cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7760251
title: A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging

description: Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast cineradiography with <em>operando</em> gas chromatography, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (2 to 3 times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gases remain unchanged. Coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical, yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications.
DOI: 10.5281/zenodo.7760250
title: A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging

description: Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast cineradiography with <em>operando</em> gas chromatography, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (2 to 3 times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gases remain unchanged. Coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical, yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications.
DOI: 10.17632/mxztrypkjc.8
title: In2Sight_WP2.Microfabrication

description: Data related to the design of the microoptics for in2sight, D2.1
DOI: 10.17632/mxgbwn4dyb.1
title: Effects of amine vapor pretreatment upon cyanoacrylate deposition onto fingerprints

description: Excel spreadsheet of deposition of cyanoacrylate onto sets of fingerprints after various amine vapor pretreatment regimens. Statistical analysis of data. Shows statistically significant increases in cyanoacrylate deposition. PDF version of spreadsheet.
DOI: 10.17632/rw6hnm6xzb.1
title: Validation of genes with a putative role in the pathophysiology of endometriosis and adenomyosis by using NanoString 

description: An RNA-Seq discovery study using endometrial samples (19 controls, 8 ovarian, 4 deep-infiltrating endometriosis, and 6 adenomyosis) identified differentially expressed genes. In the discovery study, four candidates (GADD45G, PJA2, GGT8P, and HSPA1A) correctly distinguished between disease and controls (accuracy=0.86). Eleven phenotypic characteristics (e.g. dysmenorrhea and hypermenorrhea) were used in combination with gene expression data to generate hybrid classifiers and the predictive power increased (accuracy=0.977). The validation by Nanostring (n=285) showed an accuracy=0.5 when using solely genetic data and an accuracy=0.72 with a combination of genetic and phenotypic data. Only women between 18 and 49 years old were included. A complete clinical history review was done to exclude patients with heritable diseases or with viral infections, such as HIV, VHB, and VHC. The control, endometriosis, and adenomyosis groups were women who went to the clinic because they had gynecological symptoms such as pelvic pain, hypermenorrhea, or dysmenorrhea. Thus, an endometrial biopsy was taken for histological analysis. Women presenting only one specific type of endometriosis and/or adenomyosis were included, for example, patients with endometriosis suffered only from ovarian endometriosis (OE) or deep infiltrating endometriosis (DIE) exclusively. Collected samples were selected from women without history of endometriosis or adenomyosis in the past seven to ten years from the collection of the biopsy. Endometriosis cases were proven by laparoscopy, and adenomyosis patients by laparoscopy and/or TVUS. Women who were undergoing hormone treatment, such as oral contraceptives, were not excluded. In total, 285 blocks of formalin-fixed paraffin embedded (FFPE) endometrium, including endometriosis, adenomyosis, and control samples, were obtained retrospectively from the Pathological Anatomy Department of Vall d’Hebron University Hospital. These samples comprised 110 control, 58 OE, 60 DIE and 57 Adeno (adenomyosis) specimens. Samples were collected using a pipelle under an approved protocol after obtained written informed consent. Use of specimens was approved by the Ethics Committee of Vall d’Hebron Research Institute, Barcelona (Spain) under approval number PR(AMI)410/2016 on the 7th of July 2017 and all experiments were performed in accordance with relevant guidelines and regulations. The stage of menstrual cycle was determined by histological examination according to Noyes et al.

This dataset includes the raw files from the Validation study by using a custom NanoString codeset (RCC files) (n=285), as well as the excel file with the normalized data for each gene studied and the housekeeping genes (and positive and negative controls from the manufacturer) and one excel file with the metadata of each of the 285 patients.
DOI: 10.17632/rw6hnm6xzb.2
title: Gene expression of 15 genes in eutopic endometrium of women with endometriosis, adenomyosis and controls measured by NanoString

description: We aimed to validate 15 putative markers involvement in the development of deep infiltrating endometriosis, ovarian endometriosis, and adenomyosis and evaluate their potential as biomarkers for these three conditions. An RNA-Seq discovery study using endometrial samples identified differentially expressed genes. 

The validation by Nanostring (n=285) includes 110 controls, 57 adenomyosis, 60 deep infiltrating endometriosis (DIE), and 58 ovarian endometriosis (OE). RNA was obtained from 285 blocks of formalin-fixed paraffin embedded (FFPE) eutopic endometrial samples by using High Pure FFPET-RNA Isolation Kit (Roche) and quality controls were performed. Then, they were analyzed by Nanostring following manufacturer’s instructions. Post-quality controls were also performed by using nSolver analysis software (Nanostring).

