cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84c66
title: Data from: Parent-offspring facial resemblance increases with age in rhesus macaques

description: Kin recognition is a key ability which facilitates the acquisition of
 inclusive fitness benefits and enables optimal outbreeding. In primates,
 phenotype matching is considered particularly important for the
 recognition of patrilineal relatives, as information on paternity is
 unlikely to be available via social familiarity. Phenotypic cues to both
 paternal and maternal relatedness exist in the facial features of humans
 and other primates. However, theoretical models suggest that in systems
 with parentage uncertainty it may be adaptive for offspring to conceal
 such cues when young, in order to avoid potential costs of being
 discriminated against by unrelated adults. Using experienced human raters,
 we demonstrate in a computer-based task that detection of parent-offspring
 resemblances in the faces of rhesus macaques (Macaca mulatta) increases
 significantly with offspring age. Moreover, this effect is specific to
 information about kinship, as raters were extremely successful at
 discriminating individuals even amongst the youngest animals. To our
 knowledge, this is the first evidence in non-humans for the age-dependent
 expression of visual cues used in kin recognition.
description: Ontogeny of kin
 resemblance in macaquesSee
 ReadMe.rtf
DOI: 10.5061/dryad.h8b3c
title: Data from: Development of HPLC-ELSD method for determination of phytochelatins and glutathione in Perilla frutescens under cadmium stress condition

description: A rapid, accurate and simple method was developed for the simultaneous
 determination of glutathione (GSH) and phytochelatins (PCs) by high
 performance liquid chromatography (HPLC) with evaporative light-scattering
 detector(ELSD). GSH, Phytochelatin 2 (PC2), phytochelatin 3 (PC3),
 phytochelatin 4 (PC4), phytochelatin 5 (PC5) and phytochelatin 6 (PC6) can
 be separated with baseline separation within 9 minutes using a Venusil AA
 column (250 mm × 4.6 mm i.d., 5 μm particle sizes). The acetonitrile (A)
 and water containing 0.1% trifluoroacetic acid (0.1% TFA, B) were employed
 as the mobile phase for the gradient elution. The drifttube temperature
 and flow rateofcarriergas (N2) were 50℃ and 1.5 L·min-1, respectively.
 Under the optimum conditions, good linear regression equations of six
 analytes were obtained with the detection limits ranging from 0.2 to 0.5
 µg·mL-1. The proposed method has been applied successfully for the
 quantification of GSH and PCs in Perilla frutescens (a cadmium
 hyperaccumulator) under cadmium stress. The recoveries were between 82.9%
 and 115.3%.
description: Photographs
DOI: 10.5061/dryad.r9q3b
title: Data from: Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing

description: The African parasitoid wasp Cotesia sesamiae is structured in contrasted
 populations showing differences in host range and the recent discovery of
 a specialist related species, C. typhae, provide a good framework to study
 the mechanisms that link the parasitoid and their host range. To
 investigate the genomic bases of divergence between these populations, we
 used a targeted sequencing approach on 24 samples. We targeted a specific
 genomic region encoding the bracovirus, which is deeply involved in the
 interaction with the host. High sequencing coverage was obtained for all
 samples allowing the study of genetic variations between wasp populations
 and species. Combining population genetic estimations, the diversity (π),
 the relative differentiation (FST) and the absolute differentiation (dxy),
 and branch-site dN/dS measures, we identified six divergent genes impacted
 by positive selection belonging to different gene families. These genes
 are potentially involved in host adaptation and in the specialization
 process. Fine scale analyses of the genetic variations also revealed
 deleterious mutations and large deletions on certain genes inducing
 pseudogenization and loss of function. These results highlight the crucial
 role of the bracovirus in the molecular interactions between the wasp and
 its hosts and in the evolutionary processes of specialization.
description: reads_cleaning_mapping_filteringevaluation_cumulative_curvesconsensus_phylogeny_dndscoverage_deletionpopulations_diversity_fst_dxyCotesia_sesamiae_Cotesia_typhae_whole_bracovirus_alignmentAlignment of the consensus of 98 bracovirus genes from 24 C. sesamiae, C. typhae and C. flavipes samples realized with PhyML software.Population_genetics_statistics_and_dNdSPopulation genetics statistics for 98 bracovirus genes of C. sesamiae populations and C. typhae including nucleotide diversity (π) for each population, relative (FST) and absolute (dxy) differentiation for each comparison and dNdS values for each population branch.Population_genetics_statistics.xlsx
DOI: 10.5061/dryad.5n7t4
title: Data from: Sora (Porzana carolina) autumn migration habitat use

