cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13213544
title: Supplementary Material for: Expression of β-1,4-galactosyltransferases during Aging in <b><i>Caenorhabditis elegans</i></b>

description: <b><i>Background:</i></b> Altered plasma activity of β-1,4-galac­tosyl­transferases (B4GALTs) is a novel candidate biomarker of human aging. B4GALT1 is assumed to be largely responsible for this activity increase, but how it modulates the aging process is unclear at present. <b><i>Objectives:</i></b> To determine how expression of B4GALT1 and other B4GALT enzymes changes during aging of an experimentally tractable model organism, <i>Caenorhabditis elegans</i>. <b><i>Methods:</i></b> Targeted analysis of mRNA levels of all 3 <i>C. elegans</i> B4GALT family members was performed by qPCR in wild-type and in long-lived <i>daf-2</i> (insulin/IGF1-like receptor)-deficient or germline-deficient animals. <b><i>Results:</i></b> <i>bre-4</i> (<i>B4GALT1/2/3/4</i>) is the only B4GALT whose expression increases during aging in wild-type worms. In addition, <i>bre-4</i> levels also rise during aging in long-lived <i>daf-2</i>-deficient worms, but not in animals that are long-lived due to the lack of germline stem cells. On the other hand, expression of <i>sqv-3 (B4GALT7)</i> and of <i>W02B12.11 (B4GALT5/6)</i> appears decreased or constant, respectively, in all backgrounds during aging. <b><i>Conclusions:</i></b> The age-dependent <i>bre-4</i> mRNA increase in <i>C. elegans</i> parallels the age-dependent B4GALT activity increase in humans and is consistent with <i>C. elegans</i> being a suitable experimental organism to define potentially conserved roles of B4GALT1 during aging.
DOI: 10.6084/m9.figshare.13213550
title: Supplementary Material for: Hidradenitis Suppurativa: Proposal of Classification in Two Endotypes with Two-Step Cluster Analysis

description: <b><i>Introduction:</i></b> Hidradenitis suppurativa (HS) is a chronic, inflammatory, recurrent disorder of the pilosebaceous unit. Currently, several attempts have been made to classify this disease according to its pathogenesis and clinical manifestations. We attempted at classifying 103 patients using two-step cluster analysis. <b><i>Methods:</i></b> The final model included body mass index, C-reactive protein (CRP), and serum concentrations of IL-1, IL-6, IL-17, and IL-10 as continuous variables, and sex, later/early onset, anterior/posterior lesion sites, presence/absence of sinus tracts, nodules and abscesses, positive/negative history of pilonidal sinus, and presence/absence of mutations in gamma-secretase subunits (APH1A, APH1B, MEFV, NCSTN, PSEN1, PSEN2, PSENEN, PSTPIP1) as qualitative variables. <b><i>Results:</i></b> The resultant model defined two groupings or clusters: cluster 1 (64.9% of patients) characterized by nonobese males, with nodular lesions in posterior sites, early-onset HS, higher IL-10, presence of gamma-secretase mutations, and history of pilonidal sinus; and cluster 2 (35.1% of patients) characterized by obese females or males, with lesions in anterior sites, more presence of sinus tracts and abscesses and less nodules, later-onset HS, and higher concentrations of IL-1, CRP, IL-17, and IL-6. Severity measures (Hurley, HS-PGA, and IHS4) and tobacco use were discarded because the analysis found them to be less relevant for clustering. <b><i>Conclusion:</i></b> Our resultant model confirms the clinical impression that HS is a disease spectrum with two pathogenic poles defining two clusters or endotypes. The probability of having severe disease was equally distributed in the two clusters. The variable with the highest predictive value for clustering was involvement of typical anterior sites (axillae, submammary) or atypical posterior sites (back, gluteal). Serum concentrations of interleukins, tobacco use, and sex had a lower predictive power for clustering.
DOI: 10.5281/zenodo.4265867
title: Data for "Martian oxygen and hydrogen upper atmospheres responding to solar and dust storm drivers: Hisaki space telescope observations"

description: Data files (.npy) and python codes (.ipynb) to produce the figures in the paper. Download the zip file (dataforfigures_v2.zip), open plot_figX.ipynb with Jupyter notebook, and run it.
DOI: 10.5281/zenodo.4257002
title: Data for "Martian oxygen and hydrogen upper atmospheres responding to solar and dust storm drivers: Hisaki space telescope observations"

description: Data files (.npy) and python codes (.ipynb) to produce the figures in the paper. Download the zip file (dataforfigures_v2.zip), open plot_figX.ipynb with Jupyter notebook, and run it.
DOI: 10.6084/m9.figshare.13213565
title: Supplementary Material for: Association of Proteinuria and Hematuria with Acute Kidney Injury and Mortality in Hospitalized Patients with COVID-19

