cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1g1jx4z
title: Data from: when night becomes day: artificial light at night alters insect behavior under semi-natural conditions

description: Light is the most important Zeitgeber for temporal
 synchronization in nature. Artificial light at night (ALAN) disrupts the
 natural light-dark rhythmicity and thus negatively affects animal
 behavior. However, to date, ALAN research has been mostly conducted under
 laboratory conditions in this context. Here, we used the field
 cricket, Gryllus bimaculatus, to investigate the effect of ALAN
 on insect behavior under semi-natural conditions, i.e., under shaded
 natural lighting conditions, natural temperature and soundscape. Male
 crickets were placed individually in outdoor enclosures and exposed to
 ALAN conditions ranging from &lt;0.01 to 1500 lx intensity. The
 crickets' stridulation behavior was recorded for 14 consecutive days
 and nights and their daily activity patterns were analysed. ALAN impaired
 the crickets' stridulation rhythm, evoking a change in the
 crickets' naturally synchronized daily activity period. This was
 manifested by a light-intensity-dependent increase in the proportion of
 insects demonstrating an intrinsic circadian rhythm (free-run behavior).
 This also resulted in a change in the population's median activity
 cycle period. These ALAN-induced effects occurred despite the
 crickets' exposure to almost natural conditions. Our findings provide
 further validity to our previous studies on ALAN conducted under lab
 conditions and establish the deleterious impacts of ALAN on animal
 behavioral patterns.
description: Adult male crickets raised in the laboratory under LD were put in
 enclosures in the shaded natural environment and exposed to various levels
 of ALAN for two weeks. Their stridulation activity period as well as their
 onset and offset of activity were calculated. 
description: # When night becomes day: Artificial light at night alters insect
 behavior under semi-natural conditions
 [https://doi.org/10.5061/dryad.6t1g1jx4z](https://doi.org/10.5061/dryad.6t1g1jx4z) ## Description of the data and file structure The data includes several Excel files. Each is related to a figure or results calculations, indicated in the file title. Overall, SNE means semi-natural experiment, while Tau stands for each single cricket activity rhythm calculation. Additionally, the supplementary materials such as additional figures and tables are added here. ## Code/Software Overall 4 main codes were used: 1\. running the detection of Raven as a batch detection resulting in txt files from the Raven program (covering for a bug in batch detection) 2\. Extracting stridulation data from these txt files and creating time-series for actograms 3\. Comparing the onset and offset of activity data to sunset and sunrise 4\. A code to apply CosinorPY of (Moskon 2020) on our data
DOI: 10.5061/dryad.0rxwdbs68
title: Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms

description: RNA splicing is highly prevalent in the brain and has strong links to
 neuropsychiatric disorders, yet the role of cell-type-specific splicing or
 transcript-isoform diversity during human brain development has not been
 systematically investigated. Here, we leveraged single-molecule long-read
 sequencing to deeply profile the full-length transcriptome of the germinal
 zone (GZ) and cortical plate (CP) regions of the developing human
 neocortex at tissue and single-cell resolution. We identified 214,516
 unique isoforms, of which 72.6% are novel (unannotated in Gencode-v33),
 and uncovered a substantial contribution of transcript-isoform diversity,
 regulated by RNA binding proteins, in defining cellular identity in the
 developing neocortex. We leveraged this comprehensive isoform-centric gene
 annotation to re-prioritize thousands of rare de novo risk variants and
 elucidate genetic risk mechanisms for neuropsychiatric disorders.
description: # Developmental isoform diversity in the human neocortex informs
 neuropsychiatric risk mechanisms
 [https://doi.org/10.5061/dryad.0rxwdbs68](https://doi.org/10.5061/dryad.0rxwdbs68) ## Description of the data and file structure **Data S1**: This dataset contains transcriptome annotations in General Transfer Format (gtf) generated by long-read sequencing of bulk tissue samples in this study. The annotations delineate genomic coordinates, exonic/intronic boundaries, and salient attributes for each detected transcript isoform.   **Data S2**: Full-length transcriptome of the developing human brain. (A) Transcript classification using the TALON pipeline; (B) Transcript quantification using the TALON pipeline; (C) Filtering criteria used to generate the TALON whitelist. **Data S3**: This dataset contains transcriptome annotations in General Transfer Format (gtf) generated by long-read sequencing of single cells from the human neocortex. ## Sharing/Access information See Related Works. ## Code/Software See Related Works.
DOI: 10.5061/dryad.47d7wm3m4
title: Mitochondrial DNA from Borsuka Cave

