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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. 37. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 1"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b–d) Pollen grains from stamen fragment in equatorial view showing the long colpi and well-developed, heterobrochate reticulum with very distinct large and small lumina; e) Detail of pollen wall showing orbicules with irregular projections; f) Detail of pollen wall showing smooth muri supported by short, densely spaced columellae. Specimen, Catefica 50-S170419 (a–f). Scale bars = 600 Μm (a), 6 Μm (b–d), 1.5 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 37. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 1"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b–d) Pollen grains from stamen fragment in equatorial view showing the long colpi and well-developed, heterobrochate reticulum with very distinct large and small lumina; e) Detail of pollen wall showing orbicules with irregular projections; f) Detail of pollen wall showing smooth muri supported by short, densely spaced columellae. Specimen, Catefica 50-S170419 (a–f). Scale bars = 600 Μm (a), 6 Μm (b–d), 1.5 Μm (e, f).
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d).
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g).
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d).
Developing elastic mechanisms: Ultrafast motion and cavitation emerge at the millimeter scale in juvenile snapping shrimp
<p>Organisms such as jumping froghopper insects and punching mantis shrimp use spring-based propulsion to achieve fast motion. Studies of elastic mechanisms primarily focus on fully developed and functional mechanisms in adult organisms. However, the ontogeny and development of these mechanisms can provide important insights into lower size limits of spring-based propulsion, the ecological or behavioral relevance of ultrafast movement, and the scaling of ultrafast movement. Here we examine the development of the spring-latch mechanism in the big claw snapping shrimp, <em>Alpheus</em> <em>heterochaelis</em> (Alpheidae). Adult snapping shrimp use an enlarged claw to produce high-speed strikes that generate cavitation bubbles. However, until now, it was unclear when the elastic mechanism emerges during development and whether juvenile snapping shrimp can generate cavitation at this size. We reared <em>A</em>. <em>heterochaelis</em> from eggs, through their larval and postlarval stages. Starting one month after hatching, the snapping shrimp snapping claw gradually developed a spring-actuated mechanism and began snapping. We used high-speed videography (300,000 frames s<sup>-1</sup>) to measure juvenile snaps. We discovered that juvenile snapping shrimp generate the highest recorded accelerations (5.8x10<sup>5</sup> ± 3.3x10<sup>5</sup> m s<sup>-2</sup>) for repeated use and underwater motion and are capable of producing cavitation at the millimeter scale. The angular velocity of snaps did not change as juveniles grew; however, juvenile snapping shrimp with larger claws produced faster linear speeds and generated larger, longer-lasting cavitation bubbles. These findings establish the development of the elastic mechanism and cavitation in snapping shrimp and provide insights into early life-history transitions in spring-actuated mechanisms.</p>
Supporting data for the publication "Emission ensemble approach to improve the development of multi-scale emission inventories"
<p>This dataset includes the source IDL code as well as the three emission inventory aggregated emission datasets necessary to perform the analysis presented in the publication: "Emission ensemble approach to improve the development of multi-scale emission inventories (GMD)"</p>
Figure S2 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S2. Snake genome features, related to Figure 2 (A) Evolution of chromosomes in snakes. In total, 23 proto-chromosomes of Serpentes were reconstructed using four lizards as outgroup. (B) Circos plots showing conserved synteny between the hypothesized Serpentes ancestor: Serpentes (red) and Hong Kong dwarf snake (Csep-blue). (C) Snake body lengths were significantly negatively correlated with the genome evolutionary rate (correlation coefficient = 0.50, p value = 0.011). (D) Length distribution of snake ancestor gain and lost genome segments. Length distribution of snake ancestor unique genome segments (left). Length distribution of snake ancestor lost genome segments (right).
