cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17028/rd.lboro.6551114.v1
title: Supplementary data files for "The determination of salivary oxypurines before and after exercise by combined liquid chromatography-field asymmetric waveform ion mobility spectrometry-time-of-flight mass spectrometry"

description: Article abstract:A method combining field asymmetric waveform ion mobility spectrometry with liquid chromatography-mass spectrometry (LC-FAIMS-MS) has been developed for the analysis of the oxypurine compounds hypoxanthine (HX) and xanthine (XA) in saliva. Separation of the oxypurines from interfering matrix components was investigated using FAIMS-MS. The selected FAIMS parameters were then applied to the rapid LC-FAIMS-MS analysis of HX and XA using a short chromatographic separation method (7 min). A comparison of the LC-MS method with and without FAIMS applied, resulted in improved discrimination from saliva matrix interferences and improved chromatographic peak integration for both HX and XA using a FAIMS separation. A quantitative evaluation of the LC-FAIMS-MS method was performed giving limits of detection of 2.0 ng mL −1 for HX and 1.8 ng mL −1 for XA, and limits of quantification of 6.6 ng mL −1 for HX and 6.0 ng mL −1 for XA. The developed LC-FAIMS-MS method was applied to the targeted analysis of the oxypurine metabolites in saliva collected from healthy male athletes (n = 11) before and after exercise designed to induce oxidative stress; post-exercise collection time-points included immediately after exercise, one hour and twenty-four hours’ post-exercise. The salivary concentrations of both HX and XA were lower after physical exercise, compared to the pre-exercise (rest) concentrations and returned to approximately pre-exercise levels after twenty-four hours. The method reported has the potential for monitoring the salivary oxypurines, HX and XA, as biomarkers of oxidative stress and in other clinical applications.
DOI: 10.6084/m9.figshare.6549059
title: naive RTE and non-RTE CD4 T cells subsets

description: CDR3 subsets of RTE and non-RTE sorted naive CD4 T cells. Metadata includes information about all donors. Only beta chain.
DOI: 10.6084/m9.figshare.6549059.v1
title: naive RTE and non-RTE CD4 T cells subsets

description: CDR3 subsets of RTE and non-RTE sorted naive CD4 T cells. Metadata includes information about all donors.
DOI: 10.6084/m9.figshare.6548999
title: OTU tables and metadata belonging to De Vries et al. 2018

description: OTU tables and metadata for De Vries et al. 2018. See the paper for detailed description of experimental set up. See Readme.txt for a description of all variables.
DOI: 10.6084/m9.figshare.6548999.v2
title: OTU tables and metadata belonging to De Vries et al. 2018

description: OTU tables and metadata for De Vries et al. 2018. See the paper for detailed description of experimental set up.
DOI: 10.6084/m9.figshare.6548999.v3
title: OTU tables and metadata belonging to De Vries et al. 2018

description: OTU tables and metadata for De Vries et al. 2018. See the paper for detailed description of experimental set up.
DOI: 10.6084/m9.figshare.6548921
title: Naive CD4 & CD8 subsets

description: CDR3 subsets of CD4 and CD8 sorted naive T cells. Metadata includes information about all donors. Only beta chain.
DOI: 10.6084/m9.figshare.6548921.v1
title: Naive CD4 & CD8 subsets

description: CDR3 subsets of CD4 and CD8 sorted naive T cells. Metadata includes information about all donors.
DOI: 10.6084/m9.figshare.6548921.v2
title: Naive CD4 & CD8 subsets

description: CDR3 subsets of CD4 and CD8 sorted naive T cells. Metadata includes information about all donors. Only beta chain.
DOI: 10.6084/m9.figshare.6544055
title: devcon3-index-to-youtube-movies.docx

description: Testing
DOI: 10.6084/m9.figshare.6544055.v3
title: devcon3-index-to-youtube-movies.docx

description: Testing
DOI: 10.6084/m9.figshare.6544055.v2
title: devcon3-index-to-youtube-movies.docx

description: Testing
DOI: 10.6084/m9.figshare.6542681
title: Supplementary Material for: Increased Expression of Programmed Death-Ligand 1 in Infiltrating Immune Cells in Hepatocellular Carcinoma Tissues after Sorafenib Treatment

