cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w6m905r1k
title: Data from: The inhibitory SAPS3 – AMPK interaction detected in HEK293 cells is not detectable in muscle or liver from humans or mice

description: It has been proposed that the regulatory Sit4-associated protein subunit 3
 (SAPS3) of protein phosphatase 6 (PP6C) acts as an AMP-activated protein
 kinase (AMPK) inhibitor by recruiting PP6C to dephosphorylate AMPKα-T172.
 While we confirm this interaction in HEK293 cells, we find limited
 evidence for a SAPS3–AMPK interaction in metabolically perturbed liver and
 skeletal muscle from humans and mice. Across fasting, high-fat diet
 feeding, and exercise conditions, co-immunoprecipitation assays failed to
 detect endogenous SAPS3–AMPK and PP6C–AMPK interactions. These findings
 challenge the physiological relevance of SAPS3/PP6C as regulators of AMPK
 in mature tissues and highlight the need for further investigation into
 the regulation of AMPK by protein phosphatases in vivo.
description: # The inhibitory SAPS3–AMPK interaction detected in HEK293 cells is not
 detectable in muscle or liver from humans or mice Dataset DOI:
 [10.5061/dryad.w6m905r1k](10.5061/dryad.w6m905r1k) ## Description of the
 data and file structure This dataset contains the summarized experimental
 data supporting figures in a study examining the metabolic effects of
 SAPS3 and AMPK signaling in mice subjected to either fasting or high-fat
 diet (HFD). The data are organized according to figure panels from the
 manuscript and include key physiological, biochemical, and molecular
 readouts relevant to energy metabolism and insulin sensitivity.
 Experimental groups typically include fasted/fed and chow/HFD-fed animals.
 ### Files and variables #### File: Data_summary_SAPS3-AMPK_v2.xlsx
 **Description:** This summary Excel file is intended for transparency and
 reproducibility and may serve as a reference for reviewers and
 collaborators in interpreting the figures and statistical analyses
 presented in the manuscript. Each sheet contains a description of the data
 along with related units. ## Code/software N/A
DOI: 10.5061/dryad.jwstqjqnr
title: Data from: Theory of infectious disease spillover at an ecological boundary: Impacts of seasonality and cross-boundary movement

description: Ecological boundaries are a key site for the spillover of wildlife
 pathogens into human and domestic livestock populations. Ebola virus is a
 zoonotic pathogen that is periodically introduced into humans causing
 outbreaks of a highly fatal hemorrhagic disease. There is evidence that
 spillover risk varies seasonally. Here we hypothesize that this
 seasonality may be due to periodic variations in pathogen-host
 interactions, host social behaviors, movement and contact rates, and
 demography. To better understand the dynamics of such a system, we studied
 a two-patch SIR compartmental model for the spillover of Ebola virus with
 seasonal and demographic variability. The model is expressed as a system
 of coupled ordinary differential equations (ODE) with periodic disease
 transmission and dispersal between supercritical and subcritical patches.
 The periodic ODE system is generalized to a stochastic Continuous-Time
 Markov Chain (CTMC) model. The basic reproduction number of the two-patch
 SIR model is derived at the disease-free equilibrium to illustrate the
 impact of seasonality and movement on Ebola virus outbreaks. Several
 numerical examples are investigated. We find that the seasonality strength
 and human movement are two potentially leading factors that are
 responsible for the intensity of periodic spillover risk from pathogen
 reservoirs to human settlement regions.
description: # Data from: Theory of infectious disease spillover at an ecological
 boundary: Impacts of seasonality and cross-boundary movement (Kaniz Fatema
 Nipa, Mozzamil Mohammed, Patrick R. Stephens, John M. Drake) The numerical
 implementation of a two-patch deterministic and stochastic model and the
 results are presented in the above-mentioned paper. * The deterministic
 ODE system is coded in **Two-patch_Ebola_ODE_Model.R**. * The
 Continuous-Time Markov Chain (CTMC) Model is coded in
 **CTMC_Ebola_V02.R**. * The main script
 **MainDeterministicStochastic.Rmd** is where these functions are called
 and the manuscript results are produced. * **CTMC_SeasonPersistence.R**
 codes the effect of seasonality strength on the persistence probability of
 the disease. * **CTMC_Movement_BA_Persistence.R** codes the effect of
 movement strength of human settlement (Patch B) to the reservoir region
 (Patch A) on the persistence probability of the disease. To reproduce
 results of the paper, compile **MainDeterministicStochastic.Rmd** using
 `knitr` or run the code chunks individually in a session. Compiled with R
 version 5.4.1 Dependencies: `deSolve`
DOI: 10.15468/dl.syhsuc
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Psalidodon schubarti"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004421-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2gkavk
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicyema monodi",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004422-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9ghx3ffwm
title: Data from: Mechanisms of antibiofilm compounds JG-1 and M4 across multiple species: Alterations of protein interactions essential to biofilm formation

