Find research datasets worth reusing

opencc-by-4.0Jan 2016View details →

Fig. 1 in Home range and activity patterns of Sunda scops owl in Peninsular Malaysia

Fig. 1. Location of Ayer Hitam Forest Reserve, Selangor, Peninsular Malaysia.

opencc-by-4.0Jul 2017View details →

Fig. 1 in Dependence of daily oviposition activity and total fecundity on body mass in the house cricket Acheta domesticus (L.) (Insecta: Orthoptera)

Fig. 1: Biological traits demonstrably influenced by body mass in orthopterans (WITHMAN 2008).

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.

Dataset for "Comparative Analysis of Machine Learning Models to Forecast Flaring Capability of Solar Active Regions: A Parameter Based Approach"

This CSV file contains the values of 14 selected magnetic features along with the active region class for all the regions used in our study. As discussed in the paper, these 14 magnetic features characterize the properties of active regions. All these magnetic features are obtained from the HMI SHARP data series which provides open-sourced vector magnetic field information of solar active regions. the column named 'AR_class' carries information about the class of active regions i.e., 1 for flaring regions and 0 for non-flaring regions.

opencc-zeroSep 2021View details →

Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricket Gryllus bimaculatus

This dataset contains data from a laboratory experiments described in the paper: "Levy, K., Wegrzyn, Y., Efronny, R., Barnea, A., & Ayali, A. 2021 Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricket Gryllus bimaculatus. Proc. R. Soc. B 20211626. <a href="https://doi.org/10.1098/rspb.2021.1626">https://doi.org/10.1098/rspb.2021.162</a>". Artificial light at night (ALAN) is increasing worldwide,with most of the world population living under light-polluted skies. Growing awareness of the harmful effects of ALAN calls for more comprehensive understanding of these effects. The stridulation and locomotion patterns of adult male crickets reared under different lifelong ALAN intensities were monitored simultaneously for five consecutive days in custom-made anechoic chambers. Activity periods and acrophases were compared between the experimental groups. Control crickets exhibited a robust rhythm, stridulating at night and demonstrating locomotor activity during the day. In contrast, ALAN affected both the relative level and timing of the crickets' nocturnal and diurnal activity. ALAN induced free-running patterns, manifested in significant changes in the median and variance of the activity periods, and even arrhythmic behavior. The magnitude of disruption was light intensity dependent, revealing an increase in the difference between the activity periods calculated for stridulation and locomotion in the same individual. Our results demonstrate that ecologically-relevant ALAN intensities affect crickets' behavioral patterns, and may lead to decoupling of locomotion and stridulation behaviors at the individual level, and to loss of synchronization at the population level.

Supporting data of "Temperature and barometric pressure affect the activity intensity and movement of an endangered thermoconforming lizard"

JOURNAL PUBLICATION CITATION: Daniel Ariano-Sánchez, Rasmus M. Mortensen, Rory P. Wilson, Peder Bjureke, Stefanie Reinhardt and Frank Rosell. Temperature and barometric pressure affect the activity intensity and movement of an endangered thermoconforming lizard. Ecosphere. ------------ Raw data in RDS format and R codes of movement paths and step-selection function analyses ------------- CleanDBALMM.R – R script of the LMM for VeDBA from obtained from the daily diaries in the backpack system. CleanGPSHeloderma.R – R script for calculation of step-lengths, bearings and turning angles from the GPS data of the Guatemalan Beaded Lizards tracked, including the LMM and circular-linear regressions. CleanSSF.R – R script of the step-selection functions. DBAHeloderma.rds – Raw data of the Guatemalan Beaded Lizard movement obtained from the daily diaries in the backpack system. GPSData.rds - Raw data of the Guatemalan Beaded Lizard movement obtained from GPS tags. ssf3.rds – Dataset for the step-section functions.

