cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dncjsxm68
title: Circulating KLRG1+ memory T cells retain the flexibility to become tissue-resident

description: KLRG1+ CD8 T cells persist for months after acute infections are cleared
 and maintain high levels of effector molecules, contributing essential
 protective immunity against systemic pathogens. Upon secondary infection,
 these long-lived effector cells (LLECs) are incapable of forming other
 circulating KLRG1− memory subsets such as central and effector
 memory T cells. Thus, KLRG1+ memory T cells are frequently referred to as
 a terminally differentiated population that is relatively short lived.
 Here, we show that during infection, effector cells derived from LLEC
 rapidly enter nonlymphoid tissues and reduce pathogen burden, but are
 largely dependent on receiving antigen cues from vascular endothelial
 cells. Single-cell RNA sequencing revealed that secondary memory cells in
 nonlymphoid tissues arising from either KLRG1+ or KLRG1− memory
 precursors developed a similar transcriptional signature. Thus, although
 KLRG1+ memory T cells cannot differentiate into other circulating memory
 populations, they still retain the flexibility to enter tissues and
 establish residency.
description: # Circulating KLRG1+ memory T cells retain the flexibility to become
 tissue-resident
 [https://doi.org/10.5061/dryad.dncjsxm68](https://doi.org/10.5061/dryad.dncjsxm68) The goal of this study was to determine if long-lived effector CD8 T cells (LLEC), which are usually confined to circulation will enter inflamed tissues upon infectious challenge and contribute to the resident memory T cell pool. This data set contains flow cytometry files (FCS files) and the raw tiffs from the microscopy files from each figure in the manuscript. The flow cytometry data was collected on isolated white blood cells isolated from various tissues. Briefly, purified populations of memory CD8 cell P14 or endogenous subsets were transferred into mice, and then the mice were infected with either LCMV or IAV-gp33. At differing time points tissues were harvested and processed for flow cytometry. Samples were stained with antibody cocktails that allowed for the identification of the transferred cells and the characterization of phenotypes. For microscopy, tissues were embedded in OCT and then stained with antibodies to allow for the identification of the transferred T cells and blood vessels. ## Description of the data and file structure Each .zip folder contains the data from one timepoint following cell transfer and reinfection with the virus indicated in the folder name. Abbreviations are as follows: LLEC- long lived effector cell TCM - central memory T cell TEM - effector memory T cell LN - lymph node SG - salivary gland SI-IEL - small intestine intraepithelial layer CTV - cell trace violet For the microscopy data, the raw Tiffs are provided in a zip folder.
DOI: 10.5061/dryad.zkh1893hb
title: Data from: Aboveground versus soil-mediated effects of an invasive grass on fire-dependent forbs in an oak woodland

description: Most work on plant competition intensity in general has focused on how
 aboveground and belowground competition for resources between plants
 change with soil resource availability. In contrast, much work on the
 competitive effects of non-native invasive species on native species has
 focused on other mechanisms (e.g., allelopathy, microbial changes) and has
 largely ignored how these effects interact with mechanisms of resource
 competition along productivity gradients. We examined aboveground effects
 of an invasive grass, Microstegium vimineum, along with soil
 differences between invaded and non-invaded areas on two native perennial
 herbs at a productive and an unproductive oak woodland site in north
 Mississippi, USA. We transplanted 32 individuals each of Helianthus
 silphioides and Potentilla simplex from uninvaded areas into natural
 patches dominated by M. vimineum at each of the sites. Each transplant was
 randomly assigned to a pot with either native soil or soil from around M.
 vimineum roots. Aboveground competition was manipulated by securing M.
 vimineum shoots in a non-shading position around the transplant. We
 monitored survival of all transplants weekly in the growing seasons of
 2020 and 2021. Transplant survival of H. silphioides was lowest
 in M. vimineum soil at the more productive site when M. vimineum was not
 pinned back. Transplant survival of P. simplex was lower at the more
 productive site but was mostly unresponsive to pinning and soil
 treatments. Synthesis: Our results suggest that soil-mediated legacy
 effects of an invader may reduce some native species’ ability to compete
 for light at productive sites.
description: # Data from: Aboveground versus soil-mediated effects of an invasive grass
 on fire-dependent forbs in an oak woodland (Williams & Brewer,
 2024) [https://doi.org/10.1002/ece3.11712](https://doi.org/10.1002/ece3.11712) [https://doi.org/10.5061/dryad.zkh1893hb](https://doi.org/10.5061/dryad.zkh1893hb) ## Description of the data and file structure **Appendix S1 metadata.docx** - The metadata containing the variables used in the statistical analyses and a description of what the variable represents. **Appendix_S1_data.csv -** The data used for all analyses. Specifically, this file contains the initial weight, canopy density above the transplants, survival, and flowering data for *Helianthus silphioides* and *Potentilla simplex* transplants. **Appendix_S1_code.r** - The annotated R script (created in R version 4.1.0) containing the code for all analyses performed. ## Code/Software The R script (created in R version 4.1.0) for all analyses performed in the associated manuscript titled "Aboveground versus Soil-Mediated Effects of an Invasive Grass on Fire-Dependent Forbs in an Oak Woodland Data Set". The code is annotated and contains all necessary information to replicate the analyses.
DOI: 10.5061/dryad.5qfttdzdq
title: Data from: Hematological parameters vary with life history stage in the pale-breasted thrush (Turdus leucomelas)

