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154 results for “local structure”
Dimensionality reduction of local structure in glassy binary mixtures
<p>This dataset is associated with "<em>Dimensionality reduction of local structure in glassy binary mixtures</em>", by D. Coslovich, R. L. Jack, J. Paret. It includes data and workflow to allow for the replication of the analysis and figures of the manuscript.</p> <p>To reproduce the workflow and the figures, download and extract the package sprouts.tar.gz, then execute</p> <pre><code class="language-bash">./make all</code></pre> <p>This will create the figures under plots/paper and recompile project.pdf. If the workflow fails because of missing dependencies, read the project.pdf file below and check the requirements, or download the <a href="http://www.docker.com">docker</a> image sprouts-docker.tar.gz, load the image and execute the same command within the container.</p> <p><em>Make sure you have at least 20 Gb of free space on your disk if you use the package, and 22 Gb if you use the docker image.</em></p> <p>To speed up the execution of the workflow, download the data cache (cache.tar) and extract it at the root of the project folder.</p> <p>See project.pdf below for full details about the workflow.</p> <p><strong>Changelog</strong>:</p> <ul> <li>1.0.2: use more portable she-bang in scripts</li> <li>1.0.1: fix typos, remove some dead code</li> <li>1.0.0: initial submission</li> </ul>
Figures 10–17. Chrysina spp. genital structures. 10–15 in A new species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae) from the Sierra Madre Occidental of Mexico, with notes on the type locality of Chrysina adelaida (Hope, 1841)
Figures 10–17. Chrysina spp. genital structures. 10–15) Male genital capsule dorsal (d), ventral (v) and lateral (l) habitus. 10–11) C. occidentalis holotype. 10) (d). 11) (v). 12–13) C. adelaida from Veracruz, Mexico. 12) (d). 13) (v). 14) C. occidentalis holotype (l). 15) C. adelaida from Veracruz, Mexico (l). 16–17) Female genital plates. 16) C. occidentalis from Sinaloa, Mexico. 17) C. adelaida from Veracruz, Mexico.
Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 45. Scanning electron microscope (SEM) images of "Staminate structure"; Catefica locality, Portugal. a–c) Staminate structure in oblique apical (a), oblique basal (b) and lateral (c) views showing distinct stalk and head with a cluster of about 20 stamens; note bracts at the base of the structure (asterisks) and probable secretory openings in the anther tissues (arrows). Specimen, Catefica 358-S135451 (a–c). Scale bars = 600 Μm (a–c).
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. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 33. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a, c) and scanning electron microscope (SEM, b, d) images of Paisia pantoporata (a–c) and?Paisia sp. (d); Catefica locality, Portugal. a) Lateral view (volume rendering) of flower showing the carpels (c) and the fleshy tepals (t) that have a slightly bulge near the base; b) Pollen grains in situ from stamen showing scattered pores and spiny supratectal ornamentation; c) Transverse section (orthoslice xz1024) through flower showing the pentamerous organization with five tepals (green) five stamens (yellow) and five carpels (red) all on the same radii; d) Lateral view of floral structure with three free carpels borne on the swollen receptacle that has poorly defined facets at the apex indicating the former presence of perianth parts. Specimens, Catefica 49-S101214 (a, c), Catefica 50-S170188 (b), Catefica MM125-P0292 (d). Scale bars = 300 Μm (a, c, d), 6 Μm (b).
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b).
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g).
Text-fig. 6. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Epidermal-cuticular structure of upper surface of seed-bearing capsule. a–c, e–g: cuticles of upper surface of seed-bearing capsule, b – detail of (a), notice small white spot at picture center, which could be interpreted as scar of small monocellular trichome; d: conducting strand going to seed scar. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 200 µm (a, c, d, g), 100 µm (e, f). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 6. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Epidermal-cuticular structure of upper surface of seed-bearing capsule. a–c, e–g: cuticles of upper surface of seed-bearing capsule, b – detail of (a), notice small white spot at picture center, which could be interpreted as scar of small monocellular trichome; d: conducting strand going to seed scar. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 200 µm (a, c, d, g), 100 µm (e, f).
Text-fig. 5. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a–d: epidermal-cuticular structure of upper surface of seed-bearing capsule. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 100 µm (a, c, d), 50 µm (b). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 5. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a–d: epidermal-cuticular structure of upper surface of seed-bearing capsule. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 100 µm (a, c, d), 50 µm (b).
Text-fig. 9. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seed-bearing capsule. a: general morphology; b, c: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a), 100 µm (b, c). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 9. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seed-bearing capsule. a: general morphology; b, c: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a), 100 µm (b, c).
