Find research datasets worth reusing

opennotspecifiedFeb 2023View details →

FIGURE 4 in Mangrovomyia, a new genus of long-legged flies from Iranian mangroves (Diptera: Dolichopodidae: Hydrophorinae)

FIGURE 4. Mangrovomyia mofidii sp. nov., female. A. Habitus. B. Head, anterior view. С. Antenna, lateral outer view. D. Fore leg, posterior view. E. Mid tibia and tarsus, anterior view. F. Mesonotum, dorsal view. G. Wing. H. Oviscapt, posterior view.

opencc-zeroFeb 2023View details →

Data from: Evidence of low within-pair genetic relatedness in a relict population of Thorn-tailed Rayadito despite long-term isolation

Investigating whether mating patterns are biased in relation to kinship in isolated populations can provide a better understanding of the occurrence of inbreeding avoidance mechanisms in wild populations. Here we report on the genetic relatedness (r) among breeding pairs in a relict population of Thorn-tailed Rayadito (Aphrastura spinicauda) in north-central Chile that has experienced a long-term history of isolation. We used simulations based on eight years of data to assess whether mating is random with respect to relatedness. We found that mean and median population values of pair relatedness tended to be lower than randomly generated values, suggesting that mating is not random with respect to kinship. We hypothesize that female-biased dispersal is the main mechanism reducing the likelihood of mating among kin, and that the proportion of related pairs (i.e., r > 0.125) in the study population (25%) would presumably be higher in the absence of sex-biased dispersal. The occurrence of other mechanisms such as extra-pair copulations, delayed breeding and active inbreeding avoidance through kin discrimination cannot be dismissed and require further study.

opencc-by-4.0Dec 2022View details →

Synergistic effects of warming and internal nutrient loading interfere with the long-term stability of lake restoration and induce sudden re-eutrophication

This repository contains the dataset linked to the following publication: Article title: Synergistic effects of warming and internal nutrient loading interfere with the long-term stability of lake restoration and induce sudden re-eutrophication Journal: Environmental Science & Technology DOI: 10.1021/acs.est.2c07181 Abstract: Phosphorus (P) precipitation is among the most effective treatments to mitigate lake eutrophication. However, after a period of high effectiveness, studies have shown possible re-eutrophication and the return of harmful algal blooms. While such abrupt ecological changes were attributed to the internal P loading, the role of lake warming and its potential synergistic effects with internal loading, thus far, has been understudied. Here, in a eutrophic lake in central Germany, we quantified the driving mechanisms of the abrupt re-eutrophication and cyanobacterial blooms in 2016 (30 years after the first P precipitation). A process-based lake ecosystem model (GOTM-WET) was established using a high-frequency monitoring dataset covering contrasting trophic states. Model analyses suggested that the internal P release accounted for 68% of the cyanobacterial biomass proliferation, while lake warming contributed to 32%, including direct effects via promoting growth (18%) and synergistic effects via intensifying internal P loading (14%). The model further showed that the synergy was attributed to prolonged lake hypolimnion warming and oxygen depletion. Our study unravels the substantial role of lake warming in promoting cyanobacterial blooms in re-eutrophicated lakes. The warming effects on cyanobacteria via promoting internal loading need more attention in lake management, particularly for urban lakes. SYNOPSIS: Warming synergistically promotes re-eutrophication with internal nutrient loading and exacerbates cyanobacterial blooms in urban lakes 30 years after phosphorus mitigation.   Data description by Xiangzhen Kong (<a href="mailto:xzkong@niglas.ac.cn">xzkong@niglas.ac.cn</a>), 2023-02-20 ---Wet chemical analysis on water samples taken at five depths (0.5, 2.5, 5.0, 7.0 and 9.0 m) from the deepest point in the lake (BA1) at biweekly intervals from 2018.5-2021.8.         File name: <ul> <li>BAB_BA1_TN_mgL.obs (total nitrogen concentration)</li> <li>BAB_BA1_NH4_mgL.obs (ammonium nitrogen concentration)</li> <li>BAB_BA1_NO3_mgL.obs (nitrate nitrogen concentration)</li> <li>BAB_BA1_TP_mgL.obs (total phosphorus concentration)</li> <li>BAB_BA1_SRP_mgL.obs (Soluble reactive phosphorus concentration)</li> <li>BAB_BA1_DP_mgL.obs (dissolved P concentration)</li> <li>BAB_BA1_DOC_mgL.obs (Dissolved organic carbon concentration)</li> <li>BAB_BA1_Si_mgL.obs (dissolved silicon concentration)</li> <li>BAB_BA1_Chla_HPLC_DIN_mgL.obs (Chl-a concentration)</li> </ul>   ---CTD probe profile data from the deepest point in the lake (BA1) from 2017.8 to 2021.8 at biweekly basis with approximately 0.1 m vertical resolution        File name: <ul> <li>t_prof_file_barleber_ctm644.obs (water temperature)</li> <li>oxy_prof_file_barleber_ctm644 (Dissolved oxygen)</li> <li>turb_prof_file_barleber_ctm644.obs (Turbidity)</li> <li>chla_prof_file_barleber_ctm644.obs (Chl-a concentration)</li> </ul>   ---BBE probe profile data from the deepest point in the lake (BA1) from 2017.8 to 2021.8 at biweekly basis with approximately 0.1 m vertical resolution        File name: <ul> <li>totalChla_prof_file_barleber_FP2101.obs (Chl-a concentration)</li> <li>bluegreen_prof_file_barleber_FP2101.obs (Blue-green algae Chl-a concentration)</li> <li>green_prof_file_barleber_FP2101.obs (Green algae Chl-a concentration)</li> <li>diatom_prof_file_barleber_FP2101.obs (Diatom Chl-a concentration)</li> </ul>

