Find research datasets worth reusing

Sea or summit? Wild reindeer spatial responses to changing high-arctic winters

Data for the article “Sea or summit? Wild reindeer spatial responses to changing high-arctic winters” By ÅØ Pedersen, LT Beumer, R Aanes, BB Hansen The data set includes four files: A readme file describing the data files, and three data files accompanying the above publication. For further queries please contact Åshild Ø. Pedersen: Ashild.Pedersen@npolar.no

Code and data for 'Bacillus subtilis histidine kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'

Code and data used in the paper 'Bacillus subtilis histidine  kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'  https://doi.org/10.1128/mBio.01694-21

A Repeated Measures Dataset on Public Responses to the COVID-19 Pandemic: Social Norms, Attitudes, Behaviors, Conspiracy Thinking, and (Mis)Information

We present a quantitative repeated measures dataset from intensive longitudinal research (diary survey) conducted with participants drawn from a nationally representative sample of the German population. This diary survey addresses a wide range of variables relevant to the COVID-19 pandemic, including information seeking, attitudes towards science, public health, and related behaviors.  Respondents were asked about their thoughts, challenges, concerns, and experiences related to the pandemic. Survey responses were requested every two weeks from November 2020 and September 2021 for a total of 18 stages of data collection. The diary survey responses were all matched to the same individual. Using the unique identifier for each individual, the diary survey dataset can be analyzed in concert with a larger representative survey sample that was conducted three times within the same research project over this time period. The diary dataset we present here includes socio-demographic information and other potentially relevant variables, ready for secondary analysis. Initial sample frame: N = 1,480 Initial diary survey sub-sample: N = 133

Yield and Quality Response of Cassava (Manihot esculenta Crantz) to Nitrogen and Potassium Fertilizer Rates at Arba Minch, Southern Ethiopia

Cassava (Manihot esculenta Crentz), is a major staple food crop of the people in most parts of Africa, and plays an important role in terms of food security, employment and income generation for farm families. It is one of important root crops in Ethiopian diet; however there is no research work has been done on rate of nitrogen and potassium fertilizer. Rate of N and K fertilizer are the major factor in determining the quality and quantities of cassava. Thus, this experiment was carried on the influence of nitrogen and potassium fertilizer rate on yield and qualities of cassava at Arba Minch. Four levels of N (0, 46, 92 and 138 kg N ha−1) and three levels of K (0, 60, and 120 kg K ha−1) were arranged in factorial combination in a randomized complete block design (RCBD) with three replications. The results revealed that the main effects of nitrogen fertilizer rates influences all the studied parameters, while the main effect of potassium affects number of tubers per plant and tuber diameter. Interaction effect of N and K influences fresh tuber yield of cassava. The highest fresh tuber yield of cassava was achieved from the combination of 92 kg Nha-1 with application of 0 kg K ha−1, whereas the lowest fresh tuber yield of cassava was obtained from the combination of 0 kg N ha−1 with 0 kg K ha−1. The economic analysis showed that higher net benefit and marginal rate of return were obtained from the application of 92 kg N ha−1 with 0 kg K ha−1. In order to prevent excessive production costs, the use of 92 kg Nha-1 combined with the application of 0 kg K ha−1 is recommended.

opencc-zeroNov 2021View details →

Data from: Size matters: when resource accessibility by ecosystem engineering elicits wood-boring beetle demographic responses

This data was used to investigate how the age and size of beaver disturbances act as predictors for primary wood-boring beetle abundance and species richness around beaver-altered habitat patches. To do so, we sampled beetles around 16 beaver-disturbed and unaltered watercourses within the Kouchibouguac National Park (Canada) and modeled beetle demographical responses to site conditions and their physical characteristics, distance from the watercourse, deadwood biomass, and the geographical location of the sites.

opencc-by-4.0Oct 2020View details →

Data: Responsiveness and habituation to repeated sound exposures and pulse trains in blue mussels

