cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0gb5mkmcc
title: Data and code from: Environmental drivers of wild bee reproductive performance across a South American dryland ecoregion

description: The reproductive performance of wild bees is a key determinant of their
 population persistence. However, few studies have directly examined the
 environmental drivers of demographic processes using a geographically
 broad approach. In this study, we explored how biotic and abiotic factors
 influence the reproduction of solitary, cavity-nesting bees across the
 Monte Desert ecoregion in Argentina. Using artificial wood nests and a
 standardized sampling spanning 2,000 km and 20° of latitude, we related
 key reproductive metrics—nest establishment, offspring production, and
 offspring survival—to latitude, climate, and biotic factors (flower
 abundance, vegetation cover, and brood parasitism). Climate was the most
 consistent and strongest predictor of bee reproductive performance: warm,
 humid conditions during the nesting period were associated with reduced
 nest establishment and offspring survival. Brood parasitism also emerged
 as a strong driver, significantly reducing offspring survival. Across the
 Monte Desert's latitudinal gradient, nest establishment peaked at
 mid-latitudes, while offspring production and survival increased toward
 higher latitudes. These findings highlight the sensitivity of wild bee
 reproduction to climatic conditions, particularly during the critical
 nesting period. Our study advances our understanding of the potential
 impacts of climate change on wild bees in the Neotropics, where extensive
 areas are experiencing dramatic land-use changes.
description: # Environmental drivers of wild bee reproductive performance across a
 South American dryland ecoregion
 [https://doi.org/10.5061/dryad.0gb5mkmcc](https://doi.org/10.5061/dryad.0gb5mkmcc) ## Description of the data and file structure Data and code for Aranda-Rickert et al. 2025: "Environmental Drivers of Wild Bee Reproductive Performance Across a South American Dryland Ecoregion" ### Files and variables #### File: Aranda-Rickert\_data\_Rcode\_ProceedingsB.zip **Description:**  The excel file ‘Aranda-Rickert_bee_data_column_headers’ contains 2 spreadsheets (‘raw_data’ / ‘column_headers’). Spreadsheet ‘raw_data’ contains the dataset with the response variables and the environmental predictors used in this study. Spreadsheet ‘column_headers’ explains each variable. The csv file 'Aranda-Rickert_bee_data’ contains the dataset with the response variables and the environmental predictors to run the R scripts. The R file ‘Aranda-Rickert_R_code’ contains the R scripts with the analyses to reproduce the results in this study. Missing values are indicated as N/A. ## Code/software R version and list of R packages used for the analyses and plots: We conducted all analyses with R statistical software, version 4.3.3 We used the gamm4 function from the gamm4 R package version 0.2-6 (Wood & Scheipl, 2020) to perform the GAMMs. We ussed the glmer function from the lme4 R package version 1.1-34 (Bates et al., 2015) to perform the GLMMs. We drew plots with ggplot2 R package version 0.9.3.1 (Wickham, 2016)
DOI: 10.15468/3n5ah7
title: A new species of the Neoplecostomine catfish Pareiorhaphis (Siluriformes: Loricariidae) from the Coastal basins of Espírito Santo, Eastern Brazil

description: This dataset contains the digitized treatments in Plazi based on the original journal article Pereira, Edson H. L., A., Pablo Lehmann, Reis, Roberto E. (2012): A new species of the Neoplecostomine catfish Pareiorhaphis (Siluriformes: Loricariidae) from the Coastal basins of Espírito Santo, Eastern Brazil. Neotropical Ichthyology 10 (3): 539-546, DOI: 10.1590/S1679-62252012000300006, URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252012000300006&lng=en&tlng=enPareiorhaphis ruschii, new species, is the first neoplecostomine catfish of the genus Pareiorhaphis described based on material from tributaries to the rio Piraquê-Açu and rio Reis Magos, both small coastal drainages in the State of Espírito Santo, eastern Brazil. The new species is promptly diagnosed from all its congeners by features related to the morphology of the lower lip margin, number of preadipose azygous plates, size and shape of the pectoral-fin spine, and caudal-fin skeleton. Additionally, sexual dimorphism of the new species is marked by hypertrophied odontodes on the lateral margins of head slightly directed forward in adult males.Pareiorhaphis ruschii, espécie nova, é o primeiro cascudo neoplecostomíneo do gênero Pareiorhaphis descrito de afluentes dos rios Piraquê-Açu e Reis Magos, ambos pequenas bacias costeiras do estado do Espírito Santo, leste do Brasil. A espécie nova é prontamente diagnosticada de todas as demais congêneres por caracteres relacionados à morfologia da margem do lábio inferior, número de placas ázigas pré-adiposas, forma e tamanho do raio não ramificado das nadadeiras peitorais e forma do esqueleto da nadadeira caudal. O dimorfismo sexual da espécie nova é marcado pelos odontódeos hipertrofiados na margem lateral da cabeça que são ligeiramente orientados anteriormente em machos adultos.
DOI: 10.5281/zenodo.18407858
title: COPD Anuradhapura
DOI: 10.5281/zenodo.18407857
title: COPD Anuradhapura
DOI: 10.5061/dryad.5dv41nsh7
title: Ancestral complexity and constrained diversification of the ant olfactory system

