cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26301/taz6-n215
title: Ayutthaya - Wat Phra Si Sanphet

description: The CyArk field mission to Ayutthaya took place in June 2017. The archaeological complex of Wat Phra Si Sanphet, the focus of the expedition, was impacted during a major flood event in 2011.The primary purpose of the trip was to assist UNESCO and the Fine Arts Department (FAD) of Thailand in mapping the site and providing detailed documentation surrounding the subsidence of the monuments. The documentation was conducted utilizing LiDAR and both aerial and terrestrial photogrammetry. Our work was supported through a generous grant from Seagate.
description: Founded in 1350 C.E., Ayutthaya was the Siamese capital of Thailand until the 18th century. Ayutthaya developed into a booming city starting in 1378 C.E., surpassing the old capital of Sukhothai. King Ramathibodi declared Ayutthaya the new capital and it was named after a magical kingdom from the Ramakien, an epic story about Thailand. The city was attacked and burned to the ground in 1767 C.E. by the Burmese army. The only remaining buildings in Ayutthaya are of stone, as the wood structure burned to the ground in 1767 C.E. After the destruction of Ayutthaya, the capital was moved to Bangkok and there was an effort to recreate the urban template and architecture of Ayutthaya. In Thai, the official name of Bangkok retains Ayutthaya as part of the formal name.
description: Photogrammetry - Aerial, LiDAR - Terrestrial, Photogrammetry - Terrestrial
DOI: 10.5061/dryad.zpc866tj7
title: If the tape were played again: Lineage evolution and the causes of phylogenetic similarity in two tropical assemblages of Coleoptera

description: Communities of insects around the world consist of unique sets of species
 that have evolved under different historical processes of assembly and
 lineage diversification. Whole-community phylogenetics can partition the
 shared and uniquely derived evolutionary history at sites. We used
 mitochondrial genome sequences of &gt;1000 species each from two
 assemblages of Coleoptera (beetles) in distantly situated tropical lowland
 rainforest of Malaysia and Panama for phylogenetic reconstruction and
 community ecological analysis. Assemblages were entirely distinct at
 species level but were surprisingly similar at family level in their
 overall composition and relative species richness, despite a high degree
 of phylogenetic clustering that implied independent evolution. Inclusion
 of species poor lineages reduced the level of community clustering in
 parallel in both sites, indicating lineage-specific factors to determine
 species richness and their effect on local community composition. In
 conclusion, relative species richness in local community composition and
 global clade sizes are connected, in part due to biotic exchange in deep
 time, but more likely because of intrinsic rates of diversification unique
 to each clade (family), thus making assembly composition more predictable,
 i.e. the ‘evolutionary tape’ would be similar wherever a new assemblage of
 tropical-forest Coleoptera arises.
description: # If the tape were played again: Lineage evolution and the causes of
 phylogenetic similarity in two tropical assemblages of Coleoptera
 [https://doi.org/10.5061/dryad.zpc866tj7](https://doi.org/10.5061/dryad.zpc866tj7) ## Description of the data and file structure Mitochondrial genome data were generated to assess the diversity and phylogeny of Coleoptera from tropical sites in Panama and Malaysian Borneo. Beetle specimens were collected using standardized trapping methods across 1-hectare plots at each location. From each morphospecies identified, genomic DNA was extracted and mitogenomes were retrieved through genome skimming. The mitogenomes were then assembled, annotated, and aligned for 13 protein-coding genes. To increase taxonomic and geographic diversity in phylogenetic analyses, additional mitochondrial genomes from GenBank were included, with one representative per genus selected. ### Files and variables #### File: alignment.nex **Description:** A NEXUS format file containing aligned mitogenome sequences for all taxa in the study, including both GenBank-derived and newly assembled sequences. ## Code/software Associated scripts to recreate all analyses in the manuscript are available at: [https://github.com/FLCarpenter/BorneoPanama](https://github.com/FLCarpenter/BorneoPanama).
DOI: 10.5061/dryad.sqv9s4nd0
title: Code from: Testing for normality in regression models: mistakes abound (but may not matter)

