cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/hxxpr2p337.1
title: Xeno amino acid peptide: MD with NOE restraints

description: For full details, see the manuscript. Using NMR-informed molecular dynamics, we have observed a propensity towards a short β-bend at the N-terminus (residues v3-a5) and an α-helical structure at the C-terminus (residues a18-a24). The φ and ψ dihedral angles of these residues in 10 representative structures from independent MD replicas suggest a mix of C-terminal α-helix and N-terminal β-bend, except for MD replicate number 4, the least stable structure, where we observe a shorter C-terminal α-helix starting at n20. P2 is thus the first peptide constructed entirely from a xeno amino acid alphabet that has been observed to adopt any secondary structure elements according to CD, MD, and NMR.
DOI: 10.25345/c58k75951
title: MassIVE MSV000100652 - Technical Brief: Lysis to Cleanup - A Practical Workflow for High-throughput Analytical-flow LC-MS-Based Proteomics of Caco-2 Cell Pellets and Monocyte-derived Macrophages Supernatant
title: Efficient and reproducible sample preparation is crucial for high-quality mass spectrometry-based proteomics. In this study, we systematically optimized a bottom-up workflow for both cell pellets and cell culture supernatants, specifically adapted for use with an analytical-flow high-performance liquid chromatography (HPLC) system instead of the more commonly applied nano-HPLC setups. Starting with a commercially available human protein mix, we identified a publicly available method as the most effective in terms of protein yield and reproducibility. Applying this protocol to Caco-2 cells, we optimized cell lysis and found that a urea/thiourea-based buffer without protease inhibitors provided the highest protein content and identification rates.. We further tested multiple cleanup and enrichment strategies, identifying spin column-based desalting as the most efficient for cell lysates. Magnetic bead enrichment for macrophage supernatants showed no added benefit. The final workflow is tailored for analytical-flow LC-MS setups, enabling cost-effective, robust, and scalable proteomic analyses across diverse sample types.
DOI: 10.5281/zenodo.18383997
title: 19F-NMR spectra of artificial 17-OPH biosensor (cpOHPFA_1952-20-BLA-253) in apo and holo states

description: This dataset contains 19F-NMR spectra supporting Figure 3e, Figure 3f, and Supplementary Figure 10 of the manuscript "Artificial allosteric protein switches with machine learning-designed receptors".

The data consists of spectra for the cpOHPFA_1952-20-BLA-253 chimera, an artificial allosteric biosensor composed of a machine learning-designed 17alpha hydroxy-progesterone (17-OPH) binding domain inserted into TEM-1 beta-lactamase. To probe conformational dynamics, p-(O)CF3-tyrosine was installed at specific positions (including 105, 229, 230, 256, 389, and 437) via in vivo genetic code expansion.
DOI: 10.5281/zenodo.18383998
title: 19F-NMR spectra of artificial 17-OPH biosensor (cpOHPFA_1952-20-BLA-253) in apo and holo states

description: This dataset contains 19F-NMR spectra supporting Figure 3e, Figure 3f, and Supplementary Figure 10 of the manuscript "Artificial allosteric protein switches with machine learning-designed receptors".

The data consists of spectra for the cpOHPFA_1952-20-BLA-253 chimera, an artificial allosteric biosensor composed of a machine learning-designed 17alpha hydroxy-progesterone (17-OPH) binding domain inserted into TEM-1 beta-lactamase. To probe conformational dynamics, p-(O)CF3-tyrosine was installed at specific positions (including 105, 229, 230, 256, 389, and 437) via in vivo genetic code expansion.
DOI: 10.6084/m9.figshare.31190086.v1
title: Dataset_Shaping Smooth Muscle Forces

description: This dataset accompanies the publication:<br><i>Shaping Smooth Muscle Forces: The Role of Preconditioning in Urinary Smooth Muscle</i><br>This dataset contains raw force measurements (in mN) recorded from porcine bladder smooth muscle strips subjected to three different preconditioning protocols (P<sub>CYC</sub>, P<sub>NPC</sub>, P<sub>FC</sub>).
DOI: 10.15468/dl.egry3q
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((9.56398 47.78346,9.30544 47.12274,9.67889 47.02937,11.26607 47.22328,11.07216 47.91992,9.56398 47.78346))",
 "TaxonKey is Pyrgus serratulae"
 ]
}

