cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xsj3tx9c7
title: Tree species rankings based on publication rate (North America)

description: A ranking of North American tree species based on keyword searches of
 genus and species using Web of Science, AGRICOLA, and CAB Abstracts. A
 bibliographic analysis using three bibliographic databases was conducted
 to understand the importance of North American tree species in literature
 published since 1900 and since the development of the last Silvics of
 North America in the 1980s. The Silvics of North America is the most
 comprehensive guide to North American tree-like species containing about
 200 of the 696 tree-like species found in the literature. Depending on the
 bibliographic database, over 100,000 to over 600,000 publications on the
 696 plant species can be obtained. At least half of the publication
 records are from 1985 forward. The ranking in this database is based on
 the average rank of six bibliographic searches (three bibliographic
 databases and two time frames: 1900-2020 and 1985-2020).
description: Keyword searches of genus and species using Web of Science,
 AGRICOLA, and CAB Abstracts were conducted in January and February 2020.
 Search queries were conducted in English, using contemporary taxonomy
 (genus and species identifiers and their surrogates), as suggested through
 <i>Silvics of North America</i> (Burns and Honkala 1990) and
 the U.S. Department of Agriculture PLANTS database. The initial set of
 tree species were derived from <i>SNA</i> and supplemented
 with species that were identified as having a tree-like growth quality
 from the U.S. Department of Agriculture PLANTS database. Duplications of
 genus and species identifiers were resolved by carefully examining each
 genus/species combination. Some tree species were combined as a result
 into one instance of a species, when they used the same genus/species
 combination. Other tree species had to be carefully evaluated to avoid
 double-counting search results. For example, <i>Pinus
 monophylla</i> (western white pine) is also known as a variant of
 another species, <i>Pinus edulis</i> var. fallax. Therefore,
 the query for western white pine contained a criterion using the Boolean
 operator OR (“<i>Pinus monophylla</i>” or “<i>Pinus
 edulis</i> var. fallax”). However, when <i>Pinus
 edulis</i> (twoneedle pine) was assessed, it required a criterion
 using the Boolean operator NOT (“<i>Pinus edulis</i>” not
 “<i>Pinus edulis</i> var. fallax”). Common names were
 considered for inclusion in the queries using the Boolean operator OR
 (e.g., OR “<i>common name</i>”), however several tree species
 shared common names and the query results could not be disentangled. The
 term “North America” was not used as a keyword (as topic or in “all
 fields” in these queries as it acted to severely limit the results. In
 fact, in limited tests using this term, no results were returned when
 queries included AND “North America”.
DOI: 10.5061/dryad.cjsxksn3k
title: Data from: Functional implications of the specialized staminal appendages in alpine ginger (Roscoea spp.: Zingiberaceae)

description: Floral organs are widely believed to enhance the pollination and
 reproductive success of angiosperms. However, the functional implication
 of some floral structures is still unknown. In this study, we explored the
 functional role of staminal appendages on male and female fitness of
 Himalayan Roscoea spp. and tested if their function differed between
 species with biotic pollination and autonomous selfing. Phenotypic
 manipulation is a powerful approach to test the functional effect of a
 particular trait on plant fitness. We compared various proxies of
 pollination success between intact flowers and flowers with
 manually-excised staminal appendages. We found that the rate of visitation
 did not differ between intact and manipulated flowers. Our results
 revealed that in outcrossing Roscoea spp. the staminal appendages act as
 triggering devices to facilitate pollen release and deposition and also to
 manipulate the foraging position of pollinators to ensure both male and
 female fitness. In contrast, in autonomously selfing Roscoea spp., the
 removal of staminal appendages did not affect any aspect of pollination
 processes. Our results suggest that the staminal appendages are an
 integral component of outcrossing in Roscoea spp., and are maintained by
 selection pressure through both male and female fitness. This study
 provides important insights on how variation in breeding systems can
 provoke changes in the structure and function of floral organs among
 congeners.
DOI: 10.5061/dryad.cz8w9gj17
title: Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements

description: Phospholipase Cepsilon (PLCepsilon) generates lipid-derived second
 messengers in the cardiovascular system at the plasma and perinuclear
 membranes. It is activated in response to a wide variety of signals, such
 as those conveyed by Rap1A and Ras, through a mechanism that involves its
 C-terminal Ras association (RA) domains (RA1 and RA2). However, the
 complexity and size of PLCepsilon has hindered its structural and
 functional analysis. In this manuscript, we report the 2.7 Å crystal
 structure of fragment of PLCepsilon that retains catalytic activity. The
 strutcure includes the RA1 domain, which forms an integral part of the
 conserved core. In addition, a highly conserved amphipathic helix in the
 autoinhibitory X–Y linker is shown to modulate activity in
 vitro and in cells. The studies provide
 a structural framework for  the core of this critical
 cardiovascular enzyme that will allow for a better understanding of its
 regulation and roles in disease.
description: Thermal stability of the PLCepsilon variants was measured using
 differential scanning fluorimetry. Briefly, a final concentration of 0.5
 mg/mL PLCepsilon variant protein was incubated with SYPRO Orange, and the
 increase in fluorescence was measured as a function of increasing
 temperature. The data was fit to a Boltzmann sigmoidal function, where the
 inflection point corresponds to the melting temperature of the
 protein.  <em>In vitro</em> PLCepsilon
 activity was measured using a liposome-based activity assay. In this
 assay, [3H]-PIP2 is incorporated into PE/PIP2 liposomes, and the amount of
 free [3H]-IP3 produced is quantified by scintillation counting. Activity
 was measured at 30 C using a 5 point time course (2-10 min). Control
 reactions lacked Ca2+ and provide the background [3H]-IP3. Specific
 activity was calculated as described
 in 10.1385/1-59259-430-1:67. Cell-based PLCepsilon
 activity was measured using the [3H]-inositol phosphates (IPx)
 accumulation assay. COS-7 cells are transfected with PLCe variants, and
 metabolically labelled with [3H]-myoinositol. Cells were treated with
 lithium chloride to inhibit IPx degradation, and [3H]-IPx species isolated
 by ion exchange chromatography and quantifed by scintillation counting.
 Protein expression was quantified using by western blot analysis (doi:
 10.1126/scisignal.aan1210).
DOI: 10.5061/dryad.1g1jwstsk
title: Ions release from hydroxyapatite and substituted hydroxyapatites in different immersion liquids: In vitro experiments and theoretical modelling study

description: The multi-substituted hydroxyapatites (ms-HAPs) are currently gaining more
 consideration due to their multifunctional properties and biomimetic
 structure, owning thus an enhanced biological potential in orthopedic and
 dental applications. In this study, nano hydroxyapatite (HAP) substituted
 with multiple cations (Sr2+, Mg2+ and Zn2+) for Ca2+ and anion (SiO44-)
 for PO43- and OH-, specifically HAPc-5%Sr and HAPc-10%Sr (where HAPc is
 HAP-1.5%Mg-0.2%Zn-0.2%Si), both lyophilized noncalcined and lyophilized
 calcined, were evaluated for their in vitro ions release. These
 nanomaterials were characterized by SEM, FE-SEM and EDX, as well as by AFM
 images and by surface-specific areas and porosity. Further, the release of
 cations and of phosphate anions were assessed from nano HAP and ms-HAPs,
 both in water and in simulated body fluid (SBF), in static and simulated
 dynamic conditions, using inductively coupled plasma optical emission
 spectrometry (ICP-OES). The release profiles were analyzed and the
 influence of experimental conditions was determined for each of the six
 nanomaterials and for various periods of time. The pH of the samples
 soaked in the immersion liquids was also measured. The ions release
 mechanism was theoretically investigated using the Korsmeyer-Peppas model.
 The results indicated a mechanism principally based on diffusion and
 dissolution, with possible contribution of ion exchange. The surface of
 ms-HAP nanoparticles is more susceptible to dissolution into immersion
 liquids due to the lattice strain provoked by simultaneous
 multi-substitution in HAP structure. According to the findings, it is
 rational to suggest that both materials HAPc-5%Sr and HAPc-10%Sr are
 bioactive and can be potential candidates in bone tissue regeneration.
DOI: 10.5061/dryad.cjsxksn3m
title: Data from: Seasonal and diel cycles of fin whale acoustic occurence near Elephant Island, Antarctica

