Find research datasets worth reusing

opencc-zeroJun 2020View details →

Data from: Clinical management and mortality among COVID-19 cases in sub-Saharan Africa: a retrospective study from Burkina Faso and simulated case analysis.

Absolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been relatively low. As a result, there has been limited investigation into deceased cases in the region, as well as the impacts of different case management strategies. We detail demographic, epidemiological, and clinical information derived from publicly available information on deceased cases in SSA and, for cases in Burkina Faso, from aggregate records at the Center Hospitalier Universitaire de Tengandogo. Logistic regression was conducted on a synthetic case population to evaluate the adjusted odds of survival for patients receiving oxygen therapy or convalescent plasma, based on therapeutic effectiveness observed for other respiratory illnesses. Across SSA, deceased cases have been predominantly male and over 50 years of age. After adjustment for sex, age, and underlying conditions, the odds of mortality among cases in the synthetic population not receiving oxygen therapy was significantly higher than those receiving oxygen (OR: 2.07; 95%CI: 1.56-2.75). Cases receiving convalescent plasma had 50% reduced odds of mortality (95%CI: 0.24-0.93). Investment in sustainable oxygen therapy could reduce COVID-19 deaths in SSA. Ongoing investigation into convalescent plasma is warranted, as data on its effectiveness specifically in treating COVID-19 becomes available.

opencc-by-4.0May 2020View details →

RIBuild: Survey of historic building stock - with case studies on renovation

Database prepared in Excel including four elements, as background information for RIBuild Deliverable D1.1 about the historic building stock: Historic buildings stock energy consumption (1) Historic building stock description (2) Building construction elements (3) Case studies (4) Element (1)-(3) are referring to the historic building stock in RIBuild partner countries in general, while element (4) contains examples of carried out renovation projects, involving internal insulation of a historic building. If available, the case study sheets contain information about the floor area, present use, the building envelope (thickness, materials), renovation history, pre- and post-energy usage and renovation cost. Further, information about typical defects and the main driving forces for the renovation project, planning or design tools used, whether the goal with the renovation was achieved and the satisfaction of the users. Overview of data files to be found in 'RIBuild data WP1' as part of this dataset.

opencc-by-4.0Jun 2020View details →

RIBuild: Energy saving potential, LCA and LCC - case studies

Data set from (1) Danish, Latvian and Italian desk-top case studies on energy saving potential, including description and output from building simulation using national simulation tools, referring to RIBuild Task 5.1. (2) LCA and LCC analyses on Italian case study, referring to RIBuild Task 5.2 and 5.3. Overview of data files to be found in ’RIBuild data WP5 Case studies’ as part of this dataset. Further details to be found in RIBuild deliverable D5.1 (Task 5.1 and 5.2) and D5.2 (Task 5.3).

opencc-zeroDec 2019View details →

Characterizing uncertainty in climate impact projections: a case study with seven marine species on the North American continental shelf

Projections of climate change impacts on living resources are being conducted frequently, and the goal is often to inform policy. Species projections will be more useful if uncertainty is effectively quantified. However, few studies have comprehensively characterized the projection uncertainty arising from greenhouse gas scenarios, Earth system models, and both structural and parameter uncertainty in species distribution modeling. Here we conducted 8964 unique 21st century projections for shifts in suitable habitat for seven economically important marine species including American lobster, Pacific halibut, Pacific ocean perch, and summer flounder. For all species, both the Earth system model used to simulate future temperatures and the niche modeling approach used to represent species distributions were important sources of uncertainty, while variation associated with parameter values in niche models was minor. Greenhouse gas emissions scenario contributed to uncertainty for projections at the century scale. The characteristics of projection uncertainty differed among species and also varied spatially, which underscores the need for improved multi-model approaches with a suite of Earth system models and niche models forming the basis for uncertainty around projected impacts. Ensemble projections show the potential for major shifts in future distributions. Therefore, rigorous future projections are important for informing climate adaptation efforts.

