Find research datasets worth reusing

opencc-zeroOct 2022View details →

Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish

The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra, Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations of A. mexicanus have independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use of A. mexicanus has led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. The optimization of husbandry protocols that maximize high-nutrient feed, smaller tank densities, and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high-protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of A. mexicanus as a genetic model.

opencc-by-4.0Oct 2022View details →

Data for Chandnani and Herrick, Influence of Target Properties on Wall Slumping in Lunar Impact Craters within the Simple-to-Complex Transition

Data files for Figures 3 and S1 of the manuscript.  These are craters counted in slump and ejecta units for the purpose of comparing their relative ages. The directory sf_shapefiles contains subdirectories for the 20 craters for which a slump unit and an ejecta unit had crater counts performed.  The AREA_* shapefiles are polygons that outline the area studied, and the CRATER_* files are the individual craters counted.  These files were created using CraterTools (<a href="https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html">https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html</a>) in ArcGIS, but that software is not necessary to use the shapefiles.  The subdirectory SFD_figs_color and SFC_suppl_figs_color are, respectively, the CraterStats (https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html) files used to generate Figure 3 of the main manuscript and Supplemental Figure S1.  Each crater comprises a subdirectory of those main directories.  Within each subdirectory, the *.plt file is the file directing CraterStats how to make the figure.  The *.png file is the output figure from CraterStats, and the *.jpg file is the .png file after it has been cropped and the error bars have been changed from grey to black.  The *.txt file provides the output from CraterStats that, among other things, provides the data fit of isochrons to the data.  The *.diam files are data extracted from the shapefiles and provide the input into Craterstats.  They have the lat-lon-diameter information on the craters and the counting area.  All of these are commented text files, so you don’t need CraterStats to look at them and use them.

Detectability and impact of repetitive surveys on threatened West African crocodylians: Data M1

West African crocodylians are among the most threatened and least studied crocodylian species globally. Assessing population status and establishing a basis for population monitoring is the highest priority action for this region. Monitoring of crocodiles is influenced by many factors that affect detectability, including environmental variables and individual or population-level wariness. We investigated how these factors affect detectability and counts of the Critically Endangered Mecistops cataphractus and the newly recognized Crocodylus suchus. We implemented 195 repetitive surveys at 38 sites across Côte d'Ivoire between 2014 and 2019. We used an occupancy-based approach and a count-based GLMM analysis to determine the effect of environmental and anthropogenic variables on detection, and modeled crocodile wariness over repetitive surveys. Despite their rarity and level of threat, detection probability of both species was relatively high (0.75 for M. cataphractus and 0.81 for C. suchus), but a minimum of two surveys was required to infer absence of either species with 90% confidence. We found that detection of M. cataphractus was significantly negatively influenced by fishing net encounter rate, while high temperature for the previous 48h of the day of the survey increased C. suchus detection. Precipitation and aquatic vegetation had significant negative and positive influence, respectively, on M. cataphractus counts and showed the opposite effect for C. suchus counts. We also found that fishing encounter rate had a significant negative effect on C. suchus counts. Interestingly, survey repetition did not generally affect wariness for either species, though there was some indication that at least C. suchus was more wary by the fourth replicate. These results are informative for designing future survey and monitoring protocols for these threatened crocodylians in West Africa, and for other endangered crocodylians globally.

Time scales of ecosystem impacts and recovery under individual and serial invasions

Introductions of keystone or engineering species have complex and long-term impacts on multiple ecosystem features. Anticipating these consequences requires knowledge of the magnitude and pace of a species' impacts and whether they subside as resident species and communities adapt. Managing for the effects of invasive species is particularly complicated by a paucity of long-term ecosystem studies, the fact that invaders can represent novel ecological types, and as serial invasions by new species mediate the impacts of an original invader. We resolve the impacts of quagga (Dreissena rostriformis bugensis) and zebra mussels (D. polymorpha), two of the most widespread species that increasingly co-invade and re-engineer energy flows in freshwater ecosystems. Following many-decade time series and seven ecosystem features, we find remarkably similar ecosystem responses to mussel invasion across seven lakes in Europe and North America. Lakes invaded by zebra mussels only experienced the most severe changes within 5-10 years of invasion, followed by a partial recovery of several key ecosystem features. However, recovery disappeared, and initial impacts amplified in lakes where subsequent, serial invasions by quagga mussels competitively displaced zebra mussels. Our results suggest that the impact of quagga is stronger per unit biomass due to their greater effects on phytoplankton during spring and fall. Thus, we show that the effects of species introductions on many lake ecosystem features can manifest quickly and partially subside, except when multiple species invade a system.

