cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1g1jwsv3p
title: Urban natural areas forest carbon

description: Urban natural area forests provide cities with crucial ecosystem services,
 including carbon storage and sequestration. Although previous work from a
 single city has suggested that urban natural area forests may be carbon
 rich and dominated by native species, it is unclear if that pattern is
 widespread. Indeed, little is known about the species composition and
 carbon storage in these green spaces, or how urban natural area forests
 compare to similar rural forests. Here, we use data collected by the
 Forests in Cities network to quantify carbon stored in urban natural area
 forests across 1,852 plots in eight of the most populous US cities and
 examine patterns in woody vegetation carbon storage by tree species
 composition and size class. We also compare the carbon storage in these
 urban natural area forests to similar rural forests using USDA FS Forest
 Inventory and Analysis data. We found that urban natural area forests
 store between 214-267 Mg C ha-1, with the majority (on average 55%) in the
 aboveground portion of live trees and shrubs. This carbon was primarily
 stored by native trees and increased with the proportion of native
 species, as native trees tended to be larger. The proportion of nonnative
 species was higher in smaller size classes. Overall, the woody vegetation
 carbon density in urban natural area forests was higher than similar
 forest types in rural settings, a phenomenon driven by the presence of
 more large trees. Synthesis and Applications Together these results
 demonstrate the importance of urban natural area forests as carbon-dense
 ecosystems and havens for native tree species. However, because of the
 greater number of non-native species in smaller size classes, these
 forests may also be at risk of transitioning away from native-dominated
 systems. Therefore, greater monitoring efforts and increased management
 activities such as non-native species removal will be crucial to
 maintaining the high carbon storage and health of these
 ecosystems. 
description: # Urban natural areas forest carbon
 [https://doi.org/10.5061/dryad.1g1jwsv3p](https://doi.org/10.5061/dryad.1g1jwsv3p) These data and code quantify carbon stocks in urban natural area forests in 8 US cities. The code and data are associated with the manuscript "Native trees are responsible for the high carbon density in urban natural area forests across eight United States cities". ## Description of the data and file structure There are two primary data files: "all_cities.csv" contains tree level information (e.g. each observation is an individual tree). "plots_all_cities.csv" contains plot level information (e.g. each observation is a forest monitoring plot). Metadata for both files can be found in "Metadata.csv". In addition, there are three additional .csvs that contain useful information for recoding variables that are used in the R script. In all files, "NA" represented data that is not available. ## Code/Software Annotated R code with the analyses in the manuscript is in "R_code_UNAF_carbon.R".
DOI: 10.7910/dvn/jusyjm
title: Solar and Telluric spectra for wavelength calibration

description: Files containing wavelength and transmittance for a reference Solar spectrum and Telluric absorption lines. The Solar spectrum ranges from 300 - 16,661 nm and the Telluric spectrum ranges from 350 - 5,000 nm.

The solar spectrum is derived from the work of G.C. Toon, cited in the metadata.

The telluric lines come from the synthetic spectra of T. Schad, cited in the metadata.
DOI: 10.34740/kaggle/dsv/14654891
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.cnp5hqccb
title: Paraphlomis octopus (Lamiaceae), a new species from Southern China

