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opencc-zeroFeb 2020View details →

Linking community assembly and structure across scales in a wild mouse parasite community

Understanding what processes drive community structure is fundamental to ecology. Many wild animals are simultaneously infected by multiple parasite species, so host parasite communities can be valuable tools for investigating connections between community structures at multiple scales, as each host can be considered a replicate parasite community. Like free-living communities, within-host parasite communities are hierarchical; ecological interactions between hosts and parasites can occur at multiple scales (e.g. host community, host population, parasite community within the host), therefore both extrinsic and intrinsic processes can determine parasite community structure. We combine analyses of community structure and assembly at both the host population and individual scales using extensive datasets on wild wood mice (Apodemus sylvaticus) and their parasite community. An analysis of parasite community nestedness at the host population scale provided predictions about the order of infection at the individual scale, which were then tested using parasite community assembly data from individuals hosts from the same populations. Nestedness analyses revealed parasite communities were significantly more structured than random. However, observed nestedness did not differ from null models in which parasite species abundance was kept constant. We did not find consistency between observed community structure at the host population scale and within-host order of infection. Multistate-Markov models of parasite community assembly showed that a host's likelihood of infection with one parasite was not impacted by previous parasite infection, suggesting there is not a deterministic order of infection among the species we investigated in wild wood mice. Our results demonstrate that patterns at one scale (i.e. host population) do not reliably predict processes at another scale (i.e. individual host), and that neutral or stochastic processes may be driving the patterns of nestedness observed in these communities. We suggest that experimental approaches that manipulate parasite communities are needed to better link processes at multiple ecological scales.

opencc-zeroDec 2016View details →

Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes on forest N cycling, we measured stable N isotopes in wood, a proxy for N supply relative to demand, on large spatial and temporal scales across the continental U.S.A. Here, we show that forest N availability has generally declined across much of the U.S. since at least 1850 C.E. with cool, wet forests demonstrating the greatest declines. Across sites, recent trajectories of N availability were independent of recent atmospheric N deposition rates, implying a minor role for modern N deposition on the trajectory of N status of North American forests. Our results demonstrate that current trends of global changes are likely to be consistent with forest oligotrophication into the foreseeable future, further constraining forest C fixation and potentially storage.

Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale

Raw data of nanoLC-IMS-MS/MS (DDA-PASEF) from HeLa whole proteome digest.    HeLa cells were lysed in a urea-based lysis buffer (7 M urea, 2 M thiourea, 5 mM dithiothreitol (DTT), 2% (w/v) CHAPS) assisted by sonication for 15 min at 4°C in high potency using a Bioruptor instrument (Diagenode). Proteins were digested with Trypsin using a filter-aided sample preparation (FASP) [Wisniewski et al., 2009] as previously detailed [Distler et al., 2016]. 200 ng of peptide digest were analyzed using a nanoElute UPLC coupled to a TimsTOF PRO MS (Bruker). Peptides injected directly in an Aurora 25 cm x 75 µm ID, 1.6 µm C18 column (Ionopticks) and separated using a 120 min. gradient method at 400 nL/min. Phase A consisted on water with 0.1% formic acid and phase B on acetonitrile with 0.1% formic acid. Sample was injected at 2% B, lineally increasing to 20% B at 90 min., 35% B at 105 min., 95% at 115 min. and hold at 95% until 120 min. before re-equilibrating the column at 2%B. The MS was operated in DDA-PASEF mode [Meier et al., 2018], scanning from 100 to 1700 m/z at the MS dimension and 0.60 to 1.60 1/k0 at the IMS dimension with a 100 ms TIMS ramp. Each 1.17 sec MS cycle comprised one MS1 and 10 MS2 PASEF ramps (frames). The source was operated at 1600 V, with dry gas at 3 L/min and 200°C, without nanoBooster gas. The instrument was operated using Compass Hystar version 5.1 and timsControl version 1.1.15 (Bruker).