description: <b><i>Objective:</i></b> Programmed death-ligand 1 (PD-L1) expression in the tumor microenvironment (TME) has been reported to be related to prognosis in patients with hepatocellular carcinoma (HCC) after hepatectomy. The impact of sorafenib on PD-L1 expression in the TME of advanced HCC is unclear. <b><i>Patients and Methods:</i></b> Patients with HCC who received sorafenib for advanced disease at National Taiwan University Hospital, Taipei, Taiwan, and who had paired HCC tissues obtained before and after sorafenib treatment were included in the study group. HCC patients not treated with sorafenib who had paired primary and recurrent or metastatic tissues were identified as the reference group. The membrane PD-L1 staining, detected by immunohistochemistry (IHC) using SP142 antibody, was semiquantitatively scored in tumor cells (TCs) or tumor-infiltrating immune cells (ICs). Additional IHC assays were employed to characterize the PD-L1-expressing ICs. <b><i>Results:</i></b> Twenty-three advanced HCC patients with pre- and post-sorafenib paired HCC tissues were included in the study group. The median duration of sorafenib treatment was 4.3 months (range: 1.3–18.7). PD-L1 expression in ICs was significantly higher in post-sorafenib HCC tissues than in pre-sorafenib HCC tissues (pre-sorafenib vs. post-sorafenib IHC 0/1/2/3: 11/5/5/2 vs. 5/5/2/11, <i>p</i> = 0.016). However, PD-L1 expression in TCs was not significantly different between pre- and post-sorafenib tissues (IHC 0/1/2/3: 19/2/0/2 vs. 14/5/0/4, <i>p</i> = 0.094). In the reference group of 44 patients not treated with sorafenib, PD-L1 expression in ICs and TCs was not significantly different between the paired primary and<i></i> metastatic HCC tissues. By performing IHC double staining with PD-L1 and CD68, we found the PD-L1-expressing ICs were mainly CD68-positive macrophages. PD-L1 expression levels of pre- and post-sorafenib tissues were not associated with patients’ overall survival or duration of sorafenib treatment. <b><i>Conclusions:</i></b> PD-L1 expression in ICs was significantly increased in post-sorafenib HCC tissues. The mechanisms and clinical significance of this observation warrants further investigation.
DOI: 10.6084/m9.figshare.6542624
title: Supplementary material: Strehl ratio for optical systems with ultrafast illumination

description: This fileset contains supplementary material for paper titled "Strehl ratio for optical systems with ultrafast illumination"<br><br>Last Updated in JUN 2018 by Weichuan Gao
DOI: 10.6084/m9.figshare.6542624.v1
title: Zemax and Matlab programs for SR(t)

description: Strehl ratio for optical systems with ultrafast illumination1. Zemax Macro that obtains pupil maps of alpha, beta and gamma of a complex optical system.2. Matlab code that computes SR(t).
DOI: 10.6084/m9.figshare.6542624.v2
title: Supplementary material: Strehl ratio for optical systems with ultrafast illumination

description: This fileset contains supplementary material for paper titled "Strehl ratio for optical systems with ultrafast illumination"<br>List of files:<br>1. Zemax Macro: This macro computes the pupil maps of wavefront deviation, pulsefront deviation and GDD of the optical system. These pupil maps are then used with a matlab program to calculate SR(t).<br>2. Matlab program: This program computes SR(t) with the pupil map outputs from the ZEMAX macro 'Supplementary_1.zpl'<br>3. Matlab program: This program computes the results shown in Fig. 4 and 6.<br>4. Zemax .zmx files: The zipfile contains the designs shown in Fig. 7, 8 and 9.<br>5. Seidel.m: This matlab function computes pupil maps for defocus and 4 Seidel aberrations (spherical aberration, coma, astigmatism and field curvature).<br><br>Last Updated in JUN 2018 by Weichuan Gao
DOI: 10.6084/m9.figshare.6542624.v3
title: Supplementary material: Strehl ratio for optical systems with ultrafast illumination

