cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8667959
title: Inter-observer variability in target delineation increases during adaptive treatment of head-and-neck and lung cancer

description: <b>Introduction:</b> Inter-observer variability (IOV) in target volume delineation is a well-documented source of geometric uncertainty in radiotherapy. Such variability has not yet been explored in the context of adaptive re-delineation based on imaging data acquired during treatment. We compared IOV in the pre- and mid-treatment setting using expert primary gross tumour volume (GTV) and clinical target volume (CTV) delineations in locoregionally advanced head-and-neck squamous cell carcinoma (HNSCC) and (non-)small cell lung cancer [(N)SCLC]. <b>Material and methods:</b> Five and six observers participated in the HNSCC and (N)SCLC arm, respectively, and provided delineations for five cases each. Imaging data consisted of CT studies partly complemented by FDG-PET and was provided in two separate phases for pre- and mid-treatment. Global delineation compatibility was assessed with a volume overlap metric (the Generalised Conformity Index), while local extremes of IOV were identified through the standard deviation of surface distances from observer delineations to a median consensus delineation. Details of delineation procedures, in particular, GTV to CTV expansion and adaptation strategies, were collected through a questionnaire. <b>Results:</b> Volume overlap analysis revealed a worsening of IOV in all but one case per disease site, which failed to reach significance in this small sample (<i>p</i>-value range .063–.125). Changes in agreement were propagated from GTV to CTV delineations, but correlation could not be formally demonstrated. Surface distance based analysis identified longitudinal target extent as a pervasive source of disagreement for HNSCC. High variability in (N)SCLC was often associated with tumours abutting consolidated lung tissue or potentially invading the mediastinum. Adaptation practices were variable between observers with fewer than half stating that they consistently adapted pre-treatment delineations during treatment. <b>Conclusion:</b> IOV in target volume delineation increases during treatment, where a disparity in institutional adaptation practices adds to the conventional causes of IOV. Consensus guidelines are urgently needed.
DOI: 10.6084/m9.figshare.9198974
title: Daily adaptive proton therapy – the key to innovative planning approaches for paranasal cancer treatments

description: <b>Background:</b> For proton therapy of paranasal tumors, field directions avoiding volumes that might change during therapy are typically used. If the plan is optimized on the daily anatomy using daily adapted proton therapy (DAPT) however, field directions crossing the nasal cavities might be feasible. In this study, we investigated the effectiveness of DAPT for enabling narrow-field treatment approaches. <b>Material and methods:</b> For five paranasal tumor patients, representing a wide patient spectrum, anatomically robust 4-field-star and narrow-field plans were calculated and their robustness to anatomical and setup uncertainties was compared with and without DAPT. Based on the nominal planning CTs, per patient up to 125 simulated CTs (simCTs) with different nasal cavity fillings were created and random translations and rotations due to patient setup uncertainties were further simulated. Plans were recalculated or re-optimized on all error scenarios, representing non-adapted and DAPT fractions, respectively. From these, 100 possible treatments (60 GyRBE, 30 fx) were simulated and changes in integral dose, target and organs at risk (OARs) doses evaluated. <b>Results:</b> In comparison to the 4-field-star approach, the use of narrow-fields reduced integral dose between 29% and 56%. If OARs did not overlap with the target, OAR doses were also reduced. Finally, the significantly reduced target coverage in non-adapted treatments (mean V95 reductions of up to 34%) could be almost fully restored with DAPT in all cases (differences &lt;1%). <b>Conclusions:</b> DAPT was found to be not only an effective way to increase plan robustness to anatomical and positional uncertainties, but also opened the possibility to use improved and more conformal field arrangements.
DOI: 10.6084/m9.figshare.8326064
title: Relationship between patient and physician-rated xerostomia and dose distribution to the oral cavity and salivary glands for head and neck cancer patients after radiotherapy