description: Paraphlomis octopus (Lamiaceae), a new species from the limestone area in
 Guangdong and Guangxi, China, is described and illustrated. Molecular
 phylogenetic analyses based on two nuclear ribosomal DNA sequences
 revealed that the new species is sister to P. pagantha, and the two
 species are further sister to P. kwangtungensis. All three species were
 further embedded within a clade consisting of species with hairy ovaries
 or nutlets. Morphologically, the new species can be distinguished from P.
 kwangtungensis in its acute apex of calyx tooth, from P. pagantha in its
 strongly reflexed lower corolla lip, and from both species in their
 inflorescence with peduncle-like stalks, and wider upper corolla lip.
 Based on an extensive field survey, we also found that the type locality
 of P. kwangtungensis has long been misrecorded in floras. A key
 to all species with hairy ovaries and nutlets is provided.
description: # *Paraphlomis octopus* (Lamiaceae), a new species from Southern China
 [https://doi.org/10.5061/dryad.cnp5hqccb](https://doi.org/10.5061/dryad.cnp5hqccb) This dataset includes molecular phylogenetic analysis results for all samples and sequences used in this study as well as plate details for similar species. #### Appendix S5-FIG. S1 Morphology of *Paraphlomis kwangtungensis*. A. Habitat. B. Habit. C–E. Verticillasters. F. Frontal and lateral views of flowers. G. Apical and lateral views of calyces, and a dissected calyx. H. Frontal and lateral views of corollas, and a dissected corolla. I. Stamens. J. Pistil. K. Lateral and apical views of ovaries. L. Apical and lateral views of nutlets. A–E, photographed by Qiang Fan; F–L, photographed by Ying Liu. #### Apendix S6-FIG. S2 Morphology of *Paraphlomis pagantha*. A–B. Habit. C–E. Verticillasters. F. Frontal and lateral views of flowers. G. Apical and lateral views of calyces, and a dissected calyx. H. Frontal and lateral views of corollas, and a dissected corolla. I. Stamens. J. Pistil. K. Lateral and apical views of ovaries. L. Apical and lateral views of nutlets. A, D, photographed by Jing-Min Dai; B–C, E, photographed by Lang-Xing Yuan; F–L, photographed by Ying Liu. ## Supplementary files #### Appendix S1-Table S1 Sequence information for all samples used in the present study. A “/” indicates a missing sequence. Herbarium abbreviations are listed after the vouchers. The accession numbers marked in bold represent sequences newly generated. #### Appendix S2-nrDNA Data matrix of combined ITS and ETS sequences. #### Appendix S3-nrDNA-BI The 50% majority-rule consensus tree from bayesian inference analysis of *Paraphlomis* based on combined nuclear (ITS and ETS) dataset. Multiple accessions of the same species are numbered according to the Appendix S1-Table S1. #### Appendix S4-nrDNA-ML The best-score tree from maximum likelihood analysis of *Paraphlomis* based on combined nuclear (ITS and ETS) dataset. Multiple accessions of the same species are numbered according to the Appendix S1-Table S1.
DOI: 10.5061/dryad.4xgxd25hg
title: Data for: Experiment on hydrodynamic characteristics of plunging flows in bedrock canyon bends

description: The dataset is about the hydrodynamic characteristics of plunging flows in
 bedrock bends. The dataset includes raw data of bed topography of the
 Ciping Reservoir canyon section of Jinghe River and the bed of the flume
 experiments, flow field along the center profiles of plain- and
 undulating-beds conditions, and the bed shear stress of plain- and
 undulating-beds conditions.
description: The bed topography measured at the Ciping Reservoir
 canyon section of Jinghe River, China, measured by actual survey and
 aerial survey by UAV. The bed of flume experiments
 measured by laser in undulating-bed conditions. The
 flow field measured by ADV.
description: # Data for Experiment on hydrodynamic characteristics of plunging flows in
 bedrock canyon bends A
 generalized physical model was built to investigate the hydrodynamic
 characteristics of the plunging flows in a constant curvature flume with
 flat and undulating beds, respectively. We first measured the topography
 of canyon section located near the Ciping Reservoir of Jinghe River, and
 scaled the bed topography to flume. The flow field including time-averaged
 velocity, depth-averaged velocity, and turbulence characteristics measured
 by ADV (Acoustic Doppler Velocimeter). The characteristics of plunging
 flows could obtain from flow field such as the relative of plunging flows
 (*umax/umin*) and the strength of velocity inversion (*ηmax*). ##
 Description of the data and file structure “Cross section profile” sheet
 shows the cross-section measurement in the Ciping Reservoir canyon section
 of actual survey and aerial survey by using UAV. “Plain-bed velocity”
 sheet shows the experimental results of plain-bed conditions in terms of
 time-averaged velocities (*us*, *un*, *uz*), normalized streamwise
 velocities by depth-averaged streamwise velocity (*us*/*Us*) and
 cross-section averaged velocity (*us*/*U*) along the channel centerline
 from PRUN1 to PRUN5, respectively. The corresponding values of MLW curve
 for PRUN1 to PRUN5 also list. “Undulating-bed velocity” sheet shows the
 experimental results of undulating-bed conditions in terms of
 time-averaged velocities (*us*, *un*, *uz*), normalized streamwise
 velocities by depth-averaged streamwise velocity (*us*/*Us*) and
 cross-section averaged velocity (*us*/*U*) along the channel centerline
 from URUN1 to URUN3, respectively. “Bed shear stress” sheet list the
 friction factor, *cf,bed* and the transverse shear stress (*τbs*) near the
 bed (5 mm above the bed) in plain-bed conditions (PRUN1-PRUN5) and
 undulating-bed conditions (URUN1-URUN3), respectively. “Bed topography”
 sheet shows the bed topography in the experiments of undulating-bed
 conditions. “Water depth” sheet shows the water depth along the centerline
 in the experiments of plain- and undulating-bed conditions.
 “Characteristics of plunging flows” sheet shows the relative velocity
 (umax/umin) and strength of velocity inversion (ηmax) along the centerline
 in the experiments of plain- and undulating-bed conditions.
DOI: 10.5061/dryad.h9w0vt4r4
title: Evolutionary changes of non-coding elements associated with transition of sexual mode in Caenorhabditis nematodes

