cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10219059
title: Dataset related to article "Knowledge-based DVH estimation and optimization for breast VMAT plans with and without avoidance sectors"

description: This record contains raw data related to article "Knowledge-based DVH estimation and optimization for breast VMAT plans with and without avoidance sectors"
 Abstract
Background: To analyze RapidPlan knowledge-based models for DVH estimation of organs at risk from breast cancer VMAT plans presenting arc sectors en-face to the breast with zero dose rate, feature imposed during the optimization phase (avoidance sectors AS).
Methods: CT datasets of twenty left breast patients in deep-inspiration breath-hold were selected. Two VMAT plans, PartArc and AvoidArc, were manually generated with double arcs from ~ 300 to ~ 160°, with the second having an AS en-face to the breast to avoid contralateral breast and lung direct irradiation. Two RapidPlan models were generated from the two plan sets. The two models were evaluated in a closed loop to assess the model performance on plans where the AS were selected or not in the optimization.
Results: The PartArc plans model estimated DVHs comparable with the original plans. The AvoidArc plans model estimated a DVH pattern with two steps for the contralateral structures when the plan does not contain the AS selected in the optimization phase. This feature produced mean doses of the contralateral breast, averaged over all patients, of 0.4 ± 0.1 Gy, 0.6 ± 0.2 Gy, and 1.1 ± 0.2 Gy for the AvoidArc plan, AvoidArc model estimation, RapidPlan generated plan, respectively. The same figures for the contralateral lung were 0.3 ± 0.1 Gy, 1.6 ± 0.6 Gy, and 1.2 ± 0.5 Gy. The reason was found in the possible incorrect information extracted from the model training plans due to the lack of knowledge about the AS. Conversely, in the case of plans with AS set in the optimization generated with the same AvoidArc model, the estimated and resulting DVHs were comparable. Whenever the AvoidArc model was used to generate DVH estimation for a plan with AS, while the optimization was made on the plan without the AS, the optimizer evidentiated the limitation of a minimum dose rate of 0.2 MU/°, resulting in an increased dose to the contralateral structures respect to the estimation.
Conclusions: The RapidPlan models for breast planning with VMAT can properly estimate organ at risk DVH. Attention has to be paid to the plan selection and usage for model training in the presence of avoidance sectors.
DOI: 10.5281/zenodo.10219060
title: Dataset related to article "Knowledge-based DVH estimation and optimization for breast VMAT plans with and without avoidance sectors"

description: This record contains raw data related to article "Knowledge-based DVH estimation and optimization for breast VMAT plans with and without avoidance sectors"
 Abstract
Background: To analyze RapidPlan knowledge-based models for DVH estimation of organs at risk from breast cancer VMAT plans presenting arc sectors en-face to the breast with zero dose rate, feature imposed during the optimization phase (avoidance sectors AS).
Methods: CT datasets of twenty left breast patients in deep-inspiration breath-hold were selected. Two VMAT plans, PartArc and AvoidArc, were manually generated with double arcs from ~ 300 to ~ 160°, with the second having an AS en-face to the breast to avoid contralateral breast and lung direct irradiation. Two RapidPlan models were generated from the two plan sets. The two models were evaluated in a closed loop to assess the model performance on plans where the AS were selected or not in the optimization.
Results: The PartArc plans model estimated DVHs comparable with the original plans. The AvoidArc plans model estimated a DVH pattern with two steps for the contralateral structures when the plan does not contain the AS selected in the optimization phase. This feature produced mean doses of the contralateral breast, averaged over all patients, of 0.4 ± 0.1 Gy, 0.6 ± 0.2 Gy, and 1.1 ± 0.2 Gy for the AvoidArc plan, AvoidArc model estimation, RapidPlan generated plan, respectively. The same figures for the contralateral lung were 0.3 ± 0.1 Gy, 1.6 ± 0.6 Gy, and 1.2 ± 0.5 Gy. The reason was found in the possible incorrect information extracted from the model training plans due to the lack of knowledge about the AS. Conversely, in the case of plans with AS set in the optimization generated with the same AvoidArc model, the estimated and resulting DVHs were comparable. Whenever the AvoidArc model was used to generate DVH estimation for a plan with AS, while the optimization was made on the plan without the AS, the optimizer evidentiated the limitation of a minimum dose rate of 0.2 MU/°, resulting in an increased dose to the contralateral structures respect to the estimation.
Conclusions: The RapidPlan models for breast planning with VMAT can properly estimate organ at risk DVH. Attention has to be paid to the plan selection and usage for model training in the presence of avoidance sectors.
DOI: 10.6084/m9.figshare.24461137
title: Electroluminescence data (Fig 2a)