description: This study examines the misuse of normality tests in linear regression
 within ecology and biology, focusing on common misconceptions. A
 bibliometric review found that over 70% of ecology papers and 90% of
 biology papers incorrectly applied normality tests to raw data instead of
 model residuals. To assess the impact of this error, we simulated datasets
 with normal, interval, and skewed distributions across various sample and
 effect sizes. We compared statistical power between two approaches:
 testing the whole dataset for normality (incorrect) versus testing model
 residuals (correct) to determine whether to use a parametric (t-test) or
 nonparametric (Mann-Whitney U test) method. Our results showed minimal
 differences in statistical power between the approaches, even when
 normality was incorrectly tested on raw data. However, when residuals
 violated the normality assumption, using the Mann-Whitney U test increased
 statistical power by 3–4%. Overall, the study suggests that, while
 correctly testing residuals for normality enhances model performance, the
 impact of testing raw data is negligible in terms of power loss,
 especially with large sample sizes. The findings highlight the need for
 more awareness around proper statistical practices, especially in
 evaluating the assumptions of linear models.
description: # Code for Normality Test Study
 [https://doi.org/10.5061/dryad.sqv9s4nd0](https://doi.org/10.5061/dryad.sqv9s4nd0) ## Description of the data and file structure The data files include those required to reproduce the analysis in "It’s OK Not to be Normal: Usage of Normality Tests in Linear Models" by S.R. Midway and J.W. White. ### Files and variables #### File: Normality\_Code.zip **Description:** Unzips to 5 files. "interval_sims.R", "lognormal_sims.R", and "normal_sims.R" are all R scripts that generate the data used in the study, each based on their respective distribution. "normality_comp.R" is an R script to reproduce the comparison of different tests of normality. "workflows_power.R" is an R script that reproduces the 3 analytical decisions in the manuscript. ## Code/software All code is included in the attached files. All code are R scripts that can be run through the free software R, with the associated libraries that are specified in the scripts.  ## Access information Other publicly accessible locations of the data: * None. Data was derived from the following sources: * All data is simulated.
DOI: 10.5061/dryad.wpzgmsbz6
title: Data from: Reduced soil moisture drives leaf anatomical shifts more than chronically elevated temperatures in European temperate trees

description: Chronic reductions in soil moisture combined with high air temperatures
 can modify tree carbon and water relations. However, little is known about
 how trees acclimate their foliar structure to the individual and combined
 effects of these two climatic drivers. We used open-top chambers
 to determine the multi-year effects of chronic air warming (+5 °C) and
 soil moisture reduction (-50 %) alone and in combination on the foliar
 anatomy of two European tree species. We further investigated how these
 climatic drivers affected the relationship between foliar anatomy and
 physiology/chemistry in young downy oak and European beech
 trees. After four years, reduced soil moisture led to the
 development of thinner leaves with narrower epidermis and lower gas
 exchange for oak and beech but to a lesser extent for the latter. In
 contrast, prolonged warming did not affect the anatomical and
 physiological/chemical traits in either species. Warming also did not
 exacerbate the impacts of dry soils, highlighting soil moisture as the key
 driver in leaf anatomical shifts. While soil moisture altered oak
 foliar anatomy, and physiology and chemistry of both species, our work
 revealed a limited acclimation potential towards more drought- and
 heat-tolerant leaves as conditions get drier and warmer, suggesting
 potentially high vulnerability of both species to future climate.
description: # Reduced soil moisture drives leaf anatomical shifts more than
 chronically elevated temperatures in European temperate trees
 [https://doi.org/10.5061/dryad.wpzgmsbz6](https://doi.org/10.5061/dryad.wpzgmsbz6) ## Description of the data and file structure ### Files and variables The dataset consists of two files namely: Dryard_Data_PlantBio_MargauxDidionGency and Dryard_README_PlantBio_MargauxDidionGency (contains description of variables with their corresponding units) We used open-top chambers to assess the effects of chronic air warming (+5 °C) and soil moisture reduction (-50%) on the foliar anatomy of two European tree species over multiple years. After four years, reduced soil moisture resulted in thinner leaves with narrower epidermis and lower gas exchange in both oak and beech, though the effect was less pronounced in beech. Warming did not affect leaf anatomy or physiology/chemistry, nor did it amplify the impact of reduced soil moisture, emphasizing soil moisture as the primary driver of leaf changes. Our findings show limited acclimation potential for both species, suggesting they may be highly vulnerable to future climate changes.
DOI: 10.5061/dryad.v6wwpzh5g
title: Data from: Molecular discovery of filarial nematode DNA in an endangered wild pinniped