Figure S3 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S3. Snake-specific genome structural variations (SSSVs), snake-diverged conserved non-coding elements (SD-CNEs that were diverged in snakes but were still conserved in the outgroup) (SD-CNEs), and orthologous genes used for evolutionary analysis, related to Figure 3 and STAR Methods (A) SSSVs distribution in different genome regions. (B) Genomic reads coverage of the snake-specific lost gene GHRL across four lizards (green anole [Acar], Anan's rock agama [Lsac], Komodo dragon [Vkom],and viviparous lizard [Zviv]), and 14 newly sequenced snakes. (C) Z-score cut off of SD-CNEs. (D) The enriched MGI terms that related to snake phenotypes for genes with SD-CNE (adjusted p value <0.05). SD-CNEs (dots) are located around the transcription start site of the genes enriched in eye, eyelid, ear, lung, mandible, maxillary, sternum, and tooth development-related terms. (E) Enriched GO terms (adjusted p value <0.05) for the newly evolved coding genes in snakes. Those related to dietary excess, protein digestion, and olfactory receptor activity were colored in red, blue, and brown, respectively. (F) Enriched GO terms (adjusted p value <0.05) for snake-specific coding genes that were lost. Red, blue, orange, and green were used to indicate the terms involved in vision, lens development, appetite, and bile acid biosynthetic process, respectively. (G) SSSV deletion in the potential regulatory region of RP1. (H) Counts of orthologous genes used for evolutionary analysis among 27 selected species.
Figure 3 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 3. Genetic basis of skeletal system evolution and organ adaptation in snakes PSGs, REGs, WGCNA hub genes, lost genes, SSSV-related genes, newly evolved genes, and SD-CNE-associated genes are marked in different colors and are represented by rectangles. (A) Renewal of genomic elements contributing to snake skull development and digestion. Related genes are shown in their corresponding regions. (B) The evolution of genomic elements has potentially facilitated the evolution of the elongated body plan of snakes. (C) The evolution of genes related to lung development and function. The heatmap shows the expression levels of WGCNA hub genes, PSGs, and SSSV-related genes in green anole (Acar), keeled slug snake (Pber), and many-banded krait (Bmul) (The ''_numbers'' represents the different copies of a multi-copy gene). (D) Whole-body X-ray images and relative lengths of the fourth forelimb phalanx and third hindlimb phalanx of wild and PTCH1-mutated mice (eight samples per group, the significance is indicated as *p <0.05). Mean ± SD is shown by error bar. See also Figure S4 and Table S3.
Figure S1 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S1. Phylogenetic and divergent time tree of snakes, related to Figure 1 (A) Phylogenetic tree distributions of selected snake species, topology inferred from a previous study.173 (B) Maximum likelihood (ML) phylogenetic tree inferred from the 31-taxon whole-genome alignments. Ultrafast bootstraps were repeated 3,000 times, with NNI UFBoot tree optimization and SH-like approximate likelihood ratio test (SH-aLRT) performed. SH-aLRT support rate/ultrafast bootstrap support rate is indicated at each node. (C) Inferred ML phylogenetic tree using orthologous genes. 1,980 1:1 orthologous genes were concatenated to a super gene sequence for constructing the ML phylogenetic tree using IQ-TREE. 10,000 ultrafast bootstraps were carried out and the two support rates were marked at each node. (D) ML phylogenetic tree inferred from 4d sites. 4d sites were extracted from the orthologous genes and taken as input for IQ-TREE to infer the ML phylogenetic tree. The two supports were computed by 10,000 ultrafast bootstraps and SH-aLRT. (E) Inferred ML phylogenetic tree of conserved non-coding elements (CNEs). All CNEs were identified and concatenated into a single sequence for the ML phylogenetic tree inferred using 5,000 ultrafast bootstraps and SH-aLRT. (F) Coalescent phylogenetic tree inferred from 51,302 1-kb orthologous genomic segments using ASTRAL-III. (G) Coalescent phylogenetic tree inferred from 1,980 1:1 orthologous genes using ASTRAL-III. The poorly supported nodes are indicated in red. (H) DicoVista gene tree topologies frequency analysis. The frequency of three topologies (t1–t3) is shown, and the red is the main topology. The divergence time (million years ago [mya]) of the species is estimated using r8s and the incongruent clades are in red. (I) Divergence time of the 31 species. r8s estimated divergence time using the whole-genome alignments.The estimated divergence time (million years ago [mya]) is labeled on each node and 6 calibrating nodes used are marked. (J) MCMCTree estimated divergence time of the 31 species using 4d sites. Six calibrating nodes used are marked and the estimated divergence time represented in million years is labeled.