description: Electroluminescence data (Fig 2a)
DOI: 10.6084/m9.figshare.24461137.v1
title: Electroluminescence data (Fig 2a)

description: Electroluminescence data (Fig 2a)
DOI: 10.22029/jlupub-9169
title: Supplemental Material for "Untersuchungen zur In-vitro-Chemosensitivität einer felinen Large Granular Lymphocyte (LGL)-Zelllinie unter Berücksichtigung arbeitssicherheitsrelevanter Maßgaben"

description: Supplemental material for doctoral thesis: "Untersuchungen zur In-vitro-Chemosensitivität einer felinen Large Granular Lymphocyte (LGL)-Zelllinie unter Berücksichtigung arbeitssicherheitsrelevanter Maßgaben" and related publications. The aim of the study was to determine the in vitro chemosensitivity of the feline LGL cell line S87. For this purpose the cells were seeded at a concentration of 1 Mio./ml/well in 24-well-cell-culture-plates. After 48 h the cell culture medium was changed to a medium containing six diffrent concentrations (given in the tables for each substance) of doxorubicin, 4-hydroperoxycyclophosphamide, vincristine, methotrexate, L-asparaginase or prednisolone. The cell count and the viability were determined by trypan blue staining after 24 and 48 h. Each experiment was repeated 3 times (given in the dates of the experiments). Furthermore the experiments with doxorubicin and vincristine were repeated with usage of elacridar, an inhibitor of several ATP-binding-cassette-transporters. The data sheet includes the number of living cells and the viability of four measurements per well as well as the arithmetic mean.
DOI: 10.22029/jlupub-15650
title: Supplemental Data for "Frequency and Characterisation of Anomalies and Fractures of the Caudal Spine in Sheep with Undocked Tails"

description: The dataset provided relates to the publication "Frequency and Characterisation of Anomalies and Fractures of the Caudal Spine in Sheep with Undocked Tails" in the journal Animals and is intended to increase the transparency of the data processes and allow reproducibility and traceability. At 14 weeks of age, the caudal spines of 216 undocked Merino land lambs was radiographically examined, and tail length and circumference were measured. Anomalies were documented and statistical correlation and model calculations were performed using the statistical programme SAS OnDemand for Academics (SAS, 2022). - The lamb ID represents a continuous numbering of the examined animals for targeted assignment. - Litter size is used to describe the number of lambs in this litter. - Sex can be female (w) or male (m). - We used 4 different rams (male sheep) for the mating. Ram 1 and 2 are short tailed, Ram 3 and 4 have a long tail. Therefore the number of the ram (1-4) is documented. - The parity describes the number of previous lamings of the ewe. - Tail length and tail circumference are displayed in centimeters. - The Number of vertebrae was counted on the basis of an X-ray image. - The occurence of axial deviation, blocked vertebrae, wedged vertebrae and vertebral fractures coded with 1. If no change was found, it was coded as 0. - The fracture localisation can be 1 = Caudal third of the tail, 2 = middle third of the tail, 12 = caudal and middle third of the tail or 0 = no fracture - Axial deviation was defined as any manually irreparable deviation of the tail from the medians. - A blocked vertebra was considered present if the vertebral boundaries of adjacent vertebrae were not clearly visible or were completely fused. Wedge-shaped bony structures present between two vertebrae were recorded as wedged vertebrae. A fracture was noted in any event where a vertebra demon-strated an interruption of bone structure.
DOI: 10.22029/jlupub-17614
title: Supplemental Material for "Effects of temperature-humidity index on blood metabolites of German dairy cows and their female calves"

description: The data tables are supplemental material for the research article "Effects of temperature-humidity index on blood metabolites of German dairy cows and their female calves". The aims of the present study were (a) to compare differences in blood plasma metabolite concentrations of German Holstein dairy cows either suffering from high mean THI (mTHI) on the day before blood sampling during late gestation or not suffering from high mTHI, and (b) to compare differences between blood plasma metabolite concentrations of their female calves either suffering from high mTHI on the day before blood sampling during the first week of life or not suffering from high mTHI. The supplementary data include 3 tables: Supplemental table S1: List of Metabolites: MxP® Quant 500 Kit (Biocrates Life Sciences AG, Innsbruck, Austria), Version: 2_02/2019 Supplemental table S2: Effects of fixed effects in the models 1a-c on metabolites of cows. The table includes log transformed Least-squares means (LSMeans) with corresponding SE, number of observations (n) and P-value. Supplemental table S3: Effects of fixed effects in models 2a-d on metabolites of calves. The table includes log transformed Least-squares means (LSMeans) with corresponding SE, number of observations (n) and P-value.
DOI: 10.6084/m9.figshare.24461134
title: Depth profiling of OLEDS (Fig 1c)

