cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gmsbcc2rj
title: Data from: Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish, Oryzias latipes

description: Sagittal otoliths, typically composed of aragonite, are frequently laid
 down rather as vaterite during growth in hatchery-reared fish populations.
 Sagittal vateritisation is believed to impair individual hearing/balancing
 abilities, but the causal mechanism remains unclear. Here we
 experimentally demonstrated that rearing in Sr-rich water induces sagittal
 vateritisation in the HdrR-II1 inbred strain of the Japanese rice
 fish, Oryzias latipes. Both sagittae were partly vateritised in
 70% of individuals subjected to the Sr2+ treatment (n = 10), whereas fish
 reared in normal tap water showed no sagittal vateritisation (n = 8). Our
 result is consistent with the theoretical prediction that vaterite becomes
 thermodynamically more stable than aragonite as the Sr2+ concentration in
 solution increases. A vateritic layer develops surrounding the original
 aragonitic sagitta in vateritised otoliths, some of which take on a
 comma-like shape. Electron probe microanalysis demonstrates that the
 vateritised phase is characterised by lower Sr2+ and higher Mg2+
 concentrations than the aragonitic phase. It is unlikely that increased
 environmental Sr2+ is responsible for the sagittal vateritisation in
 farmed fish. However, our findings likely help to establish an in vivo
 assay using O. latipes to understand the physiological process underlying
 the sagittal vateritisation in farmed fish.
description: Concentrations of some divalent cation species were
 sclerochronologically quantified from the core to the edge of each
 otolith, because the vateritic phase is characterised by both lower
 strontium (Sr) and higher magnesium (Mg) concentrations than the
 aragonitic phase. Prior to the analysis, the upper surface of the
 specimens was coated with platinum-palladium for 60 s in an ion-beam
 sputter coater (Hitachi E-1030) to enhance electrical conductivity.
 Chemical composition of the otoliths was obtained using a JEOL JXA-8230
 electron probe microanalyser (EPMA) at the Atmosphere and Ocean Research
 Institute, the University of Tokyo. The wavelength-dispersive spectrometry
 (WDS) method was used to measure Ca, Mg, and Sr concentrations with the
 electron beam of 5 µm in diameter with 5 µm intervals. Exposure times were
 set at 10 s for peaks and 5 s for background measurements with an
 accelerating voltage of 15 kV and a beam current of 12 nA. Wollastonite
 (CaSiO<sub>3</sub>), magnesium oxide (MgO), and strontium
 titanate (SrTiO<sub>3</sub>) were used as standard materials
 for the ZAF correction. Otoliths collected from all 18 individuals (n =
 36) were subjected to the EPMA analysis.
DOI: 10.3929/ethz-b-000681298
title: Replication data for: Association genetics and genomic prediction for resistance to the pea root rot complex in a diverse collection of Pisum sativum L.
title: Identification of a resistance QTL against a pea root rot complex in a diverse population of Pisum sativum L.

description: This repository contains genotypic and phenotypic data from a collection of 254 genotypes of pea (Pisum sativum L.). These data was used to identify genomic regions in the pea genome associated with root rot resistance.
DOI: 10.5061/dryad.6m905qg32
title: Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

description: Populations of short-lived organisms can respond to spatial and temporal
 environmental heterogeneity through local adaptation. However, the
 comparative signals of local adaptation across space and time remains
 poorly understood. Here, we examined patterns of allele frequency change
 across a latitudinal cline and between seasons at previously reported
 expression quantitative trait loci (eQTLs). We divided eQTLs into groups
 by utilizing differential expression profiles of fly populations collected
 across latitudinal clines or exposed to different environmental
 conditions. In general, we find that eQTLs are enriched for clinally
 varying polymorphisms, and that these eQTLs change in frequency in
 concordant ways across the cline and in response to starvation and
 chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms
 is more subtle, and the direction of allele frequency change at eQTLs
 appears to be somewhat idiosyncratic. Taken together, we suggest that
 clinal adaptation at eQTLs is at least partially distinct from seasonal
 adaptation.
description: 1. For original datasets, we downloaded from supplemental
 materials or websites. 2. For intermediate data, we
 wrote R scripts to re-group eQTLs by sex and estimated their directional
 effect on genes. 3. For results data, we wrote R
 scripts to do the enrichment and directionality analysis.
DOI: 10.5061/dryad.nk98sf7wj
title: Improvements in airflow characteristics and effect on the NOSE score after septoturbinoplasty: A computational fluid dynamics analysis

