Find research datasets worth reusing

Data, simulations/projections, and supporting materials for simulated hydrologic responses to climate-change projections for the Lake Tahoe basin: subbasin-scale results

This dataset contains data, simulations, projections, and supporting materials associated with simulated hydrologic responses, at the scale of 60 subbasins comprising the Lake Tahoe Basin, California and Nevada, to a 16-member ensemble of statistically-downscaled projections of climate change, 1950-2099. The process and results are described in detail in <div>Dettinger, M., & Rajagopal, S., 2023, Simulated hydrologic responses to climate-change </div> <div>projections for the Lake Tahoe Basin: Desert Research Institute Publication 41292, 99 p.,</div> <div> </div> <div>which is included here. </div> <div> </div> <div>The dataset as presented here contains 6 files, including one large zipped file that itself contains some 1,975 files, mostly simple text files of data, simulation outputs, and analytical results organized into dozens and dozens of subdirectories to allow specific elements to be identified and isolated. Beyond this large collection, the zipped file also contains copies of the report(s), selected supporting documents, graphical files, codes, and copious #readme.txt files to orient the user. </div>

Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe

Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from that of other highly visual species, such as vertebrates, and therefore the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, since there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. Examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods.

Data from: Navigating Polycrisis: long-run socio-cultural factors shape response to changing climate

These data are part of a data portal that accompanies the special issue 'Climate change adaptation needs a science of culture,' published in Philosophical Transactions of the Royal Society B in 2023. To access the data portal, please visit <a href="https://doi.org/10.5061/dryad.bnzs7h4h4">10.5061/dryad.bnzs7h4h4</a>. We have systematically collected information about the nature and consequences of societal crisis in over 150 cases covering different regions in the world in the preindustrial period. In this contribution, we discuss some critical insights arising from initial analysis of this material, which has informed the basis of our work.

Dataset for "Disentangling mechanisms responsible for wind energy effects on European bats"

Data used in the study "Disentangling mechanisms responsible for wind energy effects on European bats". site = ID attributed to the studied site ; ID_Parc = ID attributed to the studied wind farm ; night = date of the sampling ; SM4 = ID attributed to the recorder ; NbWT_1500m = number of wind turbines in a 1500m buffer ; Dist_WT = distance to the nearest wind turbine ; Dist_water = distance to the nearest water body or water course ; Dist_forest = distance to the nearest forest ; avg_temp = average temperature of the night ; Prev_wind_mod1 = prevailing wind direction of the night ; count_prev_wind22.5 = number of hours during which the wind direction was close (± 22.5°) to the prevailing wind direction (mode) of the night ; angle = angle between the axis wind-turbine - detector and the north direction ; MES_year = year of commissioning of the nearest wind turbines ; Model = model of the nearest wind turbine ; Rotor_diameter = diameter of the rotor of the nearest wind turbine ; Hub_height = height of the hub of the nearest wind turbine ; ID_WT = ID attributed to the nearest wind turbine

Runoff threshold responses in continental Boreal catchments: Nexus of sub-humid climate, low-relief, surficial geology and land cover

Revision in journal Water Resources Research,Paper # 2023WR034752RR the publication doi:  <a href="https://doi.org/10.1029/2023WR034752">doi.org/10.1029/2023WR034752</a> Abstract We examined annual runoff from 20 meso-scale catchments over 25 years, to elucidate how interactions between physiography and long-term weather patterns influence the magnitude of spatial-temporal thresholds in annual runoff responses in water-limited, low-relief, glaciated continental Boreal landscapes. Annual runoff ranged over two orders of magnitude (<3 to >300 mm) among catchments receiving similar annual precipitation. Threshold relationships were observed with cumulative regional moisture deficits that reflected spatial-temporal differences in effective storage and antecedent moisture among catchments with differing portions of glacial-deposit and land-cover types. The importance of the glacial-deposit texture and forest-peatland cover on runoff behavior among catchments varied with weather patterns and catchment antecedent moisture states. Dry states yielded low annual runoff that ranged by two orders of magnitude (0 to 80 mm), with higher values in catchments with predominantly coarse-textured deposits. During near normal antecedent moisture, annual runoff remained low (<10 mm) in catchments associated with fine-textured, hummocky landforms and deciduous forests. Annual runoff >10 mm was observed only in catchments with extensive peatlands. Infrequent wet states resulted in increased runoff in all catchments; however, ranges in maximum runoff were associated with heterogeneity in catchment landforms and land covers. Integrating cumulative precipitation with the proportion of glacial-deposit and land-cover types within catchments can: 1) represent water cycling and regional sink-source dynamics controlling runoff, and 2) provide an effective management framework for predicting climate and land-use impacts on regional runoff in water-limited, low-relief, glaciated landscapes such as the Boreal Plain.

