cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28873595
title: <b>Fig 1.</b> SPIRIT schedule of enrolment, interventions, and assessments across the 6-weeks study period.

description: <b>Figure 1.</b> SPIRIT schedule of enrolment, interventions, and assessments across the 6-weeks study period.
DOI: 10.5061/dryad.0cfxpnw9q
title: Genomic data support the revision of provenance regions delimitation for Scots pine

description: Scots pine is a key component of large ecosystems of great ecological,
 economic, and social importance in Europe and Asia, and is a major utility
 species that accounts for more than 60% of total forest production in
 Poland. To date, due to the lack of suitable molecular tools, the genetic
 relationships between ecotypes of key conservatory and commercial value in
 Poland and the genetic signatures of their variation remain unclear. We
 analysed the distribution of maternally inherited mitochondrial markers,
 nuclear microsatellite loci, and polymorphisms at thousands of SNP markers
 from the genotyping array to examine genetic relationships and divergence
 in 27 populations (842 trees) representing the most valuable Polish Scots
 pine ecotypes. They include the oldest stands and cover all 23 seed zones
 defined for the species in the country. Analysis of the distribution of
 genetic variation, population differentiation, and genetic structure in
 all markers indicates high genetic similarity and homogeneous structure
 across populations, except for a single stand from the mountain region.
 More than 99% of the genetic variation in nuclear markers was shared in
 all populations. Multilevel genomics data suggest that during the
 postglacial recolonization process, populations of different origins
 admixed in central Europe and newly established Scots pine forests did not
 diverge significantly, resulting in populations that share a common
 history. The results are important in the discussion on regionalisation of
 reforestation material, delineation of seed zone boundaries,
 and existing management strategies for the most valuable breeding
 populations of forest tree species that are under increasing pressure from
 ongoing environmental changes
description: # Genomic data support the revision of provenance regions delimitation for
 Scots pine
 [https://doi.org/10.5061/dryad.0cfxpnw9q](https://doi.org/10.5061/dryad.0cfxpnw9q) The dataset contains genotype data from 27 populations of Scots pines and 841 individual trees. Three sets of markers are provided here: mtDNA, nSSR, and SNP. The details regarding plant material collection can be found in the original manuscript. ## Description of the data and file structure The files are stored as Lasek_et_al.zip archive, which contains separate folders for each type of marker. Those folders are called: **MtDNA_dataset**, **SSR_dataset**, **SNP_dataset**. Each folder contains a genotype file and **a README file** with a brief description of its structure.
DOI: 10.6084/m9.figshare.28873595.v4
title: SPIRIT schedule of enrolment, interventions, and assessments across the 6-weeks study period.

description: figure 1 of SPIRIT schedule of enrolment, interventions, and assessments
DOI: 10.6084/m9.figshare.28873595.v5
title: <b>Fig 1.</b> SPIRIT schedule of enrolment, interventions, and assessments across the 6-weeks study period.

description: <b>Figure 1.</b> SPIRIT schedule of enrolment, interventions, and assessments across the 6-weeks study period.
DOI: 10.5061/dryad.8w9ghx3vs
title: Niche modelling and correlation analyses of climate variables

