Find research datasets worth reusing

opencc-zeroJun 2021View details →

Two decades of annual landscape-scale tree growth and dynamics in old-growth tropical rainforest in the CARBONO Project, La Selva Biological Station, 1997-2018

Here we present the complete data series from a 21-yr study of the annual growth and dynamics of trees, palms and lianas in the old-growth tropical rainforest at the La Selva Biological Station in Costa Rica. These observations were part of the CARBONO Project, a multidisciplinary team study of forest carbon cycling. The project was designed to assess forest processes at the landscape scale by sampling with replication across the within-landscape edaphic heterogeneity typical of tropical forests. Through more than two decades, forest growth and dynamics were assessed annually. The annual time-step used in the CARBONO Project effectively captured forest responses to major disturbances and to interannual and climatic variation. Annual measurements also enhanced the accuracy and long-term consistency of the data. To our knowledge, the resulting records are unique for tropical forests, where the dominant approach to studying the dynamics of a given forest has been to use a single plot and multi-year inter-census intervals. To date these CARBONO Project data have revealed: multi-decadal forest stability in spite of the short-term changes in forest structure resulting from major natural disturbances (e.g., the 1997-1998 Strong El Niño, and the extreme windstorm of May 2018); the dynamics and importance of large trees; and the responses of a major component of ecosystem productivity, aboveground wood production, to interannual and long-term climatic and atmospheric change. These data have also contributed to many remote-sensing studies. The data set consists of annual observations through the period 1997–2018 of the floristics, survival, recruitment, and growth of all woody stems (diameter > 10 cm) in a landscape-scale plot network. At completion of the study, the data spanned 6705 individuals and 21 years. The data set is complete and has been through extensive internal checks for quality assurance. Detailed data documentation and an emphasis on measurement repeatability were prioritized through the study. The metadata include an extensive README file describing the data files and the methods, a document detailing the data management and qa/qc, and the scanned original field data-sheets for the 22 annual censuses. We gratefully acknowledge the careful long-term field work and data entry and checking by paraforesters Leonel Campos Otoya and William Miranda Conejo. Logistical support and the long-term protection of the La Selva reserve were provided by the Organization for Tropical Studies. The Ministerio de Ambiente y Energía of Costa Rica granted permits to carry out this study through the years of the study (most recently: Resolución No. 037-2018-ACCVC-PI).

opencc-zeroJun 2021View details →

Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion, and influence evolution as selective pressures force adaption. Such disasters occurred on March 11th 2011, in Fukushima, Japan when an earthquake, tsunami, and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Here, we demonstrate, using genetic data, how wild boar (Sus scrofa leucomystax) have persevered against these environmental changes, including an invasion of escaped domestic pigs (Sus scrofa domesticus). Concurrently, we show evidence of successful hybridization between pigs and native wild boar in this area, however in future offspring, the pig legacy has been diluted through time. We speculate that the range expansion dynamics inhibit long-term introgression and introgressed alleles will continue to decrease at each generation while only maternally inherited organelles will persist. Using the gene flow data among wild boar, we assume that offspring from hybrid lineages will continue dispersal north at low frequencies as climates warm. We conclude that future risks for wild boar in this area include intraspecies competition, revitalization of human related disruptions, and disease outbreaks.

opencc-by-4.0Jun 2021View details →

Dynamic light scattering data

The upload archive consists of all the obtained results based on DLS measurements ( commonly known as dynamic light scattering) . More detain you could find in the cited article above.

Molecular Dynamics of SARS-CoV-2 Delta Variant Receptor Binding Domain in Complex with ACE2 Receptor

Molecular dynamics simulation for 10 ns at 37 C degrees of SARS-CoV-2 delta variant. Performed with NAMD and visualized/analyzed in ChimeraX software using Frontera supercomputer from Texas Advanced Computing Center. By Victor Padilla-Sanchez, PhD. https://www.youtube.com/watch?v=8N_MjWwxbMQ

