cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nzs7h44vq
title: Predator and destructor species of artificial bird nests in La Paz, Bolivia

description: Urbanization alters the composition of biological communities and,
 therefore, ecological processes such as predation and destruction of bird
 nests. The identification of predator and destructor species is useful for
 designing research for the understanding of the effects of urbanization on
 these ecological processes. In this study, we identify the diurnal
 predator and destructor species of artificial bird nests in urban and
 peri-urban sites of the metropolitan region of La Paz, Bolivia, using
 webcams. The House Wren (Troglodytes aedon) was the only nest-destroying
 species, recorded in both urban and peri-urban environments. This species
 affected the nests by extracting material. Besides a predation event by
 the Andean Caracara (Phalcoboenus megalopterus) in a peri-urban site and
 one by the Domestic Cat (Felis silvestris catus) in an urban site, the
 species with the highest incidence of nest predation in both urban and
 peri-urban sites was the Chiguanco Thrush (Turdus chiguanco). A behavior
 that had not been previously reported for this species, and is very rare
 for the genus. In this report, we present two films of destruction events
 by the House Wren and two films of eggs predation events by the Chiguanco
 Thrush.
description: We used artificial bird nests
 baited with three commercial eggs of Common Quail (Coturnix coturnix).
 Nest were adapted from abandoned natural nests of local wild bird species
 such as the Rufous-collared Sparrow (Zonotrichia capensis) and Eared Dove
 (Zenaida auriculata). A battery of three nests was located during two
 periods of seven days each in six study sites in the metropolitan region
 of La Paz. Individual nests were separated between them between five to 16
 m. The sites were three private urban gardens and three peri-urban private
 land. The two aforementioned periods correspond to the reproductive season
 of the birds (February 2012-May 2012 and September 2012-January 2013). We
 firmly attach each nest to the branches of trees or bushes at a height of
 1.5-2.5 m above the ground. We monitored nests between 06:00 and 18:30
 using Microsoft LifeCam HD-6000 720p HD webcams. Therefore, we recorded
 only daytime nest predators and nest destroyers. We installed the webcams
 at 30 cm from each nest, camouflaged inside a box covered with dry leaves.
 Each webcam was connected to the computer with a 10m USB cable. We
 obtained a continuous track per day using Spy v. 3.8.6.0. Software, in
 which we identified each event of nest predation or destruction plus the
 species involved.
DOI: 10.5061/dryad.2bvq83btw
title: Spiny tails and clades: A fully sampled phylogeny of hoplocercine lizards (Iguanidae/Hoplocercinae) and its taxonomic and nomenclatural implications

description: Hoplocercine lizards (Enyalioides, Morunasaurus, and Hoplocercus) form a
 clade of ca. 20 currently recognized species. The phylogenetic
 relationships among hoplocercine lizards, whose members exhibit striking
 differences in morphology (e.g., spiny vs. non-spiny tails), have not been
 clearly resolved by previous molecular phylogenetic studies. We generated
 a considerably larger dataset including 130 new DNA sequences from one
 mitochondrial and four nuclear loci for all named and two unnamed species
 of Hoplocercinae. We analyzed the data under concatenated maximum
 likelihood (RAxML) and Bayesian (MrBayes) as well as summary coalescent
 (ASTRAL) approaches. While our phylogenetic hypotheses strongly supported
 the monophyly of Hoplocercinae, neither Enyalioides nor Morunasaurus was
 supported as monophyletic. Instead, M. groi was inferred with strong
 support to form a clade with E. heterolepis and E. laticeps. This clade
 was in turn the sister taxon to other species of Morunasaurus (M.
 annularis, M. peruvianus). The remaining species of Enyalioides formed a
 separate clade with a basal split between western (3 species) and eastern
 (13 species) subclades. Tree topology tests rejected the monophyly of
 Enyalioides but failed to reject monophyly of Morunasaurus, suggesting
 that further study is needed to resolve its taxonomic status. Based on our
 results, we establish the converted clade names Hoplocercinae,
 Hoplocercus, Enyalioides, and Morunasaurus, as well as the new clade name
 Zimiamviasaurus.  
description: Polymerase Chain Reaction (PCR) amplification was performed in a
 final volume of 25 μl reactions using 1X PCR Buffer (–Mg), 3 mM
 MgCl<sub>2</sub>, 0.2 mM dNTP mix, 0.2 μM of each primer, 0.1
 U/μl of Platinum® Taq DNA Polymerase (Invitrogen, Carlsbad, CA) and 1 μl
 of extracted DNA. PCR primers and protocols are presented in Table 1.
 Double stranded sequencing of the PCR products was performed in both
 directions by Macrogen Inc. (Seoul, Korea), except for those of
 <em>H. spinosus</em>, which were performed at the Laboratório
 Temático de Biologia Molecular from the Instituto Nacional de Pesquisas da
 Amazônia (LTBM/ INPA). We also retrieved from GenBank all available
 sequences of the genes mentioned above for all species of hoplocercine
 lizards and the outgroups. All terminals in gene trees correspond to
 single specimens except for <em>Enyalioides microlepis, E.
 palpebralis </em>and<em> E. touzeti,</em> which are
 composed of sequences of two specimens from localities 204.32 km, 56.16
 km, and 35.88 km (great circle distances calculated in
 www.gpsvisualizer.com) apart, respectively. Similarly, outgroup species
 are represented by sequences of more than one specimen.
description: BBEdit (any text editor), MrBayes, RAxML
DOI: 10.5061/dryad.kkwh70s7s
title: Queens control caste allocation in the ant Cardiocondyla obscurior