description: OrbiSIMS Depth profiling of OLEDS (Fig 1c)
DOI: 10.6084/m9.figshare.24461134.v1
title: Depth profiling of OLEDS (Fig 1c)

description: OrbiSIMS Depth profiling of OLEDS (Fig 1c)
DOI: 10.58060/9zaq-cf61
title: EVA (European Vegetation Archive) and ReSurveyEurope - version 2023-09-15

description: The European Vegetation Archive is a collective database of vegetation plots from Europe and adjacent regions integrated into a single platform. Each plot contains a list of plant species in a specific small area, usually supplemented by an estimate of the cover of each species. EVA consists of individual databases owned by data contributors. Any use of the data from the individual databases is subject to the consent of the data owner. ReSurveyEurope is integrated as a subset of EVA. It contains vegetation-plot data with repeated measurements over time, including data from permanent plots and resurveys of vegetation survey plots.
DOI: 10.6084/m9.figshare.24461125
title: Delta layer for depth resolution (Fig 1b)

description: Delta layer for depth resolution (Fig 1b)
DOI: 10.6084/m9.figshare.24461125.v1
title: Delta layer for depth resolution (Fig 1b)

description: Delta layer for depth resolution (Fig 1b)
DOI: 10.6084/m9.figshare.24461110
title: Degradation study (Fig 2b-e and Fig3a-d)

description: Degradation study (Fig 2b-e and Fig3a-d)
DOI: 10.6084/m9.figshare.24461110.v1
title: Degradation study (Fig 2b-e and Fig3a-d)

description: Degradation study (Fig 2b-e and Fig3a-d)
DOI: 10.23729/5c5e62ad-7831-439e-910c-9cbf74f526ec
title: 3D histology data of mouse prostates with manually annotated tumor hotspots

description: This dataset contains six sparse 3D histology stacks of registered, H&E-stained mouse prostate samples with manually annotated tumor hotspots. The data has been processed to suit SparStVR application. Each stack has approximately 30 sections with 50 micrometer distance between sections, and highest magnification is 10x. The dataset includes high resolution png images, subsampled tumor and sample masks and correspondingly sized H&E-stained images, and Cycle-GAN generated IHC and PAS stains plus experimental translations to forested ortho images. In addition, we provide feature maps for nucleus amount, computed from hematoxylin channel with two different tile sizes. Data is from mice heterozygous for tumor suppressor Pten+/-. Prostates were collected at the age of 11 months. Samples were fixed in PAXgene paraffin and cut into 5 micrometer thick slices. Every tenth section was H&E-stained and imaged with Zeiss Axioskop40 microscope (Carl Zeiss MicroImaging, NY, USA) using CCD color camera (QICAM Fast; QImaging, Canada) and motorized specimen stage (Märzhäuser Wetzlar GmbH, Germany). Surveyor imaging system (Objective Imaging, UK) controlled the automated image acquisition. Images were registered using Elastic Stack Alignment (ESA) plugin of Fiji (ImageJ).
DOI: 10.5281/zenodo.10219245
title: Data for Bell-jar performance evaluation report

description: During the SI-Hg performance evaluation of elemental mercury gas generators on the market three generators were tested, e.g., PSA 10.536 elemental Hg generator, bell-jar and Tekran Model 3425. Key characteristics were determined e.g.; the stabilisation period, short-term drift, precision, i.e., reproducibility and repeatability of the concentration generated, linearity, bias, sensitivity to sample gas pressure, sensitivity to surrounding temperature and sensitivity to electrical voltage. All three generators could be tested according to the calibration protocol developed within the project. The results obtained with the different gas generator clearly shows the importance of a metrological calibration. All three candidate generators show a different bias for the setpoint compared to the calibrated output. 
The data obtained during the performance evaluation of the bell-jar is published in this repository. The files of the following experiments can be found here:

m1

Measurement data online mercury analyser comparison VSL and bell-jar 2023-02-20
Bell_jar_calibration_m1
m2

