cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gtht76hkf
title: Consistency of aquatic enclosed experiments

description: Aim: Marine and freshwater ecosystems are increasingly threatened by human
 activities. For over a century, scientists have been testing many
 biological, chemical and physical questions to understand various
 ecosystems and their resilience to different stressors. While the majority
 of experiments were conducted at small-scale laboratory settings, lately
 large mesocosm experiments have become more and more common. Yet, it still
 remains unclear how the scale (i.e. space) and ecological complexity (i.e.
 community vs. limited number of species) of experiments affect the results
 and to what extent different experimental types are comparable.
 Innovation: Here, we conducted two types of experiments, run at different
 scale and ecological-complexity levels (i.e. outdoor large-scale
 community-level mesocosm vs. indoor small-scale two-species laboratory
 experiment), to assess the effects of marine heatwaves on two gammarid
 species. Main Conclusions: Our approach detected differences in abundance
 and relative population growth between the two experimental types for one
 out of the two tested species, but no difference in heatwave impacts on
 any of the species, independently of which experimental type was used. The
 larger space in the mesocosm, accompanied with inclusion of the community,
 benefited this species, demonstrating stronger performance in the mesocosm
 than in the laboratory experiment. Though, our study design cannot
 directly distinguish if scale or ecological complexity of the experiments,
 or both, caused the observed discrepancy in our findings. Furthermore,
 inconsistency in results among laboratory experiments complicates the
 extrapolations and generalization of the laboratory results. Yet, our
 findings indicate the importance of space, density-dependent effects,
 biotic interactions and complexity of natural environments in buffering,
 or boosting, the direct effects of environmental stress on organisms.
 Therefore, we urge the use of large-scale community-level mesocosm
 experiments instead of small-scale single-species laboratory ones whenever
 possible, and emphasize a necessity of great caution when interpreting the
 results of laboratory experiments.
DOI: 10.5061/dryad.c2fqz616t
title: Data from: Time to market for drugs approved in Canada between 2014-2018: an observational study

description: Objectives: This study examines the length of time between when a
 patent application is filed in Canada for a new drug and when it is
 available for patients (time to market) and various components of that
 time. It also looks at whether various factors explain the time between
 patent application to New Drug Submission and compares Canadian and
 American times. Drugs approved between January 1, 2014 and December 31,
 2018 are examined.  Design: Descriptive study Data
 Sources: Websites from Health Canada, Food and Drug
 Administration, Merck Index, United States Patent and Trademark Office,
 World Health Organization and previously published articles.
 Interventions: None Primary and Secondary Outcomes: The
 primary outcomes are time to market, time from patent application to New
 Drug Submission (pre-NDS time), review time, time from approval to
 availability (postapproval time) and factors that may influence the
 pre-NDS time. The secondary outcome is a comparison of Canadian and
 American review times and times between patent application and
 approval.  Results: There were 113 drugs available for
 analysis. The median time to market was 11.80 years
 (inter-quartile range (IQR) 9.40, 14.05). The component median times were
 pre-NDS 10.00 years (IQR 8.05, 12.80), review time 0.96 years (IQR 0.75,
 1.15) and postapproval time 0.15 years (IQR 0.08, 0.28). Less than 8% of
 the pre-NDS time was explained by the factors that were analyzed in a
 multiple linear regression equation. There was no statistically
 significant difference between Canadian and American pre-NDS
 times.  Conclusion: On average, once a drug reaches the
 market companies have a median of 8.2 years before the patent expires and
 generics can reach the market. Most of the time between the filing of a
 patent application and when a drug is marketed is determined by decisions
 that are largely under the control of the company.
description: The dataset was collected from published literature, Health
 Canada's Summary Basis of Decision website, Merck Index, United
 States Patent and Trademark Office, World Health Organization
 Collaborating Centre for Drugs Statistics Methodology, Government of
 Canadad Patent Register, and Health Canada Drug Product
 Database.
description: There are no missing values. All of the information needed to
 generate the data used in the paper is in the dataset.
DOI: 10.5061/dryad.b8gtht7bg
title: Global patterns in leaf stoichiometry across coastal wetlands