This dataset includes the raw files from the validation study by using a custom NanoString codeset (RCC files) (n=285). The dataset includes the excel file with the normalized data for each gene studied, which includes 20 genes (15 candidates to validate and 5 houskeeping genes) and 14 internal controls from the manufacturer and one excel file with the metadata of each of the 285 patients.
DOI: 10.17632/6vwz4sk4rn.2
title: Supplemental material for “Salicylate suppresses monocyte chemoattractant protein-1 production by targeting phosphodiesterase 3B inhibition in TNF-α-stimulated adipocytes”

description: Our study provides compelling evidence for a hitherto unknown anti-inflammatory pathway of salicylate in obesity-related inflammation and a rationale for the application of the prodrug of salicylate in metabolic diseases. The raw data for each result is provided here for research reference.
DOI: 10.6084/m9.figshare.22331479
title: Supplementary Material for: The Effects of Mucopolysaccharide Polysulfate on Steroid-Induced Tight Junction Barrier Dysfunction in Human Epidermal Keratinocytes and a 3D Skin Model

description: Introduction: The long-term use of topical corticosteroids (TCS) is associated with side effects such as skin atrophy and barrier deterioration. Moisturizers, such as mucopolysaccharide polysulfate (MPS), have been reported to prevent relapses in atopic dermatitis (AD) when used in combination with TCS. However, the mechanisms underlying the positive effects of MPS in combination with TCS in AD are poorly understood. In the present study, we investigated the effects of MPS in combination with clobetasol 17-propionate (CP) on tight junction (TJ) barrier function in human epidermal keratinocytes (HEKa) and 3D skin models. Methods: The expression of claudin-1, which is crucial for TJ barrier function in keratinocytes, and transepithelial electrical resistance (TEER) was measured in CP-treated human keratinocytes incubated with and without MPS. A TJ permeability assay, using Sulfo-NHS-Biotin as a tracer, was also conducted in a 3D skin model. Results: CP reduced claudin-1 expression and TEER in human keratinocytes, whereas MPS inhibited these CP-induced effects. Moreover, MPS inhibited the increase in CP-induced TJ permeability in a 3D skin model. Conclusion: The present study demonstrated that MPS improved TJ barrier impairment induced by CP. The improvement of TJ barrier function may partially be responsible for the delayed relapse of AD induced by the combination of MPS and TCS.
DOI: 10.6084/m9.figshare.22331479.v1
title: Supplementary Material for: The Effects of Mucopolysaccharide Polysulfate on Steroid-Induced Tight Junction Barrier Dysfunction in Human Epidermal Keratinocytes and a 3D Skin Model

description: Introduction: The long-term use of topical corticosteroids (TCS) is associated with side effects such as skin atrophy and barrier deterioration. Moisturizers, such as mucopolysaccharide polysulfate (MPS), have been reported to prevent relapses in atopic dermatitis (AD) when used in combination with TCS. However, the mechanisms underlying the positive effects of MPS in combination with TCS in AD are poorly understood. In the present study, we investigated the effects of MPS in combination with clobetasol 17-propionate (CP) on tight junction (TJ) barrier function in human epidermal keratinocytes (HEKa) and 3D skin models. Methods: The expression of claudin-1, which is crucial for TJ barrier function in keratinocytes, and transepithelial electrical resistance (TEER) was measured in CP-treated human keratinocytes incubated with and without MPS. A TJ permeability assay, using Sulfo-NHS-Biotin as a tracer, was also conducted in a 3D skin model. Results: CP reduced claudin-1 expression and TEER in human keratinocytes, whereas MPS inhibited these CP-induced effects. Moreover, MPS inhibited the increase in CP-induced TJ permeability in a 3D skin model. Conclusion: The present study demonstrated that MPS improved TJ barrier impairment induced by CP. The improvement of TJ barrier function may partially be responsible for the delayed relapse of AD induced by the combination of MPS and TCS.
DOI: 10.6084/m9.figshare.22331488
title: Supplementary Material for: The Effects of Mucopolysaccharide Polysulfate on Steroid-Induced Tight Junction Barrier Dysfunction in Human Epidermal Keratinocytes and a 3D Skin Model

