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Figure 3 in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 3. Flow chart for extant behavioural interpolation, which enables inference of muscle-modulated behaviours in extinct animals. The certainty of behavioural inference in an extinct taxon is inversely related to the behaviour's specificity. Behaviour can be inferred by phylogenetic bracketing if similarity of muscle function is established in extant clades by kinematic and physiological considerations, and if these functions correlate with similar behaviours in the extant groups.
Figure 11. A in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 11. A, origins (dark shapes) and insertions (lighter outlined shapes) of mm. intertransversarii aponeuroses on posterior cervical vertebrae of Struthio camelus. Origins are from anterior faces of lateral tubercles, and insertions are onto posterior projections of the lateral tubercles. Arrows represent lines of action whereby insertions are drawn towards the origins to effect intervertebral lateroflexion. B, origins (dark) and insertions (lighter) of mm. inclusii on posterior cervical vertebrae of Struthio camelus. Origins are from anterior faces of the costal processes, and insertions are onto the lateral and dorsolateral tubercles. Arrows represent lines of action whereby insertions are drawn towards the origins. C, origins (dark-filled shapes) and insertions (light-filled shapes) of lateral portions of mm. intertransversarii in Caiman crocodylus. Arrows represent lines of action from origin to insertion, by which the muscles would lateroflex the anterior vertebra of each pair relative to the posterior one.
Figure 20. A in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 20. A, origin scar of m. splenius capitis from C2 of Tyrannosaurus rex (BHI 3033), in anterodorsal view. B, area of possible insertions of m. splenius capitis (medial part) on the occiput of Daspletosaurus torosus (CMN 8506; the specimen is incomplete and the image partly mirrored), with moment arms shown for dorsiflexion and lateroflexion. C, insertions of m. longus colli dorsalis/m. transversospinalis cervicis onto posterior and dorsal surfaces of epipophyses, from C2 to C5. The most prominent insertion is a posteriorly concave scar on the C2 epipophysis. D, centres of rotation (white circles) and moment arms (lines) for insertions of m. longus colli dorsalis/m. transversospinalis cervicis, on cervical vertebrae of Tyrannosaurus rex (BHI 3033). Centres of rotation are estimated to be at positions similar to those Selbie, Thomson & Richmond (1993) determined for intervertebral flexion in cats.
Figure 19. A in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 19. A, origins of m. transversospinalis capitis (C2–C9), m. complexus (C2–C5) and m. splenius capitis from C2 and possibly C3, of Tyrannosaurus rex (BHI 3033). B, rugose scarring of m. transversospinalis capitis insertion on parietals of Tyrannosaurus rex (AMNH 5029). C, insertion of m. transversospinalis capitis onto parietals of Daspletosaurus torosus (CMN 8506; the specimen is incomplete and the image partly mirrored), with moment arms for lateral and dorsiflexion. D, insertions and moment arms for m. complexus (two dorsal) and m. iliocostalis capitis (ventral) on occiput of Daspletosaurus torosus (CMN 8506; the specimen is incomplete and the image partly mirrored for clarity).
Figure 16 in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 16. Schematic diagram of major neck muscles of Tyrannosaurus rex in dorsal view. A–C represent successively deeper layers, and other conventions are as in Figure 15. M. complexus inserts dorsally on the squamosal, and m. iliocostalis capitis inserts along the ventral edge of the paroccipital process. M. longissimus capitis superficialis inserts between these on the lateral edge of the paroccipital process. In C a probable lateral part of m. spinalis capitis is signified by a '? ' .
