cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rn8pk0p7h
title: Foraging in fear: spatial variation in range use, vigilance, and perceived risk in Chacma baboons (Papio ursinus)

description: Spatial variation in predation risk can lead to behavioural modifications
 including increased vigilance and avoidance. Coined the landscape of fear,
 previous studies have suggested that an animal’s spatial perception of
 risk is the most critical landscape within their environment. Few studies
 have integrated the landscape of fear with spatial measures of risk and
 assessments of resource availability within a single analytical framework.
 We assessed whether long-term space use in chacma baboons was influenced
 by the distribution of key resources, perceived risk and the probability
 of encountering threats. We also assessed whether vigilance, varied
 spatially in response to potential threats. Contrary to expectations,
 perceived risk was primarily related to other baboon groups rather than
 predators, with the baboons modifying their range use to reduce intergroup
 encounters. In contrast, the probability of encountering leopards was the
 primary determinant of spatial variation in vigilance behaviour.
 Collectively, while other groups have a greater influence on space use,
 the baboons are critically aware of the predation risk landscape,
 modifying their vigilance strategies in response to leopards. Baboons thus
 use different long-term strategies to alleviate the risks imposed by
 different threats. Our methodological approaches provide a framework for
 future studies looking to tease apart these effects.
DOI: 10.5061/dryad.4xgxd2571
title: Data from: Healthy cardiovascular biomarkers across the lifespan in wild-born chimpanzees (Pan troglodytes)

description: Chimpanzees (Pan troglodytes) are a crucial model for understanding the
 evolution of human health and longevity. Cardiovascular disease is a major
 source of mortality during ageing in humans and therefore a key issue for
 comparative research. Current data indicate that compared to humans,
 chimpanzees have proatherogenic blood lipid profiles, an important risk
 factor for cardiovascular disease in humans. However, most work to date on
 chimpanzee lipids come from laboratory-living populations where lifestyles
 diverge from a wild context. Here, we examined cardiovascular profiles in
 chimpanzees living in African sanctuaries, who semi-free-range in large
 forested enclosures, consume a naturalistic diet, and generally experience
 conditions more similar to a wild chimpanzee lifestyle. We measured blood
 lipids, body weight and body fat in 75 sanctuary chimpanzees and compared
 them to publicly available data from laboratory-living chimpanzees from
 the Primate Ageing Database. We found that semi-free-ranging chimpanzees
 exhibited lower body weight and lower levels of lipids that are risk
 factors for human cardiovascular disease, and that some of these
 disparities increased with age. Our findings support the hypothesis that
 lifestyle can shape health indices in chimpanzees, similar to effects
 observed across human populations, and contribute to an emerging
 understanding of human cardiovascular health in evolutionary context.
description: See methods in the manuscript for all details.
description: Please see the key tab in the file for all details for usage. The
 comparison dataset used in this work is availible from the Primate Aging
 Database (https://primatedatabase.org/).
DOI: 10.5061/dryad.bvq83bk6k
title: Context-Dependent Effects of a Reintroduced Ungulate on Soil Properties are Driven by Soil Texture, Moisture and Herbivore Activity

description: Although there is considerable evidence that large mammalian herbivores
 influence ecosystem-level processes, studies have reported such widely
 varying results that generalizations have remained elusive. Here, we use
 an 18-year-old exclosure experiment – stratified across a landscape
 heterogeneous with respect to soil texture, moisture and herbivore
 activity – to understand the variable effects of tule elk (Cervus
 canadensis nannodes), a native reintroduced herbivore, on soil properties
 along the coast of northern California. Elk significantly increased soil
 bulk density and created a compacted layer at shallow soil depth, while
 decreasing infiltration rate and pH. The effects of elk on bulk density,
 penetration resistance and pH varied with soil type, being least
 pronounced in coarse, sandy loams and greatest in loose sand. The effects
 of elk on nutrient availability varied along gradients of soil texture and
 moisture. In coarser soils, elk decreased ammonium availability, but
 increased it in finer soils. Elk also decreased soil moisture content, in
 part through their positive effect on bulk density, and this effect was
 most pronounced in coarser soils. Through decreasing soil moisture
 content, elk also decreased nitrate availability in coarser soils. At
 greater levels of elk activity (as measured by dung deposition), the elk
 effect on bulk density was amplified, and this had a corresponding
 negative effect on nitrate and phosphate availability. Our study has
 demonstrated that a better understanding of spatial variation in the
 effects of herbivores on ecosystems can emerge by evaluating their
 influences across gradients of soil texture, soil moisture, and herbivore
 activity. These data enabled us to evaluate several frameworks that have
 been developed to understand the variable effects of herbivores on
 ecosystems, which is a significant step in reconciling the many competing
 ideas put forth to explain the context-dependent effects of large
 herbivores on grazed ecosystems.
description: See published article.
description: See published article.
DOI: 10.5061/dryad.31zcrjdj0
title: Data from: Foraging behaviour and habitat-use drives niche segregation in sibling seabird species