description: Palustrine wetland management across the United States is often conducted
 under a moist soil management framework aimed at providing energetic
 resources for non-breeding waterfowl. Moist soil management techniques
 typically include seasonal water-level manipulations and mechanical soil
 disturbance to create conditions conducive to germination and growth of
 early successional, seed-producing wetland plants. The assumption is that
 providing stopover and wintering habitat for non-breeding waterfowl will
 also accommodate life history needs of a broader suite of migratory
 waterbirds including shorebirds, wading birds, and marsh birds. Although
 studies of wetlands provide some evidence to support this assumption for
 shorebirds and wading birds, there is less information on how other
 marshbirds, respond. Sora (Porzana carolina) are a species of migratory
 rail that depends on wetlands year round as it migrates across North
 America. It is a species for which the consequences of wetland management
 decisions directed toward non-breeding waterfowl, is unknown. We conducted
 nocturnal surveys on 10 public properties in Missouri, USA during autumn
 migration from 2012-2016 to examine Sora habitat use in wetland
 impoundments managed to enhance production of moist soil vegetation. We
 found a positive relationship with Sora presence and mean water depth and
 annual moist soil vegetation; Sora used, on average, deeper water than was
 available across surveyed impoundments and used locations with a higher
 percentage of annual moist soil vegetation than was available. We found a
 negative relationship with Sora use and upland vegetation, woody
 vegetation, and open water. We found Sora using deeper water than have
 previously been reported for autumn migration and that moist soil
 management techniques used on Missouri’s intensively-managed public
 wetland areas may be compatible with Sora autumn migration stopover
 habitat requirements.
description: Figure 2, Analysis and
 Supplementary Materials Inputsinputs to create the
 analysis, figures and supplementary material associated with Figure 2.
 Including text files that define the columns and the
 units.fig_2.zipFigure 1 input filesInput files for creation of Figure 1. One input file is not included, but a citation to where to find the data is included in the figure 1 script.fig_1.zipR Scripts for Analysis & FiguresR scripts to reproduce the analysis and recreate the figures included in the paper.scripts.zip
DOI: 10.5061/dryad.pc054
title: Data from: Evolutionary rescue in a host-pathogen system results in coexistence not clearance

description: The evolutionary rescue of host populations may prevent extinction from
 novel pathogens. However, the conditions that facilitate rapid evolution
 of hosts, in particular the population variation in host susceptibility,
 and the effects of host evolution in response to pathogens on population
 outcomes remain largely unknown. We constructed an individual-based model
 to determine the relationships between genetic variation in host
 susceptibility and population persistence in an amphibian-fungal pathogen
 (Batrachochytrium dendrobatidis) system. We found that host populations
 can rapidly evolve reduced susceptibility to a novel pathogen and that
 this rapid evolution led to a 71 fold increase in the likelihood of
 host-pathogen coexistence. However, the increased rates of coexistence
 came at a cost to host populations; fewer populations cleared infection,
 population sizes were depressed, and neutral genetic diversity was lost.
 Larger adult host population sizes and greater adaptive genetic variation
 prior to the onset of pathogen introduction led to substantially reduced
 rates of extinction suggesting that populations with these characteristics
 should be prioritized for conservation when species are threatened by
 novel infectious diseases.
description: Model source
 codeThis zip file contains
 source code for the model used in "Evolutionary rescue in a
 host-pathogen system results in coexistence not
 clearance."chytrid_base_model.zipData from Figure 5This file contains the model output used to create Figure 5 in the paper "Evolutionary rescue in a host-pathogen system results in coexistence not clearance."Output_Figures5.txtData from Figure 6This file contains data from the model used to create Figure 6 in the paper "Evolutionary rescue in a host-pathogen system results in coexistence not clearance."Output_Figure6.txt
DOI: 10.5061/dryad.3f5q5
title: Data from: Knowledge-based prediction of protein backbone conformation using a structural alphabet