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is strongly associated with poor outcomes in hospitalized patients with coronavirus disease 2019 (COVID-19), but data on the association of proteinuria and hematuria are limited to non-US populations. In addition, admission and in-hospital measures for kidney abnormalities have not been studied separately. <b><i>Methods:</i></b> This retrospective cohort study aimed to analyze these associations in 321 patients sequentially admitted between March 7, 2020 and April 1, 2020 at Stony Brook University Medical Center, New York. We investigated the association of proteinuria, hematuria, and AKI with outcomes of inflammation, intensive care unit (ICU) admission, invasive mechanical ventilation (IMV), and in-hospital death. We used ANOVA, <i>t</i> test, χ<sup>2</sup> test, and Fisher’s exact test for bivariate analyses and logistic regression for multivariable analysis. <b><i>Results:</i></b> Three hundred patients met the inclusion criteria for the study cohort. Multivariable analysis demonstrated that admission proteinuria was significantly associated with risk of in-hospital AKI (OR 4.71, 95% CI 1.28–17.38), while admission hematuria was associated with ICU admission (OR 4.56, 95% CI 1.12–18.64), IMV (OR 8.79, 95% CI 2.08–37.00), and death (OR 18.03, 95% CI 2.84–114.57). During hospitalization, de novo proteinuria was significantly associated with increased risk of death (OR 8.94, 95% CI 1.19–114.4, <i>p</i> = 0.04). In-hospital AKI increased (OR 27.14, 95% CI 4.44–240.17) while recovery from in-hospital AKI decreased the risk of death (OR 0.001, 95% CI 0.001–0.06). <b><i>Conclusion:</i></b> Proteinuria and hematuria both at the time of admission and during hospitalization are associated with adverse clinical outcomes in hospitalized patients with COVID-19.
DOI: 10.6084/m9.figshare.13213565.v1
title: Supplementary Material for: Association of Proteinuria and Hematuria with Acute Kidney Injury and Mortality in Hospitalized Patients with COVID-19

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is strongly associated with poor outcomes in hospitalized patients with coronavirus disease 2019 (COVID-19), but data on the association of proteinuria and hematuria are limited to non-US populations. In addition, admission and in-hospital measures for kidney abnormalities have not been studied separately. <b><i>Methods:</i></b> This retrospective cohort study aimed to analyze these associations in 321 patients sequentially admitted between March 7, 2020 and April 1, 2020 at Stony Brook University Medical Center, New York. We investigated the association of proteinuria, hematuria, and AKI with outcomes of inflammation, intensive care unit (ICU) admission, invasive mechanical ventilation (IMV), and in-hospital death. We used ANOVA, <i>t</i> test, χ<sup>2</sup> test, and Fisher’s exact test for bivariate analyses and logistic regression for multivariable analysis. <b><i>Results:</i></b> Three hundred patients met the inclusion criteria for the study cohort. Multivariable analysis demonstrated that admission proteinuria was significantly associated with risk of in-hospital AKI (OR 4.71, 95% CI 1.28–17.38), while admission hematuria was associated with ICU admission (OR 4.56, 95% CI 1.12–18.64), IMV (OR 8.79, 95% CI 2.08–37.00), and death (OR 18.03, 95% CI 2.84–114.57). During hospitalization, de novo proteinuria was significantly associated with increased risk of death (OR 8.94, 95% CI 1.19–114.4, <i>p</i> = 0.04). In-hospital AKI increased (OR 27.14, 95% CI 4.44–240.17) while recovery from in-hospital AKI decreased the risk of death (OR 0.001, 95% CI 0.001–0.06). <b><i>Conclusion:</i></b> Proteinuria and hematuria both at the time of admission and during hospitalization are associated with adverse clinical outcomes in hospitalized patients with COVID-19.
DOI: 10.5281/zenodo.3960529
title: Synchrotron Diffraction During Stress Relaxation in CP Ti (grade 4)