description: Rapidly changing environments are contributing to the spread of non-native
 species and their associated pathogens into new and vulnerable ecosystems,
 such as the Galapagos archipelago. These pathogens represent a significant
 threat to emblematic species. The Galapagos sea lion (Zalophus wollebaeki)
 (GSL) is an endangered and endemic pinniped that is increasingly at risk
 of acquiring infectious diseases due to interactions with introduced
 companion animals. Previously, we reported the first detection of antigens
 from Dirofilaria immitis, the parasite that causes canine heartworm
 disease, in the GSL. To investigate further, we developed a multifilarial
 PCR assay and successfully detected DNA from D. immitis and the closely
 related D. repens in 10.7% of our sample cohort of juvenile GSLs. This
 assay, based on a conserved region in the filarial 28S gene, can be used
 in conjunction with restriction endonuclease digestion or Sanger
 sequencing to identify the species of the causative nematode. Our method
 proved effective without nonspecific amplification in a wide host range,
 and highly sensitive, detecting as little as one parasite. Further, this
 assay can be used in cases of immature, low-worm burden, or all male
 infections. Our molecular approach offers a sensitive and specific method
 for detecting filarial parasites in wild animals. Further investigations
 are necessary to confirm the pathology of filarial nematodes in the GSL
 and their prevalence in the general population. Our identification of
 Dirofilarial species in the GSL underscores the urgent need for measures
 to manage the risk of pathogen transmission from introduced species to
 native wildlife.
description: The published data set includes the metadata for 28 juvenile
 Galapagos sea lions sampled in May 2022. The supplemental appendices are
 also included. 
description: # Molecular Discovery of Filarial Nematode DNA in an Endangered Wild
 Pinniped
 [https://doi.org/10.5061/dryad.v6wwpzh5g](https://doi.org/10.5061/dryad.v6wwpzh5g) ## Description of the data and file structure Repository for the purposes of storing and sharing all data and resources pertinent to the Galapagos sea lion study. Twenty-eight juvenile Galapagos sea lions were sampled in May of 2022 by our collaborative team of researchers from the NCSU CVM, USFQ, the Galapagos National Parks, and the Galapagos Science Center. Sample collections are detailed in the associated manuscript.  The metadata file includes the * Sample ID - date collected * sex - approximate age * heart rate (beats per minute) - respiratory rate (breaths per minute), and results * of the multifilarial PCR test for each sea lion assessed
DOI: 10.15468/dl.8qkdp5
title: Occurrence Download

description: A dataset containing 23915 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Dominican Republic",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (VU, EN, CR)",
 "OccurrenceStatus is Present",
 "Year 2010-2026"
 ]
}

 The dataset includes 23915 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004183-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n63k6p
title: Occurrence Download

description: A dataset containing 920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudophycis bachus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 920 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004184-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zgmsbccnm
title: Molecular mechanism of SNHG11 in human osteosarcoma cells

