cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16910824
title: Untargeted metabolomic profile of leaves in a transplant experiment of hyperaccumulating Noccaea praecox
DOI: 10.5281/zenodo.16910823
title: Untargeted metabolomic profile of leaves in a transplant experiment of hyperaccumulating Noccaea praecox
DOI: 10.13012/b2idb-4015036_v1
title: Data for Field-Effect Transistors from Artificial Charged Domain Walls in Stacked van der Waals Ferroelectric α-In2Se3

description: <b>Note:</b> This dataset has been updated. Please visit V2 instead: https://doi.org/10.13012/B2IDB-4015036_V2

Room-temperature transfer curves; Benchmarking conductance; STEM images of charged domain walls; Temperature-dependent transfer curves; Scaling of conductance, hopping length, threshold voltage, trap density, and field-effect mobility with temperature; Magnetotransport data; Optical, AFM, and PFM image of different field-effect transistors; STEM images of contacts; Output and transfer curves of FETs; Temperature scaling of subthreshold swing and threshold voltage difference; Comparison of maximum field-effect mobility for different structures;
DOI: 10.5061/dryad.sj3tx96fs
title: Range-wide climate risk and adaptive potential in a cold-water fish species (Part 1/2)

description: Predicting extinction risk from climate change requires understanding
 adaptive variation and local adaptation across species’ ranges. We combine
 experimental and -omics approaches with climate change modeling to
 identify molecular mechanisms of local adaptation to heat stress in brook
 trout, a coldwater species experiencing extirpations due to warming
 temperatures. We identify genomic variation corresponding with thermal
 conditions across the native range, suggesting local adaptation, and
 experimentally identify variants linked with gene expression responses to
 thermal stress. Using climate projections, we find that southern brook
 trout populations are the most vulnerable to extirpation from climate
 warming and mid-range populations are the most promising candidates for
 receiving assisted gene flow to improve climate resilience. Together, this
 work highlights the importance of genomic information in managing
 populations threatened by climate change. This is Part 1 of the full
 dataset, containing the RADseq dataset.
description: # Range-wide climate risk and adaptive potential in a cold-water fish
 species (Part 1/2)
 [https://doi.org/10.5061/dryad.sj3tx96fs](https://doi.org/10.5061/dryad.sj3tx96fs) This is one of two datasets related to the same study: * Part 1 (this dataset) contains all the RADseq data, [https://doi.org/10.5061/dryad.sj3tx96fs](https://doi.org/10.5061/dryad.sj3tx96fs) * Part 2 contains all of the RNAseq data, [https://doi.org/10.5061/dryad.nk98sf84m](https://doi.org/10.5061/dryad.nk98sf84m) ## Description of the data and file structure The code and RADseq data associated with Meek et al. Nature Communications 2025 manuscript. RADseq data are contained in: * 7116_9173_35601_HG23CBGXY_all_R1.fastq.gz 31.04 GB - Forward reads Plate 1 * 7116_9173_35601_HG23CBGXY_all_R2.fastq.gz 29.34 GB - Reverse reads Plate 1 * 7117_9173_35602_HL2K7BGXY_BT_2_R1.fastq.gz 21.87 GB - Forward reads Plate 2 * 7117_9173_35602_HL2K7BGXY_BT_2_R2.fastq.gz 22.13 GB - Reverse reads Plate 2 ### Files and variables **Description:** All RADseq data generated on individuals used in the brook trout common garden experiment in Meek et al. Nature Communications 2025. File: RADseq_Brook_Trout_Barcode_Information.csv Metadata for samples: "RADseq Brook Trout Barcode Information" Column descriptions: | Variable | Description | | :--------------------- | :----------------------------- | | Library Index | NEBNext Library index used | | Library Index Sequence | Library index genetic sequence | | Individual Index | Individual barcode sequence | | Plate ID | Name of 96 well plate | | DNA well | Well in 96 well plate | | SampleID | Individual sample ID | | Date sampled | Date of individual sampling | | Location | Tank number individual was in | blank cells = NA ## Code/software "BrookTroutCommonGardenExperimentScripts.zip" contains the scripts to process the RNAseq data and do the eQTL analysis for the common garden experiment as described in Meek et al. Nature Communications 2025.
DOI: 10.5061/dryad.j3tx95xrv
title: Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created

