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opencc-zeroApr 2024View details →

Global responses of plant abundance, diversity, and fitness to increased fire severity or frequency

Database of responses of plant abundance, diversity, and fitness to increased fire frequency or severity, collected from published scientific articles or reports. The database includes 394 studies published worldwide between 1962 and 2023. Information on the following variables are also provided: fire regime component (fire frequency or severity), time since the last fire, fire type (wildfire or prescribed fire), historical fire regime type (surface or crown fire), plant life form (woody plant, herb, or bryophyte), habitat type, and climate. The database underpins the meta-analysis 'Global plant responses to intensified fire regimes', published in Global Ecology and Biogeography.

opencc-by-4.0Apr 2024View details →

Why do avian responses to changes in Arctic green-up vary

Global climate change has altered the timing of seasonal events (i.e. phenology) for a diverse range of biota. Within and among species, however, the degree to which alterations in phenology match climate variability differ substantially. To better understand factors driving these differences, we evaluated variation in timing of nesting of eight Arctic-breeding shorebird species at 18 sites over a 23-year period. We used the Normalized Difference Vegetation Index as a proxy to determine the start of spring growing season (SOS) and quantified relationships between SOS and nest initiation dates as a measure of phenological responsiveness. Among species, we tested four life history traits (migration distance, seasonal timing of breeding, female body mass, expected female reproductive effort) as species-level predictors of responsiveness. For one species (Semipalmated Sandpiper), we also evaluated whether responsiveness varied across sites. Although no species in our study completely tracked annual variation in SOS, phenological responses were strongest for Western Sandpipers, Pectoral Sandpipers, and Red Phalaropes. Migration distance was the strongest additional predictor of responsiveness, with longer-distance migrant species generally tracking variation in SOS more closely than species that migrate shorter distances. Semipalmated Sandpipers are a widely distributed species but adjustments in timing of nesting relative to variability in SOS did not vary across sites, suggesting that different breeding populations of this species were equally responsive to climate cues despite differing migration strategies. Our results unexpectedly show that long-distance migrants are more sensitive to local environmental conditions, which may help them to adapt to ongoing changes in climate.

opencc-zeroApr 2024View details →

Data for: A linear response framework for simulating bosonic and fermionic correlation functions on quantum computers

Response functions are a fundamental aspect of physics; they represent the link between experimental observations and the underlying quantum many-body state. However, this link is often under-appreciated, as the Lehmann formalism for obtaining response functions in linear response has no direct link to experiments. Within the context of quantum computing, and by using a linear response framework, we restore this link by making the experiment an inextricable part of the quantum simulation. This method can be frequency- and momentum-selective, avoids limitations on operators that can be directly measured, and is ancilla-free. As prototypical examples of response functions, we demonstrate that both bosonic and fermionic Green's functions can be obtained, and apply these ideas to the study of a charge-density-wave material on {\emph{ibm\_auckland}}. The linear response method provides a robust framework for using quantum computers to study systems in physics and chemistry.

Heatwave responses of Arctic phytoplankton communities are driven by combined impacts of warming and cooling

Marine heatwaves are increasing in frequency and intensity as climate change progresses, especially in the highly productive Arctic regions. Although their effects on primary producers will largely determine the impacts on ecosystem services, mechanistic understanding on phytoplankton responses to such extreme events is still very limited. We experimentally exposed Arctic phytoplankton assemblages to stable warming, as well as to repeated heatwaves, and measured temporally resolved productivity, physiology and composition. Our results show that even extreme stable warming increases productivity, while the response to heatwaves depends on the specific scenario applied, and are not predictable from stable warming responses. This appears to be largely due to the underestimated impact of the cool phase following a heatwave, which can be at least as important as the warm phase for the overall response. We show that physiological and compositional adjustments to both, warm and cool phases drive overall phytoplankton productivity, and need to be considered mechanistically to predict overall ecosystem impacts.