description: The avian life cycle is composed by a progressive sequence of life history
 stages (LHS). Changes in energy expenditure and exposure to stressors at
 different LHS require corresponding changes in behavior, physiology, and
 morphology. Variation in hematological parameters, such hematocrit (Hct),
 hemoglobin (Hb), and heterophil to lymphocyte ratio (H/L ratio), can have
 permissive, stimulatory, and preparative actions to help maintain
 homeostasis through different LHS. Few studies have examined differences
 in these parameters among different LHS in free-living birds, with most of
 them restricted to temperate zones. We collected blood samples and
 measured hematological parameters every week for over a year from a
 population of a common resident bird species in southeastern Brazil, the
 pale–breasted thrush (Turdus leucomelas). Hematocrit and hemoglobin
 concentration were highest during the onset of the reproduction and lowest
 during molt. Furthermore, H/L ratios were higher at the end of the
 reproduction, indicating that the breeding season could be the most
 stressful period of the year for this population of thrushes. There was no
 difference between sexes for any hematological parameter at any LHS. These
 results show that there is a permissive physiological effect for Hct and
 Hb to facilitate LHS transitions and that reproduction could be the most
 stressful event for this species. Lastly, these results mirror those from
 temperate species despite distinct environmental differences between these
 regions.
description: # Hematological parameters vary with life history stage in the
 pale-breasted thrush (Turdus leucomelas)
 [https://doi.org/10.5061/dryad.5qfttdzdq](https://doi.org/10.5061/dryad.5qfttdzdq) This dataset was collected in the Universidade Estadual Paulista (UNESP) - Rio Claro in Sao Paulo, Brazil (2017) **ID**: individual metallic band id given to each individual **day**: day of the year when capture occurred **hour and hour.ori**: **hour.ori** indicates the real hour each individual got captured. For **hour** we considered time, in minutes, after 6:00am. **Temperature**: mean temperature, in celsius, at the time of capture. **sex**: sex of each captured individual **LHS**: life history stage of each individual at the time they got captured **hematocrit**: hematocrit value (%) for each individual **hemoglobin**: hemoglobin level (g/dL) for each individual **weight**: body mass, in grams, for each individual **H_L and H_L.trans**: H/L ratio (heterophil to lymphocyte ratio) and H/L ratio values after boxcox transformation, respectively. We did not take this measurement for all individuals. Thus, missing values are denoted by NA. **wing, tail, culmen and tarsus**: morphological measurements, in mm, for each individual **SMI_Cul**: body condition index for each individual. We utilized the scaled-mass index (Peig & Green, 2009) and considered the body mass and tarsus values.
DOI: 10.5281/zenodo.18405717
title: Table 1 in Trichomycterus anhanga, a new species of miniature catfish related to T. hasemani and T. johnsoni (Siluriformes: Trichomycteridae) from the Amazon basin, Brazil

