cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cc2fqz6bx
title: Data from: Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover

description: Human activities, directly and indirectly, impact ecological engineering
 activities of subterranean rodents. As engineering activities of burrowing
 rodents are affected by, and reciprocally affect vegetation cover via
 feeding, burrowing and mound building, human influence such as settlements
 and livestock grazing, could have cascading effects on biodiversity and
 ecosystem processes such as bioturbation. However, there is limited
 understanding of the relationship between human activities and burrowing
 rodents. The aim of this study was therefore to understand how human
 activities influence the ecological engineering activity of the giant
 root-rat (Tachyoryctes macrocephalus), a subterranean rodent species
 endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We
 collected data on human impact, burrowing activity and vegetation during
 February and March of 2021. Using path analysis, we tested (1) direct
 effects of human settlement on the patterns of livestock grazing
 intensity, (2) direct and indirect impacts of humans and livestock grazing
 intensity on the root-rat burrow density, and (3) whether human settlement
 and livestock grazing influence the effects of giant root-rat burrow
 density on vegetation and vice versa. We found lower levels of livestock
 grazing intensity further from human settlement than in its proximity. We
 also found a significantly increased giant root-rat burrow density with
 increasing livestock grazing intensity. Seasonal settlement and livestock
 grazing intensity had an indirect negative and positive effect on giant
 root-rat burrow density, respectively, both via vegetation cover.
 Analysing the reciprocal effects of giant root-rat on vegetation, we found
 a significantly decreased vegetation cover with increasing density of
 giant root-rat burrows, and indirectly with increasing livestock grazing
 intensity via giant root-rat burrow density. Our results demonstrate that
 giant root-rats play a synanthropic engineering role that affects
 vegetation structure and ecosystem processes. 
description: This file contains data collected at 216 sample plots established
 along 36, 1.5km long transects in the Bale Mountains of Ethiopia. Users
 are free to reuse for scientific purposes.
description: <strong>File name: GRRData.csv</strong>
 All variables used in the analysis stored in the file are defined
 as follows:<br>site: 6 sites where data were
 collected<br>transect: 36 transects where plots were
 established<br>plot: sample plots<br>settype: settlement type
 (permanent vs seasonal)<br>distance: distance of a sample plot from
 a settlement area<br>dung: number of livestock dung counted within
 25 x 25m plot<br>freshholes: number of giant root-rat fresh burrows
 counted within 25x25m plot<br>S: plant species richness recorded
 within a plot<br>vegcvrall: vegetation cover within a plot
DOI: 10.57745/0agkkm
title: eco2adapt_Soil MicroResp_T0_Lithuania

description: This dataset presents the results of soil CLPP (Community-Level Physiological Profile) analyses performed using the MicroResp™ technique for Lithuanian LL (Marcinkonys) (Time zero - June 2023)
DOI: 10.5061/dryad.xsj3tx9mv
title: Data from: Personality determines population-level effects of microplastics consumption in a modelled population of stream-dwelling rainbow trout (Oncorhynchus mykiss)

