cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14060511
title: ICSA 2025 submission 44

description: This repository provides the dataset and results for the evaluation of the paper with submission Nr 44 of the ICSA 2025 Research track.The dataset consists of the following files:



architectural_languages.zip: contains the used architectural lanauges used in the evaulation

Additionalnformation.pdf: contains additional information on how to read the files extracted by our approach

evaluation.zip: contains the data recieved by our evalutation. It contains the ChangeTrees created for each of the given AL. For more information consider the AdditionalInformation.pdf

results.zip: contains the summerized results for each of ChangeTrees in the AL

RQ_Results.zip: contains evaulated results from each of the RQs

Tools.zip: Contains the tools used for the evalution. For an explaination how to use it read the Additionalnformation.pdf, see below or contact the authors


Running the tool:

Windows 10/11JDK 20 or above

The tools consist of three programs: 



FHIR ReconstructorThis tool consists of three different jars. Each of the jars have the different FHIR AL already preloaded. (e.g. reconstructorFHIRSTU3.jar has FHIR_STU3 preloaded)Run the jar with:java -jar reconstructor_FHIR_STU3.jarAfterward there a Console Dialog where you enter the Type and afterwards the PropertyType from which you want to detect the possible changes.


Enter Type to inspect:

Activity

Enter PropertyType where you want to detect the changes:

actionResulting

Reading Activity.actionResulting 

Encounter:Location Type Match 1 Encounter:Participant

Location Type Match 1 Hospitalization

Stage.assessment Type Match 1 Condition.asserter

Changes decked please see file !

Process finished with exit code 0

Afterwards a file called possibleChanges.json should be created that contains the detected ChangeTree.



EMF AL ReconstructorThis tool is similar to the FHIR importer. Here, you can import to EML AL versions that get imported into the system. Afterwards you can reconstruct the history of a PropertyType same as the FHIR jar. Run this tool with:


java -jar reconstructor.jar <pathToALVersion1> <pathToALVersion2>



EMF RandomChanges ReconstructorThis tool imports an EMF AL and applies random changes to it. Afterwards it generates a ChangeTree for each of the PropertyTypes and stores them in the provided Path


java -jar reconstructorRandom.jar <pathToALVersion1> <pathWhereToStore> <numberOfRandomChangesApplied>

Note: Please run both the tool and the server in a command line to receive additional information.
DOI: 10.5281/zenodo.14060512
title: ICSA 2025 submission 44

description: This repository provides the dataset and results for the evaluation of the paper with submission Nr 44 of the ICSA 2025 Research track.The dataset consists of the following files:



architectural_languages.zip: contains the used architectural lanauges used in the evaulation

Additionalnformation.pdf: contains additional information on how to read the files extracted by our approach

evaluation.zip: contains the data recieved by our evalutation. It contains the ChangeTrees created for each of the given AL. For more information consider the AdditionalInformation.pdf

results.zip: contains the summerized results for each of ChangeTrees in the AL

RQ_Results.zip: contains evaulated results from each of the RQs

Tools.zip: Contains the tools used for the evalution. For an explaination how to use it read the Additionalnformation.pdf, see below or contact the authors


Running the tool:

Windows 10/11JDK 20 or above

The tools consist of three programs: 



FHIR ReconstructorThis tool consists of three different jars. Each of the jars have the different FHIR AL already preloaded. (e.g. reconstructorFHIRSTU3.jar has FHIR_STU3 preloaded)Run the jar with:java -jar reconstructor_FHIR_STU3.jarAfterward there a Console Dialog where you enter the Type and afterwards the PropertyType from which you want to detect the possible changes.


Enter Type to inspect:

Activity

Enter PropertyType where you want to detect the changes:

actionResulting

Reading Activity.actionResulting 

Encounter:Location Type Match 1 Encounter:Participant

Location Type Match 1 Hospitalization

Stage.assessment Type Match 1 Condition.asserter

Changes decked please see file !

Process finished with exit code 0

Afterwards a file called possibleChanges.json should be created that contains the detected ChangeTree.



