cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g209
title: Flow cytometric analysis of neutrophil populations present in orthotopic KCKO cancers

description: Chronic inflammatory milieu in the tumor microenvironment (TME) leads to
 the recruitment and differentiation of myeloid-derived suppressor cells
 (MDSCs). Polymorphonuclear (PMN)-MDSCs, which are phenotypically and
 morphologically defined as a subset of neutrophils, cause major immune
 suppression in the TME, posing a significant challenge in the development
 of effective immunotherapies. Despite recent advances in our understanding
 of PMN-MDSC functions, the mechanism that gives rise to immunosuppressive
 neutrophils within the TME remains elusive. Both in vivo and in vitro,
 newly recruited neutrophils into the tumor sites remained activated and
 highly motile for several days and developed immunosuppressive phenotypes,
 as indicated by increased arginase 1 (Arg1) and dcTrail-R1 expression and
 suppressed anti-cancer CD8 T cell cytotoxicity. The strong suppressive
 function was successfully recapitulated by incubating naïve neutrophils
 with cancer cell culture supernatant in vitro. Cancer metabolite secretome
 analyses of the culture supernatant revealed that both murine and human
 cancers released lipid mediators to induce the differentiation of
 immunosuppressive neutrophils. Liquid chromatography–mass spectrometry
 (LC-MS) lipidomic analysis identified platelet activation factor (PAF;
 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) as a common tumor-derived
 lipid mediator that induces neutrophil differentiation.
 Lysophosphatidylcholine acyltransferase 2 (LPCAT2), the PAF biosynthetic
 enzyme, is upregulated in human pancreatic ductal adenocarcinoma (PDAC)
 and shows an unfavorable correlation with patient survival across multiple
 cancer types. Our study identifies PAF as a lipid-driven mechanism of MDSC
 differentiation in the TME, providing a potential target for cancer
 immunotherapy.
description: This data set contains raw fcs flow cytometric data from
 <em>in vivo</em> experiments on naive and tumor bearing
 mice. 
description: # Flow Cytometric Data set
 [https://doi.org/10.5061/dryad.866t1g209](https://doi.org/10.5061/dryad.866t1g209) Dataset contains raw fcs files from *in vivo* experiments described in the manuscript.  ## Description of the data and file structure Raw fcs files of tumor digestion. All markers are labeled in the dataset ***Name of dataset:*** (number after the name denotes biological replicate) *N_BM* (Bone marrow isolated from naive mice) *T_BM* (Bone marrow isolated from tumor bearing mice) *N_SPL* (Spleen isolated from naive mice) *T_SPL* (Spleen isolated from tumor bearing mice) *Tumor* (KCKO tumor)
DOI: 10.15468/dl.4a2p4f
title: Occurrence Download

description: A dataset containing 61172 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sprattus fuegensis",
 "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 61172 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004061-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r4xgxd2p5
title: Data from: Dipoles affect conformational equilibrium