description: The transition of the sexual mode occurs widely in animal evolution. In
 Caenorhabditis nematodes, androdioecy, a sexual polymorphism composed of
 males and hermaphrodites having the ability to self-fertilize, has evolved
 independently multiple times. Although regulatory elements in non-coding
 regions are likely involved in the evolution of hermaphroditism, their
 contribution to the transition of sexual mode is ambiguous. Here, we
 conducted a genome-wide analysis of conserved non-coding elements (CNEs)
 focusing on the evolution of hermaphroditism in Caenorhabditis nematodes.
 We found that, in androdioecious nematodes, mutations rapidly accumulated
 in CNEs neighboring genes associated with sexual traits. Expression
 analysis indicate that the identified CNEs are involved in spermatogenesis
 in hermaphrodites and associated with the transition of gene expression
 from dioecious to androdioecious nematodes. Finally, genome editing of a
 CNE neighboring laf-1 resulted in a change in its expression in the
 gonadal region undergoing spermatogenesis. Our bioinformatic and
 experimental analyses highlight the importance of CNEs to the transition
 of sexual mode.
description: # Evolutionary changes of non-coding elements associated with transition
 of sexual mode in Caenorhabditis nematodes
 ## Description of the data
 and file structure All.maf: Multiple alignment file of genome alignment of
 11 Caenorhabditis nematodes producing by Cactus. All.wig: Conserved score
 of genome alignment estimated from maf file by PhastCons.
 Csp36_Kikuchi_candidateNonCoding_cneesL10.bed: Summarized bed format file
 of CNE which is longer than 10 bp using C. niphades as reference.
 Result_three_hermaphrodite_NonCoding_L10.out: Results of detection of
 accelerated evolution in each CNE by PhyloP.
DOI: 10.5061/dryad.wm37pvmvd
title: k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase) Part 3/3

description: Wild wheat relatives of bread wheat represent genetic diversity that can
 be used for wheat crop improvement. We generated a k-mer presence/absence
 matrix of over 920 accessions of the wild wheat Aegilops tauschii, the
 donor of the bread wheat D genome. This dataset was generated under the
 aegis of Phase II of the Open Wild Wheat Consortium
 (www.openwildwheat.org).
description: The full methods are available in the related publication.
description: # ***k***-mer matrix Aegilops tauschii diversity panel (Open Wild Wheat
 Consortium Phase II) PART 3/3
 [https://doi.org/10.5061/dryad.wm37pvmvd](https://doi.org/10.5061/dryad.wm37pvmvd) ## **Description of the data and file structure** *k*-mer presence/absence matrix for the *Aegilops tauschii* diversity panel of over 920 accessions, including genetically redundant accessions. **Resequencing of the *Ae. tauschii* accessions:** We generated short-read whole genome sequencing data for 350 *Ae. tauschii* accessions.  PCR-free paired-end libraries were constructed and sequenced on an Illumina Novaseq 6000 instrument, yielding a median 8.3-fold coverage per sample (ranging from 5.87 to 16.86-fold). ***k*****-mer matrix generation.** We developed and implemented an optimised *k*-mer matrix workflow to generate a presence/absence *k*-mer matrix for large diversity panels (https://github.com/githubcbrc/KGWASMatrix). We counted *k*-mers (*k* = 51) in raw sequencing data for 350 accessions generated in this study, 306 accessions published by Gaurav et al. (2022), 275 accessions published by Zhou et al. (2021) and 24 accessions by Zhao et al. (2023). Accessions with less than 5-fold sequencing coverage were discarded to avoid affecting the *k*-mer count. *k*-mers were filtered by a minimum occurrence of six across accessions and a maximum occurrence of (N-6), being N the total number of accessions. Detailed information about this *k*-mer matrix is found in the related pre-print by Cavalet-Giorsa, Gonzalez-Munoz and Athiyannan et al. (2023) (https://doi.org/10.1101/2023.11.29.568958). The full *k*-mer matrix has a total size of ~729G and has been divided into 25 gzipped files. The full *k*-mer matrix is tab-delimited in which the first column contains 10,078,115,665 *k-*mers and the remaining columns show the presence (1) or absence (0) across the accessions that are listed in order in the matrix_acc945_samples_list.txt file available in part 1/3 (doi:10.5061/dryad.p5hqbzkvx). This dataset contains gzipped files 18 through 25 of the full *k*-mer matrix, as follow: 18_m.tsv.gz 19_m.tsv.gz 20_m.tsv.gz 21_m.tsv.gz 22_m.tsv.gz 23_m.tsv.gz 24_m.tsv.gz 25_m.tsv.gz The first and second parts of the *k*-mer matrix are available in additional related DRYAD datasets: doi:10.5061/dryad.p5hqbzkvx doi:10.5061/dryad.wpzgmsbvm
DOI: 10.5061/dryad.ngf1vhj23
title: Aedes albopictus in Zambia

