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opencc-by-3.0-usOct 2022View details →

Code and data for directed emission from uniformly excited non-Hermitian photonic meta-structures

Wolfram Mathematica notebook (.nb) used to generate figures, data, and confirm analytical results presented in the main work. Data generated from the notebook is included here as separate text files (.dat) as well.

Data from: Nature versus nurture: Structural equation modeling indicates that parental care does not mitigate consequences of poor environmental conditions in Eastern bluebirds (Sialia sialis)

1. How organisms respond to variation in environmental conditions and whether behavioral responses can mitigate negative consequences on growth, condition and other fitness measures are critical to our ability to conserve populations in changing environments. Offspring development is affected by environmental conditions and parental care behavior. When adverse environmental conditions are present, parents may alter behaviors to mitigate the impacts of poor environmental conditions on offspring. 2. We determined if parental behavior (provisioning rates, attentiveness, nest temperature) varied in relation to environmental conditions (e.g., food availability, ectoparasites) and if parental behavior mitigated negative consequences of the environment on their offspring in Eastern bluebirds (Sialia sialis). 3. We found that offspring on territories with lower food availability had higher hematocrit, and when bird blow flies (Protocalliphora spp.) were present growth rates were reduced. Parents increased provisioning and nest attendance in response to increased food availability but did not alter behavior in response to parasitism by blow flies. While parents altered behavior in response to resource availability, parents were unable to override the direct effects of negative environmental conditions on offspring growth and hematocrit. 4. Our work highlights the importance of the environment on offspring development and suggests that parents may not be able to sufficiently alter behavior to ameliorate challenging environmental conditions.

Data and scripts from: Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia

The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across ten locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.

Data from: Multiple origins of lipid-based structural colors contribute to a gradient of fruit colors in Viburnum (Adoxaceae)

Structural color is poorly known in plants relative to animals. In fruits, only a handful of cases have been described, including in Viburnum tinus where the blue color results from a disordered multilayered reflector made of lipid droplets. Here, we examine the broader evolutionary context of fruit structural color across the genus Viburnum. We obtained fresh and herbarium fruit material from 30 Viburnum species spanning the phylogeny and used transmission electron microscopy, optical simulations, and ancestral state reconstruction to (1) identify the presence/absence of photonic structures in each species, (2) understand the mechanism producing structural color in newly identified species, (3) relate the development of cell wall structure to reflectance in V. dentatum, and (4) describe the evolution of cell-wall architecture across Viburnum. We identify at least two (possibly three) origins of blue fruit color in Viburnum, both of which produce large photonic structures made of lipid droplets embedded in the cell wall and which reflect blue light. Examining species that may exhibit structural color in combination with anthocyanin and carotenoid pigments, rather than focusing on the most extreme examples, will yield further insights into the diversity, ecology and evolution of fruit color.

Data from: Variations of trophic structure and niche space in fish community along a highly regulated subtropical large river

The trophic interactions between consumers and resources play a vital role in the stability of communities. In river systems, fragmentation of natural habitats and environmental changes alters the energy basis and community composition, consequently leading to variations in the community's trophic structure and niche space. However, our understanding of how the trophic structure responds to environmental changes is still very limited. Here, based on stable isotope data, we explored and compared trophic positions (TPs), community-wide trophic metrics, and isotope niche space of fish communities in three reaches with different hydrogeomorphic conditions along a highly regulated subtropical river over three seasons. The community trophic structure and niche space showed notable spatiotemporal variations. Overall, the downstream reach had lower TPs and trophic diversity but higher trophic redundancy. The middle reach occupied a wider isotope niche space than other reaches, with the largest niche size during autumn. Furthermore, the niche overlap was relatively high in winter between reaches and in the downstream between seasons. The results implied a homogenization of feeding functional groups and energy flow pathways of species in the downstream community associated with the change of energy source and stability of hydrological conditions. The relationship between trophic structure and environmental factors suggested that the dam-induced alteration in hydrological-related aspects may drive the changes in the functional group composition, together with changes in energy basis, resulting in differences in the trophic structure of the community. The results of the present study deepen our understanding of how ecosystem functions respond to disturbance, thus contributing to an improved ability to conserve river ecosystems.