description: <b>Introduction:</b> Xerostomia is a frequent complication after curative intended radiotherapy (RT) for head and neck squamous cell carcinoma (HNSCC). Assessment of xerostomia is commonly done by the physician. The aim of this study is to investigate the relation between patient and physician-rated xerostomia and to predict the degree of xerostomia from patients with self-reported xerostomia based on delivered doses to the oral cavity, parotid, and submandibular glands. <b>Material and methods:</b> During a 2-year period, consecutive HNSCC patients attending the follow-up clinic were included. All included patients had self-reported xerostomia, and completed the disease-specific EORTC QLQ-H&N35 questionnaire. The physician assessed the degree of xerostomia with the DAHANCA toxicity scale and was blinded for the EORTC score. Oral cavity, parotid, and submandibular glands (OAR) were delineated on the planning CT according to international guidelines. DVH were extracted from treatment plans. Logistic regression tested the relation between mean doses, patient characteristics, and xerostomia scores. Differences between DVH values and scoring of xerostomia were analyzed with a Kruskal–Wallis test. The relation between xerostomia and dose distributions was further investigated using principal component analysis (PCA). <b>Results:</b> In total, 109 patients were included in the study. A weak correlation was seen between patient and physician-rated toxicity (<i>p</i> = .001), however, in general patients reported more toxicity than physicians. For EORTC score ≥2, the multi-variable analysis was significant for doses to the oral cavity, tobacco status and use of xerogenic medication. Neither the DVH analysis nor the PCA found any clear distinction between xerostomia scores for EORTC or DAHANCA and investigated OARs. <b>Conclusion:</b> Patients tended to report higher scores of xerostomia than the physician. PCA indicated a complex relation between doses to the OAR and xerostomia scores, showing e.g., that reducing doses in one organ was on the expense of increased dose to another organ.
DOI: 10.6084/m9.figshare.8948798.v1
title: Patient-reported lung symptoms and quality of life before and after radiation therapy for non-small cell lung cancer: correlation with radiation pneumonitis and functional imaging

description: Patient-reported lung symptoms and quality of life before and after radiation therapy for non-small cell lung cancer: correlation with radiation pneumonitis and functional imaging
DOI: 10.6084/m9.figshare.8481233.v3
title: Towards FLASH proton therapy: the impact of treatment planning and machine characteristics on achievable dose rates

description: <b>Background:</b> This study aimed at evaluating spatially varying instantaneous dose rates for different intensity-modulated proton therapy (IMPT) planning strategies and delivery scenarios, and comparing these with FLASH dose rates (&gt;40 Gy/s). <b>Material and methods:</b> In order to quantify dose rates in three-dimensions, we proposed the ‘dose-averaged dose rate’ (DADR) metric, defined for each voxel as the dose-weighted mean of the instantaneous dose rates of all spots (i.e., pencil beams). This concept was applied to four head-and-neck cases, each planned with clinical (4 fields) and various spot-reduced IMPT techniques: ‘standard’ (4 fields), ‘arc’ (120 fields) and ‘arc-shoot-through’ (120 fields; 229 MeV only). For all plans, different delivery scenarios were simulated: constant beam intensity, variable beam intensity for a clinical Varian ProBeam system, varied per energy layer or per spot, and theoretical spot-wise variable beam intensity (i.e., no monitor/safety limitations). DADR distributions were calculated assuming 2-Gy or 6-Gy fractions. <b>Results:</b> Spot-reduced plans contained 17–52 times fewer spots than clinical plans, with no deterioration of plan quality. For the clinical plans, the mean DADR in normal tissue for 2-Gy fractionation was 1.7 Gy/s (median over all patients) at maximum, whereas in standard spot-reduced plans it was 0.7, 4.4, 7.1, and 12.1 Gy/s, for the constant, energy-layer-wise, spot-wise, and theoretical spot-wise delivery scenarios, respectively. Similar values were observed for arc plans. Arc-shoot-through planning resulted in DADR values of 3.0, 6.0, 14.1, and 24.4 Gy/s, for the abovementioned scenarios. Hypofractionation (3×) generally resulted in higher dose rates, up to 73.2 Gy/s for arc-shoot-through plans. The DADR was inhomogeneously distributed with highest values at beam entrance and at the Bragg peak. <b>Conclusion:</b> FLASH dose rates were not achieved for conventional planning and clinical spot-scanning machines. As such, increased spot-wise beam intensities, spot-reduced planning, hypofractionation and arc-shoot-through plans were required to achieve FLASH compatible dose rates.
DOI: 10.6084/m9.figshare.9198974.v1
title: Daily adaptive proton therapy – the key to innovative planning approaches for paranasal cancer treatments

