cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48804/pzavuc
title: Replication Data for: Speech enhancement using ego-noise references with a microphone array embedded in an unmanned aerial vehicle

description: This dataset contains experimental audio recordings performed with a microphone array embedded in an unmanned aerial vehicle (UAV) in a semi-anechoic chamber used for testing the implemented methods described in the related publication. Please read the README.txt for further description and instructions.
DOI: 10.48804/dz5xag
title: Replication Data for: Algorithmic Differentiation for adjoint sensitivity calculation in plasma edge codes

description: A data-set including the input parameters and results for the paper "Algorithmic Differentiation for adjoint sensitivity calculation in plasma edge codes". 
The simulation results can be reproduced using SOLPS-ITER and TAPENADE tools with the methodology and code versions described in the paper. 
All figures can be directly reproduced with the scripts available in the related repository using MATLAB.
description: SOLPS-ITER, ea8c1a68067
description: B2.5, 01a98c0af71
description: Tapenade, 3.16
DOI: 10.48804/kqbk3r
title: Replication Data for: Interconnected and high cycling stability polypyrrole supercapacitors using cellulose nanocrystals and commonly used inorganic salts as dopants

description: Raw data for the paper of "Interconnected and high cycling stability polypyrrole supercapacitors using cellulose nanocrystals and commonly used inorganic salts as dopants"
DOI: 10.48804/tljwnd
title: Replication Data for: Using full-scale observations on footbridges to estimate the parameters governing human-structure interaction

description: This dataset contains the data for the Case study Waalse Krook South Footbridge in the above mentioned paper.
DOI: 10.48804/ihzx7d
title: Replication data for Eeklo Footbridge: Benchmark Dataset on Pedestrian-Induced Vibrations

description: The Eeklo footbridge benchmark dataset was collected on October 26th 2017 on the Eeklo footbridge (Belgium) and involves unrestricted pedestrian traffic. Two pedestrian densities were considered: 0.25 persons/m2 and 0.50 persons/m2, corresponding to approximately 75 and 150 pedestrians. All procedures were approved by the social and societal ethics committee of KU Leuven and each participant gave written informed consent prior to participation. The following data
is available: (1) Structural accelerations at 10 locations along the bridge deck, (2) Accelerations levels at the lower back of each participant, (3) Pedestrian trajectories along the bridge deck and (4) a digital twin representing the dynamic behavior of the footbridge.
DOI: 10.48804/m5yv9f
title: Replication Data for: Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes

description: The Aryl hydrocarbon receptor is an ancient transcriptional factor originally discovered as a sensor of dioxin. In addition to its function as receptor of environmental toxicants, it plays an important role in development. Although a significant amount of research has been carried out to understand AHR signal transduction pathway and its involvement in species susceptibility to environmental toxicants, none of them to date has comprehensively studied its evolutionary origins. Studying evolutionary origins of molecules can inform ancestral relationships of genes. Vertebrate genome has been shaped by two rounds of whole-genome duplications (WGD) at the base of vertebrate evolution approximately 600 million years ago (Mya), followed by lineage specific gene losses, which often complicate assignment of functional homology. It is crucial to understand evolutionary origins of this transcription factor and its partners, in order to distinguish orthologs from ancient non-orthologous homologs. In this study, we have investigated evolutionary origins of proteins involved in the AHR pathway. Our results provide evidence of gene loss and duplications, crucial for understanding functional connectivity of human and model species. Multiple studies have shown that 2R-ohnologs (genes and proteins that have survived from the 2R-WGD) are enriched in signaling components relevant to developmental disorders and cancer. Our findings provide a link between AHR pathway’s evolutionary trajectory and its possible mechanistic involvement in pathogenesis.
description: MAFFT
description: HMMER, v3.2.1
description: Gblocks, 0.91b
description: iTOL
description: taxonkit
description: ETE3
description: RAxML-NG, v1.1
description: Genomicus
description: Synteny Database
DOI: 10.48804/73uhkn
title: Replication Data for: Glycyrrhizin-based hydrogels accelerate wound healing of normoglycemic and diabetic mouse skin

description: This dataset contains microscopy (cryoSEM), rheometry and small angle X-ray scattering data on glycyrrhizin based hydrogels. This was used for the elucidation of changes in the gel structure dependent on glycyrrhizin concentration and gel temperature. The concentrations and temperatures were chosen to cover a range suitable for the final application in healing of diabetic wounds.
description: SPEC (Certified scientific software), 6.08.04
description: XSACT (Xenocs), 2.6
description: RHEOPLUS/32 (Anton Paar), 3.41D090724
DOI: 10.48804/aelrql
title: Replication Data for: Cytokine release during normothermic kidney perfusion – a scoping review.