Data abstract: Time series data on the valve gape behaviour of blue mussels (Mytilus edulis) that were exposured to sound treatments. Here, we provide the valve gape (time series data expressed in proportion open) of all mussels over the course of their trial and the timing of the sound exposures.   Paper abstract: Anthropogenic sound has been shown to affect marine animals across taxa. However, bivalves and other invertebrates received limited attention and most studies across taxa focussed on immediate, rather than long-term, effects of sound. Most bivalves adopt a sessile or sedentary lifestyle and are therefore expected to be exposed to the same sounds for long periods or repeatedly. For this reason, bivalves are an especially relevant taxonomic group to study long-term effects of sound. In the current study, we examined whether blue mussels (Mytilus edulis) habituate to repeated sound exposures and whether they recover quicker from a single pulse exposure than from a pulse train. We equipped individual mussels with sensors to monitor valve gape and exposed them to repeated sound playback. We found that mussels responded to sound by partially closing their valves. This response was consistent and repeatable, but decayed over sequential exposures to the same sound stimulus, and was stronger again with exposure to a different sound. This pattern is clear evidence for acoustic habituation in a bivalve. Additionally, we found no differences in the initial response and recovery (time to return to baseline levels) between mussels that were exposed to single pulses and pulse trains. Our results therefore show that mussels are able to habituate to sound and suggest that mussels mostly respond to the onset of a pulse train. Future research is needed to determine whether mussels also habituate in situ to actual anthropogenic sound and whether a lack of a behavioural response also implies that other negative effects are also absent.   Paper reference: Hubert, J., Booms, E., Witbaard, R., Slabbekoorn, H. (2022). Responsiveness and habituation to repeated sound exposures and pulse trains in blue mussels. Journal of Experimental Marine Biology and Ecology. 547, 151668. DOI: 10.1016/j.jembe.2021.151668

Distinct and essential roles of bZIP transcription factors in stress response and pathogenesis in Alternaria alternata

The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata un- der metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We determined the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A. alternata by analyzing targeted gene deletion mutants. Morphological analysis provides evidence that bZIPs including Gcn4, MeaB, Atf1, Hac1 and Ada1 are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover, the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings identified many crucial transcription factor genes and pathways related to cell development, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.

opencc-zeroNov 2021View details →

Dogs' looking times and pupil dilation response reveal expectations about contact causality

Contact causality is one of the fundamental principles allowing us to make sense of our physical environment. From an early age, humans perceive spatiotemporally contiguous launching events as causal. Surprisingly little is known about causal perception in nonhuman animals, particularly outside the primate order. Violation-of-expectation paradigms in combination with eye-tracking and pupillometry have been used to study physical expectations in human infants. In the current study, we establish this approach for dogs (Canis familiaris). We presented dogs with realistic 3D animations of launching events with contact (regular launching event) or without contact between the involved objects. In both conditions, the objects moved with the same timing and kinematic properties. The dogs tracked the object movements closely throughout the study but their pupils were larger in the No-contact condition and they looked longer at the object initiating the launch after the No-contact event compared to the Contact event. We conclude that dogs have implicit expectations about contact causality.

Spectral reconstruction using iteratively reweighted-regulated model from two illumination camera responses

This document shows spectral reflectance data and RGB values of 380 samples for spectral estimation, which includes 5 databases: 1) Spectral reflectance of ColorChecker semigloss chart (CCSG, 140 patches), 2) Spectral reflectance of ColorChecker DC matte chart (CCDC, 240 patches including 232 mattes, and 8 glossy patches), 3) RGB values of ColorChecker semigloss chart (CCSG, 140 patches) , 4) RGB values of ColorChecker DC matte chart (CCDC, 240 patches including 232 mattes, and 8 glossy patches), 5) Spectral Power Distribution value of  3500K & 6500K illumination conditions.