opencc-by-4.0Mar 2020View details →

Data from: A comprehensive and cost-effective approach for investigating passive dispersal in minute invertebrates with case studies of phytophagous eriophyid mites

Filename: 1_wcm_wheat_wind_.vector.xlsx Variables: 1. Variant - experimental approach: W- wind tunnel; V - vector tunnel   2. N - population size on the source patch 3. D - number of individuals that left the source patch 4. C - population size on the target patch after several generations   Filename: 2_wcm_brome_wind_.xlsx Variables: 1. N - population size on the source patch 2. D - number of individuals that left the source patch 3. C - population size on the target patch after several generations   Filename: 3_wheat_brome_dispersal_rate.xlsx Variables: 1. Host - host plant species: Brome - smooth brome (Bromopsis inermis); Wheat - common wheat (Triticum aestivum) 2. N - population size on the source patch 3. D - number of individuals that left the source patch   Filename: 4_wcm_crm_dispersal_rate.xlsx Variables: 1. Species - eriophyid mite species: WCM - wheat curl mite;  CRM - cereal rust mite 2. N - population size on the source patch 3. D - number of individuals that left the source patch

Identifying Implicit Vulnerabilities through Personas as Goal Model: Case study model

CAIRIS model to accompany 'Identifying Implicit Vulnerabilities through Personas as Goal Model: Case study model' SECPRE 2020 paper. Instructions for importing the model package: https://cairis.readthedocs.io/en/latest/io.html#importing-models Instructions for working with user goal models: https://cairis.readthedocs.io/en/latest/usergoals.html#user-goals-and-user-goal-models

opencc-by-4.0Jun 2020View details →

Strong Scaling Tools 2 Additive manufacturing case study

All data, results, and scripts from the Al-Si-Sc additive manufacturing alloy design high-throughput case study. All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. *.zip are the specimen-specific PARAPROBE results and POS rawdata. *.pdf are the PDF reports that were created with the automation of paraprobe-autoreporter. src.zip contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only! Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe https://paraprobe-toolbox.readthedocs.org

Do dense layers of invasive plants elevate the foraging intensity of small mammals in temperate deciduous forests? A case study from Pennsylvania, USA

Monospecific stands of invasive plants can dramatically restructure habitat for fauna, thereby elevating population densities or promoting foraging of consumer species who benefit in the altered habitat. For example, dense stands of invasive plants may protect small mammals from predators, which in turn could increase foraging pressure on seeds that small mammals feed upon. We used a before-after, control-impact experimental design to test whether small mammal capture rates were higher and giving-up densities (GUDs) lower beneath dense stands of Berberis thunbergii, an invasive shrub with a rapidly expanding range throughout eastern North America. Our experimental design included three plot categories: 1) plots heavily invaded by B. thunbergii, 2) control plots lacking invasive shrub cover, and 3) invaded plots where we eradicated B. thunbergii midway through the study. Although our overall small mammal capture rate was low, small mammal captures were 65% higher in B. thunbergii invaded habitat relative to control plots and eradication lowered capture rates by 77%. GUDs were also 26% higher within B. thunbergii relative to control plots and eradication decreased GUDs by 65%. Our findings suggest that small mammals perceive dense stands of B. thunbergii as relatively safe foraging habitat. Prior surveys within our study locations revealed dramatically depressed tree seedling densities under B. thunbergii, thus invasive plants may promote intensive foraging by small mammals and reduce recruitment for species with foraged seeds or seedlings.

