cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13102871
title: Changes of 70 years in the non-native and native flora of a Hungarian county seat (Pécs, Central Europe)

description: The research of European urban flora is still based on the study of Western and Central European settlements, while relatively few data are available from the southern and eastern parts of Europe. This paper presents the first grid-based approach that surveyed the spontaneous and sub-spontaneous flora and its temporal changes of a Hungarian city located in this latter region of Europe. The changes during 70 years in the flora of a Hungarian county seat, Pécs were investigated. The contemporary city areas were used as two different study areas in the analyses. Changes in species richness, proportions of dispersal types, life form traits and alien statuses were examined during the mentioned period. With 1641 vascular plant species found at 232.88 km<sup>2</sup> in the last 70 years, the flora of Pécs represents a diversity hotspot within Europe. In contrast with other European cities we found significant (19.37%) increase in the number of species over the last 70 years. As a result of temporal changes in the city flora, differnces were found only in the case of neophytes’ life forms regardless of the spatial approach. Similar to the other cities globally the number of woody species neophytes and short-lived alien plants increased.
DOI: 10.6084/m9.figshare.13102871.v1
title: Changes of 70 years in the non-native and native flora of a Hungarian county seat (Pécs, Central Europe)

description: The research of European urban flora is still based on the study of Western and Central European settlements, while relatively few data are available from the southern and eastern parts of Europe. This paper presents the first grid-based approach that surveyed the spontaneous and sub-spontaneous flora and its temporal changes of a Hungarian city located in this latter region of Europe. The changes during 70 years in the flora of a Hungarian county seat, Pécs were investigated. The contemporary city areas were used as two different study areas in the analyses. Changes in species richness, proportions of dispersal types, life form traits and alien statuses were examined during the mentioned period. With 1641 vascular plant species found at 232.88 km<sup>2</sup> in the last 70 years, the flora of Pécs represents a diversity hotspot within Europe. In contrast with other European cities we found significant (19.37%) increase in the number of species over the last 70 years. As a result of temporal changes in the city flora, differnces were found only in the case of neophytes’ life forms regardless of the spatial approach. Similar to the other cities globally the number of woody species neophytes and short-lived alien plants increased.
DOI: 10.6084/m9.figshare.13318657.v1
title: Insect pollination in temperate sedges? A case study in <i>Rhynchospora alba</i> (Cyperaceae)

description: Sedges (Cyperaceae) are commonly pollinated by wind, but some transitions from wind to insect pollination have been reported in tropical sedges. Despite being a temperate sedge, the pollination strategy of <i>Rhynchospora alba</i> may partly depend on insects, as suggested by its white-colored inflorescences. Here we quantify the contribution of insects to the reproductive fitness of <i>R. alba</i> as an exploration of the success of entomophily in temperate sedges. Honeybees and hoverflies seem to be the primary visitors of <i>R. alba</i> in the study site, and pollen of <i>R. alba</i> was recovered from the mouthparts and legs of the insects. Treatments excluding insects led to a lower reproductive fitness (regarding fruit weight and fruit viability) than those not excluding them. Therefore, insects seem to contribute significantly to the pollination of <i>R. alba</i> despite moderate morphological adaptation. We highlight the role of entomophily as an overlooked reproductive mechanism in cold-temperate sedges.
DOI: 10.6084/m9.figshare.13199865
title: A littoral grass growing inland: genetic diversity of <i>Puccinellia fasciculata</i> around mud volcanoes in Italy

description: <i>Puccinellia fasciculata</i> is a littoral miohalophyte with a Mediterranean-Atlantic distribution, uncommonly found in inland sites. The main Italian inland population is located in the Salse di Nirano Reserve, an area internationally renowned for the phenomenon of mud volcanoes. In this study, molecular markers are used to characterize this population and its possible relationships with the nearest littoral conspecific population. A survey of ISSR markers revealed low levels of genetic diversity (<i>He</i> = 0.081 in the inland population, 0.105 in the littoral one) and a weak genetic differentiation (<i>Gst</i> = 0.24 within the inland population, 0.28 among this and the littoral one). A sequence analysis of three non-coding regions of chloroplast DNA found no genetic differentiation both within the inland population and between the two populations, and revealed a common origin for the two dating back to the middle Holocene. The apparent incongruence between the results from the two approaches may be explained by differences between ISSR and non-coding cpDNA markers in capturing signatures related to gene flow; their integrated information implies a mixed reproductive strategy and a common evolutionary history for the two examined populations. Effective conservation strategies are recommended for the inland population of <i>P. fasciculata</i> and its habitat.
DOI: 10.6084/m9.figshare.13199865.v2
title: A littoral grass growing inland: genetic diversity of <i>Puccinellia fasciculata</i> around mud volcanoes in Italy