opencc-by-4.0Nov 2022View details →

The versatility of pulses: Are consumption and consumer perceptions in different European countries related to the actual climate impact of different pulse types? Author links open overlay panel

Pulses support sustainable production and consumption. Their culinary versatility creates a wide range of possibilities for new products, bridging consumers’ preparation barriers. However, this potential is often intangible for consumers who have little knowledge about plant-based foods. Based on an online survey in Denmark, Germany, Poland, Spain, and the United Kingdom (N = 4,226), this study aimed to investigate consumer utilization and perception of pulses as a versatile, low-carbon food relative to objective life cycle assessment (LCA) measures of 12 pulse types. The most popular pulse types, with specific preferences across countries, were lentils, kidney beans, and chickpeas, typically consumed at home and purchased in dried or canned form. Respondents associated pulses with being healthy and natural, but sustainability was not an essential attribute related to the perception of pulses. LCA revealed a low environmental impact caused by pulse production and consumption, with marginal variations between types and produce. Respondents were unaware of the nuances in the environmental impact of different pulse types, generally perceiving uncommon pulses to be relatively more sustainable than others. In conclusion, a low consumption combined with a misconception of pulses’ environmental impact may demand different promotional strategies including clear communication to inform consumers.

opencc-by-4.0Dec 2021View details →

Data supporting: Impacts of extreme climatic events on trophic network complexity and multidimensional stability

Data used to produce the results presented in the manuscript entitled "Impacts of extreme climatic events on trophic network complexity and multidimensional stability", published in the journal "Ecology". The data were obtained from an outdoor pond mesocosm experiment where freshwater communities were exposed to two different heatwave scenarios.

Data for: Evaluating the impact of anatomical partitioning on summary topologies obtained with Bayesian phylogenetic analyses of morphological data

Morphological data are a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task. Bayesian phylogenetic analyses require the use of evolutionary models, which have been intensively studied in the past few years, with significant improvements to our knowledge. Notwithstanding, a systematic evaluation of the performance of partitioned models for morphological data has never been performed. Here we evaluate the influence of partitioned models, defined by anatomical criteria, on the precision and accuracy of summary tree topologies considering the effects of model misspecification. We simulated datasets using partitioning schemes, trees, and other properties obtained from two empirical datasets, and conducted Bayesian phylogenetic analyses. Additionally, we reanalysed 32 empirical datasets for different groups of vertebrates, applying unpartitioned and partitioned models, and, as a focused study case, we reanalysed a dataset including living and fossil armadillos, testing alternative partitioning hypotheses based on functional and ontogenetic modules. We found that, in general, partitioning by anatomy has little influence on summary topologies analysed under alternative partitioning schemes with a varying number of partitions. Nevertheless, models with unlinked branch lengths, which account for heterotachy across partitions, improve topological precision at the cost of reducing accuracy. In some instances, more complex partitioning schemes, led to topological changes, as tested for armadillos, mostly associated with models with unlinked branch lengths. We compare our results with other empirical evaluations of morphological data and those from empirical and simulation studies of partitioning of molecular data, considering the adequacy of anatomical partitioning relative to alternative methods of partitioning morphological datasets.

Data from: Zoning has little impact on the seasonal diel activity and distribution patterns of wild boar (Sus scrofa) in an UNESCO Biosphere Reserve

Understanding the spatio‐temporal distribution of ungulates is important for effective wildlife management, particularly for economically and ecologically important species such as wild boar (Sus scrofa). Wild boars are generally considered to exhibit substantial behavioral flexibility, but it is unclear how their behavior varies across different conservation management regimes and levels of human pressure. To analyze if and how wild boars adjust their space use or their temporal niche, we surveyed wild boars across the core and buffer zones (collectively referred to as the conservation zone) and the transition zone of a biosphere reserve. These zones represent low and high levels of human pressure, respectively. Specifically, we employed a network of 53 camera traps distributed in the Schaalsee UNESCO Biosphere Reserve over a 14‐month period (19,062 trap nights) and estimated circadian activity patterns, diel activity levels, and occupancy of wild boars in both zones. To account for differences in environmental conditions and day length, we estimated these parameters separately for seven 2‐month periods. Our results showed that the wild boars were primarily nocturnal, with diurnal activity occurring dominantly during the summer months. The diel activity patterns in the two zones were very similar overall, although the wild boars were slightly less active in the transition zone than in the conservation zone. Diel activity levels also varied seasonally, ranging from 7.5 to 11.0 h day−1, and scaled positively with the length of the night (R2 = 0.66–0.67). Seasonal occupancy estimates were exceptionally high (point estimates ranged from 0.65 to 0.99) and similar across zones, suggesting that the wild boars used most of the biosphere reserve. Overall, this result suggests that different conservation management regimes (in this case, the zoning of a biosphere reserve) have little impact on wild boar behavior. This finding is relevant for wildlife management in protected areas where possibly high wild boar densities could interfere with conservation goals within these areas and those of agricultural land use in their vicinity.