description: Microplastics in freshwater habitats are consumed by fish, including
 stream-dwelling salmonids, which can alter food consumption or negatively
 affect swimming and foraging behaviour. As population-level effects are
 largely unknown, a simulated population of stream-dwelling rainbow trout
 (Oncorhynchus mykiss) was created using the agent-based model ‘inSTREAM 7’
 to model population-level effects (biomass) of behavioural changes caused
 by microplastics consumption. Individual fish were assigned all possible
 combinations of two personality traits (dominance, boldness/shyness), and
 consumed microplastics while foraging, while their abundance, body size,
 and microplastics consumption were tracked for three different life stages
 (fry, juvenile, adult) for a 10-year simulation period. Three additive
 scenarios were explored: a low-impact scenario with decreased food
 consumption, a medium-impact scenario with added lower swimming speed, and
 a high-impact scenario with added reductions in prey capture efficiency.
 Each was tested with microplastics concentrations of 0%, 1% (i.e., current
 levels), and 3% (i.e., future levels) of drift food. Overall,
 microplastics consumption did not strongly affect trout population
 abundance. Dominant adult trout consumed disproportionally more
 microplastics than all other fish, especially with higher microplastics
 concentrations. Different personality types were affected differently in
 the three scenarios: dominant and bold adults were smaller when food
 consumption was reduced, shy and subordinate adults were smaller when
 swimming speed was lowered, and all dominant adults, regardless of
 boldness, were smaller when foraging efficiency was impeded, with dominant
 and bold fry also less abundant in this scenario. However, effects on fish
 body size were only found with microplastic concentrations of 3%,
 indicating these outcomes can be prevented, as current levels of
 microplastics pollution are unlikely to affect salmonid body size.
 Nevertheless, microplastics ingestion represents an additional stressor
 that may potentially interact with a myriad of anthropogenic impacts that
 already affect wild salmonid populations.
description: This dataset was collected from 10-year model simulations using a
 modified version of the agent-based model 'inSTREAM'. The data
 comparing the abundance, body length and microplastics consumption of a
 simulated population of rainbow trout was collected annually on the census
 day (i.e., September 23) from years 3-10. The data was analyzed using
 mixed models, to see how microplastics pollution (concentrations of 0%, 1%
 and 3% of drift food) affects this fictional population of rainbow trout,
 specifically the abundance and body length of fish with all different
 combinations of two personality traits (dominance, boldness/shyness) of
 three life stages (fry, juvenile, adult).
DOI: 10.5061/dryad.s4mw6m9bp
title: 3D model radula of Gastropteron rubrum

description: The molluscan feeding structure is the radula, a chitinous membrane with
 teeth, which are highly adapted to the food and the substrate to which the
 food is attached. In Polyplacophora and Patellogastropoda, the handling of
 hard ingesta can be facilitated by high content of chemical compounds
 containing Fe or Si in the tooth cusps. Other taxa, however, possess teeth
 that are less mineralized, even though animals have to avoid structural
 failure or high wear during feeding as well. Here, we investigated the
 gastropod Gastropteron rubrum, feeding on hard Foraminifera, diatoms and
 Porifera. Tooth morphologies and wear were documented by scanning electron
 microscopy and their mechanical properties were tested by nanoindentation.
 We determined, that gradients of hard- and stiffness run along each tooth,
 decreasing from cusp to basis. We also found, that inner lateral teeth are
 harder and stiffer than the outer ones. These findings allowed us to
 propose hypotheses about the radula-ingesta interaction. In search for the
 origins of the gradients, teeth were visualized using confocal laser
 scanning microscopy, to determine the degree of tanning, and analyzed with
 energy-dispersive X-ray spectroscopy, to test the elemental composition.
 We found that the mechanical gradients do not have their origins in the
 elemental content, as the teeth did not contain high proportions of metals
 or other minerals, which indicates that their origin might in the degree
 of tanning. However, in the tooth surfaces, which interact with the
 ingesta, high Si and Ca content was determined, which is likely an
 adaptation to reduce wear.
description: For the 3D visualization, mature radular teeth of the working zone of two radulae were extracted manually with forceps. Each tooth was mounted on SEM specimen holders by double-sided adhesive carbon tape, sputter-coated with platinum (5 nm layer), and visualized under the SEM from all sides. Using the 3D software Blender v2.83 (Blender Foundation), the teeth were then modelled by hand constantly comparing the 3D visualization with the SEM images taken from different sides (see also protocol in Krings et al., 2020, 2021e). In the same manner, the position and embedment of the teeth within the membrane were reconstructed.
description: You can use any 3D program as blender, maya, modo, etc.
DOI: 10.15468/dl.xcm2rm
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Juniperus rigida"
 ]
}