description: Osteosarcoma ( OS ) is a malignant bone tumor of mesenchymal origin, which
 is common in children and adolescents.  LncRNA SNHG11 plays an
 important regulatory role in a variety of cancers and plays a key role in
 the migration, invasion, proliferation of a variety of cancer cells. At
 present, there is no report on the function and regulatory mechanism of
 lncRNA SNHG11 in osteosarcoma.We found Overexpression of SNHG11 inhibited
 the proliferation of in human osteosarcoma U2OS cells and promoted
 apoptosis.Overexpression of SNHG11 in U2OS cells resulted in significant
 differential expression of 344 genes, including 82 up-regulated genes and
 262 down regulated genes.The upregulated differentially expressed genes
 were not enriched in relevant biological processes on GO-P, among which
 HMGCS2 and IL24 deserve attention.Downregulated genes are enriched in GO-P
 for cell adhesion and migration, among which KRT17, CXCL14, TRIB2, COL5A1,
 CCL24, SOX2, and COL6A3 are worth paying attention to.  SNHG11
 may interact with KRT6 B, SERPINB12 and DCD proteins to regulate
 downstream targets. ChIRP-seq ( RNA ) sequencing revealed that SNHG11
 specifically binds to EEF2, RPS4X, and ACTG1. ChIRP-seq ( DNA ) sequencing
 showed that SNHG11 gene was mainly enriched in biological processes such
 as negative regulation of apoptosis process  in GO-P. Integrated
 analysis of ChIRP-seq ( RNA ) revealed 32 overlapping genes, and SNHG11
 may participate in the progression of osteosarcoma by binding to DCD and
 regulating these 32 target genes.  Integrated analysis of
 ChIRP-seq ( DNA ) revealed 16 overlapping genes. Combined with the results
 of protein profiling, it is speculated that SNHG11 may be involved in the
 progression of osteosarcoma by binding SERPINB12 and regulating the
 transcription.LncRNA SNHG11 plays a key role in the development of
 osteosarcoma by affecting cell information carrier molecules at three
 levels of DNA, RNA and protein.
description: # Molecular mechanism of SNHG11 in human osteosarcoma cells
 [https://doi.org/10.5061/dryad.zgmsbccnm](https://doi.org/10.5061/dryad.zgmsbccnm) ## Description of the data and file structure This project aims to detect the effect of overexpression of lncRNA SNHG11 on the proliferation and apoptosis of U2OS cells in human osteosarcoma cells. And high-throughput transcriptome sequencing was used to obtain RNA seq and ChIRP seq data affected by SNHG11. Combined with bioinformatics analysis methods, the interacting proteins, RNA, and DNA targets of SNHG11 in U2OS cells were analyzed. ## Code/software Due to the possibility of errors during data transmission, in order to ensure that the data you downloaded is intact and undamaged, it is necessary to use md5 software to verify whether the md5 value of the file you received is consistent with the md5sum.exe we sent. Inconsistencies indicate errors in data transmission. Data needs to be downloaded again.
DOI: 10.5061/dryad.jwstqjqkp
title: Non-adapted bacterial infection suppresses plant reproduction

description: Environmental stressors, including pathogens, substantially
 affect the growth of host plants. However, how non-adapted
 bacteria influence nonhost plants has not been
 reported. Here, we reveal that infection of Arabidopsis
 flowers by Xanthomonas oryzae pv.
 oryzae PXO99A, a bacterial pathogen causing rice blight disease,
 suppresses ovule initiation and reduces seed number without causing
 visible disease symptoms. TleB, secreted by the type VI secretion system
 (T6SS), interacts with plant E3 ligase PUB14,
 and disrupts the function of the PUB14-BZR1 module,
 leading to decreased ovule initiation and seed yield. In the other site,
 PUB14 concurrently promotes TleB’s degradation. Our
 findings indicate that bacterial infections in nonhost plants directly
 repress offspring production. The regulatory mechanism by
 effectors-PUB14-BZR1 is widely present, suggesting that plants may
 balance reproduction and
 defense and produce fewer offspring to conserve
 resources, thus enabling them to remain in a standby mode prepared for
 enhanced resistance.
description: This dataset primarily contains the raw data for the genomics and
 structural predictions in the article.
description: 1.Name:AlphaFoldPredictions_rawpdbs.zip Description:AlphaFold2-predicted
 protein structure files Number of pdb files:11 pdb files list:
 AtPUB14-BZR1-TleB(DC3000).pdb BnPUB14-BnBZR1-TleB.pdb
 OsPUB12-OsBZR1-TleB(PXO99A).pdb OsPUB12-OsBZR1-TleB.pdb
 PhPUB14-PhBZR1-TleB.pdb PUB14&BZR1&TleB.pdb PUB14&BZR1.pdb
 PUB14&TleB.pdb SlPUB14-SlBZR1-TleB.pdb TaPUB14-TaBZR1-TleB.pdb
 ZmPUB14-ZmBZR1-TleB.pdb 2.Name:RNA-seq_Col_PUB14_CRISPR__UBQ10-PUB14.zip
 Description:The raw data for the RNA-seqs. The transcriptome contains 3
 groups, Col(WT), PUB14_CRISPR(PUB14_crispr), and UBQ10-PUB14(PUB14_OE1).
 Raw data expression of 18 samples: PUB14_crispr_1_1.fq.gz
 PUB14_crispr_1_2.fq.gz PUB14_crispr_2_1.fq.gz PUB14_crispr_2_2.fq.gz
 PUB14_crispr_3_1.fq.gz PUB14_crispr_3_2.fq.gz PUB14_OE1_1_1.fq.gz
 PUB14_OE1_1_2.fq.gz PUB14_OE1_2_1.fq.gz PUB14_OE1_2_2.fq.gz
 PUB14_OE1_3_1.fq.gz PUB14_OE1_3_2.fq.gz WT_1_1.fq.gz WT_1_2.fq.gz
 WT_2_1.fq.gz WT_2_2.fq.gz WT_3_1.fq.gz WT_3_2.fq.gz
 3.Name:Metagenomic_sequencing_Krona_analysis.zip Description:The raw data
 for the Krona analysis Raw data of 2 samples: S2_1.fq.gz S2_2.fq.gz
 4.Name:RNA-seq_MgCl2_PXO99A_PXO99ATleAandTleB.zip Description:The raw data
 for the RNA-seqs. The transcriptome contains 3 groups, MgCl2(control),
 PXO(PXO99A), and P3234(PXO99ATleAandTleB). Raw data expression of 18
 samples: MgCl2_1.R1.fq.gz MgCl2_1.R2.fq.gz MgCl2_2.R1.fq.gz
 MgCl2_2.R2.fq.gz MgCl2_3.R1.fq.gz MgCl2_3.R2.fq.gz PXO_1.R1.fq.gz
 PXO_1.R2.fq.gz PXO_2.R1.fq.gz PXO_2.R2.fq.gz PXO_3.R1.fq.gz PXO_3.R2.fq.gz
 P3234_1.R1.fq.gz P3234_1.R2.fq.gz P3234_2.R1.fq.gz P3234_2.R2.fq.gz
 P3234_3.R1.fq.gz P3234_3.R2.fq.gz
DOI: 10.5061/dryad.rxwdbrvkd
title: Data from: Multiomics inform invasion risks under global climate change