description: This dataset is the data extraction table of a scoping review performed to assess cytokine changes during isolated normothermic kidney perfusion. The final search was carried out on July 22nd, 2022 (2022-07-22)
DOI: 10.48804/rjndza
title: Replication Data for: Inflammatory profile during normothermic kidney perfusion with whole blood versus red blood cell perfusion fluid

description: This dataset contains replication data (this is processed data) collected during normothermic perfusion of pig kidneys.
DOI: 10.48804/qqnnho
title: How negative affect does and does not lead to binge eating - the importance of craving and negative urgency in bulimia nervosa

description: Data used for the manuscript called 'How negative affect does and does not lead to binge eating - the importance of craving and negative urgency in bulimia nervosa'. This includes the data and scripts for the analyses in SAS as well as the data and the scripts used for the analyses in Mplus. Do not reuse without explicit permission.
DOI: 10.48804/n6g7if
title: MEP data PhD project: interpersonal motor resonance during social gaze conditions

description: This dataset contains corticospinal excitability measures (MEPs, rMT, background EMG) investigated via single-pulse transcranial magnetic stimulation (TMS) of 166 anonymized adult participants (141 neurotypical, 25 with a clinical autism spectrum diagnosis) included in the PhD project of the dataset author. TMS-induced MEPs were collected during rest and during different action observation settings (see ReadMe files per cohort for experimental details and stimuli descriptions). The dataset is structured per experimental cohort (1 to 6) and composed of 1 CSV file per participant, reporting raw MEP waveform characteristics and background EMG-related parameters elicited under different experimental conditions.
description: Participants' demographic characteristics, individual TMS-related parameters (rMT, hotspot coordinates) as well as self-reported raw questionnaire scores are reported in the tabular data overview. Questionnaires include the Social Responsiveness Scale (SRS), Social Phobia Inventory (SPIN) and State Adult Attachment Scale (SAAM).
description: Signal CED, version 6
description: MEP and social trait data included in the associated Exploratory Report are denoted by a 'YES' tag in the final column of the tabular data overview (.xlsx file).
DOI: 10.48804/qunnz0
title: Tidal Marsh Sediment Phosphorus Profiles

description: "Identification of the natural background of phosphorus in the Scheldt river using tidal marsh sediment cores" 


The cores were collected at Tidal Marshes along the Scheldt river, and were used to deduce the pre-industrial background of Phosphate based on deep sediment layers. 

Results obtained through these data were published in Open Access journal Biogeosciences. https://doi.org/10.5194/bg-2021-100
DOI: 10.48804/4aitp0
title: Replication Data for: Extending the dynamic response of structural input estimation by combining sensors with unmatched bandwidth

description: Raw data for the paper of "Extending the dynamic response of structural input estimation by combining sensors with unmatched bandwidth". The dataset contains the sensor readings for the experimental validation described in section 5.2 as well as the sensor and process models used in the Kalman filter. The .mat files contain detailed information about the sensor types, used timestep and unit. The data can be directly accessed via MATLAB or GNU Octave (open access). Alos .mat files for the models are included. The .csv files contain the data used in the figures of the paper.
DOI: 10.5281/zenodo.15014570
title: Microscopy and raw data for Alkane 1-monooxigenase gene alkB of Pseudomonas sp. FF2 is upregulated during colonisation of Arabidopsis thaliana leaves

description: This dataset accompanies the analysis of bacterial single-cell fluorescence and colony-forming unit (CFU) measurements in both in vitro and in planta conditions. The study focuses on the bacterial strain Pseudomonas fluorescens PFF2, evaluating its growth and promoter activity of the alkB gene using fluorescence under different growth conditions (diesel supplement growth medium and the Arabidopsis thaliana phyllosphere). The dataset supports machine learning classification models for bacterial cell identification and statistical analyses.

Codes are available at https://github.com/relab-fuberlin/alkanebioreporter

File description:




File
Data type
Description


invitro.tar.gz
Microscopy images
Images of in vitro experiments (PFF2 grown in BHB with and without diesel, and in LB)


inplanta-rep1.tar.gz
Microscopy images
Images of planta experiment 1 (PFF2 grown on Arabidopsis thaliana at 0, 2 and 7 dpi)


inplanta-rep2.tar.gz
Microscopy images
Images of planta experiment 2 (PFF2 grown on Arabidopsis thaliana at 0, 2 and 7 dpi)


in_vitro_rawdata.zip
CSV
CFU and single-cell fluorescence data of in vitro experiments


in_planta_rawdata.zip
CSV
CFU and single-cell fluorescence data of in planta experiments


trainset.zip
CSV
Ground truth-label dataset for training classification models
DOI: 10.5281/zenodo.15014571
title: Microscopy and raw data for Alkane 1-monooxigenase gene alkB of Pseudomonas sp. FF2 is upregulated during colonisation of Arabidopsis thaliana leaves

description: This dataset accompanies the analysis of bacterial single-cell fluorescence and colony-forming unit (CFU) measurements in both in vitro and in planta conditions. The study focuses on the bacterial strain Pseudomonas fluorescens PFF2, evaluating its growth and promoter activity of the alkB gene using fluorescence under different growth conditions (diesel supplement growth medium and the Arabidopsis thaliana phyllosphere). The dataset supports machine learning classification models for bacterial cell identification and statistical analyses.

