Find research datasets worth reusing

Defining the role of the miR-145 – KLF4 – αSMA axis in mitral valvular interstitial cell activation in myxomatous mitral valve prolapse using the canine model

Mitral valve prolapse (MVP) is a common valvular disease, affecting 2-3% of the adult human population and is a degenerative condition. 5-10% of the afflicted will develop severe mitral regurgitation, cardiac dysfunction, congestive heart failure, and sudden cardiac death. Naturally occurring myxomatous MVP in dogs closely resembles MVP in humans structurally, and functional consequences are similar. In both species, valvular interstitial cells (VICs) in affected valves exhibit phenotype consistent with activated myofibroblasts with increased αSMA expression. Using VICs collected from normal and MVP-affected valves of dogs, we analyzed the miRNA expression profile of the cells and their associated small extracellular vesicles (sEV) using RNA sequencing to understand the role of non-coding RNAs and sEV in MVP pathogenesis. miR-145 was shown to be upregulated in both the affected VICs and sEV, and overexpression of miR-145 by mimic transfection in quiescent VIC recapitulates the activated myofibroblastic phenotype. Concurrently, KLF4 expression was suppressed by miR-145, and KLF4 overexpression resulted in a decrease in αSMA expression, and its suppression resulted in an increase in αSMA expression, thus confirming the miR-145 – KLF4 – αSMA axis. Targeting this axis may serve as potential therapy in controlling pathologic abnormalities found in MVP valves.

Forest bat activity declines with increasing wind speed in the proximity of operating wind turbines

The increasing use of onshore wind energy is leading to an increased deployment of wind turbines in structurally rich habitats such as forests. Forest-affiliated bats, in turn, are at risk of colliding with the rotor blades. Due to the legal protection of bats in Europe, it is imperative to restrict the operation of wind turbines to periods of low bat activity to avoid collisions. However, bats have also been observed to avoid wind turbines over several hundred meters distance, indicating a displacement that cannot solely be explained by modifications to the habitat. This avoidance suggests a displacement of bats by indirect factors related to wind turbine operation, e.g., wake turbulences and noise emissions. Therefore, we investigated whether the activity of forest-affiliated bats is influenced by operation mode (on/off) under variable wind conditions along transects from 80 to 450 m distance to wind turbines. We divided recordings by foraging guild, i.e., either narrow-space (Myotis, Plecotus), edge-space (Pipistrellus, Barbastella), or open-space foraging bats (Nyctalus, Eptesicus, Vespertilio), and analyzed the effects of wind turbine operation and wind speed on the recorded bat guild activity with mixed effects models. The acoustic activity of narrow-space foraging bats decreased by 91% with increasing wind speed when wind turbines were operating, while bat activity remained unaffected by wind speed when turbines were not operating. This was neither observed for open-space foraging bats nor for edge-space foraging bats, and neither wind turbine operation nor wind speed (ranging between 0 – 4 m/s at 10 m height above ground) were found to affect bat activity when considered alone. Wind turbine noise emissions are known to increase with rotor speed and consequently, wind speed, thus presenting a likely explanation for the interactive negative effect of turbine operation and wind speed specifically on noise-sensitive narrow-space foraging bats. To understand potential ecological long-term consequences for bat populations in forest areas with wind turbines and to design effective conservation measures, future research should focus on disentangling the effects of different disturbances related to turbine operation.

Decision-related activity and movement selection in primate visual cortex

Fluctuations in the activity of sensory neurons often predict perceptual decisions. This connection can be quantified with a metric called choice probability (CP), and there has been a longstanding debate about whether CP reflects a causal influence on decisions, or an echo of decision-making activity elsewhere in the brain. Here we show that CP can actually reflect a third variable, namely the movement used to indicate the decision. In a standard visual motion discrimination task, neurons in the middle temporal (MT) area of the primate visual cortex responded more strongly during trials in which the animals executed a saccade toward their receptive fields, and less strongly for saccades directed away from the receptive fields. The resulting trial-to-trial variability accounted for much of the CP observed across the neuronal population, and it arose through training. The learned association between MT activity and oculomotor selection was causal, as pharmacological inactivation of MT neurons biased behavioral responses away from the corresponding receptive field locations. These results demonstrate that training on a task with fixed sensorimotor contingencies introduces movement-related activity in sensory brain regions, and that this plasticity can shape the neural circuitry of perceptual decision-making.

