cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18380364
title: Characterization, ultrafiltration, depolymerization and gel formulation of ulvans extracted via a novel ultrasound-enzyme assisted method
DOI: 10.15468/dl.ehqkzs
title: Occurrence Download

description: A dataset containing 14813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cedrela odorata"
 ]
}

 The dataset includes 14813 records from 431 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000369-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b30s4
title: Data from: Remotely sensed data informs red list evaluations and conservation priorities in southeast Asia

description: The IUCN Red List has assessed the global distributions of the majority of
 the world’s amphibians, birds and mammals. Yet these assessments lack
 explicit reference to widely available, remotely-sensed data that can
 sensibly inform a species’ risk of extinction. Our first goal is to add
 additional quantitative data to the existing standardised process that
 IUCN employs. Secondly, we ask: do our results suggest species of
 concern—those at considerably greater risk than hitherto appreciated?
 Thirdly, these assessments are not only important on a species-by-species
 basis. By combining distributions of species of concern, we map
 conservation priorities. We ask to what degree these areas are currently
 protected and how might knowledge from remote sensing modify the
 priorities? Finally, we develop a quick and simple method to identify and
 modify the priority setting in a landscape where natural habitats are
 disappearing rapidly and so where conventional species’ assessments might
 be too slow to respond. Tropical, mainland Southeast Asia is under
 exceptional threat, yet relatively poorly known. Here, additional
 quantitative measures may be particularly helpful. This region contains
 over 122, 183, and 214 endemic mammals, birds, and amphibians,
 respectively, of which the IUCN considers 37, 21, and 37 threatened. When
 corrected for the amount of remaining natural habitats within the known
 elevation preferences of species, the average sizes of species ranges
 shrink to &lt;40% of their published ranges. Some 79 mammal, 49 bird,
 and 184 amphibian ranges are &lt;20,000km2—an area at which IUCN
 considers most other species to be threatened. Moreover, these species are
 not better protected by the existing network of protected areas than are
 species that IUCN accepts as threatened. Simply, there appear to be
 considerably more species at risk than hitherto appreciated. Furthermore,
 incorporating remote sensing data showing where habitat loss is prevalent
 changes the locations of conservation priorities.
description: dataThese GIS data files are
 the ones shown in our figures. "Forest" is the forest cover that
 we created using the methods in our paper. Center geodatabase contains the
 files that are in the Figure 6. The other files are the data for Figure 5
 by taxa. Files ending with "IUCN" are for the first column,
 ending with "refined" are for the second column, ending with
 "concern" are the third column and "DD" for the fourth
 column.
DOI: 10.5061/dryad.8d8v4
title: Data from: Deformability assessment of waterborne protozoa using a microfluidic-enabled force microscopy probe

description: Many modern filtration technologies are incapable of the complete removal
 of Cryptosporidium oocysts from drinking-water. Consequently,
 Cryptosporidium-contaminated drinking-water supplies can severely
 implicate both water utilities and consumers. Existing methods for the
 detection of Cryptosporidium in drinking-water do not discern between
 non-pathogenic and pathogenic species, nor between viable and non-viable
 oocysts. Using FluidFM, a novel force spectroscopy method employing
 microchannelled cantilevers for single-cell level manipulation, we
 assessed the size and deformability properties of two species of
 Cryptosporidium that pose varying levels of risk to human health. A
 comparison of such characteristics demonstrated the ability of FluidFM to
 discern between Cryptosporidium muris and Cryptosporidium parvum with 86%
 efficiency, whilst using a measurement throughput which exceeded 50
 discrete oocysts per hour. In addition, we measured the deformability
 properties for untreated and temperature-inactivated oocysts of the highly
 infective, human pathogenic C. parvum to assess whether deformability may
 be a marker of viability. Our results indicate that untreated and
 temperature-inactivated C. parvum oocysts had overlapping but
 significantly different deformability distributions.
description: Cryptosporidium
 deformability - dataThe files within the ZIP
 archive are in CSV format and can be readily accessed by Microsoft Excel,
 MATLAB, and many other programs. CSV files were recorded by the CyUI
 software from Cytosurge AG (Glattbrug, Switzerland).
 "spec.fwd.csv" and "spec.bwd.csv" files refer to the
 approach or retraction phases of the force spectroscopy measurements,
 respectively. Only the "spec.fwd.csv" (approach) files were used
 in the data analysis. Cantilever spring constants, deflection
 sensitivities, and sampling frequencies are specified in the header of the
 csv files. The initial cantilever-substrate separation was 10 micron for
 the C. muris and 5.0-5.3 micron for the C. parvum
 measurements.
DOI: 10.5061/dryad.742j4
title: Data from: A comparative survey of the frequency and distribution of polymorphism in the genome of Xenopus tropicalis