description: Libraries of structural prototypes that abstract protein local structures
 are known as structural alphabets and have proven to be very useful in
 various aspects of protein structure analyses and predictions. One such
 library, Protein Blocks, is composed of 16 standard 5-residues long
 structural prototypes. This form of analyzing proteins involves drafting
 its structure as a string of Protein Blocks. Predicting the local
 structure of a protein in terms of protein blocks is the general objective
 of this work. A new approach, PB-kPRED is proposed towards this aim. It
 involves (i) organizing the structural knowledge in the form of a database
 of pentapeptide fragments extracted from all protein structures in the PDB
 and (ii) applying a knowledge-based algorithm that does not rely on any
 secondary structure predictions and/or sequence alignment profiles, to
 scan this database and predict most probable backbone conformations for
 the protein local structures. Though PB-kPRED uses the structural
 information from homologues in preference, if available. The predictions
 were evaluated rigorously on 15,544 query proteins representing a
 non-redundant subset of the PDB filtered at 30% sequence identity cut-off.
 We have shown that the kPRED method was able to achieve mean accuracies
 ranging from 40.8% to 66.3% depending on the availability of homologues.
 The impact of the different strategies for scanning the database on the
 prediction was evaluated and is discussed. Our results highlights the
 usefulness of the method in the context of proteins without any known
 structural homologues. A scoring function that gives a good estimate of
 the accuracy of prediction was further developed. This score estimates
 very well the accuracy of the algorithm (R2 of 0.82). An online version of
 the tool is provided freely for non-commercial usage at
 http://www.bo-protscience.fr/kpred/.
description: DATA SET USED IN THE
 PAPERDATA SET FOR Knowledge
 based prediction of protein backbone conformation using a structural
 alphabet Authors : Iyanar Vetrivel, Swapnil Mahajan, Manoj Tyagi, Lionel
 Hoffmann, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Alexandre G. de
 Brevern, Frédéric Cadet, Bernard Offmann Corresponding author :
 bernard.offmann@univ-nantes.fr FILES DESCRIPTIONS : 1) PDB30_aaseq.txt.
 This file contains the amino acid sequence of the PDB chains from PDB30
 dataset described in the manuscript. 2) PDB30_assigned_pb.txt. This file
 contains the PB sequence assignment of the PDB chains from the same PDB30
 dataset. PB assignment is performed according to reference [29] in the
 manuscript. 3) PDB30_predited_pb.txt. This file contains the predicted PB
 sequences of the PDB chains from the PDB30 dataset as per the hybrid
 method described in the manuscript.DATA_KPRED.tar.gz
DOI: 10.5061/dryad.qc1bc
title: Data from: Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds

description: The roan coat color pattern is described as the presence of white hairs
 intermixed with pigmented hairs. This kind of pigmentation pattern has
 been observed in many domestic species, including the goat. The molecular
 mechanisms and inheritance that underlie this pattern are known for some
 species and the KITLG gene has been shown associated with this phenotype.
 To date, no research effort has been done to find the gene(s) that
 controls roan coat color pattern in goats. In the present study, after
 genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan
 pattern and that belonged to two Pakistan breeds (Group A) were analyzed
 and then compared to 740 goats of 39 Italian and Pakistan goats breeds
 that did not have the same coat color pattern (Group B). Run of
 homozygosity-based and XP-EHH analyses were used to identify unique
 genomic regions potentially associated with the roan pattern. A total of 3
 regions on chromosomes 5, 6 and 12 were considered unique among the group
 A versus B group comparisons. The A region &gt; 1.7 Mb on chromosome 5
 was the most divergent between the two groups. This region contains six
 genes, including the KITLG gene. Our findings support the hypothesis that
 the KITLG gene may be associated with the roan phenotype in goats.
description: Genotype
 dataThe TalentiEtAl_2017.ped
 file contains the unphased genotype data for all the 929 animals described
 in the paper: "Genomic analysis suggests KITLG is responsible for a
 roan pattern in two Pakistani goat breeds". In this file, data are
 coded as following: - FID contains the breed of every individual coded as
 a number, with the exception of the Beetal Muki Cheni and Barri animals
 coded BeetalMukiCheni and Barri, respectively - IID column contains the id
 code of every individual - the phenotype column contain the information of
 the country, with 1 that indicates breeds from Italy and 2 indicates
 breeds from Pakistan The TalentiEtAl_2017.map file contain the data of all
 53K markers.TalentiEtAl_2017.zip
DOI: 10.5061/dryad.d69k7
title: Data from: Extracting coherent tree-ring climatic signals across spatial scales from extensive forest inventory data