 The dataset includes 158 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003561-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8q04
title: Data from: Phenotypic evolution of SARS-CoV-2: A statistical inference approach

description: Since its emergence in late 2019, the SARS-CoV-2 virus has spread
 globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the
 Alpha variant (lineage B.1.1.7) was detected in England and spread
 rapidly, outcompeting the previous lineage. Yet, very little is known
 about the underlying modifications of the infection process that can
 explain this selective advantage. Here, we try to quantify how the Alpha
 variant differed from its predecessor on two phenotypic traits: the
 transmission rate and the duration of infectiousness. To this end, we
 analysed the joint epidemiological and evolutionary dynamics as a function
 of the Stringency Index, a measure of the amount of Non-Pharmaceutical
 Interventions. Assuming that these control measures reduce contact rates
 and transmission, we developed a two-step approach based on SEIR models
 and the analysis of a combination of epidemiological and evolutionary
 information. First, we quantify the link between the Stringency Index and
 the reduction in viral transmission. Secondly, based on a novel
 theoretical derivation of the selection gradient in an SEIR model, we
 infer the phenotype of the Alpha variant from its frequency changes. We
 show that its selective advantage is more likely to result from a higher
 transmission than from a longer infectious period. Our work illustrates
 how the analysis of the joint epidemiological and evolutionary dynamics of
 infectious diseases can help understand the phenotypic evolution driving
 pathogen adaptation.
description: We only used publicly available data.
DOI: 10.5061/dryad.x3ffbg7qw
title: Joint quantile disease mapping with application to Malaria and G6PD deficiency

description: Statistical analysis based on quantile regression methods is more
 comprehensive, flexible, and less sensitive to outliers when compared to
 mean regression methods. When the link between different diseases are of
 interest, joint disease mapping is useful for inferring correlation
 between them. Most studies study this link through multiple correlated
 mean regressions. In this paper we propose a joint quantile regression
 framework for multiple diseases where different quantile levels can be
 considered. We are motivated by the theorized link between the presence of
 Malaria and the gene deficiency G6PD, where medical scientist have
 anecdotally discovered a possible link between high levels of G6PD and
 lower than expected levels of Malaria initially pointing towards the
 occurrence of G6PD inhibiting the occurrence of Malaria. This link cannot
 be investigated with mean regressions and thus the need for flexible joint
 quantile regression in a disease mapping framework arise. Our joint
 quantile disease mapping model can be used for linear and non-linear
 effects of covariates by stochastic splines, since we define it as a
 latent Gaussian model. We perform Bayesian inference of this model using
 the INLA framework embedded in the R software package INLA, resulting in a
 very efficient model even for large datasets. Finally, we illustrate the
 applicability of the model by analyzing the malaria and G6PD deficiency
 incidences, jointly, in 21 countries.
DOI: 10.5061/dryad.t4b8gtj70
title: Data from: Silicon supplementation and jasmonate activation synergistically increase phenolic defences against a legume herbivore

description: The accumulation of silicon (Si) is widely reported to have anti-herbivore
 defensive properties in grasses. There is emerging, but fragmentary,
 evidence that Si could play a similar role in legumes. Here, we sought to
 understand the effects of Si supplementation on anti-herbivore defensive
 properties in lucerne (Medicago sativa), especially in relation to other
 potential defences (i.e. phenolics) and the phytohormone that regulates
 anti-herbivore defences, jasmonic acid or jasmonate (JA), which is also
 linked to Si accumulation. We determined how growth, root nodulation and
 chemistry (carbon, nitrogen and phenolic concentrations) of four genotypes
 of lucerne responded to Si supplementation, with and without the
 application of JA, and we used feeding assays to determine the subsequent
 effects on the feeding success of adult Sitona discoideus weevils. Si
 supplementation increased plant mass and root nodulation of M. sativa by
 61% and 227%, respectively, and reduced relative consumption (RC) and
 frass production by S. discoideus by 38% and 30%, respectively. Si
 supplementation had no effect on foliar nitrogen concentrations, most
 likely due to the dilution effects of increased plant growth and foliar
 carbon. Phenolic concentrations were negatively correlated with leaf RC;
 RC also decreased by 34% when JA was applied to plants. When Si was
 combined with JA application, phenolics were significantly enhanced,
 demonstrating the potential to stimulate multiple anti-herbivore
 properties in M. sativa. The novel findings suggest that Si accumulation
 may play a more important role in legume resistance to herbivorous animals
 than previously thought. The ubiquity of soil Si and its emerging
 functional role in plant biology, including plant–animal interactions,
 suggest that these patterns could be common amongst legumes.
DOI: 10.5061/dryad.j6q573nkx
title: Data from: Morphological measurements and mercury levels of Saltmarsh Sparrows sampled across their breeding range