Data from: Diurnal variation of brain activity in the human suprachiasmatic nucleus

The suprachiasmatic nucleus (SCN) is the central clock for circadian rhythms. Animal studies have revealed daily rhythms in the neuronal activity in the SCN. However, the circadian activity of the human SCN has remained elusive. In this study, to reveal the diurnal variation of the SCN activity in humans, the SCN was localized, and its activity was investigated using perfusion imaging. We scanned each participant four times a day, every six hours, and higher activity was observed at noon while lower activity was recorded in the early morning. The SCN activity was then measured every thirty minutes for six hours from midnight to dawn and showed a decreasing trend and was comparable with the rodent SCN activity after switching off the lights. These results suggest that the diurnal variation of the human SCN follows the zeitgeber cycles of mammals and is modulated by physical lights rather than the local time.

Chemo- and optogenetic activation of hypothalamic Foxb1-expressing neurons and their terminal endings in the rostral-dorsolateral PAG leads to tachypnea, bradycardia, and immobility

Foxb1-expressing neurons occur in the dorsal premammillary nucleus (PMd) and further rostrally in the parvafox nucleus, a longitudinal cluster of neurons in the lateral hypothalamus of rodents. The descending projection of these Foxb1+ neurons end in the dorsolateral part of the periaqueductal gray (dlPAG). The functional role of the Foxb1+ neuronal subpopulation in the PMd and the parvafox nucleus remains elusive. In this study, the activity of the Foxb1+ neurons and of their terminal endings in the dlPAG was selectively altered by employing chemo- and optogenetic tools. Our results show that in whole-body barometric plethysmography, hM3Dq-mediated, global Foxb1+ neuron excitation activates respiration. Time-resolved optogenetic gain-of-function manipulation of the terminal endings of Foxb1+ neurons in the rostral third of the dlPAG leads to abrupt immobility and bradycardia. Chemogenetic activation of Foxb1+ cell bodies and ChR2-mediated excitation of their axonal endings in the dlPAG led to a phenotypical presentation congruent with a "freezing-like" situation during innate defensive behavior. The authors have no relevant financial or non-financial interests to disclose. This work was supported by the Swiss National Foundation grant 31003A_160325 to Marco R. Celio.

opencc-by-4.0Jan 2024View details →

Datasets for Insights into prismatic loop formation in irradiated Fe-Cr alloys from hypothesis-driven active learning and causal analysis

Datasets for irradiated Fe-Cr alloys are collected from the experimental reports on dislocation loop type and dislocation density. We have constructed a data set from experimental literature containing 182 data points. To address such challenges to predict dislocation density, we have implemented a three-step ML approach as listed in the following: <div> <div> <div> <ul> <li> impute dataset to fill in the missing data to construct a predictive model using the RF regression algorithm.  </li> <li> generate functionalized features and evaluate feature importance using the predictive model </li> <li> use the physics-based important functionalized features as hypotheses (physics-augmented GP models) in a hypothesis-driven active learning scheme to learn and predict dislocation density for all alloys.  </li> </ul> </div> </div> </div>

Data from: Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts

Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1,500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.