description: <i>Puccinellia fasciculata</i> is a littoral miohalophyte with a Mediterranean-Atlantic distribution, uncommonly found in inland sites. The main Italian inland population is located in the Salse di Nirano Reserve, an area internationally renowned for the phenomenon of mud volcanoes. In this study, molecular markers are used to characterize this population and its possible relationships with the nearest littoral conspecific population. A survey of ISSR markers revealed low levels of genetic diversity (<i>He</i> = 0.081 in the inland population, 0.105 in the littoral one) and a weak genetic differentiation (<i>Gst</i> = 0.24 within the inland population, 0.28 among this and the littoral one). A sequence analysis of three non-coding regions of chloroplast DNA found no genetic differentiation both within the inland population and between the two populations, and revealed a common origin for the two dating back to the middle Holocene. The apparent incongruence between the results from the two approaches may be explained by differences between ISSR and non-coding cpDNA markers in capturing signatures related to gene flow; their integrated information implies a mixed reproductive strategy and a common evolutionary history for the two examined populations. Effective conservation strategies are recommended for the inland population of <i>P. fasciculata</i> and its habitat.
DOI: 10.6084/m9.figshare.13199865.v1
title: A littoral grass growing inland: genetic diversity of <i>Puccinellia fasciculata</i> around mud volcanoes in Italy

description: <i>Puccinellia fasciculata</i> is a littoral miohalophyte with a Mediterranean-Atlantic distribution, uncommonly found in inland sites. The main Italian inland population is located in the “Salse di Nirano” Reserve, an area internationally renowned for the phenomenon of mud volcanoes. In this study, molecular markers are used to characterize this population and its possible relationships with the nearest littoral conspecific population. A survey of ISSR markers revealed low levels of genetic diversity (<i>He</i> = 0.081 in the inland population, 0.105 in the littoral one) and a weak genetic differentiation (<i>Gst</i> = 0.24 within the inland population, 0.28 among this and the littoral one). A sequence analysis of three non-coding regions of chloroplast DNA found no genetic differentiation both within the inland population and between the two populations, and revealed a common origin for the two dating back to the middle Holocene. The apparent incongruence between the results from the two approaches may be explained by differences between ISSR and non-coding cpDNA markers in capturing signatures related to gene flow; their integrated information implies a mixed reproductive strategy and a common evolutionary history for the two examined populations. Effective conservation strategies are recommended for the inland population of <i>P. fasciculata</i> and its habitat.
DOI: 10.6084/m9.figshare.19126655.v3
title: Human Metadata and Multi-Omic Datasets

description: This repository contains the data tables for the multi-omic datasets and metadata for the COPD multi-omic paper.
DOI: 10.6084/m9.figshare.19714435
title: The Fate of IgE Epitopes and Coeliac Toxic Motifs During Simulated Gastro-intestinal Digestion of Pizza Base

description: Information S1: Information regarding the wheat proteins identified in the different digestion timepoints from mass spectrometry including protein accession, protein description, number of peptides and the sequence coverage. Information S2: Information regarding the soy proteins identified in the different digestion timepoints from mass spectrometry including protein accession, protein description, number of peptides and the sequence coverage. Information S3: Information regarding peptides mapped to the allergen Tri a 36 with UniProt accession B2Y2Q7 in the different digestion timepoints determined from mass spectrometry.
DOI: 10.6084/m9.figshare.19714435.v1
title: The Fate of IgE Epitopes and Coeliac Toxic Motifs During Simulated Gastro-intestinal Digestion of Pizza Base

description: Information S1: Information regarding the wheat proteins identified in the different digestion timepoints from mass spectrometry including protein accession, protein description, number of peptides and the sequence coverage. Information S2: Information regarding the soy proteins identified in the different digestion timepoints from mass spectrometry including protein accession, protein description, number of peptides and the sequence coverage. Information S3: Information regarding peptides mapped to the allergen Tri a 36 with UniProt accession B2Y2Q7 in the different digestion timepoints determined from mass spectrometry.
DOI: 10.5281/zenodo.6472293
title: Molecular similarity perception based on machine-learning models

