cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22008/promice/data/ice_discharge/d/v02/1fiuyi
title: gate_D.csv

description: Gate discharge. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/aaa6bp
title: gate_err.csv

description: Gate errors. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/gwyxgh
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/s2x8zh
title: GIS_coverage.csv

description: Greenland coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/zbpzlp
title: GIS_D.csv

description: Greenland discharge. Git hash: 66fa5db
DOI: 10.5061/dryad.mw6m90602
title: A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes

description: Echinometra is the most widespread genus of sea urchin and has
 been the focus of a wide range of studies in ecology, speciation, and
 reproduction. However, available genetic data for this genus are
 generally limited to a few select loci. Here, we present a
 chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C
 sequencing for Echinometra sp. EZ from the
 Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling
 817.8 Mb with an N50 of 39.5 Mb. From this assembly we determined that
 the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO
 analysis showed that 95.3% of BUSCO genes were complete. ab initio and
 transcript-informed gene modeling and annotation identified
 29,405 genes, including a conserved Hox
 cluster. E. sp. EZ can be found in high-temperature and
 high-salinity environments, and we therefore compared gene families and
 transcription factors associated with environmental stress response
 (“defensome”) with other echinoid species with similar high-quality
 genomic resources. While the number of defensome genes was broadly similar
 for all species, we identified strong signatures of positive selection in
 non-coding elements near genes involved in environmental response pathways
 as well as losses of transcriptions factors important for environmental
 response. These data provide key insights into the biology of E.
 sp. EZ as well as the diversification
 of Echinometra more widely and will serve as a useful
 tool for the community to explore questions in this taxonomic group and
 beyond.
description: spez_chrom_genome_final.fasta -- Chromosome-level genome
 assembly spez_gene_annotations.txt -- Gene annotation
 file spez_annotations.gff -- Gene annotation file gff
 format spez_proteins.fa -- Protein file
 spez_only_sig_sites.bed -- file generated from positive selection
 analysis (adaptiphy), includes sites that are under selection in E. sp.
 EZ PFAM_SPEZ -- file generated from running hmmscan on
 spez protein files and PFAM database (includes all results)
 Please see:
 http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf for formatting
 information (page 45) PFAMs_Queried -- this is the list
 of PFAMs that we extracted from the PFAM_SPEZ file in order to look at
 'defensome' PFAMs
 spez_chrom_genome_final.fasta.mod.EDTA.TEanno.gff3 --
 Whole-genome TE annotation file which contains structurally intact and
 fragmented TE annotations (generated through EDTA)
DOI: 10.22008/promice/data/ice_discharge/d/v02/ix1ycw
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/lpwffs
title: GIS_err.csv

description: Greenland error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/4kjwyt
title: region_coverage.csv

description: Regional coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/gctxoe
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/hukvbi
title: region_D.csv

description: Regional discharge. Git hash: 66fa5db
DOI: 10.25338/b8t935
title: Experimental data used in mathematical modeling

description: The heart pumps blood into circulation against vascular resistance and
 actively regulates the contractile force to compensate for mechanical load
 changes. Our experimental data show that cardiomyocytes have a
 mechano-chemo-transduction (MCT) mechanism that increases intracellular
 Ca2+ transients to enhance contractility in response to increased
 mechanical load. This study advances the cardiac excitation-Ca2+
 signaling-contraction (E-C) coupling model on conceptual and technical
 fronts. First, we developed analytical and computational models to perform
 3-dimensional mechanical analysis of cardiomyocytes contracting in a
 viscoelastic medium under mechanical load. Next, we proposed an MCT
 feedback loop in the E-C coupling dynamic system to shift the feedforward
 paradigm of cardiac E-C coupling to an autoregulation model. Our combined
 modeling and experimental studies reveal that MCT enables autoregulation
 of E-C coupling and contractility in single cardiomyocytes, which
 underlies the heart's intrinsic autoregulation in compensatory
 response to load changes in order to maintain the stroke volume and
 cardiac output.
description: This paper focuses on developing analytic and computational
 models. The model formulation and parameters are based on experimental
 data. These experimental data have been previously published in
 experimental papers and cited in this modeling paper. Here we deposit the
 relevant experimental data used for modeling in the present
 paper.
description: Microsoft Excel.
DOI: 10.22008/promice/data/ice_discharge/d/v02/ugr0ul
title: sector_coverage.csv

description: Sector coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/o6ud0j
title: sector_D.csv

description: Sector discharge. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/zynim5
title: sector_err.csv

description: Sector error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/gjnjsn
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.5061/dryad.4b8gthtfk
title: Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): A foundation for future evolutionary study of a speciose mimicry complex

