Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Nanoporous carbon structures of different densities generated through GAP molecular dynamics

These nanoporous (NP) carbon atomic structures, in extendend XYZ format, have been generated using a melt-graphitization-quench molecular dynamics (MD) protocol using a Gaussian interatomic potential (GAP) for amorphous carbon [1]. Simulation details and characterization of structural and mechanical properties will follow shortly in a scientific paper. References [1] M.A. Caro. GAP interatomic potential for amorphous carbon (2.0) [Data set]. Zenodo, 10.5281/zenodo.5243184 (2021).

opencc-zeroSep 2021View details →

Data for: Characterizing individual tree-level snags using airborne lidar-derived forest canopy gaps within closed-canopy conifer forests

1. Airborne lidar is often used to calculate forest metrics about trees but it may also provide a wealth of information about the space between trees. Forest canopy gaps are defined by the absence of vegetative structure and serve important roles for wildlife, such as facilitating animal movement. Forest canopy gaps also occur around snags, keystone structures that provide important substrates to wildlife species for breeding, roosting, and foraging. 2. We wanted to test a method for quantifying canopy gaps around individual snags and live trees, with the working hypothesis that snags would have more gaps surrounding them overall than live trees. We evaluated canopy gaps around individual snags (n=270) and live trees (n=2186) and evaluated correlations between canopy structure and snag occurrence in dense conifer stands of the Idaho Panhandle National Forest, USA. We paired airborne lidar with ground reference data collected at fixed-radius plots (n=53) to evaluate local gap structure. The R package ForestGapR was used to quantify canopy gaps throughout the canopy to determine where the differences were greatest. A canopy space profile was created for each tree by mapping gaps (a) vertically every 2 m in height (2–50 m above ground), and (b) horizontally across small (16 m2), medium (36 m2), and large (64 m2) footprint sizes. 3. Our results suggest this method is robust for quantifying canopy gaps around individual trees. The canopy space profiles were distinctly different for snags and live trees, with more canopy gaps within the area surrounding snags relative to live trees. The greatest differences occurred at mid-canopy heights (~20 m above ground) and at the smallest footprint size (16 m2). 4. These results show potential to improve understanding of gap dynamics in closed-canopy conifer forests, and we suggest snag modeling could be improved by incorporating lidar-derived canopy gap analyses alongside existing methodologies.

opencc-by-4.0Jul 2021View details →

Characterization of photodiodes for detection of variations in part-to-part gap and weld penetration depth during remote laser welding of copper-to-steel battery tab connectors

In this folder, .csv files and Matlab scripts for processing data from experimental campaign that has been reported in the following paper: Chianese, G., Franciosa, P., Nolte, J., Ceglarek, D., and Patalano, S., “Characterization of photodiodes for detection of variations in part-to-part gap and weld penetration depth during remote laser welding of copper-to-steel battery tab connectors.” Journal of Manufacturing Science and Engineering. In-press. As the experimental campaign is made up of two phases, files are divided in two folders: (i)     Phase I - Weld penetration depth; and, (ii)    Phase II - Part-to-part gap. In each of these two folders, there are: (i)    a Matlab live script that, once the code is run, allows the user to select the signals (please, select all of them); (ii)     functions to run the code; (iii)    Matlab variable files; (iii)    a folder with .csv files that contain signals recorded during experimental campaign; (iv)      an Excel file reporting experimental setup and process parameters; (v)    a PDF file with the live script and results of the data processing for the readers that cannot run Matlab codes.

opencc-zeroOct 2022View details →

Research gaps limit understanding of invasion-fire cycles

These files provide the data underlying our publication that reviews what is currently known about plant invasion-fire cycles, including complete lists of all papers and the data we gathered from them.

