cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14235911
title: FEater dataset: A molecular fragment dataset to benchmark the robustness of 3D flexible object recognition

description: This dataset is associated with the work: Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models

# Original FEater-Single and FEater_Dual dataset. 
FEater_Single
├── TestSet_coord.h5
├── TrainingSet_coord.h5
└── ValidationSet_coord.h5
FEater_Dual
├── TestSet_coord.h5
├── TrainingSet_coord.h5
└── ValidationSet_coord.h5

# Non-redundant baseline dataset
FEater_Baseline
├── TestSet_Dual.h5
├── TestSet_Single.h5
├── TrainingSet_Dual.h5
└── TrainingSet_Single.h5

# FEater-Single and FEater_Dual in different sample size
FEater_Mini200
├── Mini200_Dual.h5
└── Mini200_Single.h5
FEater_Mini400
├── Mini400_Dual.h5
└── Mini400_Single.h5
FEater_Mini800
├── Mini800_Dual.h5
└── Mini800_Single.h5

For further details of the usage, please visit the original GitHub repository: https://github.com/miemiemmmm/FEater
DOI: 10.15468/dl.hc7pdt
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus hirsutissimus Z.P.Wang & P.X.Zhang)"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004701-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b3cmun
title: Occurrence Download

description: A dataset containing 10646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "TaxonKey is Petromyzon marinus Linnaeus, 1758"
 ]
}

 The dataset includes 10646 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004700-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23719/1531858
title: Residential greenness, asthma, and lung function among children at high risk of allergic sensitization: a prospective cohort study

description:  Personal identifying information include residential addresses and clinical data from longitudinal follow-up evaluations in a prospective cohort from the Cincinnati Childhood Allergy and Air Pollution Study.  The greenness exposure data was based on the Normalized Difference Vegetation Index (NDVI) estimated from satellite measurements.
DOI: 10.25403/upresearchdata.27908457
title: Methods for persons with acquired communication disabilities

description: A scoping review was conducted. Scoping reviews do not include people as subjects. Nonetheless, ethical considerations were acknowledged. A multi-faceted search strategy was then conducted and included database searches, hand searching, and forward citation and ancestry searches. The search results were imported into a screening tool known as Covidence used for conducting Cochrane Systematic Reviews. Two reviewers did a double-blind screening of studies at the title/abstract and full-text level, during which the eligibility criterion was applied. Data was extracted by the researcher and independently verified by reviewers at title and full-text level. Data extraction for coded data and outcomes were also done by the researcher initially and then all the data extraction was checked by the supervisor. An inductive coding analysis was conducted to code the main concepts. Some changes were made to the coding and themes. Disagreements were discussed until 100% consensus was reached.<br>
DOI: 10.25403/upresearchdata.27908457.v1
title: Methods for persons with acquired communication disabilities

description: A scoping review was conducted. Scoping reviews do not include people as subjects. Nonetheless, ethical considerations were acknowledged. A multi-faceted search strategy was then conducted and included database searches, hand searching, and forward citation and ancestry searches. The search results were imported into a screening tool known as Covidence used for conducting Cochrane Systematic Reviews. Two reviewers did a double-blind screening of studies at the title/abstract and full-text level, during which the eligibility criterion was applied. Data was extracted by the researcher and independently verified by reviewers at title and full-text level. Data extraction for coded data and outcomes were also done by the researcher initially and then all the data extraction was checked by the supervisor. An inductive coding analysis was conducted to code the main concepts. Some changes were made to the coding and themes. Disagreements were discussed until 100% consensus was reached.<br>
DOI: 10.6084/m9.figshare.25567157
title: genRCT: a statistical analysis framework for generalizing RCT findings to real-world population

description: When evaluating the real-world treatment effect, the analysis based on randomized clinical trials (RCTs) often introduces generalizability bias due to the difference in risk factors between the trial participants and the real-world patient population. This problem of lack of generalizability associated with the RCT-only analysis can be addressed by leveraging observational studies with large sample sizes that are representative of the real-world population. A set of novel statistical methods, termed “genRCT”, for improving the generalizability of the trial has been developed using calibration weighting, which enforces the covariates balance between the RCT and observational study. This paper aims to review statistical methods for generalizing the RCT findings by harnessing information from large observational studies that represent real-world patients. Specifically, we discuss the choices of data sources and variables to meet key theoretical assumptions and principles. We introduce and compare estimation methods for continuous, binary, and survival endpoints. We showcase the use of the R package genRCT through a case study that estimates the average treatment effect of adjuvant chemotherapy for the stage 1B non-small cell lung patients represented by a large cancer registry.
DOI: 10.6084/m9.figshare.25567157.v1
title: genRCT: a statistical analysis framework for generalizing RCT findings to real-world population