description: These data support the associated paper: <strong>Cold Creep of Titanium: Analysis of stress relaxation using synchrotron diffraction and crystal plasticity simulations</strong><br> Yi Xiong, Phani Karamched, Chi-Toan Nguyen, David M Collins, Christopher M Magazzeni, Edmund Tarleton, Angus J Wilkinson<br> Acta Materialia (2020) vol. 199, 561-577<br> https://doi.org/10.1016/j.actamat.2020.08.010 The Authors' Accepted Manuscript version of the paper is available open access on arXiv:<br> https://arxiv.org/ftp/arxiv/papers/2003/2003.01682.pdf This dataset arises from an in situ stress relaxation experiment on commercially pure (grade 4) Ti undertaken at the Diamond Light Source, beamline ID12, as part of experiment EE17222. The sample was loaded to just beyond the yield point, and then held at constant strain for 5 minutes over which time the stress relaxed. The sample was then reloaded elastically and a further period of stress relaxation at fixed total strain undertaken. in total five periods of stress relaxation were imposed. Throughout the mechanical testing cycle powder diffraction patterns were recorded in the transmission geometry, at 1 second intervals using a 2d Pixium detector held 1097 mm from the sample. The beam energy was determined to be 79.79 keV. Diffraction Patterns are contained as 16 bit TIF files bundled into the Patterns_72995.zip file. Macroscopic mechanical test data are in the excel file MechTest_2995.xlsx. Small EBSD map in #.ctf format converted from Bruker #bcf file in CPg4.ctf file. Matlab + MTEX script to load and make simple plots from EBSD data file in CPg4Ti_EBSDmap.m file. Details of the MTEX orientation analysis package from Matlab can be found and freely downloaded at:<br> https://mtex-toolbox.github.io/
DOI: 10.5281/zenodo.3960528
title: Synchrotron Diffraction During Stress Relaxation in CP Ti (grade 4)

description: These data support the associated paper: <strong>Cold Creep of Titanium: Analysis of stress relaxation using synchrotron diffraction and crystal plasticity simulations</strong><br> Yi Xiong, Phani Karamched, Chi-Toan Nguyen, David M Collins, Christopher M Magazzeni, Edmund Tarleton, Angus J Wilkinson<br> Acta Materialia (2020) vol. 199, 561-577<br> https://doi.org/10.1016/j.actamat.2020.08.010 The Authors' Accepted Manuscript version of the paper is available open access on arXiv:<br> https://arxiv.org/ftp/arxiv/papers/2003/2003.01682.pdf This dataset arises from an in situ stress relaxation experiment on commercially pure (grade 4) Ti undertaken at the Diamond Light Source, beamline ID12, as part of experiment EE17222. The sample was loaded to just beyond the yield point, and then held at constant strain for 5 minutes over which time the stress relaxed. The sample was then reloaded elastically and a further period of stress relaxation at fixed total strain undertaken. in total five periods of stress relaxation were imposed. Throughout the mechanical testing cycle powder diffraction patterns were recorded in the transmission geometry, at 1 second intervals using a 2d Pixium detector held 1097 mm from the sample. The beam energy was determined to be 79.79 keV. Diffraction Patterns are contained as 16 bit TIF files bundled into the Patterns_72995.zip file. Macroscopic mechanical test data are in the excel file MechTest_2995.xlsx. Small EBSD map in #.ctf format converted from Bruker #bcf file in CPg4.ctf file. Matlab + MTEX script to load and make simple plots from EBSD data file in CPg4Ti_EBSDmap.m file. Details of the MTEX orientation analysis package from Matlab can be found and freely downloaded at:<br> https://mtex-toolbox.github.io/
DOI: 10.6084/m9.figshare.8481233
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.8667899
title: Dual-energy material decomposition for cone-beam computed tomography in image-guided radiotherapy

description: <b>Background:</b> Dual-energy (DE) diagnostic computed tomography (CT) combines two scans of different photon energy spectra which can provide additional image information as compared to standard CT. We developed a DE material decomposition scan protocol for daily cone-beam CT (CBCT) of head-and-neck patients receiving radiotherapy and tested it in a clinical trial. <b>Material and methods:</b> Our DE CBCT protocol consisted of an 80 and 140 kVp scan. The material decomposition algorithm split the low and high energy scan into components of two basis materials, aluminum and acrylic. Scans of different thicknesses and overlap of the basis materials were acquired to calibrate the model which decomposed the CBCT projections into thicknesses of aluminum and acrylic on a per-pixel basis. Pseudo monochromatic projections were created from these thicknesses and the known energy dependence of the attenuation coefficient of the basis materials. A frequency selective de-noising method was further applied to the basis material projections. The DE CBCT protocol was tested on seven patients. Two DE images were chosen, one at low (50–60) keV to evaluate soft tissue image quality and one at 150 keV to assess metal artifact reduction as compared to standard CBCT. <b>Results:</b> The de-noising algorithm reduced noise by 41% and 69% in the 60 and 150 keV images, respectively, compared to images without the de-noising. The low keV image showed an increase in soft tissue contrast-to-noise ratio of 7–43% compared to the standard clinical CBCT for six of the seven patients. The 150 keV DE CBCT image reduced metal artifacts. Enhanced streaking from metal artifacts were observed in some of the DE CBCT images. <b>Conclusion:</b> Monochromatic DE images from material decomposition can improve soft tissue contrast-to-noise ratio and metal artifact reduction. Improvements are limited, however, and new artifacts were also introduced by the DE algorithm.
DOI: 10.6084/m9.figshare.8667899.v2
title: Dual-energy material decomposition for cone-beam computed tomography in image-guided radiotherapy