opencc-by-4.0Dec 2022View details →

General-purpose GAP potential for platinum

Gaussian approximation potential (GAP) [1] for platinum. It has been fitted with QUIP/GAP [1,2] by generating a new database of atomic structures containing: <ol> <li>dimers;</li> <li>fcc, bcc, hcp and simple-cubic supercells, including strained, distorted and high-temperature configurations;</li> <li>surface slabs;</li> <li>clusters (nanoparticles).</li> </ol> Version 2 of this potential included more clusters in the training set than version 1. The calculations were carried out at the PBE level of theory [3] using the VASP code [4,5]. This potential uses 2-body (distance_2b) and SOAP-type descriptors (soap_turbo) [6,7]. The files can be used both with QUIP/GAP (compiled with the soap_turbo libraries) and TurboGAP [8]. This is the reference publication for this potential: <blockquote> J. Kloppenburg, L. B. Pártay, H. Jónsson, M. A. Caro. "A general-purpose machine learning Pt interatomic potential for an accurate description of bulk, surfaces and nanoparticles". <a href="https://doi.org/10.1063/5.0143891">J. Chem. Phys. 158, 134704 (2023)</a> </blockquote> References <ol> <li>A.P. Bartók, M.C. Payne, R. Kondor, and G. Csányi. Phys. Rev. Lett. 104, 136403 (2010).</li> <li>LibAtoms: <a href="https://libatoms.github.io/">https://libatoms.github.io</a></li> <li>J.P. Perdew, K. Burke and M. Ernzerhof. Phys. Rev. Lett. 77, 3865 (1996).</li> <li>VASP: <a href="http://vasp.at/">http://vasp.at</a></li> <li>G. Kresse and J. Furthmüller. Phys. Rev. B 54, 11169 (1996).</li> <li>A.P. Bartók, R. Kondor, and G. Csányi. Phys. Rev. B 87, 184115 (2013).</li> <li>M.A. Caro. Phys. Rev. B 100, 024112 (2019).</li> <li>TurboGAP: <a href="http://turbogap.fi/">http://turbogap.fi</a></li> </ol>

Tropical bat ectoparasitism in continuous versus fragmented forests: A gap analysis and preliminary meta-analysis

Tropical regions are experiencing rapid rates of forest fragmentation, which can have several effects on wildlife, including altered parasite dynamics. Bats are a useful host group to consider these effects of fragmentation because they are abundant in the tropics, serve important ecological roles, and harbour many parasites. Nevertheless, research on the effects of fragmentation on bat ectoparasites is still limited. To help guide ongoing and future research efforts, this study had two objectives: (1) conduct a gap analysis to characterize the state of currently available research on fragmentation effects on bat ectoparasites, and (2) conduct a preliminary meta-analysis to identify current trends. We systematically highlighted several research gaps: studies comparing the effects of fragmented versus continuous forests on ectoparasites are limited and have primarily been conducted in the Neotropics, with a focus on bats in the superfamily Noctilionidea (especially frugivorous phyllostomids). Our preliminary meta-analysis suggested that ectoparasite prevalence (but not the mean or variance in intensity) was higher in fragments than in continuous forests. Moreover, prevalence increased with increasing roost duration, and mean intensity was higher for bats with higher wing aspect ratios. Intensity variance was affected by an interaction between forest type and wing aspect ratio, such that variance increased for bats with high wing aspect ratios in continuous forests but decreased in fragments. These results suggest that fragmentation can shape aspects of bat ectoparasitism and could have implications for the ecology, health, and conservation of bats in fragmented landscapes. However, existing research gaps could bias our current understanding of habitat change and bat health, and future research should thus investigate these effects in the Paleotropics and with other bat families.

The effect of flight efficiency on gap‐crossing ability in Amazonian forest birds

We used this dataset to examine the role of flight efficiency on gap-crossing ability in Amazonian forest birds. We used data from the Biological Dynamics of Forest Fragments Projects on recaptures of banded birds in an Amazonian forest bisected by a road. For a total of 45 species, we estimated flight efficiency using the hand-wing index (a proxy for the wing's aspect ratio) and used it as a predictor of the probability of road crossing in phylogenetic binomial regression models. We found that flight efficiency was a strong predictor of road-crossing probability: species with high hand-wing indices crossed the road more frequently than those with low hand-wing indices. In contrast, other characteristics such as body mass, diet, flocking behavior, and foraging stratum did not show significant associations with road crossing probability. Our results suggest that proxies of flight efficiency such as the hand-wing index can be powerful tools for predicting the vulnerability of bird species to forest fragmentation.