description: Social insect queens and workers can engage in conflict over reproductive
 allocation when they have different fitness optima. Here, we show that
 queens have control over queen-worker caste allocation in the ant
 Cardiocondyla obscurior, a species in which workers lack reproductive
 organs. We describe crystalline deposits that distinguish castes from the
 egg stage onwards, providing the first report of a discrete trait that can
 be used to identify ant caste throughout pre-imaginal development.
 Comparison of queen- and worker-destined eggs and larvae revealed size and
 weight differences in late development, but no discernible differences in
 traits that may be used in social interactions, including hair morphology
 and cuticular odors. In line with a lack of caste-specific traits, adult
 workers treated developing queens and workers indiscriminately. Together
 with previous studies demonstrating queen control over sex allocation,
 these results show that queens control reproductive allocation in C.
 obscurior and suggest that the fitness interests of colony members are
 aligned to optimise resource allocation in this ant.
DOI: 10.5281/zenodo.11618452
title: 2'O-ribose methylation of ribosomal RNA (rRNA 2'Ome) in primary human T cells from septic shock and COVID-19 patients

description: Abstract

T cell exhaustion plays a central role in sepsis-induced immunosuppression. Deciphering the precise mechanism of this cellular dysfunction could lead to new therapies. In several pathophysiological contexts, the 2’O-ribose methylation of ribosomal RNA (rRNA 2’Ome) has emerged as a level of epitranscriptomic regulation. Here, we report for the first time site-specific alterations of rRNA 2’Ome epitranscriptomic marks in T cells after sepsis, associated with impaired functionality. Using primary human T cells from septic shock and COVID-19 patients, we identified a subset of sites with high inter-individual variability, the levels of which correlated with lymphocyte effector functions. This was recapitulated in an ex vivo model of stimulated T lymphocytes from healthy donors. Finally, 2’Ome signature discriminated samples from septic patients from those of healthy donors. We describe rRNA 2’Ome regulation as a new molecular mechanism that controls T lymphocyte effector function in sepsis with high potential as biomarker and therapeutic target. 

---------------------------------------------------

Description of the data and file structure

Each folder contains the read-end counts in the sub-directory RiboMethSeq_ReadEnd_Counts and the metadata file. The metadata file describe each file contained in this sub-directory.



The read-end count file structure:





The name of the RNA on which the read end counting was performed.




The number of the position on the RNA.




The value of the read end counts at the position.



Code/Software

Using ribomethseq-nf pipeline, fastq were used to align reads on the human rRNA sequence (NR_046235), compute 5’/3’-end read counts.

