cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ffbg79cz2
title: Urbanization drives geographically heterogeneous freshwater salinization in the northeastern United States

description: Rising trends in freshwater salinity, collectively termed the Freshwater
 Salinization Syndrome (FSS), constitute a global environmental concern.
 Given that the FSS has been observed in diverse settings, key questions
 regarding the causes, trend magnitudes, and consequences remain. Prior
 work hypothesized that FSS is driven by state factors, such as
 human-centered land use change, geology, and climate. Here, we identify
 the fundamental overriding factors driving FSS within the northeastern
 United States and quantify the diversity of FSS severity within the
 region. Specifically, we analyzed decadal-scale trends in specific
 conductance (a salinity proxy) for 333 lotic sites over four 
 decades. Next, we quantified potential variables driving the rising or
 falling trends, including impervious surface cover (ISC), winter
 temperature and precipitation, watershed size, and ambient conductance.
 Temperature and ISC were considered the most likely candidates for
 predicting FSS severity because road salts have previously emerged as the
 fundamental regional driver.Most (62.5%) sites exhibited patterns of
 significantly increasing conductance; thus, the overall regional state
 reflects advancing FSS. However, others exhibited an absence of change
 (28.8%) or decreasing values (8.7%), and slope magnitude did change with
 latitude. Linear modeling demonstrated that two variables—ISC and
 watershed size—constitute the best predictors of long-termconductance
 trends and that an intercept not significantly different than zero
 suggests that the FSS does not reign in the absence of urbanization. We
 also detected areas with consistently decreasing trends despite moderate
 ISC. Therefore, within the region, advancing urbanization causes the
 typical condition of advancing FSS, but heterogeneity also exists.
description: All water quality data were collected from the Water Quality
 Portal, an online database maintained by the National Water Quality
 Monitoring Council. Data were collected using the following filters
 (selected options as listed on the portal provided in italics): states
 inclusive of the 10 listed above, site type = Stream (NWIS, STEWARDS,
 STORET), sample media = Water (NWIS, STEWARDS, STORET), characteristic =
 Specific conductance (NWIS, STORET), a date range between 1 Jan.1980 and
 12 Jan. 2021, and minimum results per site = 100. Sites with records that
 spanned &lt;10 yr were omitted from further analyses. Included here
 are also metrics depicting land use and climate attributes for each
 site.
DOI: 10.5061/dryad.c866t1g9b
title: Data from: Genome-wide association study for grain yield and component traits in wheat (Triticum aestivum L.)

description: The study material in GWAS panel with 280 common bread wheat genotypes was
 selected from All India Coordinated Research Project on Wheat and Barley
 to map the genomic regions governing days to heading (DH), grain filling
 duration (GFD), grain number per spike (GNPS), grain weight per spike
 (GWPS), plant height (PH), and grain yield (GY). Phenotypic data: The GWAS
 panel was evaluated at five different environments during the 2020-21 Rabi
 (winter) season: E1-University of Agricultural Sciences, research farm,
 Dharwad (15°29'20.71"N, 74°59'3.35"E, 750m AMSL),
 E2-ICAR-Indian Agricultural Research Institute, New Delhi (28°38′30.5″N,
 77°09′58.2″E, 228 m AMSL), E3-Indian Agricultural Research Institute,
 Jharkhand (24°16'58.4"N, 85°21'16.1"E, 651m AMSL),
 E4-ICAR-Indian Institute of Wheat and Barley, Karnal
 (29°41'8.2644''N,
 76°59'25.9692''E,  250m AMSL), and E5-Punjab
 Agricultural University, Ludhiana (30o54' N, 75o48'E, 247m
 AMSL). The genotypes were planted in an augmented block design along with
 repeated checks (DBW187, MACS6222, WH1124, and WH1142). All the genotypes
 of a GWAS panel were phenotyped for six quantitative traits i.e. GWPS
 (gm), GY (gm), PH (cm) at five locations, GFD (days), DH (days) at four
 locations and GNPS (number) at two locations. Phenotypic data were
 analyzed using the R package ‘augmentedRCBD’ Genotypic data: Genomic DNA
 of the GWAS panel was extracted from the leaves of 21 days-old seedlings
 by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped
 using Axiom Wheat Breeder’s Genotyping Array (Aﬀymetrix, Santa Clara, CA,
 United States) having 35,143 genome-wide SNPs. The monomorphic, markers
 with minor allele frequency (MAF) of &lt;5%, missing data of
 &gt;20%, and heterozygote frequency &gt;25% were removed from the
 analysis. The remaining set of 14,790 high-quality SNPs was used in GWAS
 analysis.
DOI: 10.7280/d1s69x
title: Data for: Sequencing and variant detection of eight abundant plant-infecting tobamoviruses across Southern California wastewater