opengpl-2.0Jan 2023View details →

Scaling Behavior for Electric Vehicle Chargers and Roadmap to Addressing the Infrastructure Gap

Source code and datasets for "Scaling Behavior for Electric Vehicle Chargers and Roadmap to Addressing the Infrastructure Gap"

Mapping the correlations and gaps in studies of complex life histories

For species with complex life histories, phenotypic correlations between life-history stages constrain both ecological and evolutionary trajectories. Studies that seek to understand correlations across life history differ greatly in their experimental approach: some follow individuals ("individual longitudinal"), while others follow cohorts ("cohort longitudinal"). Cohort longitudinal studies risk confounding results through Simpson's Paradox, where correlations observed at the cohort-level do not match that of the individual-level. Individual longitudinal studies are laborious in comparison, but provide a more reliable test of correlations across life-history stages. Our understanding of the prevalence, strength and direction of phenotypic correlations depends on the approaches that we use, but the relative representation of different approaches is unknown. Using marine invertebrates as a model group, we used a formal, systematic literature map to screen 17,000+ papers studying complex life histories, and characterized the study type (i.e. cohort longitudinal, individual longitudinal or single stage), as well as other factors. For 3,315 experiments from 1,716 articles, most (67.4%) focused on a single stage, and just 1.7% used an individual longitudinal approach. While life-history stages have been studied extensively, we suggest that the field prioritize individual longitudinal studies to understand the phenotypic correlations among stages.

Data for: Bridging the gap between microclimate and microrefugia: A bottom‐up approach reveals strong climatic and biological offsets

In the context of global warming, a clear understanding of microrefugia, microsites enabling the survival of species populations outside their main range limits, is crucial. Several studies have identified forcing factors that are thought to favor the existence of microrefugia. However, there is a lack of evidence to conclude whether, and to what extent, the climate encountered within existing microrefugia differs from the near surrounding climate. So, we adopt a "bottom-up" approach, linking marginal disconnected populations to microclimate. We used the southernmost disconnected and abyssal populations of the circumboreal herbaceous plant Oxalis acetosella in Southern France to study whether populations matching the definition of "microrefugia" occur in particularly favorable climatic conditions compared to neighboring control plots distant about 50 m to 100 m. Temperatures were recorded in putative microrefugia and in neighboring plots for approximately 2 years to quantify their thermal offsets. Vascular plant inventories were carried out to test whether plant communities also reflect microclimatic offsets. We found that current microclimatic dynamics are genuinely at stake in microrefugia. Microrefugia climates are systematically colder compared to those found within 50 m to 100 m distant. This pattern was more noticeable during the summer months. Abyssal populations showed stronger offsets compared to neighboring plots than the putative microrefugia occurring at higher altitudes. Plant communities demonstrate this strong spatial climatic variability, even at such a microscale approach, as species compositions systematically differed between the two plots, with species more adapted to colder and moister conditions in microrefugia compared to the surrounding area.

opencc-by-4.0Feb 2023View details →

SourceData for "Correlating the charge transfer gap to the maximum transition temperature in Bi2Sr2Can-1CunO2n+4+x"

SourceData for "Correlating the charge transfer gap to the maximum transition temperature in Bi2Sr2Can-1CunO2n+4+x"

opencc-zeroFeb 2023View details →

Bridging the gap: Optimising connectivity solutions for an arboreal gliding mammal