description: This study investigates the relevance of the Elephant Island region for
 Southern Hemisphere fin whales (Balaenoptera physalus) in their annual
 life cycle. We collected three years of passive acoustic recordings (Jan
 2013 to Feb 2016) northwest of EI to calculate time series of fin whale
 acoustic indices, daily acoustic occurrence, spectrograms, as well as
 abundance of their 20-Hz pulses. Acoustic backscatter strength, sea ice
 concentration and chlorophyll a composites provided concurrent
 environmental information for graphic comparisons. Acoustic interannual,
 seasonal and diel patterns together with visual information and literature
 resources were used to define the period of occupancy and to infer
 potential drivers for their behaviour. Spectral results suggest that these
 fin whales migrate annually to and from offshore central Chile. Acoustic
 data and visual information reveal their arrival at EI in December to feed
 without producing their typical 20-Hz pulse. For all three years, acoustic
 activity commences in February, peaks in May and decreases in August, in
 phase with the onset of their breeding season. Our results emphasize the
 importance of EI for fin whales throughout most of the year. Our
 recommendation is to consider EI for establishing a marine protected area
 to expedite the recovery of this vulnerable species.
description: See publication.
description: <strong>Description
 of data files used in Burkhardt et al. “Seasonal and diel cycles of fin
 whale acoustic occurence near Elephant Island,
 Antarctica”</strong> <strong>Daily_Acoustic_Presence.xlsx</strong> Descriptor Content Day        Date of day analyses [dd.mm.yyyy] FinWhale             1 if at least one fin whale 20-Hz call detected during that day. <strong>Call_Abundance.xlsx</strong> Descriptor Content CorrOrder           Consecutive numbering of analysed files DateFile               Date of start of analysed  file [yyyymmdd] File         Time of start of analysed file [HHMMSS] UTC Date      Consecutive number in analysed days (omitting days not analysed) UTC_long            Time of start of analysed file [HH:MM:SS] UTC UTC       Time of start of analysed file [HH:MM] UTC floored to the lesser full 10-minutes TimeEI(UTC-3.40)            Local time of start of analysed file [HH:MM] LT floored to the lesser full 10-minutes UTC+3.30fuerAchsen0PunktBei20.30 Helper variable facilitating a shift of the x-axis Obvious Calls (OC) Number of obvious 20-Hz calls in 10-min file Category Classification of OC according to legend of Fig. 6 NAN set to 1 if files not analysed for technical reasons <strong>AWI251-01_AU0231_LTS_SNR.mat</strong> Matlab data file containing Long Term Spectrogram Data from Aural 0231.  Variable naming is self-explaining. <strong>MVBS_sn5848_mooring_AWI251-1.mat</strong> Matlab data file containing mean volume backscatter data from ADCP.  Variable naming is self-explaining.
DOI: 10.5061/dryad.66t1g1k06
title: Intensive care unit patients’ opinion on enrollment in clinical research: a multicenter survey - Study data bank

description: Background: In most emergency situations or severe illness,
 patients are unable to consent for clinical trial enrollment. In such
 circumstances, the decision about whether to participate in a scientific
 study or not is made by a legally designated representative.
 Objective: To address the willingness of patients admitted to the
 intensive care unit (ICU) to be enrolled in a scientific study as
 volunteers, and to assess the agreement between patients’ and their legal
 representatives’ opinion concerning enrollment in a scientific study.
 Methods: This survey was conducted in two hospitals in São Paulo,
 Brazil. Patients (≥18 years) with preserved cognitive functions
 accompanied by a surrogate admitted to the ICU were eligible for this
 study. A survey containing 28 questions for patients and 8 questions for
 surrogates was applied within the first 48h from ICU admission. The survey
 for patients comprised three sections: demographic characteristics,
 opinion about participation in clinical research and knowledge about the
 importance of research. The survey for legal representatives contained two
 sections: demographic characteristics and assessment of legal
 representatives’ opinion in authorizing patients to be enrolled in
 research. Results: Between January 2017 and May 2018, 208 pairs
 of ICU patients and their respective legal representatives answered the
 survey. Out of 208 ICU patients answering the survey, 73.6% (153/208) were
 willing to be enrolled in the study as volunteers. Of those patients,
 65.1% (97/149) would continue participating in a research even if their
 legal representative did not support their
 enrollment.  Agreement between patients’ and surrogates’
 opinion concerning participation was poor [Kappa=0.11 (IC95% -0.02 to
 0.25)]. If a consent for study participation had been obtained, 69.1%
 (103/149) of patients would continue participating in the study until its
 conclusion, and 23.5% (35/149) would allow researchers to use data
 collected to date, but would withdraw from the study on that occasion.
 Conclusion: The majority of patients admitted to the ICU were
 willing to be enrolled in a scientific study as volunteers, also after a
 deferred informed consent procedure has been used. Nevertheless,
 contradictory opinions between patients and their and their legal
 representatives’ concerning enrollment in a scientific study were
 often observed.
DOI: 10.5061/dryad.crjdfn327
title: Effect of soil carbon amendments in reversing the legacy effect of plant invasion