description: Sesiids are a diverse group of predominantly diurnal moths, many of which
 are Batesian mimics of Hymenoptera. However, their diversity and
 relationships are poorly understood. A multi-gene phylogenetic analysis of
 48 North American sesiid species confirmed the traditional taxonomic
 tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with
 respect to several other genera, and ultimately provided minimal
 phylogenetic resolution within and between North American and European
 groups. Character support from each gene suggested inconsistency between
 the phylogenetic signal of the CAD gene and that of the other four genes.
 However, removal of CAD from subsequent phylogenetic analyses did not
 substantially change the initial phylogenetic results or return Carmenta
 and Synanthedon as reciprocally monophyletic, suggesting it was not
 impacting the overall phylogenetic signal. The lack of resolution
 using genes that are typically informative at the species level for other
 lepidopterans suggests a surprisingly rapid radiation of species in
 Carmenta/Synanthedon. This group also exhibits a wide range of mimicry
 strategies and hostplant usage, which could be fertile ground for future
 study.
description: See methods in paper for details. 
description: File opens as text.
DOI: 10.22008/promice/data/ice_discharge/d/v02/bfcai5
title: gate_coverage.csv

description: Gate coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/ngtff9
title: gate_D.csv

description: Gate discharge. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/z5fqqa
title: gate_err.csv

description: Gate errors. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/3vip4j
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/yugkic
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/0owafo
title: region_coverage.csv

description: Regional coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/dsbsbr
title: README.txt

description: README. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/6m1wsp
title: region_D.csv

description: Regional discharge. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/2b4mq4
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/hxgta0
title: region_err.csv

description: Regional error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/dxryvp
title: sector_coverage.csv

description: Sector coverage. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/43qule
title: sector_D.csv

description: Sector discharge. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/kafmzb
title: sector_err.csv

description: Sector error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/sza83y
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: 66fa5db
DOI: 10.22008/promice/data/ice_discharge/d/v02/48lhuf
title: gate_D.csv

description: Gate discharge. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/i1cazr
title: gate_coverage.csv

description: Gate coverage. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/cuvvke
title: gate_err.csv

description: Gate errors. Git hash: ed0b83b
DOI: 10.25338/b8ph0v
title: Common bean PvIND locus bisulfite sequencing reads

description: Fruit development has been central in the evolution and domestication of
 flowering plants. In common bean (Phaseolus vulgaris L.), the principal
 global grain legume staple, two main production categories are
 distinguished by fiber deposition in pods: a) dry beans, with fibrous,
 stringy pods; and b) stringless snap/green beans, with reduced fiber
 deposition, which frequently revert to the ancestral stringy state. Here,
 we identify genetic and developmental patterns associated with pod fiber
 deposition. Transcriptional, anatomical, epigenetic, and genetic
 regulation of pod strings were explored through RNA-seq, RT-qPCR,
 fluorescence microscopy, bisulfite sequencing, and whole-genome
 sequencing. Overexpression of the INDEHISCENT (“PvIND”) ortholog was
 observed in stringless types compared to isogenic stringy lines,
 associated with overspecification of weak dehiscence zone cells throughout
 the pod vascular sheath. No differences in DNA methylation were correlated
 with this phenotype. Non-stringy varieties showed a tandemly direct
 duplicated PvIND and a Ty1-copia retrotransposon inserted between the two
 repeats. These sequence features are lost during pod reversion and are
 predictive of pod phenotype in diverse materials, supporting their role in
 PvIND overexpression and reversible string phenotype. Our results give
 insight into reversible gain-of-function mutations and possible genetic
 solutions to the reversion problem, of considerable economic value for
 green bean production.
description: Genomic DNA was extracted using a modified CTAB protocol.
 Bisulfite treatment was conducted with the EZ DNA Methylation-Lightning
 Kit. Primers were designed with Zymo Bisulfite Primer Seeker 12S, PCR
 products were checked on a gel, cleaned with a QIAquick PCR Purification
 Kit, and genotyped by Sanger sequencing at the UC Davis DNA sequencing
 facility.
DOI: 10.22008/promice/data/ice_discharge/d/v02/2pszvo
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/mf9pcg
title: GIS_coverage.csv

description: Greenland coverage. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/epw7tx
title: GIS_err.csv

description: Greenland error. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/t8vyu4
title: GIS_D.csv

description: Greenland discharge. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/hqzas9
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: ed0b83b
DOI: 10.5061/dryad.2fqz612rq
title: RNA-seq of green hydra strains' ( Hydra viridissima) response to the removal or exchange of symbionts