description: Table 1. Morphometric data for holotype and paratypes of Trichomycterus anhanga (n = 9 including holotype).
HolotypeMin.Max.MeanSDStandard length (SL, mm)10.09.713.1--Percentage of SLTotal length120.7113.9126.3119.33.5Body depth16.911.616.914.01.7Peduncle length22.321.624.923.51.1Peduncle depth15.210.715.212.51.7Predorsal length66.265.569.467.81.5Preanal length68.263.571.467.42.3Dorsal-fin base length8.07.510.18.60.8Anal-fin base length7.85.59.27.71.0Head length (HL)18.417.220.218.41.0Percentage of HLHead width93.580.696.389.15.5Head depth33.033.050.340.25.3Interorbital19.517.823.220.61.7Snout length31.923.037.231.44.6Nasal babel length30.826.539.832.14.6Maxillary babel length41.637.055.045.96.0Rictal barbel length34.132.253.939.87.4Mouth width31.922.538.828.64.9Eye diameter15.113.619.015.91.7
description: Published as part of Dutra, Guilherme M., Wosiacki, Wolmar B. & de Pinna, Mario C. C., 2012, Trichomycterus anhanga, a new species of miniature catfish related to T. hasemani and T. johnsoni (Siluriformes: Trichomycteridae) from the Amazon basin, Brazil, pp. 229 in Neotropical Ichthyology 10 (2) on page 229, DOI: 10.1590/S1679-62252012000200001, http://zenodo.org/record/4647117
DOI: 10.5281/zenodo.18405718
title: Table 1 in Trichomycterus anhanga, a new species of miniature catfish related to T. hasemani and T. johnsoni (Siluriformes: Trichomycteridae) from the Amazon basin, Brazil

description: Table 1. Morphometric data for holotype and paratypes of Trichomycterus anhanga (n = 9 including holotype).
HolotypeMin.Max.MeanSDStandard length (SL, mm)10.09.713.1--Percentage of SLTotal length120.7113.9126.3119.33.5Body depth16.911.616.914.01.7Peduncle length22.321.624.923.51.1Peduncle depth15.210.715.212.51.7Predorsal length66.265.569.467.81.5Preanal length68.263.571.467.42.3Dorsal-fin base length8.07.510.18.60.8Anal-fin base length7.85.59.27.71.0Head length (HL)18.417.220.218.41.0Percentage of HLHead width93.580.696.389.15.5Head depth33.033.050.340.25.3Interorbital19.517.823.220.61.7Snout length31.923.037.231.44.6Nasal babel length30.826.539.832.14.6Maxillary babel length41.637.055.045.96.0Rictal barbel length34.132.253.939.87.4Mouth width31.922.538.828.64.9Eye diameter15.113.619.015.91.7
description: Published as part of Dutra, Guilherme M., Wosiacki, Wolmar B. & de Pinna, Mario C. C., 2012, Trichomycterus anhanga, a new species of miniature catfish related to T. hasemani and T. johnsoni (Siluriformes: Trichomycteridae) from the Amazon basin, Brazil, pp. 229 in Neotropical Ichthyology 10 (2) on page 229, DOI: 10.1590/S1679-62252012000200001, http://zenodo.org/record/4647117
DOI: 10.5061/dryad.4tmpg4fjj
title: Frugivory and seed predation of fishtail palm (Caryota mitis Lour.) on the remote oceanic island of Narcondam, India