Figure 5 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 5. Evolution of blind and infrared-sensitive snakes (A) Specialized traits of blind snakes. (B) Gene regression underlies eye degeneration in blind snakes. Lost genes are shown in green. Heatmap showing the significant down-regulation of the expression of genes in blind snake eyes (QN, quantile normalized). (C) BSD-CNE-associated genes enriched in odontogenesis and bone-development-related GO terms. (D) Amino acids sequences alignment (left) and enzymatic activity (right) of CHIA. The amino acids in red are positively selected sites in blind snakes. The error bar represents mean ± SD of enzymatic activity. The enzymatic activity is significantly higher in Diard's blind snake (Student's t-test p value = 8.78e-09). (E) Infrared sensing-related genes in infrared-sensitive snakes. PSGs, REGs, and variation-shared genes are indicated in purple, blue, and red, respectively. Average expression levels (represented by FPKM) of these genes in seven tissues of the brown-spotted pitviper are shown. See also Figure S5 and Tables S4 and S5.
Figure 4 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 4. Genome features associated with snake-specific sense organ evolution, highlighting PSGs, REGs, newly evolved genes, SD-CNEassociated genes, lost genes, and SSSV-associated genes (A) Lost and highly expressed genes in snake eyes. Diagram of the snake eye showing lost genes in blue. Heatmap of highly expressed genes (QN, quantile normalized). (B) Diagram of the snake inner ear. Twelve SD-CNE-associated genes and four SSSV-associated genes are involved in ear development. Expression levels (scaled fragments per kilobase per million mapped reads [FPKM]) of sound perception-related PSGs and REGs in 10 keeled slug snake (Pber) tissues are shown in circles. Circle size is positively correlated to the expression level. (C) Diagram of the taste transduction process. Solid lines indicate direct interactions, and dotted lines indicate indirect interactions. See also Table S3.
Figure 1 in Large-scale snake genome analyses provide insights into vertebrate development
Figure 1. Phylogeny of snakes Maximum-likelihood phylogenetic tree inferred from whole-genome sequences of 31 species. Divergence times of all nodes were estimated by r8s with whole-genome sequences using six calibration points (Figures S1I and S1J). All genomes generated in this study are in red. Maps were taken from those in a previous study.24
Figure S5 in Large-scale snake genome analyses provide insights into vertebrate development
Figure S5. Genome evolution of snake sensory system, related to Figures 4 and 5 (A) Expression patterns of genes associated with eye development in human embryos at different embryonic stages (4.7–8 weeks post conception [wpc]) and red cornsnake embryos at 10, 30, and 50 days post oviposition (dpo). (B) KMT2C specific amino acids residue lost in snakes and its associated snakes divergent CNE (SD-CNE). The black line portrays gene structure with blue blocks representing CDSs and the numbers indicate the exact positions on the European glass lizard reference genome. Three segments of snake-specific amino acid residue loss are manifested by internal numbers ''4002–4004,'' ''2110–2112,'' and ''1983–1987.'' One SD-CNE located at 30 regulate region of KMT2C is marked by a red block. (C) Alignment of SSSV that inserted into the 5 kb upstream of PDZD7 transcription start site. This SSSV conveys a new EBF1 binding site with a regulatory potential (RP) score: 0.78. (D) Taste transduction involved genes were expressed in tongue and brain of three snakes (plumbeous water snake [Hplu], keeled slug snake [Pber], and Asian vine snake [Apra]). The numbers in cells indicate the scaled FPKM values. (E) Comparison of eye structures between Diard's blind snake and Asian vine snake, keeled slug snake. The magnifications were marked as ''*×'' at the bottomright corner of each histological sections. (F) GOChord plot (produced by GOplot package) of blind snake divergent CNEs involved coding gene-enriched GO terms (p value <0.05). Left half of GOChord displayed genes of different GO terms and the right showed the GO term descriptions. Each gene was linked to a GO term by the colored bands. (G) REVIGO clusters of significantly overrepresented (p value <0.01) GO terms for blind snake REGs. (H) Expression levels of TRPV4 and TRPA1 in seven tissues of brown spotted pitviper. (I) Genome locations of pitviper diverged conserved non-coding elements (PVD-CNEs), and the infrared-sensitive python and boa divergent conserved non-coding elements (ISPBD-CNEs) in PMP22 and NFIB.