Alliance Dynamics Experiment Data

This repository contains two csv files. GAdata.csv contains per-subject/ per-period data on decisions made by participants in all our sessions. Interaction_Data.csv contains data aggregated by interactions. E.g., fraction of periods during which an interaction cooperated. ### File GAdata.csv, variables This data set contains one data point for each choice made by every subject that participated in the experiment. * Session: session ID, from 1 to 16. * Subject: session-specific subject ID, from 1 to 24 in most sessions. * GovStructure: governance structure of the alliance. Four possible values:     * 2-player: two players, no exit cost.     * 3-player: three players, no exit cost.     * 2-Exit cost: two players, exit cost.     * 3-Exit cost: three players, exit cost. * Game: the strategic properties of the alliance game played. Either CG, for coordination game, or PD, for prisoner's dilemma. * interactionDraw: the number of periods per interaction was randomly drawn in the first two sessions, and replicated afterwards. There are thus two types of ``interaction draws''. Type 1 has seven interactions, lasting 5, 14, 5, 11, 6, 12, and 37 periods each. Type 2 has six interactions, lasting 19, 4, 2, 15, 20, and 21 periods each. * interaction: session-specific interaction ID. For type 1 interaction draw, the ID goes from 1 to 7, for type 2 interaction draw it goes from 1 to 5. * Period: interaction-specific period ID, ranging from 1-2 in the shortest interaction, to 1-37 in the longest interaction. * Partnership: alliance ID. In each interaction of a session, two or three subjects interact repeatedly. Partnership is the interaction-specific ID of the group interacting repeatedly. * Profit: profit obtained by the given subject in the current interaction and period. * Matchpay: cumulative profit obtained by the given subject in the current interaction up to the current period. * Finished: if equal to 0, the current alliance has not been terminated by a partner exiting. Is larger than 0, the current alliance has been terminated in the specified period by a partner exiting. * Choice: action chosen by the subject in the current interaction and period. Five possible values: C means the subject contributes resources to the alliance, nC means the subject does not contribute resources to the alliance, E means the subject chooses to exit the alliance, E- means the subject or one of her partners chose to exit the alliance in a preceding period. * Terminator: a dummy that takes on the value of 1 if the alliance was terminated by the subject's choice to exit in the current or some preceding period. If, instead, the alliance has not been terminated, or it was terminated by a partner's choice to exit, the dummy equals 0. * PartnerChoice.Poc: choice of the single partner in two-player alliances. Choice of ``partner one'' in three-player alliances. * PTc: empty for two-player alliances. Choice of ``partner two'' in three-player alliances. * gplay: indicator of joint choice of all alliance partners.\ It takes on 7 different values for two-player alliances: 1 if both choose C, 2 if the subject chooses C and her partner nC, 4 if the subject chooses nC and her partner C, 6 if both subjects choose nC, 7 if the subject chooses E, 8 if the subject's partner chooses 8, and 9 in all other cases. \ It takes on 9 different values for three-player alliances: 1 if all players choose C, 2 if the subject and one partner choose C while another partner chooses nC, 3 if the subject chooses C and both partners choose nC, 4 if the subject chooses nC and both partners choose C, 5 if the subject and one partner choose nC while another partner chooses C, 6 if all three players choose nC, 7 if the subject chooses E, 8 if a partner chooses E, 9 in all other cases. * simplay: indicator of joint choice of all partners, treats partners symmetrically.\ For two-player alliances, the values are: 1 if both choose C, 2 if one partner chooses C and the other nC, 4 if both choose nC, 5 if one partner chooses E, 6 if E was chosen in some preceding period.\ For three-player alliances, the values are: 1 if all partners choose C, 2 if two partners choose C and one partner chooses nC, 3 if two partners choose nC and one partner chooses C, 4 if all partners choose nC, 5 if one partner chooses E, 6 if E was chosen in some preceding period. * Age: age of the subject, as collected from the exit questionnaire. * Gender: gender of the subject, as collected from the exit questionnaire. ### File Interaction_Data.csv This data set contains one data point for each interaction formed by sets of two or three subjects during all sessions of the experiment. * Session: session ID, from 1 to 16 * interaction: session-specific interaction ID. For type 1 interaction draw, the ID goes from 1 to 7, for type 2 interaction draw it goes from 1 to 5. * Partnership: alliance ID. In each interaction of a session, two or three subjects interact repeatedly. Partnership is the interaction-specific ID of the group interacting repeatedly. * gstruct: governance structure of the alliance. Four possible values:     * 2-player: two players, no exit cost.     * 3-player: three players, no exit cost.     * 2-Exit cost: two players, exit cost.     * 3-Exit cost: three players, exit cost. * game: the strategic properties of the alliance game played. Either CG, for coordination game, or PD, for prisoner's dilemma. * it_type: the number of periods per interaction was randomly drawn in the first two sessions, and replicated afterwards. There are thus two types of ``interaction draws''. Type 1 has seven interactions, lasting 5, 14, 5, 11, 6, 12, and 37 periods each. Type 2 has six interactions, lasting 19, 4, 2, 15, 20, and 21 periods each. * it_length: length, in periods, of the current interaction. * fins: period in which the alliance was terminated because a partner chose E. If equal to 0, the alliance was never terminated. * Ldum: a dummy, specified as a factor variable equal to "CC last period" if all partners chose C in the last period of the interaction, or "not CC last period" if not all partners chose C in the last period of the interaction. * startC: conditional on all partners chosing C in the last period, startC gives the first period when C was chosen by all partners, to keep on being chosen until the final period of the interaction. startC = 0 means partners did not all choose C in the last period. * cfreq: fraction of all periods of the interaction in which all partners jointly chose C. * ncfreq: fraction of all periods of the interaction in which all partners jointly chose nC. * fcdummy: dummy, equal to 1 if all partners chose C in all periods of the interaction. * sdummy: dummy equal to 1 if an alliance is "successful", meaning that all partners choose C in all periods. Its value is 0 otherwise. * tdummy: dummy, specified as a factor variable equal to "Terminated" if the alliance was terminated by a partner choosing E in some period, and "Never E" if no partner chose E in any period. * simple: dummy, specified as a factor variable equal to "2-player" if the governance structure is 2-player, and "Other" otherwise. * exitcost: dummy, specified as a factor variable equal to "2-Exit cost" if the governance structure is 2-Exit cost, and "Other" otherwise. * multi: dummy, specified as a factor variable equal to "3-player" if the governance structure is 3-player, and "Other" otherwise. * multec: dummy, specified as a factor variable equal to "3-Exit cost" if the governance structure is 3-Exit cost, and "Other" otherwise.

Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein"

Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein", Journal of Biomolecular Structure and Dynamics, 2021, 10.1080/07391102.2021.1942213 A random selection of 10 representative structures from each MSM state of STING/CDN complexes is provided in .pdb file format. The selected MSM representatives are aligned and available as PyMOL session files.

Depth dependent spatiotemporal dynamics of overwintering pelagic Microcystis in a temperate water body

Supplementary Information for the research article 'Depth dependent spatiotemporal dynamics of overwintering pelagic Microcystis in a temperate water body'.

Comparing single-species and mixed-species groups in fruit flies: differences in group dynamics but not group formation

Mixed-species groups describe active associations among individuals of two or more species at the same trophic level. Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation; and ignoring the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected. Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species groups form. Further, insects have been almost completely ignored in the study of mixed-species groups, despite their taxonomic importance and relative prominence in the study of single-species groups. Here, we measured group formation processes in Drosophila melanogaster and its sister species Drosophila simulans. Each species was studied alone, and together; and one population of D. melanogaster was also studied both alone and with another, phenotypically-distinct D. melanogaster population, in a nested-factorial design. This approach differs from typical methods of studying mixed-species groups in that we could quantitatively compare group formation between single-population, mixed-population, and mixed-species treatments. Surprisingly, we found no differences between treatments in the number, size, or composition of groups that formed, suggesting that single-species and mixed-species groups form through similar mechanisms of active attraction. However, we found that mixed-species groups showed elevated inter-species male-male interactions, relative to inter-population or inter-genotype interactions in single-species groups. Our findings expand the conceptual and taxonomic study of mixed-species groups while raising new questions about the mechanisms of group formation broadly.