Ecosystem-wide responses to fire and large mammal herbivores in an African savanna

Fire and large mammal herbivores (LMH) are the principal top-down forces maintaining savanna structure. Nonetheless, experiments designed to investigate interactions between fire and LMH are rare in savannas, and relationships between environmental variation and biodiversity in the context of fire and LMH are poorly understood. This study addresses these gaps by manipulating the presence of LMH and early and late dry season fires in a tropical African savanna. In addition, this work simultaneously explores environmental variables including soil and foliar quality, vegetation cover, and nearby water sources to more holistically describe factors affecting savanna functioning and biodiversity. After one year of experimental treatments, changes in vegetation were already apparent. Shrub abundance and richness and grass richness were higher in the absence of LMH, while grass biomass increased three-fold in burned plots as compared to unburned plots. Foliar nutrients tended to increase in open plots, while phenolics decreased. Amphibian abundance decreased with early burns and was higher with LMH. In contrast, small mammal abundance and richness increased without LMH and with time since fire. Richness and foraging of LMH were highest after late burns. These results demonstrate ecosystem-wide effects of LMH, illustrating the importance of considering multiple taxa when designing fire management programs. For example, burning negatively affected amphibians and small mammals and changed vegetation at the same time it increased LMH foraging. In the long-term, this experiment will shed light on interacting effects of fire and LMH on savanna biodiversity and function.

Behavioural changes in aposematic Heliconius melpomene butterflies in response to their predatory bird calls

Prey-predator interactions have resulted in the evolution of many anti-predatory traits. One of them is the ability of prey to listen to predators and avoid them. Although prey anti-predatory behavioural responses to predator auditory cues are well described in a wide range of taxa, studies on whether butterflies change their behaviours in response to their predatory calls are lacking. Heliconius butterflies are unpalatable and form Müllerian mimicry rings as morphological defence strategies against their avian predators. Like many other butterflies in the Nymphalidae family, some Heliconius butterflies possess auditory organs, which are hypothesized to assist with predator detection. Here we test whether Heliconius melpomene changes their behaviour in response to their predatory bird calls by observing the behaviour of male and female H. m. plessini exposed to calls of Heliconius avian predators: rufous-tailed jacamar, migratory Eastern kingbird, and resident tropical kingbird. We also exposed them to the calls of the toco toucan, a frugivorous bird as a control bird call, and an amplified greenhouse background noise as a noise control. We found that individuals changed their behaviour in response to Jacamar calls only. Males increased their walking and fluttering behaviour, while females did not change their behaviour during the playback of the jacamar call. Intersexual behaviours like courtship, copulation, and abdomen lifting did not change in response to bird calls. Our findings suggest that despite having primary predatory defences like toxicity and being in a mimicry ring, H. m. plessini butterflies changed their behaviour in response to predator calls. Furthermore, this response was predator-specific, as H. m. plesseni did not respond to either the Eastern kingbird or the tropic kingbird calls. This suggests that Heliconius butterflies may be able to differentiate predatory calls, and potentially the birds associated with those calls.

Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 hours

Aims/hypothesis: Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycemia, beta cell glucotoxicity, and subsequently type 2 diabetes. In this study, we explored the effects of in vitro hyperglycemic conditions on human pancreatic islet gene expression across 24 hours in six pancreatic cell types: alpha, beta, gamma, delta, ductal, and acinar cells. We hypothesized that genes associated with hyperglycemic conditions may be relevant to the onset and progression of diabetes. Methods: We exposed human pancreatic islets from two donors to low (2.8 mmol/l) and high (15.0 mmol/l) glucose concentrations over 24 hours in vitro. To assess the transcriptome, we performed single-cell RNA sequencing (scRNA-seq) at seven time points. We modeled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Additionally, we integrated genomic features and genetic summary statistics to nominate candidate effector genes. For three of these genes, we functionally characterized the effect on insulin production and secretion using CRISPR interference to knockdown gene expression in EndoC-βH1 cells, followed by a glucose-stimulated insulin secretion assay. Results: Across all cell types, we identified 1,447 genes associated with time, 680 genes associated with glucose exposure, and 418 genes associated with interaction effects between time and glucose. By integrating these expression profiles with summary statistics from genetic association studies, we identified 2,449 candidate effector genes for type 2 diabetes, HbA1c, random blood glucose, and fasting blood glucose. Of these candidate effector genes, we showed that three—ERO1B, HNRNPA2B1, and RHOBTB3—exhibited an effect on glucose-stimulated insulin secretion and production in EndoC-βH1 cells. Conclusions/interpretation: The findings of our study provide an in-depth characterization of the 24-hour transcriptomic response of human pancreatic islets to glucose exposure at a single-cell resolution. By integrating differentially expressed genes with genetic signals for type 2 diabetes and glucose-related traits, we provide insights into the molecular mechanisms underlying glucose homeostasis. Finally, we provide functional evidence to support the role of three candidate effector genes in insulin secretion and production.

