cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9jj84
title: Data from: Prediction and attenuation of seasonal spillover of parasites between wild and domestic ungulates in an arid mixed-use system

description: 1.Transmission of parasites between host species affects host population
 dynamics, interspecific competition, and ecosystem structure and function.
 In areas where wild and domestic herbivores share grazing land, management
 of parasites in livestock may affect or be affected by sympatric wildlife
 due to cross-species transmission. 2.We develop a novel method for
 simulating transmission potential based on both biotic and abiotic factors
 in a semi-arid system in Botswana. Optimal timing of antiparasitic
 treatment in livestock is then compared under a variety of alternative
 host scenarios, including seasonally migrating wild hosts. 3.In this
 region, rainfall is the primary driver of seasonality of transmission, but
 wildlife migration leads to spatial differences in the effectiveness of
 treatment in domestic animals. Additionally, competent migratory wildlife
 hosts move parasites across the landscape. 4.Simulated transmission
 potential matches observed patterns of clinical disease in the study area.
 Increased wildlife contact is correlated with a decrease in disease,
 suggesting that noncompetent wild hosts may attenuate transmission by
 removing infective parasite larvae from livestock pasture. 5.Optimising
 the timing of treatment according to within-year rainfall patterns was
 considerably more effective than treating at a standard time of year. By
 targeting treatment in this way, efficient control can be achieved,
 mitigating parasite spillover from wildlife where it does occur.
 6.Synthesis and applications: This model of parasite transmission
 potential enables evidence-based management of parasite spillover between
 wild and domestic species in a spatio-temporally dynamic system. It can be
 applied in other mixed-use systems to mitigate parasite transmission under
 altered climate scenarios or changes in host ranges.
description: Goat characteristics and
 FAMACHA/anemia dataData used for logistic
 regression evaluating associations with high FAMACHA score (indicating
 anemia) before and after the rainy season. Reported in paper section
 "Spatial and seasonal variability in parasite burden in
 goats".goat_famacha.xlsxparamsQ0Code for these data available at https://github.com/jogwalker/parasite_transmission_Q0paramsTreatfinalrunsCode for these data available at https://github.com/jogwalker/parasite_transmission_Q0BotsclimdatCode for these data available at https://github.com/jogwalker/parasite_transmission_Q0paramsMovementCode for these data available at https://github.com/jogwalker/parasite_transmission_Q0L3dataCode for these data available at https://github.com/jogwalker/parasite_transmission_Q0
DOI: 10.17632/sw7ppcknm8
title: Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment

description: This dataset contains all-atom molecular dynamics (MD) simulation trajectories supporting the manuscript "Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment." The data characterizes the intrinsic dynamics and allosteric pathways of the human interleukin-1 receptor (R1) in its unbound, agonist-bound, and antagonist-bound states.

The repository includes production trajectories for the following systems (identified by their starting PDB entries). Here, we use Chain IDs to distinguish between components extracted from complexes for "apo" (ligand-removed) simulations. The following table maps the repository folders to the identifiers used in the manuscript and figure legends:

Directory Component(s) Label used in the paper
1G0Y Unbound Receptor (R1) 1G0Y
1ILR Unbound Antagonist (Ra) 1ILR
9ILB Unbound Agonist (IL1) 9ILB
1IRA Antagonist-bound Complex 1IRA
1ITB Agonist-bound Complex 1ITB
4DEP Fully Assembled Ternary Complex 4DEP
4DEP_binary R1–IL1 binary subcomplex 4DEP_binary
1IRA_A Receptor (R1) freed from Ra 1IRA_apo
1ITB_A Receptor (R1) freed from IL1 1ITB_apo
4DEP_A Receptor (R1) freed from ternary complex 4DEP_apo
1IRA_B Antagonist (Ra) freed from R1 1IRA_Apo
1ITB_B Agonist (IL1) freed from R1 1ITB_Apo
4DEP_B Agonist (IL1) freed from ternary complex 4DEP_Apo