Anatomy, ontogeny, and evolution of the archosaurian respiratory system: a case study on Alligator mississippiensis and Struthio camelus

The avian lung is highly specialized and is both functionally and morphologically distinct from that of their closest extant relatives, the crocodilians. It is highly partitioned, with a unidirectionally ventilated and immobilized gas-exchanging lung, and fully decoupled, compliant, poorly vascularized ventilatory air-sacs. To understand the evolutionary history of the archosaurian (birds, crocodilians and their common ancestors) respiratory system, it is essential to determine which anatomical characteristics are shared between birds and crocodilians and the role these shared traits play in their respective respiratory biology. To begin to address this larger question, we examined the anatomy of the lung and bronchial tree of ten American alligators (Alligator mississippiensis) and eleven ostriches (Struthio camelus) across an ontogenetic series using traditional and micro-computed tomography (µCT), three-dimensional (3D) digital models, and morphometry. Intraspecific variation and left to right asymmetry were present in certain aspects of the bronchial tree of both taxa but was particularly evident in the cardiac (medial) region of the lungs of alligators and the caudal aspect of the bronchial tree in both species. The cross-sectional area of the primary bronchus at the level of the major secondary airways and cross-sectional area of ostia scaled either isometrically or negatively allometrically in alligators and isometrically or positively allometrically in ostriches with respect to body mass. Of fifteen lung metrics, five were significantly different between the alligator and ostrich, suggesting that these aspects of the lung are more interspecifically plastic in archosaurs. One metric, the distances between the carina and each of the major secondary airways, had minimal intraspecific or ontogenetic variation in both alligators and ostriches, and thus may be a conserved trait in both taxa. In contrast to previous descriptions, the 3D digital models and CT scan data demonstrate that the pulmonary diverticula pneumatize the axial skeleton of the ostrich directly from the gas-exchanging pulmonary tissues instead of the air sacs. Global and specific comparisons between the bronchial topography of the alligator and ostrich reveal multiple possible homologies, suggesting that certain structural aspects of the bronchial tree are likely conserved across Archosauria, and may have been present in the ancestral archosaurian lung.

opencc-by-4.0Jun 2020View details →

Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study

Online Data Files [ODFs] accompanying manuscript "Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study"

Datasets from PhD thesis: "Integrating classical and DNA-based approaches to advance the field of paleolimnology: Case studies of a warm monomictic lake"

The general objectives of my PhD were to evaluate the advantages and limitations to using DNA-based methods in paleolimnology and to evaluate the ecological trajectory of Cultus Lake, British Columbia, using both classical paleolimnological and DNA-based approaches. The datasets therein were generated for my PhD thesis. Firstly, a 36-month sediment trap time series was developed to evaluate which DNA taxa can be deposited in the sediments and potentially be used as indicator taxa in paleolimnological studies. Congruence between morphological and DNA identification in water and sediment trap samples was also assessed specifically for diatoms and crustaceans. The data generated include mass accumulation rate and carbon accumulation rate, carbon and nitrogen percentage, morphological counts for diatoms and cladocerans in the sediment traps, DNA quantity for water and sediment trap samples, metabarcoding of a fragment of the V7 region of the 18S rRNA gene. Secondly, a multi-proxy paleolimnological study was developed to evaluate the ecological changes in Cultus Lake and the potential drivers of the changes. From this study, sedimentary delta 15N, delta 13C, percentage of carbon, percentage of nitrogen, pigments were measured and diatoms and cladoceran remains were counted and identified from a sediment core collected in 2008. The data for this project are part of a publication accepted in May 2020 in Journal of Paleolimnology: Gauthier et al (In press) Ecological dynamics of a peri-urban lake: a multi-proxy paleolimnological study of Cultus Lake (British Columbia) over the past ~200 years. doi: 10.1007/s10933-020-00147-9. Thirdly, a paleo-genetic project was developed to compare the ecological changes observed with sedimentary DNA with those observed with classical paleolimnological approaches. The same fragment of the V7 region of the 18S rRNA gene was targeted, percentage of carbon and nitrogen were also measured as well as DNA quantity for all intervals subsampled in a sediment core collected in 2017. The datasets usually come with a description of the data and meaning of abbreviations whether needed. DNA datasets will be publicly released upon acceptance of the manuscripts. For more information about the projects, methods and results, please refer to my PhD thesis published at McGill University. The number in front of the name of each file represents the chapter for which the data were generated.

GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 1

This dataset contains 50 Hz GPS data to explore JAVAD and Leica receivers quality to reconstruct slant TEC. GNSS receiver is to some extent a “black box” when its data is used for ionospheric studies. The results based on Javad, Septentrio, Trimble and Leica GNSS receivers (which is placed in this data set) proved that the accuracy of the slant Total Electron Content (TEC) calculation can differ significantly if data used for its calculation is from different GNSS receiver make/type. This is because TEC measurements depend on the carrier phase tracking technique applied in a receiver. Based on this data it was found that: 1) Correlation coefficient between carrier phase noises in L1 and L2 channel outputs may be considered as an indicator showing whether the L1-aided tracking technique or independent tracking is applied. 2) The empirical model of TEC noise component was provided to determine TEC noise value in GNSS receivers of different make/type.

Data from: Phylogenomics in Cactaceae: a case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan/Sonoran Deserts

PREMISE OF THE STUDY: Although numerous phylogenetic studies have been conducted in Cactaceae, whole plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age and morphological evolution. METHODS: We developed a plastome dataset for most known diploid members of the chollas, 42 taxa, as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were referenced-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, which were used to build our plastome dataset that was analyzed using various methods. KEY RESULTS: Our plastome dataset resolved the phylogeny of the chollas, including most inter- and intraspecific relationships. Tribe Cylindropuntieae arose during the early Miocene in southern South America, ca. 18 mya, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya, and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series (e.g., spiny fruit) in Cylindropuntia are mostly homoplasious. CONCLUSIONS: This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although widespread throughout western North American deserts, the most recent common ancestor of the chollas s.l. likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, showing a strikingly similar pattern to other western North American Desert groups.

Data generated for the EDO chapter case study

This archive contains a ZIP archive, `data.zip`, that contains several directories and a `README`. Further details of this archive's contents are described in that file. The source code used to generate this data is available <a href="https://zenodo.org/record/4000316">here</a>.

The evolution of startle displays: a case study in praying mantises

Anti-predator defences are typically regarded as static signals that conceal prey or advertise their unprofitability. However, startle displays are performed by prey when attacked and can include a spectacular array of movements, colours, and sounds. Here we present the first phylogenetically-controlled comparative analyses of startle displays including behaviour, using praying mantises as a test case. For 58 species, with a dated phylogeny, we estimate the strength of phylogenetic signal in the presence and 'complexity' (number of display components) of displays and their components and test hypotheses on their evolutionary correlates including primary defence and body size. We report strong phylogenetic signal in display presence and complexity, and strong lability in behavioural, but not morphological, components. Body size correlates with display presence and complexity independently of phylogeny, but not in phylogenetically-controlled analyses. Finally, species in species-rich clades are more likely to have a display, and a more complex one, suggesting support for ecological displacement via behavioural traits. To further elucidate the conditions under which startle display evolve, future work should include quantitative descriptions of display components, habitat type, and predator communities. Understanding the evolution of startle displays enriches our overall understanding of predator-prey dynamics and provides scaffolding for the development of new theory.

opencc-zeroSep 2020View details →

Integrating functional connectivity in designing networks of protected areas under climate change: a caribou case-study

