Find research datasets worth reusing

opencc-by-4.0Nov 2023View details →

Data and code for replication of: "Global warming and heat extremes to exacerbate inflationary pressures. M. Kotz, F. Kuik, E. Liz, C. Nickel. Nature Communications Earth & Environment (2023)."

This repository contains secondary data and code necessary to reproduce the results of the manuscript:Global warming and heat extremes to exacerbate inflationary pressures.M. Kotz, F. Kuik, E. Liz, C. Nickel. Nature Communications Earth & Environment (2023). For further information please contact: maxkotz@pik-potsdam.de This document contains:1. An outline of the data included in the repository.2. An outline of the code included in the repository. See the README for further details. Credit and thanks go to Miles Parker, Chiara Osbat and Emanuele Franceschi for compiling the inflation data which is used in this study. Inflation data provided here has been anonymised (countries shuffled and names replaced by random letter combinations) to enable reproduction of our results, while limiting further use. Moreover, inflation in terms of the change in the logarithm of prices is included, whereas the level of price indices are excluded. For full inflation data please see the forthcoming publication by Miles Parker, Chiara Osbat,and Emanuele Franceschi (contact Miles.Parker@ecb.europa.eu for further enquiries into the raw inflation data).

opencc-by-4.0Dec 2023View details →

Data - Krieg et al. Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)

Data used in analyses and code to produce figures.

opencc-by-4.0Nov 2023View details →

Sample preservation methods for nitrous oxide concentration and isotope ratio measurements in aquatic environments

This is the raw data for the method paper submitted in Limnology and Oceanography: Methods titled "Sample preservation methods for nitrous oxide concentration and isotope ratio measurements in aquatic environments".

opencc-by-4.0Dec 2023View details →

Suspect Screening and Non-targeted Analysis of Chemical Pollutants in Botswana's Aquatic Environments

Raw HRMS data associated with the paper titled  "Suspect Screening and Non-targeted Analysis of Chemical Pollutants in Botswana’s Aquatic Environments"

opencc-by-4.0Dec 2023View details →

Data associated with the study titled "The role of micro-environments on computed vibrationally-resolved emission spectra: The case of oxazines."

This repository contains data associated with the study titled "The role of micro-environments on computed vibrationally-resolved emission spectra: The case of oxazines." Folder Structure: ========== /CV/ ========== /CV-bare/: Coordinates of the ground state (GS) and excited state (ES) for CV+ dye. ========== /DR/ ========== /DR-bare/DR-most-stable/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of DR+ dye. ========== /NB/ ========== /NB-bare/NB-most-stable/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of NB+ dye. /NB-bare/NB-other-conformers/: Coordinates of the ground state (GS) and excited state (ES) for other conformers responsible for over 90% of the total Boltzmann weighted population of NB+ dye. ========== /Ox1/ ========== /Ox1-bare/Ox1-most-stable/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of Ox1+ dye. /Ox1-bare/Ox1-other-conformers/: Coordinates of the ground state (GS) and excited state (ES) for other conformers responsible for over 90% of the total Boltzmann weighted population of Ox1+ dye. ========== /Ox4/ ========== /Ox4-bare/Ox4-most-stable/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of Ox4+ dye. /Ox4-bare/Ox4-other-conformers/: Coordinates of the ground state (GS) and excited state (ES) for other conformers responsible for over 90% of the total Boltzmann weighted population of Ox4+ dye. /Ox4-bare/Ox4-PCM/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of Ox4+ dye in the Polarizable Continuum Model (PCM). /Ox4-betaine/: Coordinates of the ground state (GS) and excited state (ES) for a betaine molecule aggregated to Ox4+ dye at different positions. /Ox4-water-gasphase/: Coordinates of the ground state (GS) and excited state (ES) for a water molecule aggregated to Ox4+ dye at different positions as well as two water mocules aggregated to Ox4+ at postion 1. /Ox4-water-PCM/: Coordinates of the ground state (GS) and excited state (ES) for a water molecule aggregated to Ox4+ dye at different positions in PCM. ========== /Ox170/ ========== /Ox170-bare/Ox170-most-stable/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of Ox170+ dye. /Ox170-bare/Ox170-other-conformers/: Coordinates of the ground state (GS) and excited state (ES) for other conformers responsible for over 90% of the total Boltzmann weighted population of Ox170+ dye. /Ox170-bare/Ox170-PCM/: Coordinates of the ground state (GS) and excited state (ES) for the most stable conformer of Ox170+ dye in the Polarizable Continuum Model (PCM). /Ox170-betaine/: Coordinates of the ground state (GS) and excited state (ES) for a betaine molecule aggregated to Ox170+ dye at different positions. /Ox170-water-gasphase/: Coordinates of the ground state (GS) and excited state (ES) for a water molecule aggregated to Ox170+ dye at different positions as well as two water mocules aggregated to Ox170+ at postion 1. /Ox170-water-PCM/: Coordinates of the ground state (GS) and excited state (ES) for a water molecule aggregated to Ox170+ dye at different positions in PCM. Notes: For any inquiries or clarifications, please contact the creators.