These files can be analyzed using standard molecular modeling suites such as AMBER (cpptraj), VMD, MDAnalysis, or MDTraj. The provided topology files are essential for interpreting the coordinate data in the NetCDF files.
DOI: 10.5061/dryad.c2j7m
title: Data from: Comparative genomics of pathogenic and nonpathogenic beetle-vectored fungi in the genus Geosmithia

description: Geosmithia morbida is an emerging fungal pathogen which serves as a model
 for examining the evolutionary processes behind pathogenicity because it
 is one of two known pathogens within a genus of mostly saprophytic,
 beetle-associated, fungi. This pathogen causes thousand cankers disease in
 black walnut trees and is vectored into the host via the walnut twig
 beetle. G. morbida was first detected in western US and currently
 threatens the timber industry concentrated in eastern US. We sequenced the
 genomes of G. morbida in a previous study and two non-pathogenic
 Geosmithia species in this work and compared these species to other fungal
 pathogens and nonpathogens to identify genes under positive selection in
 Geosmithia morbida that may be associated with pathogenicity. Geosmithia
 morbida possesses one of the smallest genomes among the fungal species
 observed in this study, and one of the smallest fungal pathogen genomes to
 date. The enzymatic profile in this pathogen is very similar to its
 non-pathogenic relatives. Our findings indicate that genome reduction or
 retention of a smaller genome may be an important adaptative force during
 the evolution of a specialized lifestyle in fungal species that occupy a
 specific niche, such as beetle vectored tree pathogens. We also present
 potential genes under selection in G. morbida that could be important for
 adaptation to a pathogenic lifestyle.
description: geosmithia.flava.proteinsIn silico generated proteins for Geosmithia flava.geosmithia.flava.transcriptsIn silico generated transcripts for Geosmithia flava.geosmithia.putterillii.proteinsIn silico generated proteins for Geosmithia putterillii.geosmithia.putterillii.transcriptsIn silico generated transcripts for Geosmithia putterillii.
DOI: 10.17632/sw7ppcknm8.1
title: Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment

description: This dataset contains all-atom molecular dynamics (MD) simulation trajectories supporting the manuscript "Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment." The data characterizes the intrinsic dynamics and allosteric pathways of the human interleukin-1 receptor (R1) in its unbound, agonist-bound, and antagonist-bound states.

The repository includes production trajectories for the following systems (identified by their starting PDB entries). Here, we use Chain IDs to distinguish between components extracted from complexes for "apo" (ligand-removed) simulations. The following table maps the repository folders to the identifiers used in the manuscript and figure legends:

Directory Component(s) Label used in the paper
1G0Y Unbound Receptor (R1) 1G0Y
1ILR Unbound Antagonist (Ra) 1ILR
9ILB Unbound Agonist (IL1) 9ILB
1IRA Antagonist-bound Complex 1IRA
1ITB Agonist-bound Complex 1ITB
4DEP Fully Assembled Ternary Complex 4DEP
4DEP_binary R1–IL1 binary subcomplex 4DEP_binary
1IRA_A Receptor (R1) freed from Ra 1IRA_apo
1ITB_A Receptor (R1) freed from IL1 1ITB_apo
4DEP_A Receptor (R1) freed from ternary complex 4DEP_apo
1IRA_B Antagonist (Ra) freed from R1 1IRA_Apo
1ITB_B Agonist (IL1) freed from R1 1ITB_Apo
4DEP_B Agonist (IL1) freed from ternary complex 4DEP_Apo

These files can be analyzed using standard molecular modeling suites such as AMBER (cpptraj), VMD, MDAnalysis, or MDTraj. The provided topology files are essential for interpreting the coordinate data in the NetCDF files.
DOI: 10.15468/dl.wsmpxw
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001519-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bt11p
title: Data from: Parasites favor intermediate nestling masses and brood sizes in cliff swallows