description: Identifying the current geographic range of disease vectors is a critical
 first step towards determining effective mechanisms for controlling and
 potentially eradicating them. This is particularly true given that
 historical vector ranges may expand due to changing climates and human
 activity. The Aedes subgenus Stegomyia contains over 100 species, and
 among them, Ae. aegypti and Ae. albopictus mosquitoes represent the
 largest concern for public health, spreading dengue, chikungunya, and Zika
 viruses. While Ae. aegypti has been observed in the country of Zambia for
 decades, Ae. albopictus has not. In 2015 we sampled four urban and three
 rural areas in Zambia for Aedes species. Using DNA barcoding, we confirmed
 the presence of immature and adult Ae. albopictus at two sites: Siavonga
 and Livingstone. These genotypes seem most closely related to specimens
 previously collected in Mozambique based on CO1 sequence from mtDNA. We
 resampled Siavonga and Livingstone sites in 2019, again observing immature
 and adult Ae. albopictus at both sites. Relative Ae. albopictus
 frequencies were similar between sites, with the exception of immature
 life stages, which were higher in Siavonga than in Livingstone in 2019.
 While Ae. albopictus frequencies did not vary through time in Livingstone,
 both immature and adult frequencies increased through time in Siavonga.
 This report serves to document the presence of Ae. albopictus in Zambia,
 which will contribute to the process of determining the potential public
 health implications of this disease vector in Central Africa.
description: # Code to reproduce results in
 [https://doi.org/10.5061/dryad.ngf1vhj23 ](https://doi.org/10.5061/dryad.ngf1vhj23) A single R script to do proportion comparisons.      ## Description of the data and file structure All the data required to execute the code appear in the code itself, in the .csv file data_zambia.csv, and also in Table 1 of Matute and Cooper 2024. Larvae were collected larvae using Mosquito dippers powdered with stainless steel (John W. Hock Company, Gainesville, FL). data_zambia.csv shows the numbers of Aedes individuals collected in Zambia in two different years. Adults were collected with CDC-type light traps (2836BQX, BioQuip; Rancho Domingo, CA) connected to a 6V as a power source. The first column is the location. Second colum is the altitude (in meters above sea level). Days represents the number of days the trapping lasted. Imm: number of collected immature states in each location; Adults: number of collected adults in each location. ## Code/Software The R code is self-contained and has all the elements required to run in R. data_zambia.csv includes the same data in tabular form.
DOI: 10.5061/dryad.k3j9kd5fx
title: Data from: Human conjunctival transcriptome in Acanthamoeba keratitis: An exploratory study