description: Naturally occurring DNA sequence variation within a species underlies
 evolutionary adaptation and can give rise to phenotypic changes that
 provide novel insight into biological questions. This variation exists in
 laboratory populations just as in wild populations and, in addition to
 being a source of useful alleles for genetic studies, can impact efforts
 to identify induced mutations in sequence-based genetic screens. The
 Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as
 a model system for studying the genetic control of embryonic development
 and a variety of other areas of research. Its diploid genome has been
 extensively sequenced and efforts are underway to isolate mutants by
 phenotype- and genotype-based approaches. Here, we describe a study of
 genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism
 was detected in the coding and non-coding regions of developmental genes
 distributed widely across the genome. Laboratory strains exhibit
 unexpectedly high frequencies of genetic polymorphism, with alleles
 carrying a variety of synonymous and non-synonymous codon substitutions
 and nucleotide insertions/deletions. Inter-strain comparisons of
 polymorphism uncover a high proportion of shared alleles between Nigerian
 and Ivory Coast strains, in spite of their distinct geographical origins.
 These observations will likely influence the design of future
 sequence-based mutation screens, particularly those using DNA
 mismatch-based detection methods which can be disrupted by the presence of
 naturally occurring sequence variants. The existence of a significant
 reservoir of alleles also suggests that existing laboratory stocks may be
 a useful source of novel alleles for mapping and functional studies.
description: Dataset
 1.tarZipped; raw ABI sequence
 data files.Dataset
 2.tarZipped; raw ABI sequence
 data files.
DOI: 10.5061/dryad.7t06c
title: Data from: The landscape of realized homologous recombination in pathogenic bacteria

description: Recombination enhances the adaptive potential of organisms by allowing
 genetic variants to be tested on multiple genomic backgrounds. Its
 distribution in the genome can provide insight into the evolutionary
 forces that underlie traits such as the emergence of pathogenicity. Here
 we examined landscapes of realized homologous recombination of 500 genomes
 from ten bacterial species, and found all species have ‘hot’ regions with
 elevated rates relative to the genome average. We examined the size, gene
 content and chromosomal features associated with these regions and the
 correlations between closely related species. The recombination landscape
 is variable and evolves rapidly. For example in Salmonella, only short
 regions of around 1kb in length are hot while in the closely related
 species Escherichia coli, some hot regions exceed 100kb, spanning many
 genes. Only Streptococcus pyogenes shows evidence for the positive
 correlation between GC content and recombination that has been reported
 for several eukaryotes. Genes with function related to the cell
 surface/membrane are often found in recombination hot regions but E. coli
 is the only species where genes annotated as “virulence associated” are
 consistently hotter. There is also evidence that some genes with
 “housekeeping” functions tend to be overrepresented in cold regions. For
 example, ribosomal proteins showed low recombination in all of the
 species. Among specific genes, transferrin binding proteins are
 recombination hot in all three of the species in which they were found,
 and are subject to inter-species recombination.
description: Campylobacter_jejuni_n50Clostridium_difficile_n50Escherichia_coli_n50Haemophilus_influenzae_n50Neisseria_gonorrhoeae_n50Neisseria_meningitidis_n50Salmonella_enterica_n50Staphylococcus_aureus_n50Streptococcus_pneumoniae_n50Streptococcus_pyogenes_n50Isolate_list
DOI: 10.5061/dryad.p03j0
title: Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait

description: We used extensive data from a long-term study of great tits (Parus major)
 in the United Kingdom and Netherlands to better understand how genetic
 signatures of selection translate into variation in fitness and
 phenotypes. We found that genomic regions under differential selection
 contained candidate genes for bill morphology and used genetic
 architecture analyses to confirm that these genes, especially the collagen
 gene COL4A5, explained variation in bill length. COL4A5 variation was
 associated with reproductive success, which, combined with spatiotemporal
 patterns of bill length, suggested ongoing selection for longer bills in
 the United Kingdom. Last, bill length and COL4A5 variation were associated
 with usage of feeders, suggesting that longer bills may have evolved in
 the United Kingdom as a response to supplementary feeding.
description: TemporalBillLength_DryadDataText file containing bill length and tarsus length of birds measured between 1982 and 2007Plink files of all typed individuals.bed file of 3015 individuals typed at 485,122 SNPs.NLUK.bedPlink files of all typed individuals.bim file of 3015 individuals typed at 485,122 SNPsNLUK.bimPlink files of all typed individuals.fam file of 3015 individuals typed at 485,122 SNPsNLUK.famPlink file for genomic prediction between NL and UK populations.bed fileBillLength_BayesR.bedPlink file for genomic prediction between NL and UK populations.bim fileBillLength_BayesR.bimPlink file for genomic prediction between NL and UK populations.fam file. Parents set as unknown and sex set as 2 (not used in analyses). Col 6 is bill length, Col 7 is UK birds bill length adjusted for repeated measurements and mean zero centred. This phenotype was also used in the GWAS. Col 8 is NL birds bill length.BillLength_BayesR.famCOL4A5_Reproductive_success.csv file of data used to explore relationship between COL4A5 and annual reproductive successBillLength_museum_specimens.csv file of bill lengths of museum specimens from UK and the NetherlandsCOL4A5_genotype_feeder_visits.csv file of data used to explore relationship between COL4A5 and visits to bird feeders2015_2016_feeder_bills.csv file of data used to explore relationship between bill length and feeder visits
DOI: 10.5061/dryad.5s77q
title: Data from: Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data

description: To characterize natural selection, various analytical methods for
 detecting candidate genomic regions have been developed. We propose to
 perform genome-wide scans of natural selection using principal component
 analysis (PCA). We show that the common FST index of genetic
 differentiation between populations can be viewed as the proportion of
 variance explained by the principal components. Considering the
 correlations between genetic variants and each principal component
 provides a conceptual framework to detect genetic variants involved in
 local adaptation without any prior definition of populations. To validate
 the PCA-based approach, we consider the 1000 Genomes data (phase 1)
 considering 850 individuals coming from Africa, Asia, and Europe. The
 number of genetic variants is of the order of 36 millions obtained with a
 low-coverage sequencing depth (3×). The correlations between genetic
 variation and each principal component provide well-known targets for
 positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate
 genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition
 to identifying genes involved in biological adaptation, we identify two
 biological pathways involved in polygenic adaptation that are related to
 the innate immune system (beta defensins) and to lipid metabolism (fatty
 acid omega oxidation). An additional analysis of European data shows that
 a genome scan based on PCA retrieves classical examples of local
 adaptation even when there are no well-defined populations. PCA-based
 statistics, implemented in the PCAdapt R package and the PCAdapt fast
 open-source software, retrieve well-known signals of human adaptation,
 which is encouraging for future whole-genome sequencing project,
 especially when defining populations is difficult.
description: loadings_1000G.txtLoadings of SNPs from the 1000 genomes data (phase 1, 36,536,154 SNPs). Each loading corresponds to the correlation between a principal component and a SNP. A principal component analysis with K=2 was performed. maf stands for minor allele frequency.
DOI: 10.5061/dryad.160mp
title: Data from: Pulmonary anatomy and a case of unilateral aplasia in a common snapping turtle (Chelydra serpentina): developmental perspectives on cryptodiran lungs

description: The common snapping turtle (Chelydra serpentina) is a well studied and
 broadly distributed member of Testudines; however, very little is known
 concerning developmental anomalies and soft tissue pathologies of turtles
 and other reptiles. Here, we present an unusual case of unilateral
 pulmonary aplasia, asymmetrical carapacial kyphosis, and mild scoliosis in
 a live adult C. serpentina. The detailed three-dimensional (3D) anatomy of
 the respiratory system in both the pathological and normal adult C.
 serpentina, and a hatchling are visualized using computed tomography (CT),
 microCT, and 3D digital anatomical models. In the pathological turtle, the
 right lung consists of an extrapulmonary bronchus that terminates in a
 blind stump with no lung present. The left lung is hyperinflated relative
 to the normal adult, occupying the extra coelomic space facilitated by the
 unusual mid-carapacial kyphotic bulge. The bronchial tree of the left lung
 retains the overall bauplan of the normal specimens, with some minor
 downstream variation in the number of secondary airways. The primary
 difference between the internal pulmonary structure of the pathological
 individual and that of a normal adult is a marked increase in the surface
 area and density of the parenchymal tissue originating from the secondary
 airways, a 14.3% increase in the surface area to volume ratio. Despite
 this, the aplasia has not had an impact upon the ability of the turtle to
 survive; however, it did interfere with aquatic locomotion and buoyancy
 control under water. This turtle represents a striking example of a
 non-fatal congenital defect and compensatory visceral hypertrophy.
description: Full body CT scan of a
 deceased normal Chelydra serpentinaFull body CT scan of a
 deceased normal Chelydra serpentina (straight-line carapacial length:
 22.62 cm) scanned on a 164 slice dual energy Siemens SOMATOM Definition
 computed tomography unit at a slice thickness of 0.6 mm, kVp 120, MA 200.
 The turtle was intubated with a 60 cc syringe and inflated until
 resistance could be felt.Normal Chelydra
 serpentina.zipFull body CT scan of a
 live Chelydra serpentina with unilateral pulmonary
 aplasiaFull body CT scan of a
 live Chelydra serpentina (straight-line carapacial length: 29.12 cm) with
 unilateral pulmonary aplasia (Wildlife Rehabilitation Center of Minnesota
 Case Number 15-11926). The live pathological turtle was scanned on a
 Toshiba TSX-101A/7D.004 CT scanner at a slice thickness of 1 mm, and
 reconstructed in a bone algorithm (FC30) and a soft tissue algorithm
 (FC05). Prior to scanning, the turtle was given an intramuscular injection
 of 2.4 ml of 10 mg/ml alfaxalone (Alfaxan, Jurox Inc., Kansas City, MO)
 for sedation, and his head was covered with a towel.Pathological Chelydra
 serpentina.zip
DOI: 10.5061/dryad.cr65v
title: Data from: How to optimize the precision of allele and haplotype frequency estimates using pooled-sequencing data