description: Molecular similarity is an particularly important notion for chemical legislation, specifically in the evaluation process for orphan drugs (i.e., drugs for rare diseases). A new molecule needs to be dissimilar from any other existing drug for a given disease to be assigned the financially advantageous status of orphan drug. Currently, there are many ways to define whether two molecules are similar or dissimilar. Thus far, the European Medicines Agency has used experts majority voting on discretional judgments of similarity when assessing new drugs for rare diseases. The decision of individual expert whether two compounds are similar is inherently subjective, depending on factors such as gender, age, state of mind, and previous experiences. It is therefore desirable, in this context, to benefit from an objective measure of similarity. To answer this need, we report a new dataset of molecular similarity assessments, that includes complex and difficult similarity scenarios. As a result, we propose new and improved models for similarity-prediction procedures, including 3D properties. These models are publicly available: https://chematlas.chimie.unistra.fr/ReadySim/. Software, 3D structures and pictures are available in the git related to this deposit: https://github.com/enricogandini/paper_similarity_prediction.git The deposit contains two files. original_training_set.csv: this is one of the dataset published initially in [doi: 10.1186/1758-2946-6-5]. new_dataset.csv: result from a new survey organized in 2020 The columns are the following: id_pair: unique identifier of the compound pair curated_smiles_molecule_a: first compound of the pair curated_smiles_molecule_b: second compound of the pair tanimoto_cdk_Extended: ECFP similarity measure TanimotoCombo: ComboScore similarity measure pchembl_distance: difference of activity of the compound pair target_name: protein to which the compound pair is binding simil_2D: similar based on ECFP (0 or 1) simil_3D: similar based on ComboScore (0 or 1) dissimil_2D: dissimilar based on ECFP (0 or 1) dissimil_3D: dissimilar based on ComboScore (0 or 1) pair_type: pairs are classified based on ECFP and ComboScore as similar or dissimilar in 2D and 3D - Sim2DSim3D, Sim2DDis3D, Dis2D,Sim3D, Dis2DSim3D n_answers: number of answers from experts n_similar: number of answers labeling the pair as similar compounds frac_similar: n_similar/n_answers
DOI: 10.5281/zenodo.6472292
title: Molecular similarity perception based on machine-learning models

description: Molecular similarity is an particularly important notion for chemical legislation, specifically in the evaluation process for orphan drugs (i.e., drugs for rare diseases). A new molecule needs to be dissimilar from any other existing drug for a given disease to be assigned the financially advantageous status of orphan drug. Currently, there are many ways to define whether two molecules are similar or dissimilar. Thus far, the European Medicines Agency has used experts majority voting on discretional judgments of similarity when assessing new drugs for rare diseases. The decision of individual expert whether two compounds are similar is inherently subjective, depending on factors such as gender, age, state of mind, and previous experiences. It is therefore desirable, in this context, to benefit from an objective measure of similarity. To answer this need, we report a new dataset of molecular similarity assessments, that includes complex and difficult similarity scenarios. As a result, we propose new and improved models for similarity-prediction procedures, including 3D properties. These models are publicly available: https://chematlas.chimie.unistra.fr/ReadySim/. Software, 3D structures and pictures are available in the git related to this deposit: https://github.com/enricogandini/paper_similarity_prediction.git The deposit contains two files. original_training_set.csv: this is one of the dataset published initially in [doi: 10.1186/1758-2946-6-5]. new_dataset.csv: result from a new survey organized in 2020 The columns are the following: id_pair: unique identifier of the compound pair curated_smiles_molecule_a: first compound of the pair curated_smiles_molecule_b: second compound of the pair tanimoto_cdk_Extended: ECFP similarity measure TanimotoCombo: ComboScore similarity measure pchembl_distance: difference of activity of the compound pair target_name: protein to which the compound pair is binding simil_2D: similar based on ECFP (0 or 1) simil_3D: similar based on ComboScore (0 or 1) dissimil_2D: dissimilar based on ECFP (0 or 1) dissimil_3D: dissimilar based on ComboScore (0 or 1) pair_type: pairs are classified based on ECFP and ComboScore as similar or dissimilar in 2D and 3D - Sim2DSim3D, Sim2DDis3D, Dis2D,Sim3D, Dis2DSim3D n_answers: number of answers from experts n_similar: number of answers labeling the pair as similar compounds frac_similar: n_similar/n_answers
DOI: 10.15151/esrf-dc-809911049
title: Multiferroic Coupling in Magnetite Single Crystal