opencc-zeroMar 2023View details →

Modelling long-distance seed dispersal of Spathodea campanulata in the Society Islands

These datasets are related to the paper "Modelling long-distance seed dispersal of the invasive tree Spathodea campanulata in the Society Islands" published in Ecological Applications. We used a 3-D kinematic trajectory model (Computing Atmospheric Trajectory tool (CAT)) initiated from regional wind field data to assess the potential for long-distance seed dispersal (LDD) of a wind-dispersed invasive tree, Spathodea campanulata (African tulip tree) across the Society Islands (French Polynesia, South Pacific Ocean) following its initial planting and spread on the island of Tahiti. The main objective of our study was to determine whether S. campanulata can be expected to spread naturally among islands. Atmospheric dynamics, seed terminal velocity, precipitation, and temperature of air masses were considered to assess the potential for LDD between oceanic islands, with the island of Tahiti serving as the island source for multiple, geographically distant invasions. These datasets contain the number of simulated seed trajectories with Computing Atmospheric Trajectory tool (CAT) in the study area as well as all data corresponding to each figure found in the paper.

opennotspecifiedMay 2018View details →

FIG. 3 in A Long-term Demographic Study of a Spotted Salamander (Ambŋstoma maculatum) Population in Central Ohio

FIG. 3.—Relationships between percent mass loss and number of days spent in Taylor–Ochs Pond, Ohio, for individually marked female (R2 ¼ 0.57, P ¼ 0.001; y ¼ 1.25x þ 6.76) and male (R2 ¼ 0.18, P ¼ 0.001, y ¼ 0.29x þ 3.39) Ambŋstoma maculatum sampled from 2005 to 2014.

opennotspecifiedMay 2018View details →

F. 1 in A Long-term Demographic Study of a Spotted Salamander (Ambŋstoma maculatum) Population in Central Ohio

F. 1.—Numbers of (a) breeding Ambŋstoma maculatum adults (R2 ¼ IG 0.46, P ¼ 0.03), (b) split by sex (females, R2 ¼ 0.02, P ¼ 0.67; males, R2 ¼ 0.68, P ¼ 0.003), and (c) counts of breeding females plotted alongside egg mass counts and numbers of emerging juveniles from 2005 to 2014 in Taylor–Ochs Pond, Ohio. Numbers near the bottom of (b) reflect sex ratios (male:female), and numbers near the bottom of (c) reflect recruitment rates (emerging juveniles per breeding female) for each year. Significant negative linear relationships of overall breeding adults (a) and breeding males (b) over time are represented by the equations y ¼ 46.1x þ 93246.0 and y ¼ 41.6x þ 84148.9, respectively.

opennotspecifiedMay 2018View details →

FIG. 2 in A Long-term Demographic Study of a Spotted Salamander (Ambŋstoma maculatum) Population in Central Ohio