Exploring the relation between fundamental frequency and spectral envelope in the perception of musical instrument sounds – sound files and participant responses

This database contains synthesized instrument sounds (sounds.zip), participant responses (data.zip), and a key for the stimulus order (stimKey.zip) as complementary data to [1]. Sounds include individual stimuli for two experiments. Experiment 1 contains stimuli used for sound pleasantness and sound brightness ratings. Every rating scale includes three acoustic conditions: congruent, incongruent, and fixed, corresponding to the relation of fundamental frequency (F0) and spectral envelope (SE). See [1] for further details on this matter. Experiment 2 contains stimuli for four synthesized instrument sounds: violin, alto voice, clarinet, and tuba. Sounds were synthesized using congruent spectral envelopes (all), and register fixed spectral envelopes (low, mid, high). All sounds are mono signals with a sampling frequency of 44100 Hz in WAV format. Data includes four sets of participant response data: sound pleasantness ratings (Exp. 1), sound brightness ratings (Exp. 1), sound pleasantness ratings (Exp. 2), and sound plausibility ratings (Exp. 2). StimKey provides values for the first and second principal components of the synthesis space for the pleasantness (1 to 81) and brightness (1 to 16) stimulus numbers for Exp. 1.   Names convention for Exp. 2 sounds: InstrumentName_congruencyCondition_F0..wav   References: [1] Jacobsen, S. and Siedenburg, K. (2024). Exploring the relation between fundamental frequency and spectral envelope in the perception of musical instrument sounds. Acta Acustica, 8, 48. <a href="https://doi.org/10.1051/aacus/2024038">https://doi.org/10.1051/aacus/2024038</a>.

Dataset and scripts from: Predicting organismal response to marine heatwaves using dynamic thermal tolerance landscape models

Marine heatwaves (MHWs) can cause thermal stress in marine organisms, experienced as extreme 'pulses' against the gradual trend of anthropogenic warming. When thermal stress exceeds organismal capacity to maintain homeostasis, organism survival becomes time-limited and can result in mass mortality events. Current methods of detecting and categorizing MHWs rely on statistical analysis of historic climatology, and do not consider biological effects as a basis of MHW severity. The reemergence of ectotherm thermal tolerance landscape models provides a physiological framework for assessing the lethal effects of MHWs by accounting for both the magnitude and duration of extreme heat events. Here, we used a simulation approach to understand the effects of a suite of MHW profiles on organism survival probability across 1) three thermal tolerance adaptive strategies, 2) interannual temperature variation, and 3) seasonal timing of MHWs. We identified survival isoclines across MHW magnitude and duration where acute (short duration-high magnitude) and chronic (long duration-low magnitude) events had equivalent lethal effects on marine organisms. While most research attention has focused on chronic MHW events, we show similar lethal effects can be experienced by more common but neglected acute marine heat spikes. Critically, a statistical definition of MHWs does not accurately categorize biological mortality. By letting organism responses define the extremeness of a MHW event, we can build a mechanistic understanding of MHW effects from a physiological basis. Organism responses can then be transferred across scales of ecological organization and better predict marine ecosystem shifts to MHWs.

Modeling the impacts of Antarctic Sea Ice Decline: Responses of Atmospheric Dynamics

Open the record for dataset details and reuse information.