Virtual Storage Plant (VSP) preliminary demonstration of active power control

This the dataset of preliminary demostration of using distributed control with consensus algorithm for dispatching a virtual storage plant. The dataset contains raw data from 4 experiments (3, 4, 5 and 6 units in a VSP) for 5 scenarios: TC_5.02.01, TC_5.02.02, TC_5.02.03, TC_5.02.04, TC_5.02.05. The experiments were conducted at the University of Zagreb's Smart Grid Laboratory (SGLab).

opencc-by-4.0Mar 2022View details →

Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files

Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms

Determining voluntary activation in synergistic muscles: new insights from a mechanomyographic approach

Aim: We propose a new approach based on the mechanomyographic (MMG) signal to detect the voluntary activation (VA) of the synergistic superficial heads of quadriceps muscle. We  hypothesised that, after a fatiguing task, the changes in MMG signal of each quadriceps’ head would correlate with the level of VA of the whole quadriceps. Methods: Twenty-five men [age:25(1) yrs; body mass:77(2) kg; stature:1.81(0.02) m] underwent a unilateral single-leg quadriceps exercise up to failure. Before and after the intervention, VA was assessed by the interpolated twitch technique via nerve stimulation during and after a maximum voluntary contraction (MVC). Along with force, the MMG signal was recorded from vastus lateralis, vastus medialis, and rectus femoris muscles. The MMG peak-to-peak was calculated and the voluntary activation index (VAMMG) as the superimposed/potentiated MMG peak-to-peak ratio, was determined from the MMG signal for each head.  Results: VAMMG presented very-high reliability (ICC:0.975-0.998) and sensitivity (MDC95%: 0.4%-4.26%). Fatigue reduced MVC and VA in both the exercised [-17(5)%, ES:-0.92 and -7(3)%, ES:-1.90 for MVC and VA, respectively] and the contralateral limb [-15(7)%, ES:-0.87 and -7(3)%, ES:-2.32 for MVC and VA, respectively]. VAMMG decreased in both the exercised [~-9(6)%, ES:-1.00] and the contralateral limb [~-5(2)%, ES:-1.12], with larger VAMMG decrements occurring in vastus medialis in the exercised limb only. Moderate to very high correlations were found between VAMMGand VA (R= 0.503-0.886) before and after fatigue.  Conclusions: VAMMG may be implemented to assess VA and could provide further information when different synergistic muscle heads are involved in a fatiguing task.

Dataset for the study Sensitive period for the plasticity of alpha activity in humans

Raw EEG data in european data format (EDF) format. Descriptive and clinical data of the subjects in textual tab delimited format. Columns report for each subject: group (blind/severely impaired, BSI or sighted, S), code, gender, age expressed in decimal years, age bin, degree of visual impairment, diagnosis, motor coordination impairment classification (MCI, 1 = not impaired, 2 = impaired), and hypotonia classification (1 = not impaired, 2 = impaired).  NA correspond to undefined classification. Visual experience is crucial for the development of neural processing. For example, alpha activity development is a vision-dependent mechanism. Indeed, studies report no alpha activity is present in blind adults. Nevertheless, studies have not investigated the developmental trajectory of this activity in infants and children with blindness. Here, we hypothesize that the difference in neural activity of blind compared to sighted subjects is: absent at birth, progressive with age, specifically occipital and linked to a gradual motor impairment. Therefore, we consider spectral power of resting-state EEG and its association with motor impairment indices, in blind subjects and in sighted controls between 0 and 11 years of age. Blind subjects show posterior alpha activity during the first three years of life, although weaker and slower maturing compared to sighted subjects. The first great differentiation between blind and sighted subjects occurs between 3 and 6 years of age. Starting in this period, reduced alpha activity increases the probability of motor impairment in blind subjects, likely because of impaired perception/interaction. These results show that visual experience mediates the neural mechanisms generating alpha oscillations during the first years of life, suggesting that it is a sensitive period for the plasticity of this process.