These files can be the input of rRMSAnalyzer package to adjust batch effect (ComBat-seq method) and calculate C-score corresponding to the end read count at the genomic position of interest normalized to the median of end read counts of the local environment (6 upstream and 6 downstream nucleotides).
DOI: 10.5281/zenodo.11618451
title: 2'O-ribose methylation of ribosomal RNA (rRNA 2'Ome) in primary human T cells from septic shock and COVID-19 patients

description: Abstract

T cell exhaustion plays a central role in sepsis-induced immunosuppression. Deciphering the precise mechanism of this cellular dysfunction could lead to new therapies. In several pathophysiological contexts, the 2’O-ribose methylation of ribosomal RNA (rRNA 2’Ome) has emerged as a level of epitranscriptomic regulation. Here, we report for the first time site-specific alterations of rRNA 2’Ome epitranscriptomic marks in T cells after sepsis, associated with impaired functionality. Using primary human T cells from septic shock and COVID-19 patients, we identified a subset of sites with high inter-individual variability, the levels of which correlated with lymphocyte effector functions. This was recapitulated in an ex vivo model of stimulated T lymphocytes from healthy donors. Finally, 2’Ome signature discriminated samples from septic patients from those of healthy donors. We describe rRNA 2’Ome regulation as a new molecular mechanism that controls T lymphocyte effector function in sepsis with high potential as biomarker and therapeutic target. 

---------------------------------------------------

Description of the data and file structure

Each folder contains the read-end counts in the sub-directory RiboMethSeq_ReadEnd_Counts and the metadata file. The metadata file describe each file contained in this sub-directory.



The read-end count file structure:





The name of the RNA on which the read end counting was performed.




The number of the position on the RNA.




The value of the read end counts at the position.



Code/Software

Using ribomethseq-nf pipeline, fastq were used to align reads on the human rRNA sequence (NR_046235), compute 5’/3’-end read counts.

These files can be the input of rRMSAnalyzer package to adjust batch effect (ComBat-seq method) and calculate C-score corresponding to the end read count at the genomic position of interest normalized to the median of end read counts of the local environment (6 upstream and 6 downstream nucleotides).
DOI: 10.15468/dl.m6kh48
title: Occurrence Download

description: A dataset containing 12992 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.39203 43.44612,3.48681 43.44612,3.48681 43.53656,3.39203 43.53656,3.39203 43.44612))",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 12992 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003418-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.w0vt4b8w2
title: Metabolic rates of Armases cinereum

description: Metabolic rate is a basic individual metric that extends beyond the
 individual to link the ecology of populations, communities and ecosystems
 via its role as a central component of energy budgets. Metabolic rates are
 often measured indirectly by quantifying respiration under simplified,
 standard laboratory conditions. This approach limits the application of
 these measurements to a small range of conditions that commonly do not
 reflect natural field conditions. We measured metabolic rates of the
 squareback marsh crab Armases cinereum under field conditions. Previous
 work highlights that movement of individual A. cinereum, especially
 females, provides a potential spatial subsidy of energy, as individuals
 consume energy in salt marshes and then transfer that energy to upland
 forest ecosystems. We show that metabolic rate increases with size for
 both males and females and that metabolic rates are influenced by
 temperature and by whether females are vitellogenic. The metabolic rates
 that we measured more closely approximate field metabolic rates than
 standard metabolic rates, and demonstrate that individual crabs experience
 high energy expenditures, reducing the amount of energy that may be
 transferred as a subsidy between marsh and forest as a result of the daily
 movements of individual crabs. Our measurements are therefore also a key
 component for the construction of an energy budget for this species.
DOI: 10.24435/materialscloud:78-2m
title: Comparative study of magnetic exchange parameters and magnon dispersions in NiO and MnO from first principles