description: Communication is a cornerstone of social living, allowing the exchange of
 information to align goals and synchronize behaviour. Ants, a group of
 highly successful social insects, have heightened olfactory abilities that
 are integral to their evolutionary success. Essential for colony cohesion
 and cooperation, a female-specific olfactory subsystem processes
 information about nestmate recognition cues (cuticular hydrocarbons),
 including basiconic sensilla on the antenna and a cluster of specific
 glomeruli in the antennal lobe. While it has often been linked to ants’
 social lifestyle, the evolutionary origins and phylogenetic distribution
 of this system remain unknown. We conducted a comparative exploration of
 the ant olfactory system across eight major subfamilies, integrating
 neuroanatomical, chemical, and behavioural analyses. Our findings reveal
 that sophistication of the ant olfactory system has deep evolutionary
 roots. Moreover, antennal lobe investment is not associated with social
 traits such as colony size, polygyny, or foraging strategies, but
 correlates with cuticular hydrocarbon profile complexity. Despite
 neuroanatomical differences, different ant species consistently excel in
 nestmate discrimination, indicating adaptation to chemical diversity while
 maintaining reliable social recognition. This suggests that cuticular
 hydrocarbon profile and neuronal investment in olfactory neuropil have
 co-evolved to sustain discrimination performance.
description: # Ancestral complexity and constrained diversification of the ant
 olfactory system Dataset DOI:
 [10.5061/dryad.5dv41nsh7](10.5061/dryad.5dv41nsh7) ## Description of the
 data and file structure This dataset includes 14 video sequences (19
 seconds each) showing the antennal lobe organisation of 14 ant species.
 Each video presents a sequence of confocal microscopy scans and the
 resulting 3D model of the antennal lobe, illustrating both raw imaging
 data and segmented glomerular structures. These data were obtained as part
 of a comparative study on the evolution of olfactory system organisation
 in ants. Full methodological details, species list, and analyses are
 provided in *Ancestral complexity and constrained diversification of the
 ant olfactory system*. ### Files and variables #### File:
 Formicidae-AL.zip **Description:** The dataset includes antennal lobe
 imaging from the following species: \* Aphaenogaster senilis \* Atta
 sexdens \* Azteca trigona \* Camponotus aethiops \* Cataglyphis cursor \*
 Cephalotes atratus \* Eciton burchellii \* Ectatoma tuberculatum \*
 Formica fusca \* Lasuis niger \* Messor barbarus \* Neoponera apicalis \*
 Paraponera clavata \* Pseudomyrmex boopis ## Code/software The videos are
 provided in MPEG format and can be viewed using a range of media players,
 including free and open-source options such as VLC Media Player (Version
 3.0 or later)
DOI: 10.5061/dryad.z08kprrr3
title: Data from: Inherent single-cell heterogeneity of the transcriptional response to hypoxia in cancer cells