description: Electric dipoles are ubiquitous. They affect charge transfer,
 self-assembly, materials performance, and enzymatic activity. Herein, we
 demonstrate dipole effects on molecular geometry. An aromatic amide,
 5-N-amide derivative of anthranilamide (Aaa), assumes two stable
 conformations with drastically different dipole moments. In non-polar
 solvents, Aaa exists predominantly as the conformer with the smaller
 dipole as nuclear Overhauser effect (NOE) and density-functional theory
 (DFT) analysis reveal. Increasing medium polarity drives the emergence of
 the other structure with the larger dipole. Splitting of the NMR signals
 at low temperature is consistent with capturing the two Aaa conformers
 upon its aggregation. Analysis employing density-functional theory
 quantifies the dynamics of the equilibrium between the two conformations
 and how solvent polarity affects it. This synergy between molecular
 electric dipoles and medium polarity reveals a paradigm for conformational
 switching.
description: # Data pertinent to manuscript "Dipoles Affect Conformational
 Equilibrium"
 [https://doi.org/10.5061/dryad.r4xgxd2p5](https://doi.org/10.5061/dryad.r4xgxd2p5) ## Description of the data and file structure **Steady-state optical absorption and emission spectra of Aaa.xlsx** Sheet 1, “Absorption spectra of Aaa,” includes the wavelength in nanometers (*λ* */* nm) and three columns with the molar extinction coefficients for different solvents (*ε*(*solvent*) / M–1 cm–1). Sheet 2, “Fluorescence spectra of Aaa,” includes the wavelength in nanometers (*λ* */* nm) and three columns with the fluorescence intensities recorded for different solvents (*F*(*solvent*)). **Pulse-radiolysis spectra of Aaa.xlsx** This file contains a matrix of two-dimensional data showing change in absorbance, Δ*A*, vs. time at different wavelengths, *λ*, i.e., Δ*A*(*λ*, *t*). The first column of this spreadsheet includes the timepoints relevant to the ionization pulse   (*time /* s), and the rest of the columns include  at each of these timepoints recorded at different wavelengths (Δ*A*(*λ *nm)).  **Proton NMR spectra of Aaa.xlsx** Sheet 1, “Proton NMR spectra (CDCl3),” includes the 1H NMR spectra of Aaa in CDCl3 recorded at different temperatures. Each spectrum is introduced as two columns: (*δ* */* ppm (temperature °C)) containing the abscissa (*x*-axis) ppm values and (temperature °C) containing the ordinate (*y*-axis) spectral intensities values recorded at the indicated temperature.  Sheet 2, “Proton NMR spectra (CD3CN),” includes the 1H NMR spectra of Aaa in CD3CN recorded at different temperatures. Each spectrum is introduced as two columns: (*δ* */* ppm (temperature °C)) containing the abscissa (*x*-axis) ppm values and (temperature °C) containing the ordinate (*y*-axis) spectral intensities values recorded at the indicated temperature.
DOI: 10.5061/dryad.bk3j9kdmt
title: Broadening the horizon of Indian mycobiota: Two new species and one new generic record in Boletoid mushrooms (Boletaceae)

description: Combined approach on morphological studies and multigene molecular
 phylogenetic analyses unveil two significant novel species of boletes
 namely, Anthracoporus indohimalayanus sp. nov. and Boletus dhakuricus sp.
 nov. from the states of Sikkim and Uttarakhand respectively. Our first
 novel species A. indohimalayanus is also the new generic record of
 Anthracoporus from India whereas, our second novel species B. dhakuricus
 is a member of wild edible porcini mushroom. Both the taxa are described
 with their morphological details and molecular phylogenetic inferences.
description: # Broadening the horizon of Indian mycobiota: Two new species and one new
 generic record in Boletoid mushrooms (Boletaceae) Authors and Contact
 Information * Dr. Kanad Das (Corresponding Author) * Email:
 [daskanadbsi@gmail.com](mailto:daskanadbsi@gmail.com) * Dr. Aniket Ghosh *
 Email: [ghosh.aniket87@gmail.com](mailto:ghosh.aniket87@gmail.com) # Date
 of Data Collection and Submission * For Boletus dhakuricus, Data
 Collection Period: August 2023 * For Anthracoporus indohimalayanus, Data
 Collection Period: July 2014 & August 2023 * Date of Submission: July
 2024 ## Sharing/Access information Data was derived from the following
 sources: * Sequences are derived from dried mushroom samples. # Abstract
 This dataset contains aligned multigene genealogical data of two wild
 mushrooms (Anthracoporus indohimalayanus and Boletus dhakuricus) from the
 states of Sikkim and Uttarakhand, India respectively. The study aimed to
 identify and classify two novel wild mushrooms using integrative
 morphotaxonomy and molecular phylogeny. # Data Description * File 1:
 Aligned file of "Boletus dhakuricus.fasta" - FASTA format file
 containing aligned multigene sequences. * File 2: Aligned file of
 "Anthracoporus indohimalayanus.fasta" - FASTA format file
 containing aligned multigene sequences.
DOI: 10.15468/dl.jbqu5g
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Conorhynchos conirostris"
 ]
}