description: The host conjunctival transcriptome of 9 patients with Acanthamoeba
 keratitis (AK) is compared to the conjunctival transcriptome of 13
 patients with keratitis and no identified pathogen. Pathway enrichment
 analysis identified thirty-six transcripts as most differentially
 expressed between patients with AK compared to patients with presumed
 sterile keratitis.
description: The host conjunctival transcriptome of 9 patients with
 <em>Acanthamoeba</em> keratitis (AK) is compared to the
 conjunctival transcriptome of 13 patients with keratitis and no identified
 pathogen. For the differential host gene expression analysis, sequencing
 reads were quality filtered and aligned to the GRCh38 human genome
 assembly using HISAT2 (version 2.1.0). Abundance of transcripts was
 calculated using the default parameters in stringtie2 (version 1.3.4d) and
 annotation of transcripts were based on ENSEMBL GRCh38.87. Gene count
 matrices were generated using the "prepDE.py" script according
 to the protocol found in the stringtie2 documentation.
description: # Data from: Human conjunctival transcriptome in Acanthamoeba keratitis:
 An exploratory study
 [https://doi.org/10.5061/dryad.k3j9kd5fx](https://doi.org/10.5061/dryad.k3j9kd5fx) ## Description of the data and file structure ### List of files ``` ENSG_ID2Name.txt conj_transcriptome_stringtie2_counts_md5-9660d96d.csv conj_transcriptome_metadata.csv ``` ### Description of data `ENSG_ID2Name.txt` is a text file containing the mapping of ENSG IDs to gene names. The CSV file `conj_transcriptome_stringtie2_counts_md5-9660d96d.csv` contains counts for human genes found in 22 conjunctival samples. RNA-Seq data was generated on an Illumina NovaSeq 6000 sequencing machine at the UCSF sequencing center. Sequencing reads were quality filtered using PriceSeqFilter, and aligned to the GRCh38 human genome assembly using HISAT2 (version 2.1.0). Abundance of genes was calculated using the default parameters in stringtie2 (version 1.3.4d). Annotation of transcripts was based on ENSEMBL GRCh38.87. The attached gene count matrix was then generated using the "prepDE.py" script according to the protocol found in the stringtie2 documentation. `conj_transcriptome_metadata.csv` is a 2-column csv file that shows the group assignments ("Negative" or "Amoeba") for each sample. ## Software Software used for determining gene counts: * PRICE Sequence Filter (version 1.2) * HISAT2 (version 2.1.0) * stringtie2 (version 1.3.4d), and stringtie2's prepDE.py script
DOI: 10.5061/dryad.vdncjsz2r
title: The spread of Aedes albopictus (Diptera: Culicidae) in the islands of São Tome and Príncipe

description: The mosquito Aedes albopictus (Diptera: Culicidae) is a vector species of
 the causal agents of Dengue, yellow fever, and Zika among other diseases
 pathogens. The species originated in Southeast Asia and has spread widely
 and rapidly in the last century. The species has been reported in
 localities from the Gulf of Guinea since the early 2000s, but systematic
 sampling has been scant. We sampled Ae. albopictus twice, in 2013 and 2023
 across the altitudinal gradient in São Tomé and found that the species was
 present in all sampled years at altitudes up to 680 meters. We also found
 some evidence of increases in proportional representation compared to Ae.
 aegypti over time. We report the presence of the species in Príncipe for
 the first time, suggesting that the range of Ae. albopictus is larger than
 previously thought. Finally, we use bioclimatic niche modeling to infer
 the potential range of Ae. albopictus and infer that the species has the
 potential to spread across a large portion of São Tomé and Príncipe. Our
 results suggest that Ae. albopictus has established itself as a resident
 species of the islands of the Gulf of Guinea and should be incorporated
 into the list of potential vectors that need to be surveyed and
 controlled.
description: # The spread of Aedes albopictus (Diptera: Culicidae) in the islands of
 São Tom and Príncipe. 
 [https://doi.org/10.5061/dryad.vdncjsz2r](https://doi.org/10.5061/dryad.vdncjsz2r) This submissions contains one dataframe relating altitude and Aedes abundance and the R code to generate linear models to quantify the effect of altitude. ## Description of the data and file structure The R code contains instructions to execute the linear models that assess the effect of altitude on the abundance of two species Aedes along the altitudinal gradient in São Tomé island. The only required data for this analysis can be found in: dataframe_aedes_ST_altitude.csv dataframe_aedes_ST_altitude.csv is a cvs file which contains the data to assess the effect of altitude on the abundance of two species Aedes along the altitudinal gradient in São Tomé island. The data constitutes collections of immature stages and adults of *Aedes* along the altitudinal transect of the island of São Tomé. Larvae were collected larvae using Mosquito dippers powdered with stainless steel (John W. Hock Company, Gainesville, FL). Adults were collected with CDC-type light traps (2836BQX, BioQuip; Rancho Domingo, CA) connected to a 6V as a power source. Coordinates: longitude and latitude of the trap. Name: locality name. altitude: elevation of the locality (In meters above sea level). year: collection year Nimm: Number of immature stages collected in the locality. Nad: Number of adults collected in the locality. # Code/Software One R script to run linear models using dataframe_aedes_ST_altitude.csv
DOI: 10.15468/dl.khwmn4
title: Occurrence Download

description: A dataset containing 1008 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Recopilación de datos e información para el Inventario Nacional de Especies de mamíferos marinos nativos de Chile 2016."
 ]
}

 The dataset includes 1008 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003864-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.