Tampere University Rotated Circular Array Impulse Response Dataset(TUNI-RCAIR)

The TUNI-RCAIR dataset consists of impulse responses collected from different spaces in the Tampere university campus, Finland.  Each folder represents a data collection environment, and it consists of impulse responses and recorded data in the form of wav files. Each space has its own three alphabet identifier, for example- Anechoic chamber is represented as AEC. The folder names indicate the space and corresponding identifier There are seven different data collection environments, and the distance between the source and receiver is varied thrice (0.7m, 1.4m, and 2.1m), which can be found in the names of the sub folders. Further details about the dataset, the characteristis of the space used for data collection, can be found in the page - https://tuni-rcair.github.io/ This dataset is accepted as a part of EUSIPCO 2021, the name of the corresponding paper is, "Tampere University Rotated Circular Array Dataset". The link to the paper will be updated. EUSIPCO paper DOI - https://doi.org/10.23919/EUSIPCO54536.2021.9616072 For citation please use - A. V. Venkatakrishnan, P. Pertilä and M. Parviainen, "Tampere University Rotated Circular Array Dataset," 2021 29th European Signal Processing Conference (EUSIPCO), 2021, pp. 201-205, doi: 10.23919/EUSIPCO54536.2021.9616072.

Wave-like global economic ripple response to Hurricane Sandy - Data supplement

This data set includes the raw data for the figures of the article "Wave-like global economic ripple response to Hurricane Sandy" (https://doi.org/10.1088/1748-9326/ac39c0).

opencc-by-4.0May 2021View details →

Instrument response files for seismic stations in South Korea (accelerometer)

To do[1.01] I have found something wrong in poles and zeros for the KG and KN networks. Please do not use them until update. I am sorry for it. (14 November 2023) Example 1 (Seismic Analysis Code)Examples to deconvolve the instrument response from raw data are below, using the Seismic Analysis Code (SAC, version sac-101.6a).  1. A unit of output is 'm/s2'r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 w acc.sac q 2. A unit of output is 'm/s'r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 TRANS FROM ACC TO VEL w vel.sac q 3. A unit of output is 'm'r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 TRANS FROM ACC TO VEL rtr rmean taper TRANS FROM VEL TO NONE w disp.sac q Note that the unit of the output is incoherent with the SAC header 'IDEP'.Example 2 (StationXML with obspy)#this is same as the code for the velocity seismometers. Update notes<ul><li>[1.01]<ul><li>Typo at INPUT UNIT for KG is modified (M/S -> M/S**2)</li><li>Stations KS.CE2A, KS.HA2B are added</li><li>StationXML file is added (ksgn.xml)</li></ul></li><li>[1.00] The files for the KG network are made based on the logs until 12 April 2019 (personal communication with the Korea Institute of Geoscience and Mineral Resources).</li></ul>OthersVelocity seismometer <a href="https://doi.org/10.5281/zenodo.3700312">https://doi.org/10.5281/zenodo.3700312</a> Accelerometer <a href="https://doi.org/10.5281/zenodo.3872436">https://doi.org/10.5281/zenodo.3872436</a> LicenseThis distribution follows the Creative Commons Attribution 4.0 International. You are free to modify and redistribute the files.

opencc-zeroDec 2021View details →

Gregarines modulate insect responses to sublethal insecticide residues

Throughout their lifetime, insects face multiple environmental challenges that influence their performance. Gregarines are prevalent endoparasites in most invertebrates that affect the fitness of their hosts, but are often overlooked in ecological studies. Next to such biotic factors, a current common challenge is anthropogenic pollution with pesticides, which causes a major threat to non-target organisms that are readily exposed to lethal or sublethal concentrations. In a laboratory study, we investigated whether the presence of gregarines modulates the food consumption and life-history traits of a (non-target) leaf beetle species, Phaedon cochleariae, in response to sublethal insecticide exposure. We show that the larval food consumption of the herbivore was neither affected by gregarine infection nor sublethal insecticide exposure. Nevertheless, infection with gregarines led to a delayed development, while insecticide exposure resulted in a lower body mass of adult males and a reduced reproduction of females. Individuals exposed to both challenges suffered most, as they had the lowest survival probability. This indicates detrimental effects on the population dynamics of non-target insects infected with naturally occurring gregarines that face additional stress from agrochemical pollution. Moreover, we found that the infection load with gregarines was higher in individuals exposed to sublethal insecticide concentrations compared to unexposed individuals. To counteract the global decline of insects, the potential of natural parasite infections in modulating insect responses to anthropogenic and non-anthropogenic environmental factors should be considered in ecological risk assessment.

opencc-zeroDec 2021View details →

Do tradeoffs govern plant species responses to different global change treatments?

