cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16923125
title: Sample simulation codes and data for Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes

description: These are the sample codes of numerical simulations and statistical data for the work presented in Yongtian Luo, Amrinder S. Nain, and Brian A. Camley, Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes, arXiv:2503.06239 and Soft Matter, 2025, DOI: 10.1039/D5SM00359H.

The Jupyter Notebook YL_cell_collision.ipynb (in Python 3) contains all the necessary components for running a full cell-cell collision simulation cycle, generating phase-field images and determining the collision outcome. The whole simulation takes roughly 6-12 hours on typical desktop/laptop computers.

In a parallel computing setting, one can use the code cell_collision.py in command line and sweep over parameter ranges (e.g. alpha, beta, and fiber spacing L) as inputs (such as "python cell_collision.py 90 0.1 10 1" for L=90, alpha=0.1, beta=10, and trajectory number 1), running multiple simulations for the same parameter set and saving the final collision outcomes ("training", "walk-past", or "reversing") as outputs to obtain a statistics of the probability of each possible collision outcome. 

The summary of our statistical results (numbers of different collision outcomes out of 96 simulation runs for each parameter set) is also included in the Excel file stat_data.xlsx.
DOI: 10.5281/zenodo.16923124
title: Sample simulation codes and data for Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes

description: These are the sample codes of numerical simulations and statistical data for the work presented in Yongtian Luo, Amrinder S. Nain, and Brian A. Camley, Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes, arXiv:2503.06239 and Soft Matter, 2025, DOI: 10.1039/D5SM00359H.

The Jupyter Notebook YL_cell_collision.ipynb (in Python 3) contains all the necessary components for running a full cell-cell collision simulation cycle, generating phase-field images and determining the collision outcome. The whole simulation takes roughly 6-12 hours on typical desktop/laptop computers.

In a parallel computing setting, one can use the code cell_collision.py in command line and sweep over parameter ranges (e.g. alpha, beta, and fiber spacing L) as inputs (such as "python cell_collision.py 90 0.1 10 1" for L=90, alpha=0.1, beta=10, and trajectory number 1), running multiple simulations for the same parameter set and saving the final collision outcomes ("training", "walk-past", or "reversing") as outputs to obtain a statistics of the probability of each possible collision outcome. 

The summary of our statistical results (numbers of different collision outcomes out of 96 simulation runs for each parameter set) is also included in the Excel file stat_data.xlsx.
DOI: 10.17632/2dc2vr3zbh
title: Hyper-Sensitive Chirality Detection via Frequency-Domain Polarization Field Mapping (FDPFM) for Bio-Molecular Assay Acceleration

description: This paper introduces Frequency-Domain Polarization Field Mapping (FDPFM), a novel technique designed to overcome the sensitivity limitations of current chiral molecule detection methods. Chirality, or a molecule's "handedness," is critical in fields like drug development and diagnostics, as different mirror-image forms (enantiomers) can have vastly different biological effects. Traditional detection methods often struggle to identify trace amounts of chiral molecules in complex biological samples.
The FDPFM system builds upon Polarization-Sensitive Optical Coherence Tomography (PS-OCT) but introduces a critical innovation: it transforms polarization state information into the frequency domain. Instead of analyzing the raw optical signal directly, the system uses a Fast Fourier Transform (FFT) to convert the time-varying Stokes parameters (which describe the light's full polarization state) into a spectral representation. This process effectively separates the subtle signal generated by chiral molecules—specifically related to circular polarization (S3)—from overwhelming background noise.
The key to its enhanced performance is a custom-designed digital filter that selectively amplifies the specific frequencies corresponding to the chiral signal while actively suppressing noise. This is analogous to isolating and boosting a single instrument's sound from a full orchestra.
Experimental validation demonstrated a remarkable 10-fold improvement in sensitivity compared to standard PS-OCT techniques. The system successfully achieved a limit of detection below 1 nM and accurately discriminated between different enantiomers with high specificity and reproducibility.
In conclusion, FDPFM represents a transformative advancement in chiral sensing. By combining frequency-domain analysis with targeted signal amplification, it has significant implications for accelerating drug discovery, developing new diagnostic biomarkers, and enhancing environmental monitoring, positioning it as a powerful, commercially-ready technology.
DOI: 10.17632/2dc2vr3zbh.1
title: Hyper-Sensitive Chirality Detection via Frequency-Domain Polarization Field Mapping (FDPFM) for Bio-Molecular Assay Acceleration

