cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t76hdr7xb
title: Heat dissipation behaviour of birds in seasonally hot, arid-zones: are there global patterns?

description: Quantifying organismal sensitivity to heat stress provides one means for
 predicting vulnerability to climate change. Birds are ideal for
 investigating this approach, as they display quantifiable fitness
 consequences associated with behavioural and physiological responses to
 heat stress. We used a recently developed method that examines
 correlations between readily-observable behaviours and air temperature
 (Tair) to investigate interspecific variation in avian responses to heat
 stress in seasonally hot, arid regions on three continents: the
 southwestern United States, the Kalahari Desert of southern Africa and the
 Gascoyne region of Western Australia. We found substantial interspecific
 variation in heat dissipation behaviours (wing-drooping, panting,
 activity-reduction, shade-seeking) across all three regions. However,
 pooling the data revealed that little of this interspecific variation was
 systematically explained by organismal traits (foraging guild, diet,
 drinking dependency, body mass, or activity levels) at the scale we
 tested. After accounting for phylogeny, we found that larger birds engaged
 in wing-drooping behaviour at lower Tair and had lower activity levels at
 high Tair compared to smaller birds, indicating an effect of body mass on
 heat dissipation behaviour (HDB). In the Kalahari, reliance on drinking
 was correlated with significantly lower Tair at which panting commenced,
 suggesting a key role of water acquisition in HDB in that region. Birds
 also tended to retreat to shade at relatively lower Tair when more active,
 suggesting a behavioural trade-off between activity, heat load, and
 microsite selection. Our results imply that the causes underlying
 interspecific variation in heat dissipation behaviours are complex. While
 the variation we observed was not systematically explained by the broad
 scale organismal traits we considered, we predict that the indices
 themselves will still reflect vulnerability to potential fitness costs of
 high air temperatures. Further research is needed on a species-specific
 basis to establish the functional significance of these indices.
DOI: 10.6078/d1q11h
title: The effect of influenza vaccination for the elderly on hospitalization and mortality: an observational study with a regression-discontinuity design

description: Replication files for "The Effect of Influenza Vaccination for the
 Elderly on Hospitalization and Mortality: An Observational Study with a
 Regression-Discontinuity Design", published in the Annals of
 Internal Medicine.
DOI: 10.5061/dryad.4qrfj6q6d
title: Data from: Cell death and survival due to cytotoxic exposure modeled as a two-state Ising system

description: Cancer chemotherapy agents are assessed for their therapeutic utility
 primarily by their ability to cause apoptosis of cancer cells and their
 potency is given by an IC50 value. Chemotherapy uses both target-specific
 and systemic-action drugs and drug combinations to treat cancer. It is
 important to judiciously choose a drug type, its dosage, and schedule for
 optimized drug selection and administration. Consequently, the precise
 mathematical formulation of cancer cells response to chemotherapy may
 assist in the selection process. In this paper, we propose a mathematical
 description of the cancer cell response to chemotherapeutic agent exposure
 based on a time-tested physical model of two-state multiple-component
 systems near criticality. We describe the Ising model methodology and
 apply it to a diverse panel of cytotoxic drugs administered against
 numerous cancer cell lines in a dose-response manner. The analyzed dataset
 was generated by the Netherlands Translational Research Center
 B.V.(Oncolines). This approach allows for an accurate and consistent
 analysis of cytotoxic agents’ effects on cancer cell lines and reveals the
 presence or absence of the bystander effect through the interaction
 constant. By calculating the susceptibility function, we see the value of
 IC50 coinciding with the peak of this measure of the system’s sensitivity
 to external perturbations.
description: The dataset has been collected by the experimental
 collaborations in Netherlands Translational Research Center B.V.
 (Oncolines), Ref. (44,45). For finding the fitting parameters of the death
 rate data in terms of the cytotoxic concentrations, analyzing and
 plotting, we used the combination of Python and MATLAB software.
description: To compare the IC50 values from the experimental data, the table
 S1 is provided in the supplementary materials. Also, some synthetic data
 are provided for running the scripts for dose-response curves.
DOI: 10.5061/dryad.h9w0vt4dt
title: Spatial and temporal variation in prey colour patterns for background-matching across a continuous heterogeneous environment

