cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2fq726m
title: Data from: Canopy spectral reflectance as a predictor of soil water potential in rice

description: Soil water potential (SWP) is a key parameter for characterizing water
 stress. Typically, a tensiometer is used to measure SWP. However, the
 measurement range for commercially available tensiometers is limited to
 -90 kPa and a tensiometer can only provide estimate of SWP at a single
 location. In this study, a new approach was developed for estimating SWP
 from spectral reflectance data of a standing rice crop over the visible to
 shortwave-infrared region (wavelength: 350 nm to 2500 nm). Five water
 stress treatments corresponding to targeted SWP of – 30 kPa, - 50 kPa, -
 70 kPa, -120 kPa and - 140 kPa were examined by withholding irrigation
 during the vegetative growth stage of three rice varieties. Tensiometers
 and mechanistic water flow model were used for monitoring SWP. Spectral
 models for SWP was developed using partial-least-squares regression
 (PLSR), support vector regression (SVR), and coupled PLSR and feature
 selection (PLSRFS) approaches. Results showed that the SVR approach was
 the best model for estimating SWP from spectral reflectance data with the
 coefficient of determination values of 0.71 and 0.55 for the calibration
 and validation datasets, respectively. Observed root-mean-squared
 residuals for the predicted SWPs were in the range of -7 to -19 kPa. A new
 spectral water stress index was also developed using the reflectance
 values at 745 nm and 2002 nm, which showed strong correlation with
 relative water contents and electrolyte leakage. This new approach is
 rapid and non-invasive and may be used for estimating SWP over large
 areas.
description: Rice canopy spectral
 data under water stressThe data file contains
 whole 780 canopy spectra and their corresponding soil water potential
 (kPa) and 72 canopy spectra and their corresponding terminal soil water
 potential (kPa), relative water content (%) and electrolyte
 leakage(%).Rice canopy spectral
 data.xlsx
DOI: 10.5061/dryad.hf06q72
title: Data from: Prognostic value of ki67 in BCG-treated non-muscle invasive bladder cancer: a meta-analysis and systematic review

description: Objectives: The aim of this study was to explore the prognostic value of
 ki67 as a marker in non-muscle-invasive bladder cancer (NMIBC) patients
 treated with Bacillus Calmette–Guérin (BCG). Methods: Studies were
 systematically retrieved from the relevant databases (Web of Science,
 PubMed, Cochrane Library, and Embase), and the expiry date was May 2017.
 The research steps referred to the Preferred Reporting Items for
 Systematic Reviews and Meta-Analysis statement. Results: A total of 11
 studies that complied with the inclusion criteria were enrolled. The
 expression of ki67 was not statistically significantly associated with
 recurrence-free survival (RFS) [hazard ratio (HR): 1.331; 95% CI:
 0.980–1.809)]. No significant heterogeneity was found among all included
 studies (I2 = 36.7%, P = 0.148). The expression of ki67 was statistically
 significantly associated with progression-free survival (PFS) (HR: 2.567;
 95% CI: 1.562–4.219), and the overexpression of ki67 was the risk factor
 for PFS. Significant heterogeneity was noted among all the included
 studies (I2 = 55.6%, P = 0.021). The studies that might cause
 heterogeneity were excluded using the Galbraith plot, and then the
 meta-analysis was performed again. The results showed that the expression
 of ki67 was still associated with PFS (HR: 2.922; 95% CI: 2.002–4.266).
 Conclusions: The overexpression of ki67 was the risk factor for PFS, and
 the relationship between the expression of ki67 and RFS was not
 statistically significant in patients with NMIBC treated with BCG
 intravesical immunotherapy. Well-designed, prospective, randomized
 controlled trials with a large sample size are still needed to validate
 the findings.
description: DataSharing_DryadWe provide all data, charts, and supplement documents for this file, including the search strategy and retrieval formula incorporated into the literature, the original data extraction process literature, the original data characteristics. The hazard ratio and 95% CI ranges extracted from the literature were included. Other data include: Quality evaluation of included literature. Detailed data on PFS and RFS forest plots and subgroup analyzes in the meta-analysis. Galbraith plot and Funnel plots. The detailed data of Meta-regression analysis. Moreover, other supplementary documents.
DOI: 10.5061/dryad.77744v3
title: Data from: Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest

description: Background: Refugial populations in Quaternary glaciations are critical to
 understanding the evolutionary history and climatic interactions of many
 extant species. Compared with the well-studied areas of Europe and
 Northern America, refugia of species in eastern Asia remain largely
 unknown. Here, we investigated the phylogeographic history of a globally
 important insect pest, the oriental fruit moth Grapholita molesta, in its
 native range of China. Results: Genetic structure analyses unveiled three
 distinct groups and a set of populations with admixture. Approximate
 Bayesian Computation (ABC) analyses support range expansion of this moth
 from southwest groups of Yunnan and Sichuan to northern and eastern China.
 A set of admixed populations was found around these two ancestral groups.
 This pattern of genetic structure points to two refugia located in the
 Yunnan region and Sichuan Basin. The split of the two refugia was dated to
 329.2 thousand years ago in the penultimate glacial period. One of the
 lineages was exclusively found around the Sichuan Basin, indicating the
 formation of endemic populations in this refugium. Ecological niche model
 analysis suggested a shrinking distribution from the past to the present
 in the Sichuan lineage but a wide and stable distribution in the other
 lineage. Conclusions: Our results for the first time suggest that Yunnan
 and Sichuan jointly served as two large-scale refugia in eastern Asia in
 Quaternary glaciations, helping to maintain genetic diversity overall.
description: Microsatellite loci
 genotyped from each individual01_microsatellite_loci_genotyped_from_each_individual.genepopAligned mitochondrial genes from all individuals02_aligned_mitochondrial_genes_from_all_individuals.fasMitochondrial haplotypes used for SplitsTree analysis03_mitochondrial_haplotypes_used_for_SplitsTree_analysis.nexMitochondrial haplotypes used for molecular dating using BEAST04_mitochondrial_haplotypes_used_for_molecular_dating_using_BEAST.fasInputfile for BAPS and STRUCTURE analysesinput_files_of_BAPS_STRUCTURE.rarR script for DAPC analysis09_R_script_for_DAPC_analysis.RFiles for DIYABC analysesfiles for DIYABC analyses.rarCommands used in IMa2 analysis12_commands_used_in_IMa2_analysis.txtScripts and input files used in IBD analysisscripts and input files used in IBD analysis.rar
DOI: 10.5061/dryad.4p9v048
title: Data from: Drivers of temporal beta diversity of a benthic community in a seasonally hypoxic ocean fjord

description: Global expansion of oxygen deficient (hypoxia) waters will have
 detrimental effects on marine life in the Northeast Pacific Ocean (NEP)
 where some of the largest proportional losses in aerobic habitat are
 predicted to occur. However, few studies have accounted for the high
 environmental variability in this region while including natural
 community-assembly dynamics. Here, we present results from a 14-month
 deployment of a benthic camera platform tethered to the VENUS cabled
 observatory in the seasonally hypoxic Saanich Inlet. Our time series
 continuously-recorded, natural cycles of deoxygenation and reoxygenation
 that allowed us to test whether a community from the NEP showed hysteresis
 in its recovery compared to hypoxia-induced decline and to address the
 processes driving temporal beta diversity under variable states of
 hypoxia. Using high-frequency ecological time series we reveal (1)
 differences in the response and recovery of the epibenthic community are
 rate-limited by recovery of the sessile species assemblage, (2) both
 environmental and biological processes influence community assembly
 patterns at multiple time-scales, and (3) interspecific processes can
 drive temporal beta diversity in seasonal hypoxia. Ultimately, our results
 illustrate how different time scale dependent drivers can influence the
 response and recovery of a marine habitat under increasing stress from
 environmental change.
description: CHONe_EF-13_ChuJ_Hypoxia_Temporal_betadiversityData are animal counts and summarized environmental measurements collected from a stationary, still camera deployment, tethered to the Ocean Networks Canada (ONC) VENUS observatory. Data were collected as part of a PhD dissertation (Chu).CHONe_EF-13_Chu_hypoxia_timeseries.xlsx
DOI: 10.5061/dryad.29j22tt
title: Data from: Visual approach computation in feeding hoverflies