description: This fileset contains supplementary material for paper titled "Strehl ratio for optical systems with ultrafast illumination"<br>List of files:<br>1. Zemax Macro: This macro computes the pupil maps of wavefront deviation, pulsefront deviation and GDD of the optical system. These pupil maps are then used with a matlab program to calculate SR(t).<br>2. Matlab program: This program computes SR(t) with the pupil map outputs from the ZEMAX macro 'Supplementary_1.zpl'<br>3. Matlab program: This program computes the results shown in Fig. 4 and 6.<br>4. Zemax .zmx files: The zipfile contains the designs shown in Fig. 7, 8 and 9.<br>5. Seidel.m: This matlab function computes pupil maps for defocus and 4 Seidel aberrations (spherical aberration, coma, astigmatism and field curvature).<br><br>Last Updated in JUN 2018 by Weichuan Gao
DOI: 10.6084/m9.figshare.6542624.v4
title: Supplementary material: Strehl ratio for optical systems with ultrafast illumination

description: This fileset contains supplementary material for paper titled "Strehl ratio for optical systems with ultrafast illumination"<br>List of files:<br>1. Zemax Macro: This macro computes the pupil maps of wavefront deviation, pulsefront deviation and GDD of the optical system. These pupil maps are then used with a matlab program to calculate SR(t).<br>2. Matlab program: This program computes SR(t) with the pupil map outputs from the ZEMAX macro 'Supplementary_1.zpl'<br>3. Matlab program: This program computes the results shown in Fig. 4 and 6.<br>4. Zemax .zmx files: The zipfile contains the designs shown in Fig. 7, 8 and 9.<br>5. Seidel.m: This matlab function computes pupil maps for defocus and 4 Seidel aberrations (spherical aberration, coma, astigmatism and field curvature).<br><br>Last Updated in JUN 2018 by Weichuan Gao
DOI: 10.6084/m9.figshare.6541865
title: Supplementary Material for: Lower Cognitive Function in Older Patients with Lower Muscle Strength and Muscle Mass

description: <b><i>Background:</i></b> Low muscle strength and muscle mass are associated with adverse outcomes in older hospitalized patients. The aim of this study was to assess the association between cognitive functioning and muscle strength and muscle mass in hospitalized older patients. <b><i>Methods:</i></b> This prospective inception cohort included 378 patients aged 70 years or older. At admission patients were assessed for cognitive functioning by use of the Six-Item Cognitive Impairment Test (6-CIT). Muscle strength and muscle mass were assessed using handheld dynamometry and segmental multifrequency bioelectrical impedance analysis, within 48 h after admission and on day 7, or earlier on the day of discharge. <b><i>Results:</i></b> The data of 371 patients (mean age ± standard deviation 80.1 ± 6.4 years, 49.3% female) were available for analyses. The median (interquartile range) 6-CIT score was 4 (0–8) points. At admission, lower cognitive functioning was associated with lower muscle strength, lower skeletal muscle mass (SMM), lower appendicular lean mass, and lower SMM index. Cognitive functioning was not associated with change in muscle strength and muscle mass during hospitalization. <b><i>Conclusion:</i></b> This study further strengthens evidence for an association between lower cognitive functioning and lower muscle strength and muscle mass, but without a further decline during hospitalization.
DOI: 10.6084/m9.figshare.6541865.v1
title: Supplementary Material for: Lower Cognitive Function in Older Patients with Lower Muscle Strength and Muscle Mass

description: <b><i>Background:</i></b> Low muscle strength and muscle mass are associated with adverse outcomes in older hospitalized patients. The aim of this study was to assess the association between cognitive functioning and muscle strength and muscle mass in hospitalized older patients. <b><i>Methods:</i></b> This prospective inception cohort included 378 patients aged 70 years or older. At admission patients were assessed for cognitive functioning by use of the Six-Item Cognitive Impairment Test (6-CIT). Muscle strength and muscle mass were assessed using handheld dynamometry and segmental multifrequency bioelectrical impedance analysis, within 48 h after admission and on day 7, or earlier on the day of discharge. <b><i>Results:</i></b> The data of 371 patients (mean age ± standard deviation 80.1 ± 6.4 years, 49.3% female) were available for analyses. The median (interquartile range) 6-CIT score was 4 (0–8) points. At admission, lower cognitive functioning was associated with lower muscle strength, lower skeletal muscle mass (SMM), lower appendicular lean mass, and lower SMM index. Cognitive functioning was not associated with change in muscle strength and muscle mass during hospitalization. <b><i>Conclusion:</i></b> This study further strengthens evidence for an association between lower cognitive functioning and lower muscle strength and muscle mass, but without a further decline during hospitalization.
DOI: 10.6084/m9.figshare.6541271
title: Dataset for: Rapid proteomic analysis for solid tumors reveals LSD1 as a drug target in an end stage cancer patient