Figure 18 in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 18. Topological appearance of (A) m. splenius capitis (medial part) and (B) m. longus colli dorsalis/ transversospinalis cervicis, on anterior vertebrae and skull of Tyrannosaurus rex skeleton (AMNH 5027). Note that the parietals are probably closer to the axial neural spine than in neutral life posture, and m. splenius capitis would be longer than shown here. C, topological appearance of m. splenius on another specimen of Tyrannosaurus rex (BHI 3033). M. complexus is also represented, and m. transversospinalis capits is depicted as though reflected back. D, E, appearance of m. longissimus capitis profundus (large anterior muscle), and cervical mm. intertransversarii (bands between transverse processes), on skeleton of Tyrannosaurus rex (AMNH 5027). A′–E′, functional inference strengths of muscles after visualization of inference space in Figure 2. A′, strength of functional inference for m. splenius capitis of tyrannosaurids, for head dorsiflexion and stabilization. The large inference space is possible by morphological and physiological bracketing between homologous muscles in birds and crocodilians. B′, strength of functional inference for m. transversospinalis cervicis of tyrannosaurids, for neck dorsiflexion. Inference strengh is particularly high for this muscle. D′, Level II′ inference for ventroflexion by m. longissimus capitis profundus. E′, inferernce for lateroflexion by mm. interntransversarii, with poor, Level III′ support from physiological data; EMG has been uninformative about mm. intertrans. lateroflexion in extant archosaurs .
Figure 23. A in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 23. A, topological appearance of m. rectus capitis ventralis (anterior muscles) and m. iliocostalis cervicis (posteroventrally originating muscles) on anterior axial skeleton of Tyrannosaurus rex (BHI 3033), ventral view. The moment arm for lateral flexion by m. iliocostalis cervicis is superimposed. B, m. r.c.v.: origins of m. rectus capitis ventralis from ventral spinous processes of Tyrannosaurus rex (BHI 3033) with arrow showing course of the muscle. m. il. cerv.: origin from ventral centra and insertions onto ventral fascia of cervical ribs of m. iliocostalis cervicis, with arrow showing course of the muscle. C, insertion of m. rectus capitis ventralis onto basioccipital of Daspletosaurus torosus (CMN 8506; the specimen is incomplete and the image partly mirrored), showing moment arms. Because the tyrannosaurid occiput slopes anteroventrally, the ventroflexion moment arm is somewhat longer than depicted in this view. D, strength of functional inference for head ventroflexion by m. rectus capitis ventralis in Tyrannosaurus rex. E, strength of functional inference for neck lateroflexion by m. iliocostalis cervicis of Tyrannosaurus rex.
Hierarchical Control for Shopping Center
<p>A diagram showing a hierarchical control approach to introduce coordination in distributed shopping center HVAC-systems.</p>
Supplementary material 3 from: Grunewald K, Schweppe-Kraft B, Syrbe R-U, Meier S, Krüger T, Schorcht M, Walz U (2020) Hierarchical classification system of Germany's ecosystems as basis for an ecosystem accounting – methods and first results. One Ecosystem 5: e50648. https://doi.org/10.3897/oneeco.5.e50648
The area and share of main ecosystem types and sub ecosystem types (ETs, see Tab. 1)) in the German land cover model (LBM-DE) for the time periods 2012, 2015 and 2018. Linear elements such as small scale structures and infrastructures from the topographic-cartographic Information system (ATKIS) were added to the land cover model.