Contrasting Responses of Particulate and Mineral-Associated Organic Carbon to Afforestation Potentially Obscure Soil Carbon Accumulation [Dataset]

This is the data repository for the manuscript “Contrasting Responses of Particulate and Mineral-Associated Organic Carbon to Afforestation Potentially Obscure Soil Carbon Accumulation” submitted to Global Biogeochemical Cycles.

opencc-by-4.0Dec 2023View details →

Research data supporting "Observation of nonlinear response and Onsager regression in a photon Bose-Einstein condensate"

This repository contains the data presented in the manuscript titled "Observation of nonlinear response and Onsager regression in a photon Bose-Einstein condensate" by A. Sazhin et al., Nature Communications 15, Article number: 4730 (2024), arXiv:2403.04705. The files named 'fig{1,2,3,4}.xlsx' contain the final data sets relevant to reproduce all plots shown in the paper.

miR-29a-3p, a new myokine orchestrating resistance exercise via coordinated metabolic responses

NGS extracelular vesicles miRNA total reads of three pooled plasma samples from sedentary(C), endurance (E) and resitance (R) 4-week trained mice.

opengpl-3.0-or-laterFeb 2024View details →

LORIS: a logistic regression-based immunotherapy-response score

This is a repository of input data and code for reproducing the paper titled "LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic, and genomic features" by Chang et al. (Nature Cancer 2024). Briefly, in this work, Chang et al. developed a new clinical score called the LOgistic Regression-based Immunotherapy-response Score (LORIS) using a transparent and concise 6-feature logistic regression model. LORIS outperforms previous signatures in ICB response prediction and can identify responsive patients, even those with low tumor mutational burden or tumor PD-L1 expression. Importantly, LORIS consistently predicts both objective responses and short-term and long-term survival across multiple cancer types. Moreover, LORIS showcases a near-monotonic relationship with ICB response probability and patient survival, enabling more precise patient stratification across the board. As the method is accurate, interpretable, and only utilizes a few readily measurable features, it could help improve clinical decision-making practices in precision medicine to maximize patient benefit.

Weak response to selection on stigma-anther distance in a primarily selfing population of yellow monkeyflower

Stebbins hypothesized that selfing lineages are evolutionary dead ends because they lack adaptive potential. While selfing populations often harbor limited nucleotide variability compared to closely related outcrossers, reductions in the genetic variability of quantitative characters remain unclear, especially for key traits determining selfing rates. Yellow monkeyflower (Mimulus guttatus) populations generally outcross and maintain extensive quantitative genetic variation in floral traits. Here, we study the Joy Road population (Bodega Bay, California, USA) of M. guttatus, where individuals exhibit stigma-anther distances typical of primarily selfing monkeyflowers. We show that this population is closely related to nearby conspecifics on the Pacific coast with a modest 33% reduction in genome-wide variation compared to a more highly outcrossing population. A five-generation artificial selection experiment challenged the hypothesis that the Joy Road population harbors comparatively low evolutionary potential in the stigma-anther distance, a critical determinant of selfing rate in Mimulus. Artificial selection generated a weak phenotypic response, with low realized heritabilities (0.020-0.028) falling 84% below those measured for floral characters in more highly outcrossing M. guttatus. These results demonstrate substantial declines in evolutionary potential with a transition toward selfing. Whether these findings explain infrequent reversals to outcrossing or general limits on adaptation in selfers requires further investigation.

Supporting Data for Viscous Mechano-Electric Response of Ferroelectric Nematic Liquid

These data correspond to the published publication entitled: Viscous Mechano-Electric Response of Ferroelectric Nematic Liquid

opencc-by-4.0Apr 2024View details →

Dataset of Room Impulse Responses from Baffled Microphone Arrays and Sound Sources at Three Elevations