description: Hypoxia-inducible factor (HIF) is a master regulator of cancer cell
 adaptation to tumor hypoxia and is involved in cancer progression.
 Single-cell (sc) differences in the HIF response allow for tumor evolution
 and cause therapy resistance. These sc-differences are usually ascribed to
 tumor microenvironmental differences and/or clonal (epi)genetic
 variability. However, the sc-heterogeneity of the HIF response in
 otherwise identical cells cultured under defined in vitro conditions has
 not yet been addressed. Therefore, we analyzed the sc-response to hypoxia
 in nonclonal cell lines and multiple clonal derivatives, including HIF-1a
 or HIF-2a knockouts. While HIF-1a and HIF-1 target mRNA sc-heterogeneity
 was slightly higher than global transcription or specific housekeeping
 mRNAs, HIF-2a and especially HIF-2 target mRNA sc-heterogeneity was
 extraordinary, and remained in independent clones and following HIFa
 knockouts. Unexpectedly, neither HIF-2a mRNA nor nuclear protein levels
 correlated with target mRNA levels. Unsupervised but not supervised HIF
 target gene dimensionality reduction revealed the initial sample
 composition after scRNAseq, demonstrating that, owing to sc-heterogeneity,
 individual HIF target genes are not sufficient to unequivocally identify
 hypoxic cancer cells. In conclusion, the pronounced intrinsic
 sc-heterogeneity of the HIF response represents a hitherto unrecognized
 feature of cancer cells that impairs clinical HIF pathway-dependent cancer
 cell identification and targeting.
description: # Data from: Inherent single-cell heterogeneity of the transcriptional
 response to hypoxia in cancer cells Dataset DOI:
 [10.5061/dryad.z08kprrr3](10.5061/dryad.z08kprrr3) **Description of the
 data and file structure** Underlying primary data for the publication Wilk
 et al., "Inherent single-cell heterogeneity of the transcriptional
 response to hypoxia in cancer cells" in NAR Cancer, 2025, 7, zcaf021.
 All information about data content and file structure can be found
 therein. **Files and variables** **File: Wilk_Figures.zip,
 PythonScript_DensityPlots.ipynb, and
 PythonScript_HeterogeneityPlots.ipynb** **Description:** Underlying
 primary data of Figures 1 to 6 of the publication Wilk et al.,
 "Inherent single-cell heterogeneity of the transcriptional response
 to hypoxia in cancer cells". **Code/software** Image viewer, Excel,
 cell profiler, Adobe acrobat, Python script (ipynb).
DOI: 10.5061/dryad.2ngf1vj0v
title: Ineffectual immunity in a resurrected mouse model of persistent viremia

description: Viruses that establish persistent (i.e., chronic) infection have evolved
 sophisticated strategies to avoid clearance by the host immune system.
 This is particularly true for viruses that infect immunocompetent mammals
 and sustain high infectious burdens in body sites under intense immune
 surveillance (i.e., the blood, a.k.a., “viremia”). Historically,
 lymphocytic choriomeningitis virus (LCMV) infection of laboratory mice has
 served as a powerful model to understand mechanisms of failed immunity,
 but other viruses may have unique and underappreciated persistence
 strategies. Here, we resurrect a bygone model of viral
 persistence––lactate dehydrogenase-elevating virus (LDV)––and use modern
 transgenic mouse technologies to investigate various aspects of anti-viral
 immunity. We find that interferons have a modest impact on LDV
 replication, with interferon-alpha blunting LDV viremia in the acute phase
 of the infection and interferon-gamma reducing LDV viral loads in the
 chronic phase of infection, but only when paired with an intact
 interferon-alpha response. Adaptive immunity, assessed in Rag-knockout
 mice, had only a modest impact on LDV viremia, and only during the
 sub-acute phase of infection. Mice lacking the critical immune checkpoint
 molecule PD-1 showed no signs of disease and supported LDV viral loads at
 levels equivalent to their wild-type counterparts. Altogether, these
 results point to a novel and highly effective mechanism of persistence
 that is minimally impacted by conventional aspects of anti-viral immunity
 or immune exhaustion––a rarity among persistent viruses. Given the
 relative paucity of chronic infection models in the laboratory mouse, LDV
 infection may be useful for exploring unique modes of immune system
 failure. 
description: # Ineffectual immunity in a resurrected mouse model of persistent viremia
 Dataset DOI: [10.5061/dryad.2ngf1vj0v](10.5061/dryad.2ngf1vj0v) ##
 Description of the data and file structure Each tab in the .csv file
 corresponds to the data from a figure in the corresponding manuscript.
 LDV= lactate dehydrogenase elevating virus of mice, Plagemann strain. PFU=
 plaque forming units. RT-qPCR= reverse transcription quantitative
 polymerase chain reaction. All blank cells are left intentionally blank. 
 Figure 1: LDV viral loads in wild-type mice over time Figure 2: LDV viral
 loads in mice with different immune-gene deficiencies over time Figure 3:
 Weight loss and LDV viral loads in mice lacking the immune checkpoint
 inhibitor PD-1.
DOI: 10.15468/dl.a773q6
title: Occurrence Download

description: A dataset containing 499 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aphyocharax dentatus"
 ]
}