description: The symbiotic hydra Hydra viridissima has a stable
 symbiotic relationship with the green alga Chlorella. This hydra appears
 to cospeciate with the symbiotic alga, and some strains are known to have
 strain-specific host/symbiont combinations. To investigate the mechanism
 of the specificity between host and symbiont, we explored the effect of
 the removal or exchange of symbionts in two distantly related H.
 viridissima strains (K10 and M9). In this study, we compared the gene
 expression of symbiont-removed, symbiont-exchanged hosts for each strain.
 The data include the raw read fastaq, assembled sequences, and read counts
 of RNA-seq.  We also attached the results of differential gene
 expression analyses for all combinations of the hosts. 
description: We used six experimental groups (K10ori, M9ori, K10apo, M9apo,
 K10exc, and M9exc) for the RNA-seq analysis. The analysis was performed
 with 150 bp paired-end reads on an Illumina HiSeq 4000 and Illumina
 MiSeq.  The low-quality reads were filtered out with
 the following criteria. 1, Low-quality ends (QV
 &lt; 30) and adapter sequences were trimmed using cutadapt. 
 2, Short reads (&lt;20 bp) were discarded for quality control
 using cutadapt.  3, Any remaining rRNA sequences were
 filtered out using SortMeRNA 2.  After quality
 filtering, de novo assembly was performed on the reads generated from
 HiSeq and MiSeq using Trinity, and the contigs less than 200 bp were
 discarded. Next, reads from HiSeq were mapped to the assembled contigs
 using salmon. Next, clustering of the assembled contigs and read counting
 were performed with Corset. Finally, a similarity search of the clustered
 contigs against UniProtKB was conducted using BLASTX with an e-value
 cut-off of 1e-5 to remove sequences from the symbiotic chlorellae and
 annotate the contigs. We calculated e-values against homologous protein
 sequences of Opisthokonta and Viridiplantae in UniProtKB and those of H.
 vulgaris in TrEMBL. Contigs whose e-values of the best hits against
 Opisthokonta and <em>Hydra</em> sequences were smaller than
 those against Viridiplantae were considered hydra contigs. These hydra
 contigs were annotated with UniProtKB Swiss-Prot. The remaining
 unannotated contigs were annotated with entries from <em>H.
 vulgaris</em>, whose whole genome was sequenced and annotated
 UniProtKB TrEMBL to find hydra-specific genes.  To find
 orthologues between K10 and M9, protein sequences translated from the
 contigs were estimated using TransDecoder (https://github.com/TransDecoder/TransDecoder), and an orthogroup, which is the set of genes that are descended from a single gene in the last common ancestor, was inferred by Orthofinder using those protein sequences and sequences from <em>H</em>. <em>vulgaris</em> in the RefSeq database.
DOI: 10.22008/promice/data/ice_discharge/d/v02/hyux4h
title: region_coverage.csv

description: Regional coverage. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/jwvreo
title: README.txt

description: README. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/n4af4p
title: region_D.csv

description: Regional discharge. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/vsyndc
title: region_err.csv

description: Regional error. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/wdb7zg
title: region.nc

description: Regional discharge, coverage, and error. Git hash: ed0b83b
DOI: 10.5061/dryad.9cnp5hqmr
title: Diversity and conservation of endemic true bugs for four family groups in China

description: Aim: Protected areas in China have typically been designed by considering
 one or several focal taxa (e.g., relict plant and vertebrate species), but
 the effectiveness of these “protective umbrellas” in safeguarding insects
 remains unclear. In this study, we aim to investigate the distribution and
 diversity of endemic true bugs for four family groups (i.e., Miridae,
 Lygaeoidea, Pentatomidae, and Reduviidae) in China, the environment
 factors shaping these diversity patterns, as well as the effectiveness of
 China’s protected areas (PAs) in safeguarding their diversity. Location:
 China. Methods: We mapped the spatial distributions of 1028 endemic true
 bugs in China using stacked species distribution models and pixel grids of
 observed points. Environment factors that influence diversity patterns
 across China were explored by generalized linear models and random forest
 models. The effectiveness of PAs in safeguarding species distribution was
 evaluated by the Zonation platform. Results: We found that most (84.9%)
 diversity hotspots for total species located in mountainous areas of
 southern China. Additionally, the diversity pattern is shaped by the
 combined effects of different environment factors, with the minimum
 temperature of the coldest month, annual precipitation and elevation
 showing the strongest effects. On average, Chinese PAs covered 10.2%
 distribution areas of these endemic true bugs. Main conclusions: In
 general, our research identifies the important roles of mountainous areas
 in southern China in maintaining the species diversity. Moreover, our
 research also suggests that PAs in China couldn’t provide sufficient
 protection for this diversity. Protecting these endemic true bugs
 diversity should be valued more in southern China's mountainous
 areas.
DOI: 10.57903/uj/vmktti
title: Ultra-Dense, Highly Ordered and Thermally Stable Anthracene Monolayers on Ag(111)The Impact of the Anchoring Group - replication data