description: Septoturbinoplasty is a surgical procedure that can improve nasal
 congestion symptoms in patients with nasal septal deviation and inferior
 turbinate hypertrophy. However, it is unclear which physical domains of
 nasal airflow after septoturbinoplasty are related to symptomatic
 improvement. This work employs computational fluid dynamics modeling to
 identify the physical variables and domains associated with symptomatic
 improvement. Sixteen numerical models were generated using eight
 patients' pre- and postoperative computed tomography scans. Changes
 in unilateral nasal resistance, surface heat flux, relative humidity, and
 air temperature and their correlations with improvement in the Nasal
 Obstruction Symptom Evaluation (NOSE) score were analyzed. The NOSE score
 significantly improved after septoturbinoplasty, from 14.4 ± 3.6 to 4.0 ±
 4.2 (p &lt; 0.001). The surgery not only increased the airflow
 partition on the more obstructed side (MOS) from 31.6 ± 9.6 to 41.9 ± 4.7%
 (p = 0.043), but also reduced the unilateral nasal resistance in the MOS
 from 0.200 ± 0.095 to 0.066 ± 0.055 Pa/(mL×s) (p = 0.004). Improvement in
 the NOSE score correlated significantly with the reduction in unilateral
 nasal resistance in the preoperative MOS (r=0.81). Also, improvement in
 the NOSE score correlated better with the increase in surface heat flux in
 the preoperative MOS region from the nasal valve to the choanae (r=0.87)
 than in the vestibule area (r=0.63). Therefore, unilateral nasal
 resistance and mucous cooling in the preoperative MOS can explain the
 perceived improvement in symptoms after septoturbinoplasty. Moreover, the
 physical domain between the nasal valve and the choanae might be more
 relevant to patient-reported patency than the vestibule area.
DOI: 10.5061/dryad.gtht76hqj
title: Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage

description: Losses in biodiversity can alter disease risk through changes in host
 species composition. Host species vary in pathogen susceptibility and
 competence. Yet how changes in diversity alter host-pathogen dynamics
 remains unclear in many systems, particularly with respect to generalist
 pathogens. Amphibians are experiencing worldwide population declines
 linked to generalist pathogens, such as ranavirus, and thus represent an
 ideal group to investigate how host species composition affects disease
 risk. We conducted experiments where individuals in the laboratory and
 assemblages of three amphibian species (Pacific tree frogs, Pseudacris
 regilla; Cascades frogs, Rana cascadae; and Western toads, Anaxyrus
 boreas) or just A. boreas alone in outdoor mesocosms were exposed to
 ranavirus as larvae. In laboratory experiment, we observed low survival
 and high viral loads in P. regilla compared to the other species
 suggesting that this species was highly susceptible to the pathogen. In
 the mesocosm experiment, we observed 41% A. boreas mortality when alone
 and 98% mortality when maintained with P. regilla and R. cascadae. Our
 results suggest that the presence of highly susceptible species can alter
 disease dynamics across multiple species, potentially increasing infection
 risk and mortality in co-occurring species.
DOI: 10.5061/dryad.pzgmsbcq9
title: Data from: Bee diversity decreases rapidly with time since harvest in intensively managed conifer forests

description: Despite widespread concern about the anthropogenic drivers of global
 pollinator declines, little information is available about the impacts of
 land management practices on wild bees outside of agricultural systems,
 including forests managed intensively for wood production. We assessed
 changes in wild bee communities with time since harvest in 60 intensively
 managed Douglas-fir (Pseudotsuga menziesii) stands across a gradient in
 stand ages spanning a typical harvest rotation. We measured bee abundance,
 species richness, and alpha and beta diversity, as well as habitat
 characteristics (i.e., floral resources, nesting substrates, understory
 vegetation, and early seral forest in the surrounding landscape) during
 the spring and summer in 2018 and 2019. We found that bee abundance and
 richness declined rapidly with stand age, decreasing by 61% and 48%,
 respectively, for every five years since timber harvest. Asymptotic
 estimates of Shannon and Simpson diversity were highest in stands 6-10 y
 post-harvest and lowest after the forest canopy had closed, approximately
 11 y post-harvest. Bee communities in older stands were nested subsets of
 bee communities found in younger stands, indicating changes were due to
 species loss, rather than turnover, as stands aged. Bee abundance – but
 not richness – was positively associated with floral resource density, and
 neither metric was associated with floral richness. The amount of early
 seral forest in the surrounding landscape seemed to enhance bee species
 richness in older, closed-canopy stands, but otherwise had little effect.
 Changes in the relative abundance of bee species did not relate to bee
 functional characteristics such as sociality, diet breadth, or nesting
 substrate. Our study demonstrates that Douglas-fir plantations develop
 diverse communities of wild bees shortly after harvest, but those
 communities erode rapidly over time as forest canopies close. Therefore,
 stand-scale management activities that prolong the pre-canopy closure
 period and enhance floral density during the initial stage of stand
 regeneration will provide the greatest opportunity to enhance bee
 diversity in landscapes dominated by intensively managed conifer forests.
DOI: 10.18112/openneuro.ds007046.v1.0.0
title: Vision for action
DOI: 10.15468/dl.xuxfg7
title: Occurrence Download