description: In this work, we explore the impact of demography and biogeographic
 history in ecological niche model interpretations, examining the potential
 of integrating genetic and ecological methodologies in elucidating the
 evolutionary dynamics of the geographic ranges of cryptic species. We
 conducted intensive sampling across the Iberian Peninsula to obtain mtDNA
 phylogeographic data, and develop fine-scale climate models for the
 cryptic earwigs Forficula dentata and F. mediterranea. The phylogeographic
 patterns revealed divergent evolutionary histories: F. dentata exhibited a
 well-established, geographically structured lineage, while F. mediterranea
 displayed a star-shape pattern typical of recent expansion. Comparison of
 current climate models and those projected into the past and future,
 indicate that F. dentata, seems to be facing a substantial reduction in
 its suitable habitat due to ongoing climate change, and potentially
 exacerbated by interaction with F. mediterranea. Our results show that
 climatic factors alone cannot determine the distribution of the two
 species. Historical and demographic factors are crucial in shaping their
 current geographical structure. Nonetheless, we cannot overlook the
 potential influence of ongoing climatic changes. Exploring the intricate
 interplay between historic, genetic and distribution is opening a new way
 to validate the predictions of climate models and to decipher
 contradictory emerging signals.
description: Two scripts are provided to build ecological niche models and project them
 to past or future conditions. The
 "occurrence_data_and_variables.R" script corresponds to the
 previous analyses to curate the occurrence data (eliminating points in
 close proximity to each other and points located in cities) to avoid as
 much bias as possible. Analyses are also performed to select uncorrelated
 variables. The second script "Model_ABSENCES_FINAL.R" provides
 the steps necessary to build the models and project them. No abbreviations
 or codes are used that are not explained throughout the script. Before
 each analysis, the title of what is to be done appears, or alternatively,
 as an explanation that accompanies the command line. As the available
 climate variables sometimes change on the web and are difficult to find,
 we provide the ones we use
 "2.5m_CNRM-ESM2-1_ssp370_2061-2080.tif". They correspond to the
 future climate variables, as their name indicates, for the period
 2061-2080, a CNRM-ESM2-1 scenario"
DOI: 10.5061/dryad.m37pvmd9z
title: Data from: Effects of nitrogen deposition, biodiversity and climate on productivity in a large temperate forest region

description: This dataset supports research on how forest productivity in temperate
 forests of Northeast China responds to atmospheric nitrogen deposition. It
 comprises survey data from 396 circular forest plots (0.1 ha each). The
 dataset includes the region of each plot, geographic coordinates
 (longitude and latitude), atmospheric nitrogen deposition (N_dep), climate
 variables (annual mean temperature, annual precipitation, precipitation of
 the driest month, precipitation seasonality, and precipitation of the
 driest quarter), soil properties (soil sand content and cation exchange
 capacity at pH 7), multiple biodiversity metrics (tree species diversity,
 tree phylogenetic diversity, tree functional diversity, and functional
 identity), and forest biomass productivity (TP). These data were used to
 examine the effects and pathways through which atmospheric nitrogen
 deposition, biodiversity, and climate influence forest productivity, as
 well as to analyze the relationship between nitrogen deposition and
 productivity along biotic and climatic gradients. Overall, the dataset
 provides new insights into patterns of temperate forest productivity
 responses to atmospheric nitrogen deposition under specific ecological and
 climatic contexts.
description: This Dryad dataset contains the data underlying the results presented in
 the paper “Effects of Nitrogen Deposition, Biodiversity and Climate on
 Productivity in a Large Temperate Forest Region," published in
 *Global Ecology and Biogeography*. ## #---Data.xlsx In the Excel file,
 Sheet1 includes the variables for 396 forest plots (0.1 ha each), and
 Sheet2 provides descriptions of these variables (as below). | 
 
 | 
 
 | | :----------- |
 :---------------------------------------------------------------- | |
 region | The mountainous area (regions) where the forest plot is located |
 | longitude | Longitude coordinates of forest plot | | latitude | latitude
 coordinates of forest plot | | Richness\_TD | Tree species diversity (Hill
 number with order q = 0) | | Richness\_PD | Tree phylogenetic diversity
 (Hill number with order q = 0) | | Richness\_FD | Tree functional
 diversity (Hill number with order q = 0) | | CWM\_LC | Community-weighted
 mean (CWM) of leaf carbon concentration (LC) | | CWM\_HM |
 Community-weighted mean (CWM) of tree maximum height (HM) | | CWM\_LN |
 Community-weighted mean (CWM) of leaf nitrogen concentration (LN) | | bio1
 | Annual mean temperature | | bio12 | Annual precipitation | | bio14 |
 Precipitation of the driest month | | bio15 | Precipitation seasonality |
 | bio17 | Precipitation of the driest quarter | | N\_dep | Atmospheric
 nitrogen deposition | | sand | Soil sand content | | cec | Exchange
 capacity at pH = 7 | | climatePC1 | The first principal component (PC1) of
 five bioclimatic variables | | TP | Forest biomass productivity |
DOI: 10.5061/dryad.dbrv15f9c
title: Data from: Iris luojiensis (Iridaceae), a new species from Southwest China