description: Aim: Coastal wetlands provide critical ecosystem functions and services,
 e.g. coastal protection, nutrient retention and C sequestration. Despite
 the important roles in global C, N and P cycling, the global variation in
 leaf stoichiometry across coastal wetlands remains unclear. Location:
 Global. Time period: 1980-2018. Major taxa studied: Vascular plants.
 Methods: By compiling a global dataset of 698 data records in 205 sites,
 we systematically analysed the world-wide trends and their determinants in
 leaf element contents and ratios of plants across coastal wetlands.
 Results: Leaf N and P contents significantly increased, but C:N, C:P and
 N:P ratios decreased with increasing latitude in coastal wetlands. Mean
 annual temperature was the predominant driver of leaf N, P and C:N, while
 soil N:P was a good predict of leaf C:P and N:P ratios. Furthermore, N
 increased faster with P in plant leaves of coastal wetlands compared to
 terrestrial ecosystems. Within coastal wetlands, herb-dominated salt
 marshes had significantly higher leaf P content, lower leaf N:P ratio and
 lower scaling exponent of leaf N to P than tree-dominated mangroves. Main
 conclusions: The similar latitudinal patterns of leaf stoichiometry in
 coastal wetlands as terrestrial ecosystems reflected the similar
 influences of temperature. However, different slopes of leaf P and N:P
 ratios and N and P scaling relationships between these two ecosystems
 suggested that different salinity and tidal inundation levels result in
 different N and P use strategies in coastal wetland plants. These
 differences in leaf stoichiometry between ecosystems and between different
 types of coastal wetlands may need to be emphasized in future
 biogeochemical modelling due to their different roles in global nutrient
 and carbon cycling.
DOI: 10.5061/dryad.pc866t1mz
title: Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs

description: Tribolium castaneum, the red flour beetle, is among the most well-studied
 eukaryotic genetic model organisms. Tribolium often
 serves as a comparative bridge from highly
 derived Drosophila traits to other organisms.
 Simultaneously, as a member of the most diverse order of metazoans,
 Coleoptera,  Tribolium informs us about
 innovations that accompany hyper diversity. However, understanding the
 tempo and mode of evolutionary innovation requires well-resolved,
 time-calibrated phylogenies, which are not available
 for Tribolium. The most recent effort to
 understand Triboliumphylogenetics used two mitochondrial and
 three nuclear markers. The study concluded that the genus may be
 paraphyletic and reported a broad range for divergence time estimates.
 Here we employ recent advances in Bayesian methods to estimate the
 relationships and divergence times among Tribolium
 castaneum, T. brevicornis, T. confusum, T.
 freemani, and Gnatocerus cornutus using 1368 orthologs
 conserved across all five species and an independent substitution rate
 estimate. We find that the most basal split
 within Tribolium occurred ~86 Mya [95% HPD 85.90–87.04
 Mya] and that the most recent split was between T.
 freemani and T. castaneum at ~14
 Mya [95% HPD 13.55-14.00]. Our results are consistent with
 broader phylogenetic analyses of insects and suggest that Cenozoic climate
 changes played a role in the Tribolium diversification.
DOI: 10.5061/dryad.79cnp5htf
title: Shared patterns of spatial accumulation of lineages across terrestrial vertebrates