description: <b>Background:</b> For proton therapy of paranasal tumors, field directions avoiding volumes that might change during therapy are typically used. If the plan is optimized on the daily anatomy using daily adapted proton therapy (DAPT) however, field directions crossing the nasal cavities might be feasible. In this study, we investigated the effectiveness of DAPT for enabling narrow-field treatment approaches. <b>Material and methods:</b> For five paranasal tumor patients, representing a wide patient spectrum, anatomically robust 4-field-star and narrow-field plans were calculated and their robustness to anatomical and setup uncertainties was compared with and without DAPT. Based on the nominal planning CTs, per patient up to 125 simulated CTs (simCTs) with different nasal cavity fillings were created and random translations and rotations due to patient setup uncertainties were further simulated. Plans were recalculated or re-optimized on all error scenarios, representing non-adapted and DAPT fractions, respectively. From these, 100 possible treatments (60 GyRBE, 30 fx) were simulated and changes in integral dose, target and organs at risk (OARs) doses evaluated. <b>Results:</b> In comparison to the 4-field-star approach, the use of narrow-fields reduced integral dose between 29% and 56%. If OARs did not overlap with the target, OAR doses were also reduced. Finally, the significantly reduced target coverage in non-adapted treatments (mean V95 reductions of up to 34%) could be almost fully restored with DAPT in all cases (differences &lt;1%). <b>Conclusions:</b> DAPT was found to be not only an effective way to increase plan robustness to anatomical and positional uncertainties, but also opened the possibility to use improved and more conformal field arrangements.
DOI: 10.6084/m9.figshare.8667959.v2
title: Inter-observer variability in target delineation increases during adaptive treatment of head-and-neck and lung cancer

description: <b>Introduction:</b> Inter-observer variability (IOV) in target volume delineation is a well-documented source of geometric uncertainty in radiotherapy. Such variability has not yet been explored in the context of adaptive re-delineation based on imaging data acquired during treatment. We compared IOV in the pre- and mid-treatment setting using expert primary gross tumour volume (GTV) and clinical target volume (CTV) delineations in locoregionally advanced head-and-neck squamous cell carcinoma (HNSCC) and (non-)small cell lung cancer [(N)SCLC]. <b>Material and methods:</b> Five and six observers participated in the HNSCC and (N)SCLC arm, respectively, and provided delineations for five cases each. Imaging data consisted of CT studies partly complemented by FDG-PET and was provided in two separate phases for pre- and mid-treatment. Global delineation compatibility was assessed with a volume overlap metric (the Generalised Conformity Index), while local extremes of IOV were identified through the standard deviation of surface distances from observer delineations to a median consensus delineation. Details of delineation procedures, in particular, GTV to CTV expansion and adaptation strategies, were collected through a questionnaire. <b>Results:</b> Volume overlap analysis revealed a worsening of IOV in all but one case per disease site, which failed to reach significance in this small sample (<i>p</i>-value range .063–.125). Changes in agreement were propagated from GTV to CTV delineations, but correlation could not be formally demonstrated. Surface distance based analysis identified longitudinal target extent as a pervasive source of disagreement for HNSCC. High variability in (N)SCLC was often associated with tumours abutting consolidated lung tissue or potentially invading the mediastinum. Adaptation practices were variable between observers with fewer than half stating that they consistently adapted pre-treatment delineations during treatment. <b>Conclusion:</b> IOV in target volume delineation increases during treatment, where a disparity in institutional adaptation practices adds to the conventional causes of IOV. Consensus guidelines are urgently needed.
DOI: 10.6084/m9.figshare.8948798
title: Patient-reported lung symptoms and quality of life before and after radiation therapy for non-small cell lung cancer: correlation with radiation pneumonitis and functional imaging