description: Magnetisation measurements from a single crystal of magnetite show unusual behaviour immediately below the Verwey transition with hysteresis loops showing anomalous hysteretic behaviour around ±0.5 T and between 80 K and 130 K. Magnetic Force Microscopy (MFM) data show different magnetic switching behaviours across this same temperature and field range as compared to that observed either above 125 K or below 80 K. The observed magnetic behaviour is therefore linked with the structural changes that occur at the Verwey transition and this is thought to arise through a magneto-elastic coupling between the ferrimagnetic domains and ferroelastic twins created at the Verwey transition. There is, unfortunately, very little experimental data exploring the structure-magnetic correlation and its evolution as a function of applied field and the effect this has on the ferroelastic twins. We therefore propose a structural characterisation using X-Ray Diffraction (XRD) as a function of field and temperature across the Verwey transition to provide new insights into the complex interplay between the ferroic orders in the vicinity of the metal-insulator Verwey transition.
DOI: 10.5281/zenodo.6518765
title: Not All Dependencies are Equal: An Empirical Study on Production Dependencies in NPM

description: This dataset contains the data and scripts we used to conduct our study on production dependencies in npm. js_projects.zip contains 100 JavaScript projects mined from GitHub in November 2021. data_and_scripts.zip contains data on all installed dependencies from the 100 JavaScript projects and the scripts to process the data and obtain the results for our study. See the README file for more details.
DOI: 10.5281/zenodo.6518764
title: Not All Dependencies are Equal: An Empirical Study on Production Dependencies in NPM

description: This dataset contains the data and scripts we used to conduct our study on production dependencies in npm. js_projects.zip contains 100 JavaScript projects mined from GitHub in November 2021. data_and_scripts.zip contains data on all installed dependencies from the 100 JavaScript projects and the scripts to process the data and obtain the results for our study. See the README file for more details.
DOI: 10.6073/pasta/2c43d15a50e56f35c4812b026f17e741
title: Point Cloud lidar DSM from UAV campaign at Niwot Ridge, 2017.

description: Elevation data from 14 August 2017 collected as part of unmanned aerial vehicle (UAV)/drone campaign during Summer 2017. Investigating snow depth varaibility and spatiotemporal variations and controls on vegetation productivity within the Niwot Ridge LTER Saddle Catchment.
DOI: 10.12751/g-node.98d6ks
title: EEGmanypipelines analysis

description: Analysis code, data and figures for manypipelines project
DOI: 10.12751/g-node.6nhr1y
title: EEGmanypipelines Preprocessing

description: Preprocessing code and data for EEGmanypipelines project
DOI: 10.5281/zenodo.6521853
title: Chalgrove Lake (Buffalo Creek Watershed) YSI Data from 2022-02-18 to 2022-03-18

description: General Metadata for Chalgrove Lake YSI Data Files Specific metadata for each deployment can be found as text files with the file format of: <pre><code>BC_chalgrove_lake_YYYY-MM-DD_YYYY-MM-DD_metadata.txt</code></pre> Where YYYY-MM-DD_YYYY-MM-DD is the date range of the deployment. File Created 2019-04-12 by KF File Modified 2019-10-31 by KF - added the descriptions of the total algae variables 2022-05-04 by KF - updated to match LEO standards and current deployment specs Description These data are from a YSI EXO2 multiparameter sonde deployed at approximatly 0.7 m in Chalgrove Lake (37.242983 N, -78.464116 W) in approximately 4 m of water. Sonde Specifics The specific sensors and SNs deployed are on the metadata specific to each deployment but generally the sonde has: Temperature Conductivity pH ODO Turbidity Measurement Parameters, units, and Variable Names date.time = the combined date and time of the measurement (YYYY-MM-DD HH:MM:SS) date = the sampling date reported by the YSI (M/D/YYYY) time = the sampling time reported by the YSI (HH:MM:SS) frac_sec = the sampling fractions of a second reported by the YSI site_name = the site name on the YSI deployment (left blank) Cond = the conductivity (uS/cm) nLF_Cond = the nLF conductivity (uS/cm) DO_perc = the percent oxygen saturation DO_percL = the percent local oxygen saturation DO_mgL = the dissolved oxygen concentration (mg/L) SAL = the salinity (psu) SPC = the specific conductivity (uS/cm) TDS = the total dissolved solids (mg/L) Turbidity = the turbidity of the water (FNU) TSS = the total suspended solids pH = the pH pH_mV = the millivolts of the pH sensor Temp = the temperature (dC) Batt_V = the battery voltage Cable_V = the cable power
DOI: 10.5281/zenodo.6521852
title: Chalgrove Lake (Buffalo Creek Watershed) YSI Data from 2022-02-18 to 2022-03-18