description: To mediate competition, similar sympatric species are assumed to utilise
 different resources, or the same but geographically separated resources.
 The two giant petrels (Macronectes spp.) are intriguing in that they are
 morphologically similar seabirds with overlapping diets and distributions.
 To better understand the mechanisms allowing their co-existence, we
 investigated intra- and interspecific niche segregation at Marion Island
 (Southern Indian Ocean), one of the few localities where they breed in
 sympatry. We used GPS tracks from 94 individuals and remote-sensed
 environmental data to quantify habitat-use, combined with blood carbon and
 nitrogen stable isotope ratios from 90 individuals to characterise their
 foraging habitat and trophic ecology. Females of both species made distant
 at sea foraging trips and fed at a similar trophic level. However, they
 used distinct pelagic habitats. In contrast, males of both species mainly
 foraged on or near land, resulting in significant sexual segregation, but
 high interspecific habitat and diet overlap. However, some males showed
 flexible behavioural strategies, also making distant, pelagic foraging
 trips. Using contemporaneous tracking, environmental and stable isotope
 data we provide a clear example of how sympatric sibling species can be
 segregated along different foraging behaviour dimensions.
DOI: 10.5061/dryad.2547d7wnz
title: Data from: Immunoreactive peptide maps of SARS-CoV-2

description: Serodiagnosis of SARS-CoV-2 infection is impeded by immunological
 cross-reactivity among the human coronaviruses (HCoVs) SARS-CoV-2,
 SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. To
 study humoral immune responses specific to SARS-CoV-2, it is
 imperative to identify peptides that may enable discrimination between
 exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide
 microarray and plasma samples collected at two time points from 50
 subjects with SARS-CoV-2 infection confirmed by qPCR, samples collected in
 2004-2005 from 11 subjects with IgG antibodies to SARS-CoV-1, 11 subjects
 with IgG antibodies to other seasonal human coronaviruses (HCoV), and 10
 healthy human subjects. The peptide microarrays consist of ~172000 12-mer
 peptide probes spanning whole viral genomes. This dataset consists of
 reactivity values for individual peptides from all 132 plasma samples for
 both IgG and IgM. Also made available is the correspondence key
 that provides a reference for all viral genome sequences that a peptide
 originated from.
description: Each peptide array is divided in 12 subarrays, with each subarray
 comprising ~172,000 twelve-amino acid (aa) nonredundant linear peptides
 that tile the proteomes of known HCoVs with 11 amino acid overlap. A total
 of 132 plasma samples were tested using eleven 12-plex peptide arrays. If
 there are three or more continuous reactive peptides (with reactivity
 values above the threshold of 10000) in samples, then those peptide
 sequences are reassembled to constitute an epitope. The length of an
 epitope depends on the number of such continuous reactive
 peptides.
description: <strong>Aggregate data for all
 samples:</strong> In peptide microarray, text
 files containing peptide probe reactivity values for individual samples
 are generated as tab-delimited text files. Data from these files was
 aggregated into CSV files for IgG and IgM. Each row contains probe
 sequences and their unique identifiers that can be matched with their
 reference in correspondence key for its source, followed by reactivity
 values for all 132 samples. 
 IgG_aggregate_file_covid_pub.csv
 IgM_aggregate_file_covid_pub.csv
 <strong>Correspondence key and header
 map:</strong> The cross-reactivity among human
 coronaviruses is because of the highly conserved nature of their genomes.
 Because of this, it is imperative to map 12-mer peptides to their source
 for proper epitope reassembly.  Correspondence key file containing probes
 sequences, their unique identifiers and the source makes it possible to
 detect the longest epitope sequence. The header map file acts as an
 additional layer of information with details of protein names and their
 locations in the genome.
 NTX-127_all_11_files_correspondence_key.txt
 Corona_chip_header_map_no_seq.txt
 <strong>Epitope re-assembly</strong>
 The software for epitope re-assembly is an R script that takes
 either IgG or IgM as an argument and makes separate epitope files for all
 coronaviruses. epitope_reassembler.R  
 <strong>Multidimensional analysis</strong>
DOI: 10.5061/dryad.tb2rbnzz4
title: De novo profiling of long non-coding RNAs involved in MC-LR–induced liver injury in whitefish: discovery and perspectives