opencc-zeroJun 2021View details →

Landscape-scale conservation mitigates the biodiversity loss of grassland birds

The decline of biodiversity from anthropogenic landscape modification is among the most pressing conservation problems world-wide. In North America, long-term population declines have elevated the recovery of the grassland avifauna to among the highest conservation priorities. Because the vast majority of grasslands of the Great Plains are privately owned, the recovery of these ecosystems and bird populations within them depend on landscape-scale conservation strategies that integrate social, economic, and biodiversity objectives. The Conservation Reserve Program (CRP) is a voluntary program for private agricultural producers administered by the United States Department of Agriculture that provides financial incentives to take cropland out of production and restore perennial grassland. We investigated spatial patterns of grassland availability and restoration to inform landscape-scale conservation for a comprehensive community of grassland birds in the Great Plains. The research objectives were to 1) determine how apparent habitat loss has affected spatial patterns of grassland bird biodiversity, 2) evaluate the effectiveness of CRP for offsetting the biodiversity declines of grassland birds and 3) develop spatially explicit predictions to estimate the biodiversity benefit of adding CRP to landscapes impacted by habitat loss. We used the Integrated Monitoring in Bird Conservation Regions program to evaluate hypotheses for the effects of habitat loss and restoration on both the occupancy and species richness of grassland specialists within a continuum modelling framework. We found the odds of community occupancy declined by 37% for every 1 Standard Deviation (SD) decrease in grassland availability [loge(km2)] and increased by 20% for every 1 SD increase in CRP land cover [loge(km2)]. There was 17% turnover in species composition between intact grasslands and CRP landscapes, suggesting grasslands restored by CRP retained considerable, but incomplete representation of biodiversity in agricultural landscapes. Spatially explicit predictions indicated absolute conservation outcomes were greatest at high latitudes in regions with high biodiversity, whereas the relative outcomes were greater at low latitudes in highly modified landscapes. By evaluating community-wide responses to landscape modification and CRP restoration at bioregional scales, our study fills key information gaps for developing collaborative strategies, and balancing conservation of avian biodiversity and social well-being in agricultural production landscapes of the Great Plains.

opencc-zeroJun 2021View details →

Two decades of annual landscape-scale tree growth and dynamics in old-growth tropical rainforest in the CARBONO Project, La Selva Biological Station, 1997-2018

Here we present the complete data series from a 21-yr study of the annual growth and dynamics of trees, palms and lianas in the old-growth tropical rainforest at the La Selva Biological Station in Costa Rica. These observations were part of the CARBONO Project, a multidisciplinary team study of forest carbon cycling. The project was designed to assess forest processes at the landscape scale by sampling with replication across the within-landscape edaphic heterogeneity typical of tropical forests. Through more than two decades, forest growth and dynamics were assessed annually. The annual time-step used in the CARBONO Project effectively captured forest responses to major disturbances and to interannual and climatic variation. Annual measurements also enhanced the accuracy and long-term consistency of the data. To our knowledge, the resulting records are unique for tropical forests, where the dominant approach to studying the dynamics of a given forest has been to use a single plot and multi-year inter-census intervals. To date these CARBONO Project data have revealed: multi-decadal forest stability in spite of the short-term changes in forest structure resulting from major natural disturbances (e.g., the 1997-1998 Strong El Niño, and the extreme windstorm of May 2018); the dynamics and importance of large trees; and the responses of a major component of ecosystem productivity, aboveground wood production, to interannual and long-term climatic and atmospheric change. These data have also contributed to many remote-sensing studies. The data set consists of annual observations through the period 1997–2018 of the floristics, survival, recruitment, and growth of all woody stems (diameter > 10 cm) in a landscape-scale plot network. At completion of the study, the data spanned 6705 individuals and 21 years. The data set is complete and has been through extensive internal checks for quality assurance. Detailed data documentation and an emphasis on measurement repeatability were prioritized through the study. The metadata include an extensive README file describing the data files and the methods, a document detailing the data management and qa/qc, and the scanned original field data-sheets for the 22 annual censuses. We gratefully acknowledge the careful long-term field work and data entry and checking by paraforesters Leonel Campos Otoya and William Miranda Conejo. Logistical support and the long-term protection of the La Selva reserve were provided by the Organization for Tropical Studies. The Ministerio de Ambiente y Energía of Costa Rica granted permits to carry out this study through the years of the study (most recently: Resolución No. 037-2018-ACCVC-PI).