FIG. 2.—Mean values (±1 SE) for mass (a) and snout–vent length (SVL, b) of inbound female and male Ambŋstoma maculatum sampled from 2005 to 2014 in Taylor–Ochs Pond, Ohio. See Table 3 for the sample size contributing to each depicted value. In all years, for both body-size indicators, females were larger than males (P <0.05). For simplicity, only differences among years (sexes combined) are reflected by different letter(s) above each pair of bars.

opencc-by-4.0Feb 2023View details →

Social structure and individuals' behavior shaped by group composition in long-term tracking of rats

Trajectory data and behavioral metrics from long-term tracking of groups of rats.  Experiments performed in 2012 at Eötvös Loránd University, Budapest, Hungary. The data here is used in the following publication. See the publication for information on experimental structure and notation. Nagy, Máté, Jacob Davidson, Gábor Vásárhelyi, Dániel Ábel, Enikő Kubinyi, Ahmed El Hady, and Tamás Vicsek. 2023. “Social Structure and Individuals’ Behavior Shaped by Group Composition in Long-Term Tracking of Rats.” bioRxiv. <a href="https://doi.org/10.1101/2023.03.18.533183">https://doi.org/10.1101/2023.03.18.533183</a>. Github repository to reproduce results in the paper: <a href="https://github.com/jacobdavidson/ratsocialgroups">github.com/jacobdavidson/ratsocialgroups</a> Github repositories used for tracking and computation of behavioral metrics: <a href="https://github.com/vasarhelyi">github.com/vasarhelyi</a> The behavioral metrics, approach-avoidance networks, individual labels and group membership information, and behavioral assay data needed to reproduce the results in the publication are included in the zip  file <a href="https://zenodo.org/api/files/969c78d4-1d30-4926-ac6e-141136cd3564/metrics-networks-labels.zip">metrics-networks-labels.zip</a>.  This includes the following files in .csv format: Naming/labels: <ul> <li>uidlabels.csv: References the ranked-mass labels used in the paper to the 3-color-code labels that identify each rat from the tracking.  "Group" is the membership during the original groups (Period 1), and "GroupG" is membership during the remixed groups (Period 3). <table> <tbody> <tr> <td> </td> <td> masslabel </td> <td> GroupMassRank-Exp7 </td> <td> Group </td> <td> GroupG </td> </tr> <tr> <td> GOB </td> <td> a5 </td> <td> 5.0 </td> <td> A1 </td> <td> G3 </td> </tr> <tr> <td>...</td> <td>...</td> <td>...</td> <td>...</td> <td>...</td> </tr> </tbody> </table> </li> <li>groupnames.csv:  Group membership information for each rat, during each experimental period <table> <tbody> <tr> <td> Experiments </td> <td> GOB </td> <td> OBG </td> <td> ... </td> </tr> <tr> <td> 1-7 </td> <td> A1 </td> <td> A1 </td> <td> ... </td> </tr> <tr> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> </tr> </tbody> </table> </li> </ul> Behavioral metrics and approach-avoidance networks: <ul> <li>metrics.csv: Behavioral metrics for each rat, calculated for each experiment. <table> <tbody> <tr> <td> Experiment </td> <td> metric </td> <td> GOB </td> <td> OBG </td> <td> ... </td> </tr> <tr> <td> 1 </td> <td> AA </td> <td> 0 </td> <td> 0.690964 </td> <td> ... </td> </tr> <tr> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> </tr> </tbody> </table> </li> <li>Networks-Period1+Period3.csv: Approach-avoidance interaction networks for the groups of 7 rats in Period 1 and Period 3.   <table> <tbody> <tr> <td> Experiment </td> <td> DayNight </td> <td> Group </td> <td> index </td> <td> winner </td> <td> loser0 </td> <td> loser1 </td> <td> loser2 </td> <td> loser3 </td> <td> loser4 </td> <td> loser5 </td> <td> loser6 </td> </tr> <tr> <td> 1 </td> <td> Day </td> <td> A1 </td> <td> 0 </td> <td> GOB </td> <td> 0 </td> <td> 0 </td> <td> 0 </td> <td> 0 </td> <td> 0 </td> <td> 0 </td> <td> 0 </td> </tr> <tr> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> </tr> </tbody> </table> </li> <li>Networks-Experiment8.csv and Networks-Experiment9.csv: Approach-avoidance interaction networks for the larger combined groups in the experiments during Period 2. </li> </ul>   Behavioral assays results: <ul> <li>IndividualTests.csv:  Individual behavioral assay test results for the black and white box, elevated plus-maze, and canopy tests. <table> <tbody> <tr> <td> ID </td> <td> BWB-All Frames </td> <td> BWB-Black </td> <td> ... </td> </tr> <tr> <td> BGP </td> <td> 7500 </td> <td> 6860 </td> <td> ... </td> </tr> <tr> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> </tr> </tbody> </table> </li> <li>PairedTests.csv:  Pairwise social interaction behavioral assay test results for tests with unfamiliar and familiar rats <table> <tbody> <tr> <td> rat_ID </td> <td> rat_group_N </td> <td> freq_standup_unfam1 </td> <td> ... </td> </tr> <tr> <td> BGP </td> <td> 2 </td> <td> 28 </td> <td> ... </td> </tr> <tr> <td> ... </td> <td> ... </td> <td> ... </td> <td> ... </td> </tr> </tbody> </table> </li> </ul>   Trajectory data is included as multiple text files for each experiment in TSV format.  #t is frame number, Color_code_name identifies each rat, Real_recognition(1)_or_virtual(0) = 1 is a detection of the rat's color codes while 0 is an interpolated value, x,y, and Orientation are the position and orientation of the rat. <table> <tbody> <tr> <td>#t</td> <td>Color_code_name</td> <td>Real_recognition(1)_or_virtual(0) </td> <td>x</td> <td>y</td> <td>Orientation</td> </tr> <tr> <td>0</td> <td>ORG</td> <td>0</td> <td>872.4000</td> <td>778.7000</td> <td>-79.5000</td> </tr> <tr> <td>...</td> <td>...</td> <td>...</td> <td>...</td> <td>...</td> <td>...</td> </tr> </tbody> </table>   Time-lapse video of the entire experiment:  <a href="https://zenodo.org/api/files/969c78d4-1d30-4926-ac6e-141136cd3564/ratlab_timelapse_entire_exp.avi?versionId=a58df78d-1291-4301-9763-86a97b9e146c">ratlab_timelapse_entire_exp.avi</a>

