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PROCRAFT Final Meeting - Case study: conservation of the Dornier 17 wreck (collaboration between institutes and volunteers) by Darren Priday, RAF Museum

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PROCRAFT Final Meeting - Choice of restoration or renovation of WWII aircraft paintwork, illustrated by two case studies Bristol Bolingbroke and Messerschmitt 163B Komet by Thilo Bürgel, National Museum of Flight

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opencc-zeroDec 2023View details →

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An inbreeding perspective on the effectiveness of wildlife population defragmentation measures: A case study on wild boar (Sus scrofa) of Veluwe, The Netherlands

Pervasive inbreeding is a major genetic threat of population fragmentation and can undermine the efficacy of population connectivity measures. Nevertheless, few studies have evaluated whether wildlife crossings can alleviate the frequency and length of genomic autozygous segments. Here, we provided a genomic inbreeding perspective on the potential effectiveness of mammal population defragmentation measures. We applied a SNP-genotyping case study on the ~2500 wild boar Sus scrofa population of Veluwe, The Netherlands, a 1000-km2 Natura 2000 protected area with many fences and roads but also, increasingly, fence openings and wildlife crossings. We combined a 20K genotyping assessment of genetic status and migration rate with a simulation that examined the potential for alleviation of isolation and inbreeding. We found that Veluwe wild boar subpopulations are significantly differentiated (FST-values of 0.02-0.07) and have low levels of gene flow. One noteworthy exception was the Central and Southeastern subpopulation, which were nearly panmictic and appeared to be effectively connected through a highway wildlife overpass. Estimated effective population sizes were at least 85 for the meta-population and ranging from 31 to 52 for the subpopulations. All subpopulations, including the two connected subpopulations, experienced substantial inbreeding, as evidenced through the occurrence of many long homozygous segments. Simulation output indicated that whereas one or few migrants per generation could undo genetic differentiation and boost effective population sizes rapidly, genomic inbreeding was only marginally reduced. The implication is that ostensibly successful connectivity restoration projects may fail to alleviate genomic breeding of fragmented mammal populations. We put forward that defragmentation projects should allow for (i) monitoring of levels of differentiation, migration and genomic inbreeding, (ii) anticipation of the inbreeding status of the meta-population, and, if inbreeding levels are high and/or haplotypes have become fixed, (iii) consideration of enhancing migration and gene flow among meta-populations, possibly through translocation.

Frictional properties of natural granite fault gouge under hydrothermal conditions: A case study of strike-slip fault from Anninghe Fault zone, southeastern Tibetan Plateau

We performed friction experiments on natural granite gouge under hydrothermal conditions to investigate roles of the Anninghe Fault (ANHF) on seismogenesis in the continental crust. In this dataset, we report processed data after correction. Detailed information about the files in the zip-files is given in the explanatory file Lei-et-al-2023-Data-Description.pdf.

opencc-zeroFeb 2024View details →

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High-precision body mass estimators for small mammals: A case study in the Mesozoic

Body mass is a pivotal quantity in palaeobiology but must be estimated from an imperfect fossil record. We analyse the precision of skeletal predictors of mammalian body mass as a mean to inform the Mesozoic mammal record, including a new eutriconodont from North America. We focus on the critical small end of the size spectrum – critical because the earliest mammals were small, because small size persisted onto the stems of the major extant radiations, and because small mammals compose a large proportion of crown diversity. Linear regressions based on extant small mammals indicate a universal correlation of body mass with observed measurements, but with clear differences in precision. Postcranial predictors outperform jaw and dental metrics, with certain femoral joint dimensions providing surprisingly precise estimations. Overall, our data indicate small-mammal evolution during the Mesozoic unfolded in patterns of underappreciated complexity. Studying these dynamics is only possible when estimating body mass within a strict, highly focused phylogenetic context. The heuristic value of the estimators we provide here are not limited to the Mesozoic but are phylogenetically justified for any small-bodied mammal regardless of age.

opencc-by-4.0Oct 2023View details →

Artifact description: CloverLeaf on Intel Multi-Core CPUs: A Case Study in Write-Allocate Evasion

In this paper we analyze the MPI-only version of the CloverLeaf code from the SPEChpc 2021 benchmark suite on recent Intel Xeon "Ice Lake" and "Sapphire Rapids" server CPUs. We observe peculiar breakdowns in performance when the number of processes is prime. Investigating this effect, we create first-principles data traffic models for each of the stencil-like hotspot loops. With application measurements and microbenchmarks to study memory data traffic behavior, we can connect the breakdowns to SpecI2M, a new write-allocate evasion feature in current Intel CPUs. For serial and full-node cases we are able to predict the memory data volume analytically with an error of a few percent. We find that if the number of processes is prime, SpecI2M fails to work properly, which we can attribute to short inner loops emerging from the one-dimensional domain decomposition in this case. We can also rule out other possible causes of the prime number effect, such as breaking layer conditions, MPI communication overhead, and load imbalance.

opencc-by-4.0Feb 2024View details →

Prospective with historical control, case-matched cohort study of the tertiary survey beneficial in critically severe trauma patients.