 The dataset includes 209 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001511-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fx7xvr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ihsanalshehbazia granatensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001512-260129131611470/datasets/export for details.
DOI: 10.6084/m9.figshare.28955087
title: Structural insights into cationic amino acid transport and viral receptor engagement by CAT1

description: The structural determination of the mCAT1–ornithine–frRBD assembly generated two principal datasets: (i) the volumetric electron density map (MRC format file) resolved at 3.65 Å resolution, and (ii) the refined atomic coordinates (PDB format file) encompassing all annotated ligands. Additionally, the compressed archive (ZIP file) contains five predicted structural models of mCAT1 generated using the AlphaFold 3 online platform.
DOI: 10.6084/m9.figshare.28955087.v1
title: Structural insights into cationic amino acid transport and viral receptor engagement by CAT1

description: The structural determination of the mCAT1–ornithine–frRBD assembly generated two principal datasets: (i) the volumetric electron density map (MRC format file) resolved at 3.65 Å resolution, and (ii) the refined atomic coordinates (PDB format file) encompassing all annotated ligands. Additionally, the compressed archive (ZIP file) contains five predicted structural models of mCAT1 generated using the AlphaFold 3 online platform.
DOI: 10.6084/m9.figshare.30618413
title: Ultra-broadband near- to mid-infrared electro-optic modulator on thin-film lithium niobate

description: This is the raw data for "Ultra-broadband near- to mid-infrared electro-optic modulator on thin-film lithium niobate"including all the data that support the plots within the paper in the main part and supplementary information.
DOI: 10.6084/m9.figshare.30618413.v1
title: Ultra-broadband near- to mid-infrared electro-optic modulator on thin-film lithium niobate

description: This is the raw data for "Ultra-broadband near- to mid-infrared electro-optic modulator on thin-film lithium niobate"including all the data that support the plots within the paper in the main part and supplementary information.
DOI: 10.17632/g3dtzddn2f
title: Effects of Arithmetic Principle Cognitive Performance on Mathematical Achievement in Elementary School Students: Controlling for Executive Functions

description: Objective: This study investigated how elementary students' understanding of core arithmetic principles (inversion, commutativity, associativity, distributivity) relates to their math achievement, while accounting for foundational skills and executive functions.

Data & Methods: 77 second-graders completed tests measuring executive functions (working memory, cognitive flexibility, inhibition), number sense, arithmetic fluency, integer computation, and a novel task assessing accuracy and speed on different arithmetic principles. Broad math achievement was also tested.

Key Findings:

Principle Difficulty Varies: The inversion principle was easiest (highest accuracy, fastest speed). Problems requiring no principle were hardest, confirming the task's validity.

Principles Predict Achievement: Even after controlling for executive functions, accuracy on the arithmetic principles task was significantly correlated with overall math achievement.

Distinct Student Profiles: Analysis revealed three distinct groups:

High Ability (25%): Excelled in both procedural fluency and principle understanding.

Moderate Ability (69%): Average performance across domains.

Low Ability (6%): Struggled severely, especially in math achievement and computation.

Interpretation & Use:
Mastering formal arithmetic principles is a key cognitive component of math success. The findings suggest classroom instruction should explicitly connect conceptual rules with procedural practice. The student profiles can help educators identify those at risk (Low Ability group) and tailor interventions. The principle task itself is a useful diagnostic tool to distinguish conceptual gaps from mere lack of practice.
DOI: 10.17632/g3dtzddn2f.1
title: Effects of Arithmetic Principle Cognitive Performance on Mathematical Achievement in Elementary School Students: Controlling for Executive Functions

description: Objective: This study investigated how elementary students' understanding of core arithmetic principles (inversion, commutativity, associativity, distributivity) relates to their math achievement, while accounting for foundational skills and executive functions.

Data & Methods: 77 second-graders completed tests measuring executive functions (working memory, cognitive flexibility, inhibition), number sense, arithmetic fluency, integer computation, and a novel task assessing accuracy and speed on different arithmetic principles. Broad math achievement was also tested.

