Find research datasets worth reusing

opencc-by-4.0Aug 2022View details →

Arbitrary-shape dielectric particles interacting in the linearized Poisson-Boltzmann framework: an analytical treatment

h_kmlsn.mat -- the coefficients hkmls,n calculated for n_max<=50: one has hkmls,n = hkmlsn(k+1,m+1,l+1,s+1,n+1), where hkmlsn is a 5D array contained in h_kmlsn.mat (note that MATLAB indices must start from 1, while mathematically indices k, m, l, s, and n are >=0). b_nml_approx.m -- it approximates $b_{nml}(\tilde r,\tilde R)$ with a given parameter n_max; derivative_b_nml_approx.m -- it approximates the derivative of $b_{nml}(\tilde r,\tilde R)$ with respect to $\tilde r$ with a given parameter n_max; linear_system_two_bodies_direct_backslash.m -- a simple example of forming the global linear system (14) and solving it directly (without regularization) using the MATLAB "mldivide" (or backslash) operation GSK3beta.zip -- zipped directory with DelPhi files related to Sec. 5.1.3 (see ReadmeGSK3beta.txt); Arginine-Glutamate -- zipped directory with DelPhi files related to Sec. 5.1.4 (see ReadmeARGGlu.txt)

Data resources for: "How career hubs shape the global corporate elite"

Here you find data resources for the article: "How career hubs shape the global corporate elite" published in Global Networks. The resources contain a merge list of IDs for firms in Boardex and links to WikiData. Data was collected in 2019. Furthermore there is R code for the variant of career networks used in the article.

opencc-by-4.0Nov 2022View details →

Bayesian Surprise Shapes Neural Responses in Somatosensory Cortical Circuit

Numerous psychophysical studies demonstrate that Bayesian inference governs sensory decision-making, however the specific neural circuitry underlying this probabilistic mechanism remains unknown. We record extracellular neural activity along the somatosensory pathway of mice while delivering sensory stimulation paradigms designed to isolate the response to the surprise generated by Bayesian inference. Our results demonstrate that laminar cortical circuits in early sensory areas encode Bayesian surprise. Systematic sensitivity to surprise is not identified in the somatosensory thalamus, rather emerging in the primary (S1) and secondary (S2) somatosensory cortices. Multiunit spiking activity and evoked potentials in layer 6 of these regions exhibit the highest sensitivity to surprise. Gamma power in S1 layer 2/3 exhibits an NMDAR-dependent scaling with surprise, as does alpha power in layers 2/3 and 6 of S2. These results demonstrate a precise spatiotemporal neural representation of Bayesian surprise and suggest that Bayesian inference is a fundamental component of cortical proc

opencc-zeroDec 2022View details →

Ecological signal in the size and shape of marine amniote teeth – 3D models and landmarks

Amniotes have been a major component of marine trophic chains from the beginning of the Triassic to present day, with hundreds of species. However, inferences of their (palaeo)ecology have mostly been qualitative, making it difficult to track how dietary niches have changed through time and across clades. Here, we tackle this issue by applying a novel geometric morphometric protocol to 3D models of tooth crowns across a wide range of raptorial marine amniotes. Our results highlight the phenomenon of dental simplification and widespread convergence in marine amniotes, implying strong functional constraints which limit the range of tooth crown morphologies. Importantly, we quantitatively demonstrate that tooth crown form (shape plus size) is strongly associated with diet, whereas crown surface complexity is not. The maximal range of tooth shapes in both mammals and reptiles is seen in medium-sized taxa; large crowns are simple and restricted to a fraction of the morphospace. We recognise four principle raptorial guilds within toothed marine amniotes (durophages, generalists, meat cutters, and flesh piercers). Moreover, even though all these feeding guilds have been convergently colonised over the last 200 million years, a series of dental morphologies are unique to the Mesozoic period, probably reflecting a distinct ecosystem structure.

Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 43. Synchrotron radiation X-ray tomographic microscopy SRXTM images of "Tricarpellate flower sp. 2"; Catefica locality, Portugal. a) Lateral view of floral structure (volume rendering) showing the apical projection of the carpels and the semiinferior organization; b) Apical view of floral structure (volume rendering) showing the triangular shape of the hypanthial rim, the tricarpellate ovary with a single apical style; note that one locule is fully developed while the other two are collapsed; note also slits of unknown nature in the corners of the triangular hypanthial rim (arrows); c) Transverse section (orthoslice xy0712) close to the floral apex showing the locule of the one fully developed carpel with ovules borne along ventral placentae; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; d) Longitudinal section (orthoslice xz0858) through the locule of the one fully developed carpel showing the semi-inferior organization and ovules arranged along the full length of the carpel; note amorphous substance (asterisk) associated with the developing ovules that fills part of the locule space; e) Tangential longitudinal section (orthoslice yz1019) through the one fully developed locule, showing the densely packed ovules and the amorphous substance (asterisk) with which they are associated. Specimen, Catefica 50-S174901 (a–e). Scale bars = 300 Μm (a–e).

Text-fig. 21. Scanning electron microscope (SEM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting structure in lateral view showing numerous small, helically arranged wedge-shaped fruitlets each with a slightly differentiated apical stigmatic region (st); no bracts or scars from bracts, perianth or stamens were observed associated with the entire structure or with individual carpels; b) Apical portions of fruitlets showing differentiation of the stigmatic region (st); c) Detail of apical portion of fruitlet showing slightly raised stigmatic region (st) and possible ventral suture. Specimen, Catefica 49-S115851 (holotype, a–c). Scale bars = 300 Μm (a, b), 100 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 21. Scanning electron microscope (SEM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting structure in lateral view showing numerous small, helically arranged wedge-shaped fruitlets each with a slightly differentiated apical stigmatic region (st); no bracts or scars from bracts, perianth or stamens were observed associated with the entire structure or with individual carpels; b) Apical portions of fruitlets showing differentiation of the stigmatic region (st); c) Detail of apical portion of fruitlet showing slightly raised stigmatic region (st) and possible ventral suture. Specimen, Catefica 49-S115851 (holotype, a–c). Scale bars = 300 Μm (a, b), 100 Μm (c).

Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).

opencc-by-4.0Jan 2023View details →

Dataset for manuscript "Responses to single and multiple temperature-, medium-, and pH-stimuli triggering reversible shape shifts in hydrogel actuators"

The dataset includes data for the article "Responses to single and multiple temperature-, medium-, and pH-stimuli triggering reversible shape shifts in hydrogel actuators", https://doi.org/10.1016/j.matdes.2022.111511

opencc-zeroJan 2023View details →

Masting is shaped by tree-level attributes and stand structure, more than climate, in a Rocky Mountain conifer species

Many tree species mast, meaning seed production is highly variable from year to year and synchronous within a stand, but this phenomenon remains poorly understood. To better understand how a changing climate, altered disturbance regimes, or novel management strategies might affect future seed production, we quantified the joint influence of both biotic (tree size, age, and neighborhood competition) and abiotic factors (climate and weather) on seed production in a widespread conifer species, Rocky Mountain ponderosa pine (Pinus ponderosa var. scopulorum). We reconstructed individual-level annual cone production across a large portion of this species' range using the cone abscission scar method, and mixed models were used to test hypotheses related to the causes and drivers of masting in this species. Our results suggest that masting in ponderosa pine is a process shaped at the individual-level, and this leads to high, local-scale variation in annual cone production. The effects of weather were strongest at climatically marginal sites, but overall, the joint effects of weather and climate only weakly described individual-level patterns of annual cone production in ponderosa pine (R2m = 1.6%, R2c = 30.1%). Rather, we found that masting was strongly influenced by tree- and stand-level factors such as diameter, age, and local neighborhood density, all of which were associated with the mean, interannual variability, and between-tree synchrony of cone production at the individual-level. Larger and older trees produced more cones, more frequently, and with less synchrony than smaller and younger trees. Open-grown trees experiencing lower levels of neighborhood competition also produced more cones with less interannual variability, but with higher between-tree synchrony. Because tree- and stand-level traits appear to regulate seed production more strongly than climate or weather in this species, management interventions targeting these factors could be powerful tools to manage future tree recruitment. Thus, current efforts to reduce stand density and conserve large trees in some ponderosa pine forests may enhance tree-level seed production and reduce variability in seed crops among years.

opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

opencc-by-4.0Jan 2023View details →

Compact metasurface-based optical pulse-shaping device

Dataset of the publication “Compact metasurface-based optical pulse-shaping device“ by René Geromel, Philip Georgi, Maximilian Protte, Shiwei Lei, Tim Bartley, Lingling Huang, and Thomas Zentgraf.  The provided data includes all the measured SHG-FROG traces at all compressor positions (SCMP) that are provided in the publication. The columns correspond to the time delay and the rows to the wavelengths. More information regarding the specific measurements can be found in the beginning of each file. A reference file containing the detected/resolved wavelength points from the used spectrometer is included in “wavelength_reference”. Besides this, the phase information of the different MS2 designs along the x-axis in steps of 300 nm (periodicity of the unit cell) is documented. The plotted data from Fig. 4 and 5 of the paper can be found in the “dispersion_data” and “double_pulse_temporal_data” file.

opencc-by-4.0Feb 2022View details →

Automatically Extracted SHACL Shapes for WikiData, DBpedia, YAGO-4, and LUBM & Associated Coverage Statistics

The uploaded datasets contain automatically extracted SHACL shapes for the following datasets: <ul> <li>WikiData (the truthy dump from September 2021 filtered by removing non-English strings) [1]</li> <li>DBpedia [2]</li> <li>YAGO-4 [3] </li> <li>LUBM (scale factor 500) [4]</li> </ul> The validating shapes for these datasets are generated by a program that parses the corresponding RDF files (in `.nt` format). The extracted shapes encode various SHACL constraints, e.g., sh:minCount, sh:path, sh:class, sh:datatype etc. For each shape we encode coverage in terms of number of entities satisfying such shape, this information is encoded using the <a href="http://vocab.deri.ie/void#entities">void:entities</a> predicate.  We have provided as executable Jar file the program we developed to extract these SHACL shapes. More details about the datasets used to extract these shapes and how to run the Jar are available on our GitHub repository <a href="https://github.com/dkw-aau/qse">https://github.com/dkw-aau/qse</a>. Read more about our Quality Shapes Extraction (QSE) tool on our website <a href="https://relweb.cs.aau.dk/qse/">https://relweb.cs.aau.dk/qse/</a> [1] Vrandečić, Denny, and Markus Krötzsch. "Wikidata: a free collaborative knowledgebase." Communications of the ACM 57.10 (2014): 78-85. [2] Auer, Sören, et al. "Dbpedia: A nucleus for a web of open data." The semantic web. Springer, Berlin, Heidelberg, 2007. 722-735. [3] Pellissier Tanon, Thomas, Gerhard Weikum, and Fabian Suchanek. "Yago 4: A reason-able knowledge base." European Semantic Web Conference. Springer, Cham, 2020. [4] Guo, Yuanbo, Zhengxiang Pan, and Jeff Heflin. "LUBM: A benchmark for OWL knowledge base systems." Journal of Web Semantics 3.2-3 (2005): 158-182.

opencc-zeroFeb 2023View details →

Data for: Stratification and recovery time jointly shape ant functional re-assembly in a Neotropical forest