description: Six infant human teeth and 112 animal tooth pendants previously found at
 Borsuka Cave in Poland were thought to be from a burial. Uncertainties
 around the dating of the assemblage and the association between the teeth
 and pendants have precluded their association to a specific archaeological
 industry. In this study, we combined dating and genetic analyses of a
 selection of the human teeth and herbivore tooth pendants to address these
 questions. We confirmed the Palaeolithic origin of the human remains and
 herbivore tooth pendants and identified the infant as female. 
description: DNA was extracted from the human tooth C7/675 following the
 automated extraction protocol in Rohland et al., 2018 with buffer
 'D'. The recovered DNA was then converted into single-stranded
 DNA libraries (Gansauge et al., 2020) and enriched for human mtDNA via
 hybridization capture before sequencing. Only putatively deaminated
 fragments were used for reconstructing an mtDNA genome. This genome was
 then aligned to the revised Cambridge reference sequence along with a
 selection of previously published human mtDNA genomes and one previously
 published Neandertal mtDNA genome. This multiple sequence alignment was
 then used for molecular branch shortening and tree building.  
description: # Multiple sequence alignment of newly reconstructed and published Human
 mtDNA: *** One multiple sequence alignments (MSA) used for tree building
 and molecular branch shortening for the associated publication. These
 contain both previously published and newly reconstructed human mtDNA
 genomes. ## 1\. Aligned\_human\_mtDNA\_Borsuka\.fst This MSA is aligned to
 the revised cambridge reference sequence and contains 54 present-day, 19
 ancient previously published human mtDNA genomes, 1 previously published
 Neandertal mtDNA genome and a newly reconstructed mtDNA genome. The newly
 reconstructed human mtDNA genome (Borsuka) is from DNA extracted from a
 human tooth (C7/675) found in Borsuka Cave.
DOI: 10.5061/dryad.02v6wwq8v
title: A master list of all indicators and metrics, with definitions, ecosystem status component(s) they inform, and source references