openmit-licenseMay 2023View details →

BRUDEX Database: Binaural Room Impulse Responses with Uniformly Distributed External Microphones

There is an emerging need for comparable data for multi-microphone processing, particularly in acoustic sensor networks. However, commonly available databases are often limited in the spatial diversity of the microphones or only allow for particular signal processing tasks. In this paper, we present a database of acoustic impulse responses and recordings for a binaural hearing aid setup, 36 spatially distributed microphones spanning a uniform grid of (5x5) m^2 and 12 source positions. This database can be used for a variety of signal processing tasks, such as (multi-microphone) noise reduction, source localization, and dereverberation, as the measurements were performed using the same setup for three different reverberation conditions (T_60≈{310, 510, 1300} ms). The usability of the database is demonstrated for a noise reduction task using a minimum variance distortionless response beamformer based on relative transfer functions, exploiting the availability of spatially distributed microphones. An example how to load a impulse responses corresponding to the 'low' reverberation condition for the speaker located at 60 deg using MATLAB:     dataStruct = loadRIR('low',60,1,<basePATH>);%<basePATH>: path where database is located on local machine For further MATLAB examples, please consider "wrapper_loadDataFromDB.m" in the "matlabScripts.zip" archive file. An example how to load a impulse responses corresponding to the 'low' reverberation condition for the speaker located at 60 deg using Python:     dataloader = wrapper.BRUDEXDataloader()# <basePATH> is implicitly set to that path, where the file "wrapper.py" is located on local machine     dataStruct = dataloader.load_rir(reverberation_condition='low', direction_of_arrival = 60, ha_av = 1,e_mic_run = None) For further Python examples, please consider "main.py" in the "pythonScripts.zip" archive file. Caution: We noticed some problems with the download of the databse when using the command line (e.g., via the zenodo_get, wget, or curl commands). These problems don't seem to appear when downloading the files with the "Download" buttons on the website instead. Caution 2: When processing microphone signals, which are recorded with microphones that are placed *behind* loudspeakers, one can expect direct-path problems. Caution 3: For the recordings of the noise signals, four loudspeakers were placed at about 170 cm from (and facing) the corners of the room. That is why the noise is approximately spatially diffuse only in the vicinity of the center of the room and rather spatially coherent in the corners of the room. Caution 4: Oppposed to Zenodos information, the database does not contain 3 TB of data but about 200 GB.   Reference: D. Fejgin, W. Middelberg, and S. Doclo, “BRUDEX database: Binaural room impulse responses with uniformly distributed external microphones,” in Proc. ITG Conference on Speech Communication, Aachen, Germany, Sep. 2023, pp. 1–5. @InProceedings{Fejgin2023,     author    = {D. {Fejgin} and W. {Middelberg} and S. {Doclo}},     booktitle = {Proc. ITG Conference on Speech Communication},     title     = {{BRUDEX} Database: Binaural Room Impulse Responses with Uniformly Distributed External Microphones},     pages     = {1-5},     month     = {Sep.},     year      = {2023},     address   = {Aachen, Germany} }

Mitochondrial responses to long-term and cyclic hypoxia depend on the oxidized fuel in a hypoxia-tolerant marine bivalve Crassostrea gigas