description: Global climate change is exacerbating biological invasions; however, the
 roles of genomic and epigenomic variations and their interactions in
 future climate adaptation remain underexplored. Using the model invasive
 ascidian Botryllus schlosseri across the Northern Hemisphere, we
 investigated genomic and epigenomic responses to future climates and
 developed a framework to assess future invasion risks. We employed
 generalized dissimilarity modeling and gradient forest analyses to assess
 genomic and epigenomic offsets under climate change. Our results showed
 that populations with genomic maladaptation did not geographically overlap
 with those experiencing epigenomic maladaptation, suggesting that genomic
 and epigenomic variations play complementary roles in adaptation to future
 climate conditions. By integrating genomic and epigenomic offsets into the
 genome-epigenomic index, we predicted that populations with lower index
 values were less maladapted, indicating a higher risk of future invasions.
 Native populations exhibited lower offsets than invasive populations,
 suggesting greater adaptive potentials and higher invasion risks under
 future climate change scenarios. These results highlight the importance of
 incorporating multiomics data into predictive models to study future
 climate (mal)adaptation and assess invasion risks under global climate
 change.
description: # Multiomics inform invasion risks under global climate change
 [https://doi.org/10.5061/dryad.rxwdbrvkd](https://doi.org/10.5061/dryad.rxwdbrvkd) ## Description of the data and file structure The table provides comprehensive information on all sampling sites for Botryllus schlosseri. The initial two columns delineate the full names of the sampling sites and the respective countries where they are situated. The "Code" column signifies the unique identifier for each sampling site, while "Latitude" and "Longitude" columns denote the geographical coordinates of these sites. Lastly, "N" indicates the total number of samples collected at each respective sampling location. ### Files and variables File: sampling_site_infromation.csv **Description:**  ##### Variables * Sampling site: * Country: * Code: * Latitude: * Longitude: * N: ## Code/software 1\. R_script for \_Genomic offset.txt: This script used for computing genomic offset (go) using the Generalised Dissimilarity Modelling (GDM) and Gradient Forest (GF) 2\. R_script for \_Epigenomic offset.txt: This script used for computing epigenomic offset (eo) using the Generalised Dissimilarity Modelling (GDM) and Gradient Forest (GF) 3\. R_script for \_Genomic-epigenomic index.txt: This script shows how to calculate the genome-epigenomic index (gei) using the Generalised Dissimilarity Modelling (GDM) and Gradient Forest (GF)