description: Aim: Whether species co-occur with closely related taxa has long been
 thought to influence both the rate of species formation and maximum clade
 diversity. However, it is unclear whether these processes act concordantly
 across entire clades, and between taxa with disparate dispersal and life
 history strategies. Quantifying these patterns will yield a better
 understanding of the factors regulating biodiversity. I investigate
 whether allopatry promotes lineage diversification leading to greater
 clade richness. I also test whether slowdowns in diversification and
 family richness are correlated with increased sympatry. Location: Global
 Taxon: Birds, mammals, and amphibians Methods: Posterior distributions of
 speciation rate estimates were compared between different definitions of
 lineage allopatry. Temporal changes in speciation rate were compared
 against family diversity as well as the mean and maximum number of
 overlapping familial ranges. Results: More diverse families accumulate
 more overlapping ranges, but this process is non-random with predominantly
 non-sister taxa overlapping. Sister species in allopatry have higher
 speciation rates, with rates generally suppressed when allopatry is
 defined using all confamilial taxa, suggesting that the effect changes
 over the course of a radiation. Slowdowns in diversification are
 uncorrelated with the maximum and mean number of regionally sympatric
 species, therefore appearing to be either an idiosyncratic feature of
 certain clades, or at least not related to spatial packing of confamilial
 species. Main conclusions: Allopatry of sister species is correlated with
 rapid diversification at 1 – 3Ma timescales. At the family level, maximal
 clade diversity is achieved through increased sympatry of member species,
 i.e. packing of related species within a single geographic area.
DOI: 10.5061/dryad.3ffbg79h2
title: Parallel molecular mechanisms for enzyme temperature adaptation

description: The mechanisms that underly the adaptation enzyme activities and
 stabilities to temperature are fundamental to our understanding of
 molecular evolution and how enzymes work. Herein, we investigate the
 molecular and evolutionary mechanisms of enzyme temperature adaption,
 combining deep mechanistic studies with comprehensive sequence analyses of
 thousands of enzymes. We show that temperature adaptation in ketosteroid
 isomerase (KSI) arises primarily from one residue change with limited,
 local epistasis and we establish the underlying physical mechanisms. This
 residue change occurs in diverse KSI backgrounds, suggesting parallel
 adaptation to temperature. We identify residues associated with organismal
 growth temperature in 1005 diverse bacterial enzyme families, suggesting
 widespread parallel adaptation. We assess the properties of these
 residues, molecular interactions and interaction networks that appear to
 underly temperature adaptation.
description: This Dryad data repository
 contains the starting datasets, analysis code and results
 (<i>p</i>-values and phylogenetic signals) for logistic
 regression models applied to 17,060,900 residue-positions in 2194 enzymes:
 Pinney, M.M, Mokhtari, D.A,  Akiva, E., Yabukarski, F., Sanchez, D.M.,
 Liang, R., Doukov, T.,  Martinez, T.J., Babbitt, P.C.,  Herschlag, D.,
 Parallel Molecular Mechanisms for Enzyme Temperature Adaptation.
 See Pinney, et. al., for
 detailed Materials and Methods on how this dataset was collected and
 analyzed and for all associated references.
description: This dataset contains two sets of files: (1) folders
 "Analysis", "Notebooks" and
 "References", which contain the datasets and step-by-step code
 used in the identification of temperature-associated residues and their
 phyogenetic signals, and (2) "SummaryCSVs", which containes
 summary csv files of the temperature-associated residues identified from
 this analysis and susbets of this dataset (see README files for all for
 more details). Detailed explanations for how this data
 was collected and processed can be found in Pinney, et. al., Materials and
 Methods.
DOI: 10.5061/dryad.931zcrjj9
title: Supplemental data: The association of dilated perivascular spaces with cognitive decline and incident dementia

description: Objective: To determine if severe perivascular space (PVS) dilation is
 associated with longitudinal cognitive decline and incident dementia over
 four and eight years respectively, we analyzed data from a prospective
 cohort study. Methods: 414 community dwelling older adults aged 72-92 were
 assessed at baseline and biennially for up to eight years, with cognitive
 assessments, consensus dementia diagnoses and 3T MRI imaging. The numbers
 of PVS in two representative slices in the basal ganglia (BG) and centrum
 semiovale (CSO) were counted and severe PVS pathology defined as the top
 quartile. The effects of severe PVS pathology in i) either region; ii)
 both regions; and those with iii) severe BG PVS and iv) severe CSO PVS
 were examined. White matter hyperintensity volume, cerebral microbleed
 number and lacune number were calculated. Results: Participants with
 severe PVS pathology in both regions or in the CSO alone had greater
 decline in global cognition over four years, even after adjustment for the
 presence of other small vessel disease neuroimaging markers. The presence
 of severe PVS pathology in both regions was an independent predictor of
 dementia across eight years (OR 2.91, 95%CI 1.43–5.95, p= 0.003). Further,
 the presence of severe PVS pathology in all groups examined was associated
 with greater dementia risk at either year four or six. Conclusions: Severe
 PVS pathology is a marker for increased risk of cognitive decline and
 dementia, independent of other small vessel disease markers. The
 differential cognitive associations for BG and CSO PVS may represent
 differences in their underlying pathology.
DOI: 10.5061/dryad.mcvdnck00
title: Data from: Induced defense and its cost in two bryophyte species