These are the metadata for a publication "Mitochondrial responses to long-term and cyclic hypoxia depend on the oxidized fuel in a hypoxia-tolerant marine bivalve Crassostrea gigas" under consideration for publication in the Scientific reports. Sessile benthic organisms like oysters inhabits intertidal zone transitioning between aquatic and terrestrial condition during tidal movements exposing the organisms to alternating hypoxia and reoxygenation (H/R) episodes thereby altering the respiratory chain activities and metabolome compositions. Our study investigated the effects of constant long-term H/R stress (90 min at ~0% O2, and 10 min reoxygenation) and constant cyclic H/R stress (5 cycles of 15 min at ~0% O2, and 10 min reoxygenation) on isolated mitochondria from the gill and the digestive gland of C. gigas respiring on different substrates (pyruvate, palmitate, and succinate). Both gill and the digestive gland mitochondria exposed to constant long-term H/R suppressed OXPHOS respiration especially during Complex I oxidation with no change in ROS efflux but an increase FEL. In the gill mitochondria oxidizing Complex I substrates, exposure to constant cyclic H/R prompted a significant drop after the first H/R cycle. In contrast, succinate-driven respiration only showed significant decline after the fifth H/R cycle. ROS efflux and FEL however saw little to no change after constant cyclic H/R. This observation from our study further suggests succinate as a potential stress fuel under H/R stress and might assist in post-hypoxic recovery of oysters mitigating oxidative stress and supporting rapid ATP re-synthesis during oxygen fluctuations such as commonly observed in intertidal zones. Additionally, our study revealed that constant long-term hypoxia is more damaging than constant cyclic hypoxia.

Investigating the local temperature response to forest management with a regional climate model

Data used in the manuscript "Investigating the local temperature response to forest management with a regional climate model" which will be submitted to Journal of Geophysical Research: Atmospheres.

The Magee 3 Equation Predicts Favorable Pathologic Response to Neoadjuvant Endocrine Therapy in Breast Cancer Patients

Supplementary Figure 1: Comparison between ROC curves of ME1, ME2, ME3, and MEm scores in a sample of breast cancer patients undergoing neoadjuvant endocrine therapy. Supplementary Figure 2: ROC curves with their respective confidence intervals and AUC values in the sample of breast cancer patients, excluding those with clinical stage IA tumors. A: ME1. B: ME2. C: ME3. D: MEm. Supplementary Figure 3: Comparison between ROC curves of ME1, ME2, ME3, and MEm scores in the sample of breast cancer patients undergoing neoadjuvant endocrine therapy (excluding those with clinical stage IA tumors).

iNaturalist data for: Multi-taxon biodiversity responses to the 2019–2020 Australian megafires

Conditions conducive to fires are becoming increasingly common and widespread under climate change. Recent fire events across the globe have occurred over unprecedented scales, affecting a diverse array of species and habitats. Understanding biodiversity responses to such fires is critical for conservation. Quantifying post-fire recovery is problematic across taxa, from insects to plants to vertebrates, especially at large geographic scales. Novel datasets can address this challenge. We use presence-only citizen science data from iNaturalist, collected before and after the 2019-2020 megafires in burnt and unburnt regions of eastern Australia, to quantify the effect of post-fire diversity responses, up to 18 months post-fire. The geographic, temporal, and taxonomic sampling of this dataset was large, but sampling effort and species discoverability were unevenly spread. We used rarefaction and prediction (iNEXT) with which we controlled sampling completeness among treatments, to estimate diversity indices (Hill numbers: q=0-2) among nine broad taxon groupings and seven habitats, including 3885 species. We estimated an increase in species diversity up to 18 months after the 2019–2020 Australian megafires in regions which were burnt, compared to before the fires in burnt and unburnt regions. Diversity estimates in dry sclerophyll forest matched and likely drove this overall increase post-fire, while no taxon groupings showed clear increases inconsistent with both control treatments post-fire. Compared to unburnt regions, overall diversity across all taxon groupings and habitats greatly decreased in areas exposed to extreme fire severity. Post-fire life histories are complex and species detectability is an important consideration in all post-fire sampling. We demonstrate how fire characteristics, distinct taxa, and habitat influence biodiversity, as seen in local-scale datasets. Further integration of large-scale datasets with small-scale studies will lead to a more robust understanding of fire recovery.

Data: Female-limited responses in remating rate and mating duration in the experimental evolution of a beetle Callosobruchus chinensis

Mating rate optima often differ between the sexes: males may increase their fitness by multiple mating, but for females, multiple mating confers little benefit and can often be costly (especially in taxa without nuptial gifts or mala parental care). Sexually antagonistic evolution is thus expected in traits related to mating rates under sexual selection. This prediction has been tested by multiple studies that applied the experimental evolution technique, which is a powerful tool to directly examine the evolutionary consequences of selection. Yet, the results so far only partly support the prediction. Here we provide another example of experimental evolution of sexual selection, by applying it for the first time to the mating behavior of a seed beetle Callsorobruchus chinensis. We found a lower remating rate in polygamy-line females than in monogamy-line (i.e. no sexual selection) females after 21 generations of selection. Polygamy-line females also showed a longer duration of first mating than monogamy-line females. We found no effect of male evolutionary lines on the remating rate or first mating duration. Though not consistent with the original prediction, the current and previous studies collectively suggest that the observed female-limited responses may be a norm, which is also consistent with the conceptual advances in the last two decades of the advantages and limitations of the experimental evolution technique.