description: Global policies increasingly focus on the importance of maintaining or
 improving the integrity of ecosystems, but defining, assessing, and
 monitoring integrity in marine protected areas (MPAs) remains a challenge.
 In this paper, we conceptualized ecological integrity along dimensions of
 heterogeneity and stability containing seven components: physical
 structure, diversity, function, persistence, resistance, resilience, and
 natural variability. Through a structured literature search, we identified
 indicators and metrics used for quantifying ecosystem status components in
 the marine environment, then reviewed MPA management plans worldwide for
 inclusion of these components. We evaluated 202 papers applying 83
 ecological indicators built from 72 metrics. Ecosystem components were
 most comprehensively addressed by metrics of taxa presence, organisms
 count, and area occupied by benthic organisms, and community structure,
 biomass, and percent cover indicators. Of the 557 MPA management plans we
 reviewed globally, 93% used at least one ecosystem status term or its
 synonym in an ecologically-relevant context, but 39% did not address any
 components of stability. In particular, resistance was mentioned in only
 1% of management plans, but in some cases it may be inferred from
 indicators and metrics used to track the best addressed component in
 management plans – diversity. Plans for MPAs with both an
 ecological/biological purpose and a research and education purpose
 contained ecosystem status terms more frequently than other plans,
 suggesting that engagement with the scientific community may have improved
 application of these terms. An improved understanding of how to
 operationalize and measure ecological integrity can help MPA monitoring
 and management.
description: ## Description of the data and file structure This dataset is structured
 as an Excel file with 2 tabs. Tab 1 represents a master list of all
 indicators and metrics, with definitions, ecosystem status component(s)
 they inform, and source references in an (author, year) format. Tab 2
 provides a full list of references. ## Sharing/Access information Data was
 derived from the following source: Primary papers for the structured
 literature search were retrieved from WebofScience
 (https://clarivate.com/webofsciencegroup/solutions/web-of-science/) using
 the following query: TS=("Search term" AND marine AND (indicat\*
 OR index OR Metric OR measur\* OR charact\* OR trait\* OR variabl\*)) NOT
 TS=Freshwater. The list of papers selected for analyses is available in
 Appendix S1: Table S1 of the manuscript as well as Tab 2 of the Excel
 file.
DOI: 10.15468/dl.u77szk
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hippocrepis prostrata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003703-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqhhrj
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000819799, K-M000195447, K-M000193549, K-M000153678, K-M000951583, K-M000202918, K-M000193552, K-M000193555, K-M000193559, K-M000202919, K-M000949144, K-M000235264, K-M000195451, K-M000036354, K-M000193564, K-M000822842, K-M000195450, K-M000235258, K-M000949121, K-M000235252, K-M000098650, K-M001441780, K-M000193560, K-M000769762, K-M000193562, K-M000195452, K-M000773932, K-M000177251, K-M000036355, K-M000202890, K-M000235257, K-M000193561, K-M000195442, K-M000951854, K-M000081495, K-M000202914, K-M000202913, K-M000954750, K-M000769680, K-M000951276, K-M000235255, K-M000122116, K-M000178414, K-M000235254, K-M000122088)"
 ]
}

 The dataset includes 45 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003706-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2c8sse
title: Occurrence Download

description: A dataset containing 285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rineloricaria parva",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 285 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003704-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqmd3h
title: Occurrence Download

description: A dataset containing 1660 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "CoordinateUncertaintyInMeters 0.0-31.0",
 "Country is Germany",
 "GadmGid is one of (DEU.10_1, DEU.11_1)",
 "Geometry POLYGON((7.10238 50.35615,7.68734 50.35615,7.68734 50.74252,7.10238 50.74252,7.10238 50.35615))",
 "HasCoordinate is true",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, bb646dff-a905-4403-a49b-6d378c2cf0d9, 28eb1a3f-1c15-4a95-931a-4af90ecb574d)",
 "TaxonKey is Orthoptera",
 "Year 2020-2026"
 ]
}

 The dataset includes 1660 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003705-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4n3uf3
title: Occurrence Download

description: A dataset containing 207871 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Observation.org, Nature data from around the World",
 "Country is Sweden"
 ]
}

 The dataset includes 207871 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003672-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.69p8cz97g
title: Viola pendulipes (Violaceae), a new species from Guangdong Province, China

description: Viola pendulipes (Violaceae), a new myrmecochous species from the Baiwan
 Nature Reserve of Guangdong Province in China, is described and
 illustrated. Morphologically the new species is most similar
 to V. nanlingensis, but it is easily distinguished by having
 truncate or cuneate leaf base (vs. cordate leaf base), robust rhizome with
 short internodes (vs. slender rhizome with long internodes), curved and
 drooping peduncles in fruit (vs. erect peduncles in fruit), and oblong
 anterior petals (vs. spatulate to rhombic anterior petals). Our
 phylogenetic analysis, based on ITS sequences, confirms that the new
 species belongs to V. subsect. Diffusae, and is most closely related to V.
 yunnanensis.
description: The dataset collected by field surveys & Sanger
 sequencing, adjusted manually, and will be released in Genbank.
description: # Viola pendulipes (Violaceae), a new species from Guangdong Province,
 China
 [https://doi.org/10.5061/dryad.69p8cz97g](https://doi.org/10.5061/dryad.69p8cz97g) These are the supply-materials of the article, contain a fastA file, a picture and a table of Genbank accessions. ## Description of the data and file structure The fastA file contains sequences used to reconstruct a phylogeny in the article. The picture contains some living photoes of Viola yunanensis & V. nanlingensis. The doc. contains a table of Genbank accessions. ## Sharing/Access information If you have any needs, please contact me by emails. * ## Code/Software I cut these sequences by using Chromas, and the made a matrix in Bioedit. I used MAFFT to align it and then adjusted it manually.
DOI: 10.5061/dryad.3bk3j9krm
title: Curcuma kakchingense (Zingiberaceae), a new species from northeast India