description: This paper introduces Frequency-Domain Polarization Field Mapping (FDPFM), a novel technique designed to overcome the sensitivity limitations of current chiral molecule detection methods. Chirality, or a molecule's "handedness," is critical in fields like drug development and diagnostics, as different mirror-image forms (enantiomers) can have vastly different biological effects. Traditional detection methods often struggle to identify trace amounts of chiral molecules in complex biological samples.
The FDPFM system builds upon Polarization-Sensitive Optical Coherence Tomography (PS-OCT) but introduces a critical innovation: it transforms polarization state information into the frequency domain. Instead of analyzing the raw optical signal directly, the system uses a Fast Fourier Transform (FFT) to convert the time-varying Stokes parameters (which describe the light's full polarization state) into a spectral representation. This process effectively separates the subtle signal generated by chiral molecules—specifically related to circular polarization (S3)—from overwhelming background noise.
The key to its enhanced performance is a custom-designed digital filter that selectively amplifies the specific frequencies corresponding to the chiral signal while actively suppressing noise. This is analogous to isolating and boosting a single instrument's sound from a full orchestra.
Experimental validation demonstrated a remarkable 10-fold improvement in sensitivity compared to standard PS-OCT techniques. The system successfully achieved a limit of detection below 1 nM and accurately discriminated between different enantiomers with high specificity and reproducibility.
In conclusion, FDPFM represents a transformative advancement in chiral sensing. By combining frequency-domain analysis with targeted signal amplification, it has significant implications for accelerating drug discovery, developing new diagnostic biomarkers, and enhancing environmental monitoring, positioning it as a powerful, commercially-ready technology.
DOI: 10.15468/dl.uxyatg
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029893-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8ytbk
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 91 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029895-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w78dtn
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029894-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17603/ds2-71av-7466
title: Research Experiences for Undergraduates (REU), NSF NHERI 2025: Unraveling Soil Dynamics with Direct Crosshole Seismic Testing  

description: My project was about completing the direct crosshole test at the Hornsby Bend site, Austin, TX to mitigate seismic hazards. My data can be used for future research regarding the site to further understand different parameters of the soil. The collected shear wave velocity can also be used to compare to other geophysical test to confirm reliability in their results. This research is unique as it discuss the soil classification on a field in Austin, TX while breaking down important aspects of understanding crosshole testing and why it’s important. My paper is targeted to those looking to understand geophysical methods used in geotechnical engineering this includes: academics, undergraduates, researchers, and geotechnical engineers.
DOI: 10.15468/dl.rywpsp
title: Occurrence Download

description: A dataset containing 17894 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17894 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029897-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jqbnra
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029896-250811113504898/datasets/export for details.
DOI: 10.15468/dl.wk42vx
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 146 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029898-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yzn3p5
title: Occurrence Download

description: A dataset containing 83888 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Silene acaulis"
 ]
}

 The dataset includes 83888 records from 431 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029809-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npfewc
title: Occurrence Download

description: A dataset containing 66472 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (EOD – eBird Observation Dataset, iNaturalist Research-grade Observations)",
 "OccurrenceStatus is Present",
 "TaxonKey is Vultur gryphus"
 ]
}

 The dataset includes 66472 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029868-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.22m6tu
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Priodontes maximus"
 ]
}

 The dataset includes 178 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029899-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cab673
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029900-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7hve9j
title: Occurrence Download

description: A dataset containing 2350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2350 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029901-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m34kxk
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029902-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rztg7e
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 63 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029903-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqd3j5
title: Occurrence Download

description: A dataset listing the 156 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Specimen)",
 "GadmGid is USA.5_1",
 "TaxonKey is Collembola"
 ]
}

 The dataset's 156 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029891-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16915852
title: A Machine Learning Method for Estimating Atmospheric Trace Gas Concentration Baselines: Training Data

description: Training data for estimating atmospheric  trace gas concentration baselines.

InTEM flags were generated as described in Manning et al. (2021). Meteorological data were extracted from the ECWMF ERA5 global reanalysis, presented in Hersbach et al. (2020). Variables were extracted around nine AGAGE atmospheric monitoring stations to match data from Prinn et al. (2025).

 

Manning et al. (2021). Evidence of a recent decline in UK emissions of hydrofluorocarbons determined by the InTEM inverse model and atmospheric measurements. Atmospheric Chemistry and Physics, 21, 12739–12755. https://doi.org/10.5194/acp-21-12739-2021

 

Herbach et al. (2020). The ERA5 global reanalysis. Quarterly Journal of the Royal Meteorological Society, 146, 1999-2049. https://doi.org/10.1002/QJ.3803

 

Prinn et al. (2025). The dataset of in-situ measurements of chemically and radiatively important atmospheric gases from the Advanced Global Atmospheric Gas Experiment (AGAGE) and affiliated stations (Version 20250123), [Data set], NASA Langley Research Center (LaRC) Data Host Facility (DHF). https://doi.org/10.60718/0FXA-QF43
DOI: 10.5281/zenodo.16915853
title: A Machine Learning Method for Estimating Atmospheric Trace Gas Concentration Baselines: Training Data

description: Training data for estimating atmospheric  trace gas concentration baselines.