Supplementary material 4 from: Grunewald K, Schweppe-Kraft B, Syrbe R-U, Meier S, Krüger T, Schorcht M, Walz U (2020) Hierarchical classification system of Germany's ecosystems as basis for an ecosystem accounting – methods and first results. One Ecosystem 5: e50648. https://doi.org/10.3897/oneeco.5.e50648
Tab. D: Detailed matrix of pre- and post-use of settlement and transportation areas in Germany in the period 2013-2018 in hectare per day (ha/d). (Data source: IOER)
Supplementary material 1 from: Grunewald K, Schweppe-Kraft B, Syrbe R-U, Meier S, Krüger T, Schorcht M, Walz U (2020) Hierarchical classification system of Germany's ecosystems as basis for an ecosystem accounting – methods and first results. One Ecosystem 5: e50648. https://doi.org/10.3897/oneeco.5.e50648
Proposal of a classification system for ecosystem types (ETs) in Germany, assignment to the European ecosystem types according to EUNIS and to the CLC types of the database LBM-DE
Supplementary material 2 from: Grunewald K, Schweppe-Kraft B, Syrbe R-U, Meier S, Krüger T, Schorcht M, Walz U (2020) Hierarchical classification system of Germany's ecosystems as basis for an ecosystem accounting – methods and first results. One Ecosystem 5: e50648. https://doi.org/10.3897/oneeco.5.e50648
Supplementation of ecosystem types (ETs) by more differentiated spatially and non-spatially explicit data (system of assignment of biotope and habitat types relevant for nature conservation to ETs
Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks
<ul> <li>Pollinator sharing can have negative consequences for plant fitness with the arrival of foreign (i.e. heterospecific) pollen, yet responses are often variable among species. Plant traits and relatedness of donor and recipient species have been suggested to drive the variations in plant fitness, but how they shape the structure of pollen competition networks has been overlooked at the community level.</li> <li>To understand the importance of reproductive traits and relatedness on the impacts of heterospecific pollen we conducted a controlled glasshouse experiment with an artificial co-flowering community. We performed 1800 reciprocal crosses by experimentally transferring 50% and 100% foreign pollen among 10 species belonging to three different plant families.</li> <li>We found a significant reduction in seed set with 50% foreign pollen for 67% of the crosses driven largely by recipient traits and the interaction between recipient-donor traits under specific circumstances of trait-matching. In general, species with shorter styles, smaller stigmas and lower pollen:ovule ratios were more impacted by foreign pollen. These traits and their differences among species led to a hierarchical (or transitive) structure of pollen competition with clear winners and losers. However, phylogenetic distance among recipient and donor species did not explain the effects.</li> <li> <i>Synthesis</i>: Our study shows that specific traits and trait combinations between donor and recipient species are important in determining fitness outcomes with heterospecific pollen deposition. Moreover, the differences in traits between species lead to a competitive structure with clear "winners" or "losers" species. The results of this study indicate the need to shift from pairwise to community level interactions to elucidate the mechanisms underlying foreign pollen impacts upon plant reproductive fitness.</li> </ul>
Data for "Magnetoencephalographic Signatures of Hierarchical Rule Learning in Newborns"
<p>Data uploaded here belongs to the manuscript "Magnetoencephalographic Signatures of Hierarchical Rule Learning in Newborns" (Moser, J., Schleger, F., Weiss, M., Sippel, K., Dehaene-Lambertz, G., & Preissl, H. (2020). Magnetoencephalographic signatures of hierarchical rule learning in newborns. <em>Developmental cognitive neuroscience</em>, <em>46</em>, 100871). It is processed MEG data and an R script, used for the analysis described in the manuscript. The content of the folder is further described in a README text file. For more information or additional data/code, please contact the authors. Additional code can be found on Github: https://github.com/moser297/fMEG_data_processing/tree/main/Code_DCN_2020_Neo.</p>
Hierarchically Porous Reduced Graphene Oxide Coated with Metal-Organic Framework HKUST-1 for Enhanced Hydrogen Gas Affinity