Data set for the article "Recently photoassimilated Carbon and fungus-delivered Nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica"

This dataset contains data that support the manuscript Mayerhofer et al (2021) "Recently photoassimilated Carbon and fungus-delivered Nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica", The New Phytologist, DOI:10.1111/nph.17591 It contains the following data: (1) NanoSIMS imaging data, which was used for Fig. 4-7, is provided in NanoSIMS_control_root_tip.zip and NanoSIMS_labelled_root_tip.zip. Each zip-files contains: <ul> <li>the original NanoSIMS images (.im)</li> <li>their related checkfiles (.chk_im)</li> <li>ROIs description (.rois.zip)</li> </ul> of the unlabelled control and the labelled root tip section, respectively. ".im" and ".chk_im" are the original image data aquisition files from the NanoSIMS instrument. "rois.zip" files describe selected regions of interests and were created utilizing the OpenMIMS plugin (Center for Nano Imaging, https://nano.bwh.harvard.edu/MIMSsoftware) for the image analysis software ImageJ (National Institutes of Health, Bethesda, MD, USA). (2) Means and standard deviations of all measured elements and isotopes of each region of interest, as obtained via the .rois.zip files from the NanoSIMS images, are reported in NanoSIMS_ROI_data.csv (used for Fig.7). (3) Linescan_data.csv contains data used for Fig. 8. (4) IRMS_roots_data.csv contains data of root segments and mycorrhizal root tips analysed with isotope-ratio mass spectrometry (EA-IRMS) (used for Fig. 2) Description of column meanings from csv data files can be found in the according "_description" files.

SPH-EXA miniapp Sedov scaling test outputs with v0.3

Output dataset for weak scaling tests on Piz Daint with 1 - 2048 compute nodes. Sedov blast wave test case with 32 million particles per node.

opencc-zeroFeb 2020View details →

Simulations of planetary-scale collisions between rotating, differentiated bodies

In the late stages of terrestrial planet formation, pairwise collisions between planetary-sized bodies act as the fundamental agent of planet growth. These collisions can lead to either growth or disruption of the bodies involved and are largely responsible for shaping the final characteristics of planets. Despite their critical role in planet formation, an accurate treatment of collisions has yet to be realized. Therefore, we simulated a new set of 10,700 smoothed-particle hydrodynamics (SPH) simulations of pairwise collisions between rotating, differentiated bodies. This dataset is an order of magnitude larger than any previous collision dataset and is intended to serve as a training dataset for machine learning models, so that accurate surrogate models for planetary-scale collisions can be developed.

A global-scale geodatabase of mine areas

Globally, the mine area include open cut pits, milling infrastructure, waste rock dumps, and tailings storage facilities of global.  Totaled 24605 polygons were studied.

Large-Scale Atmospheric Drivers of Snowfall over Thwaites Glacier, Antarctica

Monthly RACMO2 snowfall rates (1979-2015, in mm w.e. per month), as described in Lenaerts et al., 2018 (https://www.cambridge.org/core/journals/annals-of-glaciology/article/climate-and-surface-mass-balance-of-coastal-west-antarctica-resolved-by-regional-climate-modelling/E3DD6D0DA914C6031F96A548AF53603A), and used in this paper.

opencc-zeroJul 2021View details →

Springtail coloration at a finer scale: mechanisms behind vibrant Collembolan metallic colours

The mechanisms and evolution of metallic structural colours are of both fundamental and applied interest, yet most work in arthropods has focused on derived butterflies and beetles with distinct hues. In particular, basal hexapods - groups with many scaled, metallic representatives – are currently poorly studied and controversial, with some recent studies suggesting either that thin- film (lamina thickness) or diffraction grating elements (longitudinal ridges, crossribs) produce these colors in early Lepidoptera and one springtail (Collembola) species. Especially the Collembolan basal scale design, consisting of a singlelamina and longitudinal ridges with smooth valleys lacking crossribs, makes them an interesting group to explore the mechanisms of metallic colouration. Using microspectroscopy, Raman spectroscopy, electron microscopy and FDTD optical modelling we investigated scale colour in seven springtail species that show clear metallic colouration. Reflectance spectra are largely uniform and exhibit a broadband metallic/golden colouration with peaks in the violet/blue region. Our simulations confirm the role of the longitudinal ridges, working in conjunction with thin-film effects to produce a broadband metallic colouration. Broadband colouration occurs through spatial colour mixing which likely results from nanoscale variation in scale thickness and ridge height and distance. These results provide crucial insights into the colour production mechanisms in a basal scale design and highlight the need for further investigation of scaled, basal arthropods.