description: Increasing access to extensively replicated and broadly distributed
 tree-ring collections has led to a greater use of these large data sets to
 investigate climate forcing on tree growth. However, the number of
 chronologies added to large accessible databases is declining and few are
 updated, while chronologies are often sparsely distributed and are more
 representative of marginal growing environments. On the other hand,
 National Forest Inventories (NFI), although poorly replicated at the plot
 level as compared to classic dendrochronological sampling, contain a large
 amount of tree-ring data with high spatial density designed to be
 spatially representative of the forest cover. We propose an a posteriori
 approach to validating tree-ring measurements and dating, selecting
 individual tree-ring width time series, and building average chronologies
 at various spatial scales based on an extensive collection of ring width
 measurements of nearly 94,000 black spruce trees distributed over a wide
 area and collected as part of the NFI in the province of Quebec, Canada.
 Our results show that reliable signals may be derived at various spatial
 scales (from 37 to 583,000 km2) from NFI increment core samples. Signals
 from independently built chronologies are spatially coherent with each
 other and well-correlated with independent reference chronologies built at
 the stand level. We thus conclude that tree-ring data from NFIs provide an
 extraordinary opportunity to strengthen the spatial and temporal coverage
 of tree-ring data and to improve coordination with other contemporary
 measurements of forest growth to provide a better understanding of tree
 growth-climate relationships over broad spatial scales.
description: Data_DendroQuebecNFI_SignalAnalysisRegional and reference chronologies, forest land classification, annual temperature and precipitation data.
DOI: 10.5061/dryad.6h5p0
title: Data from: Two-thirds of global cropland area impacted by climate oscillations

description: The El Niño Southern Oscillation (ENSO) peaked strongly during the boreal
 winter 2015-2016, leading to food insecurity in many parts of Africa, Asia
 and Latin America. Besides ENSO, the Indian Ocean Dipole (IOD) and the
 North Atlantic Oscillation (NAO) are known to impact crop yields
 worldwide. Here, we assess for the first time in a unified framework the
 relationship between ENSO, IOD and NAO and simulated crop productivity at
 the sub-country scale. Our findings reveal that during 1961–2010, crop
 productivity is significantly influenced by at least one large-scale
 climate oscillation in two-thirds of global cropland area. Besides
 observing new possible links – especially for NAO in Africa and the Middle
 East, our analyses confirm several known relationships between crop
 productivity and these oscillations. Our results improve the understanding
 of climatological crop productivity drivers, which is essential for
 enhancing food security in many of the most vulnerable places on the
 planet.
description: Data from: Two-thirds of
 global cropland area impacted by climate oscillationsZip-file contains crop
 production and harvested areas data used in the study titled
 'Two-thirds of global cropland area impacted by climate
 oscillations'. Detailed information of the data can be found in the
 related 'README.docx' file.crops_and_oscillations_data.zip
DOI: 10.58116/uek/ugitfj
title: Emulsion Quality and Functional Properties of Natural Emulsion Systems with Xanthan Gum as a Stabilizer and Carrier of Compounds Based on Enzymatically Modified Mutton Tallow and Hemp Oil

description: This folder contains selected datasets related to a scientific publication and the research described therein.
The data are associated with a study on emulsion systems based on enzymatically modified fats and document the physical stability and rheological properties of the emulsions.
The folder includes data from Turbiscan Stability Index (TSI) measurements and dynamic viscosity determination, which were used to assess emulsion destabilization behaviour and flow characteristics as described in the article.
DOI: 10.5061/dryad.rb417
title: Data from: PCB126 inhibits the activation of AMPK-CREB signal transduction required for energy sensing in liver

