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Fig. 5 in The morphology and fine structure of the Ordovician Cephalodiscus-like genus Melanostrophus

Fig. 5. Melanostrophus fokini Öpik, 1930; Upper Ordovician (Kukruse Stage, C β), Ubja (Estonia); ZPAL Pb 6/1. SEM micrographs. Graptolite pattern of 2 tube ultrastructure. A. Broken tube wall showing layered ectocortex and fusellar layer. B. Parallel bundles of cortical fibrils covering the fusellar layer. C. Fuselli arrangement; note the oblique suture. D. Details of fusellar fabric. Abbreviations: b, bundle of cortical fibrils; cf, cortical fibril; ec, ectocortical layer; f, fusellar layer; o, oblique fusellar suture; p, pits.

Fig. 2 in The morphology and fine structure of the Ordovician Cephalodiscus-like genus Melanostrophus

Fig. 2. Melanostrophus fokini Öpik, 1930; Upper Ordovician (Kukruse Stage, C β), Ubja (Estonia); ZPAL Pb 6/1. SEM micrographs of chemically 2 isolated fragments. A. Fragment of a single tube with a fragment of apertural margin. B, C. Broken bundles of tubes. Abbreviations: a, apertural margin; f, interfusellar suture; i, interior of the tube; p, periderm perforations; t1, t2, etc., adjacent tubes. Arrows show circular cross section of the tubes.

Fig. 8 in The morphology and fine structure of the Ordovician Cephalodiscus-like genus Melanostrophus

Fig. 8. Melanostrophus fokini Öpik, 1930; Upper Ordovician (Kukruse Stage, C β), Ubja (Estonia); ZPAL Pb 6/1. SEM micrographs. A–C. Inner periderm 2 surface where removal of the enamel−like inner lining reveals cortical fibrils of endocortex beneath. D. Enlargement of cortical fabric in endocortex. Abbreviations: b1, b2, b3, adjacent bundles of cortical fibrils; c, cortical fibril; d, mineral debris; en, endocortex; i, inner lining; t, transverse connecting fibril.

Fig. 7 in The morphology and fine structure of the Ordovician Cephalodiscus-like genus Melanostrophus

Fig. 7. Melanostrophus fokini Öpik, 1930; Upper Ordovician (Kukruse Stage, C β), Ubja (Estonia); ZPAL Pb 6/1. SEM micrographs. Details of 2 cortical fabric in ectocortex. A. Bundles of cortical fibrils. B. Arrangement of cortical fibrils in bundles. Abbraviations: b, bundle of fibrils, f, cortical fibril.

Fig. 3 in The morphology and fine structure of the Ordovician Cephalodiscus-like genus Melanostrophus

Fig. 3. Melanostrophus fokini Öpik, 1930; Ordovician boulder O.148 (Wyszogród/Zakroczym, Poland); ZPAL Pb 6/1. SEM micrographs of a fragment of colony composed of numerous fused zooidal tubes. A. General view. B. Margin of the specimen showing transversely broken and strongly flattened tubes. C, D. Large openings in the tube wall. Abbreviatons: i, interior of tube; o, large opening in the wall; w, wall of zooidal tube.

publicDec 2024View details →

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Data from: Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores

Open the record for dataset details and reuse information.

opencc-by-4.0Apr 2020View details →

Fine-Grained Activities of Daily Living Data with Structural Vibration and Electrical Load Sensing

Fine-grained non-intrusive monitoring of activities of daily living (ADL) enables various smart building applications, including ADL pattern assessments for older adults at risk for loss of safety or independence. We utilize structural vibration sensing and electrical load sensing to acquire multiple fine-grained kitchen activities under a lab structure setting. Each file contains the following values: -RawData: time series of data for each channel (vibration on the table, vibration on the floor, load) -Label: manually fine-grained labels of events -Table: detected events start/stop index for vibration sensor on the table -Floor: detected events start/stop index for vibration sensor on the floor -Load: detected events start/stop index for load sensor Label notation: 1 -- operating the kettle 2 -- kettle on 3 -- operating the microwave 4 -- microwave on 5 -- put things on the stove 6 -- operating with stove 7 -- stove on 8 -- operating vacuum 9 -- sweep floor 10 -- walking/step 11 -- miscellaneous 12 -- synchronization signal (knock on the floor) 13 -- vacant 14 -- microwave door open

opencc-zeroDec 2016View details →

Data from: Fine-scale genetic structure due to adaptive divergence among microhabitats

It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic—does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3–2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate less than or equal to1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.

opencc-zeroDec 2017View details →

Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a new approach for mapping fine‐scale thermal heterogeneity. We expected that vegetation would create attenuated microclimates and that the influence of vegetation structure would vary seasonally. We measured shrub volume, horizontal cover, and operative temperature (Te) in a sagebrush‐steppe habitat in Idaho, USA, at 534 microsites across two study sites of approximately 1 km2 each. We modeled relationships between habitat structure and both mean daily maximum temperature (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0001max) and mean diurnal temperature range (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0002) for each study site during summer and winter. Aerial imagery from unmanned aerial systems was used to estimate shrub volume and canopy cover at 1‐m resolution, and we applied the best fit model to map thermal heterogeneity across broader extents. 3. Increasing shrub volume and cover was associated with lower urn:x-wiley:2041210X:media:mee313008:mee313008-math-0003max and (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0004, but strengths of the relationships differed between study sites. There was considerable heterogeneity in availability of thermal refuges across sagebrush‐steppe rangelands that have traditionally been considered relatively homogeneous. 4. This technique can help ecologists and land managers identify critical thermal refuges that large‐scale climate modelling can overlook and thus contribute to an understanding of animal‐habitat relationships under changing climates and land uses.