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

Raw data linked to the research article "ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic"

Genomic data from the Brazilian sibilator frog reveals contrasting Pleistocene dynamics and regionalism in two South American dry biomes

Aim: Knowledge about the Neotropical dry formations, particularly the Caatinga, remains rudimentary compared to other biotas in the region. Here we address several biogeographical hypotheses by combining intense geographic and genomic sampling obtained for the Brazilian sibilator frog. We specifically test predictions related to the putative roles of past climate shifts (Pleistocene and Holocene) and local geographic barriers (past and current courses of the São Francisco river, SFR) in causing population differentiation in this species. Location: Caatinga and eastern Cerrado. Taxon: Brazilian sibilator frog Leptodactylus troglodytes. Methods: We sequenced up to ~15,000 single nucleotide polymorphisms for 159 samples from 61 locations. We inferred genetic structure using spatial clustering and examined population sizes through time. We estimated the relationship among populations using phylogenetic reconstruction, estimated historical distributions with ecological niche modelling, and inferred demographic history under isolation-with-migration models. Results: Genetic diversity in L. troglodytes corresponds to biome boundaries, with one population in the Cerrado and two populations in the Caatinga, separated by the SFR. Demographic model selection indicates the Caatinga populations expanded since the end of the Pleistocene while the Cerrado population declined. Within the Caatinga, population expansion began earlier and was more extreme in the north. A continuous stability area maintained the two Caatinga populations, which share a common origin and began diverging in the mid-Pleistocene, first with symmetric gene flow and later under pronounced migration from the north. Main Conclusions: We could not reject a role of past climate change in causing diversification of relictual populations in the Cerrado, but we found no evidence of multiple refuges or long-term isolation within the Caatinga. Instead, diversification in this biome appears to be caused by the SFR acting as a "soft barrier" that constrains migration over an extended period of time.

The role of canopy cover dynamics over a decade of changes in the understory of an Atlantic beech-oak forest

This dataset hosts the main data and R codes of the analyses carried out to study the role of canopy cover dynamics over a decade of changes in the understory of an Atlantic Beech-Oak forest. We measured changes in understory taxonomical and functional composition, richness and diversity between 2006 and 2016, and relate those changes to changes in canopy coverage between both years. The data show changes between 2006 and 2016 in the species abundance, richness and diversity of 102 understory communities, and in the functional composition, richness and diversity for five functional traits (Leaf dry matter content, Specific leaf area, Leaf size, Plant height and Seed mass). Changes in canopy coverage between 2006 and 2016 were studied as an explanatory variable. The R codes show the main analyses carried out in the study: 1) The calculation of the functional composition, richness and diversity of the five traits studied (Leaf dry matter content, Specific leaf area, Leaf size, Plant height and Seed mass), 2) a Dunnett's modified Tukey-Kramer test used to test for significant relationships between four plot categories defined according to the presence or absence of canopy gaps (no gaps, gap closure, gap opening and gap persistence) and changes in the taxonomical and functional composition and diversity of the understory from 2006 to 2016. 3) An Indicator Species Analysis used to study the species that were indicators of gap opening or closure in the Atlantic Beech-Oak forest studied. 4) The calculation of the Standardized Effect Size for the functional traits of the indicator species, used to see if the species selected as gap indicators shared similar values of functional traits and had values significantly different from non-indicator species.

Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition

The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which likely played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.

opencc-zeroJan 2022View details →

Pairing functional connectivity with population dynamics to prioritize corridors for Southern California spotted owls

Aim: Land use change, climate change, and shifts to disturbance regimes make successful wildlife management challenging, particularly when ongoing urbanization constrains habitat and movement. Preserving and maintaining landscape connectivity is a potential strategy to support wildlife responding to these stressors. Using a novel model framework, we determined the population-level benefit of a set of identified potential corridors for spotted owl population viability. Location: Southern California, United States. Methods: Combining habitat suitability and dynamic metapopulation models, we compared the benefit of corridors to the Southern California spotted owl population, measured as the increase in the expected minimum abundance, both now and under a future climate. Our approach considered key corridor characteristics important to conservation decisions, namely, corridor irreplaceability and local population network benefit. Results: We identified two corridors likely to increase Southern California spotted owl expected minimum abundance under current climate conditions. At the regional scale, of the 16 corridors evaluated, one corridor was irreplaceable (i.e. no other corridors in the network could provide a similar increase in abundance when the irreplaceable corridor was removed) and one corridor was identified as redundant (i.e. remaining corridors in the network can provide some of the increases in abundance offered by the removed corridor). Both putative corridors connected two large, populous, and similarly-sized patches. Additionally, we identified two more corridors at the local scale. We found that, under climate change, population declines may limit the benefit of connectivity for a range-restricted species like the spotted owl. Main Conclusions: Our analytical approach highlights important criteria for corridor identification and prioritization, namely, irreplaceability versus redundancy, local versus regional benefit, and corridor impact in a changing landscape. With the capability of incorporating estimated functional connectivity into population dynamics, our modeling framework advances connectivity decision making for other species of conservation concern and archetypal taxa within ecological communities.