description: Oceanic islands, due to their evolutionary history and isolation, play a
 dual role of having high endemicity and being vulnerable to extinctions,
 with most known extinctions occurring on islands. Plant–animal
 interactions are particularly important on islands, as island systems
 generally have low redundancy and are more vulnerable to disruption either
 via extinction or by invasive species. Here, we examined the fruit removal
 and seed predation of a keystone palm, Caryota mitis, on
 Narcondam, a remote oceanic island. The island endemic Narcondam Hornbill
 (Rhyticeros narcondami) was the sole seed disperser of
 the palm (90 hours; N = 15 trees), with mean (±
 SE) visitation rate being 0.23 (± 0.06) individuals per hour and fruit
 removal rates of 3.5 (± 1.5; range: 0–16) fruits per visit, indicating a
 lack of redundancy in seed dispersal of the palm on this island. Whereas
 the invasive
 rodent, Rattus cf. tiomanicus, was the
 sole predator of palm seeds (N = 15 individual fruiting palms,
 416 trap nights). Overall, 17.1% of the seeds placed (N = 375 seeds) were
 removed. Seeds placed under and away from the canopy, and at different
 densities (2 plots with 10 seeds each; 1 plot with 5 seeds, respectively),
 showed similar removal rates. This indicates density-independent seed
 predation and the lack of safe regeneration sites for Caryota
 mitis, with potential deleterious effects on subsequent stages of the
 ‘seed dispersal cycle’. Here, from a data-deficient site, we provide
 baseline information on the plant–frugivore interaction of a keystone palm
 and the potential impacts of an invasive rodent.
description: # Frugivory and seed predation of fishtail palm (Caryota mitis Lour.) on
 the remote oceanic island of Narcondam, India
 [https://doi.org/10.5061/dryad.4tmpg4fjj](https://doi.org/10.5061/dryad.4tmpg4fjjGive) ## Description of the data and file structure This dataset reports the seed fates to the seed plots set up in the study. The .csv file contains the seed fate of the 7 species examined in the study. tree_sp: Name of the seven tree species that were part of the study tree_code: Unique id number for each of the tree under which the seed plots were set up lat: Latitude of the tree sampled long: Longitude of the tree sampled elev: Elevation in metres start_date:  Start date of the seed monitoring session end_date: End date of the seed monitoring session days_monitored: Number of days seed plots were surveyed plot_code: Code for the plot for each of the treatment type type: These represent the three treatments: Away_high and Away_low plots 15m away from the focal tree with 10 seeds and 5 seeds respectively, and Canopy, plots under the canopy with 10  seeds. Intact: Seeds which have remained as it is in the plot. Removed: Seeds which have been predated or removed from the plot.
DOI: 10.5061/dryad.4j0zpc8kn
title: Growth mindset and well-being during the pandemic

description: Growth mindset, the belief that abilities and attributes are changeable,
 has been implicated in better mental health and health behaviors and may
 be especially critical during challenging life events. One goal of this
 prospective longitudinal study was to investigate the role of growth
 mindset in adults’ mental health (i.e., depression, well-being, and
 adjustment of daily routines) over two years of the COVID-19 pandemic. We
 also examined this relationship in older adults who had participated in a
 prior learning intervention, including growth mindset training (compared
 with those who had not). Adults ages 19 to 89 from ethnically diverse
 backgrounds in Southern California (n = 454) were surveyed at three
 timepoints between June 2020 and September 2022. In Study 1, focusing on
 this wide age range (n = 393), we found that a growth mindset was
 associated with lower levels of depression and higher levels of well-being
 and adjustment, after accounting for various sociodemographic factors.
 Study 2, which focused on older adults (n = 174), largely replicated the
 findings from Study 1. Furthermore, the conducive effect of a growth
 mindset on well-being was marginally greater among those who had
 participated in the intervention, and those who had participated in the
 intervention showed an increase in well-being over time, while well-being
 scores decreased in the control group. Together, our findings suggest that
 a growth mindset may be an important protective factor for mental health
 during challenging times.
description: # Growth mindset and well-being during the pandemic
 [https://doi.org/10.5061/dryad.4j0zpc8kn](https://doi.org/10.5061/dryad.4j0zpc8kn) This is a minimal dataset used for this study. ## Description of the data and file structure All missing responses are indicated by NA. PID = Participant ID wave = Timepoints (1 = Wave 1, 2 = Wave 2, 3 = Wave 3) Int = Intervention status (1 = Intervention group; 0 = Control group) Gender = Gender (0 = male; 1 = female) Age = Age computed by subtracting the birth date from the survey date. Race = Dichotomized racial group (0 = Non-Hispanic white; 1 = All other groups) Retired = Retirement status (1 = Retired; 2 = Not retired) Marital = Relationship status (1 = Married or have a partner; 2 = Widowed; 3 = Separated or divorced; 4 = Never married) Income = Annual household income from last year (1 = Less than $20,000; 2 = $20,000 to $29,999 ... 6 = $100,000 to $199,999; 7 = $200,000 and over) Depression = Depression scores measured by the PHQ-9 (Higher scores representing more severe symptoms) PERMA_Overall = Overall well-being scores measured by the PERMA-Profiler (Higher scores representing greater well-being) GM_new = Growth mindset scores (Higher scores representing a greater endorsement of growth mindset) BEH4 = Adjustment of daily routines during the pandemic (Higher scores representing a greater adjustment)
DOI: 10.5281/zenodo.18383490
title: The dataset, the code, the models, and the namelist files for "Gray-Zone Simulation of the Dry Convective Boundary Layer Using Fourier Neural Operator"