Land-use change and climate change are recognized as two main drivers of the current biodiversity decline. Protected areas help safeguard the landscape from additional anthropogenic disturbances and, when properly designed, can help species cope with climate change impacts. When designed to protect the regional biodiversity rather than to conserve focal species or landscape elements, protected areas need to cover a representative sample of the regional biodiversity and be functionally connected, facilitating individual movements among protected areas in a network to maximize their effectiveness. We developed a methodology to define effective protected areas to implement in a regional network using ecological representativeness and functional connectivity as criteria. We illustrated this methodology in the Gaspésie region of Québec, Canada. We simulated movements for the endangered Atlantic-Gaspésie caribou population (Rangifer tarandus caribou), using an individual-based model, to determine functional connectivity based on this large mammal. We created multiple protected areas network scenarios and evaluated their ecological representativeness and functional connectivity for the current and future conditions. We selected a subset of the most effective network scenarios and extracted the protected areas included in them. There was a tradeoff between ecological representativeness and functional connectivity for the created networks. Only a few protected areas among those available were repeatedly chosen in the most effective networks. Protected areas maximizing both ecological representativeness and functional connectivity represented suitable areas to implement in an effective protected areas network. These areas ensured that a representative sample of the regional biodiversity was covered by the network, as well as maximizing the movement over time between and inside the protected areas for the focal population.

opencc-by-4.0Sep 2020View details →

Expanding Search-Based Software Modularization to Enterprise-Level Projects: A Case Study at Adyen (Master's Thesis)

The zip file uploaded contains the interactive 3d graphs shown in chapter 6 in the thesis. The thesis can be found on the TU Delft repository.

opencc-zeroSep 2020View details →

Data from: Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: a case study across forest plant communities of Italy

Aim. To date, despite their great potential biogeographical regionalization models have been mostly developed on descriptive and empirical bases. This paper aims at applying the beta-diversity framework on a statistically representative data set to analytically test the consistency of the biogeographical regionalization of Italian forests. Location. Italy Taxon. Vascular plants Methods. Forest plant communities were surveyed in 804 plots made in a statistically representative sample of forest communities, made by 201 sites of Italian forests across the three biogeographical regions of the country: Alpine, Continental, and Mediterranean. We conducted an ordination analysis and an analysis of beta diversity, decomposing it into its turnover and nestedness components. Results. Our results provide only partial support to the consistency of the biogeographical regionalization of Italy. While the differences in forest plant communities support the distinction between the Alpine and the other two regions, differences between Continental and Mediterranean regions had lower statistical support. Pairwise beta-diversity and its turnover component are higher between- than within biogeographical regions. This suggests that different regional species pools contribute to assembly of local communities and that spatial distance between-regions has a stronger effect than that within-regions. Main conclusions. Our findings confirm a biogeographical structure of the species pools that is captured by the biogeographical regionalization. However, non-significant differences between the Mediterranean and Continental biogeographical regions suggest that this biogeographical regionalization is not consistent for forest plant communities. Our results demonstrate that an analytical evaluation of species composition differences among regions using beta-diversity analysis is a promising approach for testing the consistency of biogeographical regionalization models. This approach is recommended to provide support to the biogeographic regionalization used in some environmental conservation polices adopted by EU.

opencc-zeroSep 2020View details →

Data from: Weighing homoplasy against alternative scenarios with the help of macroevolutionary modeling: a case study on limb bones of fossorial sciuromorph rodents

Homoplasy is a strong indicator of a phenotypic trait's adaptive significance when it can be linked to a similar function. We assessed homoplasy in functionally relevant scapular and femoral traits of Marmotini and Xerini, two sciuromorph rodent clades that independently acquired a fossorial lifestyle from an arboreal ancestor. We studied 125 species in the scapular dataset and 123 species in the femoral dataset. Pairwise evolutionary model comparison was used to evaluate whether homoplasy of trait optima is more likely than other plausible scenarios. The most likely trend of trait evolution among all traits was assessed via likelihood scoring of all considered models. The homoplasy hypothesis could never be confirmed as the single most likely model. Regarding likelihood scoring, scapular traits most frequently did not differ among Marmotini, Xerini, and arboreal species. For the majority of femoral traits, results indicate that Marmotini, but not Xerini, evolved away from the ancestral arboreal condition. We conclude on the basis of the scapular results that the forelimbs of fossorial and arboreal sciuromorphs share mostly similar functional demands, whereas the results on the femur indicate that the hind limb morphology is less constraint, perhaps depending on the specific fossorial habitat.