Find research datasets worth reusing

opencc-zeroNov 2020View details →

Data from: Modelling species distributions limited by geographic barriers: a case study with African and American primates

Aim: The boundaries of species distributions are often shaped by natural barriers such as mountains and rivers, but species distribution models usually fail to include these constraints. We tested several approaches that include barriers as explanatory variables in species distribution models. Location: Africa and South America. Time period: Current Major taxa studied: Primates Methods: We modelled the ranges of pairs of species separated by a river taking into account three explanatory components: the environment (ecosystems, topo-hydrography, climate, human pressure), the spatial structure shaped by history and population dynamics (using a trend-surface approach), and rivers as naturals barriers to dispersal (using a binary cis-trans variable that describes both sides of the river). To assess how the addition of a spatial structure and the barrier could improve distribution models, we used a nested approach by comparing models based on: a) the environment; b) the environment and the spatial structure; and c) the environment, the spatial structure and the river. These models were constructed using the favourability functions. Results: There was a decreased occurrence of high-favourability values in the opposite side of the rivers in models that included the spatial structure of distributions, compared to models based on environment alone. This decrease was more marked when the description of the spatial structure was made more flexible. However, model performance was significantly improved by the inclusion of cis-trans variables that identified areas on the opposite side as totally unfavourable. Main conclusions: The performance of distribution models can improve by the use of approaches that describe barriers. Although adding the location of geographic units in relation to a river appears to be the most accurate way to define the presence of a barrier, defining this variable may be challenging. A suitable alternative is to analyse the spatial structure of distributions using a flexible approach.

Clim2Power Austria-Germany Case Study

This archive contains neural-network-based forecasts of electricity generation and electricity market variables for a Germany-Austria case study conducted within the project Clim2Power. Depending on the selected variable (some time series are shorter), the folder named “C2P Hindcasts” contains forecast time series from 2010 to 2017 for 30 (February, May, August forecasts) respectively 10 (November forecasts) climate model ensemble members. The folder named “C2P Forecasts” contains forecast time series starting from February 2018 to May 2020 for 50 (February, May, August forecasts) respectively 10 (November forecasts) climate model ensemble members. Both folders are structured as follows: Subfolder names contain the respective variable name (Wind Electricity Generation, PV Electricity Generation, Electricity Load and Electricity Price/Climate Impact on Electricity Prices) and the short code “AT” for Austria, “DE” for Germany or “ATDE” for both. Within the subfolders, forecast time series are available in CSV, Feather and NetCDF file format. The digits in the single file names within the folder named “C2P Forecasts” denote the forecast start month and year.

opencc-by-4.0Nov 2020View details →

Implantation of a dual-chamber automatic cardioverter defibrillator in a patient with persistent left superior vena cava: case report and brief literature review

Video 1. Transthoracic echocardiography, parasternal long axis – dilated left ventricle with hypokinesia of ventricular walls and atrial enlargement; Video 2. Transthoracic echocardiography – apical view revealing the moderate functional mitral regurgitation; Video 3. Intraprocedural standard anteroposterior fluoroscopic view with the atrial and ventricular lead in place; Video 4. Intraprocedural fluoroscopic view (right anterior oblique projection at 30 degrees): atrial lead in the anterior RAA, ventricular lead at the apex of the right ventricle; Video 5. Venography performed by standard fluoroscopy through a catheter placed at the level of the left median cubital vein: left SVC draining in the right atrium via the coronary sinus; obstruction of the innominate vein, with no contrast flow; residual stenosis/kinking at the border between left SVC and CS; Video 6. Venography performed by standard fluoroscopy through a catheter placed at the level of the right median cubital vein: right SVC draining in the right atrium; obstruction of the innominate vein with no contrast flow.

Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents

Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location: North America Time period: Present-day, future Major taxa studied: Rodentia Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species, range-weighted), ecological (body size, diet, habitat), phylogenetic (mean, variance, and nearest-neighbor patristic distances, phylogenetic distance, genus-to-species ratio) and phyloendemism. We tested for correlations across dimensions and used spatial residual analyses to illustrate regions of pronounced diversity. We aggregated diversity hotspots in relation to land-use and climate-change predictions and recalculated metrics following extinctions of IUCN-listed imperiled species. Results: Topographically-complex western North America hosts high diversity across multiple dimensions: phyloendemism and ecological diversity exceed predictions based on taxonomic richness and phylogenetic variance patterns indicate steep gradients in phylogenetic turnover. While an aggregate diversity hotspot emerges in the west, spatial incongruence exists across diversity dimensions at the continental scale. Notably, phylogenetic metrics are uncorrelated with ecological diversity. Diversity hotspots overlap with land-use and climate change, and extinctions predicted by IUCN status are unevenly distributed across space, phylogeny, or ecological groups. Main conclusions: Comparison of taxonomic, ecological, and phylogenetic diversity patterns for North American rodents clearly shows the multifaceted nature of biodiversity. Testing for geographic patterns and (in)congruency across dimensions of diversity facilitates investigation into underlying ecological and evolutionary processes. The geographic scope of this analysis suggests that several explicit regional challenges face North American rodent fauna in the future. Simultaneous consideration of multidimensional biodiversity allows us to assess what critical functions or evolutionary history we might lose with future extinctions and maximize the potential of our conservation efforts.

Numerical model code, input files and output data for publication ``Mixing and Transformation in a Deep Western Boundary Current: a case study''

Contains numerical model data (code, input files, selected output) to supplement publication ``Mixing and Transformation in a Deep Western Boundary current'', by Spingys and co-authors. All umerical model data, including any errors, is the responsibility of Sonya Legg. This data set will allow reproduction of simulations used in the above-referenced paper.

Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods

Taxonomic identification of fossils is fundamental to a wide range of geological and biological disciplines. Many fossil groups are identified based on expert judgment, which requires extensive experience and is not always available for the specific taxonomic group at hand. Nerineoideans, a group of extinct gastropods that formed a major component of Mesozoic shallow marine environments, have distinctive internal spiral folds that form the basis for their classification at the genus level. However, their identification is often inconsistent because it is based on a set of selected characters reliant upon individual interpretation. This study shows a non-destructive and quantitative method for their identification using micro-CT and geometric morphometrics. We examined and micro-CT-scanned nerineoidean specimens from five main families that dominated Europe, Arabia and Africa during the Middle-Late Jurassic. Optimal longitudinal slices were selected from the tomographic reconstructions or from images of polished cross-sections compiled from fossil collections, published work and online databases. Internal whorl outlines were represented by thirty evenly distributed sliding semilandmarks and shape variations were studied using the Procrustes-based geometric morphometrics method. Multivariate analysis shows that Ceritellidae and Ptygmatididae are distinct families, whereas Nerinellidae, Eunerineidae and Nerineidae fall within the same shape variance and cannot be distinguished based on internal whorl outlines. The suggested method can be applied to images from various sources as well as to poorly preserved specimens. Our case study demonstrates the importance of quantitatively re-evaluating taxonomy in the fossil record, promoting the future utility of large datasets.

Data from: Designing monitoring protocols to measure population trends of threatened insects: a case study of the cryptic, flightless grasshopper Brachaspis robustus

Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting all adults and nymphs seen on a single ~1.5 km transect searched once annually. This method lacks spatial and temporal replication, both of which are essential to overcome detection errors in highly cryptic species like B. robustus. It also provides no information about changes in the grasshopper's distribution throughout its range. Here, we design and test new population density and site occupancy monitoring protocols by comparing a) comprehensive plot and transect searches at one site and b) transect searches at two sites representing two different habitats (gravel road and natural riverbed) occupied by the species across its remaining range. Using power analyses, we determined a) the number of transects, b) the number of repeated visits and c) the grasshopper demographic to count to accurately detect long term change in relative population density. To inform a monitoring protocol design to track trends in grasshopper distribution, we estimated the probability of detecting an individual with respect to a) search area, b) weather and c) the grasshopper demographic counted at each of the two sites. Density estimates from plots and transects did not differ significantly. Population density monitoring was found to be most informative when large adult females present in early summer were used to index population size. To detect a significant change in relative density with power > 0.8 at the gravel road habitat, at least seventeen spatial replicates (transects) and four temporal replicates (visits) were required. Density estimates at the natural braided river site performed poorly and likely require a much higher survey effort. Detection of grasshopper presence was highest (pg > 0.6) using a 100 m x 1 m transect at both sites in February under optimal (no cloud) conditions. At least three visits to a transect should be conducted per season for distribution monitoring. Monitoring protocols that inform the management of threatened species are crucial for better understanding and mitigation of the current global trends of insect decline. This study provides an exemplar of how appropriate monitoring protocols can be developed for threatened insect species.