description: Tobamoviruses are agriculturally-relevant viruses that cause crop losses
 and have infected plants in many regions of the world. These viruses are
 frequently found in municipal wastewater - likely coming from human diet
 and industrial waste across wastewater catchment areas. As part of a large
 wastewater-based epidemiology study across Southern California, we
 analyzed RNA sequence data from 275 influent wastewater samples obtained
 from eight wastewater treatment plants with a catchment area of
 approximately 16 million people from July 2020 – August 2021. We assembled
 over 1,083 high-quality genomes, enumerated viral sequencing reads, and
 detected thousands of single nucleotide variants from eight common
 tobamoviruses: Bell Pepper Mottle Virus, Cucumber Green Mottle Mosaic
 Virus, Pepper Mild Mottle Virus, Tobacco Mild Green Mosaic Virus, Tomato
 Brown Rugose Fruit Virus, Tomato Mosaic Virus, Tomato Mottle Mosaic Virus,
 and Tropical Soda Apple Mosaic Virus. We show that single nucleotide
 variants had amino acid-altering consequences along with synonymous
 mutations, which represents potential evolution with functional
 consequences in genomes of these viruses. Our study shows the importance
 of wastewater sequencing to monitor the genomic diversity of these
 plant-infecting viruses, and we suggest that our data could be used to
 continue tracking the genomic variability of such pathogens.
DOI: 10.5061/dryad.69p8cz94q
title: Data for: Single versus serial dilution SARS-CoV-2 IgG

description: Reliable and scalable seroepidemiology methods are needed to estimate
 SARS-CoV-2 incidence and monitor the dynamics of population-level immunity
 as the pandemic evolves. We aimed to evaluate the reliability of
 SARS-CoV-2 normalized ELISA optical density (nOD) at a single dilution
 compared to titers derived from serial dilutions. We conducted serial
 serosurveys within a community-based cohort in Salvador, Brazil. Anti-S
 IgG ELISA (Euroimmun AG) was performed with five serial 3-fold dilutions
 of paired sera from 54 participants. Changes in nOD reliably predicted
 increases and decreases in titers (98.1% agreement, κ = 95.8%). Fitting
 the relationship between nOD and interpolated titers to a log-log curve
 yields highly accurate predictions of titers (r2 = 0.995) and changes in
 titers (r2 = 0.975), using only one to two dilutions. This approach can
 significantly reduce the time, labor and resources needed for large-scale
 serosurveys to ascertain population-level changes in exposure and
 immunity.
description: Data can be accessed using R.
DOI: 10.5061/dryad.vhhmgqnx0
title: Data for: Fish can infer relations between colour cues in a non-social learning task

description: Transitive inference (TI) describes the ability to infer relationships
 between stimuli that have never been seen together before. Social cichlids
 can use TI in a social setting where observers assess dominance status
 after witnessing contests between different dyads of conspecifics. If
 cognitive processes are domain-general, animals should use abilities
 evolved in a social context also in a non-social context. Therefore, if TI
 is domain-general in fish, social fish should be able to use TI also in
 non-social tasks. Here we tested whether the cooperatively-breeding
 cichlid Neolamprologus pulcher can infer transitive relationships between
 artificial stimuli in a non-social context. We used an associative
 learning paradigm where the fish received a food reward when correctly
 solving a colour discrimination task. Eleven of twelve subjects chose the
 predicted outcome for TI in the first test trial and five subjects
 performed with 100% accuracy in six successive test trials. We found no
 evidence that the fish solved the TI task by value transfer. Our findings
 show that fish use TI also in non-social tasks with artificial stimuli,
 thus generalizing past results reported in a social context and hinting
 toward a domain-general cognitive mechanism.
DOI: 10.5061/dryad.zs7h44jcs
title: RNA-seq based expression of DEGs in roots and leaves of bread wheat