description: Recent advances in mass spectrometry (MS)-based technologies are now set to transform translational cancer proteomics from an idea to a practice. Here, we present a robust proteomic workflow for the analysis of clinically relevant human cancer tissues that allows quantitation of thousands of tumor proteins in several hours of measuring time and a total turnaround of a few days. We applied it to a chemorefractory metastatic case of the extremely rare urachal carcinoma. Quantitative comparison of lung metastases and surrounding tissue revealed several significantly upregulated proteins, among them lysine specific histone demethylase 1 (LSD1/KDM1A). LSD1 is an epigenetic regulator and the target of active development efforts in oncology. Thus clinical cancer proteomics can rapidly and efficiently identify actionable therapeutic options. While currently described for a single case study, we envision that it can be applied broadly to other patients in a similar condition.
DOI: 10.6084/m9.figshare.6541271.v1
title: Dataset for: Rapid proteomic analysis for solid tumors reveals LSD1 as a drug target in an end stage cancer patient

description: Recent advances in mass spectrometry (MS)-based technologies are now set to transform translational cancer proteomics from an idea to a practice. Here, we present a robust proteomic workflow for the analysis of clinically relevant human cancer tissues that allows quantitation of thousands of tumor proteins in several hours of measuring time and a total turnaround of a few days. We applied it to a chemorefractory metastatic case of the extremely rare urachal carcinoma. Quantitative comparison of lung metastases and surrounding tissue revealed several significantly upregulated proteins, among them lysine specific histone demethylase 1 (LSD1/KDM1A). LSD1 is an epigenetic regulator and the target of active development efforts in oncology. Thus clinical cancer proteomics can rapidly and efficiently identify actionable therapeutic options. While currently described for a single case study, we envision that it can be applied broadly to other patients in a similar condition.
DOI: 10.6084/m9.figshare.6541268
title: Supplementary Material for: Familial Forms of Cushing Syndrome in Primary Pigmented Nodular Adrenocortical Disease Presenting with Short Stature and Insidious Symptoms: A Clinical Series

description: Cushing syndrome (CS) is a rare disease in children, frequently associated with subtle or periodic symptoms that may delay its diagnosis. Weight gain and growth failure, the hallmarks of hypercortisolism in pediatrics, may be inconsistent, especially in ACTH-independent forms of CS. Primary pigmented nodular adrenocortical disease (PPNAD) is the rarest form of ACTH-independent CS, and can be associated with endocrine and nonendocrine tumors, forming the Carney complex (CNC). Recently, phenotype/genotype correlations have been described with particular forms of CNC where PPNAD is isolated or associated only with skin lesions. We present four familial series of CS due to isolated PPNAD, and compare them to available data from the literature. We discuss the clinical and molecular findings, and underline challenges in diagnosing PPNAD in childhood.
DOI: 10.6084/m9.figshare.6541268.v1
title: Supplementary Material for: Familial Forms of Cushing Syndrome in Primary Pigmented Nodular Adrenocortical Disease Presenting with Short Stature and Insidious Symptoms: A Clinical Series

description: Cushing syndrome (CS) is a rare disease in children, frequently associated with subtle or periodic symptoms that may delay its diagnosis. Weight gain and growth failure, the hallmarks of hypercortisolism in pediatrics, may be inconsistent, especially in ACTH-independent forms of CS. Primary pigmented nodular adrenocortical disease (PPNAD) is the rarest form of ACTH-independent CS, and can be associated with endocrine and nonendocrine tumors, forming the Carney complex (CNC). Recently, phenotype/genotype correlations have been described with particular forms of CNC where PPNAD is isolated or associated only with skin lesions. We present four familial series of CS due to isolated PPNAD, and compare them to available data from the literature. We discuss the clinical and molecular findings, and underline challenges in diagnosing PPNAD in childhood.
DOI: 10.6084/m9.figshare.6541265
title: Supplementary Material for: Validity and Reliability of the Dutch Adaptation of the Actinic Keratosis Quality of Life Questionnaire (AKQoL)