description: Introduction: The long-term use of topical corticosteroids (TCS) is associated with side effects such as skin atrophy and barrier deterioration. Moisturizers, such as mucopolysaccharide polysulfate (MPS), have been reported to prevent relapses in atopic dermatitis (AD) when used in combination with TCS. However, the mechanisms underlying the positive effects of MPS in combination with TCS in AD are poorly understood. In the present study, we investigated the effects of MPS in combination with clobetasol 17-propionate (CP) on tight junction (TJ) barrier function in human epidermal keratinocytes (HEKa) and 3D skin models. Methods: The expression of claudin-1, which is crucial for TJ barrier function in keratinocytes, and transepithelial electrical resistance (TEER) was measured in CP-treated human keratinocytes incubated with and without MPS. A TJ permeability assay, using Sulfo-NHS-Biotin as a tracer, was also conducted in a 3D skin model. Results: CP reduced claudin-1 expression and TEER in human keratinocytes, whereas MPS inhibited these CP-induced effects. Moreover, MPS inhibited the increase in CP-induced TJ permeability in a 3D skin model. Conclusion: The present study demonstrated that MPS improved TJ barrier impairment induced by CP. The improvement of TJ barrier function may partially be responsible for the delayed relapse of AD induced by the combination of MPS and TCS.
DOI: 10.6084/m9.figshare.22331488.v1
title: Supplementary Material for: The Effects of Mucopolysaccharide Polysulfate on Steroid-Induced Tight Junction Barrier Dysfunction in Human Epidermal Keratinocytes and a 3D Skin Model

description: Introduction: The long-term use of topical corticosteroids (TCS) is associated with side effects such as skin atrophy and barrier deterioration. Moisturizers, such as mucopolysaccharide polysulfate (MPS), have been reported to prevent relapses in atopic dermatitis (AD) when used in combination with TCS. However, the mechanisms underlying the positive effects of MPS in combination with TCS in AD are poorly understood. In the present study, we investigated the effects of MPS in combination with clobetasol 17-propionate (CP) on tight junction (TJ) barrier function in human epidermal keratinocytes (HEKa) and 3D skin models. Methods: The expression of claudin-1, which is crucial for TJ barrier function in keratinocytes, and transepithelial electrical resistance (TEER) was measured in CP-treated human keratinocytes incubated with and without MPS. A TJ permeability assay, using Sulfo-NHS-Biotin as a tracer, was also conducted in a 3D skin model. Results: CP reduced claudin-1 expression and TEER in human keratinocytes, whereas MPS inhibited these CP-induced effects. Moreover, MPS inhibited the increase in CP-induced TJ permeability in a 3D skin model. Conclusion: The present study demonstrated that MPS improved TJ barrier impairment induced by CP. The improvement of TJ barrier function may partially be responsible for the delayed relapse of AD induced by the combination of MPS and TCS.
DOI: 10.22008/fk2/xnebmc
title: Kort over dybden til redoxgrænsen i Danmark

description: Kortet viser det bedste estimat over dybden til redoxgrænsen i Danmark i meter under terræn. På basis af ca. 13 000 observationer af farveskift i sedimentprøver er der udviklet en model der beskriver sammenhængen mellem forskellige variable og dybden til redoxgrænsen, der beskriver overgangen fra oxiderede til reducerede jordlag. Til modellering er machine-learningmetoden ’Random Forest’ benyttet, og der er anvendt en rumlig gridopløsning på 100 m. Der er endvidere udviklet en metode til estimering af usikkerheden på kortet, som er beskrevet i de linkede publikationer. Størrelsen på datapakken er 31 MB. The map shows the depth to the redox interface in metres below ground level. The redox interface describes the transition from oxidized to reduced soil layers. Based on approximately 13,000 observations of colour change in sediment samples, a model has been developed that describes the relationship between various explanatory variables and the depth to the redox boundary. The Random Forest machine learning method has been used for the modelling task, and a spatial grid resolution of 100 meters has been applied. Additionally, a method has been developed to estimate the uncertainty of the redox map, which is described in the related, linked publications. Size of datapackage: 31 MB.
DOI: 10.22008/fk2/xnebmc/l1yy25
title: RedoxDatapakke.zip

description: :unav
DOI: 10.5517/ccdc.csd.cc27xdg1
title: CCDC 2082873: Experimental Crystal Structure Determination

description: Related Article: Chong Liu, Qi Chen, Stewart W. Schneller|2023|Bioorg.Med.Chem.Lett.|85|129219|doi:10.1016/j.bmcl.2023.129219
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27fhck
title: CCDC 2068548: Experimental Crystal Structure Determination

description: Related Article: Qian-Ya Xu, Zhifeng Xin, Meng-Jie Hu, Hua-Tian Shi, Ai-Quan Jia, Qian-Feng Zhang|2023|J.Cluster Sci.|34|285|doi:10.1007/s10876-022-02219-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27fks1
title: CCDC 2068623: Experimental Crystal Structure Determination

description: Related Article: Qian-Ya Xu, Zhifeng Xin, Meng-Jie Hu, Hua-Tian Shi, Ai-Quan Jia, Qian-Feng Zhang|2023|J.Cluster Sci.|34|285|doi:10.1007/s10876-022-02219-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27fkr0
title: CCDC 2068622: Experimental Crystal Structure Determination

description: Related Article: Qian-Ya Xu, Zhifeng Xin, Meng-Jie Hu, Hua-Tian Shi, Ai-Quan Jia, Qian-Feng Zhang|2023|J.Cluster Sci.|34|285|doi:10.1007/s10876-022-02219-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21953330
title: Supplementary Material for: Treatment of EGJ Cancer within or outside clinical trials: Does the setting matter? A monocentric prospective observational study.