description: General Metadata for Chalgrove Lake YSI Data Files Specific metadata for each deployment can be found as text files with the file format of: <pre><code>BC_chalgrove_lake_YYYY-MM-DD_YYYY-MM-DD_metadata.txt</code></pre> Where YYYY-MM-DD_YYYY-MM-DD is the date range of the deployment. File Created 2019-04-12 by KF File Modified 2019-10-31 by KF - added the descriptions of the total algae variables 2022-05-04 by KF - updated to match LEO standards and current deployment specs Description These data are from a YSI EXO2 multiparameter sonde deployed at approximatly 0.7 m in Chalgrove Lake (37.242983 N, -78.464116 W) in approximately 4 m of water. Sonde Specifics The specific sensors and SNs deployed are on the metadata specific to each deployment but generally the sonde has: Temperature Conductivity pH ODO Turbidity Measurement Parameters, units, and Variable Names date.time = the combined date and time of the measurement (YYYY-MM-DD HH:MM:SS) date = the sampling date reported by the YSI (M/D/YYYY) time = the sampling time reported by the YSI (HH:MM:SS) frac_sec = the sampling fractions of a second reported by the YSI site_name = the site name on the YSI deployment (left blank) Cond = the conductivity (uS/cm) nLF_Cond = the nLF conductivity (uS/cm) DO_perc = the percent oxygen saturation DO_percL = the percent local oxygen saturation DO_mgL = the dissolved oxygen concentration (mg/L) SAL = the salinity (psu) SPC = the specific conductivity (uS/cm) TDS = the total dissolved solids (mg/L) Turbidity = the turbidity of the water (FNU) TSS = the total suspended solids pH = the pH pH_mV = the millivolts of the pH sensor Temp = the temperature (dC) Batt_V = the battery voltage Cable_V = the cable power
DOI: 10.5281/zenodo.6518717
title: Twindroid - System calls traces - Android apps - Extention

description: TwinDroid - a dataset of system calls traces, from both benign and infected Android apps. For other traces you can visit https://zenodo.org/record/6464808#.Yls2yVyZNH4 To trace apps, you can use our script in: https://github.com/RaphaelKhoury/automated-apk-tracing
DOI: 10.26124/mitofit:2022-0018
title: Statistical analysis of instrumental reproducibility as internal quality control in high-resolution respirometry
DOI: 10.5281/zenodo.6521802
title: LAY2FORM Datasets

description: LAY2FORM compilation of datasets
DOI: 10.5281/zenodo.6521801
title: LAY2FORM Datasets

description: LAY2FORM compilation of datasets
DOI: 10.17037/data.00002878
title: Clinical codelist - other cardiovascular disease ICD9 codes

description: ICD9 codes for other cardiovascular disease.
DOI: 10.17037/data.00002879
title: Clinical codelist - other cardiovascular disease ICD10 codes

description: ICD10 codes for other cardiovascular disease.
DOI: 10.6084/m9.figshare.14955465.v2
title: Efficacy of Phonemic Awareness_Supplemental Materials_Codebook.xlsx

description: Codebook for meta-analysis of Phonemic Awareness studies
DOI: 10.15151/esrf-es-746124426
title: iNEXT Discovery: Structural biology for translational research and discovery.

description: The aim of this proposal is to provide user access to Online crystallography and fragment screening pipelines based on the combination of EMBL’s HTX Lab services and the CrystalDirect Technology and automated data collection at ESRF’s MX beamlines, supported through the collaborative EMBL-ESRF Joint Structural Biology Group (JSBG). This will include three different user access modalities: 1) Large-Scale Fragment Screening, 2) Structural characterization of ligand-target complexes and 3) Online Crystallography (automated protein-to-structure pipeline). This work will be carried out in the context of international collaborative projects. Access to these modalities will require competitive application and peer-review through projects like the E.C. funded iNEXT Discovery or the recently awarded ISIDORe.