Connectivity modelling tools are important for developing mitigation strategies to alleviate negative impacts on animal movement caused by road networks. Arboreal gliding mammals are especially vulnerable to road widening as they are unable to cross gaps beyond their gliding capacity. However, there are limitations of conventional raster-based modelling techniques when applied on this group. We developed and applied a new model that quantifies the changes in connectivity for an arboreal gliding species, the Sunda colugo, in Singapore using information on species-specific glide performance through a vector-based GIS approach. We also incorporated a genetic algorithm to determine optimal locations for sets of glide poles that could be installed to improve connectivity. Expectedly, connectivity was heavily impacted by the road widening works, with a 93.3% decrease in the total number of feasible glide paths connecting roadside trees. Nine glide poles installed during the construction phase of the project were initially uninformed by the connectivity model and they provided 26 additional connections only. Comparatively, the top nine pole locations identified through the genetic algorithm provided 247 additional connections, almost 10 times more than the amount supplied by the initial nine glide pole locations determined through qualitative methods. The multi-objective capacity of the genetic algorithm also reduced large connectivity gaps post-development, with simulated glide poles increasing the percentage of pixels covered with connectivity from 16.1% to 27.7%. Synthesis and applications: Our model fills a knowledge gap in connectivity modelling for arboreal gliding mammals whose movements are affected by varying habitat alterations. We demonstrated that locations of mitigation structures greatly influence the success of mitigation efforts and the locations can be optimized by incorporating the glide performance of the species into the genetic algorithm. Given limited conservation resources, this approach would benefit managers in formulating cost-effective efforts for arboreal gliding mammals.

opencc-by-4.0Mar 2023View details →

Poor attention: The wealth and regional gaps in event attention and coverage on Wikipedia

Repository for "Poor attention: The wealth and regional gaps in event attention and coverage on Wikipedia" (currently under review). This repository contains the preprocessed data files as well as code for the main experiments conducted during the creation of the paper. See the GitHub repository for more information: https://github.com/ruptho/wiki-event-bias

opencc-by-4.0Mar 2023View details →

Expert-annotated dataset for band gap prediction

Here we present the dataset for "Toward Accurate Interpretable Predictions of Materials Properties within Transformer Language Models" (<a href="https://doi.org/10.48550/arXiv.2303.12188">arXiv:2303.12188</a>). The dataset_annotated.json file is organized as follows: <pre><code class="language-python">{ "JARVIS-DFT id": { "text": "text description of material generated within the Robocrystallographer library", "tokens": "sequence of tokens generated by the MatBERT tokenizer", "rationales": "rationales proposed by a domain expert", "label": "label predicted by the MatBERT model", }, ...: ..., }</code></pre>

opencc-by-4.0Apr 2023View details →

ANION GAP OR SERUM LACTATE-IN SEARCH OF A BETTER PROGNOSTIC MARKER IN SEPSIS A CROSS-SECTIONAL STUDY IN A RURAL TERTIARY CARE HOSPITAL

master data sheet

opencc-zeroApr 2023View details →

Data from: Feral pigeon roosting and nesting occurrences in MRT viaduct expansion gaps and measured variables in Singapore

The feral pigeon (Columba livia) is a globally commensal bird that can cause dis-amenities such as soiling and is a potential vector of various diseases. Aside to limiting food as a management strategy, reducing the availability of roosting and nesting sites can help regulate feral pigeon populations. Despite their prevalence, current knowledge of their roosting and nesting preferences is lacking. Feral pigeons commonly use railway viaduct expansion gaps in Singapore for roosting and nesting. These gaps provided an ideal experimental platform to examine feral pigeon roost and nest site selection while controlling for differing cavity sizes which can significantly affect their reproductive success and site selection decisions. We also conducted an in-situ experiment to test the efficacy of nest removal as a management option. Our nationwide surveys of 80.3km of railway viaducts and 6,048 gaps revealed that feral pigeon day roosting and nesting preferences are influenced by structural height and more importantly, their proximity to human food sources. There was a significantly higher probability of feral pigeon roosting in a gap if it had more pigeon feeding incidences in its vicinity and was higher. The probability of feral pigeon nesting in gap was higher if it was closer to a railway station, lower and further from water bodies. In our field experiment, we did not find any significant differences in the proportions of the abundances of feral pigeon to other urban commensal bird species at the gaps before and after nests were removed. Overall, our results suggest that a concerted effort to reduce anthropogenic food availability to feral pigeons is central in limiting their reproductive success and controlling their population.

