cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rbnzs7hq
title: Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1

description: Deoxynivalenol (DON) is one of the most abundant mycotoxins and has
 adverse effects on several biological processes, posing risks of protein
 synthesis-disrupting effects and ribotoxic response. Therefore, chronic
 exposure to DON would fundamentally reshape the global expression pattern.
 Whether DON causes toxic effects on mRNA splicing, a fundamental
 biological process, remains unclear. In this study, we found that
 administration of the relative low dosage of DON dramatically changed the
 alternative splicing of pre-mRNA in HepG2 cells. The overall number of
 transcripts with aberrant selection of 3' splice sites was
 significantly increased in DON-exposed HepG2 cells. This effect was
 further confirmed in two other human cell lines, HEK293 and Caco-2,
 suggesting that this DON-induced alteration in splicing pattern is
 universal in human cells. Among these DON-induced changes in alternative
 splicing, the expression levels of two related splicing factors, SF1 and
 U2AF1, which are essential for 3' splice site recognition, were
 strongly suppressed. The expression of SF1 and U2AF1 in human cells was
 controlled by DON probably at the transcriptional level by suppressing the
 promoter activation of these two genes. Overexpression of either of the
 two splicing factors strongly alleviated the DON-induced 3' splice
 sites. Moreover, SF1 is required for human cell proliferation in DON
 exposure, and the restoration of SF1 expression partially reinstated the
 proliferation potential of DON-treated cells. In conclusion, our study
 suggests that DON, even at a low dosage, has great potential to change
 gene expression globally by affecting not only protein synthesis but also
 mRNA processing in human cells.
description: Two biological replicates for
 DON-treated and untreated control HepG2 cells were
 collected for RNA-seq. Sequencing library was constructed by NEBNext Ultra
 RNA Library Prep Kit for Illumina, assessed by gilent 2100 Bioanalyzer and
 ABI StepOnePlus Real-Time PCR System, and sequenced by Illumina
 HiSeq<sup>TM</sup> 2500 platform. The adaptor,
 ploy-N and low quality reads were removed to obtain clean reads for
 further analyses. SOAPaligner/SOAP2 were used to assemble the clean reads,
 and then the gene expression and alternative splicing analyses were
 conducted based on assembled sequences with homemade perl scripts. GO
 analysis was conducted on KOBAS 3.0 web server
 (http://kobas.cbi.pku.edu.cn/index.php). The quantitative analysis and
 statistics were conducted in R.  The comprehensive
 analyses of the transcriptomic data is included.
DOI: 10.60521/332627
title: Processed Gridded Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA163 conducted in 2024. These data files are of GeoTIFF (Raster) format and include Bathymetry data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60521/332628
title: Processed Gridded Acoustic Backscatter Data (EM302) acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA163 conducted in 2024. These data files are of GeoTIFF (Raster) format and include Acoustic Backscatter data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.5061/dryad.sf7m0cg1p
title: Insects and light interact to mediate vine colonization of fast-growing Microberlinia bisulcata tree seedlings in gaps of an African rainforest

description: Vines thrive in lowland tropical forests yet the biotic factors underlying
 their colonization of host tree seedlings and saplings remain surprisingly
 understudied. Insect herbivores presumably could influence this process,
 especially where disturbance has opened the canopy (i.e., gaps)—temporary
 areas of higher primary productivity favoring the recruitment of vines and
 trees and invertebrates in forests—but their impact on vine colonization
 has never been experimentally tested. Using data from an insect-herbivore
 exclusion (mesh-netting cages) experiment conducted in an African
 rainforest (Korup, Cameroon), I logistically modeled the probability of
 vines colonizing seedlings of three co-dominant species (Microberlinia
 bisulcatavs. Tetraberlinia bifoliolataand T. korupensis)
 in paired shaded understory and sunny gap locations (41 blocks across 80
 ha, starting n = 664 seedlings) in a 1–2-yr period (2008–2009). Vine
 colonization occurred almost exclusively in gaps, occurring on 16% of
 seedlings there. Excluding herbivores in gaps doubled colonization of the
 light-demanding and faster-growing M. bisulcatabut had negligible
 effects on the two shade-tolerant, slower-growing and less
 palatable Tetraberliniaspecies, which together were twice as
 susceptible to vines under natural forest gap conditions (controls). When
 protected from herbivores in gaps, more light to individual seedlings
 strongly increased vine colonization of M. bisulcatawhereas its
 well-lit control individuals supported significantly fewer vines. These
 results suggest vines preferably colonize taller seedlings, and because
 light-demanding tree species grow faster in height with more light, they
 are more prone to being colonized in gaps; however, insect herbivores can
 mediate this process by stunting fast-growing individuals so that
 colonization rates becomes more similar between co-occurring slow and fast
 growing tree species. Further influencing this process might be
 associational resistance or susceptibility to herbivores linked to host
 species’ leaf traits conferring shade-tolerance ability as seedlings or
 saplings. A richer understanding of how vines differentially influence
 forest regeneration and species composition may come from investigating
 vine–tree–herbivore interactions across light gradients, ideally via
 long-term studies and intercontinental comparisons.
DOI: 10.5061/dryad.1c59zw3rc
title: Seawater body dipping behaviour of the Mauritian flying fox