opencc-by-4.0Oct 2022View details →

Data for publication: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity

Original data of Figures published in: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity Journal of Colloid and Interface Science, 2022, Michal Swierczewski, Alexis Chenneviere, Lay-Theng Lee, Plinio Maroni and Thomas Bürgi*[

opencc-by-sa-4.0Nov 2017View details →

Structure, function, and control of the musculoskeletal network - Data

Supplementary data for: Structure, function, and control of the musculoskeletal network Table S8: The assigned homunculus categories and data driven community assignments of muscles. Table S9: The hypergraph of muscles and bones from the Hosford muscle tables used in the main text. Table S10: The hypergraph of muscles and bones from Grant's atlas used in the supplementary text.   Data for Figures: 2e 3a, 3b 4b, 4c, 4d S4a-h S5 S6a, S6b S7a, S7b S8 S9 S10 S11 S12

opencc-by-4.0Feb 2024View details →

Data for paper "Automated Structure Discovery for Scanning Tunneling Microscopy"

Contents of the dataset: <ul> <li>band.h5 -- keys are molecule indices, each molecule has the following keys: <ul> <li>eigs: KS eigenvalues for each state</li> <li>coefs: KS eigenvectors for each basis set</li> <li>xyz: atomic positions</li> <li>Z: atomic species</li> <li>qs: mulliken point charges</li> </ul> </li> <li>rotations_210611.pickle -- keys train/val/test <ul> <li>Each set is a dict containing id -- rotation pairs</li> <li>rotations are 3x3 numpy arrays</li> </ul> </li> <li>disks.pt -- a pretrained model for Atomic Disks predictions</li> </ul>

opencc-by-4.0Mar 2024View details →

Data from "Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family."

This data accompanies the paper entitled Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family. The zip archive contains:  1- Starting configurations of the proteins after equilibration in PDB format and trajectories of unrestrained molecular dynamics simulations with the positions of the proteins every 100 ps in XTC gromacs format are provided for all systems.  2- The free energy profiles and histograms are provided for all umbrella sampling simulations and the scripts used to run it with gromacs.

opencc-by-4.0Apr 2024View details →

Data for "Structure, short-range order, and phase stability of the Al$_x$CrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis"

Data associated with "Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis", published in npj Comput. Mater. 10, 271 (2024).

opencc-by-4.0Nov 2022View details →

Data for "Tetramine Aspect Ratio and Flexibility Determine Framework Symmetry for Zn8L6 Self-Assembled Structures"

In the following subdirectories are the input and outputs of cage and face analysis for: Published DOI: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202217987">10.1002/anie.202217987 </a> Code: <a href="https://github.com/andrewtarzia/sca_cage_assembler/tree/cubism-production">sca_cage_assembler</a> Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a> NOTES: <ul> <li>the naming convention differs from manuscript:</li> </ul> <table> <tbody> <tr> <th>manuscript tetra-aniline</th> <th>computational label</th> <th>xtal-label</th> </tr> <tr> <td>A</td> <td>5</td> <td>370</td> </tr> <tr> <td>B</td> <td>16</td> <td>326</td> </tr> <tr> <td>C</td> <td>12</td> <td>235</td> </tr> <tr> <td>D</td> <td>3</td> <td>301</td> </tr> <tr> <td>E</td> <td>8</td> <td>257</td> </tr> <tr> <td>F</td> <td>2</td> <td>354</td> </tr> </tbody> </table> <ul> <li>computational labels are often preceded by `quad2_` or `cl1_quad2_`</li> <li>much of the analysis was not used in the manuscript but remains part of the accumulated data</li> </ul>   cage_library directory: <ul> <li>_CS.json: information on all cages in the set of diastereomers - properties and whether they optimized successfully.</li> <li>_ligand_measures.json: information on the ligand associated with a set of cage diastereomers.</li> <li>_measures.json: represenets a cleaned up collation of all measures the diastereomers made from a given ligand</li> <li>C_NAME_optc.mol: optimized (at xTB level) structure of each cage.</li> <li>set_dft_run directory contains the input and output of the CP2K optimisations of one set of diastereomers</li> </ul> complex_library directory: <ul> <li>contains the optimised structures of both complexes</li> </ul> ligand_library directory: <ul> <li>contains `_opt.mol` input ligand structures for cage construction</li> <li>for cap, the input was provided manually in `manual/` directory</li> <li>in `face_analysis` directory: <ul> <li>contains manual_complex directory, with necessary input for face construction</li> <li>_long_properties.json files contains the measurements for the named face (in file name)</li> <li>_long_lopt.mol files contain the optimised structure of the named face, on which analysis was performed</li> <li>`long` corresponds to the longer restricted optimization discussed in the SI.</li> </ul> </li> </ul> xray_structures directory: <ul> <li>analysis directory: <ul> <li>contains input .pdb files for xray structure (as single molecules) used in analysis</li> <li>contains `all_xray_csv_data.csv`, which has all data needed on xray structures.</li> </ul> </li> </ul>

opencc-by-4.0May 2024View details →

Swarm-C Neutral Density Data for Large-Scale Wave (LSW) Structures

Open the record for dataset details and reuse information.