This data set contains a collection of impulse responses (stored in SOFA format) from spherical microphone arrays (SMAs), equatorial microphone arrays (EMAs), and non-spherical microphone arrays (XMAs). Thereby, impulse response sets are provided for each array type at various spatial resolutions, for a loudspeaker sound source at three source elevations, and in four diverse acoustic environments (see DATA section for a full description). The original purpose of the microphone array data is the binaural rendering in the spherical harmonics (SH) domain into ear signals for high-fidelity reproduction of the acoustic scenario via headphones. Therefore, binaural room impulse responses (BRIRs) for 360 horizontal head orientations of a G.R.A.S KEMAR acoustic dummy head are provided as a reference for each scenario. Please contact the authors for questions or additional information regarding the room setups and utilized measurement devices.   ======  DATA ====== This archive contains the processed impulse response sets of various measurement configurations, as described in this section. Directory "resources/ARIR_processed/": <ul> <li>Post-processed SMA and EMA impulse responses <ul> <li>"_SMA*_" or "_EMA*_" in the file name</li> <li>In SOFA format with "SingleRoomSRIR" convention</li> <li>From 1x DPA 4060 microphone flush mounted in a wooden spherical scattering body with an 8.5 cm radius</li> <li>High-resolution data (measured sequentially on VariSphear turntable with two degrees-of-freedom rotations): <ul> <li>Hall: 1202 channels (Lebedev grid) for maximum SH order 29</li> <li>Others: 2702 channels (Lebedev grid) for maximum SH order 44</li> </ul> </li> <li>Lower-resolution data via subsampling in the SH domain (arbitrary sampling grids and lower target orders can be achieved): <ul> <li>SH order 29: 1742 channels (t-design grid) for SMA; 59 channels (equiangular grid) for EMA</li> <li>SH order 12: 314 channels (t-design grid) for SMA; 25 channels (equiangular grid) for EMA</li> <li>SH order 8: 146 channels (t-design grid) for SMA; 17 channels (equiangular grid) for EMA</li> <li>SH order 4: 42 channels (t-design grid) for SMA; 9 channels (equiangular grid) for EMA</li> <li>SH order 2: 14 channels (t-design grid) for SMA; 5 channels (equiangular grid) for EMA</li> <li>SH order 1: 6 channels (t-design grid) for SMA; 3 channels (equiangular grid) for EMA</li> </ul> </li> </ul> </li> <li>Post-processed XMA impulse responses <ul> <li>"_XMA*_" in the file name</li> <li>In SOFA format with "SingleRoomSRIR" convention</li> <li>From 18x Rode Lavalier GO microphone mounted in an elastic band on a wooden head-shaped scattering body (7.5 cm to 10.5 cm radius)</li> <li>High-resolution data (measured simultaneously): <ul> <li>18 channels for maximum SH order 8</li> </ul> </li> <li>Lower-resolution data via integer subsets of microphones: <ul> <li>SH order 4: 9 channels</li> <li>SH order 2: 6 channels</li> </ul> </li> <li>Anechoic: For 360 horizontal scattering body orientations (measured sequentially on a VariSphear turntable with azimuth in 1-degree steps)</li> <li>Rooms: For 36 horizontal scattering body orientations (measured sequentially on VariSphear turntable with azimuth in 10-degree steps)</li> </ul> </li> <li>Generated XMA calibration filters and equalization filters <ul> <li>"_x_nm_" and "_e_nm_" in the file name</li> <li>In proprietary Matlab format</li> <li>Time-domain representation of filters in the respective orders of "real" spherical harmonics</li> </ul> </li> <li>Post-processed binaural impulse responses <ul> <li>"_KEMAR_" in the file name</li> <li>In SOFA format with "SingleRoomSRIR" convention</li> <li>From G.R.A.S KEMAR dummy head with large pinna</li> <li>For 360 horizontal head orientations (measured sequentially on VariSphear turntable with azimuth in 1-degree steps)</li> </ul> </li> <li>Thereby, impulse response sets are included for five acoustic environments <ul> <li>"Simulation_": Anechoic simulation of a plane wave impinging from the frontal direction on the array (SMA and EMA only)</li> <li>"Anechoic_": Anechoic measurement of a Genelec 8030A loudspeaker at the same height of the array</li> <li>"LabDry_": Room measurement in an acoustically damped laboratory of a Genelec 8030A loudspeaker at three different source heights (the direct floor reflection is attenuated with an additional porous absorber but otherwise identical to the following condition)</li> <li>"LabWet_": Room measurement in an acoustically damped laboratory of a Genelec 8030A loudspeaker at three different source heights (the direct reflection is not obstructed from the hard concrete floor, but otherwise identical to the former condition)</li> <li>"Hall_": Room measurement in a very reverberant hall of a Genelec 8030A loudspeaker at three different source heights</li> </ul> </li> <li>Thereby, the room impulse response sets are included for three relative source elevations (from placing the loudspeaker