Find research datasets worth reusing

Fig. 2. T-S in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 2. T-S diagram for the Mamanguá Inlet based on (a) surface and (b) bottom data of temperature and salinity from March 1990 to March 1992. Lines represent the values of the South Atlantic Central Waters, calculated from coefficients of the mean T-S expressions based in Miranda (1985).

Fig. 3 in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 3. Spatial variation of the average length of Citharichthys spilopterus in the Mamanguá Inlet. Bars= standard deviation.

Fig. 9 in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 9. Rates of follicular atresia in the ovaries of C. spilopterus captured at Mamanguá Inlet: a) percentage of females presenting á or older atresia; b) maximum rates of atresia by females in each oceanographic station on March and May 1990.

Fig. 6 in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 6. Proportion of males (a) and females (b) of the Bay whiff in each macroscopic maturity stage considered in this study. Stars means significantly different - tested by Chisquare (χ2).

Fig. 1 in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 1. Sampled area for Citharichthys spilopterus in the Mamanguá Inlet, Rio de Janeiro, Brazil. Modified from Bernardes (1995). Five oceanographic stations and four satations in the margins of the beaches are indicated with numbers.

Data from: Opposing effects of competition and selection on macroevolutionary dynamics

The diversity of species and traits is the outcome of multiple evolutionary processes operating over millions of years. These processes affect rates of trait evolution, speciation, and extinction. A key problem is identifying the relative importance of distinct processes in driving observed patterns in species traits and phylogenetic trees. Here, we show how two processes, competition and stabilising selection, can act opposingly but still leave identifiable traces in macroevolutionary data. Building on previous simulation studies, we model the joint influence of competition and stabilising selection on rates of trait evolution, speciation completion, and extinction. We find that opposing effects result in nuanced patterns of trait evolution and diversification dynamics that, when considered in isolation, could easily lead to misinterpretation. In particular, while the best fitting likelihood model of trait evolution is typically Brownian motion when competition and stabilising selection act simultaneously, we find stronger phylogenetic signal than expected under BM and trait distributions that are distinctly platykurtic. Taken together, we suggest that by considering multiple simple metrics measuring trait evolution and diversification dynamics it may be possible, though challenging, to identify the relative contribution of these two processes operating together in macroevolutionary data.

Cognitive and neural state dynamics of narrative comprehension

Functional MRI data during temporally scrambled movie watching

Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record

Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in the late Selandian-Ypresian in Dataset I indicate the onset of an ascophoran-grade radiation. Lineage-through-time plots confirm the macroevolutionary lag preceding the radiation of cheilostomes in the mid-Cretaceous, and their renewed diversification in the late Paleocene and Eocene. A multivariate birth-death model indicates that origination rates are shaped by diversity-dependent dynamics coupled with a positive correlation with sea surface temperature, while extinction rates negatively correlate with sea level. Text-mined data provide broadly similar rate dynamics as manually curated data, although discrepancies could be attributed to the omission of key literature in Dataset II, and the inclusion of new published and unpublished data, and revised ranges in Dataset I. Revision and augmentation of PBDB occurrences were necessary to generate rate profiles akin to those of Datasets I and II and highlight the risks of using unedited occurrence data. Our results support the widely held assumption that diversification dynamics are controlled by both biotic and abiotic factors and pave the way for integrating fossils with molecular phylogenies to study these processes in more detail.

Drosophila suzukii population dynamics and control efficiency of mineral dusts with a focus on grape protection