 The dataset includes 499 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004286-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc866t21f
title: Data from: The gnathosoma is a bad character rather than evidence for mite monophyly

description: In recent years, the case for the monophyly of mites or Acari
 (Parasitiformes + Acariformes) has looked increasingly weak. Much of the
 remaining doubt about the artificiality of this taxon stems from the
 importance long attributed to the gnathosoma, widely considered the most
 convincing morphological character supporting monophyly. The gnathosoma
 has long been interpreted as originating via the fusion together of the
 palpal coxae, which is thought to have contributed to the consolidation of
 the mouthparts into a compact feeding apparatus that articulates as a
 single unit. However, an investigation of the mouthparts of Acariformes,
 reported herein, revealed that fusion together of the palpal coxae is an
 uncommon state that convergently evolved in multiple acariform taxa rather
 than evolving only once, as a synapomorphy uniting Acariformes and
 Parasitiformes. Moreover, other defining features of the gnathosoma
 involve either very different modifications or structures that are not
 homologous between both main lineages of mites. Therefore, the gnathosoma
 is a bad character—poorly defined and based on a series of
 misinterpretations—that should not be treated as evidence for mite
 monophyly.
description: # The gnathosoma is a bad character rather than evidence for mite
 monophyly Dataset DOI: [10.5061/dryad.pc866t21f](10.5061/dryad.pc866t21f)
 ## Description of the data and file structure The files are confocal
 z-stacks of mite mouthparts that were generated using a Zeiss LSM 710
 (*Nanorchestes* sp. 1, and *Stigmalychus* sp.) and an Olympus Spectral
 FV1000 (*Micropsammus* sp. 1, *Nanorchestes* sp. 2, and *Tydeus* sp.). The
 files can be viewed as 3d models in ImageJ (see code/software). Excitation
 was via lasers of 405 nm (*Micropsammus* sp. 1 and *Nanorchestes* sp. 1)
 and 488 nm (*Nanorchestes* sp. 2, *Stigmalychus* sp. and *Tydeus* sp.).
 Autofluorescence was captured via broad detection bands from the
 wavelength of the laser up to around 650 nm. ## Code/software ImageJ is
 recommended because it is open source and freely available.
 [https://imagej.net/ij/](https://imagej.net/ij/) In order to view the
 models, the bio-formats plugin may need to be installed.
 [https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/installing.html](https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/installing.html) The files can be segmented and turned into mesh models using 3DSlicer (also free and open source). In order to do this the files should first be converted into a series of Tiffs or Jpegs in ImageJ.  [https://download.slicer.org/](https://download.slicer.org/)
DOI: 10.15468/dl.4sh7mg
title: Occurrence Download

description: A dataset containing 70517 records in GBIF matching the query:
SELECT
 '510' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 51.21395264452012
 AND decimalLatitude &lt;= 56.135291543055025
 AND decimalLongitude &gt;= 20.04431404917282
 AND decimalLongitude &lt;= 28.782040753409778
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 70517 records were derived from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004280-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9ghx3ffv6
title: Bulk RNA sequencing of human mesenchymal stromal cells derived from labial salivary glands, bone marrow, and adipose