Data from: Nanotube structure of AsPS4–xSex (x = 0, 1)

Single-wall nanotubes of isostructural AsPS4−xSex (x = 0, 1) are grown from solid-state reaction of stoichiometric amounts of the elements. The structure of AsPS4 was determined using single-crystal X-ray diffraction and refined in space group P1. The infinite, single-walled AsPS4 nanotubes have an outer diameter of ≈1.1 nm and are built of corner-sharing PS4 tetrahedra and AsS3 trigonal pyramids. Each nanotube is nearly hexagonal, but the ≈3.4 Å distance between S atoms on adjacent nanotubes allows them to easily slide past one another, resulting in the loss of long-range order. Substituting S with Se disrupted the crystallization of the nanotubes, resulting in amorphous products that precluded the determination of the structure for AsPS3Se. 31P solid-state NMR spectroscopy indicated a single unique tetrahedral P environment in AsPS4 and five different P environments all with different degrees of Se substitution in AsPS3Se. Optical absorption spectroscopy revealed an energy band gap of 2.7 to 2.4 eV for AsPS4 and AsPS3Se, respectively. Individual AsPS4 microfibers showed a bulk conductivity of 3.2 × 10−6 S/cm and a negative photoconductivity effect under the illumination of light (3.06 eV) in ambient conditions. Thus, intrinsic conductivity originates from hopping through empty trap states along the length of the AsPS4 nanotubes.

opencc-by-4.0May 2024View details →

Data for "Low-Energy Electronic Structure in the Unconventional Charge-Ordered State of ScV6Sn6"

The files contain the data for the paper "Low-Energy Electronic Structure in the Unconventional Charge-Ordered State of ScV6Sn6". For data Fig1c+d_topography.gwy, the data has been well plotted in a free and commonly used software Gwyddion. The raw data can also be found in Fig1_c_topography.txt and Fig_1c_FFT.txt. For the 2D data, the scales for each axes can be obtained either normalized to Bragg peaks or can be found in the published manuscript online. Any question on the data, please contact the authors.

Data from: Changes of Chinese forest-grassland ecotone in geographical scope and landscape structure from 1990 to 2020

Forest-grassland ecotone (FGE) has essential ecological and economic value. Unfortunately, it is impacted greatly by environmental changes and anthropogenic disturbance, and is considered one of the most severely threatened biomes in China. To protect Chinese FGE, identifying its exact boundary and exploring its landscape structure dynamic are badly needed, especially on nationwide scale at one-year temporal resolution. Here, we mapped the annual FGE distribution of China from 1990 to 2020, investigated its changing trends of area, location and landscape patterns, and revealed the underlying driving factors. Our results showed that FGE area over the 31 years totaled 1,011,870 km2, covering about 10.54% of China's land. The FGE area first increased from 1990 and peaked in 1999, and then kept decreasing until 2020. The FGE gravity center has moved accumulatively 590.15 km over the 31 years, with the net moving distance of 228.76 km southwestward. From 1990 to 2020, forest area increased continuously while grassland and cropland area decreased, but these three landscape types had been dominating the FGE. The increase in forest area was largely converted from grassland. The decline in grassland mainly resulted from its conversion into cropland and forest. Meanwhile, the conversion of cropland to grassland supplemented grassland loss to a certain extent. At landscape level, the total area with decreased fragmentation is larger than that with increased fragmentation. Returning Farmland to Grassland Project and land reclamation were primary drivers for changes of fragmentation in the northern and middle part of the FGE, while temperature and precipitation were primary drivers in southern part. Our results will improve the understanding into the dynamic trends of distribution and pattern of FGE at nationwide scale, and thus help to optimize the designing of ecological projects and protective schemes for FGE as a unique and integral biome.

Data from: The basic-reproduction number of infectious diseases in spatially structured host populations

The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic dynamics can be used to study the effect of host spatial pattern on the basic reproduction number of infectious diseases. As well as showing how explicit expressions for the basic reproduction number can be derived for landscapes with standard structures, our expression for the basic reproduction number is tested against a simulation model. The model structure in our simulation is motivated by the spread of a plant disease epidemic, although it is applicable more broadly. The agreement between our analytic expression for the basic reproduction number and the corresponding numeric quantity extracted from simulations is close to perfect across a wide range of landscape structures and model parameterisations, and including cases in which more than one species of host is at risk of infection.