Codes are available at https://github.com/relab-fuberlin/alkanebioreporter

File description:




File
Data type
Description


invitro.tar.gz
Microscopy images
Images of in vitro experiments (PFF2 grown in BHB with and without diesel, and in LB)


inplanta-rep1.tar.gz
Microscopy images
Images of planta experiment 1 (PFF2 grown on Arabidopsis thaliana at 0, 2 and 7 dpi)


inplanta-rep2.tar.gz
Microscopy images
Images of planta experiment 2 (PFF2 grown on Arabidopsis thaliana at 0, 2 and 7 dpi)


in_vitro_rawdata.zip
CSV
CFU and single-cell fluorescence data of in vitro experiments


in_planta_rawdata.zip
CSV
CFU and single-cell fluorescence data of in planta experiments


trainset.zip
CSV
Ground truth-label dataset for training classification models
DOI: 10.48804/cxzyhc
title: Replication Data for: Defect-Engineered Surfaces to Investigate the Formation of Self-Assembled Molecular Networks

description: The purpose of this data set is to give the reader access to the data used in the publication "Defect-Engineered Surfaces to Investigate the Formation of Self-Assembled Molecular Networks" (https://doi.org/10.1039/D2SC04599K). This folder contains a dataset of scanning tunnelling microscopy (STM) images and quantitative analysis files used for a systematic study of the effect of grafting density of covalently modified HOPG substrate on the domain size distribution of self-assembled molecular network formation at the liquid/solid interface.
DOI: 10.48804/3fhvrc
title: Interview Transcripts of Students' and Professionals' Perception of Creativity

description: Dataset containing fully anonymized transcripts of interviews of students and professionals concerning their perception of creativity in software engineering. Includes scripts used to generate key code trees and saturation graphs.
DOI: 10.48804/qebxic
title: Replication Data for: The magmatic-hydrothermal transition in pegmatites and its effects on rare-metal mineralization: Insights from melt-crystal-fluid interactions in phosphate minerals from the Buranga dike (Rwanda) - PhD Thesis

description: The enclosed datasets were acquired as part of the research of Fernando Prado Araujo towards obtaining the degree of Doctor of Science (PhD): Geology at the KU Leuven, Belgium.

The purpose of the analyses is to understand the processes occurring during the transition from a melt- to a fluid-dominated environment in phosphorus-rich rare-element pegmatites.
All measurements were performed in natural rock and mineral samples from the Buranga pegmatite, western Rwanda.
Specifications of each dataset and measurement method are provided in the following sections.
DOI: 10.48804/jsktr6
title: Replication Data for: Pathway-specific inputs to the superior colliculus support flexible responses to visual threat

description: Included here are data related to the paper entitled: Pathway-specific inputs to the superior colliculus support flexible responses to visual threat.

This includes:
1. Position of retrogradely labeled neurons, related to Figure 1.
2. Visual responses of Gad2 neurons in the superior colliculus, related to Figure 2.
3. Retinal ganglion cell dendritic diameters and molecular identities, related to Figure 2.
4. Data needed related to Figure 3.
5. Data needed related Figure 4.
6. Summary of behavioral data related to Figure 6.
7. Summary of behavioral data related to Figure 7
DOI: 10.48804/amzhsd
title: EXIMIOUS SOP for collection, storage and shipment of biological samples (updated version 3)
title: EXIMIOUS SOP

description: This deliverable presents the standard operating procedures (SOP) for the collection, processing and shipment of biological samples in the EXIMIOUS human cohort studies. 
It is first described how the sampling relates to the project’s objectives and work plan. Biological samples are collected and processed in relation to WP3, WP4 and WP5. Thereafter, the process of collection, processing and shipment is described in detail with step-by-step instructions. Partners handling the biological samples will follow the instructions presented in this deliverable.
DOI: 10.15468/dl.5zr5qr
title: Occurrence Download

description: A dataset containing 382 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salvia scapiformis Hance"
 ]
}