opencc-by-4.0Nov 2022View details →

Analyzing the Impact: Foster Grandparent Program

Foster Grandparent Program (FGP) is a multigenerational approach to community volunteerism. The study uses intergenerational solidarity to conceptualize the impact of the FGP. The study aims to examine the impact from two dimensions by analyzing data from the Assignment Assessment Forms and the New General Self-Efficacy Scale. Paired t-tests were conducted to determine whether there is a difference in the mentees’ behavior pre- and post-intervention from four years and byway of three priority areas. Results indicated that the FGP has an impact on both the mentees and volunteers. Findings suggest that the program’s activities are the vehicle for intergenerational solidarity.

Functional impact of subunit composition and compensation on Drosophila melanogaster nicotinic receptors: Targets of neonicotinoids

Neonicotinoid insecticides target insect nicotinic acetylcholine receptors (nAChRs) and their adverse effects on non-target insects are of serious concern. We recently found that cofactor TMX3 enables robust functional expression of insect nAChRs in Xenopus laevis oocytes and showed that neonicotinoids (imidacloprid, thiacloprid, and clothianidin) exhibited agonist actions on some nAChRs of the fruit fly (Drosophila melanogaster), honeybee (Apis mellifera) and bumblebee (Bombus terrestris) nAChRs with more potent actions on the pollinator nAChRs. However, other subunits from the nAChR family remain to be explored. We show that the Dα3 subunit co-exists with Dα1, Dα2, Dβ1, and Dβ2 subunits in the same neurons of adult D. melanogaster, thereby expanding the possible nAChR subtypes in these cells alone from 4 to 12. The presence of Dα1 and Dα2 subunits reduced the affinity of imidacloprid, thiacloprid, and clothianidin for nAChRs expressed in Xenopus laevis oocytes, whereas the Dα3 subunit enhanced it. RNAi targeting Dα1, Dα2, or Dα3 in adults reduced expression of targeted subunits but commonly enhanced Dβ3 expression. Also, Dα1 RNAi enhanced Dα7 expression, Dα2 RNAi reduced Dα1, Dα6, and Dα7 expression and Dα3 RNAi reduced Dα1 expression while enhancing Dα2 expression, respectively. In most cases, RNAi treatment of either Dα1 or Dα2 reduced neonicotinoid toxicity in larvae, but Dα2 RNAi enhanced neonicotinoid sensitivity in adults reflecting the affinity-reducing effect of Dα2. Substituting each of Dα1, Dα2, and Dα3 subunits by Dα4 or Dβ3 subunit mostly increased neonicotinoid affinity and reduced efficacy. Therefore, functional expression studies and RNAi targeting of subunits show that neonicotinoid action and toxicity involve the integrated actions of multiple nAChR subunit combinations, counseling caution in interpreting toxicity to insects by subunit gene modification alone.

Spatial heterogeneity in benthic foraminiferal assemblages track regional impacts of paleoenvironmental change across Cretaceous OAE2

The impact of global climate events on local ecosystems can vary spatially. Understanding this heterogeneity can illuminate which environments will be most impacted and the proximal drivers of ecosystem responses. Cenomanian-Turonian marine deposits of the Western Interior Seaway (WIS) record paleoceanographic changes associated with transgression and the onset of Oceanic Anoxic Event 2 (OAE2). They provide an ideal setting to study basinwide paleoecological responses during a global perturbation. Here, we integrate benthic foraminiferal assemblages from before, during, and after OAE2 via multivariate ordination analysis to examine spatial patterns in faunal responses across the western United States on a common scale and to interrogate a previously defined faunal marker used for basin-wide correlation, the Benthonic Zone (BZ). We identify oxygenation and organic matter quality as primary and secondary controls of variation across the 10 stratigraphic records and use this variation to infer paleoenvironmental changes. Stratigraphic trends reveal, in contrast to previous studies, deoxygenation at the onset of OAE2. They also reveal temporal patterns in oxygenation and productivity consistent with the gradual northward migration of a southern water mass into the WIS. This spatial heterogeneity hinders the use of the BZ in biostratigraphy because assemblages change in response to diachronous environmental change, and thus timing of the BZ with respect to OAE2 is not consistent across the basin. Our study demonstrates that regional processes can overshadow ecosystem responses to global events and underscores the importance of considering how changes in the position of water masses impact the expression of global biogeochemical perturbations.