description: The dataset for training and testing, the FNO code, the trained FNO model, and the namelist files are used in the paper: Gray-Zone Simulation of the Dry Convective Boundary Layer Using Fourier Neural Operator.

The FNO code is also available at https://github.com/FreyLuo/FNO-CBL. 

The LES data can be found at https://doi.org/10.5281/zenodo.18326720.
DOI: 10.5281/zenodo.18371203
title: Speculative Design and Entanglement Theories (Workshop)
DOI: 10.5281/zenodo.18371204
title: Speculative Design and Entanglement Theories (Workshop)
DOI: 10.15468/dl.ehn4yv
title: Occurrence Download

description: A dataset containing 1036 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Monitoreo de Felinos Silvestres asociados a Sistemas Agropecuarios en las Cuencas del Caño Zarzal y Caño La Vizcaína, Barrancabermeja, Santander"
 ]
}

 The dataset includes 1036 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003906-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6hdr7sr7h
title: Human primary mesothelial cells treated with TGF-β1 and with or without JPH203

description: The mesothelial-mesenchymal transition (MMT) of mesothelial cells has been
 recognized as a critical process during progression of peritoneal fibrosis
 (PF). Despite its crucial role in amino acid transport and metabolism, the
 involvement of LAT1 and the potential therapeutic role of its inhibitor,
 JPH203, in fibrotic diseases remain unexplored.
description: # Human primary mesothelial cells treated with TGF-β1 and with or without
 JPH203
 [https://doi.org/10.5061/dryad.6hdr7sr7h](https://doi.org/10.5061/dryad.6hdr7sr7h) This dataset consists of RNA sequencing data from human primary mesothelial cells treated with TGF-β1, both with and without JPH203, an LAT1 inhibitor. The fastq files in this dataset correspond to raw sequencing reads from these experimental conditions, designed to explore the effects of JPH203 on gene expression under TGF-β1-induced fibrotic conditions. It includes fastq.gz files with raw sequencing reads and a supplementary **expression.xls** file that provides processed gene expression data. ## Description of the data and file structure ### RNA-seq Fastq Files: The fastq.gz files contain paired-end reads and are organized by treatment group and replicate number. The filenames follow this structure: * **T_X_R1.fastq.gz / T_X_R2.fastq.gz**: Control group (TGF-β1 treatment only), where 'T_X' indicates the replicate number, and '_R1' and '_R2' represent paired-end reads. * **TJ_X_R1.fastq.gz / TJ_X_R2.fastq.gz**: Treated group (TGF-β1 + JPH203), with 'TJ_X' for replicate numbers. ### Expression.xls File: The **expression.xls** file includes the following key columns: * **Gene_ID**: Ensembl gene IDs. * **Read counts & FPKM values**: Gene expression values for each sample. * **Genomic and functional annotations**: Including gene names, GO terms, KEGG pathways, and other relevant metadata. The file provides a summary of gene-level expression and related biological information for each experimental condition. ## Sharing/Access information This dataset is publicly available at Dryad: DOI: 10.5061/dryad.6hdr7sr7h. ## Code/Software No specific code or software is included in this dataset. Standard RNA-seq analysis tools such as FastQC, STAR, and DESeq2 were used during data processing.
DOI: 10.15468/dl.uxy76j
title: Occurrence Download

description: A dataset containing 3513 records in GBIF matching the query:
SELECT
 '484' 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;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= 75.5327771015545
 AND decimalLongitude &lt;= 86.85869421308222
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 3513 records were derived from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003892-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.89z5hj
title: Occurrence Download

description: A dataset containing 7512 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is BCCM/IHEM - Fungi Collection: Human & Animal Health"
 ]
}

 The dataset includes 7512 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003907-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.