 The dataset includes 181 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004094-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.80gb5mkzw
title: A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics

description: Animals throughout the metazoa selectively acquire specific symbiotic gut
 bacteria from their environment that aid host fitness. Current models of
 colonization suggest these bacteria use weakly specific receptors to stick
 to host tissues and that colonization results when they stick in a region
 of the host gut that overlaps with their nutritional niche. An alternative
 model is that unique receptor-ligand binding interactions provide
 specificity for target niches. Here we use live imaging of individual
 symbiotic bacterial cells colonizing the gut of living Drosophila
 melanogaster to show that Lactiplantibacillus plantarum specifically
 recognizes a distinct physical niche in the host gut. We find that
 recognition is controlled by a colonization island that is widely
 conserved in commensals and pathogens from the Lactobacillales to the
 Clostridia. Our findings indicate a genetic mechanism of host specificity
 that is broadly conserved.
description: # A conserved genetic basis for commensal-host specificity through live
 imaging of colonization dynamics
 [https://doi.org/10.5061/dryad.80gb5mkzw](https://doi.org/10.5061/dryad.80gb5mkzw) Alignments and all the trees used to construct all the figures are available in this public repository. For further information related to the code and programs used to generate the figures, please visit: Gutierrez-Garcia, K., Aumiller, K., Dodge, R., Obadia, B., Deng, A., Agrawal, S., Yuan, X., Wolfe, R., Garud, N., & Ludington, W. B. (2024). A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics. Zenodo. [https://doi.org/10.5281/zenodo.13115916](https://doi.org/10.5281/zenodo.13115916) Or  [https://github.com/K-Gutierrez/LpColonizationIsland/](https://github.com/K-Gutierrez/LpColonizationIsland/)) #### **Files related to Figure 3:** * Fig3-SpeciesTree-36Org-rooted.tree * Fig3-SpeciesTree-36Org.fasta #### **Files related to aSec tree:** * aSec-phylogeny-based-on-the-core-genes-aln-gb.fasta * aSec-phylogeny-based-on-the-core-genes-MappingFile.txt * aSec-phylogeny-based-on-the-core-genes-rooted.tree #### **Files related to dN/dS analysis:** * Cluster1-pal2nal.fasta * Cluster1-aBSREL.json * Cluster2-pal2nal.fasta * Cluster2-aBSREL.json * Cluster3-pal2nal.fasta - Cluster3-aBSREL.json #### **Files for the core genome tree:** * Phylogeny_of_colonization_island-containing_strains-MappingFile.txt * Phylogeny_of_colonization_island-containing_strains.fasta * Phylogeny_of_colonization_island-containing_strains.tree #### **Files to perform the Co-phylogenetic analysis** * aSecTree1-rooted.tree * aSecTree1.fasta * SpeciesTree1-rooted.tree * SpeciesTree1.fasta * aSecTree2-rooted.tree * aSecTree2.fasta * SpeciesTree2-rooted.tree * SpeciesTree2.fasta * aSecTree3-rooted.tree * aSecTree3.fasta * SpeciesTree3-rooted.tree * SpeciesTree3.fasta * aSecTree4-rooted.tree * aSecTree4.fasta * SpeciesTree4-rooted.tree * SpeciesTree4.fasta
DOI: 10.5061/dryad.05qfttfc0
title: Data from: PicoCam: High-resolution 3D imaging of live animals and preserved specimens

description: The PicoCam system is a multi-camera photogrammetry rig used for
 generating high-resolution 3D models of animals in the field, or preserved
 specimens in laboratory or museum settings. The digital measurement of 3D
 models is increasingly useful for studying body shape. However, methods
 that capture sub-millimetric detail often do so at the cost of portability
 and versatility; this system aims to bridge this gap. The PicoCam
 system employs 3D digital photogrammetry, a process that generates
 accurate, full-color,  3D models from sequences of photographs.
 By using six cameras and a rotating base, the system is able to capture
 multiple angles in rapid succession – a key advantage for both 3D-imaging
 live specimens and efficiently scanning museum specimens. Through the use
 of macro lenses and high-resolution camera sensors, this system can
 capture sub-millimetric detail without sacrificing portability. In this
 study, we 3D imaged the bills of 19 species of hummingbirds using the
 PicoCam system and measured the length, height, width, surface area, and
 volume of their bills. We examined eight species in the field and 11 from
 the Burke Museum in Seattle. We chose Hummingbird bills as a model system,
 as their fine-scale interspecific differences in 3D shape can have
 significant functional and behavioral implications, and could tell us more
 about how these traits predict habitat and resource use. The
 prospect of a common 3D-imaging method for both museum and field use is
 compelling when documenting structures’ shape within and among species.
 The PicoCam system is also valuable for quantifying the 3D shape of
 fine-scale phenotypes (like hummingbird bills) that benefit from digital
 measurement, preservation, and improved accessibility. Lastly, the PicoCam
 system allows “digital 3D collection”, by which the shape of biological
 structures in the field can be recorded and stored in a public database
 without the need to collect a specimen. This opens the door to studies in
 which multiple 3D image captures of the same individual across different
 time scales permit 3D shape/color comparisons (e.g., seasonal, ontogenetic
 changes).
description: # PicoCam We submitted our raw data (PicoCam_measurements.csv), as well as
 our 3D models in .OBJ format used to collect the data
 (PicoCam_models.zip). ## Descriptions ### PicoCam\_measurements *
 *Species*: species scanned to produce the 3D model * *Dataset*: whether
 the scan was generated from live animals in the field, or a museum
 specimen * *Length*: length of the bill in mm * *Width*: width of the base
 of the bill in mm * *Height*: height of the base of the bill in mm *
 *Volume*: volume of the bill in cubic mm * *SA*: surface area of the bill
 in square mm ### PicoCam\_models PicoCam_models.zip contains 3D models for
 19 species of hummingbirds assembled in a combined .OBJ format. The 3D
 models were arranged in Blender (Version 4.1), which can also be used to
 view, measure, and export the individual models.
DOI: 10.5061/dryad.0rxwdbs97
title: Data from: Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)