Appendix II for: Social context modulates scale-free walks in a social insect

Plots from the MLE (Maximum likelihood estimation) analysis for the step-lengths of the focal termite workers. Two competing models were tested: Truncated Pareto Lévy (TP - red line) vs exponential (EX - blue dashed line) for both (X and Y) axis. Data series are identified with "S" plus a number from 1 to 75). The Lévy exponent ($1 < \mu \leq 3.0$) and the Akaike weights (wAIC) for the competing models (1 for full support, 0 for not support) are shown in the plots.

opencc-by-4.0Dec 2020View details →

Dataset (46 analyzed core studies) of the publication "Conservation perspectives of small-scale private forest owners in Europe: A systematic review"

The dataset contains the data collected to conduct the review "Conservation perspectives of small-scale private forest owners in Europe: A systematic review".

opencc-zeroJul 2021View details →

Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius

In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.

Dataset: A multi-scale probabilistic atlas of the human connectome

This repository complements the paper submitted to Scientific Data named A multi-scale probabilistic atlas of the human connectome. Introduction The assessment of the networks underlying brain processes is key to understand brain-related disorders. However, groundbreaking connectomics research is highly demanding in terms of equipment and expertise. The aim of this work is to create a multiscale probabilistic atlas of the human white matter (WM) to carry out network analyses in the context of clinical research, particularly when diffusion data is not directly available. Methods Sixty six subjects from the Human Connectome Project (HCP) database (29 males, age: 22-36 years old) were used to build the WM probabilistic atlas. MRI acquisition protocols are described in (Van Essen et al, 2012). Besides T1-, T2- and diffusion-weighted (DW) images, the HCP database provides the FreeSurfer outputs (Glasser et al, 2016) namely cortical surfaces (pial and white), subcortical segmentation and a cortical surface parcellation containing 34 structures for each hemisphere (Desikan et al, 2006). For each subject, the DWIs were employed to segment each thalamus in seven nuclei (Battistella et al, 2016) and to estimate the WM streamlines distribution. The constrained spherical deconvolution (Tournier et al, 2007) algorithm was used to compute the intravoxel fiber distribution functions for the anatomically-constrained particle-filter tractography approach (Descoteaux et al, 2009) to compute the WM streamlines. Subcortical, thalamic and multiscale cortical (Cammoun et al, 2012) parcellations were gathered to obtain four individual gray matter (GM) parcellations. Finally, for each scale, individual fiber bundles, were created by selecting the streamlines connecting each pair of GM regions (Figure 1a). Atlas construction The T1 and T2 images were non-linearly warped to their corresponding MNI templates (Evans et al, 2012, mni_icbm152_tal_nlin_asym_09c version) using ANTs (Avants et al, 2010). The resulting spatial transformations were applied to warp the individual fiber bundles to stereotactic space and the normalized tract density images (TDIs) were created. In these images, each voxel contains the number of streamlines passing through it. Finally, the spatial probability map for each bundle was obtained by binarizing and averaging the bundle TDIs across the subjects (Figure. 1b). Different views of the developed probabilistic multi-scale connectome atlas are shown in Figure 2.

Raw data for "X-ray studies bridge the molecular and macro length scales during the emergence of CoO assemblies"