Data from: Camera traps reveal seasonal variation in activity and occupancy of the Alpine mountain hare (Lepus timidus varronis)

Mountain hare is a cold-adapted species threatened by climate change, but despite its emblematic nature, our understanding of the causes of population decline remains limited. Camera traps are increasingly used in ecology as a tool for monitoring animal populations at large spatial and temporal scales. In mountain environments where field work is constrained by difficult access and harsh conditions, camera traps constitute a promising tool for surveying rare and elusive species such as the mountain hare. Our study explored the use of camera traps as a tool for studying seasonal habitat occupancy and daily activity patterns of the mountain hare, in order to carry out long-term monitoring of populations. We installed 46 camera traps along elevation gradients in the Mont-Blanc massif (France) from January 2018 to June 2022. We measured habitat variables at each camera trap site in order to define vegetation composition and habitat structure. We performed multi-season and single-season occupancy models to respectively describe habitat occupancy of the mountain hare throughout the year and identify the environmental variables influencing mountain hare presence during the breeding season. Mountain hares occupy coniferous forest in winter, and then switch to mixed areas of shrubland and grassland above treeline in spring and the beginning of summer. In spring, occupancy probability of the mountain hare increases with relative cover of mixed low shrub and herbaceous layer (i.e. the 10-40 cm vegetation layer), suggesting a link to food resources and protection from predation. Our results also confirm the nocturnal and crepuscular activity of the mountain hare during the breeding season, and strictly nocturnal activity in winter. Our results demonstrate the efficiency of camera traps as tools for monitoring mountain hare habitat occupancy in mountain environments and underline the importance of diverse habitat mosaics for the preservation of the species.

Social network shrinking is explained by active and passive effects but not increasing selectivity with age in wild macaques

Evidence of social disengagement, network narrowing, and social selectivity with advancing age in several non-human animals challenges our understanding of the causes of social ageing. Natural animal populations are needed to test whether social ageing and selectivity occur under natural predation and extrinsic mortality pressures, and longitudinal studies are particularly valuable to disentangle the contribution of within-individual ageing from the demographic processes that shape social ageing at the population level. Data on wild Assamese macaques (Macaca assamensis) were collected between 2013 and 2020 at the Phu Khieo Wildlife Sanctuary, Thailand. We investigated the social behaviour of 61 adult females observed for 13,270 hours to test several mechanistic hypotheses of social ageing and evaluated the consistency between patterns from mixed-longitudinal and within-individual analyses. With advancing age, females reduced the size of their social network, which could not be explained by an overall increase in the time spent alone, but by an age-related decline in mostly active, but also passive, behaviour, best demonstrated by within-individual analyses. A selective tendency to approach preferred partners was maintained into old age but did not increase. Our results contribute to our understanding of the driver of social ageing in natural animal populations and suggest that social disengagement and selectivity follow independent trajectories during ageing.

Data from: The Drosophila Genetic Reference Panel (DGRP) on locomotor activity across different environmental conditions

In nature, organisms are exposed to variable and occasionally stressful environmental conditions. Responses to diurnal and seasonal fluctuations, such as temperature and food accessibility, involve adaptive behavioral and physiological changes. While much work has been done on understanding the genetic architecture and evolutionary potential of stress tolerance traits under constant thermal conditions, there has been less focus on the quantitative genetic background in variable environments. In this study, we use the Drosophila Genetic Reference Panel (DGRP) to investigate locomotor activity, a key behavioral trait, under variable natural thermal conditions during the summer in a temperate environment. Male flies from 100 DGRP lines were exposed to natural thermal and light conditions in Drosophila activity monitors across three experimental days. We found that activity was highly temperature- and time-dependent and varied between lines both within and between days. Further, we observed variation in genetic and environmental variance components, with low to moderate estimates of the heritability for locomotor activity, consistently peaking in the afternoons. Moreover, we showed that the estimated genetic correlations of locomotor activity between two time points decreased as the absolute differences in ambient temperature was increased. In conclusion, we find that the genetic background for locomotor activity is environment specific and we conclude that more variable and unpredictable future temperatures will likely have a strong impact on the evolutionary trajectories of behavioral traits in ectotherms.

opencc-by-4.0Dec 2023View details →

Raw data: The novel gammaproteobacterial methanotroph "Ca. Methylocalor cossyra" CH1 actively coexists with verrucomicrobial methanotrophs in acidic and hot geothermal soil

Open the record for dataset details and reuse information.