description: Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap
 in knowledge persists regarding the underlying molecular mechanisms of
 liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have
 been extensively studied in model organisms, our knowledge concerning the
 role of lncRNAs in liver injury is limited. Given that lncRNAs show low
 levels of sequence conservation, their role becomes even more unclear in
 non-model organisms without an annotated genome, like whitefish (Coregonus
 lavaretus). The objective of this study was to discover and profile
 aberrantly expressed polyadenylated lncRNAs that are involved in
 MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq)
 data, we de novo assembled a high-quality whitefish liver transcriptome.
 This enabled us to find 94 differentially expressed (DE) putative
 evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC,
 and 4429 DE putative novel whitefish lncRNAs, which differed from
 annotated protein-coding transcripts (PCTs) in terms of minimum free
 energy, guanine-cytosine (GC) base-pair content and length. Additionally,
 we identified DE non-coding transcripts that might be 3′ autonomous
 untranslated regions (3′UTRs) of mRNAs. We found both evolutionary
 conserved lncRNAs as well as novel whitefish lncRNAs that could serve as
 biomarkers of liver injury.
description: File list: 
 <strong>Cla_52_samples_liver_transcriptome.fasta</strong> - 
 de novo assembled and filtered liver transcriptome of Coregonus
 lavaretus 
 <strong>Cla_novel_lncRNAs.fasta</strong> - list of
 putative novel lncRNAs of Coregonus lavaretus 
 
 <strong>Cla_malat1.fasta</strong> - sequence of malat1
 discovered in this study 
 
 <strong>qPCR-housekeeping-transcript.fasta</strong> - sequence
 of transcirpt used for normalizing qPCR results
DOI: 10.5061/dryad.cfxpnvx3m
title: Traits mediate a tradeoff in seedling growth response to light and conspecific density in a diverse subtropical forest

description: Understanding tree species responses to biotic and abiotic factors is
 fundamental for stronger predictions of community assembly and dynamics.
 However, several challenges remain. These include a failure to investigate
 whether there is evidence for key hypothesized life-history tradeoffs and
 to link these tradeoffs to functional traits. In this study, we seek to
 explicitly address the above outstanding challenges by constructing models
 for individual seedling growth in response to abiotic and biotic factors
 using three years of seedling census data from a 20-ha subtropical forest
 dynamics plot in a diverse subtropical forest and correlated these
 responses with functional traits. We found that light and conspecific
 neighbours increase and decrease the relative growth rate of tree
 seedlings, respectively. We also found that the ability of a species to
 positively respond to canopy openness trades off against susceptibility to
 CNDD. This tradeoff was evident across seasons and could be predicted on
 functional trait - stem and leaf dry matter content. Synthesis. Our
 findings indicate species that can grow quickly in high light environments
 also tend to suffer more conspecific negative density dependence. The
 results highlight strong evidence of a tradeoff relating to growth and
 defence widely hypothesized to be of importance in diverse tree
 communities and that this tradeoff occurs across seasons and can be linked
 to a commonly measured functional trait.
DOI: 10.5061/dryad.dncjsxkx5
title: Vegetation changes from private forestland management can increase species richness and abundance

