, however there was important differentiation at a finer scale cats did not reduce their spatial activity but shifted diel patterns when localised fox activity was high. Cats were crepuscular on average. However, across dry vegetation types of both regions (where foxes were nocturnal), cats shifted to diurnal behaviour with increasing fox activity. In contrast, fox activity was relatively consistent throughout the daily cycle in the wet forest; here cats avoided dawn when fox activity was high. Changes in cat diel activity patterns may facilitate spatial coexistence between these two invasive predators, potentially shifting feral cat impacts onto different native prey. It is well-appreciated that predator activity varies spatially and fluctuates throughout the daily cycle. However, our study demonstrates that diel activity patterns also vary across space, likely mediated by both landscape-context and fear. Dominant predator avoidance in time appears to be spatially dynamic a key nuance which is overlooked when simply comparing the average activity overlap between two species.

closedIPD-NOFeb 2026View details →

Gut-level Antiinflammatory Activities of Green Tea in Metabolic Syndrome

ClinicalTrials.gov study NCT03973996. IPD Sharing: NO. Countries: 1. Publications: 4.

controlledIPD-YESFeb 2026View details →

Using Smartphones to Improve Physical Activity Levels of Individuals With Spinal Cord Injury

ClinicalTrials.gov study NCT05317832. IPD Sharing: YES. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

The Relationship Between Dual-task Gait Performance, Physical Activity Levels, Sleep and Aging in Healthy Adults

ClinicalTrials.gov study NCT04144647. IPD Sharing: NO. Countries: 1. Publications: 27.

restrictedIPD-UNDECIDEDFeb 2026View details →

Evaluate Protein C Levels in Severe Sepsis Patients on Drotrecogin Alfa (Activated)

ClinicalTrials.gov study NCT00386425. IPD Sharing: Not stated. Countries: 9. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

Study to Evaluate Activity of 2 Dose Levels of Imetelstat in Participants With Intermediate-2 or High-Risk Myelofibrosis (MF) Previously Treated With Janus Kinase (JAK) Inhibitor

ClinicalTrials.gov study NCT02426086. IPD Sharing: Not stated. Countries: 11. Publications: 1.