opencc-by-4.0Nov 2022View details →

Data for How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland

Raw and processed data for the paper "How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland" The raw trade data file is named TradeDataAggregated.rds The raw greenhouse gas footprint data is contained in Output_all.xlsx

opencc-by-4.0Oct 2022View details →

Impact planning using logic models and theory of change - Webinar

As part of Project Ô's communication efforts, two international events were organised aimed at extended networks with a focus on political communication and science advocacy relevant to water reuse. These online public events were recorded and edited for publication on the YouTube channel. -- Making an effective plan for impact can considerably increase your likelihood of success. This training introduces you to two powerful tools that will enable you to think systematically about your pathway to impact, including risks and assumptions you might need to take into account and indicators to help you track your progress. Mark Reed (SRUC and Fast Track Impact) introduces you to logic models based on his widely used impact planning template, and Eric Jensen (University of Illinois at Urbana-Champaign, University of Warwick and Methods for Change) introduces the theory of change approach. Mark then explains how you can co-produce a more detailed theory of change with stakeholders, and Eric shows how theory of change can be used to evaluate impact, using a case study of water research. You then have an opportunity to see examples of logic models and theory of change developed with researchers by Sarah Bowman (Trinity College Dublin).

openDec 2022View details →

Seismic Inverted Impact force and Digital Elevation Models before and after the 2018 Baige Landslide

For the data of inverted seismic force, the seismic signals recorded by the broadband seismic stations were prepared for the inversion of the force-time function by the following series of actions: <ul> <li>Removing the instrumental response</li> <li>Resampling to 0.5 s</li> <li>Integrating the signals from velocity to displacement</li> <li>Rotating the horizontal components to the radial and transverse direction</li> <li>Filtering the signals between periods of 30 and 140 s</li> </ul> For the digital elevation models (DEMs) of the Baige landslide, the pre-failure DEM with 10 m grid spacing was obtained from the Sichuan Bureau of Surveying Mapping and Geoinformation (SBSMG). At the same time, the post-failure DEM was derived from the UAV-based photogrammetry.

Timing of hydrologic anomalies direct impacts on migration traits in a flood pulse fishery system

1. Understanding adaptive reservoir management strategies that balance ecological outcomes with other objectives necessitates properly articulated environmental objectives. Aside from flood pulse extent-related metrics, residual-based descriptors provide robust descriptions of fish assemblage structure and harvest. 2. We proposed a model framework based on spectral analysis of hydrologic variation and the Multivariate AutoRegressive State Space (MARSS) model to statistically quantify the effect sizes of hydrologic variation impacts on total fish catch and functional group (migration types) fish harvest and applied it to 17 years of fish harvest data from the Lower Mekong River Basin (LMB). 3. Our findings suggest that duration and timing of hydrologic anomalies matter as much as their magnitude. Anomaly droughts coupled with strong pulse can benefit species if timed correctly. Longitudinal migrators were more sensitive to anomalous floods and droughts than other migratory species. Fish catch projections using effect sizes derived from historical data revealed that a well-timed and protracted flood followed by a powerful flood pulse would be advantageous to the fishery, but a flood delay could negate such benefits. 4. Our results add to a growing body of research that suggests ecological flows can be engineered. For most dams, the rule curve describing reservoir releases and resulting downstream hydrograph is designed in an ecological vacuum in which the objectives are to maximize human services—power production, flood control or navigation. Our work demonstrates that hydrograph can be designed to manage aspects of functional biodiversity directly. Though the exact shape of our hydrograph may not apply to other engineered river systems, we suggest that the approach can be applied generally, and globally both to developed and developing river basins. Specifically, a functional biodiversity rule curve could be optimized as an additional objective function in a multi-objective optimization framework. Our methodology provides a quantitative method for deriving an ecological flow for this larger tradeoff analysis.

The impacts of fine-tuning, phylogenetic distance, and sample size on big-data bioacoustics

Vocalizations in animals, particularly birds, are critically important behaviors that influence their reproductive fitness. While recordings of bioacoustic data have been captured and stored in collections for decades, the automated extraction of data from these recordings has only recently been facilitated by artificial intelligence methods. These have yet to be evaluated with respect to accuracy of different automation strategies and features. Here, we use a recently published machine learning framework to extract syllables from ten bird species ranging in their phylogenetic relatedness from 1 to 85 million years, to compare how phylogenetic relatedness influences accuracy. We also evaluate the utility of applying trained models to novel species. Our results indicate that model performance is best on conspecifics, with accuracy progressively decreasing as phylogenetic distance increases between taxa. However, we also find that the application of models trained on multiple distantly related species can improve the overall accuracy to levels near that of training and analyzing a model on the same species. When planning big-data bioacoustics studies, care must be taken in sample design to maximize sample size and minimize human labor without sacrificing accuracy.