The invasive pest Drosophila suzukii is threatening berry production. It is mainly managed via chemical control, which is associated with consumer and environmental concerns. Here, we tested the efficiency of mineral dusts under field and laboratory conditions. Furthermore, population dynamics were studied in a vineyard and its surroundings. The kaolin products Cutisan and Surround®, as well as the CaCO3 product Carboliq had neither insecticidal nor repellent effects on Drosophila suzukii adults in laboratory choice tests with grapes at concentrations of up to 2% (w/v). Cutisan and Surround® significantly reduced the number of deposited eggs (-41.9% and -49.3%, respectively) while Carboliq had no effect on the oviposition under laboratory conditions. The Surround® treatment significantly reduced the number of flies trapped on 09/09/2020 at a test vineyard. Depending on the assessment date and treatment, between 59 and 84% of the flies in the bait traps were females. The number of eggs found in fruit treated with Carboliq in the field was higher at each assessment date than in the control but this difference was not statistically significant. Cutisan and Surround® applications in the field showed an equivalent or lower average number of eggs compared to the control but this difference was only significant on 24/09/2020. The highest number of D. suzukii adults was observed around September in the field and a decline of the population occurred in the winter months until July. In epidemic years, temperature - humidity - combinations prior to population peaks were quite stable with low humidity being associated with a high temperature and vice-versa. In non-epidemic years, humidity fluctuated more than in epidemic years and temperatures were lower before population peaks. The effect of global radiation on population maxima seemed to be minor.

Data from: Mass extinctions alter extinction and origination dynamics with respect to body size

Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. Previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa, and scales with organismal traits. Here, we test for shifts in selectivity between background intervals and the "Big Five" mass extinction events using capture-mark-recapture models. Our body-size data cover 10,203 fossil marine animal genera spanning 10 Linnaean classes with occurrences ranging from Early Ordovician to Late Pleistocene (485–1 Mya). Most classes exhibit differences in both origination and extinction selectivity between background intervals and mass extinctions, with the direction of selectivity varying among classes and overall exhibiting stronger selectivity during origination after mass extinction than extinction during mass extinction. Thus, not only do mass extinction events shift the marine biosphere into a new macroevolutionary regime, the dynamics of recovery from mass extinction also appear to play an underappreciated role in shaping the biosphere in their aftermath.

NGS Data Accompanying "Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome Dynamics"

NGS Data Accompanying "Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome Dynamics", currently in review.

COVID-19++: A Citation-Aware Covid-19 Dataset for the Analysis of Research Dynamics

COVID-19++ is a citation-aware COVID-19 dataset for the analysis of research dynamics. In addition to primary COVID-19 related articles and preprints from 2020, it includes citations and the metadata of first-order cited work. All publications are annotated with MeSH terms, either from the ground truth, or via ConceptMapper, if no ground truth was available.  The data is organized in CSV files - Paper metadata (paper_id, publdate, title, data_source): paper.csv - Annotation data, mapping paper_id to MeSH terms: annotation.csv  - Authorship data, mapping paper_id to author, optionally with ORCID: authorship.csv - Paired DOIs of citing and cited papers: references.csv The column data source within the paper metadata has the value KE (for metadata from ZB MED KE), PP (for preprints) or CR (for cited resources from CrossRef)   This work was supported by BMBF within the programme ``Quantitative Wissenschaftsforschung'' under grant numbers 01PU17013A, 01PU17013B, 01PU17013C.

Data for: Tracking the temporal dynamics of insect defoliation by high-resolution radar satellite data

1. Quantifying tree defoliation by insects over large areas is a major challenge in forest management, but it is essential in ecosystem assessments of disturbance and resistance against herbivory. However, the trajectory from leaf-flush to insect defoliation to refoliation in broadleaf trees is highly variable. Its tracking requires high temporal- and spatial-resolution data, particularly in fragmented forests. 2. In a unique replicated field experiment manipulating gypsy moth Lymantria dispar densities in mixed-oak forests, we examined the utility of publicly accessible satellite-borne radar (Sentinel-1) to track the fine-scale temporal trajectory of defoliation. The ratio of backscatter intensity between two polarizations from radar data of the growing season constituted a canopy development index (CDI) and a normalized CDI (NCDI), which were validated by optical (Sentinel-2) and terrestrial laser scanning (TLS) data as well by intensive caterpillar sampling from canopy fogging. 3. The CDI and NCDI strongly correlated with optical and TLS data (Spearman's ρ=0.79 and 0.84, respectively). The ∆NCDIDefoliation (A-C) significantly explained caterpillar abundance (R2=0.52). The NCDI at critical time-steps and ΔNCDI related to defoliation and refoliation well discriminated between heavily and lightly defoliated forests. 4. We demonstrate that the high spatial and temporal resolution and the cloud independence of Sentinel-1 radar potentially enable spatially unrestricted measurements of the highly dynamic canopy herbivory. This can help monitor insect pests, improve the prediction of outbreaks, and facilitate the monitoring of forest disturbance, one of the high priority Essential Biodiversity Variables, in the near future.