Active sensing in bees through antennal movements is independent of odor molecule (source videos)

Videos of restrained bombus terrestris stimulated by odors to record their antennal movements. The video were used in the following preprint: https://www.biorxiv.org/content/10.1101/2021.09.13.460114v1

Data from: Historical human activities reshape evolutionary trajectories across both native and introduced ranges

The same vectors that introduce species to new ranges could move them among native populations, but how human‐mediated dispersal impacts native ranges has been difficult to address because human‐mediated dispersal and natural dispersal can simultaneously shape patterns of gene flow. Here, we disentangle human‐mediated dispersal from natural dispersal by exploiting a system where the primary vector was once extensive but has since ceased. From 10th to 19th Centuries, ships in the North Atlantic exchanged sediments dredged from the intertidal for ballast, which ended when seawater ballast tanks were adopted. We investigate genetic patterns from RADseq‐derived SNPs in the amphipod Corophium volutator (n = 121; 4,870 SNPs) and the annelid Hediste diversicolor (n = 78; 3,820 SNPs), which were introduced from Europe to North America, have limited natural dispersal capabilities, are abundant in intertidal sediments, but not commonly found in modern water ballast tanks. We detect similar levels of genetic subdivision among introduced North American populations and among native European populations. Phylogenetic networks and clustering analyses reveal population structure between sites, a high degree of phylogenetic reticulation within ranges, and phylogenetic splits between European and North American populations. These patterns are inconsistent with phylogeographic structure expected to arise from natural dispersal alone, suggesting human activity eroded ancestral phylogeographic structure between native populations, but was insufficient to overcome divergent processes between naturalized populations and their sources. Our results suggest human activity may alter species' evolutionary trajectories on a broad geographic scale via regional homogenization and global diversification, in some cases precluding historical inference from genetic data.

openDec 2019View details →

Dataset relating the Social activity of Open Research Data on ResearchGate

The potential of Open Research Data (ORD) within the context of open science and digital scholarship can be frustrated if data remains unused. Although current research has investigated the way ORD is being published,  researchers’ behaviour of ORD publishing and sharing on academic social networks (ASN) remains insufficiently explored. The research to which this dataset is connected aims to illustrate some parameters of social activity around self-archived ORDs on ResearchGate. The study analyses whether the ORDs publication leads to social activity (reads and citations) around the ORDs and their linked published articles, including eventual associations between the social activity and the researchers’ profile (scientific domain, gender, region, professional position, reputation) as well as the quality of the ORD published. The current dataset is composed by: A- The .csv file, extracted as a random sample of 752 ORD items from ResearchGate. The dataset has been polished and anonymized. The variables relating the researchers' profiles and citations to the ORD lined research were got from the researchers' profiles and published research. However, for the purpose of anonymisation, these variables have been coded and the original information removed. B- The codebook explaining the variables and metrics contained in the file (A) C- The R script. This script contains a number of explorations not reported in the final paper. The quantitative techniques applied include descriptive statistics, logistic regression and K-means cluster analysis. D- Five tables, three figures and two annexes (Logistic Regression I and II) created over the basis of the dataset (A) The results have been interpreted in terms of three main aspects. <ul> <li>Firstly, there is still an underdeveloped social activity around self-archived ORD in ResearchGate (operationalized as reads and citations) overall and in spite of the published ORDs quality.</li> <li>Secondly, it was found an uncovering of the relevance of the moderating effects over ORD, which spots traditional dynamics within the “innovative” practice of engaging with data practices.</li> <li>Thirdly, a rather similar situation of ResearchGate as ASN with regard to other data platforms and repositories in terms of social activity around ORD was detected.</li> </ul> The potential of Open Research Data (ORD) within the context of open science and digital scholarship can be frustrated if data remains unused.

Data from: Seasonality of floral resources in relation to bee activity in agroecosystems

The contribution of wild insects to crop pollination is becoming increasingly important as global demand for crops dependent on animal pollination increases. If wild insect populations are to persist in agricultural landscapes, there must be sufficient resources over time and space. The temporal, within‐season component of floral resource availability has rarely been investigated, despite growing recognition of its likely importance for pollinator populations. Here, we examined the visitation rates of common bee genera and the spatiotemporal availability of floral resources in agroecosystems over one season to determine whether local wild bee activity was limited by landscape floral resource abundance, and if so, whether it was limited by the present or past abundance of landscape floral resources. Visitation rates and landscape floral resources were measured in 27 agricultural sites in Ontario and Québec, Canada, across four time periods and three spatial scales. Floral resources were determined based on species‐specific floral volume measurements, which we found to be highly correlated with published measurements of nectar sugar mass and pollen volume. Total floral volume at varying spatial scales predicted visits for commonly observed bee genera. We found Lasioglossum and Halictus visits were highest in landscapes that provided either a stable or increasing amount of floral resources over the season. Andrena visits were highest in landscapes with high floral resources at the start of the season, and Bombus visits appeared to be positively related to greater cumulative seasonal abundance of floral resources. These findings together suggest the importance of early‐season floral resources to bees. Megachile visits were negatively associated with the present abundance of floral resources, perhaps reflecting pollinator movement or dilution. Our research provides insight into how seasonal fluctuations in floral resources affect bee activity and how life history traits of bee genera influence their responses to food availability within agroecosystems.