to varying heights on the same vertical axis) <ul> <li>"_SrcHigh": The source is located above the horizon of the receiver</li> <li>"_SrcEar": The source and receiver are located at the same height</li> <li>"_SrcLow": The source is located below the horizon of the receiver</li> </ul> </li> <li>Additionally, anechoic impulse responses of the measurement loudspeaker and the utilized microphones are included <ul> <li>"Anechoic_MicSMAnoTape_": SMA measurement microphone without the applied tape (the source was compensated)</li> <li>"Anechoic_MicSMAwithTape_": SMA measurement microphone with the applied tape (the source was compensated)</li> <li>"Anechoic_MicXMAmic19_": XMA measurement microphone (the source was compensated)</li> <li>"Anechoic_SrcFreeField_": Measurement source (on-axis) (the influence of the utilized high-quality free-field measurement microphone can be neglected)</li> <li>"Anechoic_SrcFreeField+MicSMAnoTape_": Measurement source and SMA measurement microphone without the tape applied</li> <li>"Anechoic_SrcFreeField+MicSMAwithTape_": Measurement source and SMA measurement microphone with the tape applied</li> <li>"Anechoic_SrcFreeField+MicXMAmic19_": Measurement source and XMA measurement microphone</li> <li>Overall, the resulting impulse response sets contain the following compensations (including exact compensation of the phase/time behavior): <ul> <li>Anechoic KEMAR: Source</li> <li>Anechoic SMA/EMA/XMA: Source and array microphones</li> <li>Rooms KEMAR: None</li> <li>Rooms SMA/EMA/XMA: Array microphones</li> <li>There is the option to compensate for the source's on-axis response in the room measurement data. However, the direction-dependent directivity of the loudspeaker cannot be compensated. Therefore, we decided not to compensate for the source in the room measurement data since the on-axis frequency response of the utilized loudspeaker is reasonably flat.</li> </ul> </li> </ul> </li> </ul>   ===========   DATA_RAW =========== This archive is too large to be uploaded to Zotero (around 77.5 GB). Please get in touch with the authors to request the data. The archive contains the raw acoustic data of all measurement configurations captured by the measurement scripts (see section CODE_AND_PLOTS). The data yields the final impulse responses (see section DATA), as described in this section. Directory "resources/ARIR_raw/": <ul> <li>Subdirectories by room and source position containing the raw SMA, XMA, and KEMAR acoustic measurement data</li> <li>In proprietary Matlab format, separate for every measurement position of each configuration</li> <li>Each data file contains extensive metadata, e.g., describing the utilized hardware devices, input/output ports, and descriptions.</li> <li>Each data file contains the raw utilized exponential sweep signal and the resulting captured microphone signals. Each impulse response may be recomputed with alternative deconvolution and post-processing parameters.</li> </ul> Directory "resources/ARIR_raw/Logs_temp_humidity/": <ul> <li>Air temperature and humidity data were captured in 5-second intervals during all acoustic measurements</li> <li>In CSV format (automatically loaded and included in the final impulse response sets as part of the measurement post-processing; see section CODE_AND_PLOTS)</li> <li>This data is not further utilized at the moment but seemed worthwhile to capture since some acoustic measurements (particularly the high-resolution SMA data sets) were conducted over multiple hours.</li> </ul>   ==================  CODE_AND_PLOTS ================== This archive contains the code required to gather the raw acoustic measurement data (see section DATA_RAW), the code to post-process and yield the final impulse response data (see section DATA), and the resulting plots as described in this section. Directory "dependencies/": <ul> <li>Matlab and Python functions that are utilized in the code</li> <li>Additional dependencies of available open-source projects may be required for certain code functions. If so, the source and setup process for the necessary dependencies are documented in the code header.</li> </ul> Directory "plots/": <ul> <li>Plots that were exported (and that may be regenerated) by the following scripts to validate different stages of the data simulation, measurement, and subsampling.</li> </ul> Shell script "x1_Start_Jupyter.sh": <ul> <li>Prepare a Python environment with the required tools described as dependencies.</li> <li>Activate the prepared Python environment to perform impulse response measurements using Jupyter Notebooks setup for different acoustic settings.</li> </ul> Python Jupyter notebook "x1a_Measure_Microphones.ipynb": <ul> <li>Setup and test the utilized acoustic measurement hardware.</li> <li>Perform a series of acoustic measurements of all utilized microphones in an anechoic environment.</li> <li>Export the raw acoustic data and processed impulse responses.