description: The majority of human bacterial pathogens have the ability to form
 biofilms in vivo on body tissues and implantable medical devices.
 Biofilm-mediated chronic bacterial infections are difficult to treat due
 to their recalcitrance to antimicrobials and immune effectors, often
 requiring invasive surgical intervention to clear the infection. The
 difficulty in effectively executing these treatment strategies underscores
 the need for therapeutic agents that specifically target the biofilm
 state. To this end, we previously identified two small molecules, JG-1 and
 M4, that in vitro effectively inhibit and disperse biofilms of Salmonella
 Typhimurium and members of the ESKAPE pathogen group, including
 Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii.
 In addition to its antibiofilm effects, M4 has a bactericidal effect on
 Staphylococcus aureus and Enterococcus faecium. While these compounds have
 promising utility as antimicrobial agents, their mechanism of action
 remains unknown. By employing multiple techniques including RNAseq,
 thermal proteome profiling, and site directed mutagenesis, we identified
 multiple proteins essential to biofilm formation and evaluated their role
 in the presence of JG-1 and M4 in mutant and wildtype backgrounds. We
 report that the JG-1 and M4 actions are influenced by proteins important
 to biofilm maintenance, including OmpA, OmpC, and TrxA. Compound-bacteria
 interactions cause transcriptional changes that result in biofilm
 dispersal, and modulation of other virulence mechanisms, including
 invasion and motility. Additionally, we report that M4 interacts with S.
 aureus CodY, which promotes cell death, while the specific targets in S.
 Typhimurium and E. cloacae remain elusive. Collectively, this study
 presents an empirical investigation into JG-1 and M4’s mechanism of action
 in S. Typhimurium, E. cloacae, and S. aureus, and how the antibiofilm
 compounds disrupt microbial community dynamics, ultimately driving biofilm
 dispersal or cell death. 
description: # Data from: Mechanisms of antibiofilm compounds JG-1 and M4 across
 multiple species: Alterations of protein interactions essential to biofilm
 formation Dataset DOI: [10.5061/dryad.9ghx3ffwm](10.5061/dryad.9ghx3ffwm)
 ## Description of the data and file structure This dataset includes
 additional data collected and included in figures in Bennett et. al. 2025
 (10.3389/fcimb.2025.1631575).  Data was complied using GraphPad Prism
 software and is available in the following files: * Figure_1_Data.prism *
 Figure_3_Data.prism * Supplemental_Figure_2_Data.prism *
 Supplemental_Figure_3_Data.prism * Supplemental_Figure_5_Data.prism
 Additional explanation of data sources and analysis techniques can be
 found within each file.
DOI: 10.5061/dryad.jwstqjqnt
title: Data from: An integrated analysis of mammalophilic blackflies in the <em>Simulium variegatum</em> group (Diptera: Simuliidae) in Laos

