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Supplementary material 6 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S6. Average nucleotide diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa

Supplementary material 5 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S5. Average haplotype diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa

Supplementary material 7 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S7 – part 1. Haplotype network of the two most frequent EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa

Supplementary material 4 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S4. Average haplotype number per OTU for the four different datasets of shared OTUs. Datasets are split into EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa

Supplementary material 3 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S3. Average haplotype number per OTU for the four different datasets of shared OTUs. Values are illustrated for all sample sites including all shared OTUs

Supplementary material 2 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S2. Four different datasets including shared OTUs between the different river systems (Emscher-Ennepe-Sieg, Emscher-Ennepe, Emscher-Sieg, Sieg-Ennepe). Number of OTUs is illustrated with taxonomic assignment on order level

Supplementary material 1 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925

Figure S1. Total number of aquatic macroinvertebrate individuals per sample and season plotted against the average haplotype number per OTU. Different colours indicate the three river systems

Data from: Agroforestry coffee soils increase the insect-suppressive potential offered by entomopathogenic fungi over full-sun soils: a case proposing a "bait-survival technique"

Entomopathogenic fungi are important natural enemies of insects. However, there is little information on the insect-suppressive potential of these fungi and possible effects of farming management on this. Meanwhile, changes in natural landscapes due to agricultural intensification have caused considerable biodiversity loss and consequent decay of ecosystem services. However, the adoption of practices such as agroforestry in agroecosystems can foster abiotic and biotic conditions that conserve biodiversity, consequently restoring the provision of ecosystems services. Here, we assessed the effect of management systems (agroforestry or full-sun) on the pest-suppressive potential of entomopathogenic fungi in Brazilian coffee plantations. We used the insect-bait method coupled with survival analyses to assess the speed of kill by entomopathogenic fungi and their presence in soil samples from both farming systems. We found that insects exposed to agroforestry soils died more quickly than insects exposed to full-sun soils. Of the fungi isolated from the insect-baits, Metarhizium was found most frequently, followed by Beauveria. Meanwhile, Fusarium was frequently isolated as primary or secondary infections. We propose that the differential survival of insects is indicative of a greater suppressive potential by entomopathogenic fungi in agroforestry, and that this could be promoted by the diversified landscape, microclimatic stability and reduced soil disturbance in agroforestry systems. Furthermore, our results provide a useful demonstration of the potential use of the insect bait method to investigate pest suppressive potential through insect-bait mortality, and we term this the "bait survival technique".

opencc-by-4.0Apr 2020View details →

Cantemist corpus: gold standard of oncology clinical cases annotated with CIE-O 3 terminology

Intro: Cantemist shared task dataset (divided in train, dev1, dev2 and test). In addition, we include here the Cantemist background set. It contains the train, development and test sets of the three subtasks: cantemist-ner, cantemist-norm and cantemist-coding with Gold Standard annotations. In addition, it contains the documents of the background set, without annotations.   Please cite if you use this dataset: Miranda-Escalada, A., Farré, E., & Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings. <pre><code>@inproceedings{miranda2020named, title={Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results}, author={Miranda-Escalada, A and Farr{\'e}, E and Krallinger, M}, booktitle={Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings}, year={2020} }</code></pre>   Format: For subtasks cantemist-norm and cantemist-ner, annotations are distributed in Brat format. See <a href="https://brat.nlplab.org/standoff.html">Brat webpage</a> for more information For subtask cantemist-coding, codes are grouped in a TSV file with the following columns (this follows the format used in <a href="https://temu.bsc.es/codiesp/">CodiEsp shared task</a>):  <blockquote> filename    code </blockquote>   Shared task goal: In the three subtasks, the goal will be to predict the annotations (either the ANN files or the TSV with the codes) given only the plain text files.    Resources: <ul> <li><a href="https://temu.bsc.es/cantemist/">Web</a></li> <li><a href="http://ceur-ws.org/Vol-2664/cantemist_overview.pdf">Citation</a>: Miranda-Escalada, A., Farré, E., & Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings.</li> <li><a href="https://doi.org/10.5281/zenodo.4010899">Silver Standard corpus</a></li> <li><a href="https://doi.org/10.5281/zenodo.3878178">Annotation guidelines</a></li> <li><a href="https://www.youtube.com/playlist?list=PL5uSCzf1azhC24g5dsp5eVMp8BZFWCraX">YouTube presentations</a></li> <li><a href="https://temu.bsc.es/cantemist/?p=4606">Participant codes</a></li> </ul>   For further information, please visit <a href="https://temu.bsc.es/cantemist/">https://temu.bsc.es/cantemist/</a> or email us at encargo-pln-life@bsc.es

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

The importance of wetland margin microhabitat mosaics; the case of shorebirds and thermoregulation

<ol> <li>Wetlands, and the species that rely upon them, are under significant threat worldwide, with wetlands often being completely removed or drastically altered. Successful wetland management requires an understanding of the interactions between wetland species and the microhabitats they use. The use of microhabitats for thermoregulation in wetland species is poorly studied, though anthropogenic influence on wetlands can reduce the diversity of microhabitats and thus the thermoregulatory options for animals. At high ambient temperatures birds may use the water-logged wetland margins to help with thermoregulation, and are often observed roosting in the sitting position within this microhabitat. However, whether sitting on the wet substrate helps in thermoregulation is unknown. </li> <li>In this study, we tested whether birds selectively use microhabitats across temperatures by conducting field observations of nine species of shorebirds. We use comparative analysis to determine whether birds roost more on wet substrate in the sitting posture, i.e. 'wet-sitting', at high ambient temperatures. </li> <li>We found substrate type across the wetland margins to be important in shorebird thermoregulation, with the time spent sitting being significantly mediated by the substrate on which the bird roosted. Individuals tended to sit on bare, wet ground much more under high ambient temperatures compared with low ambient temperatures. Vegetation on the other hand was used similarly across temperatures, and likely does not provide the same thermoregulatory benefits. </li> <li>By roosting on wet substrate at high ambient temperatures, birds may increase the potential for heat dissipation across the uninsulated legs, as water-logged wetland margins are known to remain cooler than the ambient temperature or vegetated microhabitats under hot climatic conditions. </li> <li>Synthesis and applications. Wetland creation and management requires an understanding of the functional significance of such microhabitats, not only for foraging and breeding, but also for roosting. We demonstrate that managing wetland margins is likely important in minimising heat stress in birds, with our findings emphasising the importance of maintaining open spaces in habitat mosaics for birds to use for thermoregulation. The ability of wetland species to manage heat stress is becoming exceedingly important as they are threatened by both decreased wetland availability and increasing ambient temperatures under climate change.</li> </ol>

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.