description: Curcuma kakchingense Bidyaleima, Kishor & Sharma, a new species of
 Curcuma subg. Curcuma (Zingiberaceae) from Manipur, Northeast India is
 described and illustrated. The species has close resemblance to C.
 phrayawan and C. longa but is distinguished by having
 lemon-yellow-coloured rhizomes with a very bitter taste, glabrous dark
 reddish-brown bladeless sheaths, reddish-brown petiole fading towards the
 edges, densely pubescent coma and upper fertile bracts on both surfaces
 with mucronate tip, broadly ovate bracteole, elongated and revolute apex
 of the middle lobe of the labellum and stigma protruding through the
 anther lobes. The chromosome number is established as 2n = 3x = 63.
description: The morphological parameters were recorded from the type specimen
 collected from the natural habitat. Further, the material was pressed and
 prepared as a herbarium.
description: # <i>Curcuma kakchingense</i> (Zingiberaceae), a new species
 from northeast India
 [https://doi.org/10.5061/dryad.3bk3j](https://doi.org/10.5061/dryad.3bk3j9krm) Raw\_data\_of\_morphological\_characters of\_*Curcuma\_kakchingense* ## Description of the data and file structure In this study, we documented (in centimeters) the morphological data of one matured plant from each population consisting of 10 individuals during July of 2015, 2016, and 2017. ## ##
DOI: 10.15468/dl.q4ygt8
title: Occurrence Download

description: A dataset containing 1084244 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungal Records Database of Britain and Ireland"
 ]
}

 The dataset includes 1084244 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003682-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.w9ghx3fvw
title: Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing

description: Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to
 identify the taxonomic composition of microbial communities. We compared
 the metagenome and 16S rDNA amplicon results to demonstrate the features
 of this animal. In general, relatively consistent patterns and reliability
 could be identified by both sequencing methods, but the results varied
 following the refinement of taxonomic levels. Metagenomic sequencing was
 more suitable for the discovery and detection of pathogenic bacteria of
 gut microbiota in seagulls. Although there were large differences in the
 numbers and abundance of bacterial species of the two methods in terms of
 taxonomic levels, the patterns and reliability results of the samples were
 consistent.
description: # Comparative seagulls of gut microbiota by using metagenomics and 16S
 rDNA sequencing
 [https://doi.org/10.5061/dryad.w9ghx3fvw](https://doi.org/10.5061/dryad.w9ghx3fvw) We compared the metagenome and 16S rDNA amplicon results to identify the taxonomic composition of microbial communities. ## Description of the data and file structure Table1. The total taxa abundance of all samples in this study. -sheet1. The total taxa abundance of all samples for metagenomics -sheet2. The total taxa abundance of all samples for 16S rDNA sequencing Table2. The original data of cladogram for common and unique taxa composition between the two methods. ## Sharing/Access information Data was derived from the following sources: The sequence data have been deposited into the National Center for Biotechnology Information (NCBI), [https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/) with BioProject accession number: PRJNA849401 for metagenome and PRJNA849758 for 16S rDNA sequencing. ## Code/Software We have run the scripts files according to the request.
DOI: 10.5061/dryad.931zcrjs2
title: The qPCR results of Asian arowana eDNA detection in Muda Lake, Kedah, Malaysia