Enhancing pay quality: Development of a physical environment rating scale for children's folk games in chinese neighborhoods
Open the record for dataset details and reuse information.
Developing elastic mechanisms: Ultrafast motion and cavitation emerge at the millimeter scale in juvenile snapping shrimp
Open the record for dataset details and reuse information.
Experimental data for "Development of Experimental Techniques for Parameterization of Multi-scale Lithium-ion Battery Models"
<p>This dataset is for the validation data in Chen et al. (2020). It contains data for three different LG M50 cells undergoing an experiment in which the cells are charged in a constant-current/constant-voltage fashion and discharge at a constant current for different C-rates (C/10, C/2, 1C and 1.5C). Apart from the current and voltage, the temperatures of the cell surface and the thermal chamber in which they are cycled is recorded too.</p> <p><strong>References:</strong></p> <p>Chang-Hui Chen <em>et al</em> 2020 <em>J. Electrochem. Soc.</em> <strong>167</strong> 080534 (<a href="https://doi.org/10.1149/1945-7111/ab9050">https://doi.org/10.1149/1945-7111/ab9050</a>)</p>
Developing hierarchical density-structured models to study the national-scale dynamics of an arable weed
<p class="BodyText1">Population dynamics can be highly variable in the face of environmental heterogeneity, and understanding this variation is central in the study of ecology. Robust management decisions require that we understand how populations respond to management at a range of scales, and under a broad suite of conditions. Population models are potentially valuable tools in addressing this challenge. However, without adequate data, models can fail to produce useful results. Populations of arable weeds are particularly problematic in this respect, as they are widespread and their dynamics are extremely variable. Owing to the inherent cost of collecting data, most studies of weed population dynamics are derived from localized experiments under a small range of environmental conditions, limiting the extent to which variance in population dynamics can be measured. Density-structured models provide a route to rapid, large-scale analysis of population dynamics, and can expand the scale of ecological models that are directly tied to data. Here we extend previous density-structured models to include environmental heterogeneity, variation in management, and to account for inter-population variation. We develop, parameterize and test hierarchical density-structured models for a common agricultural weed, black-grass (<i>Alopecurus myosuroides</i>). We model the dynamics of this species in response to crop management, using survey data gathered over 4 years from 364 fields across a network of 45 UK farms. We show that hierarchical density-structured models provide a substantial improvement over their non-hierarchical counterparts. Using these models, we demonstrate that several alternative crop-rotations are effective in reducing weed densities. Rotations with high wheat prevalence exhibit the most severe infestations, and diverse rotations generally have lower weed densities. However, a key outcome is that in many cases the effect of crop rotation is small compared to the high variability arising from spatio-temporal heterogeneity. This result highlights the need to monitor and model population dynamics across large spatial and temporal scales in order to account for variation in the drivers of plant dynamics. Our framework for data collection and modelling provides a means to achieve this.</p>
Figure 11. - Fruits and galls produced by Epicephala species on Glochidionobovatum. A Fruit produced after pollination by Epicephalaobovatella (Tomogashima, Wakayama) B Gall induced on female flower by Epicephalacorruptrix (Takae, Okinawa) C Cross section of the gall induced by Epicephalacorruptrix. Arrow indicates the galled locule with feeding trace of Epicephala larva. Note that the irregularly developed ovules of the galled locule have merged indistinguishablly to septa. Scale bar 2 mm.
Figure 11. - Fruits and galls produced by Epicephala species on Glochidionobovatum. A Fruit produced after pollination by Epicephalaobovatella (Tomogashima, Wakayama) B Gall induced on female flower by Epicephalacorruptrix (Takae, Okinawa) C Cross section of the gall induced by Epicephalacorruptrix. Arrow indicates the galled locule with feeding trace of Epicephala larva. Note that the irregularly developed ovules of the galled locule have merged indistinguishablly to septa. Scale bar 2 mm.
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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.