Key Findings:

Principle Difficulty Varies: The inversion principle was easiest (highest accuracy, fastest speed). Problems requiring no principle were hardest, confirming the task's validity.

Principles Predict Achievement: Even after controlling for executive functions, accuracy on the arithmetic principles task was significantly correlated with overall math achievement.

Distinct Student Profiles: Analysis revealed three distinct groups:

High Ability (25%): Excelled in both procedural fluency and principle understanding.

Moderate Ability (69%): Average performance across domains.

Low Ability (6%): Struggled severely, especially in math achievement and computation.

Interpretation & Use:
Mastering formal arithmetic principles is a key cognitive component of math success. The findings suggest classroom instruction should explicitly connect conceptual rules with procedural practice. The student profiles can help educators identify those at risk (Low Ability group) and tailor interventions. The principle task itself is a useful diagnostic tool to distinguish conceptual gaps from mere lack of practice.
DOI: 10.6084/m9.figshare.28869281
title: Telomere-to-Telomere genome assembly of an endangered tree Berchemiella wilsonii (Rhamnaceae)

description: Genome assembly and annotation of Berchemiella wilsonii .
DOI: 10.6084/m9.figshare.28869281.v1
title: Telomere-to-Telomere genome assembly of an endangered tree Berchemiella wilsonii (Rhamnaceae)

description: Genome assembly and annotation of Berchemiella wilsonii .
DOI: 10.6084/m9.figshare.29642135
title: Global Ensemble Fire Emission Product Version 1.0 (EnsemFire V1.0)

description: The EnsemFire dataset is a daily global 0.1° × 0.1° biomass burning emission dataset stored in the Network Common Data Form (NetCDF). The dataset includes ensemble mean estimates for a range of chemical species emitted from biomass burning, as well as their corresponding standard deviations. Specifically, the file contains variables for PM2.5, BC, OC, CO, NH3, NOx, SO2, CO2 and CH4, and FRP. For each species, the ensemble mean is provided in units of kg s⁻¹ m⁻², except for FRP which is given in megawatts (MW). Standard deviation fields are included to represent the spread across ensemble members, aiding uncertainty quantification.

The data is available from 2012 to 2021, with a filename of EnsemFire_v1.0_YYYYMMDD.nc, where YYYYMMDD denotes the calendar date in the format of four-digit year (YYYY), two-digit month (MM), and two-digit day (DD). The data is structured on a regular latitude–longitude grid with dimensions of 1791 grid points in latitude and 3600 in longitude, covering the global domain. The temporal dimension includes a single time step representing one full day. The time variable is defined in hours since YYYY-MM-DD 00:00:00 using the Gregorian calendar. All variables use a fill value of -9999 to indicate missing or undefined data. The coordinate variables include latitude (in degrees north), longitude (in degrees east), and time.

The dataset integrates seven widely used biomass burning emission inventories: five global datasets (GFAS, FINN, FEER, QFED, GBBEPx) and two regional products (EPA and CFFEPS). By applying an ensemble approach, EnsemFire addresses the substantial variability and uncertainty across individual inventories, offering a more robust and consistent emission estimate.
DOI: 10.6084/m9.figshare.29642135.v1
title: Global Ensemble Fire Emission Product Version 1.0 (EnsemFire V1.0)

description: The EnsemFire dataset is a daily global 0.1° × 0.1° biomass burning emission dataset stored in the Network Common Data Form (NetCDF). The dataset includes ensemble mean estimates for a range of chemical species emitted from biomass burning, as well as their corresponding standard deviations. Specifically, the file contains variables for PM2.5, BC, OC, CO, NH3, NOx, SO2, CO2 and CH4, and FRP. For each species, the ensemble mean is provided in units of kg s⁻¹ m⁻², except for FRP which is given in megawatts (MW). Standard deviation fields are included to represent the spread across ensemble members, aiding uncertainty quantification.