description: Iris luojiensis, sp. nov. from Southwest China is described and
 illustrated. This species occurs on shrub slopes in mountainous regions of
 southwest China. Iris luojiensis is morphologically similar to Iris
 japonica Thunb., Iris calcicola Z.C.Lu, Z.P.Huang & Yan Liu and
 Iris watii Baker, but easily distinguished from them by its bluish-violet
 flowers, 3-6 flowering-stem branches, leaf size, particularly the upper
 leaves, and by only having two to three (seldom one) flowers per bract. A
 phylogenetic analysis based on the complete plastid genome supports the
 separation of I. luojiensis from other morphologically related species.
 According to morphological and molecular evidence, I. luojiensis can be
 placed in the I. sect. Lophiris.
description: Phylogenetic analysis of chloroplast genomes: CTAB (Cetyl
 Trimethyl Ammonium Bromide) method (Doyle and Doyle, 1987). The total
 extracted DNA was sent to Wuhan BGI for further database construction and
 sequencing. A 300-400 bp DNA small fragment library was constructed using
 the BGISEQ-500 platform. Subsequently, paired-end 150 (PE150) sequencing
 was performed using the MGISEQ-2000 platform, resulting in 2G paired-end
 data in fastq format.
description: # Iris luojiensis (Iridaceae), a new species from Southwest China
 [https://doi.org/10.1111/njb.04389](https://doi.org/10.1111/njb.04389)
 Iris luojiensis is a new species from Southwest China. ## Description of
 the data and file structure In this dataset, all photos from published
 articles on this species and the photo of the type specimen are
 included. Also contains the fasta file of seven (CQIris_fasta,
 GIris_fasta, HHIris_fasta, Iris_fasta, LuoIris_fasta, WUIris_fasta, XHIris_fasta) newly sequenced iris species. Our dataset can be used for taxonomic and phylogenetic studies of Iris.
DOI: 10.15468/dl.5bjatw
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyhypopomus bullocki",
 "Year 2006-2026"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004013-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4tmpg4fk8
title: Analogous above- and belowground traits for twelve boreal tree species

description: It is heavily debated whether analagous aboveground and belowground traits
 are coordinated. Here, we collected trait data (above- and belowground)
 for twelve boreal forest tree species to assess trait coordination in
 leaves and roots. We find only partial evidence for above-belowground
 coordination for "fast-slow economic traits", such that N
 content and dry matter content were positively correlated with each other.
 However, root dry matter content and leaf N had no significant
 relationship. For reseource acquisition traits we found no strong evidence
 for trait cordination, as specific root length and specific leaf area were
 not positively correlated.Site explained little of the total trait
 variation, whereas within-site variation contributed substantially to the
 total trait variation for a large number of traits, more so for
 morphological root traits than leaf traits.
description: # Analogous above- and belowground traits for twelve boreal tree species
 [https://doi.org/10.5061/dryad.4tmpg4fk8](https://doi.org/10.5061/dryad.4tmpg4fk8) ## Description of the data and file structure The data were collected at two sites within Sweden (one northern and one central site). In this dataset, the northern site is Vindeln (abbreviated "VI") and the central site was located in Garpenberg (abbreviated "GA"). Each site consisted of 3 blocks each with plots consisting of monocultures of twelve different species. Six species were common between the two sites. In the dataset, the species are Pinus contorta (CO), Pseudotsuga menziesii (DO), Picea abies (SP), Larix sibirica (LS), Betula pendula (BI), Pinus sylvestris (PN), Larix sp. (LH), Picea glauca (WS), Picea mariana (PM), Abies lasciocarpa (AL), Abies sibirica (AS), and Pinus banksianna (PB). The measured traits and their units are leaf carbon content (C_Leaf; %); leaf nitrogen content (N_Leaf; %); specific leaf area (SLA; cm2 g-1); leaf dry matter content (LDMC; g g-1); leaf carbon to nitrogen ratio (CN_Leaf); average root diameter (AD; mm); root nitrogen content (N_Root; %); specific root area (SRA; cm2 g-1); specific root length (SRL; cm g-1); root carbon content (C_Root; %); root carbon to nitrogen ratio (CN_Root), and root dry matter content (RDMC; g g-1).
DOI: 10.15468/dl.wd8me9
title: Occurrence Download