description: We obtained mesenchymal stromal cells from digested human tissue derived
 from bone marrow (n=3), adipose (n=3), and labial salivary glands (n=9).
 The salivary gland derived MSCs were from participants who met 2016
 ACR/EULAR criteria for SjD (n=3), participants who had dry eye or dry
 mouth but no evidence of a systemic autoimmune disease (n=3), and
 participants who had no symptoms of dryness as controls (n=3). The samples
 were subjected to bulk RNA sequencing.
description: # Bulk RNA sequencing of human mesenchymal stromal cells derived from
 labial salivary glands, bone marrow, and adipose Dataset DOI:
 [10.5061/dryad.9ghx3ffv6](10.5061/dryad.9ghx3ffv6) ## Description of the
 data and file structure We collected tissue from bone marrow (n=3),
 omental adipose (n=3), or labial salivary gland tissue (n=9). The tissue
 was digested, and mesenchymal stromal cells were isolated, verified, and
 cryopreserved. The cells were sent to Novogene. They purified mRNA from
 total RNA with poly -T oligo attached magnetic beads and synthesized cDNA
 and generated a library. They checked the library with Qubit and rtPCR.
 the quantified library was pooled and sequenced using an Illumina
 platform. They followed their standard bioinformatics work flow that
 includes generation of raw data, data QC, mapping to reference genome,
 gene expression quantification, differential gene analysis, and functional
 analysis. Also, we provide FASTQ files with nucleotide sequences and
 quality scores (forward and reverse) for each subject and treatment
 condition. Differentially expressed genes (DEGs) are included for multiple
 comparisons: markers_humanmsc_all lists DEGs for each cytokine treatment
 vs. all others; markers_ifng_vs_vehicle, markers_tnfa_vs_vehicle, and
 markers_it10_vs_vehicle compare DEGs for IFN-γ, TNF-α, and combined
 IFN-γ/TNF-α treatments versus vehicle, respectively and the data is
 available at: https://doi.org/10.5061/dryad.9ghx3ffv4 ### Files and
 variables #### File: gene_fpkm_dryad.txt **Description:**  ##### Variables
 * gene_id: ID of gene * 1ns: 1st labial salivary gland MSC subject that
 did not have dryness (nonsicca control) * 2ns: 2nd MSC from nonsicca
 control  * 3ns: 3rd MSC from nonsicca control * 1siccact: 1st MSC from a
 sicca control (dryness but no autoimmunity) * 2siccact: 2nd MSC from a
 sicca control * 3siccact: 3rd MSC from a sicca control * 1Sj: 1st MSC from
 a SjD patient * 2Sj: 2nd MSC from a SjD patient * 3Sj: 3rd MSC from a SjD
 patient * 1BM: 1st bone marrow MSC * 2BM: 2nd bone marrow MSC * 3BM: 3rd
 bone marrow MSC * 1Ad: 1st adipose MSC * 2Ad: 2nd adipose MSC * 3Ad: 3rd
 adipose MSC * gene_name: gene symbol * gene_chr: the chromosome of the
 gene * gene_start: the start site of the gene * gene_end: the end site of
 the gene * gene_strand: the direction of the gene chain * gene_length: the
 length of the gene * gene_biotype: the biotype of gene * gene_description:
 the description of gene * tf_family: the transcription factor of gene
DOI: 10.5061/dryad.0rxwdbsbz
title: Spectroscopic data for the total synthesis of brevianamide S

description: # Spectroscopic data for the total synthesis of brevianamide S Data is
 grouped in appropriately named folders according to the compound it
 relates to. FID folders are named for the NMR experiment. A folder named
 “HMBC” would therefore be the FID for a HMBC spectrum. For compounds that
 are reported in more than one solvent, the solvent is also included in the
 folder name. The FID folders can be processed and interpreted using
 MestReNova or TopSpin. Primary IR data is recorded in .txt or .tsv files
 in folders named “IR”. These files contain x and y coordinates, which can
 be plotted to display the IR spectra.
description: The first total synthesis of the alkaloid brevianamide S has been achieved
 in eight steps. This natural product, isolated from Aspergillus
 versicolor, exhibits selective antibacterial activity against Bacille
 Calmette-Guérin (BCG), a commonly used surrogate for Mycobacterium
 tuberculosis. Brevianamide S is proposed to act through a novel,
 yet-to-be-elucidated mechanism, making it a promising lead in the
 development of next-generation antitubercular agents. Our approach employs
 a bidirectional synthetic strategy, involving a bespoke alkenyl-alkenyl
 Stille cross-coupling reaction and a double aldol condensation. This
 represents a flexible and efficient platform for the future synthesis of
 structurally diverse analogues.
DOI: 10.15468/dl.e5w7y2
title: Occurrence Download

description: A dataset containing 66999 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Hesperocyparis forbesii, Polioptila californica)"
 ]
}

 The dataset includes 66999 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004242-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.