Find research datasets worth reusing

Three-dimensional stratification pattern in an old-growth lowland forest: how does height in canopy and season influence temperate bat activity?

The study of animal-habitat interactions is of primary importance for the formulation of conservation recommendations. Flying, gliding and climbing animals have the ability to exploit their habitat in a three-dimensional way and the vertical canopy structure in forests plays an essential role for habitat suitability. Forest bats as flying mammals may seasonally shift their microhabitat use due to differing energy demands or changing prey availability, but the patterns are not well understood. We investigated three-dimensional and seasonal habitat use by insectivorous bats in a temperate lowland old-growth forest, the Belovezhskaya Pushcha in Belarus. We acoustically sampled broadleaved and mixed coniferous plots in the forest interior and in gaps in three heights during two reproductive periods (pregnancy/lactation versus post-lactation). In canopy gaps, vertical stratification in bat activity was less pronounced than in the forest interior. Vertical activity patterns differed among species. The upper canopy levels were important foraging habitats for the open-space forager guild and for some edge-space foragers like the Barbastelle bat Barbastella barbastellus and the soprano pipistrelle Pipistrellus pygmaeus. Myotis species had highest activity levels near the ground in forest gaps. Moreover, we found species-dependent seasonal microhabitat shifts. Generally, all species and species groups considered except Myotis species showed higher activity levels during post-lactation. Myotis species tended towards higher activity in the forest interior during post-lactation. P. pygmaeus switched from high activity levels in the upper canopy during pregnancy and lactation to high activity levels near the ground during post-lactation. We conclude that a full comprehension of forest bat habitat use is only possible when height in canopy and seasonal patterns are considered.

Activity of forest specialist bats decreases towards wind turbines at forest sites

Worldwide, wind turbines are increasingly being built at forest sites to meet the goals of national climate strategies. Yet, the impact on forest ecosystems and biodiversity is barely understood. Bats may be heavily affected by wind turbines in forests, because many species depend on forest ecosystems for roosting and hunting and can experience high fatality rates at wind turbines. We performed acoustic surveys in 24 temperate forests in the low mountain ranges of Central Germany to monitor changes in the acoustic activity of bats in relation to wind turbine proximity, rotor size, vegetation structure and season. Call sequences were identified and assigned to one of three functional guilds: open-space, edge-space and narrow-space foragers, the latter being mainly forest specialists. Based on the response behaviour of bats towards wind turbines in open landscapes, we predicted decreasing bat activity towards wind turbines at forest sites, especially for narrow-space foragers. Vertical vegetation heterogeneity had a strong positive effect on all bats, yet responses to wind turbines in forests varied across foraging guilds. Activity of narrow-space foragers decreased towards turbines over distances of several hundred meters, especially towards turbines with large rotors and during midsummer months. The activity of edge-space foragers did not change with distance to turbines or season, whereas the activity of open-space foragers increased close to turbines only in late summer. Synthesis and applications: We show that narrow-space foragers avoid wind turbines in forests over a spatial scale of several hundred meters. This response was most apparent towards turbines with large rotors. Since forests are an important habitat for this guild, we advise to exclude forests with diverse vegetation structure as potential wind turbine sites and to consider compensation measures to account for habitat degradation associated with the operation of wind turbines in forests.

opencc-by-4.0Jul 2022View details →

Active Power Control from Wind Farms for Damping Very Low-Frequency Oscillations

Dataset used for results in paper "Active Power Control from Wind Farms for Damping Very Low-Frequency Oscillations"

Active season body mass patterns of Little Brown Bats and Northern Myotis: Raw and fitted mass values, environmental conditions and inflection point estimates

Animals are expected to adjust their behavioural patterns to improve fitness outcomes, such as fecundity or offspring survival. For long-lived hibernators, decisions made in each annual cycle may reflect considerations not just for concurrent survival and reproduction, but also the pressure to maximize overwinter survival and future reproductive success. We examined how these elements manifest themselves in the body mass variation patterns of North American northern latitude temperate bats, whose size and roosting habits present considerable monitoring challenges. We characterized and compared the summer and fall mass variation patterns of little brown myotis (Myotis lucifugus) and northern myotis (M. septentrionalis) from a historic dataset. In summer, the estimated date of parturition was strongly associated with spring foraging conditions (low wind, low precipitation, warm temperatures), and mass gain associated with female reproduction conferred considerable differentiation between the mass variation patterns of females and males. In fall, differences were most apparent among species, although adults exhibited a greater capacity for rapid mass gain than juveniles. These results demonstrate how reproductive constraints and interannual survival have important influences on the behaviour of temperate bats. Future work should seek to quantify the fitness benefits of patterns identified in this study, such as the rate of prehibernation mass gain.