opencc-byApr 2021View details →

Cannon Environment Textured

My Textured Environment with Textured Cannon model for my W10: Create Textures Assignment for DIG4324C class. Source: Objaverse 1.0 / Sketchfab

opencc-byMar 2021View details →

Cannon Environment Low

My Low poly Environment with my Textured Cannon model for my W8: Create Low Poly and UV Assignment for DIG4324C class. Source: Objaverse 1.0 / Sketchfab

opencc-byJan 2020View details →

Environment Rocks

Some environment rocks as part of a gangplank inspired shipwreck diorama otherwise found (albeit heavily decimated) on my profile. Any and all models of this diorama can be downloaded for free, and upon request, I can also send you the non decimated / non sculpted versions as well. Though keep in mind for this particular model, the non sculpted version is just a block :/ Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Jan 2024View details →

Supplementary data for "Increasing risks of extreme salt intrusion events across European estuaries in a warming climate", published in Communications Earth & Environment

This data repository contains python scripts and post-processed climate model and salt intrusion length data to reproduce figures in the paper below. ==================== Title: Increasing risks of extreme salt intrusion events across European estuaries in a warming climate (<a href="https://www.nature.com/articles/s43247-024-01225-w">Link to the full paper</a>) Author: Jiyong Lee, Bouke Biemond, Huib de Swart, and Henk A. Dijkstra Journal: Communications Earth & Environment Year: 2024 Publisher: Nature ====================

opencc-zeroJan 2024View details →

N-cadherin dynamically regulates pediatric glioma cell migration in complex environments

Pediatric high-grade gliomas are highly invasive and essentially incurable. Glioma cells migrate between neurons and glia, along axon tracts, and through extracellular matrix surrounding blood vessels and underlying the pia. Mechanisms that allow adaptation to such complex environments are poorly understood. N-cadherin is highly expressed in pediatric gliomas and is associated with shorter survival. We found that inter-cellular homotypic N-cadherin interactions differentially regulate glioma migration according to the microenvironment, stimulating migration on cultured neurons or astrocytes but inhibiting invasion into reconstituted or astrocyte-deposited extracellular matrix. N-cadherin localizes to filamentous connections between migrating leader cells but to epithelial-like junctions between followers. Leader cells have more surface and recycling N-cadherin, increased YAP1/TAZ signaling, and increased proliferation relative to followers. YAP1/TAZ signaling is dynamically regulated as leaders and followers change position, leading to altered N-cadherin levels and organization. Together, the results suggest that pediatric glioma cells adapt to different microenvironments by regulating N-cadherin dynamics and cell-cell contacts.

opencc-zeroJan 2024View details →

Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation

The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of Cornus from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of Cornus. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in Liriodendron and Cornus, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in Cornus. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.

opencc-zeroFeb 2024View details →

Synthetic eco-evolutionary dynamics in simple molecular environment

The understanding of eco-evolutionary dynamics, and in particular the mechanism of emergence of species, is still fragmentary and in need of test bench model systems. To this aim, we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10^15 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼ 10^12 DNA oligomers of fixed sequence ('resources') over which they compete. At each cycle ('generation'), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences ('species') drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions becomes important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.