description: The data contained collection sites for larvae and pupae of three species
 in the Simulium variegatum group in Laos and Thailand. Stream
 characteristics of the habitats of the immature stages of the Simulium
 variegatum group in Laos and Thailand. Chromosomal rearrangement
 frequencies in larvae of three species of the Simulium variegatum
 group in Laos and Thailand. Sex chromosomes of Simulium chamlongi in Laos
 with test for random assortment and mitochondrial cytochrome oxidase I
 gene sequences of two black fly species: Simulium luculentum and Simulium
 chamlongi.
description: # Data from: An integrated analysis of mammalophilic blackflies in the
 *Simulium variegatum* group (Diptera: Simuliidae) in Laos Dataset DOI:
 [10.5061/dryad.jwstqjqnt](10.5061/dryad.jwstqjqnt) ## Description of the
 data and file structure The data contained collection sites for larvae and
 pupae of three species in the *Simulium variegatum* group in Laos and
 Thailand. Stream characteristics of the habitats of the immature stages of
 the *Simulium variegatum* group in Laos and Thailand. Chromosomal
 rearrangement frequencies in larvae of three species of the *Simulium
 variegatum* group in Laos and Thailand. Sex chromosomes of *Simulium
 chamlongi* in Laos with test for random assortment and mitochondrial
 cytochrome oxidase I gene sequences of two black fly species, *Simulium
 luculentum*, and *Simulium chamlongi*. ### Files and variables #### File:
 COI_seqeunces.txt **Description:** Mitochondrial cytochrome oxidase I
 sequences of two black fly species: *Simulium chamlongi* and *Simulium
 luculentum*. ##### Variables * NCBI GenBank accession numbers
 PV528918–PV528931, PV565542, and PV565543 #### File:
 Data_for_MVE-25-3301.docx **Description:** Collection sites for larvae and
 pupae of three species in the Simulium variegatum group in Laos and
 Thailand. Stream characteristics of the habitats of the immature stages of
 the Simulium variegatum group in Laos and Thailand. Chromosomal
 rearrangement frequencies in larvae of three species of the Simulium
 variegatum group in Laos and Thailand. Sex chromosomes of *Simulium
 chamlongi* in Laos with test for random assortment ## Access information
 Other publicly accessible locations of the data: * NCBI GenBank * NCBI
 GenBank accession nos. PV528918–PV528931, PV565542, and PV565543
DOI: 10.15468/dl.rzzg48
title: Occurrence Download

description: A dataset containing 27009 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-124.47827 49.44352,-123.73874 49.34809,-123.32523 49.13339,-123.13438 48.90278,-122.76464 48.99792,-122.65834 49.00072,-122.34045 49.00269,-122.33267 49.00221,-122.16835 49.00318,-122.00208 49.00075,-121.90533 48.99977,-121.46027 49.00001,-121.41054 49.4483,-121.38229 49.75031,-121.57067 50.13314,-121.72716 50.19954,-121.81945 50.24055,-121.93125 50.26729,-122.11111 50.32562,-122.29339 50.41312,-122.4611 50.43743,-122.71293 50.48523,-122.83059 50.52887,-122.95642 50.51489,-123.0473 50.51489,-123.22906 50.53586,-123.29896 50.52188,-123.31993 50.52887,-123.40382 50.53586,-123.42479 50.52887,-123.64849 50.54285,-123.74636 50.54285,-123.99103 50.59877,-124.05395 50.64771,-124.39649 50.75956,-124.52232 50.8015,-124.75857 50.91474,-124.78856 50.85476,-124.83054 50.80278,-124.81655 50.67484,-124.85653 50.58288,-124.89251 50.56289,-124.99047 50.51691,-125.04445 50.49492,-125.11242 50.35298,-125.07223 50.29137,-125.00247 50.33098,-124.84254 50.289,-124.66769 50.33821,-124.62085 50.18917,-124.63687 50.17903,-124.80821 50.10827,-124.86783 50.06142,-124.73273 49.75364,-124.47827 49.44352))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Melittidae, Megachilidae, Colletidae, Halictidae, Andrenidae, Apidae)"
 ]
}

 The dataset includes 27009 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004423-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4dnx3w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicyema moschatum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004424-260126135527185/datasets/export for details.
DOI: 10.5281/zenodo.18407898
title: Pacote de Dados - Efeitos da estimulação cognitiva nos processos de categorização e compreensão de metáforas em pessoas idosas
DOI: 10.5281/zenodo.18407897
title: Pacote de Dados - Efeitos da estimulação cognitiva nos processos de categorização e compreensão de metáforas em pessoas idosas
DOI: 10.15468/dl.jqqakv
title: Occurrence Download

description: A dataset containing 4190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Lutzomyia cruciata"
 ]
}