description: 1. Invasive plant species are key drivers of global environmental changes
 leading to the disruption of ecosystems they invade. Many invasive species
 engage in novel niche construction through plant-soil feedbacks
 facilitated by the input of secondary compounds, which help their further
 spread and survival. These compounds can persist in soil even after the
 removal of the invader thus creating a legacy effect that inhibits the
 return of native flora and fauna. Thus, formulating active intervention
 strategies that can reverse niche construction is critical for the
 restoration of these invaded ecosystems. 2. We hypothesized that the
 management practices that can reverse the soil carbon and nutrient cycling
 in invaded ecosystems can facilitate the rapid restoration of the invaded
 sites. We predicted that adding soil C amendments such as activated carbon
 and biochar can alter the microbial functional activity and nutrient
 cycling leading to the restoration of invaded habitats. We tested this
 hypothesis in an old-field in Massachusetts that has been invaded by
 Japanese knotweed (Polygonum cuspidatum) for &gt;20 years. 3. After
 two years of treatment application, the activated carbon and biochar
 amended plots had 80% more biomass of the prairie species than the control
 plots. The C amendments also altered soil nutrient cycling and fungal
 biomass and enzyme activity compared to the control plots. The nitrate
 content of C amended plots was 5 times higher than the non-amended control
 plots indicating an increased nitrogen mineralization in C amended plots
 potentially due to the sorption of phenolic compounds by activated carbon
 and biochar that makes them unavailable. This was further supported by the
 increased phenol oxidase activity which might have been less inhibited by
 tannins and led to increased organic matter decomposition. 4. Synthesis
 and conclusions: Our results thus reveal the potential of soil C
 amendments in reversing niche construction and legacy effects of
 polyphenol-rich invasive species and indicate that biochar could be a more
 economically feasible alternative to activated carbon in restoring invaded
 ecosystems. Our results also emphasize that understanding the mechanism
 through which invasive species engage in niche construction is vital in
 formulating suitable knowledge-based restoration practices for invaded
 ecosystems.
DOI: 10.5061/dryad.02v6wwq16
title: Genetic and phenotypic variation in Bathygobius cocosensis from East Australia (2014–2016)

description: Genetic and phenotypic data from an East Australian metapopulation of the
 intertidal goby, Bathygobius cocosensis (Bleeker 1854). Data was collected
 over three years (2014–2016) from juveniles and adult subpopulations at
 three sites: Point Cartwright, Hastings Point and Shellharbour. Genetic
 variation was characterised using genome-wide SNPs, obtained through
 pooled ezRAD sequencing. Phenotypic variation was characterised using
 geometric morphometric analysis of head shape morphology. The analyses
 contained in this repository are for a manuscript submitted
 to Molecular Ecology.
DOI: 10.5061/dryad.83bk3j9p7
title: Microsatellite data for Aedes aegypti populations in Florida and southern California