Larval and adult traits coevolve in response to asymmetric coastal currents to shape marine dispersal kernels

Dispersal emerges as an outcome of organismal traits and external forcings. However, it remains unclear how the emergent dispersal kernel evolves as a by-product of selection on the underlying traits. This question is particularly compelling in coastal marine systems where dispersal is tied to development and reproduction, and where directional currents bias larval dispersal downstream causing selection for retention. We modelled the dynamics of a metapopulation along a finite coastline using an integral projection model and adaptive dynamics to understand how asymmetric coastal currents influence the evolution of larval (pelagic larval duration) and adult (spawning frequency) life history traits, which indirectly shape the evolution of marine dispersal kernels. Selection induced by alongshore currents favors the release of larvae over multiple time periods, allowing long pelagic larval durations and long-distance dispersal to be maintained in marine life cycles in situations where they were previously predicted to be selected against. Two evolutionary stable strategies emerged: one with a long pelagic larval duration and many spawning events resulting in a dispersal kernel with a larger mean and variance, and another with a short pelagic larval duration and few spawning events resulting in a dispersal kernel with a smaller mean and variance. Our theory shows how coastal ocean flows are important agents of selection that can generate multiple, often co-occurring, evolutionary outcomes for marine life history traits that affect dispersal.

Hyper PUF with multi-level operation: Challenge-Response Pair Library

An optical PUF with multi level operation (that we named as Hyper PUF) is interrogated with a set of 100 Random Probing Challenges producing in the far field an optical response, the speckle pattern. The multi-level operation is induced by modifying the scattering properties of the PUF with a second light pattern, the Transforming Level. Per each Transforming Level, we acquired the Responses to the 100 Random Probing Challenges. In this repository, we collect the Random Probing Challenges, the ten Transforming Levels and the relative Responses to the Probing Challenges per each Transforming Level.

Thallus hydrophobicity: a low-cost method for understanding lichen ecophysiological responses to environmental changes

Premise: Methods to evaluate lichen thalli hydrophobicity were described in the past, but only recently this was shown to be an important functional trait related to water regulation dynamics that could be used to predict future climate change effects. Methods and Results: Our protocol requires only a micropipette, distilled water, a tripod and a phone or camera. Hydrophobicity is inferred from multiple metrics associated with absorption times of standardized droplets (initial and total absorption time). We used a dataset of 93 lichen taxa with different growth forms and from different biomes and demonstrated that this method is well suited for capturing different levels of hydrophobicity, including very hydrophilic species. Conclusions: Our results show that the measurement of lichen hydrophobicity is a rapid and low-cost method to assess an ecophysiologically based lichen functional trait that can be used with almost no limitations, including in different climates, lichen species, and growth forms.

Upconversion FRET quantitation: the role of donor photoexcitation mode and compositional architecture on the decay and intensity based responses

Abstract Lanthanide-doped colloidal nanoparticles capable of photon upconversion (UC) offer long luminescence lifetimes, narrowband absorption and emission spectra, and efficient anti-Stokes emission. These features are highly advantageous for Förster Resonance Energy Transfer (FRET) based detection. Upconverting nanoparticles (UCNPs) as donors may solve the existing problems of molecular FRET systems, such as photobleaching and limitations in quantitative analysis, but these new labels also bring new challenges. Here we have studied the impact of the core-shell compositional architecture of upconverting nanoparticle donors and the mode of photoexcitation on the performance of UC-FRET from UCNPs to Rose Bengal (RB) molecular acceptor. We have quantitatively compared luminescence rise and decay kinetics of Er3+ emission using core-only NaYF4: 20% Yb, 2% Er and core-shell NaYF4: 20% Yb @ NaYF4: 20% Yb, 5% Er donor UCNPs under three photoexcitation schemes: (1) direct short-pulse photoexcitation of Er3+ at 520 nm; indirect photoexcitation of Er3+ through Yb3+ sensitizer with (2) 980 nm short (5–7 ns) or (3) 980 nm long (4 ms) laser pulses. The donor luminescence kinetics and steady-state emission spectra differed between the UCNP architectures and excitation schemes. Aiming for highly sensitive kinetic upconversion FRET-based biomolecular assays, the experimental results underline the complexity of the excitation and energy-migration mechanisms affecting the Er3+ donor responses and suggest ways to optimize the photoexcitation scheme and the architecture of the UCNPs used as luminescent donors.