description: A dataset containing 7837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hyperlophus vittatus",
 "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 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 7837 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004014-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kh18932fz
title: SCC3 is an axial element essential for homologous chromosome pairing and synapsis

description: Cohesin is a multi-subunit protein that plays a pivotal role in holding
 sister chromatids together during cell division. Sister chromatid cohesion
 3 (SCC3), constituents of cohesin complex, is highly conserved from yeast
 to mammals. Since the deletion of individual cohesin subunit always causes
 lethality, it is difficult to dissect its biological function in both
 mitosis and meiosis. Here, we obtained scc3 weak mutants using CRISPR-Cas9
 system to explore its function during rice mitosis and meiosis. The scc3
 weak mutants displayed obvious vegetative defects and complete sterility,
 underscoring the essential roles of SCC3 in both mitosis and meiosis. SCC3
 is localized on chromatin from interphase to prometaphase in mitosis.
 However, in meiosis, SCC3 acts as an axial element during early prophase I
 and subsequently situates onto centromeric regions following the
 disassembly of the synaptonemal complex. The loading of SCC3 onto meiotic
 chromosomes depends on REC8. scc3 shows severe defects in homologous
 pairing and synapsis. Consequently, SCC3 functions as an axial element
 that is essential for maintaining homologous chromosome pairing and
 synapsis during meiosis.
description: The immunoﬂuorescence signals were analyzed and captured using a
 ZEISS A2 microscope imaging system. Chromosome images were captured using
 an Olympus (Shinjuku-ku, Tokyo, Japan) BX51 fluorescence microscope with a
 micro CCD camera using software IPLAB4.0 (BD Biosciences, San Jose, CA,
 USA). STED images were acquired using Abberior STEDYCON (Abberior
 Instruments GmbH, Göttingen, Germany) fluorescence microscope built on an
 upright microscope BX53 (Olympus UPlanXAPO 100x, NA1.45, Tokyo, Japan).
 All STED images were processed by deconvolution approach. All raw
 microscopy images were combined and adjusted for brightness and contrast
 using Photoshop software.
description: # SCC3 is an axial element essential for homologous chromosome pairing and
 synapsis-raw microscopy images
 [https://doi.org/10.5061/dryad.kh18932fz](https://doi.org/10.5061/dryad.kh18932fz) ## Description of the data and file structure This dataset contains all the raw images of fluorescence microscopy in this manuscript. All raw microscopy images were captured using the following methods: The immunofluorescence images were analyzed and captured using a ZEISS A2 microscope imaging system. STED images were acquired using Abberior STEDYCON (Abberior Instruments GmbH, Göttingen, Germany) fluorescence microscope built on an upright microscope BX53 (Olympus UPlanXAPO 100x, NA1.45, Tokyo, Japan).  ## Code/Software The combination of microscopy images utilizes Photoshop and ZEN software. The distance between sister chromatids were measured using ImageJ software.
DOI: 10.5061/dryad.s4mw6m9f5
title: Data from: Beyond the colony-forming-unit: Rapid bacterial evaluation in Osteomyelitis