description: Malaria parasites (genus Plasmodium) are important agents of infectious
 disease in birds and multiple factors including warming temperatures and
 environmental contamination may act to increase their geographic and host
 ranges. Here, we examined the role of geographical variation and
 environmental mercury exposure in malaria parasite infection dynamics in
 an imperiled songbird species with high mercury exposition, the Saltmarsh
 Sparrow (Ammospiza caudacutus). Using PCR methods, we screened 280
 Saltmarsh Sparrows from across their breeding range for malaria parasite
 infection. We detected malaria parasites in 17% of sampled birds and a
 total of six Plasmodium lineages. Prevalence of infection and diversity of
 parasite lineages varied across the breeding range of the Saltmarsh
 Sparrow and increased at more northern latitudes. Although mercury is a
 known immunosuppressant and has been documented to alter an individual’s
 susceptibility to pathogens, we did not find a significant difference in
 blood mercury levels between infected and not infected birds, perhaps due
 to sampling methods and/or small sample sizes. As a specialist of coastal
 wetlands, the Saltmarsh Sparrow is an excellent indicator species for
 ecological health, and the patterns of malaria parasite infection with
 host distribution and mercury suggest that birds at northern latitudes are
 at greater risk of disease and should be priorities for conservation,
 habitat, and pathogen monitoring.
DOI: 10.5061/dryad.kwh70rz9d
title: Data from: Vitamin D induces SIRT1 activation through K610 deacetylation in colon cancer

description: Posttranslational modifications of epigenetic modifiers provide a flexible
 and timely mechanism for rapid adaptations to the dynamic environment of
 cancer cells. SIRT1 is an NAD+-dependent epigenetic modifier whose
 activity is classically associated with healthy aging and longevity, but
 its function in cancer is not well understood. Here, we reveal that
 1a,25-dihydroxyvitamin D3 (1,25(OH)2D3, calcitriol), the active metabolite
 of vitamin D (VD), promotes SIRT1 activation through auto-deacetylation in
 human colon carcinoma cells, and identify lysine 610 as an essential
 driver of SIRT1 activity. Remarkably, our data show that the
 post-translational control of SIRT1 activity mediates the
 antiproliferative action of 1,25(OH)2D3. This effect is reproduced by the
 SIRT1 activator SRT1720, suggesting that SIRT1 activators may offer new
 therapeutic possibilities for colon cancer patients who are VD deficient
 or unresponsive. Moreover, this might be extrapolated to inflammation and
 other VD deficiency-associated and highly prevalent diseases in which
 SIRT1 plays a prominent role.
description: For Immunofluorescences, datasets were collected with ImageJ
 software as fluorescence intensity corrected by cell number. For each experiment (named in the excel n1 to
 nx), 3 different fields were evaluated per slide. Statistical methods are
 detailed in the Excel file. For western blots, bands were measured by
 densitometry and analyzed with ImageJ software. Statistical methods are
 detailed in the Excel file. For Deacetylase assays and NAD+ levels, datasets
 were collected from the luminometer. Statistical methods are detailed in
 the Excel file. For TMAs in
 Figure 3C-E: immunoreactivity was quantified blind with a Histoscore (H
 score) that considers both the intensity and percentage of cells stained
 for each intensity (low, medium, or high) following this algorithm (range
 0–300): H score = (low%) × 1 + (medium%) × 2 + (high %) × 3.
 Quantification for each patient biopsy was calculated blindly by 2
 investigators. Statistical analysis was
 performed with Chi-square test. For the TNM plots, data was collected from Gene Expression Omnibus
 of the National Center for Biotechnology Information (NCBI-GEO)
  (https://www.ncbi.nlm.nih.gov/geo/) repository for datasets containing
 “cancer” samples. Only datasets utilizing the Affymetrix HGU133,
 HGU133A_2, and HGU133A platforms were considered.
 For cell cycle, data were
 collected and analyzed using CXP
 software (Becton-Dickinson). Statistical methods are detailed in the Excel
 file. For
 proliferation curves datasets were collected with Spectra FLUOR (Tecan) at
 542 nm and analyzed in Excel. Statistical methods are detailed in the
 Excel file.
description: Datasets are presented in Excel. For TNM
 plots we used this link: https://tnmplot.com/analysis/ Rawdata: original data are presented in PowerPoint No additional software is required.
DOI: 10.5061/dryad.02v6wwq7x
title: Data from: Decadienal afforestation and risks to montane grassland amphibians in the Udzungwa Plateau, Tanzania