description: The Laufeia clade is a peculiar lineage of euophryine jumping spiders
 showing elevated divergence of male genitalic structures, especially the
 embolic complex that directly interacts with female genitalia during sperm
 transfer. With the rapid growth of species discovery in the Laufeia clade,
 the controversy in its classification has become a crucial problem. In
 this study, we applied a phylogenomic approach using ultra-conserved
 element data to infer the phylogeny of the Laufeia clade with extensive
 taxon sampling. A comparative morphological study was also performed to
 evaluate diagnostic characters and understand the evolution of male
 embolic complex within the Laufeia clade. The results provide a strongly
 supported phylogenetic framework and updated generic concepts for the
 Laufeia clade. The updated genera within the Laufeia clade were all
 recovered as monophyletic with well-defined synapomorphies identified
 through character mapping on the phylogeny. Ancestral state reconstruction
 analyses revealed that the Type I embolic complex was ancestral and
 gradually evolved into the Type II and III embolic complex, and that some
 shapes of embolus often evolved multiple times independently in different
 lineages of the Laufeia clade. The shift from foliage dwelling to tree
 trunk dwelling at the common ancestor of the Laufeia clade may have
 facilitated the divergent evolution of male embolic complex in the Laufeia
 clade. This study provides a solid foundation for future studies of
 systematics and evolution of this group.
description: # Data from: Robust phylogenomics settles controversies of classification
 and reveals evolution of male embolic complex of the Laufeia clade
 (Araneae, Salticidae, Euophryini)
 [https://doi.org/10.5061/dryad.0rxwdbs97](https://doi.org/10.5061/dryad.0rxwdbs97) Description of the data and file structure LaufeiaUCE_98taxa.mafft.alignments.rename.zip: contains all the alignments for the UCE loci; LaufeiaUCE_98taxa_proofed.2431loci.alignments.rename.zip: contains the 2431 trimmed and proof-checked UCE loci (alignments) for the final phylogenetic analyses LaufeiaUCE_98taxa.Concat2431loci.rename.phy: final concatenated UCE dataset with 2431 loci for the phylogenetic analyses; LaufeiaUCE_98taxa.Concat2431loci.partitiont: partition file for the concatenated 2431-UCE dataset; LaufeiaUCE_98taxa.2431loci.PhylogeneticTrees.rename.zip: Contains the results from ML, MP, Bayesian, ASTRAL and concordance factor (gene-wise and site-wise) analyses.
DOI: 10.5061/dryad.fxpnvx127
title: Needs assessment of advanced practice provider education in allergy & immunology