<p>Metal organic frameworks (MOFs) are crystalline porous materials with interconnected pores and have been actively explored for various gas storage, separation and conversion applications due to their structural tunability. While the micropores (<2 nm) in MOFs are essential for increased gas affinity, these small pores significantly decrease the mass transport kinetics. One way to address this challenge is to develop hierarchically porous MOFs with interconnected micro-, meso- and macropores. Whereas these MOFs can be formed by using soft/hard templates or by creating pores through post-modification, it can also be achieved by growing MOFs on structural templates such as porous carbons i.e., reduced graphene oxide. The latter strategy can enable the introduction of hierarchical porosity, while creating a synergistic effect to simultaneously improve both mechanical property and gas affinity by creating pores at the interface. In this direction, we demonstrated that the coating of HKUST-1 onto a porous reduced graphene oxide (HRGO) led to the formation of a hierarchically porous structure, namely, HKUST-1@HRGO with increased affinity towards H2 gas. While the isosteric heats of adsorption (<em>Q</em><sub>st</sub>) values for H2 were found to be 7.7, 6.9 and 6.7 kJ mol<sup>-1</sup> for HRGO, HKUST-1 and the physical mixture of HKUST-1 and HRGO, respectively, at zero coverage, that of HKUST-1@HRGO composite revealed a significant increase up to 9.26 kJ mol<sup>-1 </sup>,<sup> </sup>thus clearly demonstrating not only the synergetic effect between HKUST-1 and the reduced graphene oxide and also the critical role interfacial pores as high affinity binding sites.</p> <p> </p>
Figure 9. A in Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach
Figure 9. A, insertions of (dark grey) m. longus colli dorsalis pars cranialis onto anterior cervical epipophyses of Haliaeetus leucocephalus. B, schematic origin (light grey) of m. longus colli dorsalis pars cranialis, from cervicodorsal region of Struthio camelus. C, schematic origins (dark grey) of m. longus colli dorsalis pars cranialis from epipophyses (processes dorsales) of posterior cervicals in Struthio camelus. Slips from these origins coalasce with the main belly of the muscle, as demarcated by the light-shaded lines. The main belly of the muscle continues dorsally. D, schematic origin and insertions of m. longus colli dorsalis pars caudalis. This muscle subsystem originates from the cervicodorsal region and sends multiple bellies to insert on posterior cervical epipophyses. E, origins of m. longissimus cervicis/m interarticulares of Caiman crocodylus. The gradient-filled slips represent association of origins with the fascia surrounding the muscles. F, anteriormost insertions (dark grey) of m. longissimus cervicis/m. interarticulares, and m. transversospinalis cervicis, of Caiman crocodylus.
Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model
<p>Individual differences in male reproductive success drive genetic drift and natural selection, altering genetic variation and phenotypic trait distributions in future generations. Therefore, identifying the determinants of reproductive success is important for understanding the ecology and evolution of plants. Here, based on the spatially-explicit mating model (the neighborhood model), we develop a hierarchical probability model that links co-dominant genotypes of offspring and candidate parents with the phenotypic determinants of male reproductive success. The model accounts for pollen dispersal, genotyping errors as well as individual variation in selfing, pollen immigration, and differentiation of immigrant pollen pools. Unlike the classic neighborhood model approach, our approach is specially designed to account for excessive variation (overdispersion) in male reproductive success. Using the Bayesian framework, we implemented the estimation method that, among others, allows the selection of phenotypic variables important for male reproductive success as well as the computation of the fraction of total variance in fecundity (<i>R</i><sup>2</sup>) explained by selected variables. Computer simulations showed that our method outperforms both the classic neighborhood model and the two-step approach, where individual fecundities and the effects of phenotypic variables are estimated in separate steps. The analysis of two data examples showed that in wind-pollinated trees, male reproductive success depends on both the amount of produced pollen and the ability to pollen spread. However, despite that the tree size was positively correlated with male fecundity, it explained only a fraction of the total variance in reproductive success, indicating the presence of significant unmeasured factors. Finally, case studies highlighted the importance of accounting for pollen dispersal in the estimation of determinants of plant reproductive success.</p>
Data from: Hierarchical Bayesian model reveals the distributional shifts of Arctic marine mammals