description: In-context promoter bashing via genome editing is a route to identify and
 characterize critical regulatory regions that govern expression of genes
 of interest. The outcomes of in-context promoter bashing can be used to
 inform editing strategies to modulate the expression of selected gene
 models in a desired fashion. Here we employed in-context promoter bashing
 to characterize the proximal upstream regulatory regions of sorghum genes
 encoding phosphoenolpyruvate carboxykinase (Sb.PEPCK.BS,
 SbiTx430.01G455400) and alanine aminotransferase (SbiTx430.02G006600,
 SbAlaAT.BS), two proteins involved in the PCK C4 pathway. Characterized
 germinal edits within the targeted regions upstream of these two genes
 ranged in size from 138 bp up to 1790 bp. A 138 bp within the Sb.PEPCK.BS
 upstream region and a 1643 bp element within the Sb.AlaAT.BS upstream
 region were determined to be important for maintenance of transcription
 levels. No change in development or various physiological parameters was
 observed in characterized lineages carrying promoter edits. However,
 significant changes in seed reserves and a reduction in 100 seed weight
 were consistently observed, under both greenhouse and field environments,
 in plants carrying an edit in the promoter of Sb.PEPCK.BS gene were
 significantly reduced in transcript accumulation for this gene.
description: # Supplementary table, figures and DNA sequences of sorghum gene models
 SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and
 indels created
 [https://doi.org/10.5061/dryad.j3tx95xrv](https://doi.org/10.5061/dryad.j3tx95xrv) ## Description of the data and file structure DNA sequence of edited sorghum gene models*Sb*.PEPCK.BS, SbiTx430.01G455400 & *Sb*AlaAT.BS SbiTx430.02G006600 Supplementary dataset document contains the supplemental Tables and Figures described in the manuscript.   ### Files and variables #### File: Crop\_Sci\_DNA.zip \**Description:***DNA sequences of sorghum gene models SbPEPCK.BS and Sb.AlaAT.BS with features highlighting edits created and various reagents used in the study (primers, gRNAs)* ## Code/software none ## Access information Data was derived from the following sources: * The DNA sequece files are comprerssed/ SnapGene format (v 8.0.2). Supplementary dataset file is in MS word format (v.16.95).
DOI: 10.5061/dryad.6hdr7srbm
title: Data for: Genomic insights into inbreeding and adaptive divergence of trout populations to inform genetic rescue

description: Genetic rescue, specifically translocation to facilitate gene flow among
 populations and reduce the effects of inbreeding, is an increasingly used
 approach in conservation. However, this approach comes with tradeoffs,
 wherein gene flow may reduce fitness when populations have adaptive
 differentiation (i.e., outbreeding depression). A better understanding of
 the interaction between isolation, inbreeding, and adaptive divergence in
 key traits, such as life history traits, will help to inform genetic
 rescue efforts. Stream dwelling salmonids, such as the westslope cutthroat
 trout (Oncorhynchus lewisi;WCT), are well-suited for examining these
 tradeoffs because they are increasingly isolated by habitat degradation,
 exhibit substantial variation in life history traits among populations,
 and include many species of conservation concern. However, few genomic
 studies have examined the potential tradeoffs in inbreeding versus
 outbreeding depression in salmonids. We used &gt;150,000 SNPs to
 examine genomic variation and inbreeding coefficients in 565 individuals
 across 25 WCT populations that differed in their isolation status and
 demographic histories. Analyses of runs of homozygosity revealed that
 several isolated WCT populations had ‘flatlined’, having extremely low
 genetic variation and high inbreeding coefficients. Additionally, we
 conducted genome scans to identify potential outlier loci that could
 explain life-history differences among ten isolated populations. Genome
 scans identified one candidate genomic region that influenced maximum
 length and age-1 to age-2 growth. However, the limited number of candidate
 loci suggests that the life history traits examined may be driven by many
 genes of small effect or phenotypic plasticity. Although adaptive
 differentiation should be considered, the high inbreeding coefficients in
 several populations suggest that genetic rescue may benefit the most
 genetically depauperate WCT populations.
description: Methods for data collection and processing are provided in the
 manuscript: Genomic insights into inbreeding and adaptive divergence of
 trout populations to inform genetic rescue.
description: # Data for Genomic insights into inbreeding and adaptive divergence of
 trout populations to inform genetic rescue
 [https://doi.org/10.5061/dryad.6hdr7srbm](https://doi.org/10.5061/dryad.6hdr7srbm) ## Description of the data and file structure Genetic samples of westslope cutthroat trout were collected during random sampling of 25 populations. Genotypes were generated using BestRAD protocol.  #### File: belletal\_genotypes.txt **Description:** Sample_id provides unique IDs for all individuals used in the final analyses. The remaining columns are 0, 1, 2 format genotypes with column names corresponding to the position on a rainbow trout reference genome (NCBI OmykA_1.1).
DOI: 10.15468/dl.72jfcn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Breizacanthus golvani",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004274-260126135527185/datasets/export for details.
DOI: 10.25934/pr00011350
title: Modified Multiplier Simple Endoscopic Score for Crohn's Disease (MM-SES-CD) Thresholds as Predictors of Delayed Clinical Response to Upadacitinib in Patients with Crohn’s Disease

