Find research datasets worth reusing

opencc-zeroSep 2020View details →

Data from: The effects of climate warming on the migratory status of early summer populations of Mythimna separata(Walker) moths: a case-study of enhanced corn damage in central-northern China, 1980 - 2016

Mythimna separata (Walker) moths captured in light-traps were monitored in Luohe, central-northern China, from 1980 to 2016. Annual average temperature recorded an increase of 0.298 oC/10 years in this region in the period. Our results indicate that a rising Apr and May avarage temprature and earlier occurrences of days recording the highest day temperature (30℃) caused an advanced peak and increasing proportion of high ovarian development levels of first generation females in earlier summers. Results using Johnson's formulation of 'oogenesis-flight syndrome' indicate that increasing sexual maturity proportion has resulted in more emigrant individuals in the local first generaton moth becoming residents, and then increased individuls repidly in the local second generation moth since 2006. Consequences of this action have a boom in corn damage since 2007 in this region. Advanced peak dates of the first and second generation moth revealed the same response to increasing average monthly temperatures in the monitoring period. Increasing temperatures, the avarage May temperature exceeds or equal to 22℃, during the early 2000's may represent a physiological threshold for M. separata development. Our results suggest that climate warming may impact M. separata migratory status and cause a problem of crop production in this region.

opencc-zeroSep 2020View details →

Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds

1. Efforts to monitor and conserve populations and ecosystems in human-dominated landscapes can benefit from an empirical social-ecological systems approach. 2. Here we illustrate how latent variable structural equation modelling of regional time series data can effectively describe interconnected drivers of population fluctuations in dynamic landscapes and can help to reveal previously unknown system drivers. 3. Using a declining farmland-dependent bird species (Ammodramus savannarum) in the eastern United States (1994-2015) as a case study, our analysis reveals how farm management decisions drive population fluctuations (R2 = 20%), while management is in turn highly influenced by climate (R2 = 23-51%), but not by regional conservation spending. 4. Synthesis and applications. Structural equation modelling revealed potential social-ecological pathways for halting regional population declines in a grassland bird, the Grasshopper Sparrow. Lower population growth rates followed years of higher hay yields (~4 percentage points per metric ton increase in hay yield) and later harvests (~2 percentage points per 10-day delay in harvest). Thus, one pathway for stabilising regional populations could involve compensating farmers for reducing hay harvests, potentially requiring a six-fold increase in current annual agri-environmental conservation spending.

opencc-by-4.0Oct 2020View details →

Incremental Development of Safety Cases: a Mapping Study

Video presentation for Research Track article "Incremental Development of Safety Cases: a Mapping Study"

opencc-by-4.0Apr 2020View details →

On the impact of release policies on bug handing activity: A case study of Eclipse

This repository contains the data used in our paper entitled ["On the impact of release policies on bug handing activity: A case study of Eclipse"] # Structure The repository contains : 1. `raw_data`: a repository containing all the raw data of our study before processing. 2. `data_processing`: a repository containing all the raw data of our study during processing. 3. `data`: a repository containing all the data of our study after all processing steps. 4. `figs`: The generated figures from the notebooks for the paper. 5. The various Jupyter notebooks containing all the scripts used to gather the data and answer each research question.

opencc-zeroOct 2020View details →

Supplementary material 1 from: Brock KC, Daehler CC (2020) Applying an invasion and risk framework to track non-native island floras: a case study of challenges and solutions in Hawai'i. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 55-79. https://doi.org/10.3897/neobiota.62.52764

Guidance on the status confidence rating and adapting a regional checklist to track invasion statuses

opencc-by-4.0Oct 2020View details →

Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation

Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation. For the model code, see https://github.com/YaleCIE/RECC-ODYM. The model results archived here were calculated by running the ODYM-RECC scripts of commit no. cb3a388 with the data in this archive.

opencc-by-4.0Nov 2020View details →

Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels

Dataset accompanying "Ryan Brate, Paul Groth and Marieke van Erp (2020) Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels. LaTeCH-CLfL 2020. Barcelona, December 2020." Abstract: Environmental factors determine the smells we perceive, but societal factors factors shape the importance, sentiment and biases we give to them. Descriptions of smells in text, or as we call them `smell experiences', offer a window into these factors, but they must first be identified. To the best of our knowledge, no tool exists to extract references to smell experiences from text. In this paper, we present two variations on a semi-supervised approach to identify smell experiences in English literature. The combined set of patterns from both implementations offer significantly better performance than a keyword-based baseline.

opencc-zeroNov 2020View details →

Data from: Exceptional preservation requires fast biodegradation: the case study of thylacocephalan specimens from La Voulte-sur-Rhône (Callovian, Jurassic, France)

Konservat-Lagerstätten are seen as snapshots of past biodiversity for a given location and time. Yet, processes leading to the exceptional morphological preservation of fossils in these deposits remain incompletely understood. This results in the deficient assessment of taphonomic biases and limits the robustness/relevance of palaeobiological reconstructions. Here, we report the mineralogical characterization of crustacean fossils preserved within carbonate-rich concretions from the Jurassic Konservat-Lagerstätte of La Voulte-sur-Rhône (Ardèche, France). The combination of SEM-EDS, TEM, synchrotron-based XRF, XRD and XANES allows identifying the mineralogical phases composing these fossils (i.e. fluorapatite, Fe-sulfides (pyrite, pyrrhotite) and Mg-calcite) and the surrounding matrix (i.e. Mg-calcite, clays and detrital silicates). Fluorapatite and pyrite (and pyrrhotite) precipitated during decay under anoxic conditions, replacing delicate organic structures and preserving anatomical details. These mineral structures were subsequently consolidated by a Mg-calcite cement. Of note, histologically similar tissues were replaced by the same mineral phases, confirming that 'fossilization [in La Voulte] occurred rapidly enough to be influenced by tissue composition'. Altogether, the present study shows that exceptional preservation requires fast biodegradation, thereby confirming recent experimental evidence.

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.

opencc-by-4.0Dec 2020View details →

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.

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.

opencc-by-4.0Dec 2020View details →

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.

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.

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.

opencc-by-4.0Jan 2021View details →

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"

opencc-by-4.0Dec 2020View details →

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>