description: Examination of bacteria/host cell interactions is important for
 understanding the aetiology of many infectious diseases. The
 colony-forming-unit (CFU) has been the standard for quantifying bacterial
 burden for the past century, however, this suffers from low sensitivity
 and is dependent on bacterial culturability in vitro. Our data demonstrate
 the discrepancy between the CFU and bacterial genome copy number in an
 osteomyelitis-relevant co-culture system and we confirm diagnosis and
 quantify bacterial load in clinical bone specimens. This study provides
 insight into improving the quantification of bacterial burden in such
 cases.
description: The DNA sequences were generated by Oxford Nanopore sequencing
 platform, using the PCR amplicons following the enrichment of bacterial
 signal from total DNA isolated from clinical bone specimens.
description: # Beyond the Colony-Forming-Unit: Rapid Bacterial Evaluation in
 Osteomyelitis
 [https://doi.org/10.5061/dryad.s4mw6m9f5](https://doi.org/10.5061/dryad.s4mw6m9f5) The DNA sequences were generated by Oxford Nanopore sequencing platform related to the bacterial presence of 3 prothethic joint infection (PJI) patients. The DNA materials for input to sequencing were PCR amplicons by bacterial targeted PCRs using the total genomic DNA isolated from the clinical bone specimens from those 3 PJI patients. Inside the .zip file, there are three folders, namely PJI 1-3, which are correlated to sequencing results from the three PJI patients (PJI I-III) in figure 3 in our paper. Sequencing results were analysed by the onboard module "what-in-my-port" provided by Oxford Nanopore.
DOI: 10.15139/s3/w9vzxi
title: Data Management and Sharing Plan for: Prevalence and Adherence for the Control of HepaTitis B and D in the DRC (PACT-DRC)

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.5tb2rbpch
title: Hydroacoustic data from Inglefield Bredning Fjord, Northwest Greenland (Oct 2022 - Jul 2023): Part B

description: Here, we archive long-term oceanographic and acoustic data from moorings
 deployed to the seafloor in NW Greenland (August 2022 - July 2023). The
 data document local biophony, geophony, and anthrophony in the glacial
 fjords of NW Greenland. The primary targets of acoustic monitoring are
 marine mammals, such as narwhals and seals, icebergs, and boats.
description: This oceanographic dataset was collected by autonomous stations
 deployed to the seafloor in NW Greenland (August 2022 - July 2023). It has
 not been processed.
description: # Hydroacoustic data from Inglefield Bredning Fjord, Northwest Greenland
 (Oct 2022 - Jul 2023): Part B We have submitted our raw acoustic data
 (BowdoinCalFr_6229.zip), collected in Inglefield Bredning Fjord, Northwest
 Greenland; Oct 2022 - Jul 2023). Please note that the first half of this
 dataset (Part A; specifically, data for Aug-Sep 2022 @ sensor #6229;
 Aug-Nov 2022 @ sensor #6230) is available at:
 [https://doi.org/10.5061/dryad.qz612jmqd](https://doi.org/10.5061/dryad.qz612jmqd) ## Description of the data and file structure For recording sound, Soundtrap#6229 was deployed near the calving front of Bowdoin Glacier (77.67 deg N, 68.63 deg W; water depth = 192 m). The sound recorder was programmed to store 4.5 minutes of continuous sound every 20 minutes at a sampling rate of 64 kHz. Zipped acoustic data is stored in standard audio files (e.g., 6229.220806030000.wav), which corresponds to a recorder's serial number and UTC time stamp (XXXX.YYMMDDHHmmss.wav). Our data are structured in the following way: **BowdoinCalFr_6229.zip** The archive contains all audio files (6229.*.wav) recorded between October 2022 and July 2023 by Soundtrap#6229 at Bowdoin Fjord (see "Part A" for August - October 2022). For example,  the data set includes a series of files: *6229.221001000000.wav* *6229.2212..................wav* *6229.2301..................wav* *6229.230802010000.wav* where "6229" is the serial number of the used Soundrtap hydrophone separated by a dot (.) from a corresponding time stamp information, interpreted as, e.g., "*221001000000" = 10 October 2022, 00:00:00 UTC*. Each individual audio data file contains 4.5 minutes of acoustic amplitudes [in units re. Pa]. ## Code/Software Acoustic data files *.sud were converted to *.wav using the free software SoundTrap Host (Release 4.0.17), which is offered at [http://oceaninstruments.co.nz/downloads/(opens in new window)](http://oceaninstruments.co.nz/downloads/). Data processing and visualizations were made with commercially available Matlab R2022b, Kaleidoscope Pro 5.6.2, and Raven (Lite 2.0 is openly available).