description: Patient-reported lung symptoms and quality of life before and after radiation therapy for non-small cell lung cancer: correlation with radiation pneumonitis and functional imaging
DOI: 10.6084/m9.figshare.8667959.v1
title: Inter-observer variability in target delineation increases during adaptive treatment of head-and-neck and lung cancer

description: <b>Introduction:</b> Inter-observer variability (IOV) in target volume delineation is a well-documented source of geometric uncertainty in radiotherapy. Such variability has not yet been explored in the context of adaptive re-delineation based on imaging data acquired during treatment. We compared IOV in the pre- and mid-treatment setting using expert primary gross tumour volume (GTV) and clinical target volume (CTV) delineations in locoregionally advanced head-and-neck squamous cell carcinoma (HNSCC) and (non-)small cell lung cancer [(N)SCLC]. <b>Material and methods:</b> Five and six observers participated in the HNSCC and (N)SCLC arm, respectively, and provided delineations for five cases each. Imaging data consisted of CT studies partly complemented by FDG-PET and was provided in two separate phases for pre- and mid-treatment. Global delineation compatibility was assessed with a volume overlap metric (the Generalised Conformity Index), while local extremes of IOV were identified through the standard deviation of surface distances from observer delineations to a median consensus delineation. Details of delineation procedures, in particular, GTV to CTV expansion and adaptation strategies, were collected through a questionnaire. <b>Results:</b> Volume overlap analysis revealed a worsening of IOV in all but one case per disease site, which failed to reach significance in this small sample (<i>p</i>-value range .063–.125). Changes in agreement were propagated from GTV to CTV delineations, but correlation could not be formally demonstrated. Surface distance based analysis identified longitudinal target extent as a pervasive source of disagreement for HNSCC. High variability in (N)SCLC was often associated with tumours abutting consolidated lung tissue or potentially invading the mediastinum. Adaptation practices were variable between observers with fewer than half stating that they consistently adapted pre-treatment delineations during treatment. <b>Conclusion:</b> IOV in target volume delineation increases during treatment, where a disparity in institutional adaptation practices adds to the conventional causes of IOV. Consensus guidelines are urgently needed.
DOI: 10.6084/m9.figshare.13213535
title: plus.bw

description: proliferating homo cell
DOI: 10.6084/m9.figshare.13213535.v1
title: plus.bw

description: proliferating homo cell
DOI: 10.6084/m9.figshare.13213571
title: Genetic Interactions Between BEN1- and Cytochrome P450-Mediated Brassinosteroid Inactivation.

description: Dataset for the indicated paper.
DOI: 10.6084/m9.figshare.13213571.v1
title: Genetic Interactions Between BEN1- and Cytochrome P450-Mediated Brassinosteroid Inactivation.

description: Dataset for the indicated paper.
DOI: 10.5281/zenodo.4053151
title: Eclipse Static Analysis - 10 Java projects

description: This dataset consists of Eclipse's static analysis performed on 10 Java projects. For each <em>.java</em> file of a test project, we ran a static analysis using Eclipse JDT Core allows us to retrieve all the possible function calls based on typing/imports for a given completion site). Each java project has three files structured as follows: <strong>*.json file. </strong>The file contains all the method declarations of the project and the function calls in their body. For each function call, the file lists all the possible function call that could have been made at that place in the source code. For practical purposes, we splitted this file into two text files. <strong>*_sequences.txt file. </strong>This file consists of all the method declaration + function call sequences in the project. The last element of each line corresponds to a completion site. <strong>*_proposals.txt file.</strong> Each line is made of the function-call suggestions retrieved by static analysis for the corresponding line in the <em>*_sequences.txt</em> file. The corpus was used for the experiments in the paper <strong>Combining Code Embedding with Static Analysis for Function-Call Completion</strong>. Github repository to replicate the experiments: https://github.com/mweyssow/cse-saner
DOI: 10.5281/zenodo.4053150
title: Eclipse Static Analysis - 10 Java projects