description: PREMISE: Current knowledge about defense strategies in plants under
 herbivore pressure is predominantly based on vascular plants. Bryophytes
 are rarely consumed by herbivores since they have ample secondary
 metabolites. However, it is unknown whether bryophytes have induced
 defenses against herbivory, and whether there is a trade-off between
 growth and defense in bryophytes. METHODS: We carried out an experiment
 with two peatland bryophytes, Sphagnum magellanicum Brid. and S. fuscum
 (Schimp.) H. Klinggr. Two kinds of herbivory, clipping with scissors and
 grazing by mealworms (Tenebrio molitor L.) were simulated. At the end of
 the experiment we measured growth traits, carbon-based defense compounds
 (total phenolics and cellulose) and storage compounds (total
 non-structural carbohydrates) of these two Sphagnum species. RESULTS:
 Grazing but not clipping increased total phenolics and C:N ratio and
 reduced biomass production and height increment. A negative relationship
 between biomass production and total phenolics was found in S.
 magellanicum but not in S. fuscum, indicating a growth-defense trade-off
 which is species-specific. Grazing reduced the starch content of S.
 magellanicum and the sugar of S. fuscum. Either clipping or grazing had no
 effect on chlorophyll fluorescence (including actual and maximum
 photochemical efficiency of photosystem II) except that a significant
 effect of clipping on actual photochemical efficiency in S. fuscum was
 observed. CONCLUSIONS: Our results suggest that Sphagnum can have induced
 defense against herbivory, and that this defense can come at a cost of
 growth. These findings advance our knowledge about induced defense in
 bryophytes, the earliest land plants.
description: See full article for complete methodological details.
DOI: 10.5061/dryad.5dv41ns56
title: Aridity mediates biocrusts' effects on soil multifunctionality in northern China

description: 1. Soil biocrusts, as the fundamental component of drylands, alter soil
 microbial and plant community compositions, thus profoundly affecting soil
 multifunctionality (SMF). Biocrust development regulates microbial
 composition and eco-physiological effects, but there have been limited
 assessments regarding how biocrust development impacts SMF through
 microbial communities and plant species. 2. We investigated the geographic
 patterns of plant diversity, soil bacterial diversity, biocrust
 development, and SMF along an aridity gradient, spanning 2,200 km in
 northern China, and evaluated how biocrust development modulated multiple
 soil functions related to carbon, nitrogen, and phosphorus cycles. 3.
 Plant species richness and SMF decreased linearly with increasing aridity
 (1-AI), but the relationship of soil bacterial diversity and biocrust
 development index (BSCDI) with aridity differed between arid region and
 semi-arid region. 4. Plant diversity and soil bacterial diversity
 increased linearly with BSCDI in arid regions, but decreased linearly with
 BSCDI in semi-arid regions. 5. Both plant species and soil bacterial
 diversity exerted positive effects on SMF in arid regions, but soil
 bacterial diversity, rather than plant species, did not explain any
 variation in SMF in semi-arid regions. Most importantly, biocrust
 development exerted direct effects on SMF in arid regions, but only
 indirect effects through changing soil microbial biomass carbon in
 semi-arid regions. 6. Our findings suggest that the effects and
 influencing pathways of biocrusts on SMF are different between arid and
 semi-arid regions, these results give a comprehensive view of how biocrust
 development facilitates soil multifunctionality improvement and ultimately
 promote a deeper understanding of the dependence of biodiversity-SMF
 relationship on aridity.
DOI: 10.5061/dryad.8gtht76nm
title: Data from: Toward the development of cavitation technology for gas hydrate prevention