description: Conservation efforts on private lands are important for biodiversity
 conservation. On private lands in South Carolina, forestry management
 practices (prescribed burning, thinning, herbicide application) are used
 to improve upland pine habitat for wildlife and timber harvest and are
 incentivized through United States Department of Agriculture Farm Bill
 cost-share programs. Because many forest-dependent bird species have
 habitat requirements created primarily through forest management, data are
 needed on the effectiveness of these management activities. We studied
 privately-owned loblolly pine (Pinus taeda) stands in the South Carolina
 Piedmont region. Our objective was to understand how management practices
 influence avian species richness and abundance at local (forest stand) and
 landscape levels in relatively small stands (average ~28 hectares). We
 surveyed 49 forest stands during two bird breeding seasons with
 traditional point counts and vegetation surveys. We evaluated the effects
 of management on pine stand characteristics, avian species richness, and
 abundance of state-designated bird species of concern. Repeated burning
 and thinning shifted stand conditions to open pine woodlands with reduced
 basal area and herbaceous understories. Stands with lower basal area
 supported greater avian species richness. Some species increased in
 abundance in response to active management (e.g., Brown-headed Nuthatch,
 Sitta pusilla, and Indigo Bunting, Passerina cyanea), but relationships
 varied. Some species responded positively to increases in forest quantity
 at a landscape scale (1–5 km, e.g., Northern Bobwhite, Colinus
 virginianus). We found species-rich avian communities and species of
 conservation concern on working timber lands, indicating that incentivized
 forest management on private lands can provide valuable habitat for
 wildlife.   
description: Data were collected through point counts and vegetation sampling.
 See manuscript for more details.
description: See README.txt for more details about data
DOI: 10.5061/dryad.18931zcv8
title: Dataset for Body size impacts critical thermal maximum measurements in lizards

description: Understanding the mechanisms behind critical thermal maxima (CTmax, the
 high body temperature at which neuromuscular coordination is lost) of
 organisms is central to understanding ectotherm thermal tolerance. Body
 size is an often overlooked variable that may affect interpretation of
 CTmax, and consequently, how CTmax is used to evaluate mechanistic
 hypotheses of thermal tolerance. We tested the hypothesis that body size
 affects CTmax and its interpretation in two experimental contexts. First,
 in four Sceloporus species, we examined how inter- and intra-specific
 variation in body size affected CTmax at normoxic and
 experimentally-induced hypoxic conditions, and cloacal heating rate under
 normoxic conditions. Negative relationships between body size and CTmax
 were exaggerated in larger species, and hypoxia-related reductions in
 CTmax were unaffected by body size. Smaller individuals had faster cloacal
 heating rates and higher CTmax, and variation in cloacal heating rate
 affected CTmax in the largest species. Second, we examined how body size
 interacted with the location of body temperature measurements (i.e.,
 cloaca versus brain) in Sceloporus occidentalis, then compared this in
 living and deceased lizards. Brain temperatures were consistently lower
 than cloacal temperatures. Smaller lizards had larger brain-cloacal
 temperature differences than larger lizards, due to a slower cloacal
 heating rate in large lizards. Both live and dead lizards had lower brain
 than cloacal temperatures, suggesting living lizards do not actively
 maintain lower brain temperatures when they cannot pant. Thermal inertia
 influences CTmax data in complex ways, and body size should therefore be
 considered in studies involving CTmax data on species with variable sizes.
description: See Claunch et al., Body size impacts critical thermal maximum
 measurements in lizards 2020 Journal of Experimental Zoology  for
 details.
description: This dataset includes three .csv files and a .R file.
 The .R file (scelop_body_ctmax_code.R) reproduces the analyses
 and graphs using the .csv files, and includes descriptions of variables
 within each dataset.  scelop_body_exp1.csv includes the
 data for Experiment 1 models 1 (full data) and 2 (normoxia
 subset). scelop_body_exp2_living.csv includes the data
 for Experiment 2 model 1- living lizards.
 scelop_body_exp2_livedead.csv includes the data for Experiment 2
 model 2: lizards with living and dead data
DOI: 10.5281/zenodo.18290574
title: Code Repository for 'A Case for an Inhomogeneous Einstein-de Sitter Universe'

description: The repository contains Python code to test the iEdS and flat ΛCDM cosmological models against the DESI DR2 BAO and Pantheon+ SNIa datasets. Parameter estimation is performed with dynesty’s DynamicNestedSampler (see the article and documentation). Additionally, we evaluate the goodness of a camb fit (see the article and documentation) with respect to the Planck 2018 CMB TT power spectrum. Detailed descriptions and usage instructions are included within the code file.