description: In heterogeneous habitats, camouflage via background-matching can be
 challenging because visual characteristics can vary dramatically across
 small spatial scales. Additionally, temporal variation in signalling
 functions of colouration can affect crypsis, especially when animals use
 colouration seasonally for intraspecific signalling (e.g. mate selection).
 We currently have a poor understanding of how wild prey optimise
 background-matching within continuously heterogeneous habitats, and
 whether this is affected by requirements of intraspecific signalling
 across biological seasons. Here, we quantified colour patterns of a wild
 population of shore skink (Oligosoma smithi), a variably coloured lizard
 endemic to New Zealand, to 1) investigate whether background-matching
 varies across a vegetation gradient; 2) assess potential signalling
 functions of colour; and 3) to determine whether there is a trade-off
 between requirements for crypsis and intraspecific signalling in
 colouration across seasons. Although all pattern types occurred throughout
 the vegetation gradient, we found evidence for background-matching in
 skinks across the vegetation gradient, where dorsal brightness and pattern
 complexity corresponded with the proportion of vegetation cover. There was
 also a significant disparity between ventral colour (saturation) of
 juveniles and adults, and also between sexes, suggestive of sex
 recognition. However, there was little indication that colour was
 condition-dependent in adults. Despite some evidence for a potential role
 in signalling, crypsis did not greatly differ across seasons. Our study
 suggests that selection favours a mix of generalist and specialist
 background-matching strategies across continuously heterogeneous habitats.
DOI: 10.15468/dl.vxkzcb
title: Occurrence Download

description: A dataset containing 423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, 6ea87510-0561-11d8-b851-b8a03c50a862, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862)",
 "TaxonKey is Melanoplus borealis",
 "Year 1900-2026"
 ]
}

 The dataset includes 423 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002126-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q83bk3jdt
title: Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice

description: To investigate the genetic architecture underlying cold tolerance during
 germination in rice (Oryza sativa), we conducted a genome-wide association
 study (GWAS) using a novel diversity panel of 257 rice accessions from
 around the world and 5,185 SNP markers from a 7K SNP marker array.
 Genotyping was performed using a 7K Illumina iSelect custom-designed array
 by following the Infinium HD Array Ultra Protocol. The 7K array, called
 the C7AIR, was designed by Dr. Susan McCouch’s Lab at Cornell University
 and consists of 7,098 SNPs (Morales et al. 2020, under review). After
 genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing
 SNP markers (SNPs of call rate &lt;90%; minor allele frequency
 &lt;5%; or heterozygosity &gt;20%) were removed from the dataset.
 For our study, a subset of 5,185 high-quality SNP markers obtained after
 filtering was used to perform the genome-wide association
 analysis.  The dataset representing the genotype data of 5,185
 SNP markers by 257 rice accessions is presented here.
DOI: 10.5061/dryad.0gb5mkkxf
title: Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms

description: Background:Houseflies (Musca domesticaL.) live in intimate association
 with numerous microorganisms and is a vector of human pathogens. In
 temperate areas, houseflies willoverwinter in environments constructed by
 humans and recolonize surrounding areas in early summer. However,
 the dispersal patterns and associated bacteria across season and
 location are unclear.We used genotyping-by-sequencing (GBS) for
 the simultaneous identification and genotyping of thousands of Single
 Nucleotide Polymorphisms (SNPs) to establish dispersal patterns
 of houseflies across farms. Secondly, we used16S rRNA gene amplicon
 sequencing to establish the variation and association between bacterial
 communities and the housefly across farms. 
 Results: Using GBS we identified 18,000 SNPs across 400
 individualssampled within and between 11 dairy farms in Denmark. There was
 evidence for sub-structuring of Danish housefly populations and with
 genetic structure that differed across season and sex. Further, there was
 a strong isolation by distance (IBD) effect, but with large variation
 suggesting that other hidden geographic barriers are important. Large
 individual variations were observed in the community structure of
 the microbiome and it was found to be dependent on location, sex,
 and collection time. Furthermore, the relative prevalence of putative
 pathogens was highly dependent on location and collection time.
 Conclusion:We were able to identify SNPs for the determination of
 the spatiotemporal housefly genetic structure, and to establish
 the variation and association between bacterial communities and the
 housefly across farms using novel next‐generation sequencing
 (NGS)techniques. These results are important for disease prevention given
 the fine-scale population structure and IBD for the housefly, and that
 individual houseflies carry location specific bacteria including putative
 pathogens.
DOI: 10.5061/dryad.ttdz08ktf
title: High-efficient fabrication of core-shell-shell structured SiO2@GdPO4:Tb@SiO2 nanoparticles with improved luminescence