description: Introduction. RCTs support neoadjuvant chemoradiotherapy (nCRT) followed by surgery in Locally Advanced Esophago-Gastric Junction (LA-EGJ) adenocarcinoma. However, RCTs are performed in highly controlled settings with limited representativeness of real-life patients (RLS). Aim: To compare the outcomes in RLS and clinical trial settings. Methods. The outcomes of RLS, which comprised 125 patients consequently treated for LA-EGJ adenocarcinoma between 2012 and 2017, were compared with the phase II trial (PIIS), performed on 65 patients from 2003 to 2011. Results. About half of RLS (51.2%) were treated with nCRT according to VR-protocol, 20.8% with standard-CRT according to CROSS/Al-Sarraf, 20% with CT alone. pCR was 36.8%, 28.6% and 9.1% after VR-protocol, standard-CRT, and chemotherapy respectively (p=0.082), while three-year overall survival (OS) was 58.6% (95% CI 43.2-71.1%), 32.8% (14.6-52.4%) and 44.8% (21.3-65.9%) respectively (p=0.030). With respect to PIIS, RLS had a higher proportion of cN+ (94% versus 54%; p&lt;0.001), and a lower proportion of pCR after CT/CRT (23% versus 39%; p=0.041). Three-year OS was slightly higher, although not significantly, in PIIS (58.9%, 45.1-70.2%) than RLS (47.9%, 37.4-57.7%) and nearly identical to 3-year OS in RLS treated with VR-protocol. Discussion/Conclusion. Real-life patients with EGJ adenocarcinoma have more advanced cancer at baseline, lower pathologic response to neoadjuvant treatment than patients enrolled in clinical trials, but similar survival.
DOI: 10.6084/m9.figshare.22331374
title: Adatfüggelék - Társadalmi különbségek a magyarországi gyerekek fogainak állapotában és egészségmagatartásában

description: Adatfüggelék a "Társadalmi különbségek a magyarországi gyerekek fogainak állapotában és egészségmagatartásában" c. tanulmányhoz <br>
DOI: 10.5281/zenodo.7108099
title: The Svalbox Digital Model Database (DMDb)

description: <strong>The Svalbox Digital Model Database</strong><br> The Svalbox Digital Model Database (DMDb) is a regional DOM database geographically constrained to the Norwegian High Arctic Archipelago of Svalbard at 74-81 °N and 10-35 °E. Svalbard offers exceptional quality, vegetation-free outcrops with a wide range of lithologies and tectono-magmatic styles including extension, compression and magmatism. Data and metadata of the systematically digitized outcrops across Svalbard are shared according to FAIR principles through the Svalbox DMDb. Fully open-access and downloadable DOMs include not just the DOM itself but also the input data, processing reports and projects, and other data products such as footprints and orthomosaics. Rich metadata for each DOM comprises both the technical and geological parameters (metadata), enabling visualisation and integration with regional geoscientific data on the Svalbox portal.<br> <br> <strong>Release information</strong><br> The v2022.9 release of the Svalbox DMDb, documented in this contribution, covers 131 DOMs cumulatively covering 110 km2 and offering Proterozoic to Cenozoic stratigraphy.<br> <br> <strong>Release documentation</strong><br> The Svalbox DMDb vv2022.9 is shared in the following formats: GeoJSON (.geojson) Geopackage (.gpkg) Documentation of the types and units associated with the data columns is documented through the SvalboxDMDb parameters files, available in: Comma-separated values (.csv) JSON (.json) Updated metadata is continuously updated to the Svalbox server and made available through: https://www.svalbox.no/map/ Svalbox ArcGIS REST access point (https://svalbox.unis.no/arcgis/rest/services/) <strong>Citation</strong><br> In addition to model-specific DOIs, please cite the following papers when using the Svalbox DMDb and its models: Betlem, et al. "The Svalbox Digital Model Database: a geoscientific window to the High Arctic." Geosphere (in review). Senger, et al. "Using digital outcrops to make the high Arctic more accessible through the Svalbox database." Journal of Geoscience Education 69.2 (2021): 123-137.