description: Advanced practice providers (APPs) are increasingly utilized throughout
 the health care system. At present there is no nationally sanctioned
 curriculum for APPs providing Allergy & Immunology (A&I)
 care. A nationwide gap analysis and targeted needs assessment
 were conducted to examine the current level of education/training of APPs
 in A&I. At present, training in A&I in NP/PA schools is
 quite limited. The formal education and clinical training APPs receive at
 practice sites varies significantly with most APPs feeling only somewhat
 comfortable providing A&I care upon completion of their training
 period. Results of a nationwide gap analysis and targeted needs assessment
 identify the need for providing education specific for A&I to APPs
 practicing in this field.
description: To examine the current state of education/training for APPs
 within A&I on a national level, gap analysis, and targeted needs
 assessment were performed with the recruitment of APPs on a national level
 through the American Academy of Allergy, Asthma & Immunology
 (AAAAI) Allied Health Listserve.  This was done as an initial step in the
 development of a Core Curriculum for APPs within A&I through the
 AAAAI Educator Development award. The gap analysis consisted of a series
 of 20 qualitative interviews with APPs and 5 physicians (who had recently
 trained APPs in A&I) using open-ended questions to better
 understand the current level of education/clinical training. The data has
 not been processed.
description: # Needs assessment of advanced practice provider education in allergy
 & immunology
 [https://doi.org/10.5061/dryad.fxpnvx127](https://doi.org/10.5061/dryad.fxpnvx127) ## Description of the data and file structure A case for specific education of advanced practice providers in allergy & immunology: results of a gap analysis and targeted needs assessment ### Files and variables This data seeks to understand the current training experience of Advanced Practice Providers (APPs) in Allergy & Immunology. Each horizontal line indicates the responses of each participant with the question itself indicated in row #2. All free-form responses have been removed as they could contain potentially identifying information. The response of each participant indicates their selection in a multiple-choice response.  Acronyms: APP: Advanced Practice Provider A&I. Allergy & Immunology Empty Cells: Response was not entered by the participant.  Columns with NA listed at the top included potentially identifying information so were removed from the published data set. Examples include freeform responses, IP addresses, etc.  #### File: Data\_for\_publication.xlsx **Description:** Targeted Needs Assessment ##### Variables * Listed across row 1, and defined across row 2  ## Code/software Excel ## Access information Other publicly accessible locations of the data: * NA Data was collected from the following sources: * AAAAI Allied Health Listserve
DOI: 10.5061/dryad.b2rbnzsqd
title: Data from: The impact of aid sanctions on maternal and child mortality, 1990–2019: A panel analysis

description: To build this dataset, we searched four established sanctions databases –
 HSE/HSEO Database, the Threat and Imposition of Economic Sanctions (TIES)
 database, The Targeted Sanctions Consortium (TSC) database, and the
 EUSANCT database – for evidence of an aid sanction and extracted the
 identity of the sanctioning and sanctioned countries, the year imposed,
 and the year lifted (if not on-going) for each sanction case. We checked
 for additional aid sanctions not captured in these four databases by
 searching for cases imposed by the European Union and the United States in
 the online content of the European Parliament and US Department of State,
 respectively. For other individual nations and regional bodies imposing
 aid sanctions, we screened online search engines to gather information
 about these cases and then confirmed the information with official
 government documents such as policy orders on government websites. To
 ensure consistency and reliability, three additional co-authors reviewed
 the aid sanctions dataset independently.
description: The replication files require the user to request the Global
 Sanctions Database directly from the Global Sanctions Database team, which
 can be obtained by emailing - GSDB@drexel.edu
description: # Data from: The impact of aid sanctions on maternal and child mortality,
 1990–2019: A panel analysis
 [https://doi.org/10.5061/dryad.b2rbnzsqd](https://doi.org/10.5061/dryad.b2rbnzsqd) ## Description of the data and replication files To build this dataset, we searched four established sanctions databases – HSE/HSEO Database, the Threat and Imposition of Economic Sanctions (TIES) database, The Targeted Sanctions Consortium (TSC) database, and the EUSANCT database – for evidence of an aid sanction and extracted the identity of the sanctioning (Sanctioning state) and sanctioned countries (Sanctioned state), the year imposed (Begin), and the year lifted (End) (if not on-going) for each sanction case.  We checked for additional aid sanctions not captured in these four databases by searching for cases imposed by the European Union and the United States in the online content of the European Parliament and US Department of State, respectively. For other individual nations and regional bodies imposing aid sanctions, we screened online search engines to gather information about these cases and then confirmed the information with official government documents such as policy orders on government websites. To ensure consistency and reliability, three additional co-authors reviewed the aid sanctions dataset independently. We include the replication package for other researchers. Please cite this study when using our replication files for other work.  All files included in this replication package and datasets comply with CC0 license waiver. To run the associated code, you will need to make a direct request for the Global Sanctions Database by emailing - [GSDB@drexel.edu](mailto:GSDB@drexel.edu "Request GSDB Data")