The data is available from 2012 to 2021, with a filename of EnsemFire_v1.0_YYYYMMDD.nc, where YYYYMMDD denotes the calendar date in the format of four-digit year (YYYY), two-digit month (MM), and two-digit day (DD). The data is structured on a regular latitude–longitude grid with dimensions of 1791 grid points in latitude and 3600 in longitude, covering the global domain. The temporal dimension includes a single time step representing one full day. The time variable is defined in hours since YYYY-MM-DD 00:00:00 using the Gregorian calendar. All variables use a fill value of -9999 to indicate missing or undefined data. The coordinate variables include latitude (in degrees north), longitude (in degrees east), and time.

The dataset integrates seven widely used biomass burning emission inventories: five global datasets (GFAS, FINN, FEER, QFED, GBBEPx) and two regional products (EPA and CFFEPS). By applying an ensemble approach, EnsemFire addresses the substantial variability and uncertainty across individual inventories, offering a more robust and consistent emission estimate.
DOI: 10.15468/dl.uzmznm
title: Occurrence Download

description: A dataset containing 4222937 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Passer montanus"
 ]
}

 The dataset includes 4222937 records from 1704 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001484-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g8d5h
title: Data from: Association of polyandry and sex-ratio drive prevalence in natural populations of Drosophila neotestacea

description: Selfish genetic elements bias their own transmission to the next
 generation, even at the expense of the fitness of their carrier. Sex-ratio
 (SR) meiotic drive occurs when an X-chromosome causes Y-bearing sperm to
 die during male spermatogenesis, so that it is passed on to all of the
 male's offspring, which are all daughters. How SR is maintained as a
 stable polymorphism in the absence of genetic suppressors of drive is
 unknown. Here, we investigate the potential for the female remating rate
 to affect SR dynamics in natural populations, using the fly Drosophila
 neotestacea. In controlled laboratory conditions, females from populations
 where SR is rare mate more often than females from populations where SR is
 common. Furthermore, only when males mate multiply does the average
 fertility of SR males relative to wild-type males decrease to a level that
 can prevent SR from spreading. Our results suggest that differences in the
 female mating rate among populations may contribute to SR dynamics in the
 wild, and thus also affect the outcome of this intragenomic conflict. In
 line with this, we also present evidence of a localized population crash
 due to SR that may have resulted from habitat fragmentation along with a
 reduced mating rate.
description: Fertility of Sex-ratio
 and Standard male Drosophila neotestaeaoffspring counted in the
 laboratorymale_fertility.txtMating frequencies for Drosophila neotestacea femalesMating observations were performed in the laboratoryfemale_remating.txtAutosomal microsatellite loci for 5 populations of Drosophila neotestaceaFlies were collected in the field, sacrificed and genotyped in the laboratory.autosomal_loci.txt
DOI: 10.5061/dryad.kv7qp23
title: Data from: Urbanization and individual differences in exploration and plasticity

description: Urban environments impose novel challenges on animals and, as a result,
 the behaviors of urban wildlife are changing. In particular, high
 exploratory tendencies and an ability to gather more information from the
 environment may facilitate adoption of novel ecological opportunities. As
 of yet, very few studies have examined if urbanization predicts the way in
 which animals explore novel environments, or the extent of
 among-individual variation within habitats. Here, we assess exploration
 and it’s temporal plasticity in black-capped chickadees (Poecile
 atricapillus; N=169 individuals, 14 sites) caught along an urban gradient
 to examine individual differences in exploration and changes in
 exploration over time and assays under a reaction-norm framework. As
 predicted, urban birds were significantly faster explorers in a novel
 environment (contacted more features and moved more), however urbanization
 did not predict individual differences in the change in exploration over
 time. Exploration score was moderately repeatable; interestingly, urban
 chickadees were more repeatable in their initial exploration behaviors,
 but seemed less repeatable in how they explored over time between assays
 in comparison to forest birds. Our results support the importance of high
 exploratory tendencies for urban animals, and suggest, for the first time,
 that individuals from urban and non-urban habitats differ in the amount of
 among-individual variation in exploration, and thus urban individuals may
 benefit from diverging more from one another in their behaviour. Future
 work should examine the extent to which this variation in exploration and
 plasticity of exploration behaviors represent differences in how
 individuals gather information from their environment.
description: Urbanization,
 Exploration, and Corticosterone DataThompson-et-al-2018-Behav-Eco.zip
DOI: 10.5061/dryad.f4324
title: Data from: Uncovering spatial variation in acoustic environments using sound mapping