opencc-zeroDec 2016View details →

Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion

Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use.

opencc-by-4.0May 2016View details →

Quasar spectra and absorption profile fits of HE 0515-4414 for limiting fine-structure constant variability

This is the first public pre-release upon submission to MNRAS and to obtain a DOI.

opencc-zeroNov 2023View details →

Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants

Premise: 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. Methods: 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. Results: 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%. EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. Conclusions: 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 G. conopsea.

opencc-by-4.0Aug 2022View details →

Data and code for the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models"

This is the repository for the data and code to reproduce the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models". Summary: ·  Background and Aims Lidar is a promising tool for fast and accurate measurements of trees. There are several approaches to estimate aboveground woody biomass using lidar point clouds. One of the most widely used methods involves fitting geometric primitives (e.g. cylinders) to the point cloud, thereby reconstructing both the geometry and topology of the tree. However, current algorithms are not suited for accurate estimation of the volume of finer branches, because of the unreliable point dispersions from e.g. beam footprint compared to the structure diameter. ·  Methods We propose a new method that couples point cloud-based skeletonization and multi-linear statistical modelling based on structural data to make a model (structural model) that accurately estimates the aboveground woody biomass of trees from high-quality lidar point clouds, including finer branches. The structural model was tested at segment, axis, and branch level, and compared to a cylinder fitting algorithm and to the pipe model theory. ·  Key Results The model accurately predicted the biomass with 1.6% nRMSE at the segment scale from a k-fold cross-validation. It also gave satisfactory results when up-scaled to the branch level with a significantly lower error (13% nRMSE) and bias (-5%) compared to conventional cylinder fitting to the point cloud (nRMSE: 92%, bias: 82%), or using the pipe model theory (nRMSE: 31%, bias: -27%). The model was then applied to the whole-tree scale and showed that the sampled trees had more than 1.7km of structures on average and that 96% of that length was coming from the twigs (i.e. <5 cm diameter). Our results showed that neglecting twigs can lead to a significant underestimation of tree aboveground woody biomass (-21%). ·  Conclusions The structural model approach is an effective method that allows a more accurate estimation of the volumes of smaller branches from lidar point clouds. This method is versatile but requires manual measurements on branches for calibration. Nevertheless, once the model is calibrated, it can provide unbiased and large-scale estimations of tree structure volumes, making it an excellent choice for accurate 3D reconstruction of trees and estimating standing biomass.

opencc-by-4.0Mar 2024View details →

Dataset for Bright Excitonic Fine Structure in Metal-Halide Perovskites: From Two-Dimensional to Bulk

This is the dataset of Posmyk, Katarzyna, et al. "Bright Excitonic Fine Structure in Metal-Halide Perovskites: From Two-Dimensional to Bulk." Journal of the American Chemical Society (2024). It consists of multiple subfolders, in which polarization resolved optical spectra and high magnetic field optical spectra can be found. In each subfolder, one can find raw data for photoluminescence and reflectivity spectra. n1 indicates the thickness of the inorganic quantum well (in this case n=1). filename structure:  Spot6_A_pol_win527_1uW_number of aquisitions _ aquisition time _HW_X.csv A:photoluminescence (PL) or reflectance (R) X: degree on the half-wave plate pol/nonpol - polarised/nonpolarised Excitation power: x uW  Spoty6 - spot on the sample Grating center: win527 - 527 nm

opencc-by-4.0Mar 2024View details →

Dataset for Exciton Fine Structure in 2D Perovskites: The Out‐of‐Plane Excitonic State

This dataset includes raw photoluminescence and transmission spectra acquired at zero and high magnetic field (identified by the folder name). Samples of different origins have been identified and the folder name includes the institution where the sample was synthetized. In the filename, one can find the information concerning the excitation power used, the wavelength of the excitation laser, the acquisition time, the degree read out on the half-wavelength plate. PL _ 5K_0.5uW_511.5nm_spot8 _aquisition time _ number of aquisitions _ X.csv   R _5K_ 1uW_511.5nm _ aquisition time _ number of aquisitions _spot8 _ X.csv   X: degree on the half-wave plate   Temperature:5K Excitation power: x uW Spot y - spot on a sample Grating center: zzz nm

opencc-by-4.0Nov 2021View details →

R scripts for "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (Panurus biarmicus)"

Dataset which contains R scripts and R package SDMaps used for data preparation and modelling in the methodology described in my MSc thesis "Using LiDAR to assess the influence of fine-scale habitat structure on the abundance of the bearded reedling (Panurus biarmicus)". The project involved creating Species Distribution Models to test whether and how fine-scale habitat structure - in the form of LiDAR derived variable - influences the relative abundance of the bearded reedling in the Netherlands, beyond other variables such as land use, soil type and climate data. These scripts can serve as an example of how the SDMaps package can be used to build Species Distribution Models that include LiDAR derived variables, and to replicate some of the methodologies described in the thesis. The SDMaps package contains an installation guide, manual, tutorial and examples.

opencc-zeroJul 2022View details →

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

opencc-zeroJul 2022View details →

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

opencc-zeroSep 2022View details →

High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.