description: <b>Background:</b> Dual-energy (DE) diagnostic computed tomography (CT) combines two scans of different photon energy spectra which can provide additional image information as compared to standard CT. We developed a DE material decomposition scan protocol for daily cone-beam CT (CBCT) of head-and-neck patients receiving radiotherapy and tested it in a clinical trial. <b>Material and methods:</b> Our DE CBCT protocol consisted of an 80 and 140 kVp scan. The material decomposition algorithm split the low and high energy scan into components of two basis materials, aluminum and acrylic. Scans of different thicknesses and overlap of the basis materials were acquired to calibrate the model which decomposed the CBCT projections into thicknesses of aluminum and acrylic on a per-pixel basis. Pseudo monochromatic projections were created from these thicknesses and the known energy dependence of the attenuation coefficient of the basis materials. A frequency selective de-noising method was further applied to the basis material projections. The DE CBCT protocol was tested on seven patients. Two DE images were chosen, one at low (50–60) keV to evaluate soft tissue image quality and one at 150 keV to assess metal artifact reduction as compared to standard CBCT. <b>Results:</b> The de-noising algorithm reduced noise by 41% and 69% in the 60 and 150 keV images, respectively, compared to images without the de-noising. The low keV image showed an increase in soft tissue contrast-to-noise ratio of 7–43% compared to the standard clinical CBCT for six of the seven patients. The 150 keV DE CBCT image reduced metal artifacts. Enhanced streaking from metal artifacts were observed in some of the DE CBCT images. <b>Conclusion:</b> Monochromatic DE images from material decomposition can improve soft tissue contrast-to-noise ratio and metal artifact reduction. Improvements are limited, however, and new artifacts were also introduced by the DE algorithm.
DOI: 10.6084/m9.figshare.8667899.v1
title: Dual-energy material decomposition for cone-beam computed tomography in image-guided radiotherapy

description: <b>Background:</b> Dual-energy (DE) diagnostic computed tomography (CT) combines two scans of different photon energy spectra which can provide additional image information as compared to standard CT. We developed a DE material decomposition scan protocol for daily cone-beam CT (CBCT) of head-and-neck patients receiving radiotherapy and tested it in a clinical trial. <b>Material and methods:</b> Our DE CBCT protocol consisted of an 80 and 140 kVp scan. The material decomposition algorithm split the low and high energy scan into components of two basis materials, aluminum and acrylic. Scans of different thicknesses and overlap of the basis materials were acquired to calibrate the model which decomposed the CBCT projections into thicknesses of aluminum and acrylic on a per-pixel basis. Pseudo monochromatic projections were created from these thicknesses and the known energy dependence of the attenuation coefficient of the basis materials. A frequency selective de-noising method was further applied to the basis material projections. The DE CBCT protocol was tested on seven patients. Two DE images were chosen, one at low (50–60) keV to evaluate soft tissue image quality and one at 150 keV to assess metal artifact reduction as compared to standard CBCT. <b>Results:</b> The de-noising algorithm reduced noise by 41% and 69% in the 60 and 150 keV images, respectively, compared to images without the de-noising. The low keV image showed an increase in soft tissue contrast-to-noise ratio of 7–43% compared to the standard clinical CBCT for six of the seven patients. The 150 keV DE CBCT image reduced metal artifacts. Enhanced streaking from metal artifacts were observed in some of the DE CBCT images. <b>Conclusion:</b> Monochromatic DE images from material decomposition can improve soft tissue contrast-to-noise ratio and metal artifact reduction. Improvements are limited, however, and new artifacts were also introduced by the DE algorithm.
DOI: 10.6084/m9.figshare.8326064.v1
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.v2
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