description: When evaluating the real-world treatment effect, the analysis based on randomized clinical trials (RCTs) often introduces generalizability bias due to the difference in risk factors between the trial participants and the real-world patient population. This problem of lack of generalizability associated with the RCT-only analysis can be addressed by leveraging observational studies with large sample sizes that are representative of the real-world population. A set of novel statistical methods, termed “genRCT”, for improving the generalizability of the trial has been developed using calibration weighting, which enforces the covariates balance between the RCT and observational study. This paper aims to review statistical methods for generalizing the RCT findings by harnessing information from large observational studies that represent real-world patients. Specifically, we discuss the choices of data sources and variables to meet key theoretical assumptions and principles. We introduce and compare estimation methods for continuous, binary, and survival endpoints. We showcase the use of the R package genRCT through a case study that estimates the average treatment effect of adjuvant chemotherapy for the stage 1B non-small cell lung patients represented by a large cancer registry.
DOI: 10.15468/dl.agqe3y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus hirtivaginatus H.R.Zhao & Y.L.Yang)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004702-241126133413365/datasets/export for details.
DOI: 10.58132/u9kqhc
title: Chronology of the settlement areas at hunter-gather Stone Age site Dudka, Masuria, NE-Poland

description: Data set includes results of AMS radiocarbon measurements - 14C Age (yrBP) along with calibrated age (cal. BC) as well as isotope measurements (15N, 13C) in case of unburned bone samples (collagen). Table include the information about the sampled material and the archaeological data connected with the samples. All results of radiocarbon measurements were obtained in 2024 year thanks to the NCN grant project: Absolute chronology of burials and loose human bones from the hunter-gatherer Stone Age sites Dudka and Szczepanki in Masuria (NE-Poland), Grant no. 2020/39/B/HS3/02375.12 bones were selected for radiocarbon dating and stable isotope measurement. Three heavily cremated human bones coming from different layers, one human unburned bone and 8 animal bones and teeth from each layer with archeological finds to establish the chronology of the settlement. The set of animal remains include one dog tooth. Finaly, 4 samples failed due to too low collagen content and 8 samples were measured. One measured sample - of individual XIII-B, shows slightly increased C:N value and shall be interpreted with caution.Bone and tooth samples were measured mostly in Tandem Laboratory of Uppsala University in Sweden. Eight samples were sent to the laboratory and finally 5 of them could be measured. Three samples were analysed in the Aarhus AMS Centre of Aarhus University in Denmark. Both laboratories made AMS measurements along with precise stable isotope (13C, 15N) measurements EA-IRMS. Additionally, one bone sample was measured in the Vilnius Radiocarbon Laboratory in Lithuania.More detailed information about the methods used by laboratories are included in the instruction to the table (readme.txt).Bones used for sampling were osteologically elaborated by Karolina Bugajska.
DOI: 10.15468/dl.egd7cv
title: Occurrence Download

description: A dataset containing 31339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corbicula fluminea (O.F.Müller, 1774)",
 "Country is United States of America",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 31339 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004703-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8bfzeg
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helminthophis praeocularis Amaral, 1924"
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004704-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6dkw8r
title: Occurrence Download

description: A dataset containing 40055 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leistes superciliaris (Bonaparte, 1850)"
 ]
}

 The dataset includes 40055 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004705-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/1371
title: Dataset for 'Coexistence of Competing Microbial Strains under Twofold Environmental Variability and Demographic Fluctuations'

description: Dataset for 'Coexistence of Competing Microbial Strains under Twofold Environmental Variability and Demographic Fluctuations'. A full description of the data, methods, and interpretation may be found in the related publication. Computational data: raw results from stochastic simulations of our full model and of the effective Moran model at fixed total population.
DOI: 10.15468/dl.nbq8fr
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus hispidus H.R.Zhao & Y.L.Yang)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004706-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14234809
title: Whole body gait kinematics in patients with bilateral and chronic unilateral vestibulopathy

description: This dataset contains whole body kinematics and 3D ground reaction forces and moments from 30 subjects (10 with bilateral vestibulopathy, 10 with unilateral vestibulopathy, and 10 healthy subjects) during gait at three different walking speed: slow, comfortable, and fast. Three repetitions of these gait were performed by each subject. They were instrumented with 35 reflective placed on the whole body according to the Convention Gait Model 1.0. A 12-camera motion capture system (Oqus 7+, Qualisys, Göteborg, Sweden), set at a 100 Hz sampling frequency, was used to track cutaneous reflective markers. The marker trajectories were labeled using Qualisys Tracking Manager software (QTM 2019.3, Qualisys, Göteborg, Sweden) and exported in the C3D file format. Three force plates sampled at 1000 Hz (AMTI Accugait, Watertown, MA, USA) were used to record 3D ground reaction forces and moments. Results of gait standard deviation (GaitSD) and anchoring index (AI), as well as the kinematics data, are included in this dataset in csv file format.
DOI: 10.5281/zenodo.14236617
title: Whole body gait kinematics in patients with bilateral and chronic unilateral vestibulopathy