Text-fig. 4. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a: line drawing explaining female cone morphology after holotype; b: suggested reconstruction showing arrangement and vascularization of seed-bearing discs (left), and section through seed-bearing discs exhibiting seed attachment and marginal limb structure (right); c: seed scar structure (after Textfig. 3c), 1 – subepidermal and epidermal tissues under the cuticle, 2 – coaly tissues of mesophyll. Oval form at seed scar center is possible exit of conducting strand. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 cm (a, b), 100 µm (c). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 4. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a: line drawing explaining female cone morphology after holotype; b: suggested reconstruction showing arrangement and vascularization of seed-bearing discs (left), and section through seed-bearing discs exhibiting seed attachment and marginal limb structure (right); c: seed scar structure (after Textfig. 3c), 1 – subepidermal and epidermal tissues under the cuticle, 2 – coaly tissues of mesophyll. Oval form at seed scar center is possible exit of conducting strand. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 cm (a, b), 100 µm (c).
Simulation data and code used for the publication in Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes"
<p>Simulation data used in the publication Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes". The simulation data set, and the code developed to generate such data, are included. Details in the published paper </p>
Data from: Seascape genomics of red abalone: Limited range-wide population structure and evidence for local adaptation
Open the record for dataset details and reuse information.
Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
<p>Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.</p>
Sequence-structure-function relationships in class I MHC: a local frustration perspective
<p>Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, the Human Leukocyte Antigen (HLA) chain of MHC is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with pMHC in a common diagonal binding mode, and KIR-pMHC interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or Tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.</p>
Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. Part I: Adaptive local approximate models
<p>The global search stage of Crystal Structure Prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II (Habgood, M., Sugden, I. J., Kazantsev, A. V., Adjiman, C. S. & Pantelides, C. C. (2015).<em> J Chem Theory Comput</em> <strong>11</strong>, 1957-1969) program is presented, where the most efficient use of computational effort is ensured via the use of adaptive Local Approximate Model (LAM) placement. The entire search space of relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimise the computational effort expended in high energy regions whilst maximising the accuracy in low energy regions. As the size, complexity, and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule XXVI from the sixth blind test (Reilly <em>et al.</em>, (2016).<em> Acta Cryst. B, accepted</em>.), which is challenging due its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. </p>
Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants
<p><span><strong>Premise</strong>:</span><span> Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self-pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression.</span></p> <p><span><strong>Methods</strong>: </span><span>To evaluate whether relatedness decreases with local density, we analysed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m.</span></p> <p><span><strong>Results</strong>: </span><span>There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation-by-distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%.</span> <span>EEMS suggested that rocks and bushes may act as barriers to gene flow within a population.</span></p> <p><span><strong>Conclusions</strong>: </span><span>The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates, or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in <em>G. conopsea</em>.</span></p>
Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 1
<p>Model data from the numerical setup of the tidal Elbe presented in Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]</p><p>PART 1</p><p>Each file contains data for a full month, as given through the file naming convention: description.YYYYMMDD.nc4</p><p>The numerical model uses terrain-following sigma coordniates, with sigma level 0 being the bottommost layer.</p><p>Certain variables are also given in salinity class bins of dimension salt_s instead of vertical coordinates.</p><p>Explanation of each data type:</p><ul><li> 2D_elv_all: Spatially resolved simulated surface elevation from 08/2012 to 12/2013: Tidal analysis Fig. 4, Table 1 (simulated surface elevation vs. time)<ul><li>5 min snapshots</li></ul></li><li>Elbe_dia_getm_all: Diahaline analysis Fig. 8, 11: on-line GETM computation of u_dia,z^S in September 2012 and June 2013<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>Elbe_TEF_mean_all: Total Exchange Flow analysis in September 2012 and June 2013, Fig.s 7, 8<ul><li>1-hourly averages</li></ul></li><li>Mixing_mean_all: Physical and numerical Mixing from 08/2012 to 12/2013. Fig. 7, 8, 9, 10, 11<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>ST_stations: Surface elevation at given location for comparison with observational data at named station from 08/2012 to 12/2013<ul><li>5 min snapshots</li></ul></li><li>SST_stations: Salinity and temperature at given location for comparison with observational data at named station from 08/2012 to 12/2013; Fig. 3, Fig. 5, Table 2<ul><li>30-min snapshots</li></ul></li></ul><p> </p><p>[1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023:</p><p> Local mixing determines spatial structure of diahaline exchange flow in a</p><p> mesotidal estuary – a study of extreme runoff conditions.</p><p> J. Phys. Oceanogr., in press.</p>
Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 2
<p>Model data from the numerical setup of the tidal Elbe presented in Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]</p><p>PART 2</p><p>Each file contains data for a full month, as given through the file naming convention: description.YYYYMMDD.nc4</p><p>The numerical model uses terrain-following sigma coordniates, with sigma level 0 being the bottommost layer.</p><p>Certain variables are also given in salinity class bins of dimension salt_s instead of vertical coordinates.</p><p>Explanation of each data type:</p><ul><li>Mean_all: Spatially resolved, temporally varying salt distribution in the Elbe estuary: Fig. 6, 10<ul><li>1-hourly averages</li></ul></li></ul><p> </p><p>[1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023:</p><p> Local mixing determines spatial structure of diahaline exchange flow in a</p><p> mesotidal estuary – a study of extreme runoff conditions.</p><p> J. Phys. Oceanogr., in press.</p>
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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.