description: On warm sunny days female hoverflies are often observed feeding from a
 wide range of wild and cultivated flowers. In doing so, hoverflies serve a
 vital role as alternative pollinators, and suggested to be the most
 important after bees and bumblebees. Unless the flower hoverflies are
 feeding from is large, they do not readily share the space with other
 insects, but instead opt to leave. We have used high-speed videography
 followed by 3D reconstruction of flight trajectories to quantify how
 female Eristalis hoverflies respond to approaching bees, wasps and two
 different hoverfly species. We found that in 94% of the interactions the
 occupant female left the flower when approached by another insect. We
 found that compared to spontaneous take-offs, the occupant hoverfly's
 escape response was performed at ca. 3 times higher speed (spontaneous
 take-off at 0.2 +/- 0.05 m/s compared with 0.55 +/- 0.08 m/s when
 approached by another Eristalis). The hoverflies tended to take off upward
 and forward, while taking the incomer's approach angle into account.
 Intriguingly, we found when approached by wasps that the occupant
 Eristalis took off at a higher speed and when the wasp was further away.
 This suggests that feeding hoverflies may be able to distinguish these
 predators, demanding impressive visual capabilities. Our results,
 including quantification of the visual information available before
 occupant take-off, provide important insight into how freely behaving
 hoverflies perform escape responses from competitors and predators (e.g.
 wasps) in the wild.
description: Figure
 1AA
 Prism file with the data in figure 1a.Figure 1B and Video
 S1Matlab
 file.Figure
 2BPrism
 file.Figure
 3BPrism
 fileFigure
 2APrism
 fileFigure
 3APrism
 fileFigure
 4APrism
 fileFigure
 4BPrism
 fileFigure
 4CPrism
 fileFigure
 4DPrism
 fileFigure
 S2Prism
 fileFigure 3C, D and
 S1Matlab data and script
 showing the interactions in Figure 3C, D and S1.
DOI: 10.5061/dryad.k1k1732
title: Data from: Preparation, characterisation and antioxidant activities of rutin-loaded zein-sodium caseinate nanoparticles

description: Novel rutin-loaded zein-sodium caseinate nanoparticles (ZP) that release
 slowly in simulated gastric/intestinal solutions with antioxidant activity
 in aqueous medium were investigated. The results showed that the sodium
 caseinate concentrations, dosages of rutin and ethanol volume fractions
 significantly affected the zein nanoparticles' characteristics. A
 slower rutin cumulative release (14.8-19.8%) in simulated gastric
 solutions and a relatively faster one (19.8-26.1%) in simulated intestinal
 solutions for 3 h from rutin loaded ZP with different dosages (0.05-0.20
 g) were observed. Concerning the antioxidant properties, the highest
 values of rutin loaded ZP obtained using 2, 2-diphenyl-1-picrylhydrazyl
 scavenging and 2 and 2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic
 acid) decolourisation assays were 52.7% and 71.2%, respectively, and the
 total antioxidant capacity was 0.40nmol g-1. The results suggest that
 zein-sodium caseinate nanoparticles can be used as a new nano delivery
 system for rutin or other water insoluble active ingredients for a
 controlled release.
description: FTIR
 DataThe FTIR data of
 manuscripts “Preparation, characterisation and antioxidant activities of
 rutin-loaded zein-sodium caseinate nanoparticles”in journal Plos
 One.
DOI: 10.5061/dryad.67gk284
title: Data from: Genome-wide analysis and endo-β-mannanase gene families expression profiling of tomato and soybean

description: Endo-β-mannanase is a type of cell wall degrading enzyme and it plays
 varied roles in different developmental events and/or different plants.
 Evolutionary analysis of the gene family will provide an insight into gene
 function and speciation. In this study, genome-wide analysis and
 expression profiling of tomato and soybean endo-β-mannanase gene families
 were performed. We have identified 11 and 20 endo-β-mannanase genes in the
 tomato and soybean genomes, respectively. Sequence alignment revealed
 three α-helices (αA, αB, and αC) of plant endo-β-mannanases were conserved
 in tomato, soybean and Arabidopsis. Gene structure and phylogenetic
 analysis implied that loss of introns play an important role in the
 evolution of endo-β-mannanases. Evolutionary analysis of endo-β-mannanases
 from various plant species showed that they diversified before the
 division of lower and higher plants. Promoter sequence analysis and
 expression patterns analysis found that endo-β-mannanases are not only
 involving in growth and development process of tomato, but also associated
 with the stress response in plants.
description: NJB-01580-R
 data
DOI: 10.5061/dryad.ck21rk8
title: Data from: Leafing patterns and leaf exchange strategies of a cerrado woody community