opencc-by-4.0Mar 2022View details →

Data of Mitochondrial respirometric data of adult males of Octopus maya: supporting the method to evaluate heart metabolic activity

Mitochondrial respirometry is key to understanding how environmental factors model energetic cellular processes. Until now, no reports have shown temperature effects and other environmental variables on cephalopod mitochondria activity because of the lack of a method to evaluate mitochondrial respiratory parameters on those groups of species. In this sense and for the first time, it showed the mitochondrial respirometry data of adult Octopus maya’s heart. Following the protocol is illustrated a step-by-step procedure to get the corresponding respiratory parameters.

Data from: IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α

RNA sequencing dataset from "Van Dis et al., IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α. 2022" The prevailing model of protective immunity to tuberculosis is that CD4 T cells produce the cytokine IFN-γ to activate bactericidal mechanisms in infected macrophages. Although IFN-γ-independent CD4 T cell based control of M. tuberculosis infection has been demonstrated in vivo it is unclear whether CD4 T cells are capable of directly activating macrophages to control infection in the absence of IFN-γ. We developed a co-culture model using CD4 T cells isolated from the lungs of infected mice and M. tuberculosis-infected murine bone marrow-derived macrophages (BMDMs) to investigate mechanisms of CD4 dependent control of infection. This dataset represents RNA sequencing data from M. tuberculosis-infected wild-type and Ifngr-/- murine bone marrow-derived macrophages (BMDMs) after 24 hours of lung CD4 T cell co-culture. CD4 T cells induced differential regulation of 1825 genes in wild-type BMDMs and 1142 genes in Ifngr-/- BMDMs compared to untreated. Although wild-type and Ifngr-/- BMDMs infected with M. tuberculosis were transcriptionally very similar prior to activation, the transcriptome of these genotypes of macrophages diverged after CD4 T cell co-culture. This is likely due in part to the presence or absence of IFN-γ signaling as IFN-γ alone regulates the expression of >2500 genes during M. tuberculosis infection. Still, 769 genes were altered in an IFN-γ-independent manner, with >2-fold upregulation in both wild-type and Ifngr-/- BMDMs. We found no difference in macrophage polarization between untreated M. tuberculosis-infected wild-type and Ifngr-/- BMDMs, and no significant increase in the expression of genes associated with M2 macrophages after CD4 T cell co-culture in either genotype. However, there was significant upregulation of genes associated with M1 macrophages after CD4 T cell co-culture in both genotypes, with wild-type BMDMs slightly more polarized. Collectively, these results show comparable patterns of activation in wild-type and Ifngr-/- macrophage during CD4 T cell co-culture, indicating that CD4 T cells elicit significant polarizing, inflammatory and antimicrobial effects in M. tuberculosis-infected macrophages irrespective of IFN-γ signaling.

opencc-by-4.0Jan 2022View details →

GitRanking: A Ranking of GitHub Topics for Software Classification using Active Sampling

Replication package for our paper: GitRanking: A Ranking of GitHub Topics for Software Classification using Active Sampling

Micro and macroclimatic constraints on the activity of a vulnerable tortoise: a mechanistic approach under a thermal niche view

1. Thermal constraints imposed by the environment limit the activity time of ectotherms and have been a central issue in ecophysiology. Assessing these restrictions is key to determining the vulnerability of species to changing thermal niches and developing conservation strategies. 2. We generate an explicit tortoise model of thermal constraints at both micro and macroclimate scales based on thermophysiology parameters and environmental operative temperatures during a biologically significant period. As a study model, we use a vulnerable species of gopher tortoise (Gopherus evgoodei), whose primary habitat is the tropical dry forests in northwestern Mexico. 4. Our mechanistic model is based on a monitoring of 5-years of environmental operative temperatures (Te). Here, we use the hours of activity (ha) and hours of thermal restriction (hr), calculated from the voluntary temperature range of G. evgoodei with respect to Te, to project and compare the thermal constraints across space and time. In addition, this model was projected using a pessimistic climate change scenario for 2070 (RCP 8.5). 5. The results show that the period of activity of G. evgoodei, predicted by ha and hr, is limited by the frequency and availability of Te and differs significantly throughout the year and among years. In addition, under the RCP 8.5 scenario, we predict that hr will increase considerably and exceed the critical value (3.11 hr) placing this species as highly vulnerable. 6. We discuss and compare the period of potential activity, thermoregulation strategies, and costs and benefits with other Gopherus species. Finally, we identify critical areas to develop management strategies for protecting this Mexican endemic tortoise.