Raw data for &bdquo;X-ray studies bridge the molecular and macro length scales during the emergence of CoO assemblies“ TEM and SEM <ul> <li>SEM image of CoO assemblies after 90 min</li> <li>TEM images of CoO assemblies after 5, 10, 15, 20, 40, 60 and 90 min</li> <li>HR-TEM images of CoO assemblies after 90 min</li> <li>ED patterns of CoO assemblies after 10, 15 and 20 min</li> </ul> HERFD-XANES In situ spectra for the CoO synthesis at 160°C were recorded at beamline ID26 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. Using a Si (111) double crystal monochromator, the incident energy was varied from 7.70 to 7.78 keV. The emitted fluorescence was measured with an emission spectrometer in Rowland geometry with five Si (531) analyzer crystals aligned at the Bragg angle of 77°. HERFD-XANES spectra were recorded in continuous scan mode every 80 s with average energy steps of 0.05 eV. The data set consists of one file containing a sequential set of energy scans, representing the pre- and main edge regions of the HERFD-XANES spectra. Important column identifiers: <ul> <li>incident energy: “arr_hdh_ene”</li> <li>incident intensity: “I02”</li> <li>fluorescence intensity: “apd”</li> </ul> X-ray total scattering Data was taken at beamline P21.1 of PETRA III at Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany. Diffraction patterns were recorded every 10 s at an X-ray energy of 102.92 keV (λ = 0.121 Å) with an XRD1621 detector (Perkin Elmer Inc., USA) with a pixel size of 200 × 200 μm² and a sample-to-detector distance of 0.411 m. The dataset consist of <ul> <li>in situ data set of CoO nanoassembly synthesis at 160°C</li> <li>in situ data set of CoO nanoassembly synthesis at 140°C</li> <li>ex situ samples prepared at 160 °C at different times</li> <li>commercial reference compounds in powder and 0.1 M BnOH solution</li> </ul> data format: 2D scattering patterns in .tif format The total scattering data is split into individual archives for the above subsets. SAXS and PXRD data set “laboratory_SAXS_data”: Data were recorded with the laboratory molybdenum anode microfocus X-ray setup at LMU, Munich. SAXS data are multiple successive 20 min exposures. Transmission data are 10 s exposures with the beamstop removed. data format: .tif detector images recorded with a Dectris Pilatus 300K. X-ray wavelength: 0.71075 Angstrom Calibrant for sample-to-detector distance, beam center and detector tilt: Silver behenate (AgBeh) data set “synchrotron_SAXS_data”: Data were recorded at beamline P03 at PETRA III, DESY, Hamburg. Data are recorded separately at a long and a short sample-to-detector distance. At the long distance, the exposure time is 5x0.1s. At the short distance, the exposure time is 1x0.5s. data format: .cbf detector images recorded with a Dectris Pilatus 1M. X-ray wavelength: 0.961 Angstrom Calibrant for sample-to-detector distance, beam center and detector tilt: Silver behenate (AgBeh)  data set “laboratory_PXRD_data”: Data were recorded with the laboratory molybdenum anode microfocus X-ray setup at LMU, Munich. The overlap for stitching is 10 px in both horizontal and vertical direction. The recording sequence is 01 02 07 03 04 08 05 06 09 10 11 12 13 14 15 with 3 images at each position, to take the median. The exposure time per image is 1200 s. For LaB6 the sequence is 01 02 03 04 05 06 07 08 09 10 with 5 images at each position, to take the median. The exposure time per image is 300 s. data format: .tif detector images recorded with a Dectris Pilatus 100K. X-ray wavelength: 0.71 Angstrom Calibrant for sample-to-detector distance, beam center and detector tilt: Lanthanum hexaboride NIST SRM 660c (LaB6)

opencc-by-4.0Jun 2014View details →

Fig. 4 in A taxonomic review of the species of Charax Scopoli, 1777 (Teleostei: Characidae: Characinae) with description of a new species from the rio Negro bearing superficial neuromasts on body scales, Amazon basin, Brazil

Fig. 4. Orbital diameter as a function of head length for species of Charax.

opencc-by-4.0Aug 2021View details →

Study on corrosion behavior and corrosion scale characteristics of P110S steel in CO2-H2S saturated high-salt aqueous with pH buffer

The corrosion behavior of P110S steel in CO2-H2S saturated high-salt aqueous with pH buffer was investigated using an autoclave. SEM, EDS, XRD, and Pourbaix diagrams were used to analyze the corrosion scale characteristics. P110S steel experienced severe localized corrosion in high-salt aqueous containing saturated with CO2-H2S despite the addition of pH buffer. The main component of the corrosion scale was mackinawite and FeCO3. The corrosion scale with mackinawite as the main component was dense and had a good protective effect. The corrosion was very light in the area covered by this corrosion scale. However, this corrosion scale was poorly bonded to the matrix and is prone to partial cracking and peeling, which was the cause of severe localized corrosion of P110S steel.

opencc-by-4.0Aug 2021View details →

French Validation of the Boyd and Zimbardo (1997) Transcendental-Future Time Perspective Scale.

Focusing on future temporal perspectives, the Transcendantal-Future Time Perspective scale (TFTP; Boyd and Zimbardo 1997) is specifically designed to measure beliefs about life after death as a one-dimensional, 10-item instrument. We sought in this study to contribute to the French validation of the TFTP scale in a French sample of 256 participants (202 females, 54 males) with a mean age of 34,44 years (SD = 12.62). Content validity was assessed using CFC-14, ZTPI-15, and Schwartz’s ten value measure. Independent variables such as religious affiliation and level of religious practice were also included, as well as control variables related to past experience of confrontation with death. Confirmatory Factor Analysis validated the unidimensionality of the French version of the TFTP scale. Content validity was demonstrated with ZTPI-Future, and nomological validity was confirmed. The findings from this study support the validity of TFTP for assessing cognitions about the future in a French context, in reference to the imagined death of the body and beyond.