Aim: Our aim involved developing a method to analyze spatiotemporal distributions of Arctic marine mammals (AMMs) using heterogeneous open source data, such as scientific papers and open repositories. Another aim was to quantitatively estimate the effects of environmental covariates on AMMs' distributions and to analyze whether their distributions have shifted along with environmental changes. Location: Arctic shelf area. The Kara Sea. Methods: Our literature search focused on survey data regarding polar bears (Ursus maritimus), Atlantic walruses (Odobenus rosmarus rosmarus) and ringed seals (Phoca hispida). We mapped the data on a grid and built a hierarchical Poisson point process model to analyze species' densities. The heterogeneous data lacked information on survey intensity and we could model only the relative density of each species. We explained relative densities with environmental covariates and random effects reflecting excess spatiotemporal variation and the unknown, varying sampling effort. The relative density of polar bears was explained also by the relative density of seals. Results: The most important covariates explaining AMMs' relative densities were ice concentration and distance to the coast, and regarding polar bears, also the relative density of seals. The results suggest that due to the decrease in the average ice concentration, the relative densities of polar bears and walruses slightly decreased or stayed constant during the 17-yearlong study period, whereas seals shifted their distribution from the Eastern to the Western Kara Sea. Main conclusions: Point process modelling is a robust methodology to estimate distributions from heterogeneous observations, providing spatially explicit information about ecosystems and thus serves advances for conservation efforts in the Arctic. In a simple trophic system, a distribution model of a top predator benefits from utilizing prey species' distributions compared to a solely environmental model. The decreasing ice cover seems to have led to changes in AMMs' distributions in the marginal Arctic region.
Data from: A Bayesian hierarchical approach to quantifying stakeholder attitudes toward conservation in the presence of reporting error
Stakeholder support is vital for achieving conservation success, yet there are few reliable mechanisms to monitor stakeholder attitudes towards conservation. Importantly, few approaches account for bias arising from reporting errors; that is, reporting a positive attitude towards conservation when the respondent actually does not have one (a false positive error), or not reporting a positive attitude when the respondent is positive towards conservation (a false negative error). We borrow from developments in applied conservation science to use a Bayesian hierarchical model to quantify stakeholder attitudes as the probability of having a positive attitude towards wildlife, notionally (or in abstract terms) and at localized scales. The model allows us to assess stakeholder attitudes, and factors influencing these attitudes, while accounting for false negative and false positive reporting errors. We show through simulations that this method has lower bias than naïve estimates of the proportion of respondents who are positive towards wildlife, or Likert‐scores. We demonstrate the utility of the model by applying it to questionnaire surveys on Asian elephants Elephas maximus in the Kaziranga–Karbi Anglong landscape, Northeast India. After accounting for reporting errors, we estimated the probability of being positive towards elephants notionally as 0.85; at a localized scale, however, the proportion of respondents that were positive towards elephants was 50%. In comparison, without accounting for reporting errors, the proportion of respondents professing positive attitudes towards elephants in at least one of the certain questions, was 0.69 and 0.23, notionally and at local scales, respectively. False (positive and negative) reporting probabilities were consistently non‐zero (0.22–0.68). We submit that regular and reliable assessment of stakeholder attitudes––combined with an understanding of factors contributing to variation in attitudes––can feed into participatory conservation monitoring programs, help assess the success of initiatives aimed at facilitating human behavioral change, and inform conservation decision‐making.
Data from: Key players and hierarchical organization of prairie dog social networks
The use of social network theory in evaluating animal social groups has gained traction in recent years. Despite the utility of social network analysis in describing attributes of social groups, it remains unclear how comparable this approach is to traditional behavioral observational studies. Using data on Gunnison's prairie dog (Cynomys gunnisoni) social interactions we describe social networks from three populations. We then compare those social networks to groups identified by traditional behavioral approaches and explore whether individuals group together based on similarities. The social network social groups identified by social network analysis were consistent with those identified by more traditional behavioral approaches. However, fine-grained social sub-structuring was revealed only with social network analysis. We found variation in the patterns of interactions among prairie dog social groups that was largely independent of the behavioral attributes or genetics of the individuals within those groups. We detected that some social groups include disproportionately well-connected individuals acting as hubs or bridges. This study contributes to a growing body of evidence that social networks analysis is a robust and efficient tool for examining social dynamics.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.