Microhabitat differentiation of species communities such as vertical stratification in tropical forests contributes to species coexistence and thus biodiversity. However, little is known about how the extent of stratification changes during forest recovery and influences community reassembly. Environmental filtering determines community reassembly in time (succession) and in space (stratification), hence functional and phylogenetic composition of species communities are highly dynamic. It is poorly understood if and how these two concurrent filters – forest recovery and stratification – interact. In a tropical forest chronosequence in Ecuador spanning 34 years of natural recovery, we investigated the recovery trajectory of ant communities in three overlapping strata (ground, leaf litter, lower tree trunk) by quantifying 13 traits, as well as the functional and phylogenetic diversity of the ants. We expected that functional and phylogenetic diversity increase with recovery time and that each ant community within each stratum shows a distinct functional reassembly. We predicted that traits related to ant diet show divergent trajectories reflecting an increase in niche differentiation with recovery time. On the other hand, traits related to the abiotic environment were predicted to show convergent trajectories due to a more similar microclimate across strata with increasing recovery age. Most of the functional traits and the phylogenetic diversity of the ants were clearly stratified, confirming previous findings. However, neither functional nor phylogenetic diversity increased with recovery time. Community-weighted trait means had complex relationships to recovery time and the majority were shaped by a statistical interaction between recovery time and stratum, confirming our expectations. However, most trait trajectories converged among strata with increasing recovery time regardless of whether they were related to ant diet or environmental conditions. We confirm the hypothesized interaction among environmental filters during the functional reassembly in tropical forests. Communities in individual strata respond differently to recovery, and possible filter mechanisms likely arise from both abiotic (e.g., microclimate) and biotic (e.g., diet) conditions. Since vertical stratification is prevalent across animal and plant taxa, our results highlight the importance of stratum-specific analysis in dynamic ecosystems and may generalize beyond ants.

Fig. 19 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 19. Lacronia tenuis (Roewer, 1917) comb. nov., ♂ (MNRJ 260). A. Habitus, dorsal view. B. Ocularium, frontal view. C. Armature of mesotergum area III, posterior view. D. Habitus, lateral view. E. Left Fe–Ti III, proventral view. F. Right Fe–Ti IV, dorsal view. G. Same, prolateral view. H. Same, ventral view. I. Same, retro-lateral view. J. Right Mt–Ta IV, retro-lateral view. Scale bars: A, D–J = 3 mm; B–C = 1 mm.

Fig. 14 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 14. South America, showing the distribution of the Lacronia nigra (B. Soares, 1942) comb. nov. non-type specimens (as white circles). The legend refers to the type localities of Discocyrtus niger B. Soares, 1942 (Piraí) and Discocyrtus rarus B. Soares, 1944 (Alto da Serra). The area shaded in magenta represents Chile, the type locality of Discocyrtus fazi Piza, 1942.

Fig. 15. Lacronia ricardoi Kury, 2003 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 15. Lacronia ricardoi Kury, 2003 (MZSP 21373), specimens in alcohol. A–C. Holotype, ♂ (MZSP 21373). A. Habitus, dorsal view. B. Same, lateral view. C. Same, ventral view. D–F. Paratype, ♀ (MZSP 10589). D. Habitus, dorsal view. E. Same, lateral view. F. Same, ventral view. Scale bars = 1 mm.

Fig. 18 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 18. Lacronia serripes (Mello-Leitão, 1923), ♂ (MNRJ 9973), penis, distal part. A. Dorsal view. B. Right lateral view. C. Ventral view. D. Left lateral view. Scale bars = 100 μm.

Fig. 13 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 13. Lacronia nigra (B. Soares, 1942) comb. nov., ♂ (MNRJ 9207ꜝ), penis, distal part. A. Dorsal view. B. Lateral view. C. Ventral view. Scale bars = 20 μm.

Fig. 10. Lacronia spp. A. L. camboriu Kury, 2003 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 10. Lacronia spp. A. L. camboriu Kury, 2003, ♂, holotype (MNRJ 4956ꜝ), specimen in alcohol, from Brazil, Santa Catarina, Balneário Camboriú. B. L. ceci Kury & Orrico, 2006, ♂, specimen in vivo, from Brazil, Rio de Janeiro, Teresópolis. Photographs by Adriano Kury (A) and Glauco Machado (B).

Fig. 9 in Between areolated and band-shaped spots: a revision of Lacronia Strand, 1942 (Opiliones, Gonyleptidae)

Fig. 9. Lacronia spp., female specimens, dorsal habitus. A. L. boraceae (B. Soares, 1942) comb. nov., holotype (MZSP 114ꜝ), schematic illustration. B. L. nigra (Mello-Leitão, 1923) comb. nov., holotype of Discocyrtus fazi Piza, 1942 (MZSP 1549ꜝ), schematic illustration. C. L. serripes Mello-Leitão, 1923 (MZSP 9973). Scale bars = 3 mm.