description: This dataset consists of Eclipse's static analysis performed on 10 Java projects. For each <em>.java</em> file of a test project, we ran a static analysis using Eclipse JDT Core allows us to retrieve all the possible function calls based on typing/imports for a given completion site). Each java project has three files structured as follows: <strong>*.json file. </strong>The file contains all the method declarations of the project and the function calls in their body. For each function call, the file lists all the possible function call that could have been made at that place in the source code. For practical purposes, we splitted this file into two text files. <strong>*_sequences.txt file. </strong>This file consists of all the method declaration + function call sequences in the project. The last element of each line corresponds to a completion site. <strong>*_proposals.txt file.</strong> Each line is made of the function-call suggestions retrieved by static analysis for the corresponding line in the <em>*_sequences.txt</em> file. The corpus was used for the experiments in the paper <strong>Combining Code Embedding with Static Analysis for Function-Call Completion</strong>. Github repository to replicate the experiments: https://github.com/mweyssow/cse-saner
DOI: 10.34777/r7zr-ef05
title: PSF Estimation and deconvolution: models, microscopy images, and datasets

description: This is the accompanying dataset for the publication Adrian Shajkofci, Michael Liebling, “Spatially-Variant CNN-Based Point Spread Function Estimation for Blind Deconvolution and Depth Estimation in Optical Microscopy,” IEEE Transactions on Image Processing, vol. 29, pp. 5848-5861, 2020. 

Publications based on this data must cite the above paper.
DOI: 10.5281/zenodo.4265866
title: Digital Cores and Fractal Dimensions

description: This is a supplementary data sets for a manuscript submitted to JGR: Solid Earth entitled "A Fractal Reference Model Based on 3D Process-Based Digital Core for Evaluating the Complexity of Rock Pore Structure". This data sets present the digital core construction and fractal dimension calculation in detail, including process-based modeling program, CT digital core data, fractal dimension calculation program and analysis statistics worksheet.
DOI: 10.5281/zenodo.4265865
title: Digital Cores and Fractal Dimensions

description: This is a supplementary data sets for a manuscript submitted to JGR: Solid Earth entitled "A Fractal Reference Model Based on 3D Process-Based Digital Core for Evaluating the Complexity of Rock Pore Structure". This data sets present the digital core construction and fractal dimension calculation in detail, including process-based modeling program, CT digital core data, fractal dimension calculation program and analysis statistics worksheet.
DOI: 10.5281/zenodo.4084570
title: GitHub Java Corpus - Function Identifiers

description: This dataset contains function identifiers extracted from the GitHub Java Corpus (http://groups.inf.ed.ac.uk/cup/javaGithub/). Each line corresponds to a method declaration. A line contains the name of the method declaration followed by the function identifiers (i.e., function calls) contained within the method body. The corpus was used for the experiments in the paper <strong>Combining Code Embedding with Static Analysis for Function-Call Completion</strong>. Github repository to replicate the experiments: https://github.com/mweyssow/cse-saner
DOI: 10.5281/zenodo.4265506
title: Avaliação da Arquitetura do SMartyModeling

description: Pacote experimental com os artefatos da avaliação qualitativa da arquitetura do SMartyModeling.
DOI: 10.5281/zenodo.4265505
title: Avaliação da Arquitetura do SMartyModeling

description: Pacote experimental com os artefatos da avaliação qualitativa da arquitetura do SMartyModeling.
DOI: 10.5281/zenodo.4265918
title: Field-based evidence for intra-slab high-permeability channel formation at eclogite-facies conditions during subduction

description: Bulk rock analysis of metamorphic rock samples (major and trace element)
DOI: 10.5281/zenodo.4265917
title: Field-based evidence for intra-slab high-permeability channel formation at eclogite-facies conditions during subduction

description: Bulk rock analysis of metamorphic rock samples (major and trace element)