 The dataset includes 4190 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004425-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z08kprrs5
title: A sensory and motor neuropathy caused by a genetic variant of NAMPT

description: Nicotinamide phosphoribosyl transferase (NAMPT) is the rate-limiting
 enzyme in the salvage pathway of NAD+ biosynthesis in mammalian cells and
 is essential for survival. Here, we report on a novel axonal sensory and
 motor neuropathy likely caused by a homozygous genetic variant of missense
 mutation (c.472G&gt;C, p.P158A) in NAMPT. The two affected siblings
 presented with a range of clinical features, including impaired motor
 coordination, muscle atrophy, foot deformities, and positive Babinski
 sign. Using different preparations including recombinant NAMPT proteins,
 patient fibroblasts (FBs), and mouse model, we showed that the p.P158A
 mutation decreased NAMPT enzyme activity, caused mitochondrial
 dysfunction, disrupted cellular bioenergetic and metabolic homeostasis,
 and increased oxidative stress. Moreover, the p.P158A mutation caused
 impairments of excitability and synaptic function and motor neuron
 degeneration in the mouse model. This Mutation in NAMPT Axonopathy (MINA)
 syndrome is the first human hereditary neurological disease linking to a
 NAMPT variant and has significant clinical implications.
description: # A sensory and motor neuropathy caused by a genetic variant of NAMPT
 Dataset DOI: [10.5061/dryad.z08kprrs5](10.5061/dryad.z08kprrs5) ##
 Description of the data and file structure DEG data set of patient
 fibroblasts (P-FBs) and LD control fibroblasts (C-FBs(LD)). ### Files and
 variables #### File: P-FBs_vs_C-FBs(LD)_DEG.xlsx **Description:**  #####
 Variables * Fold change * Padj value * Gene names * NS (19997) * Down
 (1795) * Up (3181) * '--'s in cells are meaningless ## Human
 subjects data We received explicit consent from participants. We
 de-identified data using the names of P-FBs for patient fibroblasts and
 C-FBs(LD) for fibroblasts of healthy control individual.
DOI: 10.5061/dryad.gtht76j06
title: UNO experimental dataset for: Multiscale bedform reorganization at the onset of substantial suspended sediment transport

description: We collected data from three experiments that tracked bedform evolution in
 a 22-m-long, 0.56-m-wide, and 0.9-m-deep flume at the University of New
 Orleans' Dynamics of Sedimentation laboratory. Each experiment was
 run at equilibrium conditions under steady, uniform, normal flow in a
 fully closed system recirculating flume. All three experiments were run at
 20cm mean flow depth, the same bed material sediment, but with varied
 discharge: 20cm 30Hz experiment at 45 L/s, 20cm 35Hz experiment
 at 51 L/s, 20cm 40Hz experiment at 56 L/s. We measured
 topography using a 3D laser scanning system along an approximately
 5.5-m-long test section, with scans repeated approximately every 165
 seconds. We analyzed bed topography for the 2D centerline profile at 1 mm
 horizontal resolution.
description: # UNO experimental dataset for: Multiscale bedform reorganization at the
 onset of substantial suspended sediment transport Dataset DOI:
 [10.5061/dryad.gtht76j06](10.5061/dryad.gtht76j06) ## Description of the
 data and file structure #### Files and variables *
 20cm_30Hz_experiment.zip * 20cm_35Hz_experiment.zip *
 20cm_40Hz_experiment.zip * Grain_size_analysis_reports The data folder has
 three folders- one for each experiment condition (‘20cm 30Hz experiment’,
 ‘20cm 35Hz experiment’, and ‘20cm 40Hz experiment’) with one subfolder
 each titled ‘[experiment name] csvs’ in which individual variables from
 the .mat array are exported as .csv files.  **Description of the data and
 file structure:** 20cmcenterline.mat This mat file
 contains four variables: * *t_minutes_sorted* - vector representing the
 time at which the scan was captured in seconds.  * *x *- vector
 representing coordinates in the longitudinal or downstream direction along
 the study section at 1 mm resolution. * *z_centerline -* 2-dimensional
 matrix containing time series of longitudinal profiles of bed elevation
 used for computing bedform geometry and kinematics, and the power spectral
 density of bed elevation. Within *z_centerline*, the first and second
 dimensions represent the bed elevation along a longitudinal profile and
 the time step, respectively. * *z_centerline_slopecorrected* -
 2-dimensional matrix containing time series of longitudinal profiles of
 bed elevation used for computing bedform geometry and kinematics, and the
 power spectral density of bed elevation. Within
 *z_centerline_slopecorrected*, the first and second dimensions represent
 the bed elevation along a longitudinal profile and the time step,
 respectively.
DOI: 10.15468/dl.ga6ntj
title: Occurrence Download