EMF AL ReconstructorThis tool is similar to the FHIR importer. Here, you can import to EML AL versions that get imported into the system. Afterwards you can reconstruct the history of a PropertyType same as the FHIR jar. Run this tool with:


java -jar reconstructor.jar <pathToALVersion1> <pathToALVersion2>



EMF RandomChanges ReconstructorThis tool imports an EMF AL and applies random changes to it. Afterwards it generates a ChangeTree for each of the PropertyTypes and stores them in the provided Path


java -jar reconstructorRandom.jar <pathToALVersion1> <pathWhereToStore> <numberOfRandomChangesApplied>

Note: Please run both the tool and the server in a command line to receive additional information.
DOI: 10.4121/6a346720-d5a5-4ec6-9887-0a9fc745fb44
title: River Dune Behavior in Dredged Areas: Data and scripts

description: Scripts and derived data belonging to the paper named: River Dune Behavior in Dredged Areas.<br>The raw bed elevation and dredging data can be requested from Rijkswaterstaat through their service desk data (https://www.rijkswaterstaat.nl/formulieren/contactformulier-servicedesk-data). The scripts are made to analyze these data, the derived data resulting from the scripts are enclosed in this publication.<br>
DOI: 10.4121/6a346720-d5a5-4ec6-9887-0a9fc745fb44.v1
title: River Dune Behavior in Dredged Areas: Data and scripts

description: Scripts and derived data belonging to the paper named: River Dune Behavior in Dredged Areas.<br>The raw bed elevation and dredging data can be requested from Rijkswaterstaat through their service desk data (https://www.rijkswaterstaat.nl/formulieren/contactformulier-servicedesk-data). The scripts are made to analyze these data, the derived data resulting from the scripts are enclosed in this publication.<br>
DOI: 10.15468/dl.wtrnws
title: Occurrence Download

description: A dataset containing 634257 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Inventario Español de Especies Terrestres (MAGRAMA)"
 ]
}

 The dataset includes 634257 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016310-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14168474
title: D1.2.1_AGROECOseqC overall dataset_10.5281zenodo.14162190
DOI: 10.6084/m9.figshare.24936474.v3
title: Supplementary code

description: R code for the article "Developing a tool to operationalize seed provenancing for ecosystem restoration: a case study in the Brazilian Cerrado"
DOI: 10.15468/dl.hkf83h
title: Occurrence Download

description: A dataset listing the 124934 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "BasisOfRecord is one of (Human Observation)"
 ]
}

 The dataset's 124934 records were derived from 1240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016332-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/l31lp7
title: Pros and Cons of (NH4)2S Solution Treatment of p-GaN/Metallization Interface: Perspectives for Laser Diode

description: The impact of wet treatment using an (NH4)2S-alcohol solution on the interface state of the p-GaN/Ni/Au/Pt contact system and laser diode processing was investigated. Sulfur wet cleaning resulted in reduced surface roughness and contact resistivity. The lowest specific contact resistance (ρc &lt; 1 × 10−4 Ω·cm2) was achieved with samples treated with an (NH4)2S-isopropanol solution, whereas the highest resistivity (ρc = 3.3 × 10−4 Ω·cm2) and surface roughness (Ra = 16 nm) were observed in samples prepared by standard methods. Annealing the contact system in an N2 + O2 + H2O atmosphere caused degradation through species inter-diffusion and metal-metal solid solution formation, irrespective of the preparation method. Standard prepared substrates developed a thin GaN-Au intermediate layer at the interface after heat treatment. Enhanced adhesion and the absence of GaN decomposition were observed in samples additionally cleaned with the (NH4)2S-solvent solution. Complete oxidation of nickel to NiO was observed in samples that underwent additional sulfur solution treatment. The intensity of metal species mixing and nickel oxidation was influenced by the metal diffusion rate and was affected by the initial state of the GaN substrate obtained through different wet treatment methods.The names of files corespond to the numbering of the figures in the paper Iryna Levchenko,Serhii Kryvyi,Eliana Kamińska,Julita Smalc-Koziorowska,Szymon Grzanka,Jacek Kacperski,Grzegorz Nowak,Sławomir Kret,Łucja Marona and Piotr Perlin. Pros and Cons of (NH4)2S Solution Treatment of p-GaN/Metallization Interface: Perspectives for Laser Diode. https://doi.org/10.3390/ma17184520.Files include next collection:Figure 1. AFM overview scan of p-GaN surface after (a) standard cleaning and (b) standard and (NH4)2S-t-(CH3)3COH treatment.Figure 2. AFM maps (a–d) and SEM images (e–h) of the surface of annealed p-GaN/Ni/Au/Pt contact system.Figure 3. c-AFM current maps (a–d) and AFM images (e–h) of annealed p-GaN/Ni/Au/Pt.Figure 4. STEM image of annealed p-GaN/Ni/Au/Pt, after standard preparation (a) and with additional treatment by (NH4)2S solution (b).Figure 5. STEM image (a) and EDX maps of the element propagation (b–f) for the annealed p-GaN/Ni/Au/Pt system with treatment in (NH4)2S-based solution.Figure 6. Schematic view on evolution of the annealed p-GaN/Ni/Au/Pt system with treatment in (NH4)2S-based solution (grey circles represent the voids).Figure 7. STEM image (a) and EDX maps of the element dispersion (b–f) for the annealed p-GaN/Ni/Au/Pt system after standard cleaning.Figure 8. Schematic view on evolution of the annealed p-GaN/Ni/Au/Pt system after standard cleaning.
DOI: 10.5281/zenodo.13302258
title: Zebrafish embryos time-course, 5'UTR nup43

description: This Zenodo file contains data for the 5′ UTR-nup43-sfGFP mRNA reporter. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.

Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.

Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.
DOI: 10.5281/zenodo.13302259
title: Zebrafish embryos time-course, 5'UTR nup43

description: This Zenodo file contains data for the 5′ UTR-nup43-sfGFP mRNA reporter. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.

Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.

Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.
DOI: 10.6084/m9.figshare.24936474.v4
title: Supplementary code

description: R code for the article "Developing a tool to operationalize seed provenancing for ecosystem restoration: a case study in the Brazilian Cerrado"
DOI: 10.5284/1124316
title: Images from a Watching Brief at Harwich Electric Palace Theatre, Harwich, Essex, December 2021

description: This archive consists of images from an archaeological watching brief by Cotswold Archaeology at Harwich Electric Palace Theatre, Harwich, Essex in December 2021
DOI: 10.15129/68379534-815b-448f-a7ca-a458750c944f
title: Data for "Atomic scale observation of threading dislocations in α-Ga2O3"

description: This study presents a statistically significant investigation of threading dislocations in α-Ga2O3 using high-resolution transmission electron microscopy. All the dislocations, observed end-on, exhibit a projected Burgers vector be = 1/3 ⟨1-100⟩, with data revealing that the dislocations fall into three categories: perfect mixed (b = 1/3 ⟨1-101⟩) dislocations and edge (b = ⟨1-100⟩ and b = 1/3 ⟨11-20⟩) dislocations which dissociate into combinations of b = 1/3 ⟨1-100⟩ partials. High-resolution analysis of the core region of the dislocations identifies that all the dislocations exhibit a similar 5-atom core, when looking at the cation sites. This is the first investigation of its kind in this material system, which will inform future work to, for example, understand the electronic properties of dislocations in α-Ga2O3 and other epitaxial corundum-structured materials.
DOI: 10.5281/zenodo.14168514
title: D1.2.1_AGROECOseqC overall dataset_10.5281zenodo.14168515
DOI: 10.15468/dl.t5zk78
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 (Aspidistra atroviolacea Tillich)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016346-241107131044228/datasets/export for details.
DOI: 10.5281/zenodo.7788026
title: Fruit-feeding butterfly community data analysed in "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration"

description: Community data of fruit-feeding butterflies collected from Kibale National Park, Uganda, in the periods 2011-2012 and 2020-2021 analysed in our paper Korkiatupa et al. 2023: "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration" (Ecosphere 14(5): e4514. https://doi.org/10.1002/ecs2.4514).

The table consists of two parts. First part shows counts of individuals of butterfly species in each study site. Second part shows the metadata: code of studysite, census (2011-2012/2020-2021), planting year (planting year or "Primary forest"), and coordinates (WGS 84 coordinate system).
DOI: 10.5281/zenodo.7788027
title: Fruit-feeding butterfly community data analysed in "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration"

description: Community data of fruit-feeding butterflies collected from Kibale National Park, Uganda, in the periods 2011-2012 and 2020-2021 analysed in our paper Korkiatupa et al. 2023: "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration" (Ecosphere 14(5): e4514. https://doi.org/10.1002/ecs2.4514).

The table consists of two parts. First part shows counts of individuals of butterfly species in each study site. Second part shows the metadata: code of studysite, census (2011-2012/2020-2021), planting year (planting year or "Primary forest"), and coordinates (WGS 84 coordinate system).
DOI: 10.15468/dl.dwkrk7
title: Occurrence Download

description: A dataset containing 1571 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fallopia aubertii (L.Henry) Holub"
 ]
}

 The dataset includes 1571 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016347-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24936474
title: COSST code

description: R code for the article "COSST – a tool to facilitate seed provenancing for climate-smart ecosystem restoration"
DOI: 10.6084/m9.figshare.24936474.v6
title: COSST code

description: R code for the article "COSST – a tool to facilitate seed provenancing for climate-smart ecosystem restoration"
DOI: 10.6084/m9.figshare.24936474.v5
title: COSST code

description: R code for the article "COSST – a tool to facilitate seed provenancing for climate-smart ecosystem restoration"