Plants are subject to tradeoffs among growth strategies such that adaptations for optimal growth in one condition can preclude optimal growth in another. Thus, we hypothesized that the response of plant species abundance to one global change treatment would relate inversely to the response to a second treatment, particularly for treatment combinations that accentuate distinct traits. To address this hypothesis, we examined plant species abundances in 39 global change experiments manipulating CO2, nitrogen, phosphorus, water, temperature, or disturbance. Overall, the directional response of a species to one treatment was 13% more likely than expected to oppose its response to a second. This tendency was detectable across the global dataset but held little predictive power for individual treatment combinations or within individual experiments. While tradeoffs in the ability to respond to different global change drivers exert detectable effects globally, other forces may obscure their influence in local communities.

opencc-by-4.0Dec 2021View details →

Raw recordings for electrophysiological characterization of CNO-DREADD mediated responses in noradrenergic locus coeruleus (LC) neurons from lines RR1(P), RR2(P), and RC::FPDi (P).

Whole-cell recordings were performed as described previously by the Jiang lab. Briefly, patch pipettes (2-7 MΩ) were filled with an internal solution containing 120 mM potassium gluconate, 10 mM HEPES, 4 mM KCl, 4 mM MgATP, 0.3 mM Na3GTP, 10 mM sodium phosphocreatine and 0.5% biocytin (pH 7.25). Whole-cell recordings from up to 8 LC neurons were performed using two Quadro EPC 10 amplifiers (HEKA Electronic, Germany). PatchMaster (HEKA) and custom-written Matlab-based programs (Mathworks) were used to operate the recording system and perform online and offline data analysis. In current-clamp recordings, neurons were first current clamped at ~-40pA to prevent spontaneous firing. Prior to investigating the effect of drugs, we calculated spike thresholds and recorded firing patterns in response to sustained depolarizing currents by injecting increasing current steps (+10pA). Continuous recordings were obtained from LC neurons current clamped at -40 to 0 pA during drug wash-on experiments. We also calculated other intrinsic electrophysiological parameters, such as the input resistance, membrane time constant, spike amplitude, after-hyperpolarization (AHP) etc.

opencc-by-4.0May 2020View details →

Instrument response files for seismic stations in South Korea

Citation If you use it, please cite the following article in your work:  Lim and Kim (2020), A dataset of seismic sensor responses of South Korea seismic stations. Journal of the Geological Society of Korea, 56(4), 515-524, http://dx.doi.org/10.14770/jgsk.2020.56.4.515 (Korean with English abstract)   Example 1 (Seismic Analysis Code) Examples to deconvolve the instrument response from raw data are below, using the Seismic Analysis Code (SAC, version sac-101.6a).    1. A unit of output is 'm/s' <pre><code>r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 w vel.sac q</code></pre>   2. A unit of output is 'm' <pre><code>r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 TRANS FROM VEL TO NONE w disp.sac q</code></pre>   3. A unit of output is 'm/s2' <pre><code>r $input rtr rmean taper TRANS FROM POLEZERO S $pzfile TO none FREQ 0.05 0.1 1.5 3.0 TRANS FROM VEL TO ACC w acc.sac q</code></pre> Note that the unit of the output is incoherent with the SAC header 'IDEP'.   Example 2 (StationXML with obspy) <pre><code class="language-python">#!/usr/bin/env python3 from obspy import read_inventory from obspy import read st = read('/path/to/waveforms') inv = read_inventory('ksgn.xml') st.detrend(type="linear") st.detrend(type="demean") pref = [0.1, 0.2, 15, 20] #output = m/s**2 st2 = st.copy() st2.remove_response(inventory=inv,output='ACC',pre_filt=pref,taper=True,zero_mean=False) st2[0].write('acc.sac',format="SAC") #... #output = m/s st2 = st.copy() st2.remove_response(inventory=inv,output='VEL',pre_filt=pref,taper=True,zero_mean=False) st2[0].write('vel.sac',format="SAC") #... #output = m st2 = st.copy() st2.remove_response(inventory=inv,output='DISP',pre_filt=pref,taper=True,zero_mean=False) st2[0].write('disp.sac',format="SAC") #...</code></pre>   Update notes <ul> <li>[1.02] Typo in station name of KS.HA2B is modified (KS.HA2B -> HA2B)</li> <li>[1.01] <ul> <li>Files for the sensor JC-V100 are provided from Won-Young Kim (2 Dec 2021)</li> <li>Station KS.HA2B is added</li> <li>StationXML file is added (ksgn.xml)</li> </ul> </li> <li>[1.00] The files for the KG network are made based on the logs until 12 April 2019 (personal communication with the Korea Institute of Geoscience and Mineral Resources). </li> </ul>   Pending works Reflecting a change in logger of KS.DGY2   Others Velocity seismometer <a href="https://doi.org/10.5281/zenodo.3700312">https://doi.org/10.5281/zenodo.3700312</a> Accelerometer <a href="https://doi.org/10.5281/zenodo.3872436">https://doi.org/10.5281/zenodo.3872436</a>   License This distribution follows the Creative Commons Attribution 4.0 International. You are free to modify and redistribute the files.