The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species

DNA metabarcoding has become a powerful approach for analyzing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation, which can lead to over-splitting of species during DNA metabarcoding analyses. Here we assess the effects of intraspecific sequence variation in DNA metabarcoding, by analyzing local populations of eleven fungal species. We investigated the allelic diversity of ITS2 haplotypes using both Sanger sequencing and high throughput sequencing (HTS) coupled with error correction with the software dada2. All focal species, except one, included some level of intraspecific variation in the ITS2 region. Overall, we observed a high correspondence between haplotypes generated by Sanger sequencing and HTS, with the exception of a few additional haplotypes detected using either approach. These extra haplotypes, often occurring in low frequencies, were likely due to PCR and sequencing errors or intragenomic variation in the rDNA region. The presence of intraspecific (and possibly intragenomic) variation in ITS2 suggest that haplotypes (or ASVs) should not be used as basic units in ITS-based fungal community analyses, but an extra clustering step is needed to reach species-level resolution.

Plume spreading test case data

The plume test case output data from the models Thetis, FESOM-C and GETM are presented. Additionally, the key scripts to perform the numerical mixing analysis are provided.

Data from: A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian saber-tooth

Morphological convergence can be assessed through a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here we introduce a new method to chart patterns of convergence on three-dimensional models, deployed with the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well-known case study, the saber-tooth morphotype which has evolved independently among distinct mammalian clades, from placentals to metatherians. Although previous authors have concluded that saber-tooths kill using a stabbing 'bite' to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the saber-tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among saber-tooths than for any other taxa. We found that the morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence implies similarity in function among these phylogenetically distant species. In our view this function is most likely the killing of relatively large prey by a stabbing bite.

opennotspecifiedSep 2020View details →

FIGURE 16. Phylloicus passulatus Prather 2003, larval case. 16a–16c in Immature stages of three species and new records of five species of Phylloicus Müller (Trichoptera, Calamoceratidae) in the northern region of Brazil

FIGURE 16. Phylloicus passulatus Prather 2003, larval case. 16a–16c, ventral, right lateral and anterior, respectively (scale bar = 2 mm).

opennotspecifiedSep 2020View details →

FIGURE 4. Phylloicus amazonas Prather 2003, larval case. 4a–4c in Immature stages of three species and new records of five species of Phylloicus Müller (Trichoptera, Calamoceratidae) in the northern region of Brazil

FIGURE 4. Phylloicus amazonas Prather 2003, larval case. 4a–4c, ventral, left lateral, and anterior, respectively (scale bar = 4 mm); 4d, case partially built with plastic material (marking tape).

opencc-zeroJan 2021View details →

Data from: Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling, and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mtDNA haplotype—one that is rare in the Western Indian Ocean—thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in a sperm whale social group: 13 first-degree and 34 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e., vocal clans) is the next step in our research program to elucidate and better apprehend the complex organization of sperm whale social groups.

opennotspecifiedJan 2021View details →

FIGURES 1–5. Trichoptera larvae and linear regression. Figure 1, Ithytrichia lamellaris Eaton 1873, fifth instar larva with case. Figure 2, Hydropsyche tabacarui Botosaneanu 1960 in Tools for instar determination of European caddisfly larvae (Insecta: Trichoptera)

FIGURES 1–5. Trichoptera larvae and linear regression. Figure 1, Ithytrichia lamellaris Eaton 1873, fifth instar larva with case. Figure 2, Hydropsyche tabacarui Botosaneanu 1960, fifth instar larva, abdominal segments VI–IX (white ovals = pupal gill buds). Figure 3, Athripsodes longispinosus paleochora (Malicky 1972), fifth instar larva, head, right anterolateral (arrow = subocular ecdysial line). Figure 4, Halesus rubricollis (Pictet 1834), first instar larva, pronotum, dorsal (white numerals refer to setal positions; arrows indicate pits). Scale bars: 0.5 mm in Figs. 1 and 3, 1 mm in Fig. 2, 0.1 mm in Fig. 4. Figure 5, linear regression (with 95% confidence bands) of forewing length versus final instar head width, based on pooled data of 451 European Trichoptera species across all families, showing the regression equation, the coefficient of determination, and the probability level for the relationship.