description: SiO2@GdPO4:Tb@SiO2 nanoparticles with core-shell-shell structure were
 successfully synthesized by a cheap silane coupling agent grafting method
 at room temperature. This method not only homogeneously coated rare earth
 phosphate nanoparticles on the surface of silica spheres, but also saved
 the use of rare earth resources. The obtained nanoparticles are consisted
 of SiO2 core with a diameter of ~210 nm, GdPO4:Tb intermediate shell with
 thickness of ~7 nm, and SiO2 outer shell with thickness of ~20 nm. This
 unique core-shell-shell structured nanoparticles exhibited strong
 luminescence properties compared with GdPO4:Tb nanoparticles. The
 core-shell-shell structured nanoparticles can effectively quench the
 intrinsic fluorescence of bovine serum albumin (BSA) through a static
 quenching mode. The as-synthesized nanoparticles show great potential in
 biological cell imaging and cancer treatment.
DOI: 10.5061/dryad.pzgmsbcgc
title: Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver

description: The classical drug development pipeline necessitates studies using animal
 models of human disease to gauge future efficacy in humans, however there
 is a low conversion rate from success in animals to humans. Non-alcoholic
 fatty liver disease (NAFLD) is a complex chronic disease without any
 established therapies and a major field of animal research. We performed a
 meta-analysis with meta-regression of 603 interventional rodent studies
 (10,364 animals) in NAFLD to assess which variables influenced treatment
 response. Weight loss and alleviation of insulin resistance were
 consistently associated with improvement in NAFLD. Multiple drug classes
 that do not affect weight in humans caused weight loss in animals. Other
 study design variables, such as age of animals and dietary composition,
 influenced the magnitude of treatment effect. Publication bias may have
 increased effect estimates by 37-79%. These findings help to explain the
 challenge of reproducibility and translation within the field of
 metabolism.
description: This dataset can be analysed using the added code for R
 4.0.2. See README file.
DOI: 10.5061/dryad.ngf1vhhqk
title: Titanium dioxide (TiO2) thin films study, deposited by laser ablation on glass substrates in the form of prismatic figures type pyramidal

description: Thin films are something that is very close to the atomic dimensions in
 thickness, therefore if it is possible to further reduce the width of
 these, in a controlled way and monitor the behavior of some physical law
 associated with the variation in thickness, the results can be as expected
 or maybe adjustments must be applied. For this reason in this work, thin
 films of titanium dioxide (TiO2) are studied, deposited by laser ablation,
 on glass substrates in the form of prismatic figures. The main objective
 was to confine the plasma plume to produce a continuous trail with varying
 thicknesses that could be analyzed. Growth times of the films were 5, 10,
 15, 20 and 30 minutes at room temperature in a low vacuum. The deposited
 films presented a color pattern related to the expected thickness
 variation, thus the theory of optical interference was applied to the
 continuous trace to calculate thicknesses. Characterization process was
 carried out by: X-ray diffraction to know the crystalline structure of the
 films, ultraviolet-visible spectroscopy to verify the variation of
 thicknesses, X-ray photoelectron spectroscopy to know the composition and
 scanning electron microscopy, to measure the thicknesses of the films
 transversely.
DOI: 10.5061/dryad.p81m1
title: Phylogeography of lionfishes (Pterois) indicate taxonomic over splitting and hybrid origin of the invasive Pterois volitans

