Find research datasets worth reusing

opencc-by-4.0Sep 2020View details →

Tropical cyclones significantly alleviate mega-deltaic erosion induced by high riverine flow

Research repository of the paper entitled "Tropical cyclones significantly alleviate mega-deltaic erosion induced by high riverine flow" that published in Geophysical Research Letters by Wang et al. The statistical and analytical data mainly include bathymetric change magnitudes, morphodynamic characteristics, detailed information of tropical cyclones and the monthly water-sediment discharges of the Changjiang at Datong, etc.

opennotspecifiedSep 2020View details →

Figure 4 in Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society

Figure 4. Graphical representation of original and recently modified pathways for feedback regarding Primary Biodiversity Data, showing information transfer among users, providers, and aggregators. Such feedback consists of suggested improvements or additions to data fields, for example a change in species identification or a newly determined georeference. The diagrams contrast two complementary mechanisms: (a) the original feedback loop (currently dominant); and (b) the emerging feedback pendulum (proposed for expansion). In a: (1) the user sends feedback to the provider (e.g., a given natural history museum); (2) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (3) that information becomes available for query by all users. In practice, because many providers do not consistently make such changes (denoted by an X), users do have access to updated information (dashed line). In b: (1) the user sends feedback to the aggregator; (2) the aggregator simultaneously both annotates the record (visible to all users) and sends the suggested information to the provider; (3) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (4) the aggregator makes the updated information available for query by all users. Note that even if a provider takes no action regarding the suggested information, the annotations placed by the aggregator are nevertheless available to users. Additionally, because the quantifications of data quality and use described in the text allow for benchmarks that can be tracked over time, we anticipate that the feedback pendulum will help providers become more successful in justifying and securing funding to make data improvements based on feedback from users.

opencc-by-4.0Dec 2019View details →

Representation model of wind velocity fluctuations and saltation sand transport in aeolian sand flow

The data of the figures in the article.

opencc-by-4.0Oct 2020View details →

Volumetric measurements of the flow over a slanted cylinder

Thank you for the interest in the experimental data set used in my dissertation! This data set was acquired during my PhD dissertation work, published in 2020. For details of the acquisition and interpretation, please check the dissertation referenced below: "Characterization of the slanted cylinder afterbody wake and goal-based experimental optimization of open-loop wake control" - Fernando Zigunov - Florida State University - PhD Dissertation - 2020 Please cite this repository and/or the dissertation document if you use the data set in your work! _________________________ This data set contains flow visualization and pressure measurements performed on a cylinder with a slanted afterbody,  a simplified geometry used for aircraft fuselage "tail" studies. It contains Particle Image Velocimetry (PIV) data with  volumetric mesurements, which allow for great insight of the flow field.  Please contact fzigunov@fsu.edu for queries and questions.

opencc-by-4.0Jun 2020View details →

Discrete flow cytometry from the Gradients 2017 cruise using a BD Influx Cell Sorter

The dataset consists of BD Influx-based analysis of phytoplankton populations and heterotrophic bacteria from discrete flow cytometry data collected during the Gradients 2017 (Gradients 2/MGL1704) oceanographic research cruise in the Northeast Pacific Ocean. The analysis includes cell abundance, forward light scatter, and pigment fluorescence of individual cells, including bacteria, picoeukaryotes and the cyanobacteria Prochlorococcus and Synechococcus. Time is in UTC format, latitude and longitude are in decimal degrees, and depth is in meters. Further information can be found here: https://github.com/fribalet/FCSplankton

opencc-by-4.0Jun 2020View details →

Discrete flow cytometry from the Gradients 2016 cruise using a BD Influx Cell Sorter

The dataset consists of BD Influx-based analysis of phytoplankton populations and heterotrophic bacteria from discrete flow cytometry data collected during the Gradients 2016 (Gradients 1/KOK1606) oceanographic research cruise in the Northeast Pacific Ocean. The analysis includes cell abundance, forward light scatter, and pigment fluorescence of individual cells, including bacteria, picoeukaryotes, and the cyanobacteria Prochlorococcus and Synechococcus. Time is in UTC format, latitude and longitude are in decimal degrees, and depth is in meters. Further information can be found here: https://github.com/fribalet/FCSplankton