description: A challenge of life-history theory is to explain why animal body size does
 not continue to increase, given various advantages of larger size. In
 birds, body size of nestlings and the number of nestlings produced (brood
 size) have occasionally been shown to be constrained by higher predation
 on larger nestlings and those from larger broods. Parasites also are known
 to have strong effects on life-history traits in birds, but whether
 parasitism can be a driver for stabilizing selection on nestling body size
 or brood size is unknown. We studied patterns of first-year survival in
 cliff swallows (Petrochelidon pyrrhonota) in western Nebraska in relation
 to brood size and nestling body mass in nests under natural conditions and
 in those in which hematophagous ectoparasites had been removed by
 fumigation. Birds from parasitized nests showed highest first-year
 survival at the most common, intermediate brood-size and nestling-mass
 categories, but cliff swallows from non-parasitized nests had highest
 survival at the heaviest nestling masses and no relationship with brood
 size. A survival analysis suggested stabilizing selection on brood size
 and nestling mass in the presence (but not in the absence) of parasites.
 Parasites apparently favor intermediate offspring size and number in cliff
 swallows and produce the observed distributions of these traits, although
 the mechanisms are unclear. Our results emphasize the importance of
 parasites in life-history evolution.
description: Nestlings from
 non-fumigated nestsThis file contains the
 capture histories and co-variates for all nestlings from non-fumigated
 nests.NF
 nestlings (1).xlsxNestlings from fumigated
 nestsThis file contains the
 capture histories and co-variates for all birds from fumigated
 nests.F
 nestlings (1).xlsx
DOI: 10.17632/wn5775n9ys
title: Astragalin Nutrition and Cancer

description: Data showing the anti-migratory effect of astragalin against two glioblastoma cell lines, U87 and T98, as well results on the cell cycle control by astragalin. Data are depicted as the mean of at least 3 indepent experiments.
DOI: 10.15468/dl.z8ghzw
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001523-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmr4df
title: Occurrence Download

description: A dataset containing 4266 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potentilla stolonifera"
 ]
}

 The dataset includes 4266 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001520-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/wn5775n9ys.1
title: Astragalin Nutrition and Cancer

description: Data showing the anti-migratory effect of astragalin against two glioblastoma cell lines, U87 and T98, as well results on the cell cycle control by astragalin. Data are depicted as the mean of at least 3 indepent experiments.
DOI: 10.5061/dryad.f5s54
title: Data from: A novel solution configuration on liquid-based endometrial cytology

description: Objective: Early detection and diagnosis of endometrial carcinoma and
 precancerous change would undoubtedly become the most alluring part for
 researchers. With the emergence of endometrial brush samplers, a new
 upsurge in endometrial cytology is in the making. But endometrial
 specimens obtained by the endometrial brush samplers require special
 preservation solution. The objective of this study is to develop a new
 kind of endometrial-cell preservation solution and to test the
 availability compared with a patented liquid-based cell preservation
 solution. Methods: In this controlled study, we had 5 endometrial cases
 collected with Li Brush from the First Affiliated Hospital of Xi'an
 Jiaotong University (09/2016 to 12/2016). The samples of each case were
 collected 2 times separately and perserved in different perservation
 solutions. One was a kind of novel endometrial cell preservation solution
 and the other was a kind of patented liquid-based cell (LBC) preservation
 solution. The endometrial cells were smeared on slides by using the ZP-C
 automated slide preparation system and stained with Papanicolaou stain. A
 semi-quantitative scoring system was used to analyze the quality of
 slides. Statistical analysis was performed using the Wilcoxon signed rank
 test on the SPSS program (SPSS 18.0). In all LBC preparations, endometrial
 cells from the novel endometrial cells preservation solution had more cell
 quantity, less red blood cell fragments, and the background was cleaner
 compared with control group. Although the novel endometrial-cell
 preservation solution showed cellularity and absence of blood and debris
 expressed by no statistically significant differences (p = 0.063 and 0.102
 respectively). The preservation period of the two kinds of liquids was
 equivalent. Conclusions: The novel endometrial-cell preservation solution
 is superior to the liquid-base cell preservation solution for cervical
 cells, with clear background, diagnostic cells and low cost.
description: Experimental record of
 solution configurationIn the spreadsheet
 "Reading score.xlsx," which is part of this data, 实验组 translates
 to test group in English, and 对照组 translates to control
 group.
DOI: 10.17632/xw2d73z2w7
title: Sounding Space