opencc-by-4.0Jul 2022View details →

DFT Calculated xyz Files in Support of "Bidentate Rh(I)-Phosphine Complexes for the C-H Activation of Alkanes: Computational Modelling and Mechanistic Insight"

Theoretically calculated xyz files for propane, carbon monoxide, butyraldehyde and multiple Rh-phosphine complexes as well as transition states relevant for the C-H activation and subsequent carbonylation of alkanes. All quantum chemical simulations were performed using the Gaussian 16 software package. Closed-shell equilibrium structures, i.e., minima and transition states (TSs) as well as electronic properties of educts, intermediates, and products involved in the C-H activation of propane (methyl group activation) and subsequent steps mediated by the Rh complexes were obtained at the DFT level of theory. The range-separated B97XD functional was employed. The def2-SVP basis set and the respective effective core potential (ECP) were utilized for all atoms. TSs were fully optimized at the same level of theory using the rational function optimization (RFO) approach as well as nudged elastic band (NEB) method as implemented in the pysisyphus software suite. Subsequently, a vibrational analysis was carried out for each stationary point to verify that a minimum or first-order saddle point was obtained on the 3N-6-dimensional potential energy (hyper)surface (PES).

opencc-by-4.0Apr 2022View details →

From a microscopic inertial active matter model to the Schrödinger equation

Supplementary data for the following manuscript: Michael te Vrugt, Tobias Frohoff-Hülsmann, Eyal Heifetz, Uwe Thiele, Raphael Wittkowski, "From a microscopic inertial active matter model to the Schrödinger equation".

Alarm cues and alarmed conspecifics: Neural activity during social learning from different cues in Trinidadian guppies

Learning to respond appropriately to novel dangers is often essential to survival and success, but carries risks. Learning about novel threats from others (social learning) can reduce these risks. Many species, including the Trinidadian guppy (Poecilia reticulata), respond defensively to both conspecific chemical alarm cues and conspecifix anti-predator behaviours, and in other fish such social information can lead to a learned aversion to novel threats. However, relatively little is known about the neural substrates underlying social learning and the degree to which different forms of learning share similar neural mechanisms. Here, we explored the neural substrates mediating social learning of novel threats from two different conspecific cues (i.e. social cue-based threat learning). We first demonstrated that guppies rapidly learn about threats paired with either alarm cues or with conspecific threat responses (demonstration). Then, focusing on acquisition rather than recall, we discovered that phospho-S6 expression, a marker of neural activity, was elevated in guppies during learning from alarm cues in the putative homologue of the mammalian lateral septum and the preoptic area. Surprisingly, these changes in neural activity were not observed in fish learning from conspecific demonstration. Together, these results implicate forebrain areas in social learning about threat but raise the possibility that circuits contribute to such learning in a stimulus-specific manner.

opencc-by-4.0Jul 2021View details →

The dataset for an article - An Evaluation of 3D-Printed Materials' Structural Properties Using Active Infrared Thermography and Deep Neural Networks Trained on the Numerical Data

Dataset used in the research presented in the article: Szymanik, Barbara. 2022. "An Evaluation of 3D-Printed Materials’ Structural Properties Using Active Infrared Thermography and Deep Neural Networks Trained on the Numerical Data" Materials 15, no. 10: 3727. https://doi.org/10.3390/ma15103727 The database in the .mat (matlab) format contains arrays of double type related to: A - original thermograms obtained for the plate made with the 3D printing technique Ar - thermograms with ROI included FITorg - approximation of original thermograms ImDiff, ImInt, ImProp - data obtained after subtracting the approximation.