description: A dataset containing 199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dunbaria punctata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 199 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003249-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh78k
title: Large-scale reforestation can increase water yield and reduce drought risk for water-insecure regions in the Asia-Pacific

description: Large-scale reforestation can potentially bring both benefits and risks to
 the water cycle, which needs to be better quantified under future climates
 to inform reforestation decisions. We identified 477 water-insecure basins
 worldwide accounting for 44.6% (380.2 Mha) of the global reforestation
 potential. As many of these basins are in the Asia-Pacific, we used
 regional coupled land-climate modelling for the period 2041–2070 to reveal
 that reforestation increases evapotranspiration and precipitation for most
 water-insecure regions over the Asia-Pacific. This resulted in a
 statistically significant increase in water yield (p &lt; 0.05) for
 the Loess Plateau-North China Plain, Yangtze Plain, Southeast China and
 Irrawaddy regions. Precipitation feedback was influenced by the degree of
 initial moisture limitation affecting soil moisture response and thus
 evapotranspiration, as well as precipitation advection from other
 reforested regions and moisture transport away from the local region.
 Reforestation also reduces the probability of extremely dry months in most
 of the water-insecure regions. However, some regions experience
 non-significant declines in net water yield due to heightened
 evapotranspiration outstripping increases in precipitation, or declines in
 soil moisture and advected precipitation.
description: This dataset contains raw data outputs for Teo et al. (2022),
 Global Change Biology. Please see the published paper for further details
 on methods. For enquiries, please contact the corresponding authors:
 hcteo [at]
 u.nus.edu or lianpinkoh [at]
 nus.edu.sg. 
description: Shapefiles can be opened with any GIS program such as ArcMap or
 QGIS.  CSV files can be opened with any spreadsheet
 program such as Microsoft Excel or OpenOffice.
DOI: 10.15468/dl.xnhdbb
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quadrulella",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003248-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rbnzs7hf0
title: Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure

description: Biochar can significantly change soil properties and improve soil quality.
 However, the effects of long-term combined application of biochar (B) and
 nitrogen (N) fertilizer on relationships between soil enzyme activity,
 microbial community structure and crop yield are still obscure. We
 characterized these relationships in a long-term (8 years) field
 experiment with rice, two biochar rates of 0 and 13.5 t ha-1 year-1 (B0
 and B) and two N fertilizer rates of 0 and 300 kg N ha-1 year-1 (N0 and
 N). The repeated, long-term combined applications of biochar and N
 fertilizer significantly increased microbial biomass carbon and nitrogen
 (MBC and MBN), but biochar decreased the abundance of total bacteria,
 fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as
 the amount of total phospholipid fatty acids. The activity of leucine
 aminopeptidase (LAP) decreased significantly in the biochar-amended and N
 fertilized treatment, but the LAP activity either remained unchanged or
 increased with biochar amendment at N0. The relative abundance of
 bacterial phylum Chloroflexi was increased in the combined biochar and N
 fertilizer treatment. The changes in soil organic matter and the activity
 of α-1,4-xylosidase were the major properties influencing soil bacterial
 community composition, whereas the structure of fungal community was
 governed by MBC, MBN and LAP activity. In addition, long-term biochar and
 N fertilizer applied together significantly increased rice yield (more
 than biochar and nitrogen fertilizer applied alone). Yield was
 significantly positively correlated with LAP activity, but significantly
 negatively correlated with the relative abundance of Chloroflexi. In
 conclusion, long-term biochar and nitrogen fertilizer applications
 increased rice yield, which was associated with altered soil microbial
 community and enhanced activity of some enzymes.
description: The basic physical and chemical indexes were measured by the test
 method and recorded directly in the excel table.  For soil microbial data,
 it was provided  by a third party company.
DOI: 10.5061/dryad.fqz612jvz
title: A mechanism of uncompetitive inhibition of the serotonin transporter