description: RNA from roots and leaves of twenty eight bread wheat genotypes was
 extracted, purified, quantified and sent to Beijing Genomics Institute
 (BGI) for sequencing. Briefly, mRNAs were isolated and fragmented from
 total RNA using the oligo (dT) method for cDNA synthesis. The 75-bp
 single-end sequencing libraries were constructed, and sequencing was
 performed on HiSeq X Ten (Illumina, San Diego, USA) using standard
 protocols. Adapters with unknown bases (N’s &gt; 5%) and low quality
 were removed from raw reads to produce ‘clean data’ as FastQ data files
 using a quality control software, SOAPnuke version 2.1.6. High quality
 single-end reads were mapped to the bread wheat reference genome (IWGSC,
 INSDC Assembly GCA_900519105.1) using HISAT2 (Hierarchical
 Indexing for Spliced Alignment of Transcripts) software version
 2.2.1. Alignment of the reference sequence with reads were performed using
 Bowtie. Quantification of the reads was performed using featureCounts
 software program. Differentially expressed genes (DEGs) were identified
 using DeSEQ2 in R version  4.1.1. DEGs were then filtered based
 on their adjusted p-value. A total of 120744 DEGs were identified with
 varying expression in roots and leaves. The threshold value for filtering
 was set at 0.1.
description: The dataset was collected by
 RNA-sequencing and subsequently subjected to quality control
 using SOAPnuke software.
 The high quality reads were mapped and aligned to wheat reference genome
 using HISAT2. Alignment and quantification of reads were performed using
 Bowtie and featureCounts and DEGs were identified usimg DeSEQ2 in R
 software.
description: The dataset can be opened in "Excel"
DOI: 10.5061/dryad.fxpnvx0vw
title: A bibliometric analysis of systematic reviews and meta-analyses in ophthalmology, from 2000 to 2020

description: Objectives: To establish the scientometric landscape of systematic reviews
 and meta-analyses (SRMAs) published in the field of ophthalmology over
 time. Results: A total of 2,660 SRMAs were included, and the average
 annual growth rate was 21.26%. China and the USA were the most productive
 countries, while Singapore was the country with the highest average
 citations per document. Wong TY was not only the most productive, but also
 the most frequently cited author. The most productive affiliation was
 National University of Singapore (n=236). SRMA output in most
 subspecialties had steadily increased with retina/vitreous (n=986),
 glaucoma (n=411) and cornea/external diseases (n=303) constantly as the
 most dominant fields. Rates of pre-registration and guideline compliance
 had dramatically increased over time, with 20.0% and 63.5% of SRMA being
 pre-registered and reported guideline in 2020, respectively. However,
 SRMAs published on ophthalmic journals tended to be less frequently
 pre-registered and guideline complied than those on non-ophthalmic
 journals (both P &lt; 0.05). Conclusions: The annual output of SRMAs
 has been rapidly increasing over the past two decades. China and the USA
 were the most productive countries, whereas Singapore had the most
 prolific and influential scholar and institution. Raising awareness and
 implementation of SRMA pre-registration and guideline compliance is still
 necessary to ensure quality, especially for ophthalmic journals.
description: We retrieved relevant ophthalmic SRMAs and the corresponding
 bibliometric parameters during 2000 to 2020 from Web of Science Core
 Collection. Bibliometric analysis was performed using bibliometrix
 package. Pre-registration and guideline compliance of each SRMA was
 independently assessed by two investigators.
DOI: 10.5061/dryad.wpzgmsbqm
title: Seasonal and ontological variation in diet and age-related differences in prey choice, by an insectivorous songbird