</li> </ul> Python Jupyter notebook "x1b_Measure_BRIRs.ipynb": <ul> <li>Setup and test the utilized acoustic measurement hardware.</li> <li>Generate a horizontal grid of measurement orientations for the VariSphear turntable according to the desired dummy head orientations.</li> <li>Perform a series of acoustic measurements of the dummy head at the pre-defined grid in anechoic and various room environments.</li> <li>Export the raw acoustic data and processed impulse responses.</li> </ul> Python Jupyter notebook "x1c_Measure_SMAs.ipynb": <ul> <li>Setup and test the utilized acoustic measurement hardware.</li> <li>Generate a spherical grid of measurement orientations for the VariSphear turntable according to the desired SMA sampling grid.</li> <li>Perform a series of acoustic measurements of the SMA microphone at the pre-defined grid in anechoic and various room environments.</li> <li>Export the raw acoustic data and processed impulse responses.</li> </ul> Python Jupyter notebook "x1d_Measure_XMAs.ipynb": <ul> <li>Setup and test the utilized acoustic measurement hardware.</li> <li>Generate a horizontal grid of measurement orientations for the VariSphear turntable according to the desired scattering body orientations.</li> <li>Perform a series of acoustic measurements of the XMA microphones at the pre-defined grid in anechoic and various room environments.</li> <li>Export the raw acoustic data and processed impulse responses.</li> </ul> Matlab script "x1e_Simulate_SMAs.m": <ul> <li>Simulate a plane wave impinging from an arbitrary direction on SMAs and EMAs with a desired sampling grid in an anechoic environment.</li> <li>The simulations are helpful to evaluate the rendering method and to investigate the influence of different sampling grids and equalization methods on the rendered binaural signals.</li> </ul> Matlab script "x2_Gather_And_Plot_Measurements.m": <ul> <li>Gather the stored single files with individually measured impulse responses and the according metadata into a combined data set.</li> <li>The initial impulse responses can be recomputed with pre- and post-processing parameters tuned towards the specific acoustic scenario, including compensation of provided source and receiver impulse responses.</li> <li>Many plots may be generated during the processing to validate the input and output data.</li> </ul> Matlab script "x2a_Compare_Measurement_Lengths.m": <ul> <li>Compare the length of the resulting impulse responses of designated measurement configurations.</li> <li>This may be helpful for the tuning of pre-processing and post-processing parameters of the measured impulse responses.</li> </ul> Matlab script "x3_Subsample_Measurements.m": <ul> <li>Spatially subsample a high-resolution directional impulse response data set into a different (lower-resolution) sampling grid in the spherical harmonics domain.</li> <li>This is suitable for array and HRIR data sets.</li> <li>The script also compares the subsampled data against a reference set if available. In the current data set, an evaluation is performed for an anechoic simulation and a room measurement of an SMA at SH order 8.</li> </ul> Matlab script "x3a_Gather_XMA_Measurements.m": <ul> <li> Transform anechoic XMA measurement data from SOFA into the data format required by the processing scripts to calculate the respective calibration and equalization filters. </li> </ul> Readme file "x3b_Generate_XMA_Filters.txt": <ul> <li>The code for this functionality follows the publication [1] but is currently not polished enough for publication. Please contact Jens Ahrens (jens.ahrens@chalmers.se) for questions regarding this functionality.</li> <li>[1] J. Ahrens, H. Helmholz, D. Lou Alon, and S. V. Amengual Garí, “Spherical Harmonic Decomposition of a Sound Field Using Microphones on a Circumferential Contour Around a Non-Spherical Baffle,” IEEE/ACM Trans. Audio, Speech, Lang. Process., vol. 30, pp. 3110–3119, 2022, doi: 10.1109/TASLP.2022.3209940.</li> </ul> Matlab script "x3c_Gather_XMA_Filters.m": <ul> <li>Rename the files containing the computed calibration and equalization filters into a suitable convention for this collection of scripts.</li> <li>The generated name includes an incremental index to track different versions of provided filter sets.</li> </ul> Matlab script "x3d_Compare_XMA_Filters.m": <ul> <li> Generate various time domain and frequency domain plots to compare different versions of the generated XMA calibration and equalization filters. </li> </ul>   ================  DOCUMENTATION ================ This archive contains additional documentation of the setups and processes while conducting the acoustic measurements, as described in this section. Directory "documentation/": <ul> <li>Various photographs of the different room, source, and receiver arrangements of the data set</li> <li>The room dimensions and source and receiver positions are documented in the form of the original measurement notes (this may be improved in the future).</li> </ul>