opencc-zeroDec 2021View details →

Long-term study shows that increasing body size in response to warmer summers is associated with a higher mortality risk in a long-lived bat species

Change in body size is one of the universal responses to global warming, with most species becoming smaller. While small size in most species corresponds to low individual fitness, small species typically show high population growth rates in cross-species comparisons. It is unclear, there- fore, how climate-induced changes in body size ultimately affect population persistence. Unravelling the relationship between body size, ambient temperature and individual survival is especially important for the conservation of endangered long-lived mammals such as bats. Using an individual-based 24-year dataset from four free-ranging Bechstein'sbat colonies (Myotis bechsteinii), we show for the first time a link between warmer summer temperatures, larger body sizes and increased mortality risk. Our data reveal a crucial time window in June–July, when juveniles grow to larger body sizes in warmer conditions. Body size is also affected by colony size, with larger colonies raising larger offspring. At the same time, larger bats have higher mortality risks throughout their lives. Our results highlight the importance of understanding the link between warmer weather and body size as a fitness-relevant trait for predicting species-specific extinction risks as consequences of global warming.

opencc-zeroJan 2022View details →

Leaf economics in a three‐dimensional environment: Testing leaf trait responses in vascular epiphytes to land use, climate, and tree zone

1. The study of functional traits offers predictive power for community ecology. Particularly in cases where individual species are difficult to study, known properties of trait spectra, such as the leaf economics spectrum (LES), and trait-environment relationships can provide crucial generalizable information that can contribute to forecasts of distributional shifts in response to the abiotic effects of climate and land use changes. 2. Vascular epiphytes have been proposed as indicators of environmental change, but we know little about the ecology of most species. Key functional trait assumptions are based on terrestrial plants; testing these in epiphytes verifies their universality and will inform applying functional traits in predicting epiphyte responses to climate and land use change. 3. In this study, we use functional traits from 37 vascular epiphyte species from forests and shade coffee farms at two sites in northern Nicaragua. We compare correlations among traits and intraspecific trait variances with those of terrestrial plants and among epiphyte taxonomic groups. We also test trait responses to environmental differences between sites and land use types, and within zones of the tree. 4. We find that epiphyte leaf traits fall toward the slower end of the LES, but with about one-third lower leaf nitrogen per change in specific leaf area (SLA) relative to terrestrial herbaceous plants. Bromeliads show less relationship between these traits than other epiphyte groups and also deviate in other trait interrelationships, suggesting unique leaf construction. 5. Trait-environment relationships varied most strongly along vertical gradients within trees, but some traits, including SLA and carbon isotope ratio, also responded to land use and site differences. 6. We present evidence that trait relationships established for terrestrial plants appear to translate to epiphytes, but identify some possible caveats. Strong trait response to vertical gradients within trees suggests that within-canopy shifts could provide resilience to climate and land use changes for some epiphyte species.

opencc-by-4.0Jan 2022View details →

Human ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects"

Human axial and sagittal ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects". Code to process and reconstruct the data is available here: <a href="https://github.com/usc-mrel/lowfield_maxgirf">https://github.com/usc-mrel/lowfield_maxgirf</a>