description: The evolutionary consequences of hybridization are poorly understood,
 especially in the marine realm where hybridization was once thought to be
 a rare occurrence. Previous research indicated that the lionfishes Pterois
 volitans and P. miles are sister species, both of which have been detected
 in the recent invasion of the Atlantic. Anecdotal data from the invasive
 range indicates they may hybridize, but previous studies have not examined
 the potential for these species to hybridize in the native range, or how
 such hybridization affects the distribution of genetic diversity. Here we
 address evolutionary divergence and population structure using mtDNA COI
 and two nuclear introns from 214 lionfish including four putative sister
 species (36 P. miles, 90 P. volitans, 32 P. lunulata, and 56 P. russelii)
 collected at 10 locations. Genetic data are supplemented with a
 re-examination of key morphological characters: dorsal, anal and pectoral
 fin ray counts. These data reveal two lineages (d = 0.041 in COI) among
 the four putative species: an Indian Ocean lineage, represented by P.
 miles and a Pacific Ocean lineage represented by P. lunulata and P.
 russelii. Lionfish identified as P. volitans appear to be hybrids between
 the sister linages of P. miles and P. lunulata/russelii, a conclusion
 supported by both the genetic data and morphology. The degree and
 geographic extent of introgression indicates widespread hybridization, or
 the absence of valid species distinctions between all four species. These
 findings also indicate that the lionfish invading tropical Atlantic Ocean,
 usually labeled P. volitans, is a hybrid.
description: Lionfish specimen
 information Lionfish specimen
 information for samples used in this study, including sample collection
 information.
DOI: 10.5061/dryad.8kprr4xjh
title: Leaf vibrations produced by chewing provide a consistent acoustic target for plant recognition of herbivores

description: Plant defenses that respond to the threat of herbivory require accurate
 sensing of the presence of herbivores. Herbivory cues include mechanical
 damage, elicitors from insect saliva or eggs, and airborne volatiles
 emitted by wounded plants. Plants can also respond to the leaf vibrations
 produced by chewing herbivores. However, previous studies of the influence
 of feeding vibrations on plant defenses have been limited to single
 species pairs. In this study we test the hypothesis that chewing
 vibrations differ among herbivore species, both in their acoustic features
 and in their effect on plant defense responses. We first compare the
 acoustic traits of larval feeding vibrations in ten species from six
 families of Lepidoptera and one family of Hymenoptera. We then test
 responses of A. thaliana plants to variation among feeding vibrations of
 different individuals of one species, and to feeding vibrations of two
 species, including a pierid butterfly and a noctuid moth. All feeding
 vibrations consisted of repetitive pulses of vibration associated with
 leaf tissue removal, although chewing rates varied between species and
 between large and small individuals within species. The frequency spectra
 of the vibrations generated by leaf feeding were similar across all ten
 species. Induced defenses of A. thaliana did not differ when plants were
 played vibrations from different individuals, or vibrations of two species
 of herbivores with different chewing rates, when amplitude was held
 constant. These results suggest that feeding vibrations provide a
 consistent set of cues for plant recognition of herbivores.
DOI: 10.5061/dryad.gmsbcc2j6
title: Association of leaf silicon content with chronic wind exposure across and within herbaceous plant species

description: Aim: High foliar silicon (henceforth Si) concentration protects plant
 tissues against herbivory but protection against several abiotic stressors
 has been proposed too, though the adaptive significance of these functions
 is still being debated. We aimed to explore the potential relationships
 between foliar Si content and chronic wind exposure across a large scale
 and multiple species, and analyze an overlooked alternative or
 complementary function of silicon in leaves: mechanical protection against
 wind. Location: Mainland China. Time period: From July to September during
 2012–2014. Major taxa studied: 282 vascular plant species in predominantly
 herbaceous communities. Methods: We compiled a dataset for leaf silicon
 concentration [Si] across 27 sites and 153 herbaceous plots comprising the
 major climate zones of China. We hypothesized that evolutionary lineages
 that generally have high [Si] should show positive relationships between
 leaf [Si] and mean annual wind speed. Results: Within major families with
 generally high [Si] (especially grasses, sedges and composites), leaf [Si]
 is consistently positively correlated with mean wind speed among species
 across China. For the seven widespread monocot species with high leaf
 [Si], including the globally widely distributed common reed (Phragmites
 australis), intraspecific variation in leaf [Si] follows the same
 consistent positive correlation with mean wind speed. Main conclusions:
 Our findings suggest high leaf [Si] is likely to have widespread adaptive
 value for wind exposure of leaves, at least in several very widespread
 families and species of herbaceous plants. Damage from wind is a danger
 for plants in many ecosystems, and hence these findings are of global
 significance and indicate further research into large scale variation of
 leaf Si and mechanical traits in relation to wind exposure will likely be
 illuminating.
DOI: 10.5061/dryad.dr7sqv9v8
title: Large-scale metabolic interaction network of the mouse and human gut microbiota