description: 3,3’,4,4’,5-pentachlorobiphenyl (PCB126), a dioxin-like PCB, elicits
 toxicity through a wide array of non-carcinogenic effects, including
 metabolic syndrome, wasting, and non-alcoholic fatty-liver disease
 (NAFLD). Previously, we reported decreases in the transcription of several
 enzymes involved in gluconeogenesis, before the early onset of lipid
 accumulation. Hence, this study was aimed at understanding the impact of
 resultant decreases gluconeogenic enzymes on growth, weight and metabolism
 in the liver, upon extended exposure. Male Sprague-Dawley rats (75-100 g),
 fed a defined AIN-93G diet, were injected (ip) with single dose of soy oil
 (5 ml/kg body weight; n=14) or PCB126 (5 µmol/kg; n=15), 28 d, prior
 euthanasia. A subset of rats from each group were fasted for 12h (vehicle
 (n=6) and PCB126 (n=4)). Rats only showed significant weight loss between
 days 14 and 28 (P&lt;0.05) and some mortality (P=0.0413). As in our
 previous studies, the expression levels of enzymes involved in
 gluconeogenesis (Pepck-c, G6Pase, Sds, Pc and Ldh-A) and glycogenolysis
 (Pygl) were strongly downregulated. The decreased expression of these
 enzymes in PCB126 treated rats after a 12 h fast decreased hepatic glucose
 production from glycogen and gluconeogenic substrates, exacerbating the
 hypoglycemia. Additionally, PCB126 caused hepatic steatosis and decreased
 the expression of the transcription factor Pparα and its targets,
 necessary for fatty-acid oxidation. The observed metabolic disruption
 across multiple branches of fasting metabolism resulted from inhibition in
 the activation of enzyme AMPK and transcription factor CREB signaling,
 necessary for “sensing” energy-deprivation and the induction of enzymes
 that respond to the PCB126 triggered fuel crisis in liver.
description: Supplementary
 DataSupplementary Data file
 associated with the manuscript PCB126 inhibits the activation of AMPK-CREB
 signal transduction required for energy sensing in
 liver,
DOI: 10.5061/dryad.f81c5
title: Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

description: Pathogens are recognized as major drivers of local adaptation in wildlife
 systems. By determining which gene variants are favored in local
 interactions among populations with and without disease, spatially
 explicit adaptive responses to pathogens can be elucidated. Much of our
 current understanding of host responses to disease comes from a small
 number of genes associated with an immune response. High-throughput
 sequencing (HTS) technologies, such as genotype-by-sequencing (GBS),
 facilitate expanded explorations of genomic variation among populations.
 Hybridization-based GBS techniques can be leveraged in systems not well
 characterized for specific variants associated with disease outcome to
 “capture” specific genes and regulatory regions known to influence
 expression and disease outcome. We developed a multiplexed, sequence
 capture assay for red foxes to simultaneously assess ~300-kbp of genomic
 sequence from 116 adaptive, intrinsic, and innate immunity genes of
 predicted adaptive significance and their putative upstream regulatory
 regions along with 23 neutral microsatellite regions to control for
 demographic effects. The assay was applied to 45 fox DNA samples from
 Alaska, where three arctic rabies strains are geographically restricted
 and endemic to coastal tundra regions, yet absent from the boreal
 interior. The assay provided 61.5% on-target enrichment with relatively
 even sequence coverage across all targeted loci and samples (mean = 50×),
 which allowed us to elucidate genetic variation across introns, exons, and
 potential regulatory regions (4,819 SNPs). Challenges remained in
 accurately describing microsatellite variation using this technique;
 however, longer-read HTS technologies should overcome these issues. We
 used these data to conduct preliminary analyses and detected genetic
 structure in a subset of red fox immune-related genes between regions with
 and without endemic arctic rabies. This assay provides a template to
 assess immunogenetic variation in wildlife disease systems.
description: Red fox immune-gene
 sequencesRed fox immune-gene
 sequences (2,229,152 bp) used to design the sequence capture
 assay.red_fox_immune-gene_sequences.fastaRed fox immune-gene SNPsRed fox SNP variant call information.red_fox_immune-gene_SNPs.vcfRed fox NimbleGen SeqCap EZ_probesCoordinates used to design the overlapping NimbleGen SeqCap EZ probes.red_fox_NimbleGen_SeqCap_EZ_probes.bed
DOI: 10.5281/zenodo.18389039
title: INTA-AFOLU ARGENTINA_AFOLU Argentina_revision

description: Agricultura, Silvicultura y Otros Usos de la Tierra
DOI: 10.5281/zenodo.18389040
title: INTA-AFOLU ARGENTINA_AFOLU Argentina_revision

description: Agricultura, Silvicultura y Otros Usos de la Tierra