description: The serotonin transporter (SERT/SLC6A4) is arguably the most extensively
 studied solute carrier (SLC). During its eponymous action - i.e., the
 retrieval of serotonin from the extracellular space - SERT undergoes a
 conformational cycle. Typical inhibitors (antidepressant drugs and
 cocaine), partial and full substrates (amphetamines and their derivatives)
 and atypical inhibitors (ibogaine analogues) bind preferentially to
 different states in this cycle. This results in competitive or
 non-competitive transport inhibition. Here, we explored the action of
 N-formyl-1,3-bis (3,4-methylenedioxyphenyl)-prop-2-yl-amine (ECSI#6) on
 SERT: inhibition of serotonin uptake by ECSI#6 was enhanced with
 increasing serotonin concentration. Conversely, the KM for serotonin was
 lowered by augmenting ECSI#6. ECSI#6 bound with low affinity to the
 outward-facing state of SERT but with increased affinity to a
 potassium-bound state. Electrophysiological recordings showed that ECSI#6
 preferentially interacted with the inward-facing state. Kinetic modeling
 recapitulated the experimental data and verified that uncompetitive
 inhibition arose from preferential binding of ECSI#6 to the K+-bound,
 inward-facing conformation of SERT. This binding mode predicted a
 pharmacochaperoning action of ECSI#6, which was confirmed by examining its
 effect on the folding-deficient mutant SERT-PG601,602AA: pre-incubation of
 HEK293 cells with ECSI#6 restored export of SERT-PG601,602AA from the
 endoplasmic reticulum and substrate transport. Similarly, in transgenic
 flies, administration of ECSI#6 promoted delivery of SERT-PG601,602AA to
 the presynaptic specialization of serotonergic neurons. To the best of our
 knowledge, ECSI#6 is the first example of an uncompetitive SLC inhibitor.
 Pharmacochaperones endowed with the binding mode of ECSI#6 are attractive
 because they can rescue misfolded transporters at concentrations, which
 cause modest transport inhibition.
description: Microsoft Office pClamp10
 GraphPad_Prism
DOI: 10.5061/dryad.sbcc2fr9d
title: Quantifying the ecological impacts of alien aquatic macrophytes: A global meta‐analysis of effects on fish, macroinvertebrate and macrophyte assemblages

description: Biological invasions constitute a pervasive and growing threat to the
 biodiversity and functioning of freshwater ecosystems. Macrophytes are key
 primary producers and ecosystem engineers in freshwaters, meaning that
 alien macrophyte invasions have the capacity to alter the structure and
 function of recipient aquatic ecosystems profoundly. Although prevailing
 wisdom holds that alien macrophyte invasions tend to compromise freshwater
 ecosystem structure and function, the ecological impacts of alien
 macrophyte invasion have not been quantitatively reviewed to date. Here we
 present a global meta-analysis of 202 cases from 53 research articles,
 exploring the impacts of alien macrophyte invasion on the abundance and
 diversity of three ubiquitous and ecologically important focal groups,
 which together comprise the bulk of non-microbial freshwater biodiversity:
 resident macrophytes, macroinvertebrates and fish. Our synthesis includes
 data from all continents except Antarctica and Asia, covering 25 alien
 macrophyte species, but reveals considerable taxonomic and geographical
 biases in knowledge. Meta-analysis results reveal that invasion by alien
 macrophytes has an overall negative impact on taxonomic diversity of the
 three focal groups, but no consistent effect on abundance. At a finer
 resolution, we detect a strong negative effect of alien macrophyte
 invasion on resident macrophyte abundance and diversity, and a significant
 but smaller positive effect of submerged alien macrophyte invasion on
 macroinvertebrates. Effects on fish appear inconsistent. Our findings
 emphasise the importance of context- and taxon-specific ecological
 research in informing appropriate and proportionate management of alien
 macrophyte invasions, since alien macrophyte impacts are not consistently
 negative. We also identify significant geographical and taxonomic
 limitations in existing studies, quantitative data being lacking for many
 alien taxa.
DOI: 10.5061/dryad.fj6q573z3
title: Data from: Phylogenomics of superrosids and core rosids based on nuclear sequences and synteny

description: Superrosids form one of the largest clades of angiosperms, including 18
 orders (Vitales, Saxifragales and core rosids) which exhibits remarkable
 morphological and ecological diversity. However, phylogenetic
 relationships within superrosids remain unclear. To resolve the phylogeny
 of superrosids, we screened 122 single copy nuclear genes from 37 species,
 representing all 18 orders. Vitales was revealed as sister to all other
 superrosids. Within core rosids, the fabids should be restricted only to
 the nitrogen-fixing clade, while Picramniales, the CM clade, Huerteales,
 Oxalidales, Sapindales, Malvales and Brassicales composed an “expanded”
 malvids. The COM clade (sensu APG IV) did not form a monophyletic group.
 Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to
 either malvids or fabids. The difficult phylogeny of superrosids is likely
 due to the combined effects of ancient reticulation and incomplete lineage
 sorting. To provide broader genomic representation of Saxifragales, we
 constructed a high-quality chromosome-level genome assembly for Tiarella
 polyphylla (Saxifragaceae). Whole genome microsynteny analysis of
 superrosids showed that Saxifragales shared more synteny clusters with
 core rosids than Vitales, which also indicated that Saxifragales has a
 closer relationship with core rosids. Our findings contribute to a better
 understanding of the phylogeny and evolution of angiosperms.