opencc-zeroOct 2020View details →

Data for the effect of optic flow cues on honeybee flight control in wind

To minimise the risk of colliding with the ground or other obstacles, flying animals need to control both their ground speed and ground height. This task is particularly challenging in wind, where head winds require an animal to increase its airspeed to maintain a constant ground speed and tail winds may generate negative airspeeds, rendering flight more difficult to control. In this study, we investigate how head and tail winds affect flight control in the honeybee Apis mellifera, which is known to rely on the pattern of visual motion generated across the eye – known as optic flow – to maintain constant ground speeds and heights. We find that, when provided with optic flow cues in both the longitudinal and transverse directions of flight, honeybees maintain a constant ground speed but fly lower in head winds and higher in tail winds, a response that is also observed when longitudinal optic flow cues are minimised. This change in height with wind does not appear to result in a constant rate of optic flow in the ventral visual field, suggesting that honeybees may rely on a combination of mechanosensory and visual information when controlling flight in wind. We also find that, when the transverse component of optic flow is minimised, or when all optic flow cues are minimised, the effect of wind on ground height is abolished. We propose that the regular sidewards oscillations that the bees make as they fly may be used to extract information about the distance to the ground, independently of the longitudinal optic flow that they use for ground speed control. This computationally simple strategy could have potential uses in the development of lightweight and robust systems for guiding autonomous flying vehicles in natural environments.

opencc-by-4.0Oct 2020View details →

Dataset for formation of amorphous materials causes parallel brittle-viscous flow of crustal rocks: Experiments on quartz – feldspar aggregates

Mechanical and microstructural data saved as .mat data files together with scripts used for plotting saved as .m filed (MATLAB). Experiments are described in Pec and Al Nasser, JGR, 2021.

opencc-zeroOct 2020View details →

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 15%, 52%, and 32% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)

Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers to gene flow. These studies may conclude absence of population structure, lineage structure that indicates unique species have been discovered, or suggest more research is needed prior to delimitation. Comparative risks of delimiting species incorrectly or failing to delimit species are usually not weighed and a more detailed return to these problems with more data often does not occur. With genomic data and better modeling capabilities we can more clearly delimit species by understanding causes of speciation with respect to biogeography and migration between lineages, the location of hybrid zones in relationship to the ecology of parental lineages, and differential introgression of genes between taxa. Here we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, L. triangulum, and L. gentilis) using genomic-scale data to better understand the diversification of these taxa previously delimited based on a smaller genetic dataset. Methods that reject pure isolation by distance in favor of environmentally driven reduction in gene flow clearly indicate that all three lineages should continue to be recognized as unique species. These results underscore conspicuous environmental changes that occur between the sister-taxa forming due to changes in habitat from the Great Plains (GP) to the forested regions of the Eastern Nearctic (ENA). This area has been recognized for turnover of reptile and amphibian species but with few phylogeographic studies examining environmental-genetic structure in this region. We show that the two species meeting at the GP/ENA, L. triangulum and L. gentilis, likely formed in the mid-Pleistocene and have maintained partial reproductive isolation over much of this time, exchanging fewer than one migrant/generation, and formed a hybrid zone with differential introgression of loci. We also show that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. We conclude that phylogenetic reticulation in this genus, and likely for many other taxa, is common across throughout time. Furthermore, the application of the biological species concept to the whole genome will give rise to grave misunderstandings of the complexities of how species form and remain unique even in the face of gene flow.

Effect of space diffuser on flow characteristics of a centrifugal pump by computational fluid dynamic analysis

Achieving an optimal configuration of the diffuser is indispensable for high pump performances. In this work, a numerical study on diffuser configuration is conducted for a high pump performance using a computational fluid dynamics code, and the effects of the wrap angle and the relative position of the diffuser vane to the impeller on pump performances are included. The results indicate that the modified diffuser with a suitable wrap angle may improve the pump hydraulic efficiency and the head by approximately 4% and 8%, respectively, while a suitable position of the diffuser vane can enhance the pump head by more than 4%. Meanwhile, the pressure recovery coefficient and the local Euler head of the diffuser are adopted to evaluate the diffuser performance. For a high pump performance, the local Euler head of the diffuser has a peak value at the leading edge with the change rate of zero along the meridian streamline, meaning that no blade loading at the leading edge of the diffuser guarantees a better match between the impeller and the diffuser.

Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus

The final formation of the Central American Isthmus (CAI) about 3.5 Ma altered global ocean circulation, connected North and South America terrestrial biotas and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile Crocodylus acutus, to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: 1) Caribbean and the Panama Canal, 2) Pacific coast, and 3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20 ka, which is two orders of magnitude younger than the formation of the CAI, but coincides with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.

A re-evaluation of management units based on gene flow of a rare waterbird in the Americas

The maintenance of gene flow in species that have experienced population contractions and are geographically fragmented is important to the maintenance of genetic variation and evolutionary potential; thus, gene flow is also important to conservation and management of these species. For example, the Reddish Egret (Egretta rufescens) has recovered after severe population reductions during the 19th and 20th centuries, but population numbers remain below historic levels. In this study, we characterized gene flow among management units of the Reddish Egret by using ten nuclear microsatellite markers and part of the mitochondrial (mtDNA) control region from 176 nestlings captured at eight localities in Mexico (Baja California, Chiapas, Tamaulipas, and Yucatan), the U.S.A. (Texas, Louisiana, and Florida), and the Bahamas. We found evidence of population structure and that males disperse more often and across longer distances compared to females, which is congruent with previous banding and telemetry data. The maternally inherited mtDNA and biparentally inherited microsatellite data supported slightly different MU models; however, when interpreted together, a four MU model that considered population structure and geographic proximity was most optimal. Namely, MU 1 (Baja California); MU 2 (Chiapas); MU 3 (Yucatan, Tamaulipas, Texas, and Louisiana); and MU 4 (Florida and the Bahamas). Regions outside our sampled localities (e.g., the Greater Antilles and South America) require additional sampling to fully understand gene flow and movement of individuals across the species' entire range. However, the four MUs we have defined group nesting localities into genetically similar subpopulations, which can guide future management plans.

Stemming the Fake Flow: How Unistem Day Reveals the Importance of Science Communication to Students

Episode Summary In this episode we cover UniStem Day, a pan European outreach event that bring stem cell research and high school students together. We talk to the organisers of UniStem Day at the Max-Delbrück-Center for Molecular Medicine, Stefanie Mahler and Dr Daniel Besser, as well as teachers and pupils who attended.  Episode Links <a href="https://gscn.org/en/HOME.aspx">German Stem Cell Network</a>

Supporting dataset: A framework to quantify flow through coral reefs of varying coral cover and morphology

This dataset contains the STL files and data from the numerical and laboratory models used in the related publication.

Raw data for reference flow experiments

Raw results data for the reference flow study. Reference flow used public sequence data, where is specified in the manuscript, to generate the results. The figures shown in the manuscript were plotted using the provided processed data.   Reference flow manuscript: https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4 Reference flow software: https://github.com/langmead-lab/reference_flow Software for reference flow experiments: https://github.com/langmead-lab/reference_flow-experiments An archived version of the software for experiments: https://doi.org/10.5281/zenodo.4287729

Reference flow VCF for pre-built genomes

Pre-built genomes (in VCF format) for the RandFlow-LD and RandFlow-LD-26 methods in reference flow. The references can be built using the reference flow software (https://github.com/langmead-lab/reference_flow). An archival version of the software is available at http://doi.org/10.5281/zenodo.4287778   The reference flow method is described at https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4

opencc-by-4.0Dec 2020View details →

Soil water retention and water flow simulation data

The data is for the manuscript of a paper entitled "Simulation of water flow and calculation of the related physical quality indices as influenced by soil water retention curve fitting methods". Accurate fitting of soil water retention curve (SWRC) parameters is crucial in the modeling of soil water flow and the assessment of soil quality. The un-weighted least squares regression (ULS) is the most common approach applied for fitting the SWRC functions to the observed data-points in order to optimize their parameters. However, the variance of SWRC data varies in different water contents; therefore, unlike the wet-end of the SWRC, the ULS method may not be sufficiently effective in estimating its dry-end. This study examined the differences between parameter approximations achieved by the ULS and the weighted least-squares (WLS) in the SWRC. Then, an analysis of both approaches in the simulation of water redistribution and the related soil physical quality indicators (SPQIs) was done. Accordingly

opencc-zeroDec 2020View details →

Defining species when there is gene flow

Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with migration or introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive isolation mechanisms and to define species boundaries.