Data from: Coordinated ARP2/3 and glycolytic activities regulate the morphological and functional fitness of human CD8+ T cells

CD8+ T cells rely on actin cytoskeleton remodeling to search for target cells and assemble the immunological synapse (IS) for lethal hit delivery. We here investigated how the energy expenditure related to actin remodeling might influence the fitness of human cytotoxic T cells. We first established that the spreading ability of CD8+ T cells in conditions of LFA-1 and TCR engagement mirrored the cytotoxic potential of these cells. Morphological and functional fitness were both potentiated by IL-2, which co-stimulated the transcription of glycolytic enzymes, actin isoforms and the subunits of the ARP2/3 complex. This molecular program scaled with F-actin content and cell spreading. Blockade of glycolysis impaired F-actin remodeling at the lamellipodium, chemokine-driven motility and synaptic adhesion, while blockade of mitochondrial OXPHOS affected F-actin less severely and selectively reduced cell elongation during confined migration. Although T cells deficient for the ARP2/3 subunit ARPC1B increased their ATP content upon IL-2 exposure, their morphological and functional defects were only partially corrected, pointing to the pivotal position of ARP2/3 mediated actin polymerization as integrator of T cell energetic state. Our study therefore highlights that the ability of effector T cells to migrate, form IS and ultimately kill target cells depends on a tight coordination of their metabolic and actin remodeling activities.

opencc-by-4.0Feb 2024View details →

An activity-specificity trade-off encoded in human transcription factors

Data repository for the publication "An activity-specificity trade-off encoded in human transcription factors".  Imaging datasets with larger sizes can be downloaded here: https://owww.molgen.mpg.de/~TFsuboptimization/

Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - raw data

Dataset for the study Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors <ol> <li>environmental variables of the research plots</li> <li>vascular plant species composition of the research plots</li> <li>mcirobial activity on the research plots</li> <li>CLPP profiles of the research plots</li> </ol>

What controls active faulting in Tertiary and Quaternary sequences ?

Structural, geomechanical and XRD datasets obtained from outcrop investigations of Galera Fault zone located in the Guadix-Baza basin, SE Spain is presented here.

NOAA PSL thermodynamic profiles retrieved from a combination of active and passive remote sensors and numerical weather prediction models with the optimal estimation physical retrieval TROPoe at Platteville, CO, USA

This dataset contains retrieved profiles of thermodynamic variables obtained using the Tropospheric Remotely Observed Profiling via Optimal Estimation (TROPoe) physical retrieval from various combinations of input data collected by passive and active remote sensing instruments, in-situ surface platforms, and numerical weather prediction models deployed at the Platteville, CO, USA, site in fall 20221-winter 2022. Among the employed instruments are Microwave Radiometers (MWRs), Infrared Spectrometers (IRS), Radio Acoustic Sounding Systems (RASS), ceilometers, surface sensors, and information from the operational Rapid Refresh numerical weather prediction model. The dataset also includes 15 radiosounding launched for assessing the retrievals. For further information, please see: Bianco, L., Adler, B., Bariteau, L., Djalalova, I. V., Myers, T., Pezoa, S., Turner, D. D., and Wilczak, J. M.: Sensitivity of thermodynamic profiles retrieved from ground-based microwave and infrared observations to additional input data from active remote sensing instruments and numerical weather prediction models, Atmos. Meas. Tech. Discuss. [preprint], https://doi.org/10.5194/amt-2023-263, in review, 2024.

opencc-by-4.0Dec 2023View details →

Stellar chromospheric activity database of solar-like stars based on the Ca II H and K lines of LAMOST Low-Resolution Spectroscopic Survey: the bolometric and photospheric calibration