description: This dataset contains whole body kinematics and 3D ground reaction forces and moments from 30 subjects (10 with bilateral vestibulopathy, 10 with unilateral vestibulopathy, and 10 healthy subjects) during gait at three different walking speed: slow, comfortable, and fast. Three repetitions of these gait were performed by each subject. They were instrumented with 35 reflective placed on the whole body according to the Convention Gait Model 1.0. A 12-camera motion capture system (Oqus 7+, Qualisys, Göteborg, Sweden), set at a 100 Hz sampling frequency, was used to track cutaneous reflective markers. The marker trajectories were labeled using Qualisys Tracking Manager software (QTM 2019.3, Qualisys, Göteborg, Sweden) and exported in the C3D file format. Three force plates sampled at 1000 Hz (AMTI Accugait, Watertown, MA, USA) were used to record 3D ground reaction forces and moments. Results of gait standard deviation (GaitSD) and anchoring index (AI), as well as the kinematics data, are included in this dataset in csv file format.
DOI: 10.15468/dl.7jf9k7
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus hunanensis B.M.Yang)"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004707-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ak4bb4
title: Occurrence Download

description: A dataset containing 1635 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chortoicetes terminifera (Walker, 1870)"
 ]
}

 The dataset includes 1635 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004709-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.32zmby
title: Occurrence Download

description: A dataset containing 16261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cycas pectinata Buch.-Ham., Cycas pectinata Griff., Abies delavayi Franch., Abies delavayi Diels, Apios delavayi Franch., Abies ernestii Rehd., Abies georgei Orr, Abies georgei Hand.-Mazz., Abies nukiangensis W.C.Cheng & L.K.Fu, Abies likiangensis Franch., Picea brachytyla (Franch.) E.Pritz., Picea brachytila Masters, Picea brachyphylla hort. ex Mast., Picea brachyphylla (Maxim.) Godr., Picea brachyphylla (Maxim.) Gordon, Picea brachyphylla hort., Pilea brachypila Urb., Pinus armandii Franch., Pinus bhutanica Grierson et al., Pyrus bhutanica W.W.Sm., Pinus densata Mast., Pinus densa (Little & Dorman) Gaussen, Pinus densa (Little & K.W.Dorman) Silba, Pinus yunnanensis Franch., Prunus yunnanensis Franch., Pyrus yunnanensis Franch., Pseudotsuga forrestii Craib, Tsuga dumosa (D.Don) Eichler, Thuja dumosa Godr., Thuja dumosa Gordon, Taiwania cryptomerioides Hayata, Taiwania cryptomeriodes Hyata, 1906, Calocedrus macrolepis Kurz, Cupressus duclouxiana Hickel, Juniperus indica Bertol., Juniperus andina Nutt., Juniperus recurva Buch.-Ham. ex D.Don, Juniperus recurva Buch.-Ham., Juniperus incurva Buch.-Ham., Juniperus incurva Buch.-Ham. ex Endl., Juniperus saltuaria Rehd. & E.H.Wilson, Juniperus squamata Buch.-Ham. ex D.Don, Juniperus squamata Buch.-Ham., Juniperus squamata Buch.Ham. ex Lamb., Juniperus squamata Gordon, Juniperus squamosa Buch.-Ham., Juniperus squamosa Buch.-Ham. ex Wall., Platycladus orientalis (L.) Franco, Podocarpus neriifolius D.Don, Podocarpus ensifolius R.Br. ex Mirb., 1825, Podocarpus ensifolius R.Br., Podocarpus ensifolius R.Br. ex Carrière, Cephalotaxus fortunei Hook., Cephalotaxus lanceolata K.M.Feng, Cephalotaxus lanceolata K.M.Feng ex W.C.Cheng, L.K.Fu & C.Y.Cheng, Cephalotaxus mannii Hook.f., Cephalotaxus mannii E.Pritz., Cephalotaxus mannii E.Pritz. ex Diels, Cephalotaxus nana Nakai, Cephalotaxus sinensis (Rehd. & E.H.Wilson) H.L.Li, Taxus wallichiana Zucc., Torreya fargesii Franch., Ephedra likiangensis Florin)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 16261 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004708-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vy73xq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus inaequilaterus W.T.Lin & Z.M.Wu)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004710-241126133413365/datasets/export for details.
DOI: 10.15468/dl.adhk7n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Indocalamus jinpingensis T.P.Yi & J.Y.Shi)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004711-241126133413365/datasets/export for details.
DOI: 10.5281/zenodo.13362097
title: Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'

description: Melike Berksoz, Canan Atilgan* 

Faculty of Engineering and Natural Sciences, Sabanci University 

*Correspondance: Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu

Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes in vivo. A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.

Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd).