Find research datasets worth reusing

opencc-zeroOct 2022View details →

Data from: Simulating climate change in situ in a tropical rainforest understorey using active air warming and CO2 addition

Background: Future climate-change effects on plant growth are most effectively studied using microclimate-manipulation experiments, the design of which has seen much advance in recent years. For tropical forests, however, such experiments are particularly hard to install and have hence not been widely used. We present a system of active heating and CO2 fertilisation for use in tropical forest understoreys, where passive heating is not possible. The system was run for two years to study climate-change effects on epiphytic bryophytes, but is also deemed suitable to study other understorey plants. Methods: Warm-air and CO2 addition were applied in 1.6-m tall, 1.2-m diameter hexagonal open-top chambers and the microclimate in the chambers compared to outside air. Warming was regulated with a feedback system while CO2 addition was fixed. Results: The setup successfully heated the air by 2.8K and increased CO2 by 250 ppm, on average, with +3K and +300 ppm as the targets. Variation was high, especially due to technical break-downs, but not biased to times of the day or year. In the warming treatment, absolute humidity slightly increased but relative humidity dropped by between 6 to 15% (and the vapour-pressure deficit increased) compared to ambient, depending on the level of warming achieved in each chamber. Conclusions: Compared to other heating systems, the chambers provide a realistic warming and CO2 treatment, but moistening the incoming air would be needed to avoid drying as a confounding factor. The method is preferable over infrared heating in the radiation-poor forest understory, particularly when combined with CO2 fertilisation. It is suitable for plant-level studies, but ecosystem-level studies in forests may require chamber-less approaches like infrared heating and free-air CO2 enrichment. By presenting the advantages and limitations of our approach we aim to facilitate further climate-change experiments in tropical forests, which are urgently needed to understand the processes determining future element fluxes and biodiversity changes in these ecosystems.

opencc-by-4.0Jun 2022View details →

Nitrogen activation and cleavage by a multimetallic uranium complex

Multimetallic-multielectron cooperativity plays a key role in the metal-mediated cleavage of N2 to nitrides (N3-) In particular, low-valent uranium complexes coupled with strong alkali metal reducing agents can lead to N2 cleavage, but often, it is ambiguous how many electrons are transferred from the uranium centers to cleave N2. Herein, we designed new dinuclear uranium nitride complexes presenting a combination of electronically diverse ancillary ligands to promote the multielectron transformation of N2. Two heteroleptic diuranium nitride complexes, [K{UIV(OSi(OtBu)3)(N(SiMe3)2)2}2(m-N)] (1) and [Cs{UIV(OSi(OtBu)3)2(N(SiMe3)2)}2(u-N)] (3-Cs), containing different combinations of OSi(OtBu)3 and N(SiMe3)2 ancillary ligands, were synthesized. We found that both complexes could be reduced to their U(III)/U(IV) analogues, and the complex, [K2{UIV/III(OSi(OtBu)3)2(N(SiMe3)2)}2(m-N)] (6-K), could be further reduced to a putative U(III)/U(III) species that is capable of promoting the 4e reduction of N , yielding the N24- complex [K3{UV(OSi(OtBu)3)2(N(SiMe3)2)}2(m-N)(m-h2:h2-N2)], 7. Parallel N2 reduction pathways were also identified, leading to the isolation of N2 cleavage products, [K3{UVI(OSi(OtBu)3)2(N(SiMe3)2)(^N)}(m- N)2{UV(OSi(OtBu)3)2(N(SiMe3)2)}]2, 8, and [K4{(OSi(OtBu)3)2UV)(^N)}(m-NH)(m-k2:C,N-CH2SiMe2NSiMe3)- {UV(OSi(OtBu)3)2][K(N(SiMe3)2]2, 9. These complexes provide the first example of N2 cleavage to nitride by a uranium complex in the absence of reducing alkali metals,

Accompanying data for "Non-cyanobacterial diazotrophs: Global diversity, distribution, ecophysiology, and activity in marine waters"

Data accompanying the manuscript "Non-cyanobacterial diazotrophs: Global diversity, distribution, ecophysiology, and activity in marine waters," submitted to FEMS Microbiology Reviews. Contents include: - A compilation of available marine water column qPCR/ddPCR nifH gene abundance data from published studies with metadata colocalized using the Simons Collaborative Marine Atlas Project (see NCDReview_SupplTable4.pdf for a description of variables): NCDReview_qPCR_database.xlsx - Nucleotide and amino acid sequences for the assembled nifH gene catalog (NCDReview_SupplTable1_caption.docx, NCDReview_TableS1_nt.fasta, NCDReview_TableS1_aa.fasta) - Table of nifH clusters and subclusters, with corresponding phyla and genera (NCDReview_Table1.xlsx)

Role of Counterions in the Structural Stabilisation of Redox-Active Metal-Organic Frameworks

Preliminary dataset for "Role of Counterions in the Structural Stabilisation of Redox-Active Metal-Organic Frameworks"

Data from: Zoning has little impact on the seasonal diel activity and distribution patterns of wild boar (Sus scrofa) in an UNESCO Biosphere Reserve

Understanding the spatio‐temporal distribution of ungulates is important for effective wildlife management, particularly for economically and ecologically important species such as wild boar (Sus scrofa). Wild boars are generally considered to exhibit substantial behavioral flexibility, but it is unclear how their behavior varies across different conservation management regimes and levels of human pressure. To analyze if and how wild boars adjust their space use or their temporal niche, we surveyed wild boars across the core and buffer zones (collectively referred to as the conservation zone) and the transition zone of a biosphere reserve. These zones represent low and high levels of human pressure, respectively. Specifically, we employed a network of 53 camera traps distributed in the Schaalsee UNESCO Biosphere Reserve over a 14‐month period (19,062 trap nights) and estimated circadian activity patterns, diel activity levels, and occupancy of wild boars in both zones. To account for differences in environmental conditions and day length, we estimated these parameters separately for seven 2‐month periods. Our results showed that the wild boars were primarily nocturnal, with diurnal activity occurring dominantly during the summer months. The diel activity patterns in the two zones were very similar overall, although the wild boars were slightly less active in the transition zone than in the conservation zone. Diel activity levels also varied seasonally, ranging from 7.5 to 11.0 h day−1, and scaled positively with the length of the night (R2 = 0.66–0.67). Seasonal occupancy estimates were exceptionally high (point estimates ranged from 0.65 to 0.99) and similar across zones, suggesting that the wild boars used most of the biosphere reserve. Overall, this result suggests that different conservation management regimes (in this case, the zoning of a biosphere reserve) have little impact on wild boar behavior. This finding is relevant for wildlife management in protected areas where possibly high wild boar densities could interfere with conservation goals within these areas and those of agricultural land use in their vicinity.

Lightning activity and wind speed variations in Tropical Cyclones of the Southwest Pacific Region

Lightning data used in 'Lightning activity and wind speed variations in Tropical Cyclones of the Southwest Pacific Region'.

Activation patterns of afferent synapses on layer 5 tufted pyramidal cells in a biologically detailed simulation

The data set is based on a biologically detailed simulation of a circuit of cortical neurons. The circuit was activated by thalamo-cortical inputs every 1 s for 500 ms. We report for a number of exemplary tufted pyramidal cells in layer 5 the pattern activation of their afferent synapses. Specifically, we report for all afferent excitatory synapses the pairwise path distances along the dendrite / soma (note that the soma was simplified to a point for the purpose of calculating path distances, but not during the simulation), and the times of activation of each of these synapses. The simulation is based on the model described in <a href="https://www.biorxiv.org/content/10.1101/2022.08.11.503144v1">this preprint</a>. The model can also be found <a href="https://zenodo.org/record/6906785">here on Zenodo</a>. For more details on the simulation, contact the author. For more details about the format of the data, refer to the included jupyter notebook.

Data and code for: Uncovering commercial activity in informal cities

Knowledge of the spatial organisation of economic activity within a city is key to policy concerns. However, in developing cities with high levels of informality, this information is often unavailable. Recent progress in machine learning together with the availability of street imagery offers an affordable and easily automated solution. Here we propose an algorithm that can detect what we call visible firms using street view imagery. Using Medellín, Colombia as a case study, we illustrate how this approach can be used to uncover previously unseen economic activity. This dataset contains the data and code required to replicate our analysis for the manuscript: "Uncovering commercial activity in informal cities."

opencc-by-4.0Sep 2022View details →

Raw data for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents "

Raw computational, NMR, IR and MS  data  for the article "Substrate-Controlled C-H or C-C Alkynylation of Cyclopropanes: Generation of Aryl Radical Cations by Direct Light Activation of Hypervalent Iodine Reagents " published in Chemical Science, DOI:  <a href="https://doi.org/10.1039/D2SC04344K">https://doi.org/10.1039/D2SC04344K</a> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

Airborne and drone from Asiago (Italy) forest area before and after logging activities (ZIPPED archive version)

<ul> <li>lidar DSM and DTM (tif format) from airborne laser scanning before logging activities</li> <li>drone DSM (tif format) from photogrammetry after logging activities</li> <li><a href="https://zenodo.org/api/files/58082214-481c-44ce-9d3f-3dfdb311aa70/tarif_forest_parcels.gpkg">tarif_forest_parcels.gpkg</a> : tarif parcels polygons in geopackage format</li> <li>trees32632.csv: tree positions in delimited text format</li> <li>tarifVolumeTables.xlsx: tarif look-up-tables</li> <li><a href="https://zenodo.org/api/files/58082214-481c-44ce-9d3f-3dfdb311aa70/treeExtractionFromDSM_DTM_version02Dec2022.R">treeExtractionFromDSM_DTM_version02Dec2022.R</a> - R script to extract tree positions from a CHM</li> </ul>

Test dataset for "Rapid estimation of cortical neuron activation thresholds by transcranial magnetic stimulation using convolutional neural networks"

Data corresponding to test dataset used in Aberra AS, Lopez A, Grill WM, Peterchev AV. (2022). "Rapid estimation of cortical neuron activation thresholds by transcranial magnetic stimulation using convolutional neural networks". bioRxiv. Dataset includes: <ul> <li>simnibs/ - SimNIBS mesh and E-field solution file used in test dataset (posterior-anterior TMS of M1 in ernie example mesh, meshed with mri2mesh pipeline)</li> <li>layer_data/ - surface meshes used for placing and orienting neuron models and corresponding sampling grids for CNNs</li> <li>nrn_sim_data/ - Thresholds from NEURON simulations for all 25 model neurons included in the study, each at 4,999-5,000 positions and 12 azimuthal orientations ("ground truth" for CNN) </li> <li>cell_data/ - Coordinates and morphology information for all model neurons</li> <li>weights/  - Trained 3D convolutional neural networks for estimating neuron model-specific TMS thresholds given input E-field distributions on a 3D grid (see code/manuscript for dimensions)</li> <li>est_data/ - Output of trained CNNs on all E-field data for test dataset  </li> </ul>

Green synthesis of ZnO nanoparticles using Cocos nucifera leaf extract: Characterization, antimicrobial, antioxidant, and photocatalytic activity

Zinc oxide nanoparticles (ZnO NPs) have been successfully prepared using Cocos nucifera leaf extract and investigated with their antimicrobial, antioxidant, and photocatalytic activity. The structural, compositional, and morphological properties of the NPs were recorded and studied systematically to confirm the synthesis. The aqueous suspension of NPs showed a UV-Vis. absorption maxima of 370 nm indicating primarily its formation. The XRD analysis identified the NPs with hexagonal wurtzite structure with an average particle size of 16.6 nm. The FTIR analysis identified some biomolecules and functional groups in the leaf extract as responsible for the encapsulation and stabilization of ZnO NPs. The EDX analysis showed the desired elemental compositions in the material. A flower-shaped morphology of ZnO NPs was observed by SEM with a grain size of around 15 nm. The optical properties of the NPs were studied by UV-Vis spectroscopy and the bandgap was calculated as 3.37 eV. The Prepared ZnO NPs have demonstrated antimicrobial activity against T. harzianum, and S. aureus with a ZOI (zone of inhibition) of 14 and 10 mm, respectively. The photocatalytic behavior of ZnO NPs showed absorbance degradation at around 640 nm and discolored methylene blue dye after one hour with a degradation maximum of 84.29 %. Thus, the prepared ZnO NPs could be used potentially in antibiotic development, pharmaceutical industries, and as photocatalysts.

opencc-by-4.0Jul 2022View details →

Stellar chromospheric activity database of solar-like stars based on the LAMOST Low-Resolution Spectroscopic Survey

A stellar chromospheric activity database of solar-like stars is constructed based on the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) Low-Resolution Spectroscopic Survey (LRS). The database contains spectral bandpass fluxes and indexes of Ca II H and K lines derived from 1,330,654 high-quality LRS spectra of solar-like stars. We measure the mean fluxes at line cores of the Ca II H and K lines using a 1 Å rectangular bandpass and a 1.09 Å FWHM triangular bandpass, as well as the mean fluxes of two 20 Å wide pseudocontinuum bands on the two sides of the lines. Three activity indexes of Ca II H and K lines, Srec based on the 1 Å rectangular bandpass and Stri and SL based on the 1.09 Å FWHM triangular bandpass, are evaluated from the measured fluxes to quantitatively indicate the chromospheric activity level. The uncertainties of all the obtained parameters are estimated. We also produce spectrum diagrams of Ca II H and K lines for all the spectra in the database. This database, with more than one million high-quality LAMOST LRS spectra of Ca II H and K lines and basal chromospheric activity parameters, can be further used for investigating activity characteristics of solar-like stars and solar-stellar connection.   The entity of the database is composed of (1) a catalog of spectral sample and activity parameters, and (2) a library of spectrum diagrams of Ca II H and K lines. (1) Catalog of Spectral Sample and Activity Parameters CaIIHK_Sindex_LAMOST_DR7_LRS.csv (see Table3 in the paper 2022_ApJS_263_12 for description of the columns) (2) Library of Spectrum Diagrams of Ca II H and K lines spectrum_diagrams_000-049.zip  (46 subfolders) spectrum_diagrams_050-099.zip  (40 subfolders) spectrum_diagrams_100-149.zip  (47 subfolders) spectrum_diagrams_150-174.zip  (25 subfolders) spectrum_diagrams_175-199.zip  (24 subfolders) spectrum_diagrams_200-224.zip  (24 subfolders) spectrum_diagrams_225-249.zip  (23 subfolders) spectrum_diagrams_250-259.zip  (10 subfolders) spectrum_diagrams_260-274.zip  (12 subfolders) spectrum_diagrams_275-299.zip  (23 subfolders) spectrum_diagrams_300-349.zip  (41 subfolders) spectrum_diagrams_350-374.zip  (20 subfolders) spectrum_diagrams_375-399.zip  (19 subfolders) spectrum_diagrams_400-424.zip  (23 subfolders) spectrum_diagrams_425-449.zip  (22 subfolders) spectrum_diagrams_450-499.zip  (35 subfolders) spectrum_diagrams_500-549.zip  (27 subfolders) spectrum_diagrams_550-599.zip  (38 subfolders) spectrum_diagrams_600-649.zip  (32 subfolders) spectrum_diagrams_650-699.zip  (26 subfolders) spectrum_diagrams_700-749.zip  (28 subfolders)

opencc-by-4.0Jul 2022View details →

CHROMATIN ACTIVATION PROFILING OF STEREOTYPED CHRONIC LYMPHOCYTIC LEUKEMIAS

We used chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) with an antibody for the H3K27ac (a bona fide histone mark for regulatory element activation) in sorted CLL cells from 46 CLL, including 21 cases from stereotyped subsets #1, #2, #4, and #8, and 15 normal B cell subpopulations. To understand their functional impact, we integrated our data with 16 RNA-seq data. Files description: - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/H3K27ac_freq2_FDR_consensus_2022.txt?versionId=887e281e-526d-403d-a59d-4ac3e5773305">H3K27ac_freq2_FDR_consensus_2022.txt</a> count matrix from H3K27ac signals - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/H3K27ac_FDR_consensus_norm.Combat_2022.txt?versionId=4a17abb5-0c95-42cc-b573-d11e0de2f484">H3K27ac_FDR_consensus_norm.Combat_2022.txt</a> count matrix from H3K27ac signals after batch effect correction - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/RNAseq_norm.Combat_results.txt">RNAseq_norm.Combat_results.txt</a> count matrix from RNAseq after batch effect correction - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/signature_RESAMPLING_ss8VSucll_2022.txt?versionId=806b1776-1571-4675-bc1c-3f0c29bf892e">signature_RESAMPLING_ss8VSucll_2022.txt</a> differentially acetylated regions between U-CLL and stereotyped subset #8 applying random sampling 100 times with a range of samples from 5 to n-1 in each category. The regions showing frequency >=20% were considered significant regions.

Six hundred years of reconstructed atmospheric river activity on the US west coast

These are the reconstruction data from the article: Six hundred years of reconstructed atmospheric river activity along the US West Coast (under review at the Journal of Geophysical Research: Atmosphere). The earliest start year of the reconstruction are mentioned in the files (either 1916 or 1400) and the corresponding models are mentioned as PCR (Regression) or NN (Neural Network).

Data from: Smoke-driven changes in photosynthetically active radiation during the U.S. agricultural growing season

Wildfire smoke is frequently present over the U.S. during the agricultural growing season and will likely increase with climate change. Studies of smoke impacts have largely focused on air quality and human health; however, understanding smoke's impact on photosynthetically active radiation (PAR) is essential for predicting how smoke affects plant growth. We compare surface shortwave irradiance and diffuse fraction (DF) on smoke-impacted and smoke-free days from 2006-2020 using data from multifilter rotating shadowband radiometers at ten U.S. Department of Agriculture (USDA) UV-B Monitoring and Research Program stations and smoke plume locations from operational satellite products. On average, 20% of growing season days are smoke-impacted, but smoke prevalence increases over time (r = 0.60, p < 0.05). Smoke presence peaks in the mid- to late growing season (i.e., July, August), particularly over the northern Rocky Mountains, Great Plains, and Midwest. We find an increase in the distribution of PAR DF on smoke-impacted days, with larger increases at lower cloud fractions. On clear-sky days, daily average PAR DF increases by 10 percentage points when smoke is present. Spectral analysis of clear-sky days shows smoke increases DF (average: +45%) and decreases total irradiance (average: -6%) across all six wavelengths measured from 368-870 nm. Optical depth measurements from ground and satellite observations both indicate that spectral DF increases and total spectral irradiance decreases with increasing smoke plume optical depth. Our analysis provides a foundation for understanding smoke's impact on PAR, which carries implications for agricultural crop productivity under a changing climate.