description: In the affiliated paper we compare likely the oldest populations
 of Aedes aegypti in continental North America with some of the newest to
 illuminate the range of genetic diversity and structure that can be found
 within the invasive range of this important disease vector. Aedes aegypti
 populations in Florida have likely persisted since the 1600-1700s, while
 populations in southern California derive from new invasions that occurred
 in the last ten years. For this comparison, we genotyped 1,193 individuals
 from 29 sites at 12 highly variable microsatellites and a subset of these
 individuals at 23,961 single nucleotide polymorphisms (SNPs).
description: As in Brown <i>et al.</i> (2011), all
 individuals were genotyped at 12 highly variable microsatellite loci: four
 with trinucleotide repeats (A1, B2, B3, and A9) and eight with
 di-nucleotide repeats (AC2, CT2, AG2, AC4, AC1, AC5, AG1, and AG4).
 Microsatellite calls were made using GeneMapper. Any individuals that
 genotyped at fewer than 10 loci were excluded from analysis.
description: The file is in STRUCTURE format, and missing data is represented
 with -9. See Table 1 in the manuscript or the other attachment to
 understand the population abbreviations and learn more about the
 sites.
DOI: 10.5061/dryad.s4mw6m94r
title: The validation of new phase-dependent gait stability measures: a modelling approach

description: Identification of individuals at risk of falling is important when
 designing fall prevention methods. Current stability measures that
 estimate gait stability and robustness appear limited in predicting falls
 in older adults. Inspired by recent findings of phase-dependent local
 stability changes within a gait cycle, we used compass-walker models to
 test several phase-dependent stability metrics for their usefulness to
 predict gait robustness. These metrics are closely related to the
 often-employed maximum finite-time Lyapunov exponent and maximum Floquet
 multiplier. They entail linearizing the system in a rotating hypersurface
 orthogonal to the period-one solution, and estimating the local divergence
 rate of the swing phases and the foot strikes. We correlated the metrics
 with the gait robustness of two compass walker models with either point or
 circular feet to estimate their prediction accuracy. To also test for the
 metrics’ invariance under coordinate transform, we represented the
 point-feet walker in both Euler-Lagrange and Hamiltonian canonical form.
 Our simulations revealed that for most of the metrics, correlations differ
 between models and also change under coordinate transforms, severely
 limiting the prediction accuracy of gait robustness. The only exception
 that consistently correlated with gait robustness is the divergence of
 foot strikes. These results admit challenges of using phase-dependent
 stability metrics as objective measure to quantify gait robustness.
description: All code were writen in Matlab and all data was simulated and
 generated in Matlab.
description: The preprint has been uploaded to Biorxiv
 (https://www.biorxiv.org/content/10.1101/2020.06.18.156950v1). All code
 and data is also accessible via the link https://surfdrive.surf.nl/files/index.php/s/DK68NlvcEDGYaUu
DOI: 10.5061/dryad.2547d7wnj
title: Cerebral small vessel disease MRI features do not improve the prediction of stroke outcome

description: Objective: To determine whether the total small vessel disease (SVD) score
 adds information to the prediction of stroke outcome compared to validated
 predictors, we tested different predictive models of outcome in stroke
 patients. Methods: White matter hyperintensity, lacunes, perivascular
 spaces, microbleeds, and atrophy were quantified in two prospective
 datasets of 428 and 197 first-ever stroke patients, using MRI collected
 24-to-72 hours after stroke onset. Functional, cognitive, and
 psychological status were assessed at the 3–6 month follow-up. The
 predictive accuracy (in terms of calibration and discrimination) of age,
 baseline NIHSS, and infarct volume was quantified (model-1) on dataset-1,
 the total SVD score was added (model-2), and the improvement in predictive
 accuracy was evaluated. These two models were also developed in dataset-2
 for replication. Finally, in model-3, the MRI features of cerebral SVD
 were included rather than the total SVD score. Results: Model-1 showed
 excellent performance for discriminating poor vs. good functional outcomes
 (AUC=0.915), and fair performance for identifying cognitively impaired and
 depressed patients (AUCs, 0.750 and 0.688 respectively). A higher SVD
 score was associated with a poorer outcome (odds ratio=1.30 [1.07, 1.58],
 p=0.0090 at best for functional outcome). However, adding the total SVD
 score (model-2) or individual MRI features (model-3) did not improve the
 prediction over model-1. Results for dataset-2 were similar. Conclusions:
 Cerebral SVD was independently associated with functional, cognitive, and
 psychological outcomes, but had no clinically relevant added value to
 predict the individual outcomes of patients when compared to the usual
 predictors, such as age and baseline NIHSS.
DOI: 10.15468/dl.jhp7us
title: Occurrence Download

description: A dataset containing 4847 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biobanco de ADN Vegetal de la Universidad de Salamanca: SALA-DNA"
 ]
}

 The dataset includes 4847 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007285-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.