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3D wireframe plot - Tegnùa AL06

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa AL06" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa TM4

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa TM4" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa P208b

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa P208b" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa P204

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa P204" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa MR20

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa MR20" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa P213

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa P213" obtained from single beam echo sounding bathymetry.

3D wireframe plot - Tegnùa P237

3D wireframe plot of the northern Adriatic mesophotic biogenic reef "Tegnùa P237" obtained from single beam echo sounding bathymetry.

opencc-by-4.0Jul 2020View details →

Reproducible Validation and Replication Studies in Nanoscale Physics (repro results plots - Rockstuhl et al., 2005)

This archive contains the Jupyter notebooks needed to reproduce the figures of the paper that are related to the replication of Rockstuhl et al. 2005. For further information direct to the README.md file.

opencc-zeroNov 2020View details →

Presence-absence sampling for estimating plant density using survey data with variable plot size

1. Presence-absence sampling is an important method for monitoring state and change of both individual plant species and communities. With this method only the presence or absence of the target species is recorded on plots and thus the method is straightforward to apply and less prone to surveyor judgment compared to other vegetation monitoring methods. However, in the basic setting all plots must be equally large or otherwise it is unclear how data should be analyzed. In this study we propose and evaluate five different methods for estimating plant density based on presence-absence registrations from surveys with variable plot sizes. 2. Using artificial plant population data as well as empirical data from the Swedish National Forest Inventory we evaluated the performance of the proposed methods. The main analysis was conducted through sampling simulation in the artificial populations, whereby bias and variance of density estimators for the different methods were quantified and compared. 3. Both for state and change estimation of plant density, we found that the best method to handle variable plot size was to perform generalized least squares regression, using plot size as an independent variable. Methods where plots smaller than a certain threshold were excluded or their registrations recalculated were, however, almost as good. Using all registrations as if they were obtained from plots with the nominal plot size resulted in substantial bias. 4. Our findings are important for plant population studies in a wide range of environmental monitoring programmes. In these programmes plots are typically randomly laid out and may be located across boundaries between different land use or land cover classes, resulting in subplots of variable size. Such splitting of plots is common when large plots are used, e.g. with the 100 m2 plots used in the Swedish National Forest Inventory. Our methods overcome problems to estimate plant density from presence-absence data observed in plots that vary in size.

opencc-zeroDec 2020View details →

Abundance of trees and seedlings, climatic, and soil variables in 36 20x20 m permanent plots in peri-urban Andean forests of Colombia

The study was conducted on the Eastern Andean Cordillera of Colombia, in remnant forests occurring in the high-plain where Bogotá lies, one of the largest cities in Latin America. The high-plain covers an area of about 185,000 ha at an average altitude of 2600 meters above sea level (m a.s.l.). We selected six study sites, distributed in the Eastern and Western slopes of the mountain range that surrounds the high-plain, which exhibit different climatic and edaphic characteristics. Five of the sites were located in the suburban municipalities of Soacha (So), San Francisco (Sf), Guasca (Gu), Tabio (Ta), and the last one, Torca (To), located in a large forest fragment at the periphery of Bogotá. Sites were selected so that they encompassed both early- and late-successional or old-growth forest patches. Within each site, we established three 20 m x 20 m plots in early-successional forests (E) and three 20 m x 20 m plots in late-successional (L) for a total of 36 permanent plots. Here, we present climatic and soil variables for each plot and also the abundances of all tree, shrub, palm, and tree-fern individuals with DAH> 5 cm included in each plot. For simplicity we refer to these as "trees" (-t). Within each plot, we additionally established four subplots of 2 m x 2 m, where we tagged and measured all seedlings> 5 cm in height and DAH ≤ 1 cm; we also present the abundances of the seedlings (-s). Vouchers were collected for each tree and seedling species or morphospecies and identified with the help of an expert botanist and using the resources of the herbarium of the Bogotá Botanical Garden (JBB). Vouchers specimens were stored at the herbarium of the Alexander von Humboldt Biological Resources Research Institute (FMB). Overall, we recorded Vouchers that were not identified to species were assigned a standardized morphospecies and were all included in the analyzes.

opencc-by-4.0Dec 2020View details →

RNA Adsorption plot data

Data for plots of RNA adsorption simulations, after analysis

opencc-zeroDec 2020View details →

The plot thickens: Haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction in Letharia. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

opencc-by-4.0Jan 2021View details →

plot

This is plot

opencc-zeroDec 2017View details →

Data from: Accurate geometries for "mountain pass" regions of the Ramachandran plot using quantum chemical calculations

Unusual local arrangements of protein in Ramachandran space is not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. By contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. For conformations along transition regions – ϕ from -60 to 60° – a very good agreement with representative high-resolution experimental X-ray (≤1.5 Å) protein structures is obtained for both backbone C^{-1}-N-C_{alpha} angle and the nonbonded O^{-1}…C distance, while "standard geometry" leads to the "clashing" of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.

opencc-zeroJun 2021View details →

Transect and plot data from: Fruit trees drive small-scale movement of elephants in Kibale National Park, Uganda

Understanding what motivates animal spatial behavior requires discerning the relationship between animals and the landscape in which they move. Many studies have focused on large scale trends that drive migrations and movement across broad landscapes, but few studies have focused on drivers of local movement within smaller areas based on fine–scale landscape heterogeneity. This is especially true for African elephants (Loxodonta africana), whose movements in relation to landscape variables have frequently been studied across vast areas, but infrequently on a small scale. We report on how the local distribution of an important resource—fruit trees—shapes elephant movement patterns in Kibale National Park, Uganda. We hypothesized that the spatial location of elephant trails, and especially intersections in the network of trails, would be heavily associated with fruit trees, with trail density being higher in areas with greater fruit availability. Elephant trails and nearby fruit trees were mapped within a 64-km2 area within the interior of the Park. Trail and fruit tree sampling were conducted along sixteen evenly spaced one-km control transects and compared to 28.6 km of elephant trails arrayed throughout the park. Fruit tree basal area was higher along trails and at trail intersections. Trail density was also positively correlated with fruit tree density. Fruit trees may thus serve as a determinant of small-scale elephant movement and could be used to predict patterns of elephant spatial behavior across forested habitat, which has potential implications for elephant management in the area.

opennotspecifiedDec 2013View details →

FIGURE 23. L–H scatter plot for Neonesidea plumulosa n in New and poorly known species of Neonesidea (Bairdiidae, Ostracoda, Crustacea) from French Frigate Shoals, the Hawaiian Islands

FIGURE 23. L–H scatter plot for Neonesidea plumulosa n. sp. and similar Indo-Pacific species.

opencc-by-4.0Oct 2024View details →

Northwest Pacific ROMSv3.9–TOPAZv2 version 1.0 (NPRTv1.0) -plot scripts

This data is plot scripts for the manuscript

opencc-by-4.0Nov 2023View details →

Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants"

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opencc-by-4.0Dec 2023View details →

Matlab plots

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