Data from: Association between gut health and gut microbiota in a polluted environment

Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, aid in digestion of otherwise indigestible foodstuffs, and even changing host behaviour. Stress, such as environmental pollution, parasites, predators, and intraspecies competition, can alter the composition of the gut microbiome, which in turn can change host-microbiome interactions in ways that are detrimental to the host such as causing metabolic dysfunction and inflammation. While host-microbiome interactions have been extensively studied in humans and captive animals, studies into wild animal microbiomes have been scarce. We assessed the effects of disturbed environment on gut health of bank voles exposed to radionuclides in natural habitat using a combined approach of transcriptomics, microbial community analysis by 16S amplicon sequencing, histological staining analyses of colon tissue, and quantification of gut microbiota -produced short-chain fatty acids in faecal matter and blood that act as mediators of host-microbiome interactions. We found signs of weakened mucus layer and related changes in Clca1 and Agr2 gene expression and microbiome composition in animals exposed to radionuclides. These results imply that disturbed environment can have widely reaching effects through gut health.

Data from: thyroid hormone concentrations in female baboons: metabolic consequences of living in a highly seasonal environment

How female mammals adapt metabolically in response to environmental variation remains understudied in the wild, because direct measures of metabolic activity are difficult to obtain in wild populations. However, recent advances in the non-invasive measurement of fecal thyroid hormones, triiodothyronine (T3), an important regulator of metabolism, provide an opportunity to understand how female baboons living in the harsh Amboseli ecosystem in southern Kenya adapt to environmental variability and escape strict reproductive seasonality. Specifically, we assessed how a female's activity budget, diet, and concentrations of fecal T3 metabolites (mT3) changed over the course of the year and between years. We then tested which of several environmental variables (season, rainfall, and temperature) and behavioral variables (female activity budget and diet) best predicted mT3 concentrations. Finally, we determined if two important reproductive events – onset of ovarian cycling and conception of an offspring – were preceded by changes in female mT3 concentrations. We found female baboons' mT3 concentrations varied markedly across the year and between years as a function of environmental conditions. Further, changes in a female's behavior and diet only partially mediated the metabolic response to the environment. Finally, mT3 concentrations increased in the weeks prior to menarche and cycling resumption, regardless of the month or season in which cycling started. This pattern indicates that metabolic activation may be an indicator of reproductive readiness in female baboons as their energy balance is restored.

Data from: Vertically inherited microbiota and environment modifying behaviors conceal genetic variation in dung beetle life history

Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feedback on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating i) physical environmental modifications, and ii) the vertical inheritance of microbes, we assess how environment modifying behavior and microbiome transmission shape heritable variation. We found that depriving larvae from symbionts and environment modifying behaviors increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that alter the degree to which they can be manipulated. Furthermore, we found heritable variation for the response to the elimination of environmental modifications, indicating that genotypes differ in their dependence on the ability to manipulate their environment. Our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.

Small-scale fires interact with herbivore feedbacks to create persistent grazing lawn environments

Fire-herbivory feedbacks strongly influence the formation of grazing lawns in savanna ecosystems. Preliminary findings suggest that small-scale (< 25 ha) fires can engineer grazing lawns by concentrating herbivores on the post-burn green flush; however, the persistence of such grazing lawns over the longer term and without repeated fire is unknown. We used high-resolution Light Detection and Ranging (LiDAR) to investigate the long-term effects of fire manipulation on short grass structure (height, cover, volume, and spatial continuity) and grazing lawn establishment in Kruger National Park, South Africa. We analysed the effects of fire exclusion and experimental burns applied over a 7-year period (2013-2019) followed by a one-year cessation of burning at varying spatial scales during the early and late dry seasons. Fires contributed a fourfold increase in short grass cover, regardless of fire season or size. The distribution of grass height differed significantly between fire-induced grazing lawns and recently unburnt parts of the landscape where controlled fires were excluded over the experimental period. The volume (corresponding to bulk density) of short grass on the landscape responded strongly to fires, with grass volume <20 cm in height increasing with both early and late dry season fires. Early dry season fires caused larger and more homogeneous short grass patches. Furthermore, early dry season fires were more influential in increasing the cover of the shortest grass height class (1-5 cm). Synthesis and applications. Our results demonstrate that fire-induced grazing lawns can persist over the longer-term, even when fires are no longer applied, leading to the creation of vertical and horizontal heterogeneity in the grass layer. Small-scale fires, therefore, represent a feasible management approach to expanding grazing lawn extent, potentially benefiting grazer coexistence and diversity.