description: The role of our gut microbiota in health and disease is largely attributed
 to the collective metabolic activities of the inhabitant microbes. A
 system-level framework of the microbial community structure, mediated
 through metabolite transport, would provide important insights into the
 complex microbe-microbe and host-microbe chemical interactions. This
 framework, if adaptable to both mouse and human systems, would be useful
 for mechanistic interpretations of the vast amounts of experimental data
 from gut microbiomes in murine animal models, whether humanized or not.
 Here, we constructed a literature-curated, interspecies network of the
 mammalian gut microbiota for mouse and human hosts, called NJC19. This
 network is an extensive data resource, encompassing 838 microbial species
 (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types,
 interacting through 8,224 small-molecule transport and macromolecule
 degradation events. Moreover, we compiled 912 negative associations
 between organisms and metabolic compounds that are not transportable or
 degradable by those organisms. Our network may facilitate experimental and
 computational endeavors for the mechanistic investigations of
 host-associated microbial communities.
DOI: 10.5061/dryad.2bvq83bm2
title: Prediction of Cerebral Venous Thrombosis with a new clinical score and D-dimer levels

description: OBJECTIVE:To investigate prediction of cerebral venous thrombosis (CVT) by
 clinical variables and D-dimer levels. METHODS:This prospective
 multicentre study included consecutive patients with clinically possible
 CVT. On admission, patients underwent clinical examination, blood-sampling
 for D-dimers-measuring (ELISA-test), and MR-/CT-venography. Predictive
 value of clinical variables and D-dimers for CVT were calculated. A
 clinical score to stratify patients into groups with low, moderate, or
 high CVT risk was established using multivariate logistic regression.
 RESULTS:CVT was confirmed in 25.8% (94/359) patients by neuroimaging. The
 optimal estimate of clinical probability was based on 6 variables:
 seizure(s) at presentation (4 points), known thrombophilia (4 points),
 oral contraception (2 points), duration of symptoms &gt;6 days (2
 points), worst headache ever (1 point) and focal neurological deficit at
 presentation (1 point) (AUC 0.889). We defined 0-2 points as low CVT
 probability (NPV 94.1%). 186 (51.8%) patients had a low probability score,
 of whom 11 (5.9%) had CVT. The frequency of CVT was 28.3% (34/120) in
 patients with a moderate (3-5 points) and 92.5% (49/53) in patients with a
 high (6-12 points) probability score. All low CVT probability patients
 with CVT had D-dimers &gt;500µg/L. Predictive value of D-dimers for
 CVT for ≥675µg/l (best cut-off) vs. ≥500µg/l respectively was:
 Sens:77.7%/Spec:77%/NPV:90.7%/ACC:77.2% vs.
 Sens:89.4%/Spec:66.4%/NPV:94.6%/ACC:72.4%. To the clinical score added
 D-dimers &gt;500µg/L resulted in the best CVT prediction score
 explored (at the cut-off≥6 points:
 Sens:83%/Spec:86.8%/NPV:93.5%/ACC:84.4%/AUC:0.937). CONCLUSION:The
 proposed new clinical score in combination with D-dimers may be helpful
 for prediction of CVT as a pretest score;none of the CVT patients showed
 low clinical probability for CVT and D-dimers &lt;500µg/L.