description: A dataset containing 5740 records in GBIF matching the query:
SELECT
 '517' 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;= 66.81438016390939
 AND decimalLongitude &lt;= 79.15061207187689
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 5740 records were derived from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004413-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/4fjetx
title: test

description: test
DOI: 10.7910/dvn/aedrxn
title: Replication Data for: Ethnic Visibility

description: The political utility of ethnicity is typically attributed to the ease with which it can be observed. However, ethnic visibility is not universal, and I argue that its variation has political implications; namely that more visible group members support ethnic parties at higher rates because they have the most to gain (or lose) from ethnopolitical competition. Using original data from Malawi, I find that individual-level ethnic visibility is indeed strongly associated with ethnic party support. I provide further evidence that visibility induces party support instrumentally by shaping expectations about others’ ability to correctly infer ethnic belonging. I also show that the theory generalizes to the group level, with more visible ethnic groups across Africa being more likely to vote ethnically. These results qualify a central assumption in instrumental theories of ethnic politics – that ethnic identities are always visible – and help explain variation in the success of ethnic political mobilization.
description: This dataset underwent an independent verification process that replicated the tables and figures in the primary article. For the supplementary materials, verification was performed solely for the successful execution of code. The verification process was carried out by the Odum Institute for Research in Social Science at the University of North Carolina at Chapel Hill. 
<br>
The associated article has been awarded Open Materials and Open Data Badges. Learn more about the Open Practice Badges from the Center for Open Science.<br>
DOI: 10.7910/dvn/kthhc7
title: A12_21260.JPG

description: Link to OCHRE database: &lt;a href = ''http://pi.lib.uchicago.edu/1001/org/ochre/52c39c1d-7ba0-4859-ab9e-84e59ec21d77'&gt;http://pi.lib.uchicago.edu/1001/org/ochre/52c39c1d-7ba0-4859-ab9e-84e59ec21d77
DOI: 10.7910/dvn/qshx6o
title: Survival data

description: All raw survival data for Metformin Treatment of Diverse Caenorhabditis Species Reveals the Importance of Genetic Background in Longevity and Healthspan Extension Outcomes
DOI: 10.7910/dvn/xgxen6
title: Replication Data for: Abstraction and Detail in Experimental Design

description: Political scientists designing experiments often face the question of how abstract or detailed their experimental stimuli should be. Typically, this question is framed in terms of tradeoffs relating to experimental control and generalizability: the more context introduced into studies, the less control, and the more difficulty generalizing the results. Yet, we have reason to question this tradeoff, and there is relatively little systematic evidence to rely on when calibrating the degree of abstraction in studies. We make two contributions. First, we provide a theoretical framework which identifies and considers the consequences of three dimensions of abstraction in experimental design: situational hypotheticality, actor identity, and contextual detail. Second, we replicate and extend a range of survey experiments, varying these levels of abstraction. We find no evidence that situational hypotheticality substantively changes experimental results, but increased contextual detail dampens treatment effects and the salience of actor identities moderates results in specific situations.
description: This dataset underwent an independent verification process that replicated the tables and figures in the primary article. For the supplementary materials, verification was performed solely for the successful execution of code. The verification process was carried out by the Odum Institute for Research in Social Science at the University of North Carolina at Chapel Hill. 
<br>
The associated article has been awarded Open Materials and Open Data Badges. Learn more about the Open Practice Badges from the Center for Open Science.<br>