Required input files:



BAO measurements and covariance: DESI_DR2_BAO.txt and DESI_DR2_BAO_Cov.txt (included in this repository). Source: CobayaSampler/bao_data/desi_bao_dr2;

SN data and covariance: available at PantheonPlusSH0ES/DataRelease;

CMB baseline Planck TT power spectra can be obtained from: COM_PowerSpect_CMB-TT-full_R3.01.txt;

camb fit results (included): camb_iEdS.dat, camb_LCDM.dat;camb fits use Planck best fit parameters from planck_2018.ini and COM_PowerSpect_CMB-base-plikHM-TTTEEE-lowl-lowE-lensing-minimum_R3.01.txt.


The repository includes a zipped archive of fit outputs: results.zip. A detailed description of all files inside the archive is provided in results.zip/README.rtf.

The repository also includes PDF files that present the fit results as corner plots, illustrating the posterior distributions of the fitted parameters. These plots display the projections of the dynesty samples in one- and two-dimensional parameter spaces. The 1D histograms show the median of the posterior parameter distributions, along with the 1σ uncertainties represented by the 16th and 84th percentiles. In the 2D distribution panels, contours are plotted at 0.5σ, 1σ, 1.5σ, and 2σ levels.

In addition to the baseline BAO analysis, we also provide posterior distributions obtained when including the DESI DR2 LRG1 BAO data point (see Posteriors_BAO_incl_LRG1.pdf). These results are shown separately and are discussed in Appendix B of the article.

The repository also includes a supplementary document containing the detailed mathematical derivations of the iEdS model equations used in the analysis (iEdS_math_notes.pdf).

Corresponding author of the article: Peter Raffai, peter.raffai@ttk.elte.huCorresponding author of the repository: Adrienn Pataki, patakia@student.elte.hu
DOI: 10.5281/zenodo.17288918
title: Code Repository for 'A Case for an Inhomogeneous Einstein-de Sitter Universe'

description: The repository contains Python code to test the iEdS and flat ΛCDM cosmological models against the DESI DR2 BAO and Pantheon+ SNIa datasets. Parameter estimation is performed with dynesty’s DynamicNestedSampler (see the article and documentation). Additionally, we evaluate the goodness of a camb fit (see the article and documentation) with respect to the Planck 2018 CMB TT power spectrum. Detailed descriptions and usage instructions are included within the code file.

Required input files:



BAO measurements and covariance: DESI_DR2_BAO.txt and DESI_DR2_BAO_Cov.txt (included in this repository). Source: CobayaSampler/bao_data/desi_bao_dr2;

SN data and covariance: available at PantheonPlusSH0ES/DataRelease;

CMB baseline Planck TT power spectra can be obtained from: COM_PowerSpect_CMB-TT-full_R3.01.txt;

camb fit results (included): camb_iEdS.dat, camb_LCDM.dat;camb fits use Planck best fit parameters from planck_2018.ini and COM_PowerSpect_CMB-base-plikHM-TTTEEE-lowl-lowE-lensing-minimum_R3.01.txt.


The repository includes a zipped archive of fit outputs: results.zip. A detailed description of all files inside the archive is provided in results.zip/README.rtf.

The repository also includes PDF files that present the fit results as corner plots, illustrating the posterior distributions of the fitted parameters. These plots display the projections of the dynesty samples in one- and two-dimensional parameter spaces. The 1D histograms show the median of the posterior parameter distributions, along with the 1σ uncertainties represented by the 16th and 84th percentiles. In the 2D distribution panels, contours are plotted at 0.5σ, 1σ, 1.5σ, and 2σ levels.

In addition to the baseline BAO analysis, we also provide posterior distributions obtained when including the DESI DR2 LRG1 BAO data point (see Posteriors_BAO_incl_LRG1.pdf). These results are shown separately and are discussed in Appendix B of the article.

The repository also includes a supplementary document containing the detailed mathematical derivations of the iEdS model equations used in the analysis (iEdS_math_notes.pdf).

Corresponding author of the article: Peter Raffai, peter.raffai@ttk.elte.huCorresponding author of the repository: Adrienn Pataki, patakia@student.elte.hu