description: How can we use interaction and experiential design to create immersive experiences that elucidate sound as a physical phenomenon in space? We encourage our students to create both material and conceptual interventions for sound artists, along with various analytical methods to examine and contemplate the urban environment, in order to assess which acts are preferable and most effective.
DOI: 10.17632/xw2d73z2w7.2
title: Sounding Space

description: How can we use interaction and experiential design to create immersive experiences that elucidate sound as a physical phenomenon in space? We encourage our students to create both material and conceptual interventions for sound artists, along with various analytical methods to examine and contemplate the urban environment, in order to assess which acts are preferable and most effective.
DOI: 10.17632/dy85vj4377
title: Grid-Based Analysis of Urban Block Morphology and Built Environment Associations: A Building Morphology Study in Mulltple Chinese Cities

description: This dataset supports the analyses presented in “Grid-Based Analysis of Urban Block Morphology and Built Environment Associations: A Multi-City Study in China”. It provides three groups of data used to quantify (i) urban built-environment conditions, (ii) urban block building morphology, and (iii) footprint-based feature representations after dimensionality reduction.
DOI: 10.5061/dryad.qf3g0
title: Data from: Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data

description: Species diversification may be determined by many different variables,
 including the traits of the diversifying lineages. The State-dependent
 Speciation and Extinction (SSE) framework contains methods to detect the
 dependence of diversification on these traits. For the analysis of traits
 with multiple states, MuSSE (Multiple-States dependent Speciation and
 Extinction) was developed. However, MuSSE and other state-dependent
 speciation and extinction models have been shown to yield false positives,
 because they cannot separate differential diversification rates from
 dependence of diversification on the observed traits. The recently
 introduced method HiSSE (Hidden- State dependent Speciation and
 Extinction) resolves this problem by allowing a hidden state to affect
 diversification rates. Unfortunately, HiSSE does not allow traits with
 more than two states, and, perhaps more interestingly, the simultaneous
 action of multiple traits on diversification. Here, we introduce an R
 package (SecSSE: Several examined and concealed States-dependent
 Speciation and Extinction) that combines the features of HiSSE and MuSSE
 to simultaneously infer state-dependent diversification across two or more
 examined (observed) traits or states while accounting for the role of a
 possible concealed (hidden) trait. Moreover, SecSSE also has improved
 functionality compared to its two 'parents'. First, it allows
 for an observed trait being in two or more states simultaneously, which is
 useful for example when a taxon is a generalist or when the exact state is
 not precisely known. Second, it provides the correct likelihood when
 conditioned on non-extinction, which has been incorrectly implemented in
 HiSSE and other SSE models. To illustrate our method we apply SecSSE to 7
 previous studies that used MuSSE, and find that in 5 out of 7 cases, the
 conclusions drawn based on MuSSE were premature. We test with simulations
 whether SecSSE sacrifices statistical power to avoid the high type I error
 problem of MuSSE, but we find that this is not the case: for the majority
 of simulations where the observed traits affect diversification, SecSSE
 detects this.
description: Simulated
 datasetsFor each empirical
 datasets, we fit three models Constant-rate (CR), Concealed
 Trait-Dependent (CTD) and Examined Trait-Dependent (ETD) diversification.
 Using the parameters that maximize the likelihood, we simulated 100 trees
 under the three models.Supplementary
 Figures
DOI: 10.17632/dy85vj4377.2
title: Grid-Based Analysis of Urban Block Morphology and Built Environment Associations: A Building Morphology Study in Mulltple Chinese Cities

description: This dataset supports the analyses presented in “Grid-Based Analysis of Urban Block Morphology and Built Environment Associations: A Multi-City Study in China”. It provides three groups of data used to quantify (i) urban built-environment conditions, (ii) urban block building morphology, and (iii) footprint-based feature representations after dimensionality reduction.
DOI: 10.5061/dryad.678rp
title: Data from: Island- and lake-like parallel adaptive radiations replicated in rivers