This database contains the stellar chromospheric activity parameters of solar-like stars based on the Ca II H and K lines from the spectra of the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) Low-Resolution Spectroscopic Survey (LRS). We extract 1,122,495 LRS spectra of solar-like stars from the LAMOST Data Release 8 v2.0 and provide the chromospheric activity parameters $S_{\rm tri}$, $S_{\rm MWO}$, $R_{\rm HK}$ and $R'_{\rm HK}$, as well as their uncertainties in the database. $R_{\rm HK}$ and $R'_{\rm HK}$ are derived from the method in the classic literature (denoted with classic) and the method based on the PHOENIX model (denoted with PHOENIX). These stellar chromospheric activity indexes and their uncertainties, along with the relevant spectroscopic parameters from the LAMOST catalogs, are saved in a CSV-format file (name: CaIIHK_Activity_Indexes_LAMOST_DR8_LRS.csv).   Columns in the catalog of the database: obsid - Unique observation identifier of LAMOST LRS spectrum obsdate-Spectral observation date fitsname - FITS file name of LAMOST LRS spectrum snrg - Signal-to-noise ratio in the $g$ band ($\mathrm{S/N}_g$) of LAMOST LRS spectrum snrr - Signal-to-noise ratio in the $r$ band ($\mathrm{S/N}_r$) of LAMOST LRS spectrum teff - Effective temperature ($T_\mathrm{eff}$) derived from the LASP (unit: K) teff_err - Uncertainty of $T_\mathrm{eff}$ derived from the LASP (unit: K) logg - Surface gravity ($\log\,g$) derived from the LASP (unit: dex) logg_err - Uncertainty of $\log\,g$ derived from the LASP (unit: dex) feh - Metallicity ([Fe/H]) derived from the LASP (unit: dex) feh_err - Uncertainty of [Fe/H] derived from the LASP (unit: dex) rv - Radial velocity ($V_r$) derived from the LASP (unit: km/s) rv_err - Uncertainty of $V_r$ derived from the LASP (unit: km/s) ra_obs - Right ascension (RA) of fiber pointing (unit: degree) dec_obs - Declination (DEC) of fiber pointing (unit: degree)   gaia_source_id - Source identifier in Gaia DR3 catalog gaia_g_mean_mag - $G$ magnitude in Gaia DR3 catalog S_tri* - $S_{\rm tri}$ index  of LAMOST LRS   S_tri_err* - Uncertainty of $S_{\rm tri}$   S_MWO* - $S_{\rm MWO}$   S_MWO_err* - Uncertainty of $S_{\rm MWO}$   log_R_HK_classic* - $\log\,R_{\rm HK,classic}$   log_R_HK_classic_err* - Uncertainty of $\log\,R_{\rm HK,classic}$   log_R_p_HK_classic* - $\log\,R'_{\rm HK,classic}$   log_R_p_HK_classic_err* - Uncertainty of $\log\,R'_{\rm HK,classic}$   log_R_HK_PHOENIX* - $\log\,R_{\rm HK,PHOENIX}$   log_R_HK_PHOENIX_err* - Uncertainty of $\log\,R_{\rm HK,PHOENIX}$   log_R_p_HK_PHOENIX* - $\log\,R'_{\rm HK,PHOENIX}$   log_R_p_HK_PHOENIX_err* - Uncertainty of $\log\,R'_{\rm HK,PHOENIX}$   (Note: The columns denoted by an asterisk represent the parameters provided by this database, and the remaining columns are collected from the data release of LAMOST DR8 V2.0. If the values are not available, they will be filled with '-9999' in this database.)

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.

Example data set for Replay-triggered Brain-wide Activation in Humans

Example data set for Replay-triggered Brain-wide Activation in Humans  Unzip the file and place it in the directory named "example_data_code".