opennotspecifiedMar 2023View details →

FIGURE 1 in Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil

FIGURE 1. Location of the municipalities of the sampling sites in Paraná, Brazil. Light grey = Faxinal (FX), Black = Mauá da Serra (MS), Dark grey = Palmeira (PL)

opencc-zeroJan 2023View details →

Simulated eukaryotic genomic sequencing, long and short reads

As accuracy and throughput of nanopore sequencing improves, it is increasingly common to perform long-read-first de novo genome assemblies followed by polishing with accurate short reads (Kim et al. 2021). We briefly introduce FMLRC2, the successor to the original FM-index Long Read Corrector (FMLRC), and illustrate its performance as a fast and accurate de novo assembly polisher for both bacterial and eukaryotic genomes.

opencc-by-4.0Mar 2023View details →

Synthetic data for Aligning Distant Sequences to Graphs using Long Seed Sketches

Each directory inside the folder correponds to the number of levels used to generate the dataset (for more details, see the description written in the publication). Inside each directory, the files "reference_X" and "mutated_X" correpond to the sequences reference and mutated at rate X, respectively.

opencc-zeroMar 2023View details →

High-resolution quasi-idealized experiments for future and present-day based upon composites from a decades-long set of recurving landfalling (RCL) North Atlantic ET cases

We present a high-resolution quasi-idealized experiment based upon composites from a decades-long set of recurving landfalling (RCL) North Atlantic extratropical transition (ET) cases. Following Jung and Lackmann (2021), we apply the track-based classification method of Colbert and Soden (2012) to the historical database (1979 to 2018) of North Atlantic RCL ET events; recurving landfalling tropical cyclones (TCs) are defined as those which cross 70°W north of 25°N or cross 65W north of 40N and threaten the U.S. East Coast. We use the Atlantic Hurricane Database (HURDAT2) best-track data (Landsea and Franklin 2013); the track-based classification procedure yields 37 RCL ET cases over the 40-year period. To minimize the spread of the selected ET cases in terms of time to complete transition, we apply a threshold of 36 h as in Jung and Lackmann (2021). As HURDAT2 only specifies when transition is complete but does not provide the timeline of the transition, we supplement it with the cyclone phase space (CPS) method of Hart (2003) to diagnose onset and completion times of ET; ET events are first identified by HURDAT2 and then we compute the CPS parameters to confirm the ET timeline for each event using the ERA5 reanalysis dataset (Hersbach et al. 2020). This filtering process yields 21 RCL ET cases. This dataset is initialized by randomized 15-case composites selected from the 21 RCL ET cases as in Jung and Lackmann (2021). This dataset was used to produce figures and tables in the manuscript of Jung and Lackmann (2023, in review). Due to storage limitations, the full dataset is much too large to be published (~ 500GB). Instead, a subset consisting of 3-hourly atmospheric temperature at 17 vertical levels, zonal and meridional wind at 17 vertical levels, 3 hourly accumulated precipitation, mean sea level pressure, 10-m zonal and meridional wind, sea surface temperature, and relative humidity at 17 vertical levels is presented. If you wish to access the full dataset, please contact one of the authors.