 The dataset includes 382 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001703-250324175209820/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48804/6grwwe
title: Replication Data for: Accuracy-speed-stability trade-offs in a targeted stepping task are similar in young and older adults

description: Data set of 25 young and 25 older adults performed a target stepping task. In this study we aimed to test whether accuracy-speed-stability trade-offs are larger in older compared to young individuals. Since sensorimotor function degrades with age, we hypothesized that poor sensorimotor function would be associated with larger accuracy-speed-stability trade-offs. The dataset contains marker and force plate data from subjects performing a stepping task in which they stepped into projected targets starting from quiet standing. Additionally, we quantified sensorimotor function by measuring motor variability using a torque matching task on the Biodex, proprioception using a joint position matching task, and reliance on sensory information during standing using the Sensory Organization Test on the NeuroCom balance master.
description: MATLAB, 2021a
description: R, 4.1.3
description: OpenSim, 4.1
DOI: 10.48804/jl85tf
title: Replication Data for: Efficient depolymerization of glass fiber reinforced PET composites

description: This dataset is the raw data of the experimental evidence collected to proof the nature of chemical depolymerization of PET composites. The dataset is composed of txt files, containing the information needed to reproduce the data in the manuscript. This information mainly relates to experimental measurements of masses and signals from characterization equipment in the form of XY columns of easy access to the broad public. It also contains the source files for the calculation of crystallinity degree as calculated by different techniques. The structure of the dataset permits easy and fast location of the data, and a README file was placed in each folder to help understanding the nature and structure of files. The purpose of this data set is to give the reader access to the data used in the publication "Efficient depolymerization of glass fiber reinforced pet composites".
DOI: 10.48804/5w0txe
title: Normothermic perfusion of pig kidney

description: First, the pig is sedated. After intubation and general anaesthesia, a midline laparotomy is performed and the kidney is freed from the surrounding tissue. Then the renal artery and vein are ligated and the kidney is removed. On the back-table, the kidney is placed on melting ice and the renal artery is canulated with an armoured vascular cannula. The ureter is also cannulated with a small tube. Then the kidney is flushed with a cold preservation solution via the renal artery at a hydrostatic pressure of 100 cm H2O to rinse out any blood. In the meantime the normothermic perfusion circuit has been primed with the perfusion solution (Table S1) and heated to 38°C. The kidney is mounted on the circuit by connecting the arterial cannula with the inflow cannula of the circuit. The tube in the ureter is connected to a collection bag allowing urinary drainage. Then the arterial inflow cannula is opened and the kidney is perfused. This is noticeable by pinking up of the kidney once reperfusion is established.
DOI: 10.48804/9s65kb
title: EPHOR Deliverable D3.1- Protocols for collection, pre-processing and storage of biological samples (WP3)

description: The document submitted as part of EU- EPHOR (https://www.ephor-project.eu/) deliverable D3.1 describes the protocol for the collection, pre-processing and storage of biological samples in WP6, WP7.
DOI: 10.48804/kkfws9
title: Replication Data for: Charting the lipopeptidome of non-pathogenic Pseudomonas

description: A major source of pseudomonad specialized metabolites are the non-ribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with - but not restricted to - phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in non-pathogenic Pseudomonas genomes, covering thirteen chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin-family members (nepenthesin, oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in fifteen (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin- and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges.
description: MUSCLE, 3.8.425
description: IQ-TREE, 2.1.3
description: Geneious, 2022.2.2
description: iTOL
description: antiSMASH
description: NRPS-PKS
DOI: 10.48804/bl2imo
title: Code for: Algorithmic Differentiation for adjoint sensitivity calculation in plasma edge codes

description: A data-set including the post-processing scripts for the paper "Algorithmic Differentiation for adjoint sensitivity calculation in plasma edge codes". All figures can be directly reproduced with these scripts and the data available in the related repository using MATLAB.
description: Matlab, R2018a
DOI: 10.48804/do1brq
title: Replication Data for: Nonlinear topology optimization of District Heating Networks: A benchmark of a mixed-integer and a density-based approach

description: A data-set containing the structure, input parameters and optimization results of the heating networks used in benchmark of the paper "Nonlinear topology optimization of District Heating Networks: A benchmark of a mixed-integer and a density-based approach". This data can be used to replicate the results of the publication.
DOI: 10.15468/dl.avmyta
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Bubalus arnee (Kerr, 1792)"
 ]
}

 The dataset includes 251 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001704-250324175209820/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvk7cv
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Prosopis cineraria (L.) Druce"
 ]
}

 The dataset includes 225 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001706-250324175209820/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x4rvsc
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Prosopis cineraria (L.) Druce"
 ]
}

 The dataset includes 225 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001707-250324175209820/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.