Measurement data online mercury analyser comparison VSL and bell-jar 2023-02-28
Bell_jar_calibration_m2
m3

Measurement data online mercury analyser comparison VSL and bell-jar 2023-03-09
Bell_jar_calibration_m3
short-term drift

m1

Calibration bell-jar short term drif_m1
Bell_jar_drift_m1
m2

Calibration bell-jar short term drif_m2
Bell_jar_drift_m2
m3

Calibration bell-jar short term drif_m3
Bell_jar_drift_m3
m4

Calibration bell-jar short term drif_m4
Bell_jar_drift_m4
stability

Measurement data online mercury analyser comparison VSL and bell-jar stability
DOI: 10.5281/zenodo.10219244
title: Data for Bell-jar performance evaluation report

description: During the SI-Hg performance evaluation of elemental mercury gas generators on the market three generators were tested, e.g., PSA 10.536 elemental Hg generator, bell-jar and Tekran Model 3425. Key characteristics were determined e.g.; the stabilisation period, short-term drift, precision, i.e., reproducibility and repeatability of the concentration generated, linearity, bias, sensitivity to sample gas pressure, sensitivity to surrounding temperature and sensitivity to electrical voltage. All three generators could be tested according to the calibration protocol developed within the project. The results obtained with the different gas generator clearly shows the importance of a metrological calibration. All three candidate generators show a different bias for the setpoint compared to the calibrated output. 
The data obtained during the performance evaluation of the bell-jar is published in this repository. The files of the following experiments can be found here:

m1

Measurement data online mercury analyser comparison VSL and bell-jar 2023-02-20
Bell_jar_calibration_m1
m2

Measurement data online mercury analyser comparison VSL and bell-jar 2023-02-28
Bell_jar_calibration_m2
m3

Measurement data online mercury analyser comparison VSL and bell-jar 2023-03-09
Bell_jar_calibration_m3
short-term drift

m1

Calibration bell-jar short term drif_m1
Bell_jar_drift_m1
m2

Calibration bell-jar short term drif_m2
Bell_jar_drift_m2
m3

Calibration bell-jar short term drif_m3
Bell_jar_drift_m3
m4

Calibration bell-jar short term drif_m4
Bell_jar_drift_m4
stability

Measurement data online mercury analyser comparison VSL and bell-jar stability
DOI: 10.5281/zenodo.10214123
title: Dataset related to article "Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis"

description: Dataset related to article "Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis"
Abstract
Hepatic metastasis is a clinical challenge for colorectal cancer (CRC). Senescent cancer cells accumulate in CRC favoring tumor dissemination. Whether this mechanism progresses also in metastasis is unexplored. Here, we integrated spatial transcriptomics, 3D-microscopy, and multicellular transcriptomics to study the role of cellular senescence in human colorectal liver metastasis (CRLM). We discovered two distinct senescent metastatic cancer cell (SMCC) subtypes, transcriptionally located at the opposite pole of epithelial (e) to mesenchymal (m) transition. SMCCs differ in chemotherapy susceptibility, biological program, and prognostic roles. Mechanistically, epithelial (e)SMCC initiation relies on nucleolar stress, whereby c- myc dependent oncogene hyperactivation induces ribosomal RPL11 accumulation and DNA damage response. In a 2D pre-clinical model, we demonstrated that RPL11 co-localized with HDM2, a p53-specific ubiquitin ligase, leading to senescence activation in (e)SMCCs. On the contrary, mesenchymal (m)SMCCs undergo TGFβ paracrine activation of NOX4-p15 effectors. SMCCs display opposing effects also in the immune regulation of neighboring cells, establishing an immunosuppressive environment or leading to an active immune workflow. Both SMCC signatures are predictive biomarkers whose unbalanced ratio determined the clinical outcome in CRLM and CRC patients. Altogether, we provide a comprehensive new understanding of the role of SMCCs in CRLM and highlight their potential as new therapeutic targets to limit CRLM progression.
DOI: 10.5281/zenodo.10214124
title: Dataset related to article "Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis"