description: Crohn’s disease (CD) is a long-term condition that causes inflammation in the digestive system, leading to symptoms such as severe stomach pain, diarrhea, weight loss, and fatigue. It is a chronic illness, meaning it persists over time and can affect a person's quality of life. Many people with CD are treated with medications such as corticosteroids, immune system-modulating drugs, or biologics.

Corticosteroids are a class of synthetic hormones that mimic natural hormones produced by the body and are widely used to reduce inflammation.
Immune system-modulating drugs alter the way the immune system works, either enhancing or suppressing its activity to control inflammation.
Biologics are a type of medication made from living organisms or their components (like proteins) and are designed to target specific parts of the immune system involved in inflammation.

These medications aim to reduce inflammation by targeting the immune system, but not all patients respond well to these treatments. This creates a need for better treatments and ways to personalize care for each patient.

One medication that has shown promise in treating CD is upadacitinib, which works by blocking proteins called Janus Kinases (JAKs). JAKs are enzymes that act as messengers, transmitting signals from outside the cell to the inside. In CD, these signals can lead to an overactive immune response and chronic inflammation in the digestive tract. By blocking JAKs, upadacitinib helps reduce this immune system overactivity and the associated inflammation.

Although upadacitinib helps many patients feel better by the 12th week of treatment, some people take longer to see improvements. These individuals are referred to as “delayed responders.” Understanding why some people respond more slowly to treatment could help doctors decide on the best course of action, ensuring that patients receive the most effective care.

Recent evidence suggests that improvements in a specific endoscopic score, the Modified Multiplier of the Simple Endoscopic Score for Crohn’s Disease (MM-SES-CD), may help predict delayed response. This study will focus on whether changes in MM-SES-CD at week 12 can reliably identify patients who will experience clinical improvement by week 24, even if they haven’t yet shown symptomatic response.

To conduct this research, we will collect data from a group of patients who are receiving upadacitinib for CD. We will track their responses to treatment over time and compare those who respond quickly with those who take longer. This comparison will help us identify patterns and factors that might influence how well a patient responds to the medication
DOI: 10.25934/pr00009778
title: A Multicenter, Randomized, Double-Blind, Placebo-Controlled Induction Study of the Efficacy and Safety of Upadacitinib (ABT-494) in Subjects With Moderately to Severely Active Crohn's Disease Who Have Inadequately Responded to or Are Intolerant to Biologic Therapy

description: The objective of this study is to evaluate the efficacy and safety of upadacitinib compared to placebo as induction therapy in participants with moderately and severely active Crohn's disease (CD).
DOI: 10.25934/pr00009779
title: A Multicenter, Randomized, Double-Blind, Placebo-Controlled Induction Study of the Efficacy and Safety of Upadacitinib (ABT-494) in Subjects With Moderately to Severely Active Crohn's Disease Who Have Inadequately Responded to or Are Intolerant to Conventional and/or Biologic Therapies

description: The objective of this study is to evaluate the efficacy and safety of upadacitinib compared to placebo as induction therapy in adults with moderately and severely active Crohn's disease (CD).
DOI: 10.25919/et02-wn34
title: Simple Electricity Model