description: In offshore gas well drilling and production, methane hydrate may block
 the tubing, resulting in the stoppage of gas production. Conventional
 methods such as injection of thermal hydrate inhibitors, thermal
 insulating or heating, gas dehydration, and reducing pressure are
 time-consuming and expensive, and sometimes they are not realistic in
 production conditions. New methods are needed to lower the cost of gas
 hydrate prevention and to overcome these limitations. The thermal effect
 of cavitation was applied to the prevention of gas hydrate in this study.
 The thermal impact of cavitation, supposed to heat the fluids and prevent
 the formation of gas hydrate, was evaluated. Numerical simulation was
 performed to study the thermal performance of cavitation. Furthermore,
 experimental studies of the influence of initial temperature, flow rate,
 fluid volume, and fluid viscosity on the thermal effect of cavitation were
 performed, and the results were analyzed.
description: During the cavitating process, tiny bubbles collapse with extreme
 high-temperature and high-pressure shock-wave. To analyze and make use of
 the thermal effect during the cavitation, experiments were performed by
 recording the heat generated at fixed time interval (2 minutes) with
 different working conditions (initial temperature, liquid volume, et
 al.). Several sets of experiments have been performed
 and data have been collected. The final dataset used in the paper is the
 averaged one of all sets of experimental data.
description: Current dataset is acquired under the condition of fixed
 rotational speed of the cavitator. No missing values have been found
 according to the authors.
DOI: 10.5061/dryad.0zpc866wm
title: Effect of maternal infection on progeny growth and resistance mediated by maternal genotype and nutrient availability

description: 1. Maternal effects of pathogen infection on progeny development
 and disease resistance may be adaptive and have important consequences for
 population dynamics. However, these effects are often context dependent
 and examples of adaptive transgenerational responses from perennials are
 scarce, although they may be a particularly important mechanism generating
 variation in the offspring of long-lived species. 2. Here, we
 studied the effect of maternal infection of Plantago lanceolata by
 Podosphaera plantaginis, a fungal parasite, on the growth, flower
 production and resistance of the progeny of six maternal genotypes in
 nutrient rich and poor environments. For this purpose, we combined a
 common garden study with automated phenotyping measurements of early
 life-stages, and an inoculation experiment. 3. Our results show that the
 effects of infection on the mother plants transcend to impact their
 progeny. Although maternal infection decreased total leaf and flower
 production of the progeny by the end of the growing season, it accelerated
 early growth and enhanced resistance to the pathogen P. plantaginis.
 4. We also discovered that the effects of maternal infection
 affected progeny development and resistance both directly, and through a
 three way-interaction between maternal genotype, maternal infection status
 and nutrient availability.   5. Synthesis: Our results emphasize
 the importance of maternal effects mediated through genotypic and
 environmental factors in long living perennials and suggest that maternal
 infection can create a layer of phenotypic diversity in resistance. These
 results may have important implications for both epidemiological and
 evolutionary dynamics of host–parasite interactions in the wild.
DOI: 10.5061/dryad.vt4b8gtqv
title: Diatoms define a novel freshwater biogeography of the Antarctic

description: Terrestrial biota in the Antarctic are more globally distinct and highly
 structured biogeographically than previously believed, but information on
 biogeographic patterns and endemism in freshwater communities is largely
 lacking. We studied biogeographic patterns of Antarctic freshwater diatoms
 based on the analysis of species occurrences in a dataset of 439 lakes
 spread across the Antarctic realm. Highly distinct diatom floras, both in
 terms of composition and richness, characterize Continental Antarctica,
 Maritime Antarctica and the sub-Antarctic islands, with marked
 biogeographic provincialism in each region. A total of 44% of all species
 is estimated to be endemic to the Antarctic, and most of them are confined
 to a single biogeographic region. The level of endemism significantly
 increases with increasing latitude and geographic isolation. Our results
 have implications for conservation planning, and suggest that successful
 dispersal of freshwater diatoms to and within the Antarctic is limited,
 fostering the evolution of highly endemic diatom floras