description: Parallel adaptive radiations have arisen following the colonization of
 islands by lizards and lakes by fishes. In these classic examples,
 adaptive radiation is a response to the ecological opportunities afforded
 by the colonization of novel ecosystems and similar adaptive landscapes
 that favor the evolution of similar suites of ecomorphs despite
 independent evolutionary histories. Here, we demonstrate that parallel
 adaptive radiations of cichlid fishes arose in South American rivers.
 Speciation-assembled assemblages of pike cichlids (Crenicichla) have
 independently diversified into similar suites of novel ecomorphs in the
 Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers,
 and molluscivores. There were bursts in phenotypic evolution associated
 with the colonization of each river and the subsequent expansion of
 morphospace following the evolution of the ecomorphs. These riverine
 clades demonstrate that characteristics emblematic of textbook parallel
 adaptive radiations of island- and lake-dwelling assemblages are feasible
 evolutionary outcomes even in labile ecosystems such as rivers.
description: Figure_S1_RADseq_SVDquartets_trees_high_resHigh resolution version of Figure S1 depicting the Crenicichla phylogeny across different matrix sizes and dataBurress_et_al_Supporting_InformationThis file contains the supplemental tables and figures referenced in the main text as well as Methods and Results associated with the SVDquartets trees. A high resolution version of figure S1 is provided separately.Crenicichla_dated_ML_treeThe unpruned time-calibrated maximum likelihood tree used for phylogenetic comparative analyses in the paper. File is in tree format.Crenicichla_SVDquartets_50percent_allvariablesitesThis file contains the unrooted RADseq Crenicichla phylogeny based on a 50% matrix from all variable sites. File is in tree format. See the supplementary material for details.Crenicichla_SVDquartets_50percent_fixedsitesThis file contains the unrooted RADseq Crenicichla phylogeny based on a 50% matrix from fixed sites only. File is in tree format. See the supplementary material for details.Crenicichla_SVDquartets_70percent_allvariablesitesThis file contains the unrooted RADseq Crenicichla phylogeny based on a 70% matrix from all variable sites. File is in tree format. See the supplementary material for details.Crenicichla_SVDquartets_70percent_fixedsitesThis file contains the unrooted RADseq Crenicichla phylogeny based on a 70% matrix from fixed sites only. File is in tree format. See the supplementary material for details.
DOI: 10.5061/dryad.v0108
title: Data from: Effect of Relaxation-Dependent Adhesion on Pre-Sliding Response of Cartilage

description: Possible links between adhesive properties and pre-sliding (static)
 friction response of cartilage are not fully understood in the literature.
 The aims of this study are to investigate the relation between adhesion
 and relaxation time in articular cartilage, and to investigate the effect
 of relaxation-dependent adhesion on pre-sliding response of cartilage.
 Adhesion tests were performed to evaluate the work of adhesion of
 cartilage at different relaxation times. Friction tests were conducted to
 identify the pre-sliding friction response of cartilage at relaxation
 times corresponding to adhesion tests. The pre-sliding friction response
 of cartilage was systematically linked to the work of adhesion and contact
 conditions by a slip-based failure model. It was found that the work of
 adhesion increases with relaxation time. Also, the work of adhesion is
 linearly correlated to the resistance to slip-based failure. In addition,
 as the work of adhesion increases, the critical adhered area at the moment
 of failure increases, and the propagation rate of the annular slip (crack)
 area toward its center increases. These findings offer the mechanistic
 explanation of the pre-sliding friction behavior and stick-slip response
 of soft hydrated interfaces such as articular cartilage and hydrogels.
 Besides, the linear correlation between adhesion and threshold to
 slip-based failure enables estimation of adhesive strength of such
 interfaces directly from pre-sliding friction response (e.g., shear wave
 elastography).
description: Data used for
 results
DOI: 10.15468/dl.z773fm
title: Occurrence Download

description: A dataset containing 1963 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mellivora capensis"
 ]
}

 The dataset includes 1963 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001522-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.