description: Simple Electricity Model (SEM) was designed to be the simplest electricity model that could be used to reliably project the future National Electricity Market (NEM) generation mix and average cost of generation, calculating results within no more than 1 hour. In making this model available the objective is to provide more transparency around how estimates of the future cost of generation are calculated. The collection includes model data and software files. The software files themselves are not capable of running the model. Users must obtain licences to the underlying software environment which is available from external parties. See the user guide provided for more details.
DOI: 10.5281/zenodo.18403320
title: LEED IV data for "Large Hole Borophene Formation on Ni surface via Edge-Orientation Control"

description: LEED IV data set obtained from Ni(111)-(3x3)-B as a function of incident electron energy.

The diffraction spot index are provided at the 1st row.
DOI: 10.5281/zenodo.18403319
title: LEED IV data for "Large Hole Borophene Formation on Ni surface via Edge-Orientation Control"

description: LEED IV data set obtained from Ni(111)-(3x3)-B as a function of incident electron energy.

The diffraction spot index are provided at the 1st row.
DOI: 10.5061/dryad.xd2547dtg
title: Data from: Stock composition of juvenile salmon taken by an abundant, pursuit-diving seabird in the coastal waters of British

description: We determined the stock composition of the juvenile salmon delivered to
 offspring by a pursuit-diving seabird, the Rhinoceros Auklet (Cerorhinca
 monocerata) on five breeding colonies in British Columbia, in 2012-2014.
 We obtained 778 meals (bill-loads) in 11 colony-years, of which 215 (28%)
 included salmon, and estimated stock composition for 126 pink, 101
 sockeye, and 113 chum. The number, species, and stock composition of
 salmon taken by the birds varied markedly among colonies and years. On the
 two southernmost colonies there was a dramatic increase in the amount of
 Fraser River sockeye in diets in 2012, the offspring of the exceptionally
 large run up the river in 2010. The biennial cycle in pink salmon was also
 evident: individuals from Puget Sound stocks featured prominently in diets
 on colonies in 2012 and 2014, but were virtually absent in 2013 and
 replaced by pinks from more northerly stocks. Salmon generally comprise a
 minor proportion of Rhinoceros Auklet diets, but our results show that
 these seabirds will respond to pulses of increased abundance of juvenile
 salmon.
description: # Data from: Stock composition of juvenile salmon taken by an abundant,
 pursuit-diving seabird in the coastal waters of British
 [https://doi.org/10.5061/dryad.xd2547dtg](https://doi.org/10.5061/dryad.xd2547dtg) ## Description of the data and file structure Composition of food loads (number of fish species) delivered to rhinoceros auklet nestlings on breeding colonies in British Columbia Canada in 2012-2014 ### Files and variables #### File: Rhinoceros_Auklet_Food_loads_British_Columbia_2012-2014.csv **Description:** Food loads delivered to rhinoceros auklet nestlings on colonies in British Columbia from 2012 to 2014 ##### Variables * Colony name (column A) * Year of sampling (column B) * Observers initials (column C) * Date of sampling (column D) * Food load number (column E) * Number of individual items of fish species (columns F to T including an Other column) ## Code/software Excel
DOI: 10.5061/dryad.wm37pvmzh
title: Begonia himalaica: A new species from Indian Eastern Himalayas