description: Replication data for publication "Ultra-Dense, Highly Ordered and Thermally Stable Anthracene Monolayers on Ag(111)The Impact of the Anchoring Group"
DOI: 10.22008/promice/data/ice_discharge/d/v02/l16bwf
title: sector_coverage.csv

description: Sector coverage. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/xit26i
title: sector_D.csv

description: Sector discharge. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/rhe10l
title: sector_err.csv

description: Sector error. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/v1oxai
title: gate_coverage.csv

description: Gate coverage. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/zimj2k
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: ed0b83b
DOI: 10.22008/promice/data/ice_discharge/d/v02/atsdgq
title: gate_err.csv

description: Gate errors. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/z0zsjs
title: gate_D.csv

description: Gate discharge. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/cdhmfz
title: GIS_coverage.csv

description: Greenland coverage. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/zakqsk
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/hsy0q3
title: GIS_err.csv

description: Greenland error. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/mzqrc5
title: GIS_D.csv

description: Greenland discharge. Git hash: c2c886d
DOI: 10.7272/q62805w5
title: RNA seq data set of chick, quail, and duck mandibular primordia at embryonic stage (HH) 37

description: Jaws are among the most highly adapted and modified structures of
 vertebrates, and they facilitate complex behaviors like feeding,
 respiration, and vocalization. For this reason, precise developmental
 regulation of jaw length is crucial for survival. By comparing jaw
 development between white Pekin duck (Anas platyrhynchos domestica),
 Japanese quail (Coturnix coturnix japonica), and chick (Gallus gallus) we
 have shown in prior work that neural crest mesenchyme (NCM), which is the
 embryonic progenitor population that gives rise to the jaw skeleton,
 employs a variety of stage- and species-specific mechanisms to govern jaw
 length. Duck have much longer jaws compared to those of quail, and during
 the early migration of NCM from the anterior neural tube, duck embryos
 allocate more progenitors to the presumptive jaw region. Once these NCM
 populations arrive, their growth trajectories further diverge due to
 autonomous molecular programs for proliferation and differentiation that
 are tied to intrinsic rates of maturation and species-specific regulation
 of multiple-signaling pathways. To analyze the species-specific
 differential expression and regulation of the signaling pathways, which
 direct jaw morphology, we performed an RNA-seq experiment on chick, quail,
 and duck mandibular primordia at stage (HH) 37. To increase the spatial
 resolution the lower jaws were dissected into proximal and distal
 portions. Oxford Nanopore Technology sequencing was used to preserve the
 full-length mRNA sequence so that spatial and species-specific differences
 in the distribution of isoforms could be assayed.
description: Lower jaw primordia were dissected from HH37 chick,
 quail, and duck. The lower jaw primordia were cut in half along the
 distal-proximal axis and RNA was extracted using RNeasy plus kit. cDNA
 from HH37 chick, quail, and duck lower jaws was synthesized using an NEB
 Next Single Cell/Low Input cDNA Synthesis Amplification Module (E6421, New
 England BioLabs, Ipswich, MA) following PacBio Iso-Seq template
 preparation guidelines. cDNA was barcoded using the PCR barcoding
 expansion 1-96 kit (EXP-PBC096, Oxford Nanopore Technologies, Oxford, UK).
 cDNA samples were pooled, and a sequencing library was prepared using the
 ligation sequencing kit (SQK-LSK110, Oxford Nanopore Technologies, Oxford,
 UK). 50 fmol of the final library was loaded onto each of the two
 PromethION flowcells (v R9.4.1) and the run was performed for 72 hours.
 Basecalling and de-multiplexing were performed live on the PromethION
 compute module (Basecaller Version ont-Guppy-for-minKNOW
 4.0.11).
description: Data are sequencing results from long read Oxford Nanopore
 PromethION RNA seq of the distal and proximal portions of mandibular
 primordia at embryonic stage (HH) 37. Data are in FASTQ file format that
 have been Gzipped. If necessary, 7-Zip can be used to unzip the files.
 Software that can read FASTQ files should be able to open this
 dataset.
DOI: 10.22008/promice/data/ice_discharge/d/v02/qs4xqv
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/5hbf1r
title: README.txt

description: README. Git hash: c2c886d
DOI: 10.22008/promice/data/ice_discharge/d/v02/8ejptb
title: region_coverage.csv

description: Regional coverage. Git hash: c2c886d