description: The Mauritian flying fox (Pteropus niger) is the last surviving fruit bat
 species on Mauritius and is currently Endangered. The species faces
 threats as only 4.4% of habitats with high native content remains, however
 highly fragmented and invaded by alien species. Furthermore, stochastic
 events such as cyclones negatively impact food resources availability and
 likely encourage flying foxes to explore alternative ways to complement
 their diet in situation of food shortages. We organized various trips
 after extensive stochastic events to observe flying foxes attempting to
 dip their lower body part in the sea. Around 15 seawater body dipping
 instances were observed. Each time, the flying fox would clumsily dip
 itself into the water and lick their wet fur immediately after. This shows
 the species’ behavioral versatility and plausibly their resilience ability
 and local adaptation to particular opportunities within their environment.
 These observations potentially unravel an alternative way for flying foxes
 to complement minerals intake. The situation might also emphasize the
 decline in the species native foraging habitats quality and consequently
 prompts long-term conservation measures. Restoration of native forests
 from invasive alien species could maximize diverse native fruits
 availability all year round, thus limiting chances of food shortages for
 flying foxes.
description: All data collected were based on observation
DOI: 10.60521/332631
title: Google Earth files of Acoustic Backscatter and Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA163 conducted in 2024. These data files are of Google Earth (KML/KMZ) format and include Acoustic Backscatter and Bathymetry data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60521/332632
title: ROV Hercules Navigation Data acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Navigation System on ROV Hercules during E/V Nautilus expedition NA163 conducted in 2024. These data files are of Text File (ASCII) format and include Navigation data that have not been processed. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.15468/dl.2vkbr5
title: Occurrence Download

description: A dataset containing 5327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (KAZ.2_1, KAZ.10_1, KAZ.7_1, KAZ.8_1, KAZ.9_1, KAZ.9.8_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Arthropoda"
 ]
}

 The dataset includes 5327 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001977-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60521/332634
title: Dive Documentation acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Navigation System on ROV Hercules during E/V Nautilus expedition NA163 conducted in 2024. These data files are of Text File (ASCII) format and include Documentation. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60905/c690r0
title: ��Duque chao!

description: &lt;p&gt;Acciones del Movimiento Barrial Zona 2 en articulaci��n con otras organizaciones del territorio e invitaciones a sus integrantes para conversar en medios de otros sectores sociales movilizados en el Paro. &lt;/p&gt;

&lt;p&gt;Movimiento Barrial Zona 2 - CONPAZ - TallerarTe &lt;/p&gt;
description: <br>Inicio y ascenso de la Paro Nacional #28A. 28 de abril al 28 de julio de 2021
DOI: 10.15468/dl.njde59
title: Occurrence Download

description: A dataset containing 1580 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Living Specimen, Occurrence evidence)",
 "DatasetKey is one of (A global database for the distributions of crop wild relatives, iNaturalist Research-grade Observations, International Barcode of Life project (iBOL), Vegetación de sistemas cársticos en el municipio de El Peñón, Santander - Proyecto Colombia BIO, Tejidos de sistemas cársticos en el municipio de El Peñón, Santander - Proyecto Colombia BIO, EOD – eBird Observation Dataset)",
 "Geometry POLYGON((-73.83936 5.95981,-73.7864 5.9595,-73.7436 6.10298,-73.82027 6.10667,-73.83936 5.95981))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1580 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001976-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2280gb5n4
title: A report for the ontogeny of schooling behavior in homo- and heterogeneous tadpole groups