Traits mediate environmental responses of benthic ciliates in dynamic coastal habitats

Aim: Understanding how species' traits mediate environmental responses provides a mechanistic perspective on community assembly processes. Although traits that influence the response of multicellular organisms to environments have been studied, the identification of such traits in unicellular organisms, like ciliates, is underexplored. Since ciliates are dominate animals at coastal sandy sediments and contribute significantly to interstitial community respiration, identifying links between their occurrence and sandy-coast characteristics is crucial for conserving biodiversity and protecting coastal habitats. Location: Coasts of China. Methods: We used Hierarchical Modeling of Species Communities, a trait-based joint species distribution model, to analyze ciliate community data collected from 344 sites belonging to 31 beaches across the Chinese coastline. Results: We found that physical variables play the most important role in determining ciliate occurrence. The beach index which combines the tidal range, sediment grain size and beach slope of beach selected species based on body size as well as feeding type, while sediment grain size constrained different mobility types, with swimming species favoring fine sandy sediments. The significant contribution of phylogeny in explaining the residual variation among species responses indicates that there are phylogenetically conserved but unmeasured traits too that influence species' responses. Species richness of benthic ciliates was higher in dissipative beaches with high primary productivity. Main conclusions: Based on our research, ciliate occurrence in coastal beaches is mediated by their traits which are filtered by local environmental variables. The beach index is essential in predicting distribution patterns and species richness of benthic ciliates. Nevertheless, further research is needed to identify additional traits that will enhance the accuracy of predicting ciliate niches. Our study provides insights into the mechanisms driving ciliate community assembly processes and has implications for the conservation of biodiversity in sandy coastal habitats.

Data associated with manuscript: "Foliar flavonoids across an elevation gradient: plasticity in response to UV, and links with floral pigmentation patterning"

There are two datasets provided in this excel file. The data are flavonoid abundances of Argentina anserina [=Potentilla anserina] exposed to two levels of ultraviolet light in a greenhouse. The "leaf only data" tab has the combined foliar abundances of the major classes of flavonoids detected: chalcone, flavonone, flavone, flavonol, flavon-3-ol, and proanthocyanidin. This dataset was used to analyze the effect of UV treatment and elevation on flavonoid production in leaves. The "leaf and petal matching cmpnds" is the abundance of the major flavonoid classes in leaves and petals for only the compounds that were detected in both tissue types. This dataset was used for all analyses that related leaf flavonoids with petal flavonoids and petal UV pigmentation.

Optokinetic response in D. Melanogaster reveals the nature of common repellent odorants

Pre-processed data for the paper "Optokinetic response in D. Melanogaster reveals the nature of common repellent odorants" by Menti et al. (https://doi.org/10.1038/s41598-024-73221-1)