description: Human modification of the environment has drastically changed ecosystems
 around the globe. While forest-loss (deforestation) has been well studied
 for its effects on ecosystems, afforestation also has major impacts on
 ecosystems. The Udzungwa Plateau in Tanzania is naturally a mix of forests
 and grasslands. However, non-native pine plantations have recently
 increased in the area displacing the native grasslands of the montane
 plateau. In this study, we explored the effects of land use change on
 amphibian communities by comparing amphibian surveys before non-native
 plantations were introduced (~ 2000) and after (2017-2019). To put these
 amphibian surveys into wider context across the plateau, to distinguish
 local population loss compared to plateau-wide extinctions, we compared
 new sampling locations and broader surveys and assessed landscape change
 through remotely sensed data. Amphibian encounter surveys found
 approximately the same species diversity across all sampling locations,
 but local extinctions appear likely. Remaining amphibians appear to be
 limited to small refugia in non-pine wetlands. Approximately half (45%) of
 the species found have limited distributional ranges (&lt;72,000 km2)
 and are described as habitat specialists by the IUCN Red List. Monitoring
 pine plantation growth using remote sensing techniques suggested only
 limited extensions of plantations between 2000 through to 2013-2016, but
 ground-surveys found small pines (&lt;3 years old) throughout almost
 all areas identified as grasslands on satellite imagery. Our study
 highlights the plight of this narrowing biome on the African continent and
 calls for more intensive research on the impact of non-native plantations
 on natural communities.
description: This dataset consists of new amphibian surveys in the Udzungwa
 Plateau of Tanzania (2017 & 2019), comparisons to previously
 published amphibian surveys in the area (2000 onward, outlined in the
 text) and surveys found on vertnet.org using the spatial selection of
 records tool. To these survey, landuse change and the rise of plantations
 were calculated using land cover rasters from ESRI which were clipped to
 the shapefile of the Udzungwa Plateau.
description: Missing data in the data file
 "Vertnet_udzungwa_amphibia_list" are coded as
 "null".
DOI: 10.5061/dryad.h9w0vt4pp
title: Data from: Hydraulic vulnerability of tropical forests is largely independent of water availability

description: Tropical rainforest woody plants have been thought to have uniformly low
 resistance to hydraulic failure and to function near the edge of their
 hydraulic safety margin, making these ecosystems vulnerable to drought;
 however, this may not be the case. Using data collected at 30 tropical
 forest sites for three key traits associated with drought tolerance, we
 show that site-level hydraulic diversity of leaf turgor loss point,
 resistance to embolism (P50), and hydraulic safety margins (HSMs) is high
 across tropical forests and largely independent of water availability.
 Species with high HSMs (&gt;1 MPa) and low P50 values (&lt;-2 MPa)
 are common across the wet and dry tropics. This high site-level hydraulic
 diversity, largely decoupled from water stress, could influence which
 species are favored and become dominant under a drying climate. High
 hydraulic diversity could also make these ecosystems more resilient to
 variable rainfall regimes.
DOI: 10.15468/dl.nf9aaj
title: Occurrence Download

description: A dataset containing 370 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Philippines",
 "TaxonKey is Kappaphycus alvarezii"
 ]
}

 The dataset includes 370 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003562-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cjxayp
title: Occurrence Download

description: A dataset containing 552 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Artemisia desertorum"
 ]
}

 The dataset includes 552 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003563-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.