opencc-by-4.0Aug 2021View details →

Lumped Element Rigid Panel Dynamics Model

This code is a lumped element rigid panel dynamics model calculating natural frequencies and mode shapes for radiator panels connected by thin kinked tubes. The panels are connected by torsional spring elements, and this work is compared against a continuous equivalent stiffness beam model. Data is included for the example being calculated, however, it can be easily modified for any number of panels. This work is part of Kyle Marquis' 2021 Master's Thesis at the University of Colorado Boulder, titled "A Novel Deployable Radiator Architecture for High-Power Spacecraft Missions by Connecting Tapered and Layered Panels with Thin Kinked Tubes".

opencc-by-4.0Aug 2021View details →

Dynamic Evolution of Changbaishan Volcanism in Northeast China Illuminated by Machine Learning

This dataset is for our work entitled "Dynamic Evolution of Changbaishan Volcanism in Northeast China Illuminated by Machine Learning". This dataset includes: 1) The Cenozoic basalts in Changbaishan area used for predicting, 2) The IAB (Island Arc Basalts) and OIB (Ocean Island Basalts) samples used for training machine learning models.

opencc-by-4.0Apr 2021View details →

Model output data for compressible EULAG dynamical core in COSMO: convective-scale Alpine weather forecasts

The archive contains model output data for article "Compressible EULAG dynamical core in COSMO: convective-scale Alpine weather forecasts" to be published in Monthly Weather Review. The article presents the semi-implicit compressible EULAGas a newdynamical core for convective-scale numerical weather prediction. The core is implemented within the infrastructure of the operational model of the Consortium for Small Scale Modeling (COSMO), forming the NWP COSMO-EULAG model (CE). This regional high-resolution implementation of the dynamical core complements its global implementation in the Finite-Volume Module of ECMWF’s Integrated Forecasting System. The paper documents the first operational-like application of the dynamical core for realistic weather forecasts. After discussing the formulation of the core and its coupling with the host model, the paper considers several high-resolution prognostic experiments over complex Alpine orography. Standard verification experiments examine the sensitivity of the CE forecast to the choice of the advection routine and assess the forecast skills against those of the default COSMO Runge-Kutta dynamical core at the 2.2 km grid showing a general improvement. The skills are also compared using satellite observations for a weak-flow convective Alpine weather case-study, showing favorable results. Additional validation of the new CE framework for partly convection-resolving forecasts using 1.1 km, 0.55 km, 0.22 km, and 0.1 km grids, designed to challenge its numerics and test the dynamics-physics coupling, demonstrates its high robustness in simulating multi-phase flows over complex mountain terrain, with slopes reaching 85 degrees, and the flow’s realistic representation.

TCTracer: Establishing Test-to-Code Traceability Links Using Dynamic and Static Techniques - Evaluation Data - Empirical Software Engineering 2021

This repository provides the data artefacts for the experiments conducted using our tool TCTracer for the journal paper "TCTracer: Establishing Test-to-Code Traceability links Using Dynamic and Static Techniques" as submitted to the Empirical Software Engineering journal in 2021.

Comparing the Influence of Global Warming and Urban Anthropogenic Heat on Extreme Precipitation in Urbanized Pearl River Delta Area Based on WRF Dynamical Downscaling

The simulation outputs from the Weather Research and Forecasting (WRF) v3.8.1 coupled with single layer urban canopy model from three experiments (HIST_AH300, HIST_AH0, and RCP85_AH300). Variables include hourly precipitation, wind, specific humidity, relative humidity, convective available potential energy, convective inhibition, temperature, model height, land use land cover, and topography.

opencc-by-4.0Dec 2010View details →

Figure 3 in Population dynamics, age structure and sex ratio of the bromeliad-dwelling jumping spider, Psecas chapoda (Salticidae)

Figure 3. Climatic data from Itauna farm (5 km from the study site), from May 1998 to April 2000.