description: The deciduousness of tropical trees and communities depend on ecosystems
 characteristics such as plant species diversity, and strength of the dry
 season. Based on seven-years of phenological observations we provide the
 first long-term description of leafing patterns of a woody cerrado
 community, aiming to investigate: (1) the leaf exchange strategies
 considering the inter-annual variation on the degree of deciduousness of
 individuals and species and quantify the community deciduousness; (2) the
 relationship between inter-annual patterns of leaf fall and leaf flush
 according to the species` leaf exchange strategies and climate; (3) the
 onset of cerrado growing season and its relation to climate seasonality.
 To detect seasonality and leafing onset we applied circular statistics and
 to understand the relationships between environmental predictors and leaf
 exchange strategies, we used generalized additive models. From 106 species
 observed, we classified 69 as deciduous (26 species), semi-deciduous (25)
 or evergreen (18) and defined the studied cerrado as a semi-deciduous
 vegetation. Leaf phenology was markedly seasonal, and similar among years.
 Leaf fall peaked in the dry season, and leaf flush in the dry-to-wet
 transition. Leaf fall patterns related to temperature and leaf flush to
 day length and rainfall. Semi-deciduous and deciduous species were more
 constrained by climate then the evergreen ones. The cerrado growing season
 started in the dry-to-wet season transition. Inter-annual variations in
 rainfall and temperature affected the individuals’ and, consequently,
 species’ degree of deciduousness, highlighting individual and species
 variability, and suggesting that cerrado leafing patterns is likely
 susceptible to future climate change scenarios.
description: Leaf phenology data and
 climate variables of a cerrado areaThe file contain two
 spreadsheets, one with vegetative phenological ground observations, and
 another with climate variables (Temperature and Precipitation) and
 daylenght of a cerrado vegetation community. The spreadsheet with the
 phenological data presents the leaf exchange strategies and leaf fall and
 leaf flushing intensities at the individual level. Classes of intensity
 (0, 1 and 2) are based on Opler et al., (1980).Veget_Data_Camargo_etal.xlsx
DOI: 10.5061/dryad.2hr3jp7
title: Data from: Novel amphiphilic polyvinylpyrrolidone (PVP) functionalized silicone particles as carrier for low cost lipase immobilization

description: The high catalytic activity, specificity and stability of immobilization
 lipase have been drawn a great interests. How to reduce the cost of
 support materials has always been a hot topic in this field. Herein, for
 the development of low-cost immobilized lipase, we demonstrate an
 amphiphilic polyvinylpyrrolidone (PVP) grafted on silicone particles (SP)
 surface materials (SP-PVP) with rational design based on interfacial
 activation and solution polymerization. Meanwhile, the hydrophilic
 pristine SP and hydrophobic polystyrene-corded silicone particles (SP-Pst)
 were also prepared for lipase immobilization. The SP-PVP were
 characterized by X-ray diffraction, scanning electron microscopy, X-ray
 photoelectron spectroscopy, Fourier transforms infrared spectroscopy and
 thermogravimetry. Our results indicated that the lipase loading amount on
 the SP-PVP composites was about 215 mg of protein per g. In the activity
 assay, the immobilized lipase SP-PVP@CRL exhibited higher catalysis
 activity, better thermostability and reusability than that of SP@CRL and
 SP-Pst@CRL. The immobilized lipase retained more than 54 % of its initial
 activities after 10 times reuse and approximately trended to a steady in
 the following cycles. By introducing the interesting amphiphilic polymer
 to these cheap and easily obtained silicone particles (SP) surface, the
 relative performance of immobilized lipase can be significantly improved,
 rendering interactions between the low cost supports materials and lipase.
description: data of article and
 supporting informationThe files of SEM-PSP, IR
 and TG, data of performance, XPS and XRD are the data of articles. While
 the files of supporting information-IR and supporting information-data of
 recycle performance are the data of supporting
 informaton.data.rar
DOI: 10.5061/dryad.hq77h24
title: Data from: Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes

description: Recent theoretical advances have hypothesized a central role of habitat
 persistence on population genetic structure and resulting biodiversity
 patterns of freshwater organisms. Here, we address the hypothesis that
 lotic species, or lineages adapted to comparably geologically stable
 running water habitats (streams and their marginal habitats), have high
 levels of endemicity and phylogeographic structure due to the persistent
 nature of their habitat. We use a nextRAD sequencing approach to
 investigate the population structure and phylogeography of a putatively
 widespread New Guinean species of diving beetle, Philaccolilus ameliae
 (Dytiscidae). We find that P. ameliae is a complex of morphologically
 cryptic, but geographically and genetically well-differentiated clades.
 The pattern of population connectivity is consistent with theoretical
 predictions associated with stable lotic habitats. However, in two clades,
 we find a more complex pattern of low population differentiation,
 revealing dispersal across rugged mountains and watersheds of New Guinea
 up to 430 km apart. These results, while surprising, were also consistent
 with the original formulation of the Habitat Template Concept by
 Southwood, involving lineage-idiosyncratic evolution in response to
 abiotic factors. In our system, low population differentiation might
 reflect a young species in a phase of range expansion utilizing vast
 available habitat. We suggest that predictions of life history variation
 resulting from the dichotomy between lotic and lentic organisms require
 more attention to habitat characterization and microhabitat choice. Our
 results also underpin the necessity to study fine-scale processes but at a
 larger geographic scale, as compared to solely documenting
 macro-ecological patterns, to understand ecological drivers of regional
 biodiversity. Comprehensive sampling especially of tropical lineages in
 complex and threatened environments such as New Guinea, remains a critical
 challenge.
description: divingbeetleVCF file of Phillaccolilus nextRAD datasetStructure input fileInput file for the program STRUCTUREAll_structureinput.txtBayescan input fileInput file for the program Bayescan used to identify outlier loci that may be undergoing selectionbayescan_fst.txtMrBayes input fileInput file for MrBayes.divingbeetle_one_Oct8_Mrb (1).nexGenetix input fileInput file for the program Genetix used to calculate FstGenetix_all.gtx
DOI: 10.5061/dryad.9mv6d51
title: Data from: Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes.

description: Modern syntheses of eukaryote diversity assign almost all taxa to one of
 three groups: Amorphea, Diaphoretickes, and Excavata (comprising Discoba
 and Metamonada). The most glaring exception is Malawimonadidae, small
 heterotrophic flagellates that resemble Excavata by morphology, but group
 with Amorphea in most phylogenomic analyses. However, just one
 malawimonad, Malawimonas jakobiformis, has been studied with both
 morphological and molecular-phylogenetic approaches, raising the spectre
 of interpretation errors and phylogenetic artefacts from low taxon
 sampling. We report a morphological and phylogenomic study of a new
 deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron
 microscopy revealed all canonical features of ‘typical excavates’,
 including two opposed flagellar vanes (unlike M. jakobiformis but like
 many metamonads) and a composite fibre. Initial phylogenomic analyses
 grouped malawimonads with the Amorphea-related orphan lineage
 Collodictyon, separate from a Metamonada+Discoba clade. However, support
 for this topology weakened when more sophisticated evolutionary models
 were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were
 excluded. Analyses of ‘-FS/LB’ datasets instead suggested a relationship
 between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in
 morphological and molecular data argues against a Metamonada+Discoba clade
 (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade
 should therefore not be assumed when inferring deep-level evolutionary
 history in eukaryotes.
description: Unmasked single-gene
 alignmentsCompressed file
 containing unmasked single-gene alignments used to generate the concatened
 phylogenomic datasetsMal_single.unmasked.tar.gzConcatenated datasets used for phylogenomic analysisCompressed file containing the two masked concatenated datasets used in the full phylogenomic analysesMal_concat.masked.zip