Aerosol–cloud interactions: the representation of heterogeneous ice activation in cloud models

The files contain the data sets shown in the publication "Aerosol–cloud interactions: the representation of heterogeneous ice activation in cloud models" to appear in final form in the journal Atmos. Chem. Phys. in 2021. A preliminary discussion version of the manuscript is available under  https://doi.org/10.5194/acp-21-1-2021. The files include a power point slide containing the schematic Fig.1 and xmgrace plot files containing the research data (ASCII) shown in Figs.2,3,4, and A1. Specifically (Gn means graph #n, Sm means set # m): in Fig.2, the black solid curve is listed under G0.S0; the blue solid curve G0.S1; dashed = G0.S2; dot-dashed = G0.S3 in Fig.3, curve (a) = G0.S0; black curve (b) = G1.S0, red curve (b) = G1.S1; black solid (c) = G2.S0 black dashed (c) = G2.S3; red solid (c) = G2.S1, red dashed (c) = G2.S2; curve (d) = G3.S0, black curve (e) = G4.S0; red curve (e) = G4.S1, black solid (f) = G5.S0, black dashed (f) = G5.S4, red solid (f) = G5.S1, red dashed (f) = G5.S2 in Fig.4, solid orange curve (a) = G0.S0, dashed orange (a) = G0.S1, solid red (a) G0.S2, dashed red (a) = G0.S3, solid blue (a) = G0.S4, dashed blue (a) = G0.S5; solid curve (b) = G1.S0, dashed (b) = G1.S1 in Fig.A1, solid black curve = G0.S0, solid blue = G0.S1

A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-Lymphedema-Telangiectasia-Renal Syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

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>

The predator activity landscape predicts the anti‐predator behavior and distribution of prey in a tundra community

Predation shapes communities through consumptive and non-consumptive effects. In the latter case, prey respond to perceived predation risk through proactive or reactive risk management strategies occurring at different spatial and temporal scales. The predator-prey space race and landscape of fear concepts are useful to better understand how predation risk affects prey behavioral decisions and distribution. We assessed predation-risk effects in a terrestrial Arctic community, where the arctic fox is the main predator of ground-nesting birds. Using high frequency GPS data, we estimated a predator activity landscape corresponding to fox space use patterns, and validated with an artificial prey experiment that this predator activity landscape correlated with the predation risk landscape. We then investigated the effects of the fox activity landscape on multiple prey species, by assessing the anti-predator behavior of a main prey (snow goose) actively searched for by foxes, and the nest distribution of several incidental prey species. We first found that snow geese showed a stronger level of nest defense in areas highly used by foxes, possibly responding with a reactive strategy to variation in predation risk. Then, nests of incidental prey reproducing in habitats easily accessed by foxes had a lower probability of occurrence in areas highly used by foxes, suggesting these birds may use a proactive risk management strategy by shifting their distribution away from risky areas. For incidental prey species nesting in microhabitat refuges difficult to access by foxes, probability of nest occurrence was independent of predation risk in the surrounding area, as they avoid risk at a finer spatial scale. By tracking all individuals of the dominant predator species in our study area, we demonstrated the value of using predator space use patterns to infer spatial variation in predation risk. Overall, we highlight the diversity of risk management strategies in prey sharing a common predator, hence refining our understanding of the mechanisms driving species distribution and community structure.

Dataset: Discriminating Types of Volcanic Electrical Activity

This data set contains Lightning Mapping Array data and broadband VHF waveforms of electrical activity during three explosive eruptions of Sakurajima volcano in Japan in 2019 and 2020. The included README file contains pertinent information about each data set.