Predictive neural computations in cerebellar circuits contribute to motor planning and faster behavioral responses in larval zebrafish

This dataset contains raw and processed data along with jupyter notebooks to generate figures in Narayanan et al., 2023. Instructions for navigating through the dataset and for running the analysis codes are in README.pdf.

opencc-zeroOct 2023View details →

Data from: Habitat-based biodiversity responses to macroclimate and edaphic factors in European fen ecosystems

Understanding large-scale drivers of biodiversity in palustrine wetlands is challenging due to the combined effects of macroclimate and local edaphic conditions. In boreal and temperate fen ecosystems, the influence of macroclimate on biodiversity is modulated by hydrological settings across habitats, making It difficult to assess their vulnerability to climate change. Here, we investigate the influence of macroclimate and edaphic factors on three Essential Biodiversity Variables across eight ecologically defined habitats that align with ecosystem classifications and red lists. We used 27,555 vegetation plot samples from European fens to assess the influence of macroclimate and groundwater pH predictors on the geographic distribution of each habitat type. Additionally, we modeled the relative influence of macroclimate, water pH and water table depth on community species richness and composition, focusing on 309 plant specialists. Our models reveal strong effects of mean annual temperature, diurnal thermal range and summer temperature on biodiversity variables, with contrasting differences among habitats. While macroclimatic factors primarily shape geographic distributions and species richness, edaphic factors emerge as the primary drivers of composition for vascular plants and bryophytes. Annual precipitation exhibits non-linear effects on fen biodiversity, with varying impact across habitats with different hydrological characteristics, suggesting a minimum requirement of 600 mm of annual precipitation for the occurrence of fen ecosystems. Our results anticipate potential impacts of climate warming on European fens, with predictable changes among habitat types and geographic regions. Moreover, we provide evidence that the drivers of biodiversity in boreal and temperate fens are closely tied to the ecological characteristics of each habitat type and the dispersal abilities of bryophytes and vascular plants. Given that the influence of macroclimate and edaphic factors on fen ecosystems is habitat-specific, climate change research and conservation actions should consider ecological differentiation within functional IUCN ecosystems at continental and regional scales.

opencc-zeroOct 2023View details →

Dataset for: Asymmetric response of aboveground and belowground temporal stability to nitrogen and phosphorus addition in a Tibetan alpine grassland

Anthropogenic eutrophication is known to impair the stability of aboveground net primary productivity (ANPP), but its effects on the stability of belowground (BNPP) and total (TNPP) net primary productivity remain poorly understood. Based on a nitrogen and phosphorus addition experiment in a Tibetan alpine grassland, we show that nitrogen addition had little impact on the temporal stability of ANPP, BNPP and TNPP, whereas phosphorus addition reduced the temporal stability of BNPP and TNPP, but not ANPP. Significant interactive effects of nitrogen and phosphorus addition were observed on the stability of ANPP because of the opposite phosphorus effects under ambient and enriched nitrogen conditions. We found that the stability of TNPP was primarily driven by that of BNPP rather than that of ANPP. The responses of BNPP stability cannot be predicted by those of ANPP stability, as the variations in responses of ANPP and BNPP to enriched nutrients, with ANPP increased while BNPP remained unaffected, resulted in asymmetric responses in their stability. The dynamics of grasses, the most abundant plant functional group, instead of community species diversity, largely contributed to the ANPP stability. Under the enriched nutrient condition, the synchronization of grasses reduced the grass stability, while the latter had a significant but weak negative impact on the BNPP stability. These findings challenge the prevalent view that species diversity regulates the responses of ecosystem stability to nutrient enrichment. Our findings also suggest that the ecological consequences of nutrient enrichment on ecosystem stability cannot be accurately predicted from the responses of aboveground components, and highlight the need for a better understanding of the belowground ecosystem dynamics.

opencc-by-4.0Oct 2023View details →

The Responses of Students using Online Loans at the Institut Teknologi Sepuluh Nopember

The dataset of responses of students using online loans at the ITS. We remove privacy information, such as the birth of data and home address. We only store the gender. The dataset is in CSV file