A previously undescribed scene-selective site is the key to encoding ego-motion in naturalistic environments

Current models of scene processing in the human brain include three scene-selective areas: the Parahippocampal Place Area (or the temporal place areas; PPA/TPA), the restrosplenial cortex (or the medial place area; RSC/MPA) and the transverse occipital sulcus (or the occipital place area; TOS/OPA). Here, we challenged this model by showing that at least one other scene-selective site can also be detected within the human posterior intraparietal gyrus. Despite the smaller size of this site compared to the other scene-selective areas, the posterior intraparietal gyrus scene-selective (PIGS) site was detected consistently in a large pool of subjects (n=59; 33 females). The reproducibility of this finding was tested based on multiple criteria, including comparing the results across sessions, utilizing different scanners (3T and 7T) and stimulus sets. Furthermore, we found that this site (but not the other three scene-selective areas) is significantly sensitive to ego-motion in scenes, thus distinguishing the role of PIGS in scene perception relative to other scene-selective areas. These results highlight the importance of including finer scale scene-selective sites in models of scene processing – a crucial step toward a more comprehensive understanding of how scenes are encoded under dynamic conditions.

Galaxias maculatus occurrence data in marine and freshwater environments in rivers of southern Chile

In the present study, we assessed ecological and historical factors (Gondwanan vicariance, marine dispersion) and potential dispersion (niche-tracking) that explain distribution of Galaxias maculatus in the Southern Hemisphere based on occurrences available in the Global Biodiversity Information Facility (GBIF; period 1980 to 2022) and ichthyological sampling in five river systems in southern Chile between March and November 2019. Ocurrence data extracted from GBIF are available at <a href="http://www.gbif.org">http://www.gbif.org</a> and additional ichthyological sampling data that were used are provided here. Data provided here are based on sampling of Galaxias maculatus at 12 sites in five river systems in southern Chile during March, May, August, and November 2019. Sampling sites were selected to cover a continuous river gradient, including (whenever possible) the lower, middle, and upper sections of each river system. Fish were captured using beach seines (5 m long, 1.5 m high, and 10 mm stretched mesh) in shoreline habitats of each evaluated river system.

opencc-by-4.0Mar 2024View details →

Symbiodiniaceae diversity varies by host and environment across thermally distinct reefs

Analysis for Coral population ecology predicts Symbiodiniaceae diversity across thermally distinct reefs Authors: Magena R. Marzonie, Matthew R. Nitschke, Line K. Bay, David G. Bourne, Hugo B. Harrison 1_Analysis.Rmd contains all scripts required to run analyses within the manuscript. Analysis are structured as follows within the Rmd: (use Outline tab in Rmd for easy navigating) <ol> <li>Library statistics for ITS2 type profiles/DIVs <br</li> <li>UPGMA trees for ITS2 type profiles/DIVs</li> <li>Marker alignment tanglegram psba-ITS2</li> <li>PCoAs with UniFrac distance</li> <li>distance-based RDAs</li> <li>Procrustes rotation analysis</li> <li>distance-based RDA subset models with host genetic data</li> </ol>   2_R2Analyses.Rmd <ol> <li>Scripts to run host NJ (neighbour-joining trees)</li> <li>Run final distance based RDA models (host and environmental conditional models)</li> </ol> Other files needed to run scripts> O_SymPortal folder contains post-med sequence analysis of symbiont DIVs and Type Profiles which are required to run 1_Analysis Metadata.csv contains environmental and host species data associated with each sample. Note that 'Vial' refers to each coral individual sample collected Metadata_mtorf.csv contains environmental and host species data associated with each sample, with updated mtORF alignment. Both metadata files are required for 1_Analysis. Note that 'Vial' refers to each coral individual sample collected psba txt files are required to run the marker alignment PverDart_CSS/ PmeaDart_CSS/ AcroDart_AlCluster_CSS contains the scripts required to run host filtering These files are not needed to directly run 1_Analysis.Rmd scripts, but show the pre-filtering steps prior to importing host genetic data.