description: Sequencing pools of individuals rather than individuals separately reduces
 the costs of estimating allele frequencies at many loci in many
 populations. Theoretical and empirical studies show that sequencing pools
 comprising a limited number of individuals (typically fewer than 50)
 provides reliable allele frequency estimates, provided that the DNA
 pooling and DNA sequencing steps are carefully controlled. Unequal
 contributions of different individuals to the DNA pool and the mean and
 variance in sequencing depth both can affect the standard error of allele
 frequency estimates. To our knowledge, no study separately investigated
 the effect of these two factors on allele frequency estimates; so that
 there is currently no method to a priori estimate the relative importance
 of unequal individual DNA contributions independently of sequencing depth.
 We develop a new analytical model for allele frequency estimation that
 explicitly distinguishes these two effects. Our model shows that the DNA
 pooling variance in a pooled sequencing experiment depends solely on two
 factors: the number of individuals within the pool and the coefficient of
 variation of individual DNA contributions to the pool. We present a new
 method to experimentally estimate this coefficient of variation when
 planning a pooled sequencing design where samples are either pooled before
 or after DNA extraction. Using this analytical and experimental framework,
 we provide guidelines to optimize the design of pooled sequencing
 experiments. Finally, we sequence replicated pools of inbred lines of the
 plant Medicago truncatula and show that the predictions from our model
 generally hold true when estimating the frequency of known multilocus
 haplotypes using pooled sequencing.
description: Simulation
 scriptScript for the
 simulations used to verify the analytical model.Simulation_script_Fig.1Fig.S1-4.RmdHTML output of simulation scriptHTML output when knitting the file "Simulation_script_Fig.1Fig.S1-4.Rmd" using RstudioSimulation_script_Fig.1Fig.S1-4.htmlDNA concentration data (Hoechst)DNA concentration dataset (Hoechst) used to estimate the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction.DataHoechst.csvDNA concentration data (Picogreen)DNA concentration dataset (Picogreen) used to estimate the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction.DataPicogreen.csvPipette calibration dataPipetteMetrology.csvCVbefore and CVafter estimation scriptScript for estimating the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction based on PipetteMetrology.csv and DataHoechst.csv or DataPicogreen.csv.DNAconcentration_estimation_script_Fig.2-3.RmdHTML output of the script to estimate CVbefore/CVafterDNAconcentration_estimation_script_Fig.2-3.htmlGenomic dataConcatenated Medicago truncatula reference genome (v4), VCF, BAM and DGRP files used for HARP analyses.GenomicData.zip
DOI: 10.5061/dryad.02dq2
title: Data from: Weighing trees with lasers: advances, challenges and opportunities

description: Terrestrial laser scanning (TLS) is providing exciting new ways to
 quantify tree and forest structure, particularly above-ground biomass
 (AGB). We show how TLS can address some of the key uncertainties and
 limitations of current approaches to estimating AGB based on empirical
 allometric scaling equations (ASEs) that underpin all large-scale
 estimates of AGB. TLS provides extremely detailed non-destructive
 measurements of tree form independent of tree size and shape. We show
 examples of three-dimensional (3D) TLS measurements from various tropical
 and temperate forests and describe how the resulting TLS point clouds can
 be used to produce quantitative 3D models of branch and trunk size, shape
 and distribution. These models can drastically improve estimates of AGB,
 provide new, improved large-scale ASEs, and deliver insights into a range
 of fundamental tree properties related to structure. Large quantities of
 detailed measurements of individual 3D tree structure also have the
 potential to open new and exciting avenues of research in areas where
 difficulties of measurement have until now prevented statistical
 approaches to detecting and understanding underlying patterns of scaling,
 form and function. We discuss these opportunities and some of the
 challenges that remain to be overcome to enable wider adoption of TLS
 methods.
description: Data for Weighing Trees
 with LasersData used in
 publication, including lidar point clouds, resulting matlab quantitative
 structural models (QSMs) and Jupyter notebook and associated python code
 for reading and plotting these data, with worked
 examples.data.tgz