description: The diet of an individual animal is subject to change over time, both in
 response to short-term food fluctuations and over longer time scales as an
 individual ages and meets different challenges over its life cycle. A
 metabarcoding approach was used to elucidate the diet of different life
 stages of a migratory songbird, the Eurasian reed warbler (Acrocephalus
 scirpaceus) over the 2017 summer breeding season in Somerset, UK. The
 faeces of adult, juvenile and nestling warblers were screened for
 invertebrate DNA, enabling the identification of prey species. Dietary
 analysis was coupled with monitoring of Diptera in the field using yellow
 sticky traps. Seasonal changes in warbler diet were subtle whereas age
 class had a greater influence on overall diet composition. Age classes
 showed high dietary overlap, but significant dietary differences were
 mediated through the selection of prey; i) from different taxonomic
 groups, ii) with different habitat origins (aquatic versus terrestrial)
 and iii) of different average approximate sizes. Our results highlight the
 value of metabarcoding data for enhancing ecological studies of
 insectivores in dynamic environments. 
description: The dataset comprises the raw Paired-end Illumina sequencing
 reads from reed warbler dietary samples collected in Somerset in 2017.
 High-throughput sequencing was carried out on an Illumina MiSeq in 2019 at
 Cardiff University, Genomics Hub. Details of the bioinformatics pipeline
 used to process this data can be found with the publication (scripts in
 Supplemental
 Information). Along with the sequence data, an oligos file and
 fasta file are provided for use in the bioinformatics pipeline. These have
 the sample IDs and MID-tagged primers used in the Mothur step and for
 demultiplexing. 
description: Files can be opened with any text editor. For details of the
 programs used in the bioinformatics pipeline, please refer to the original
 publication.
DOI: 10.15468/dl.qy46ab
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "TaxonKey is Diploclisia"
 ]
}

 The dataset includes 160 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003180-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7wm37q46
title: Unpacking the "black box": improving ecological interpretation of regression based models

description: AimMany tree species distribution models use black-box machine learning
 techniques that often neglect interpretative aspects and instead focus
 mainly on maximising predictive accuracy. In this study, we outline an
 interpretative modelling framework to gain better ecological insights
 while mapping abundance patterns of six North American species.
 LocationContinental United States and Canada MethodsWe develop an
 innovative procedure using regression trees by stabilising variance and
 mapping dominant rules which we term ‘optimized regression tree bagging
 for interpretation and mapping’ (ORTBIM). We apply this technique to
 understand ecological features influencing the abundance patterns of three
 eastern (Pinus strobus, Acer saccharum, and Quercus montana), and three
 western (Picea engelmannii, Pinus ponderosa, and Pseudotsuga menziesii)
 tree species in North America. For these species, we assess and map the
 dominant climate-terrain interactions that partly determine abundance
 patterns in the eastern and western regions. In the process, we examine
 the role of varying responses and scales and explore finer-scale species
 climate-terrain niches and non-linear relationships. ResultsOur study
 emphasizes the prominent role of elevation and heat-moisture variables in
 the west and the greater importance of seasonal precipitation and seasonal
 temperature in the east. The abundance patterns under future climate
 (SSP5–8.5) show climate-terrain habitats shifting northward and westward
 into Canada and Alaska for the eastern species, and predominantly
 north-westward for the western species. ConclusionOur interpretative
 modelling framework can be used to gain a more comprehensive understanding
 of the abundance patterns across the full species range, to formulate
 better predictive models, and to facilitate improved management practices
 under climate change.
description: The data is from the Forest Inventory Analysis of the USDA Forest
 Service. We also use data from the AdaptWest climate and USGS elevational
 data.
description: R - https://cran.r-project.org/
DOI: 10.5061/dryad.wm37pvmqr
title: Confirmation that eagle fatalities can be reduced by automated curtailment of wind turbines

description: 1. Automated curtailment is potentially a powerful technique to reduce
 collision mortality of wildlife with wind turbines. Previously, we used a
 before-after-control-impact framework to demonstrate that eagle fatalities
 declined after automated curtailment was implemented with the IdentiFlight
 system at a wind power facility in Wyoming, USA. We received substantial
 interest and feedback regarding our study and, here, we implement several
 analytical suggestions and include more recent data that strengthen the
 inference we draw from our results. 2. The five main analytical
 suggestions we received were to 1) exclude from analysis data that were
 collected during the period when automated curtailment was only partially
 implemented; 2) only analyze data from a single make and model of turbine;
 3) evaluate changes in the rate of fatality, instead of the yearly numbers
 of fatalities that result from fluctuations around that rate; 4) calculate
 the standard measure determining effects of a treatment in a
 before-after-control-impact study; and, 5) examine yearly fluctuations of
 the fatality rate during the before period. 3. After incorporating these
 suggestions and including additional data collected since the prior paper
 was published, our results confirm prior work. We demonstrate that eagle
 fatalities were reduced by 85% (95% highest density interval = 12%, 100%)
 after implementation of automated curtailment. Rate of fatalities declined
 by 2.85 eagles per year (-0.67, 5.70) between before and after periods at
 the treatment site and increased by 2.26 eagles per year (-7.37, 1.77) at
 the control site. Overall, the fatality rate declined by 4.91 (-0.27,
 11.27) more eagles per year at the treatment site than at the control
 site. The probability that the fatality rate declined at the treatment
 site relative to the control site was 0.97. 4. Our re-analysis strengthens
 our inference by using more robust analyses and data to support the
 conclusions of the prior study suggesting that automated curtailment was
 effective at reducing eagle fatalities at our treatment site. Because of
 the site- and species-specific nature of our work, future research should
 examine the efficacy of automated curtailment at other sites, with other
 species, and under different curtailment regimes.
description: Detailes are in the paper, which is open access. 
description: Microsoft Excel or Open Office
DOI: 10.5061/dryad.z08kprrgc
title: DNA-stimulated liquid-liquid phase separation by eukaryotic topoisomerase II modulates catalytic function