description: We present a qPCR-based eDNA method to detect the presence of the
 endangered Asian arowana (Teleostei: Osteoglossidae: Scleropages formosus)
 in Muda Lake, where resides one of its last wild populations on the west
 side of Peninsular Malaysia. Flanked by a pair of newly developed
 species-specific primer, a 163-base pair fragment of the cytochrome
 oxidase subunit I (COI) gene was selected as the eDNA marker. We applied
 our eDNA method at five sampling sites throughout Muda Lake and at five
 different periods. The study observed a marked seasonal variation in
 detection rates, with significantly higher rates during the wet months of
 August, January, and December compared to the dry season spanning May and
 June. The Asian arowana is known to breed during the rainy season and we
 therefore hypothesize its reproductive biology influences the
 concentration of eDNA in the lake. Our results also highlight the possible
 impact of abiotic factors in tropical freshwater ecosystems (such as
 high-water temperature) on eDNA persistence. In conclusion, future
 applications of qPCR-based eDNA methods in tropical environments would
 benefit from locally evaluating the effects of both biotic and abiotic
 factors on species detection.
description: This dataset was obtained by conducting a qPCR amplification on
 environmental DNA (eDNA) samples collected from Muda Lake, Kedah in
 Peninsular Malaysia.
description: # The qPCR results of Asian arowana eDNA detection in Muda Lake, Kedah,
 Malaysia
 [https://doi.org/10.5061/dryad.931zcrjs2](https://doi.org/10.5061/dryad.931zcrjs2) ## Description of the data and file structure The dataset contents are to show detailed results of environmental DNA (eDNA) detection from several tests performed in a current study to detect the presence of Asian arowana in the lacustrine area in Peninsular Malaysia. The dataset contains detailed qPCR results of eDNA samples collected from aquaria, ponds, and a lake in a tropical environment of Peninsular Malaysia. The results are representing the Cq and melt peak values of each qPCR replicate from each water sample replicate. A detailed explanation of each eDNA detection was provided in the main document of the research article.
DOI: 10.21223/p3/3wapnu
title: Dataset for: Participatory Varietal Selection of 11 late blight resistant clones (B1C5) in the locality of Pamparacra in La Libertad, Peru

description: The Mother and Baby (M&B) trial methodology was adapted by CIP for Participatory Variety Selection (PVS) through decentralized evaluation networks and multi-year evaluations in potato growing areas in the Andean region. The M&B trial design encourages active participation of farmers through the application of treatments through systematic evaluations and selections of treatments in their own plots called "Baby trials" (i.e. farmer managed trials) and in fields with an experimental design called "Mother trials" (i.e. researcher managed trials). Objective: Analyze characteristics, attributes and preferences that men and women have when selecting a new potato variety at the phase of flowering and harvesting. A M&B trial was performed to evaluate 11 clones of the population B1C5 with late blight resistance at the locality of Pamparacra, in Pataz province, in La Libertad department, Peru. The trial design was a Randomized Complete Block Design (RCBD) with 3 replicates for Mother trials and 3 replicates for Baby trials during 2012-2013. During 2012-2014 a selection of 5 clones were evaluated in in 3 experiments. In this experiment, characteristics of plant (size, type of foliage), yield, quality, and pest and disease resistance during flowering and harvesting were evaluated. The number of participants at flowering phase was 15 (men=7 and women=8), 26 (men=16, women =10), and 11 (men=6, women = 5); and the number of participants at harvesting phase was 19 (men=11 and women=8), 29 (men=17, women = 12) and 20 (men=13, women = 7) in the experiments 1 to 3 respectively. Additionally, an organoleptic evaluation was assessed at harvesting to evaluate appearance, taste and texture. The number of panelists was 10 (men=5, women=5) for the organoleptic evaluation.
DOI: 10.5517/ccdc.csd.cc2np24l
title: CCDC 2463109: Experimental Crystal Structure Determination

description: Related Article: Danica B. Trollip, Benita Barton, Mino R. Caira, Eric C. Hosten |2025|J.Inclusion Phenom.Macrocyclic Chem.|||doi:10.1007/s10847-025-01324-x
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.