opencc-zeroJan 2021View details →

Integrating stable isotopes, parasite and ring-reencounter data to quantify migratory connectivity - a case study with Barn Swallows breeding in Switzerland, Germany, Sweden and Finland

Ecosystems around the world are connected by seasonal migration. The migrant animals themselves are influenced by migratory connectivity through effects on the individual and the population level. Measuring migratory connectivity is notoriously difficult due to the simple requirement of data conveying information about the non-breeding distribution of many individuals from several breeding populations. Explicit integration of data derived from different methods increases the precision and the reliability of parameter estimates. We combine ring-reencounter, stable isotope and blood parasite data of Barn Swallows Hirundo rustica in a single integrated model to estimate migratory connectivity for three large scale breeding populations across a latitudinal gradient from Central Europe and Scandinavia. To this end, we integrated a non-Markovian multi-state mark-recovery model for the ring-reencounter data with normal and binomial mixture models for the stable isotope and parasite data. The integration of different data sources within a mark-recapture modelling framework enables the most precise quantification of migratory connectivity on the given broad spatial scale. The results show that northern breeding populations and Southern Africa as well as southern breeding populations and Western-Central Africa are more strongly connected through Barn Swallow migration than central European breeding populations with any of the African wintering areas. The non-breeding distribution of Barn Swallows from central European breeding populations seems to be a mixture of those populations breeding further North and South, indicating a migratory divide.

Supplementary materials for the paper "Benefit of Self-Stabilizing Protocols in Eventually Consistent Key-Value Stores: A Case Study"

Supplementary materials for the paper "Benefit of Self-Stabilizing Protocols in Eventually Consistent Key-Value Stores: A Case Study"

Criminal Cases Tel Aviv Magistrate Court 2010-2011 Public

nn

Data Show Case Study

This dataset includes trace information as well as details about the code structure for four open source projects (Chess, Gantt, iTrust, JHotDraw). Each subfolder that starts with JSON contains the following JSON files:  <ul> <li>classes.json:This file specifies the list of Java classes for each case study.</li> <li>superclasses.json: This file specifies the list of Java superclasses andn subclasses within a Java project.</li> <li>interfaces.json: This file specifies the list of Java interfaces and implementations within a Java project.</li> <li>fieldclasses.json: This file specifies the list of variables declared within a class.</li> <li>fieldmethods.json: This file specifies the list of variables used within a method.</li> <li>parameters.json: This file specifies the list of parameters and return values within a method.</li> <li>methods.json: This file specifies the list of Java methods, along with the class that each method belongs to for every system.</li> <li>methodcalls.json: This file specifies the list of method calls made within a Java project.</li> <li>requirements.json: This file specifies the list of requirements under consideration for each system.</li> <li>traces.json: This file specifies the requirement-to-method trace values for each requirement-to-method entry within the trace matrix for each system. </li> </ul> Each subfolder that starts with MYSQL contains the equivalent MYSQL scripts for the JSON files above:  <ul> <li>classes.sql</li> <li>fieldclasses.sql</li> <li>interfaces.sql</li> <li>methodcalls.sql</li> <li>methodcallsexecuted.sql</li> <li>methods.sql</li> <li>parameters.sql</li> <li>requirements.sql</li> <li>fieldmethods.sql</li> <li>superclasses.sql</li> <li>traces.sql</li> <li>tracesclasses.sql</li> </ul>

NMR spectroscopy of coin cell batteries with metal casings

Raw NMR data in Bruker format for experiments on coin cells with metal casings. Operando experiment on COTS cell: 20201112-LiAlCell3/19

Demographics of Galaxies in the Nearby Universe: A case study with AGN and post-mergers

Here I present a volume limited catalog of ~113,600 visually classified galaxies from SDSS and the NOAO legacy survey. The classifications include identifications of bars, rings, spiral arms, tidal tails, etc.  I compare my classifications to those from other crowd sourced surveys and machine learning based catalogs to verify classification accuracy.  Using this catalog, I will show results on the systematics which affect quantitative/ML classifications and implications for the Nancy Grace Roman space telescope galaxy surveys. Time permitting I will discuss (a) bar fractions in the local Universe and role of close pair interactions in triggering bars  (b) the role of mergers in triggering AGN and the frequency of dual AGN in the local Universe.