opencc-zeroDec 2022View details →

Assisted sexual reproduction of Acropora cervicornis for active restoration on Florida's Coral Reef

Given the rapid, global decline in the health and abundance of coral reefs, increased investments in restoration-based interventions – including asexual and sexual propagation – are being made by coral reef scientists at research institutions, but also at zoos and aquariums. Mote Marine Laboratory & Aquarium is an independent, non-profit marine science organization dedicated to the conservation and restoration of Florida's Coral Reef, and does so, using science-based strategies. In order to promote the long-term persistence, resilience, and adaptive potential of restored coral populations on Florida's Coral Reef, Mote scientists are performing critical research and restoration activities related to assisted sexual reproduction (ASR). The objective of this study was to optimize ASR of Acropora cervicornis by (1) evaluating broodstock compatibility for genets actively used within Mote's restoration gene pool, (2) optimizing larval settlement by testing spectral cues, (3) and optimizing the grow-out of sexual recruits by testing the impact of light on growth, survival, and algal symbiont uptake in the presence of adult corals or not. Overall, we found that corals and genets spawned with high synchrony, both within and across years, and in terms of predicted spawning times related to nights after the full moon and minutes after sunset. Across two years, overall fertilization success was high (~95%), but we did find one pair of genets that was not compatible. During settlement, larvae preferred pink and purple-colored substrates, which was consistent with our expectation that they would select substrates similar in color to crustose coralline algae (CCA). Interestingly though, they only did so when a matching chemical cue from CCA was also present, indicating that larvae integrate multiple cues simultaneously to determine the most appropriate place to settle. Growth and symbiont uptake were faster in recruits reared in the presence of adult corals and additional lighting, but survivorship was not different through the first ten weeks post-settlement between treatments. A subset of corals was outplanted using two different techniques based on single or clustered corals. We report the initial 1-month survival results. We also provide a detailed protocol and general recommendations for ASR based on years of coral sexual propagation experience.

opencc-by-4.0Dec 2022View details →

Dataset supporting publication: "The Problem of Geothermal Power Installation on Buildings: Structural Building Monitoring and Assessment During Drilling Activities"

Dataset supporting publication: “The Problem of Geothermal Power Installation on Buildings: Structural Building Monitoring and Assessment During Drilling Activities” (publication available in <a href="https://zenodo.org/record/7266386#.Y1_e1XbMJPY">GEOFIT Zenodo</a>) Datasets resultant from structural health monitoring activities (accelerometer data). The current European Union (EU) policy aims to increase the use of “green” energies, and within this strategy the exploitation of the geothermal energy is a well promising approach. The European Horizon2020 project GEOFIT (Deployment of novel GEOthermal systems, technologies and tools for energy efficient building retroFITting) aims among the others to deploy and to integrate advanced methods of worksite inspection, ground research, and building structural monitoring, drilling and worksite characterization into advanced geothermal based retrofitting methods. When dealing with “plants of power production”, one needs to develop a Life Cycle Analysis and to apply a Life Cycle Assessment (LCA) for evaluating any environmental aspects and potential influences throughout the whole life cycle of a product or process or service. The paper first provides a preliminary discussion on this aspect. Then it focuses attention on a pilot site made available within the GEOFIT Consortium. The results from a structural monitoring campaign in this pilot site before and during the drilling operations associated to the implementation of the geothermal power system are presented discussed.

opencc-by-4.0Dec 2022View details →

shemakes activities: record of activities and participation in the learning paths and innovation services.

Shemakes record of activities and participation dataset contains the number of participants for each event or activity during the project duration collected mainly from the WP2 learning paths and WP3 innovation services, which are the WPs with a high amount of activities and events related to the shemakes development. It does not contain personal or sensitive data, as it is focused on the event's typology. Participants are aggregated per activity. Besides, the dataset includes information about 1) the country where the activity is carried out and 2) it mentions the type of activity and its title. The data about the participants comprises the number of females, whether the females were adults or minors and the percentage of female participants.