description: Spin-wave excitations are fundamental to understanding the behavior of magnetic materials and hold promise for future information and communication technologies. Yet, modeling these accurately in transition-metal compounds remains challenging, starting from the self-interaction errors affecting localized and partially filled $d$-orbitals in density-functional theory (DFT) with (semi-)local functionals. In this work, we compare three advanced first-principles approaches for computing magnetic exchange parameters and magnon dispersions in NiO and MnO, all based on a common DFT+$U$ ground state with ab initio Hubbard $U$ values obtained from density-functional perturbation theory. Two methods extract exchange parameters directly: one via total-energy differences using the four-state mapping ($\Delta E$), and the other via the magnetic force theorem (MFT) using infinitesimal spin rotations. Magnon dispersions are then obtained from a Heisenberg Hamiltonian through linear spin-wave theory (LSWT). The third approach, time-dependent density-functional perturbation theory with $U$ (TDDFPT+$U$), yields magnon dispersions directly from the dynamical spin susceptibility, with exchange parameters fitted a posteriori, for comparison, via LSWT. Our results show that TDDFPT+$U$ and the Heisenberg model based on $\Delta E$-derived parameters align well with experimental neutron scattering data, whereas the MFT-based approach shows larger discrepancies, possibly due to some inherent approximations and limitations of the particular implementation used. This study benchmarks the accuracy of state-of-the-art first-principles techniques for spin-wave modeling and contributes to advancing reliable computational tools for the study and design of magnetic materials.
DOI: 10.24435/materialscloud:jw-h1
title: Comparative study of magnetic exchange parameters and magnon dispersions in NiO and MnO from first principles

description: Spin-wave excitations are fundamental to understanding the behavior of magnetic materials and hold promise for future information and communication technologies. Yet, modeling these accurately in transition-metal compounds remains challenging, starting from the self-interaction errors affecting localized and partially filled $d$-orbitals in density-functional theory (DFT) with (semi-)local functionals. In this work, we compare three advanced first-principles approaches for computing magnetic exchange parameters and magnon dispersions in NiO and MnO, all based on a common DFT+$U$ ground state with ab initio Hubbard $U$ values obtained from density-functional perturbation theory. Two methods extract exchange parameters directly: one via total-energy differences using the four-state mapping ($\Delta E$), and the other via the magnetic force theorem (MFT) using infinitesimal spin rotations. Magnon dispersions are then obtained from a Heisenberg Hamiltonian through linear spin-wave theory (LSWT). The third approach, time-dependent density-functional perturbation theory with $U$ (TDDFPT+$U$), yields magnon dispersions directly from the dynamical spin susceptibility, with exchange parameters fitted a posteriori, for comparison, via LSWT. Our results show that TDDFPT+$U$ and the Heisenberg model based on $\Delta E$-derived parameters align well with experimental neutron scattering data, whereas the MFT-based approach shows larger discrepancies, possibly due to some inherent approximations and limitations of the particular implementation used. This study benchmarks the accuracy of state-of-the-art first-principles techniques for spin-wave modeling and contributes to advancing reliable computational tools for the study and design of magnetic materials.
DOI: 10.5061/dryad.qfttdz0mr
title: Data from: The ecology of hybrid incompatibilities

description: Ecologically-mediated selection against hybrids, caused by hybrid
 phenotypes fitting poorly into available niches, is typically viewed as
 distinct from selection caused by epistatic Dobzhansky-Muller hybrid
 incompatibilities. Here, we illustrate how selection against transgressive
 phenotypes in hybrids manifests as incompatibility.  After
 outlining our logic, we summarize current approaches for studying
 ecology-based selection on hybrids. We then quantitatively review
 QTL-mapping studies and find traits differing between parent taxa are
 typically polygenic. Next, we describe how verbal models of selection on
 hybrids translate to phenotypic and genetic fitness landscapes,
 highlighting emerging approaches for detecting polygenic
 incompatibilities. Finally, in a synthesis of published data, we report
 that trait transgression—and thus possibly extrinsic hybrid
 incompatibility—in hybrids escalates with the phenotypic divergence
 between parents. We discuss conceptual implications and conclude that
 studying the ecological basis of hybrid incompatibility will facilitate
 new discoveries about mechanisms of speciation.
description: Full methods / details about data collection are given in the
 supplementary materials (within repository). The
 dataset contains raw data and analysis/simulation code for three
 quantitative 'vignettes' within the paper. Two are syntheses of
 existing data, and one is an original small-scale simulation
 study. For the analysis of transgression, raw trait
 data for hybrids from each study are included. For the analysis of QTL,
 summary tables from papers are reproduced. Other
 authors on the paper transcribed QTL tables and produced referential
 datasheets, but KAT curated and checked all data and bears sole
 responsibility for any and all inconsistencies.
description: 'R' v 4.1.2<br>        package 'broom'
 v 0.7.12<br>        package 'cowplot' v 1.1.1<br>   
     package 'ggforce' v 0.3.3<br>        package
 'metafor' v 3.8-1<br>        package 'tidyverse'
 v 1.3.1<br>Admix'em v 1.0.2.3
DOI: 10.5061/dryad.8cz8w9gvq
title: RNAseq from normal human epidermal keratinocytes treated with C. acnes 6919 conditioned media and propionic acid