description: To compare the ontogeny of schooling behavior between homo- and
 heterogeneous tadpole groups of the Japanese mountain frog (Rana
 ornativentris), I measured the schooling behavior of a pure group
 consisting only of siblings and a mixed group consisting of siblings and
 non-siblings weekly for 5 weeks. The mean individual and nearest-neighbor
 distances decreased with increasing ontogeny up to hindlimb development.
 However, there were no significant differences in mean distances between
 the pure and mixed tadpole groups. The heterogeneity prepared in this
 study did not affect the schooling behavior of this species.
DOI: 10.60521/332635
title: Dive Documentation acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with an Ocean Exploration Trust Hercules Event Logger on ROV Hercules during E/V Nautilus expedition NA163 conducted in 2024. These data files are of Text File (ASCII) format and include Documentation. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60521/332636
title: Dive Documentation acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with an Ocean Exploration Trust Hercules Event Logger on ROV Hercules during E/V Nautilus expedition NA163 conducted in 2024. These data files are of PDF format and include Documentation. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.5061/dryad.2jm63xsjh
title: Data from: Do benefits of seed dispersal and caching by scatterhoarders outweigh the costs of predation? An example with oaks and yellow-necked mice

description: Numerous interactions between plants and animals vary in their outcome
 between antagonism and mutualism. Interactions between plants and
 scatterhoarding animals provide a prime example of this phenomenon.
 Scatterhoarders consume large quantities of seeds (potentially reducing
 plant establishment), yet also disperse seeds and bury them in shallow
 caches (potentially improving recruitment). Despite intense work on
 mechanisms that cause these interactions to shift along an
 antagonism-mutualism continuum, it remains difficult to quantify their
 final outcomes. We demonstrate how readily available field data can be
 used to reach this goal, with interactions between rodents and two oaks
 species (sessile oak Quercus petraea, and red oak Q. rubra) as an
 empirical example. Our approach consists of quantifying the net outcome of
 the interaction through collecting data on different vital rates (e.g.
 probability that cached seeds survive to germination, probability of
 seedling recruitment with and without rodents; near and far from
 conspecific trees; with and without seed pilferage) and assembling them in
 a simple mathematical model. We found that during the period of the study,
 interactions between scatterhoarding rodents and both focal oaks were
 antagonistic. Even though caching increased the likelihood of seedling
 establishment, this effect was not strong enough to compensate for the
 costs of seed predation. Furthermore, there was no evidence that the
 short-distance transportation that is usually provided by small mammals
 benefited early oak recruitment. Synthesis. Our empirical results
 demonstrated that certain common assumptions -- that caching by rodents
 invariably benefits plant recruitment; that improved seedling
 establishment after seed burial is sufficient to make plant-scatterhoarder
 interactions mutualistic; that transportation away from maternal plants is
 highly beneficial -- do not always hold and should be tested rather than
 taken for granted.
description: site - study site species - native (Quercus
 petraea) and invasive (Q. rubra) burial - buried (seeds
 sowed in the topsoil), surface - (seeds sown on litter surface)
 access - open (rodent access allowed),closed (rodent access
 excluded) seedlings - number of seedlings
 established distance - distance from the mother
 tree set - set number tree - tree
 number
DOI: 10.60521/332637
title: Processed Google Earth Visualization Data acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Navigation System on ROV Hercules during E/V Nautilus expedition NA163 conducted in 2024. These data files are of Google Earth (KML/KMZ) format and include Google Earth Visualization data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.5061/dryad.jh9w0vt6m
title: Tyrosine phosphorylation levels in primary human myometrial cells

description: Context. Preterm birth is one of the most common complications during
 human pregnancy and labor, and associated with a dramatic switch within
 the uterus from quiescence to contractility. However, the mechanisms
 underlying uterine remodeling are largely unknown. Objective. To define
 the roles of src-homology phosphatase type-1 (SHP-1, PTPN6) in regulating
 the phosphorylation of proteins involved in the uterine smooth muscle cell
 functions. Design and Setting. Human myometrial tissues, primary uterine
 smooth muscle cells, and myometrium-specific Ptpn6-KO mice were used to
 study SHP-1 regulation of uterine remodeling and labor. Patients. Patients
 who underwent elective cesarean section (n=20) and emergency cesarean
 section at term (37-42 wks, n=20) were recruited with no evidence of
 underlying diseases. Results. We found that SHP-1 was significantly
 decreased in human myometrium in labor compared with that not in labor.
 Timed-pregnant mice injected intraperitoneally with the specific SHP-1
 inhibitor, PTPI-1, or those with a myometrium-specific Ptpn6-KO manifested
 significantly preterm labor, with enriched plasmalemmal dense plaques
 between myometrial cells and increased phosphorylation at Tyr397 and
 Tyr576/577 sites of focal adhesion kinase (FAK), which remained to the
 time of labor. Knockdown of SHP-1 dramatically increased the spontaneous
 contraction of HUSMCs, which was reversed by co-infection of a
 FAK-knockdown lentivirus. PGF2a could downregulate SHP-1 via PI3K-NF-kB
 pathway. Conclusions. SHP-1 plays important roles in uterine remodeling
 and plasticity by activating focal adhesion pathway. The aberrant decrease
 of SHP-1 may be one of the reasons for spontaneous preterm labor, and
 interventions for modulation of SHP-1 provide a potential strategy for
 preventing preterm birth.
DOI: 10.5061/dryad.cfxpnvx25
title: Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses

description: Our knowledge of the diversity and frequency of genomic structural
 variation segregating in populations of large double stranded (ds) DNA
 viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV)
 purified from beet armyworm (Spodoptera exigua) larvae at depths
 &gt;195,000X using both short-read (Illumina) and long-read (PacBio)
 technologies. Using a pipeline relying on hierarchical clustering of
 structural variants (SVs) detected in individual short- and long-reads by
 six variant callers, we identified a total of 1,141 SVs in AcMNPV,
 including 464 deletions, 443 inversions, 160 duplications and 74
 insertions. These variants are considered robust and unlikely to result
 from technical artifacts because they were independently detected in at
 least three long reads as well as at least three short reads. SVs are
 distributed along the entire AcMNPV genome and may involve large genomic
 regions (30,496 bp on average). We show that no less than 39.9% of genomes
 carry at least one SV in AcMNPV populations, that the vast majority of SVs
 (75%) segregate at very low frequency (&lt;0.01%) and that very few
 SVs persist after 10 replication cycles, consistent with a negative impact
 of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we
 then show that populations of two iridoviruses and one herpesvirus are
 also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4
 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify
 1,757 transposable elements (TEs) insertions, 895 of which are truncated
 and occur at one extremity of the reads. This further supports the role of
 baculoviruses as possible vectors of horizontal transfer of TEs.
 Altogether, we found that SVs, which evolve mostly under rapid dynamics of
 gain and loss in viral populations, represent an important feature in the
 biology of large dsDNA viruses.
description: The supplementary materials include the R script used to perform
 the hierarchical clustering of structural variants detected by six
 variants callers, Figures S1 - S17, Tables S1 - S6, the assembly of
 AcMNPV, IIV6, IIV31 and HCMV genomes as well as there associated gff
 annoation files. The supplementary tables contain
 information on the genomic structural variants we have detected in
 populations of four large double stranded DNA viruses: the baculovirus
 AcMNPV, the iridoviruses IIV6 and IIV31 and the herpesvirus HCMV. The
 tables are provided in .xlsx format and can be open in Excel.
DOI: 10.5061/dryad.ngf1vhhpx
title: An unbiased molecular approach using 3’UTRs resolves the avian family-level tree of life

description: Presumably, due to a rapid early diversification, major parts of the
 higher-level phylogeny of birds are still resolved controversially in
 different analyses or are considered unresolvable. To address this
 problem, we produced an avian tree of life, which includes molecular
 sequences of one or several species of ∼ 90% of the currently recognized
 family-level taxa (429 species, 379 genera) including all 106 for the
 non-passerines and 115 for the passerines (Passeriformes). The
 unconstrained analyses of noncoding 3-prime untranslated region (3’UTR)
 sequences and those of coding sequences yielded different trees. In
 contrast to the coding sequences, the 3’UTR sequences resulted in a
 well-resolved and stable tree topology. The 3’UTR contained, unexpectedly,
 transcription factor binding motifs that were specific for different
 higher-level taxa. In this tree, grebes and flamingos are the sister clade
 of all other Neoaves, which are subdivided into five major clades. All
 non-passerine taxa were placed with robust statistical support including
 the long-time enigmatic hoatzin (Opisthocomiformes), which was found being
 the sister taxon of the Caprimulgiformes. The comparatively late radiation
 of family-level clades of the songbirds (oscine Passeriformes) contrasts
 with the attenuated diversification of non-passeriform taxa since the
 early Miocene. This correlates with the evolution of vocal production
 learning, an important speciation factor, which is ancestral for songbirds
 and evolved convergent only in hummingbirds and parrots. Since 3’UTR-based
 phylotranscriptomics resolved the avian family-level tree of life, we
 suggest that this procedure will also resolve the all-species avian tree
 of life