Dataset for Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods

This dataset contains the Matlab codes used in "Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods". The zip file contains Matlab codes used in simulation and numerical solutions of the replicator dynamics. The zip file "Figures" contains the Matlab code and data used to produce figures in this study.

opencc-by-4.0Aug 2020View details →

Development of a global dataset of Wetland Area and Dynamics for Methane Modeling (WAD2M)

Seasonal and interannual variations in global wetland area is a strong driver of fluctuations in global methane (CH4) emissions. Current maps of global wetland extent vary with wetland definition, causing substantial disagreement and large uncertainty in estimates of wetland methane emissions. To reconcile these differences for large-scale wetland CH4 modeling, we developed a global Wetland Area and Dynamics for Methane Modeling (WAD2M) dataset at ~25 km resolution at equator (0.25 arc-degree) at monthly time-step for 2000-2018. WAD2M combines a time series of surface inundation based on active and passive microwave remote sensing at coarse resolution (~25 km) with six static datasets that discriminate inland waters, agriculture, shoreline, and non-inundated wetlands. We exclude all permanent water bodies (e.g. lakes, ponds, rivers, and reservoirs), coastal wetlands (e.g., mangroves and seagrasses), and rice paddies to only represent spatiotemporal patterns of inundated and non-inundated vegetated wetlands. Globally, WAD2M estimates the long-term maximum wetland area at 13.0 million km2 (Mkm2), which can be separated into three categories: mean annual minimum of inundated and non-inundated wetlands at 3.5 Mkm2, seasonally inundated wetlands at 4.0 Mkm2 (mean annual maximum minus mean annual minimum), and intermittently inundated wetlands at 5.5 Mkm2 (long-term maximum minus mean annual maximum). WAD2M has good spatial agreements with independent wetland inventories for major wetland complexes, i.e., the Amazon Lowland Basin and West Siberian Lowlands, with high Cohen’s kappa coefficient of 0.54 and 0.70 respectively among multiple wetlands products. By evaluating the temporal variation of WAD2M against modeled prognostic inundation (i.e., TOPMODEL) and satellite observations of inundation and soil moisture, we show that it adequately represents interannual variation as well as the effect of El Niño-Southern Oscillation on global wetland extent. This wetland extent dataset will improve estimates of wetland CH4 fluxes for global-scale land surface modeling.    Update: Oct.08.2021 Documentation for WAD2M Version 2.0 can be found at <a href="https://drive.google.com/file/d/1adoAnuqu6uBWnTYKI8u_S4OAQSdgOtd6/view?usp=sharing">WAD2M_V2_update</a>

Engineering the Radiative Dynamics of Thermalized Excitons with Metal Interfaces

Here we analyze the emission properties of excitons in two metal structures: placed near a single metal (silver) interface and placed symmetrically at the center of a Fabry-Perot microcavity. The exciton is modeled as a point dipole and as an extended 2D dipole. With the momentum dependent emission rates for the extended exciton, we can also examine its temperature dependent behavior by applying a momentum distribution. We investigate the cases of a Maxwell-Boltzmann statistical distribution and a Bose-Einstein statistical distribution (since excitons form composite bosons).  The dataset provided are the Mathematica codes used to generate the plots in our paper. The point dipole results are contained in the notebook files: Emission Rate 2, Multiple Interfaces, Multiple Interfaces_Par (1), and Multiple Interfaces_Perp. The extended exciton results are contained in the notebook files: Extended Exciton 2-3 and BE stats.