description: Repeated expeditions conducted in Arunachal Pradesh resulted in the
 discovery of a unique Begonia, Begonia himalaica D.Borah, Chowlu, A.Shenoy
 & Taram, belonging to sect. Platycentrum. It is close to Begonia
 rockii Irmsch. in having broadly ovate leaves, hairy petioles, and bearing
 inflorescences directly from the rhizome, but differs in having leaves
 glabrous adaxially and sparsely setose abaxially, irregular purplish red
 patches between veins, 20–40 cm long petiole covered with setose hairs,
 large glabrous navicular bracts at the base of the inflorescence, and
 glabrous ovary. This species is described here based on collections made
 in Chayang Tajo, East Kameng District of Arunachal Pradesh. The new
 species is assessed as Data Deficient according to IUCN Guidelines for
 Using the IUCN Red List Categories and Criteria.
description: The geographical scope of these expeditions covered the region
 between latitude 26°28′ N and29°30′ N, and longitude between 91°30′ E
 and97°30′ E. Upon collection, the specimens underwent meticulous
 processing, including the creation of mounted herbarium-sheets. This
 process adhered to the established methodologies outlined by Jain and Rao
 (1977). All the collected specimens were handled using conventional
 herbarium techniques, and type specimens have been officially deposited at
 ARUN and CAL (acronyms following Thiers 2024 continuously updated).
 Morphological examinations and measurements were conducted on both freshly
 collected and dried specimens. During this analysis, comparisons were
 drawn with the protologues of similar species found in India and its
 neighbouring countries. Additionally, reference was made to digital images
 of type specimens stored at renowned herbaria, such as BM, E, G, K, L, P,
 and PE. Provisional conservation status assessment was carried out as per
 the IUCN guidelines (IUCN, 2024).
description: # Begonia himalaica: A new species from Indian Eastern Himalayas Herbaria
 ARUN contains the voucher specimens.
 [https://doi.org/10.5061/dryad.wm37pvmzh](https://doi.org/10.5061/dryad.wm37pvmzh) ## Description of the data and file structure Type: INDIA. Arunachal Pradesh: Chayang Tajo, East Kameng district, 27°38’45.07”N& 93°03’30.02”E, elev., 1200 m, 15. Sep. 2024, K. Chowlu, A.Shenoy & A.Ray* (Holotype: ARUN, barcode ARUN000038320!; Isotype: CAL).
DOI: 10.5061/dryad.gb5mkkx1t
title: Data from: Evidence of centromeric histone 3 chaperone involved in DNA damage repair pathway in budding yeast

description: The centromeric protein-A (CENP-A) is an evolutionary conserved histone H3
 variant that marks the identity of the centromeres. Several mechanisms
 regulate the centromeric deposition of CENP-A as its mislocalization
 causes erroneous chromosome segregation, leading to aneuploidy-based
 diseases, including cancers. The most crucial deposition factor is a
 CENP-A specific chaperone, HJURP (Scm3 in budding yeast), which
 specifically binds to CENP-A. However, the discovery of HJURP as a DDR
 (DNA damage repair) protein and evidence of its binding to Holliday
 junctions in vitro indicate a CENP-A-deposition-independent role of these
 chaperones. In this study, using budding yeast, we demonstrate that Scm3
 is crucial for the DDR pathway as scm3 cells are sensitive to DNA damage.
 We further observe that the scm3 mutant genetically interacts with the
 rad52 DDR mutant and is compromised in activating DDR-mediated arrest. We
 demonstrate that Scm3 associates with the DNA damage sites and undergoes
 posttranslational modifications upon DNA damage. Overall, from this report
 and earlier studies on HJURP, we conclude that DDR functions of CENP-A
 chaperones are conserved across eukaryotes. Thus, the revelation that
 these chaperones confer genome stability in more than one pathway has
 clinical significance.
description: # Data from: Evidence of centromeric histone 3 chaperone involved in DNA
 damage repair pathway in budding yeast
 [https://doi.org/10.5061/dryad.gb5mkkx1t](https://doi.org/10.5061/dryad.gb5mkkx1t) ## Description of the data and file structure The genome-wide binding of Scm3 was evaluated from MMS-treated or untreated cells using ChIP-seq assay. ### Files and variables #### File: Input_MMS_treated-1.fastq.gz **Description:** Input fasta files from MMS treated sample #### File: Input_MMS_treated-2.fastq.gz **Description:** Input fasta files from MMS treated sample #### File: Input_MMS_untreated-1.fastq.gz **Description:** Input fasta files from untreated sample #### File: Input_MMS_untreated-2.fastq.gz **Description:** Input fasta files from untreated sample #### File: MMS_treated-1.fastq.gz **Description:** IP fasta files from MMS treated sample #### File: MMS_treated-2.fastq.gz **Description:** IP fasta files from MMS treated sample #### File: MMS_untreated-1.fastq.gz **Description:** IP fasta files from untreated sample #### File: MMS_untreated-2.fastq.gz **Description:** IP fasta files from untreated sample ## Code/software The raw reads from ChIP-seq data were processed using FastQC (Andrews S., 2010) for quality assessment and pre-processing, which includes removing the adapter sequences and low quality bases (