description: Lipid synthesis is necessary for formation of epithelial barriers and
 homeostasis with external microbes. An analysis of the response of human
 keratinocytes to several different commensal bacteria on the skin revealed
 that Cutibacterium acnes induced a large increase in essential lipids
 including triglycerides, ceramides, cholesterol, and free fatty acids. A
 similar response occurred in mouse epidermis and in human skin affected
 with acne. Further analysis showed that this increase in lipids was
 mediated by short-chain fatty acids produced by Cutibacterium acnes and
 was dependent on increased expression of several lipid synthesis genes
 including glycerol3-phosphate-acyltransferase-3. Inhibition or RNA
 silencing of peroxisome proliferator–activated receptor–α (PPARα), but not
 PPARβ and PPARγ, blocked this response. The increase in keratinocyte lipid
 content improved innate barrier functions including antimicrobial
 activity, paracellular diffusion, and transepidermal water loss. These
 results reveal that metabolites from a common commensal bacterium have a
 previously unappreciated influence on the composition of epidermal lipids.
description: Normal neonatal human epidermal keratinocytes (NHEKs) were
 treated with 8mM of propionic acid or with 15% of <em>C.
 acnes</em> conditioned media or RCM media (control) for 4 days in
 triplicate. Then, RNA was extracted using the PureLink RNA mini kit.
 Isolated RNA was submitted to the UCSD IGM Genomics Center for
 RNA-sequencing performed on a high-output run V4 platform (Illumina, USA)
 with a single read 100 cycle runs.
description: Partek Flow Software
DOI: 10.5061/dryad.fbg79cnzs
title: Data for: Multiple antipredator behaviors in red-tailed monkeys reveal spatially distinct landscapes of fear

description: Foraging opportunity and predation risk act as opposing influences on an
 animal’s habitat use. “Landscapes of fear” (LOF), whereby one predicts the
 spatial distribution of predators or perceived predator presence using
 prey responses, are an important tool for modeling this conflict. LOF
 models examining perceived predation risk are often generated using a
 single behavioral metric, even though individuals can respond to predation
 pressure with multiple potential behaviors. Here, we expanded traditional
 LOF approaches by measuring three antipredator behaviors in wild
 red-tailed monkeys (Cercopithecus ascanius): aggregation, alarm calling,
 and vigilance. We predicted that each behavior would reveal spatially
 explicit regions of high risk, as each behavior may attend to different
 aspects of perceived predation risk. The use of different behaviors may
 depend upon factors such as vegetation type, age/sex class of an
 individual, and which other antipredator behaviors are being exhibited by
 group members. We collected data on two troops of monkeys in the Issa
 Valley, Tanzania for over 19 months and conducted 3,189 group follows. We
 found that vegetation type varied in its effect on antipredator behavior.
 Monkeys conducted more antipredator behavior in more open vegetation types
 compared to more closed, riparian forests. The LOF models generated for
 each behavior mapped distinct and predominantly non-overlapping spatial
 regions of perceived predation risk, which was replicated across the two
 groups. This suggested that monkeys responded differently across their
 home range to specific perceived risks. Such spatially explicit behavior
 may indicate vegetation-specific predation risk or unique trade-offs in
 antipredator behavior throughout a heterogenous habitat.
description: Behavioural observastions of individual red-tailed monkeys across
 vegetation types.