Multi-scale Fractures and Water Invasion Dynamics in Buried-Hill Bedrock Gas Reservoirs of the Jianbei Slope, Qaidam Basin, China

In this study, efforts are made to comprehensively analyze the multi-scale fracture development, the dynamic water intrusion, and the favorable remaining gas areas in the ancient buried-hill bedrock gas reservoir in the Jianbei slope of the Qaidam Basin, based on integrated analyses of thin sections, FMI imaging logging, three-dimensional seismic data, and dynamic production data. Fractures in the bedrock are demonstrated to be controlled by tectonic stress, magma intrusion, hydrothermal activity, and weathering and leaching. The complex fracture genesis leads to differences in the scale and type of bedrock fractures with multiple scales and high angles. The dip angle of the fracture gradually increases from the unconformity on the top of the bedrock downward inside the bedrock. Meanwhile, the dip angle may decrease from the center to both sides due to the difference in the fracture strength of the fault zone. Fractures are mostly near-east-west oriented and they normally intersect with the ground stress at an acute angle. Effective fractures can provide advantageous seepage channels for fluids. Formation water is demonstrated to rapidly channel through large-scale fractures while laterally invading through small-scale fractures in the gas reservoir. The western area of the reservoir is featured by intensive water invasion, rapid pressure drop, and fast production decline, while the eastern area is characterized by weak water invasion as well as relatively stable pressure and productivity. Three relatively independent water-seal gas systems with JB1-3, JBH1-3 and J3 Wells as the center are formed, and the remaining gas is enriched.

Exploring the interaction of a curcumin azobioisostere with Abeta42 dimers using replica exchange molecular dynamics simulations

Structural data and parameters relative to the evaluation of the interaction of an anti aggregating azobioisostere compound with the full-length Aβ42 peptide by replica-exchange molecular dynamics (REMD) simulations. Two different force fields (Amber and CHARMM) were used to simulate the azobioisostere-Abeta42 (AZ-Ab42) complex in a monomeric and dimeric assembly. A brief description of the shared output data is reported below: 1. Amber and CHARMM-adapted parameters for the simulated azobioisostere (AZ) compound. 2. Modified version of the CHARMM36m FF - (CHARMM36mW) 3. Starting (equilibrated) structures (first 5 T-replicas) for REMD on each of the following three systems (PDB):  <ul> <li>Amber: AZ-Ab42 (monomeric ensemble): Repl.0 (315.0 K), Repl.1 (316.7 K), Repl.2 (318.4 K), Repl.3 (320.1 K), Repl.4 (321.8 K) </li> <li>Amber: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K) </li> <li>CHARMM: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K)</li> </ul> 4. Most populated clusters for the three simulated systems (PDB): <ul> <li>Amber AZ-Ab42 (monomeric ensemble): 7 clusters (Cl.0: 12.4%, Cl.1: 10.1%, Cl.2: 9.8%, Cl.3: 5.4%, Cl.4: 3.7%, Cl.5: 3.6%, Cl.6: 2.0%) </li> <li>Amber AZ-Ab42 (dimeric ensemble): 5 clusters (Cl.0: 7.1%, Cl.1: 4.3%, Cl.2: 3.5%, Cl.3: 3.2%, Cl.4: 2.4%) </li> <li>CHARMM: AZ-Ab42 (dimeric ensemble): 3 clusters (Cl.0: 4.7%, Cl.1: 4.6%, Cl.2: 2.5%) </li> </ul>

Molecular dynamics simulation of chitin nanocrystal-water interfaces

This is the data repository for the paper "Probing the structural details of chitin nanocrystal-water interfaces by three-dimensional atomic force microscopy" by Ayhan Yurtsever, Pei-Xi Wang, Fabio Priante, Ygor Morais Jaques, Kazuki Miyata, Mark J. MacLachlan, Adam S. Foster, and Takeshi Fukuma. It contains: - The system's starting geometry (water-chitin.pdb) - The production trajectory, in .dcd format (nvt_prod_chitin.tar.xz, uncompressed size 1.9 GB) - The resulting water density, in .cube format, computed on each of the chitin surfaces (chitin_cube_densities_vmd.tar.xz, uncompressed size 3.1 GB)