Data from: Increased intake of tree forage by moose is associated with intake of crops rich in non-structural carbohydrates

Animals representing a wide range of taxonomic groups are known to select specific food combinations to achieve a nutritionally balanced diet. The nutrient balancing hypothesis suggests that, when given the opportunity, animals select foods to achieve a particular target nutrient balance, and that balancing occurs between meals and between days. For wild ruminants who inhabit landscapes dominated by human land use, nutritionally imbalanced diets can result from ingesting agricultural crops rich in starch and sugar (non-structural carbohydrates, NC), which can be provided to them by people as supplementary feeds. Here, we test the nutrient balancing hypothesis by assessing potential effects that the ingestion of such crops by Alces alces (moose) may have on forage intake. We predicted that moose compensate for an imbalanced intake of excess NC by selecting tree forage with macro-nutritional content better suited for their rumen microbiome during wintertime. We applied DNA metabarcoding to identify plants in faecal and rumen content from the same moose during winter in Sweden. We found that the concentration of NC-rich crops in faeces predicted the presence of Picea abies (Norway spruce) in rumen samples. The finding is consistent with the prediction that moose use tree forage as a nutritionally complementary resource to balance their intake of NC-rich foods, and that they ingested P. abies in particular (normally a forage rarely eaten by moose) because it was the most readily available tree. Our finding sheds new light on the foraging behaviour of a model species in herbivore ecology, and on how habitat alterations by humans may change the behaviour of wildlife.

opencc-zeroJun 2024View details →

Data from: Tracking shifts in forest structural complexity through space and time in human-modified tropical landscapes

Habitat structural complexity is an emergent property of ecosystems that directly shapes their biodiversity, functioning and resilience to disturbance. Yet despite its importance, we continue to lack consensus on how best to define structural complexity, nor do we have a generalised approach to measure habitat complexity across ecosystems. To bridge this gap, here we adapt a geometric framework developed to quantify the surface complexity of coral reefs and apply it to the canopies of tropical rainforests. Using high-resolution, repeat-acquisition airborne laser scanning data collected over 450 km2 of human-modified tropical landscapes in Borneo, we generated 3D canopy height models of forests at varying stages of recovery from logging. We then tested whether the geometric framework of habitat complexity – which characterises 3D surfaces according to their height range, rugosity and fractal dimension – was able to detect how both human and natural disturbances drive variation in canopy structure through space and time across these landscapes. We found that together, these three metrics of surface complexity captured major differences in canopy 3D structure between highly-degraded, selectively logged and old-growth forests. Moreover, the three metrics were able to track distinct temporal patterns of structural recovery following logging and wind disturbance. However, in the process we also uncovered several important conceptual and methodological limitations with the geometric framework of habitat complexity. We found that fractal dimension was highly sensitive to small variations in data inputs and was ecologically counteractive (e.g., higher fractal dimension in oil palms than old-growth forests), while rugosity and height range were tightly correlated (r=0.75) due to their strong dependency on maximum tree height. Our results suggest that forest structural complexity cannot be summarised using these three descriptors alone, as they overlook key features of canopy vertical and horizontal structure that arise from the way trees fill 3D space.

opencc-zeroJun 2024View details →

Data from: Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor

Calcium-sensing receptor (CaSR) is a class C G protein-coupled receptor (GPCR) that plays an important role in calcium homeostasis and parathyroid hormone secretion. Here, we present multiple cryo-electron microscopy structures of full-length CaSR in distinct ligand-bound states. Ligands (Ca2+ and l-tryptophan) bind to the extracellular domain of CaSR and induce large-scale conformational changes, leading to the closure of two heptahelical transmembrane domains (7TMDs) for activation. The positive modulator (evocalcet) and the negative allosteric modulator (NPS-2143) occupy the similar binding pocket in 7TMD. The binding of NPS-2143 causes a considerable rearrangement of two 7TMDs, forming an inactivated TM6/TM6 interface. Moreover, a total of 305 disease-causing missense mutations of CaSR have been mapped to the structure in the active state, creating hotspot maps of five clinical endocrine disorders. Our results provide a structural framework for understanding the activation, allosteric modulation mechanism, and disease therapy for class C GPCRs.