opencc-by-4.0Nov 2019View details →

Figure 3 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia

Figure 3. Periophthalmus variabilis, Sugihan estuary, southern Sumatra (© M. Iqbal).

opencc-zeroJul 2023View details →

Data from: A wide megafauna gap undermines China's expanding coastal ecosystem conservation

To fulfill sustainable development goals, many countries are expanding efforts to conserve ecologically and societally critical coastal ecosystems. Although megafauna profoundly impact the functioning of ecosystems, they are neglected as a key component in the conservation scheme for coastal ecosystems in many geographic contexts. Here, we reveal a rich diversity of extant megafauna associated with all major types of coastal ecosystems in China, including 218 species of mammals, birds, reptiles, cephalopods and fishes across terrestrial and marine environments. However, 44% of these species are globally threatened and 78% have not yet been assessed in China for extinction risk. More worrisome, 73% of these megafauna have not been designated as nationally protected species, and <10% of their most important habitats are protected. Filling this wide "megafauna gap" in China, and globally, would be a leading step as humanity strives to thrive with coastal ecosystems.

opencc-by-4.0Jul 2023View details →

Investigating the Lower Mass Gap with Low Mass X-ray Binary Population Synthesis

Title: Investigating the Lower Mass Gap with Low Mass X-ray Binary Population Synthesis  Authors: Jared C. Siegel, Ilia Kiato, Vicky Kalogera, Christopher P. L. Berry,          Thomas J. Maccarone, Katelyn Breivik, Jeff J. Andrews, Simone S. Bavera,          Aaron Dotter, Tassos Fragos, Konstantinos Kovlakas, Devina Misra,          Kyle A. Rocha, Philipp M. Srivastava, Meng Sun, Zepei Xing,          and Emmanouil Zapartas           Table: Summary of Population Synthesis Models Columns:     Population parameters:         CE: efficiency of common envelope unbinding, either:             * 1 or 5         CE merge: stars without a distinct core-envelope boundary that instigate a CE                    event are either assumed to survive the CE (Optimistic) or are                    assumed to merge (Pessimistic).         QMIN: minimum ZAMS ratio, either:             * 0.01             * Lifetime limited (pre-main-sequence lifetime of the secondary is shorter               than the main-sequence lifetime of the primary)         BRK: prescription for magnetic braking of a tidally coupled magnetic wind, either:             * H02: Hurley et al. 2002             * IT03: Ivanova & Taam 2003         ACC: amount of mass accreted during Roche-lobe overflow, either:             * 50% efficiency             * State dependent: (i) limited to ten-times the thermal rate if the accretor is a main-sequence,                Hertzsprung gap or core helium burning star, or (ii) unlimited if the accretor is a giant branch,                early asymptotic giant branch or asymptotic giant branch star.                Compact objects also experience conservative mass transfer, provided the                mass-transfer rate is sub-Eddington.              Selection effect parameters:         weighting: logs what selection effects were considered for the detection weighted results, either:             *prob_occ: the probability that an outburst occurs and turns off during the survey             *prob_see: the probability that the outburst is bright enough to be detected             *prob: the product of prob_occ and prob_see                             RIA_nu: determines when the transition to radiatively inefficient accretion occurs, either:             *0 (no transition) or 0.05                  Results:         f_gap_N: fraction of LMXB systems with a mass gap BH (M<4.5Msol)         f_AIC_N: fraction of LMXB systems where the BH formed through accretion induced collapse of a NS         f_AIC_gap_N: fraction of LMXB systems where the BH formed through accretion induced collapse of a NS and                      the BH is in the mass gap         fw_X_N: detection weighted fraction of X (e.g., gap, AIC, AIC_gap)          Notes:      Each quantity is calculated for 5000 snapshots of the evolution tracks.       Here we report the Nth percentiles (e.g., 16, 50, 84) of each quantity.