description: Type II topoisomerases modulate chromosome supercoiling, condensation, and
 catenation by moving one double-stranded DNA segment through a transient
 break in a second duplex. How DNA strands are chosen and selectively
 passed to yield appropriate topological outcomes – e.g., decatenation vs.
 catenation – is poorly understood. Here we show that at physiological
 enzyme concentrations, eukaryotic type IIA topoisomerases (topo IIs)
 readily coalesce into condensed bodies. DNA stimulates condensation and
 fluidizes these assemblies to impart liquid-like behavior. Condensation
 induces both budding yeast and human topo IIs to switch from DNA unlinking
 to active DNA catenation, and depends on an unstructured C-terminal
 region, the loss of which leads to high levels of knotting and reduced
 catenation. Our findings establish that local protein concentration and
 phase separation can regulate how topo II creates or dissolves DNA links,
 behaviors that can account for the varied roles of the enzyme in
 supporting transcription, replication, and chromosome compaction.
description: Microscopy data was collected on an LSM 800 Confocal microscope,
 processed through FIJI, and all data were analyzed in R studio.
 Biochemical assays were run on a gel, imaged, and images were edited in
 Adobe illustrator. All statistical analysis was done using
 PRISM. 
description: FIJI, R Studio, Adobe Illustrator, Prism.
DOI: 10.5061/dryad.12jm63z1m
title: Wildfire disturbance reveals evidence of ecosystem resilience and precariousness in a forest-grassland mosaic

description: Forest and grassland ecosystems are sometimes located adjacently within
 the same climate. In interior British Columbia, Canada, there are complex
 forest-grassland mosaics within the Interior Douglas-fir biogeoclimatic
 zone. Historically, both grassland and forest ecosystems experienced
 high-frequency, low-severity fire regimes. Since European settlement and
 introduction of livestock grazing and fire exclusion, trees have
 encroached on grasslands, and tree densities in forests have increased. In
 this study, we characterize plant communities and near-surface soil
 moisture in forest and grassland sites, and in historical grassland sites
 affected by tree encroachment. We hypothesized that spatial and temporal
 patterns of near-surface soil moisture are reflected in above-ground plant
 community composition and structure. After initial sampling of soil
 moisture and plant communities, the study area was burned in a wildfire.
 Applying a multifactorial approach to comparing adjacent grassland and
 forest sites, we treated the wildfire event as a natural experiment,
 sampling post-wildfire plant species composition and soil moisture, and
 measuring the severity and spatial heterogeneity of surface burn
 conditions. Evidence supports the concept of mutually exclusive
 fire-reinforced bi-stable grassland and forest states, with greater
 spatial heterogeneity of soil moisture and burn severity in forests, and
 highly uniform patterns of soil moisture, vegetation, and burn severity in
 grasslands. Areas of forest encroachment on grasslands had understory
 plant communities dominated by exotic species, while restored grasslands
 had native bunchgrass cover like typical grasslands of the region.
 Additionally, there was post-wildfire divergence of forest- and grassland-
 associated plant communities. Viewed through a resilience theory
 conceptual framework, we suggest that ecosystem legacies are reinforcing
 post-wildfire ecosystem identity and associated native plant communities.
 External factors - particularly past heavy livestock grazing and fire
 suppression - have caused ecosystem precariousness that can be addressed
 with management actions.
description: For statistical tests we used SAS Version 14.3 (SAS Institute
 Inc. 2019).