Raw data, Tertiary survey record form, and STROBE checklist of "Prospective with historical control, case-matched cohort study of the tertiary survey beneficial in critically severe trauma patients" study.

opencc-by-4.0Feb 2024View details →

METIS case study PSHA: openquake hdf5 output files for Conditional Spectra

This dataset (V2) contains the disaggregation results, the hdf5 files for the Conditional Spectra are in V1

Figures 1 in Biogeographical affinities and evolution of terrestrial fauna in the Qinghai-Tibetan Plateau and the Himalayas: a case study of Aphidomorpha

Figures 1. Generalized tracks and nodes based on the global distributions of aphid species in the QTPH. Generalized tracks are indicated by colored lines, and nodes are indicated with orange dots. A generalized track is a summary of replicated distribution patterns of different taxa (species); a node is a distribution area where two or more generalized tracks intersect. Generalized tracks and nodes together indicate biogeographical affinities between aphid faunas in the QTPH and other regions.

opencc-by-4.0Apr 2024View details →

Understanding the risks of co-exposures in a changing world: A case study of dual monitoring of the biotoxin domoic acid and Vibrio spp. in Pacific oyster

<div> Assessing the co-occurrence of multiple health risk factors in coastal ecosystems is challenging due to the complexity of multi-factor interactions and limited availability simultaneously collected data. Understanding co-occurrence is particularly important for risk factors that may be associated with or occur in similar environmental conditions. In marine ecosystems, the co-occurrence of harmful algal bloom toxins and bacterial pathogens within the genus Vibrio may impact both ecosystem and human health. This study examined the co-occurrence of Vibrio spp. and domoic acid (DA) produced by the harmful algae Pseudonitzschia by 1) analyzing existing California Department of Public Health monitoring data for V. parahaemolyticus and DA in oysters; 2) and conducting a one-year seasonal monitoring of these risk factors across two Southern California embayments. Existing public health monitoring efforts in the state were robust for individual risk factors; however, it was difficult to evaluate the co-occurrence of these risk factors in oysters due to low number of co-monitoring instances between 2015 and 2020. Seasonal co-monitoring of that DA and Vibrio spp. (V. vulnificus or V. parahaemolyticus) at two embayments revealed the co-occurrence of these health risk factors in 35% of sampled oysters in most seasons. Interestingly, both the overall detection frequency and co-occurrence of these risk factors was considerably less frequent in water samples. These findings may in part suggest the slow depuration of Vibrio spp. and DA in oysters as residual levels may be retained. This study expanded our understanding of the simultaneous presence of DA and Vibrio spp. in bivalves and demonstrate the feasibility of co-monitoring different risk factors from the same sample. Individual programs monitoring for different risk factors from the same sample matrix may consider combining efforts to reduce cost, streamline the process, and better understand the prevalence of co-occurring health risk factors. </div>

opencc-by-4.0Jul 2021View details →

Figure 2 in Differences in the soil seed bank of a mining area and its surroundings: a case study inserted in the Cerrado domain

Figure 2. Curves of species accumulation for the seed bank of Vazante city, northwest of the state of Minas Gerais, Brazil. A. Accumulation curve for the seed bank and confidence interval in a mining area and surrounding area separated; B. Accumulation curve for the seed bank, confidence interval and first-order Jackknife richness estimator in a mining area and surrounding area together.

opencc-by-4.0Jul 2021View details →

Figure 3 in Differences in the soil seed bank of a mining area and its surroundings: a case study inserted in the Cerrado domain

Figure 3. Two-dimensional ordination diagram based on the nonmetric multidimensional scaling (nMDS) for species density of the seed bank from a mining pit and surrounding areas in Vazante municipality, northwest of the state of Minas Gerais, Brazil.

Figure 5 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 5. Cedarosaurus site field sketch, in which the gastrolith cluster is clearly visible. Three isolated gastroliths were dispersed throughout the skeleton. Redrawn and modified from Sanders et al. (2001).

Figure 7 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 7. Plan-view map of the SI Quarry showing a scavenged juvenile Camarasaurus with vertebrate tracks, abundant theropod teeth, and gastroliths. Redrawn and modified from Jennings and Hasiotis (2006).

Figure 4. Carbonized material with a in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 4. Carbonized material with a single gastrolith from Howe Quarry. The presence of plant matter surrounding the clast is interpreted as evidence of former stomach contents. This is specimen number D18-15 in the Sauriermuseum Aathal.

Figure 3 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 3. Section of R. T. Bird's Howe Quarry map showing the Barosaurus bones (yellow; A – pubis; B – abdominal rib?) as well as the gastroliths seen in the photograph in Fig. 2. The bones of the Barosaurus individual were partially articulated. Redrawn and modified from Rice and Bierwert (1935) and Michelis (2003).

Figure 6 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 6. Distribution of bones and stones at the Diplodocus "Seismosaurus" longus locality (a) and cross section of the quarry (b). Note that bone-bearing blocks occurred below the first pebble lag and that there are two concentrations of gastroliths. A defined cluster was found in the pelvic area, whereas the majority of the stones were dispersed in the area north of the bone material. Redrawn and modified from Lucas (2000), and including information from Gillette (1994) (in a) and Schwartz and Manley (1992) (in b).

Figure 1 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 1. Studied dinosaur localities in the western USA. The surrounding line represents the extension of the Morrison Formation. Abbreviations: BCQ – Bone Cabin Quarry; CLDQ – Cleveland- Lloyd Dinosaur Quarry; DMDQ – Dry Mesa Dinosaur Quarry; DNM (CQ) – Dinosaur National Monument (Carnegie Quarry); Howe Q and HSQ – Howe Quarry and Howe Stephens Quarry; SIQ – "Something Interesting Quarry" (Camarasaurus). The red bones represent sites where gastroliths have been found in association with bones. Redrawn and modified from Dodson et al. (1980b).

Figure 2 in The rarity of gastroliths in sauropod dinosaurs - a case study in the Late Jurassic Morrison Formation, western USA

Figure 2. Photograph of gastroliths found at Howe Quarry. Next to a Barosaurus pubis (a) and an elongated bone (b), probably an abdominal rib, the cluster of 64 stones is visible. Modified from Bird (1985).