InTEM flags were generated as described in Manning et al. (2021). Meteorological data were extracted from the ECWMF ERA5 global reanalysis, presented in Hersbach et al. (2020). Variables were extracted around nine AGAGE atmospheric monitoring stations to match data from Prinn et al. (2025).

 

Manning et al. (2021). Evidence of a recent decline in UK emissions of hydrofluorocarbons determined by the InTEM inverse model and atmospheric measurements. Atmospheric Chemistry and Physics, 21, 12739–12755. https://doi.org/10.5194/acp-21-12739-2021

 

Herbach et al. (2020). The ERA5 global reanalysis. Quarterly Journal of the Royal Meteorological Society, 146, 1999-2049. https://doi.org/10.1002/QJ.3803

 

Prinn et al. (2025). The dataset of in-situ measurements of chemically and radiatively important atmospheric gases from the Advanced Global Atmospheric Gas Experiment (AGAGE) and affiliated stations (Version 20250123), [Data set], NASA Langley Research Center (LaRC) Data Host Facility (DHF). https://doi.org/10.60718/0FXA-QF43
DOI: 10.15468/dl.rp956u
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry MULTIPOLYGON(((-74.42762 4.79447,-74.43804 4.78183,-74.44246 4.76923,-74.44175 4.74648,-74.43698 4.72435,-74.43242 4.71287,-74.42401 4.69968,-74.41557 4.69093,-74.41091 4.68009,-74.40366 4.66903,-74.38519 4.65307,-74.37876 4.64436,-74.3673 4.61879,-74.35323 4.60342,-74.34203 4.59568,-74.32123 4.58732,-74.30827 4.585,-74.29401 4.58643,-74.28195 4.59163,-74.27189 4.60008,-74.26469 4.61109,-74.26094 4.62371,-74.26098 4.63688,-74.28143 4.6971,-74.29009 4.70943,-74.30291 4.7208,-74.31079 4.725,-74.31323 4.7364,-74.31884 4.7486,-74.3332 4.76396,-74.32825 4.79322,-74.32959 4.80654,-74.33476 4.81888,-74.34331 4.82917,-74.35448 4.83649,-74.3673 4.84022,-74.38525 4.83905,-74.39962 4.83307,-74.41139 4.82359,-74.42065 4.81106,-74.42762 4.79447)))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 159 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029904-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.svuny9
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029905-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bd7g6
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029907-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hwpvyc
title: Occurrence Download

description: A dataset containing 1588 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is Finland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1588 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029908-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g69c8z
title: Occurrence Download

description: A dataset containing 351 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficopomatus enigmaticus",
 "Country is Korea, Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 351 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029906-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16923163
title: Interviewtranskript - Masterarbeit GenAI im B2B-Leadmanagementprozess
DOI: 10.5281/zenodo.16923162
title: Interviewtranskript - Masterarbeit GenAI im B2B-Leadmanagementprozess
DOI: 10.17595/20180208.001
title: Atmospheric CO2 mole fraction data of CONTRAIL-CME

description: This data set contains CO2 mole fractions observed by Continuous CO2 Measuring Equipment (CME) onboard commercial aircraft under the CONTRAIL (Comprehensive Observation Network for TRace gases by AIrLiner) project. The project started in 2005 with two Boeing 747-400 aircraft and three 777-200ER aircraft operated by Japan Airlines (JAL) between Japan and Europe, Asia, Australia, Hawaii and North America. As of 2017, eight 777-200ER and two 777-300ER aircraft are used for the CME observation. The mole fraction values are obtained from 10-second average values of the CME signals for the ascending and descending portion of the flight and from 1-minute averages for the cruise. This data set contains the most recently obtained data, whose QA/QC is still in progress. Because of this, the citation policy and format are different from those of the regular data (Machida et al., 2018). Please read carefully the citation policy written below. Furthermore, a password is required to download the data, which can be obtained by contacting the CONTRAIL PIs (contrail_pi@nies.go.jp). Note that these data will be merged into the regular data set at the next major update.
DOI: 10.17595/20230725.001
title: Atmospheric trace gas data from the CONTRAIL flask air sampling

description: This data set contains trace gas mole fractions observed over the Eurasian continent by the flask air sampling of the CONTRAIL (Comprehensive Observation Network for TRace gases by AIrLiner) project. Air samples were collected by the Automatic air Sampling Equipment (ASE) and manually by the Manual air Sampling Equipment (MSE) on board commercial aircraft of Japan Airlines (JAL).
DOI: 10.15468/dl.ed5424
title: Occurrence Download

description: A dataset containing 14314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neogobius melanostomus",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14314 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029909-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.