description: Dataset related to article "Spatial resolution of cellular senescence dynamics in human colorectal liver metastasis"
Abstract
Hepatic metastasis is a clinical challenge for colorectal cancer (CRC). Senescent cancer cells accumulate in CRC favoring tumor dissemination. Whether this mechanism progresses also in metastasis is unexplored. Here, we integrated spatial transcriptomics, 3D-microscopy, and multicellular transcriptomics to study the role of cellular senescence in human colorectal liver metastasis (CRLM). We discovered two distinct senescent metastatic cancer cell (SMCC) subtypes, transcriptionally located at the opposite pole of epithelial (e) to mesenchymal (m) transition. SMCCs differ in chemotherapy susceptibility, biological program, and prognostic roles. Mechanistically, epithelial (e)SMCC initiation relies on nucleolar stress, whereby c- myc dependent oncogene hyperactivation induces ribosomal RPL11 accumulation and DNA damage response. In a 2D pre-clinical model, we demonstrated that RPL11 co-localized with HDM2, a p53-specific ubiquitin ligase, leading to senescence activation in (e)SMCCs. On the contrary, mesenchymal (m)SMCCs undergo TGFβ paracrine activation of NOX4-p15 effectors. SMCCs display opposing effects also in the immune regulation of neighboring cells, establishing an immunosuppressive environment or leading to an active immune workflow. Both SMCC signatures are predictive biomarkers whose unbalanced ratio determined the clinical outcome in CRLM and CRC patients. Altogether, we provide a comprehensive new understanding of the role of SMCCs in CRLM and highlight their potential as new therapeutic targets to limit CRLM progression.
DOI: 10.5278/7e93e42e-38fc-4d87-ad68-ff1a2d1091aa
title: Dataset of smart heat and water meter data with accompanying building characteristics

description: This dataset include data from 34,884 commercial smart heat meters and 10,765 commercial smart water meters, covering a period of up to 5 years (2018 - 2022). The data originates from single-family houses in Aalborg Municipality, Denmark. Additionally, comprehensive building characteristics were collected for each building, where available, from the Danish Building and Dwelling Register (BBR) and Energy Performance Certificate (EPC) input data. As a result, up to 86 distinct characteristics per building are available. A well-established methodology was applied to process all smart meter data, resulting in equidistant hourly data with no erroneous or missing values. Rule sets were further employed to filter the building characteristics derived from the EPCs, enhancing the data quality. For a more extensive description, we would like to refer to our peer-reviewed open-access article describing the dataset and its processing: Schaffer, M., Veit, M., Marszal-Pomianowska, A., Frandsen, M., Zbigniew Pomianowski, Dichmann, E., Grau Sørensen, C., & Kragh, J. (in press). Dataset of smart heat and water meter data with accompanying building characteristics. Data in Brief. Please also consider citing this article if you use this dataset. Please note that access to the data is restricted, and researchers interested in using the data should contact Anna Marszal-Pomianowska (ajm@build.aau.dk).
DOI: 10.6084/m9.figshare.19243899.v5
title: Air cargo load and route planning in pickup and delivery operations

description: Military aviation faces risks of cargo unbalancing due to the urgency required on loading for rapid take-off and mission accomplishment, especially in times of crisis, armed conflict or public calamity. We model and solve the problem of planning the loading of an aircraft according to utility score, weight and balance principles, confer agility to pallet assembly under safety requirements, and also serving multiple bases in a tour of simultaneous Pickup and Delivery at intermediate airfields. This research result may be applicable by military and also by commercial companies in dynamic environments, especially on handling catastrophic events, sometimes as a government contractor. This problem encompasses four sub-problems: Air Palletization, Weight and Balance, Pickup and Delivery, and Sequencing. This hard problem, named Military Air Cargo Load Planning Problem, is mathematically modeled in real scenarios, using a standardized pallet, considering the possible presence of troops, ensures that torque and center of gravity constraints are obeyed, and each item is delivered to its destination. In our approach, we carry out experiments with a commercial solver, four well known meta-heuristics, and a proposed heuristic, on benchmarks based on statistical data from the Brazilian Air Force.
DOI: 10.5281/zenodo.10219348
title: Input files for T4 lysozyme free energy calculations with DMBIS non-bonded force field parameters
DOI: 10.5281/zenodo.10219349
title: Input files for T4 lysozyme free energy calculations with DMBIS non-bonded force field parameters
DOI: 10.58060/tyn5-3914
title: EVA project # 170 ReSurveyEurope – 2022-12-20 Dynamics of multi-dimensional diversity (richness, phylogenetic and functional diversity) of native and alien species along elevation and latitudinal gradients - W. Guo
title: SELECTION 2023-02-04

description: Final approved selection from European Vegetation Archive (EVA, incl. ReSurveyEurope) database for this EVA project specified with selection date. The EVA data are available on request using procedure described at How to obtain data (https://euroveg.org/eva-database/obtaining-data).