description: Animals select and use habitats based on environmental features relevant
 to their ecology and behavior. For animals that use acoustic
 communication, the sound environment itself may be a critical feature, yet
 acoustic characteristics are not commonly measured when describing
 habitats and as a result, how habitats vary acoustically over space and
 time is poorly known. Such considerations are timely, given worldwide
 increases in anthropogenic noise combined with rapidly accumulating
 evidence that noise hampers the ability of animals to detect and interpret
 natural sounds. Here, we used microphone arrays to record the sound
 environment in three terrestrial habitats (forest, prairie, and urban)
 under ambient conditions and during experimental noise introductions. We
 mapped sound pressure levels (SPLs) over spatial scales relevant to
 diverse taxa to explore spatial variation in acoustic habitats and to
 evaluate the number of microphones needed within arrays to capture this
 variation under both ambient and noisy conditions. Even at small spatial
 scales and over relatively short time spans, SPLs varied considerably,
 especially in forest and urban habitats, suggesting that quantifying and
 mapping acoustic features could improve habitat descriptions. Subset maps
 based on input from 4, 8, 12 and 16 microphones differed slightly
 (&lt; 2 dBA/pixel) from those based on full arrays of 24 microphones
 under ambient conditions across habitats. Map differences were more
 pronounced with noise introductions, particularly in forests; maps made
 from only 4-microphones differed more (&gt; 4 dBA/pixel) from full
 maps than the remaining subset maps, but maps with input from eight
 microphones resulted in smaller differences. Thus, acoustic environments
 varied over small spatial scales and variation could be mapped with input
 from 4–8 microphones. Mapping sound in different environments will improve
 understanding of acoustic environments and allow us to explore the
 influence of spatial variation in sound on animal ecology and behavior.
description: PlosOne_Data_JobData were collected from audio recordings made in the field in Kalamazoo County, MI during the summer of 2013 using Wildlife Acoustics Song Meter 2. Values were extracted from recordings using custom script written in MatLab, as well as ArcMap by ESRI. 'Subset' refers to the number of microphones used to make maps, 'Additional Microphones' refer to the presence (Y) or absence (N) of additional flanking microphones, 'PlaybackLocation' refers to the location of the noise playback either within (Inside) or at the edge of arrays (Outside), and 'SPL' refers to sound pressure level in decibels (dB).
DOI: 10.15468/dl.h57srx
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aulacaspis tubercularis)"
 ]
}

 The dataset includes 486 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001150-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mn3gq21
title: Data from: Dietary choices are influenced by genotype, mating status, and sex in Drosophila melanogaster

description: Mating causes many changes in physiology, behaviour and gene expression in
 a wide range of organisms. These changes are predicted to be sex-specific,
 influenced by the divergent reproductive roles of the sexes. In female
 insects, mating is associated with an increase in egg production which
 requires high levels of nutritional input with direct consequences for the
 physiological needs of individual females. Consequently, females alter
 their nutritional acquisition in line with the physiological demands
 imposed by mating. Although much is known about the female mating-induced
 nutritional response, far less is known about changes in males. In
 addition, it is unknown whether variation between genotypes translates
 into variation in dietary behavioral responses. Here we examine
 mating-induced shifts in male and female dietary preferences across
 genotypes of Drosophila melanogaster. We find sex- and genotype-specific
 effects on both the quantity and quality of the chosen diet. These results
 contribute to our understanding of sex-specific metabolism and reveal
 genotypic variation that influences responses to physiological demands.
description: Female preference
 dataHere we have the total
 amount of protein and carbohydrate consumed for each genotype in a virgin
 or mated state. We also include the residuals from the preliminary
 model.female.dryad.csvMale preference dataHere we have the total amount of protein and carbohydrate consumed for each genotype in a virgin or mated state. We also include the residuals from the preliminary model.male-dryad.csv