opencc-by-4.0Dec 2021View details →

Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation

This Dataset contains primary data used for the publication "Rapid increase in transferrin receptor recycling promotes adhesion during T cell activation" accepted for publication in BMC Biology on 15. July 2022 Abstract: Background T cell activation leads to increased expression of the receptor for the iron transporter transferrin (TfR) to provide iron required for the cell differentiation and clonal expansion that takes place during the days after encounter with a cognate antigen. However, T cells mobilise TfR to their surface within minutes after activation, although the reason and mechanism driving this process remain unclear. Results Here we show that T cells transiently increase endocytic uptake and recycling of TfR upon activation, thereby boosting their capacity to import iron. We demonstrate that increased TfR recycling is powered by a fast endocytic sorting pathway relying on the membrane proteins flotillins, Rab5 and Rab11a-positive endosomes. Our data further reveal that iron import is required for a non-canonical signalling pathway involving the kinases Zap70 and PAK, which controls adhesion of the integrin LFA-1 and eventually leads to conjugation with antigen-presenting cells. Conclusions Altogether, our data suggest that T cells boost their iron importing capacity immediately upon activation to promote adhesion to antigen-presenting cells.   Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication. Programs we recommend to view the files are: .fcs files:    FlowJo software v10 (Tree Star, Ashland, OR, USA) .lsm and .czi files: ZEN 2012 SP1 and higher (Carl Zeiss, Jena, Germany) .lif files:       LAS X v3 (Leica Microsystems, Wetzlar, Germany) .pzfx files:   Prism v7 software (GraphPad, San Diego, CA, USA)

opencc-zeroAug 2022View details →

Flooding triggers increased surface activity in a bottom-dwelling turtle

Mexican giant musk turtles (Staurotypus triporcatus) are large, bottom-dwelling turtles in Central America. Following a flooding event, they were frequently seen at the surface, wherease they were never seen prior to the flooding. The data were collected using a motorized canoe to search for turtles at the surface. When possible, notes were made about size. In some cases, it was possible to capture the turtles and measure them. Observations of times, dates, sexes, and sizes of turtles are presented, as well as a measure of search effort (times of day searched and distance of creek searched). Missing values are reported as NA.

opencc-by-4.0Aug 2022View details →

EFS Care Activities Dataset

Dataset of care activities as described in the following paper: "Dataset and Methods for Recognizing Care Actvitities", Sylvia Kaczmarek, Martin Fiedler, Andreas Bongers, Sebastian Wibbeling and Rene Grzeszick, iWOAR, 2022.   This dataset has been created as part of the project "Eingabefreie Station -  Bewegungsbasierte Aufnahme von Pflegetätigkeiten zur automatisierten Dokumentation im Krankenhaus". This project is funded by the European Union and the State of Northrhine-Westphalia as part of the "Leitmarkt Gesundheit.NRW" (EFRE.NRW).   See also: https://www.eingabefreie-station.de/

opencc-by-4.0Jul 2022View details →

Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst - XYZ Structure files

XYZ Structures corresponding to DOI: 10.1002/cctc.202200662

opencc-by-4.0Aug 2022View details →

Video demonstrating results of applying show view updates on Android Activity without Fibonacci Computation on the main thread

Video demonstrating results of applying show view updates on Android Activity without Fibonacci Computation on the main thread

opencc-by-4.0Aug 2022View details →

Video demonstrating results of applying show view updates on Android Activity with Fibonacci Computation on the main thread

Video demonstrating results of applying show view updates on Android Activity with Fibonacci Computation on the main thread

opencc-by-4.0May 2022View details →

Replication stalling activates SSB for recruitment of DNA damage tolerance factors

This repository contains four zipped folders with data and code related to this manuscript in the form of MATLAB files. The folders contain: <ol> <li>By figure: plotted data organized by figure in the manuscript (as MATLAB workspaces, .mat files).</li> <li>Variables: plotted data organized by strain number and description (as MATLAB workspaces, .mat files).</li> <li>Functions: MATLAB functions needed to 1) integrate MicrobeTracker(1) cell segmentation analysis with u-track point source detection(2) and tracking(3) analysis and 2) perform subsequent processing of u-track analysis results (as MATLAB scripts, .m files)</li> <li>Scripts: MATLAB scripts needed to perform different types of data analysis (as MATLAB scripts, .m files). These scripts are organized by integration time (short vs. long exposure) and by type of analysis (radial distribution functional analysis, diffusion coefficient analysis, etc)</li> </ol>