opencc-by-4.0Sep 2022View details →

Replication package for: Optimal Long-Term Health Insurance Contracts: Characterization, Computation, and Welfare Effects

This is a replication package for:  Ghili, S., Handel, B., Hendel, I. and Whinston, M. "Optimal Long-Term Health Insurance Contracts: Characterization, Computation, and Welfare Effects."  The replication package .zip file contains a ReadMe, which provides instructions, and data matrices and code for the paper.

Fig. 3 in Age- and sex-specific survivorship of the Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii)

Fig. 3.—Age-specific mortality rates (qx) for male and female longfinned pilot whales (Globicephala melas edwardii) mass-stranded on the New Zealand coast between 2006 and 2017. Points are based on traditional life table calculations (qx) and smoothed curves were fitted using the Siler model (Siler qx). Age-class = age x to x + 1.

Fig. 1 in Age- and sex-specific survivorship of the Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii)

Fig. 1.—Age distribution of female (n = 227), male (n = 154), and unknown sex (n = 3) long-finned pilot whales (Globicephala melas edwardii) mass-stranded on the New Zealand coast between 2006 and 2017.

Fig. 2 in Age- and sex-specific survivorship of the Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii)

Fig. 2.—Age-specific survivorship (lx) for male and female longfinned pilot whales (Globicephala melas edwardii) mass-stranded on the New Zealand coast between 2006 and 2017. Points are based on traditional life table calculations (lx) and smoothed curves were fitted using the Siler model (Siler lx). Age-class = age x to x + 1.

Fig. 2 in Demographic and environmental correlates of home ranges and long-distance movements of Mohave ground squirrels

Fig. 2.—Back-transformed model fitted values from the best-performing model of size of annual home ranges (a) by sex (mean ± SE) and (b) the standard deviation (SD) of elevation for Mohave ground squirrels in the Freeman Gulch study area, Mojave Desert, California, 2003–2004. Gray bands in (b) represent 95% confidence intervals.

Fig. 1 in Demographic and environmental correlates of home ranges and long-distance movements of Mohave ground squirrels

Fig. 1.—Map of the Freeman Gulch study area in the west-central portion of the geographic range of the Mohave ground squirrel (MGS) in the Mojave Desert, California. The study area is approximately indicated by a minimum convex polygon drawn around all MGS radiotelemetry locations collected in 2003–2004. The Coso Range, in which MGS studies were conducted in the 1990s, is located in the northern portion of the MGS range. The top inset map shows juvenile and adult MGS locations within the Freeman Gulch study area. The cluster of locations in the extreme northeast of the inset was from a single individual that made a long-distance movement as a juvenile in 2003 and established a home range as an adult the following year. The bottom inset map shows the location of the MGS range in southern California.

opennotspecifiedAug 2020View details →

Figure 3 in A forgotten rodent from the Garden of Eden: what really happened to the long-tailed nesokia rat in the Mesopotamian marshes?

Figure 3: The two most abundant rat-sized rodents in the Mesopotamian seasonally flooded marshes are (A) the short-tailed nesokia (Nesokia indica; photographed at Hoor Ol-Ezeem on the Iranian side of Hawizeh Marsh; photo by Sayed B. Mousavi) and (B) the brown rat (Rattus norvegicus; captured at Mashab in the Eastern Hammar Marsh, Basra Province, Iraq; photo by Omar F. Al-Sheikhly). Compare with the longtailed nesokia rat in Figures 1, 4B.