Data for: Impact of alpha crystallin loss on zebrafish lens development

The α-crystallin small heat shock proteins contribute to the transparency and refractive properties of the vertebrate eye lens and prevent the protein aggregation that would otherwise produce lens cataracts, the leading cause of human blindness. There are conflicting data in the literature as to what role the α-crystallins may play in early lens development. In this study, we used CRISPR gene editing to produce zebrafish lines with mutations in each of the three a-crystallin genes (cryaa, cryaba and cryabb) to prevent protein production. The absence of each α-crystallin protein was analyzed by mass spectrometry, and lens phenotypes were assessed with differential interference contrast microscopy and histology. Loss of αA-crystallin produced a variety of lens defects with varying severity in larval lenses at 3 and 4 dpf but little substantial change in normal fiber cell denucleation. Loss of αBa-crystallin produced no substantial lens defects. Our cryabb mutant produced a truncated aBb-crystallin protein and showed no substantial change in lens development. Mutation of each α-crystallin gene did not alter the mRNA levels of the remaining two, suggesting a lack of genetic compensation. These data suggest that αA-crystallin plays some role in lens development, but the range of phenotype severity in null mutants indicates its loss simply increases the chance for defects and that the protein is not essential. Our finding that cryaba and cryabb mutants lack noticeable lens defects is congruent with insubstantial transcript levels for these genes in lens epithelial and fiber cells through five days of development. Future experiments can explore the molecular mechanisms leading to lens defects in cryaa null mutants and the impact of αA-crystallin loss during zebrafish lens aging.

opencc-by-4.0Mar 2022View details →

Dataset for the pubblication "Impact of DC Transient Disturbances on Harmonic Performance of Voltage Transformers for AC Railway Applications"

This is the dataset for the paper published: Letizia, P.S.; Signorino, D.; Crotti, G. Impact of DC Transient Disturbances on Harmonic Performance of Voltage Transformers for AC Railway Applications. Sensors 2022, 22, 2270. https://doi.org/10.3390/s22062270

opencc-by-4.0Dec 2022View details →

Supplementary Material for the Article "Field, Capital, and Habitus: The Impact of Pierre Bourdieu on Bibliometrics"

The full dataset of the review "Field, Capital, and Habitus: The Impact of Pierre Bourdieu on Bibliometrics" published in the journal Quantitive Science Studies (Appendix A), as well as the coding scheme (Appendix B), and a list of suggested readings based on the finding of the study (Appendix C).

Data for: Transboundary conservation hotspots in China and potential impacts of the Belt and Road Initiative

Aim: Biodiversity hotspots often span international borders, thus conservation efforts must as well. China is one of the most biodiverse countries and the length of its international land borders is the longest in the world; thus, there is a strong need for transboundary conservation. We identify China's transboundary conservation hotspots and analyze the potential effects of the Belt and Road Initiative (BRI) on them to provide recommendations for conservation actions. Location: China, Asia Methods: We compiled a species list of terrestrial vertebrates that span China's borders. Using their distribution, we extracted the top 30% of the area with the highest richness value weighted by Red List category and considered these transboundary hotspots for conservation priority. Then we analyzed protected area (PA) coverage and connectivity to identify conservation gaps. To measure the potential impact of the BRI, we counted the species whose distribution range is traversed by the BRI and calculated the aggregation index, proportion of natural land, and night light index along its routes. Results: We identified 1,964 terrestrial vertebrate species living in the border region. We identified four transboundary hotspots and found insufficient PA coverage and low connectivity in three of them. The BRI routes intersected all four hotspots and traversed 82.4% (1,619/1,964) of the transboundary species, half of which (918) are sensitive to the potential risks brought by the BRI. Night light index increased generally along the BRI. However, the proportion of natural land and the aggregation index near the BRI showed different trends in hotspots. Main conclusions: There is an urgent need for conservation action in China's transboundary region. The BRI should put biodiversity conservation at the core of its development strategy. Furthermore, we suggest using the planned BRI as a platform for dialogue and consultation, knowledge and data sharing, and joint planning to promote transboundary conservation.