description: <b><i>Background:</i></b> The Actinic Keratosis Quality of Life Questionnaire (AKQoL) is a disease-specific instrument to measure the impact of actinic keratosis (AK) on patients’ lives. <b><i>Objective:</i></b> To validate and test the psychometric properties of the AKQoL translated into the Dutch language (AKQoL-NL). <b><i>Methods:</i></b> All new patients ≥50 years of age with untreated AK in a university medical center and a general hospital between August 2014 and August 2015 were eligible. The AKQoL was obtained and repeated after 2 weeks. The feasibility was tested by missing responses and response distribution. The internal consistency reliability of each domain was investigated with the Cronbach alpha, and test-retest reliability and validity with the Spearman correlation coefficient. AKQoL scores were compared to the Skindex-17 for convergent validity and to the Groningen Frailty Indicator scores for divergent validity. <b><i>Results:</i></b> A total of 153 of 190 eligible patients consented to participate. Feasibility analysis showed that none of the items missed ≥10% of responses but 5 of the 9 items showed floor effect. The AKQoL subscales showed a moderate internal consistency (Cronbach α = 0.235–0.468) and an excellent test-retest reliability (interclass correlation coefficient = 0.997–1). The AKQoL correlated poorly with the symptom component and moderately with the psychosocial component of the Skindex-17 (ρ = –0.015 to 0.346 and 0.324 to 0.501, respectively), which is less than expected. The AKQoL scored poorly in both of the Groningen Frailty Indicator (GFI) components (ρ = –0.97 to 0.12 and 0.185 to 0.276, respectively), as expected. <b><i>Conclusion:</i></b> The AKQoL-NL is a feasible, moderately valid, and moderately reliable health-related quality of life questionnaire.
DOI: 10.6084/m9.figshare.6541265.v1
title: Supplementary Material for: Validity and Reliability of the Dutch Adaptation of the Actinic Keratosis Quality of Life Questionnaire (AKQoL)

description: <b><i>Background:</i></b> The Actinic Keratosis Quality of Life Questionnaire (AKQoL) is a disease-specific instrument to measure the impact of actinic keratosis (AK) on patients’ lives. <b><i>Objective:</i></b> To validate and test the psychometric properties of the AKQoL translated into the Dutch language (AKQoL-NL). <b><i>Methods:</i></b> All new patients ≥50 years of age with untreated AK in a university medical center and a general hospital between August 2014 and August 2015 were eligible. The AKQoL was obtained and repeated after 2 weeks. The feasibility was tested by missing responses and response distribution. The internal consistency reliability of each domain was investigated with the Cronbach alpha, and test-retest reliability and validity with the Spearman correlation coefficient. AKQoL scores were compared to the Skindex-17 for convergent validity and to the Groningen Frailty Indicator scores for divergent validity. <b><i>Results:</i></b> A total of 153 of 190 eligible patients consented to participate. Feasibility analysis showed that none of the items missed ≥10% of responses but 5 of the 9 items showed floor effect. The AKQoL subscales showed a moderate internal consistency (Cronbach α = 0.235–0.468) and an excellent test-retest reliability (interclass correlation coefficient = 0.997–1). The AKQoL correlated poorly with the symptom component and moderately with the psychosocial component of the Skindex-17 (ρ = –0.015 to 0.346 and 0.324 to 0.501, respectively), which is less than expected. The AKQoL scored poorly in both of the Groningen Frailty Indicator (GFI) components (ρ = –0.97 to 0.12 and 0.185 to 0.276, respectively), as expected. <b><i>Conclusion:</i></b> The AKQoL-NL is a feasible, moderately valid, and moderately reliable health-related quality of life questionnaire.
DOI: 10.6084/m9.figshare.6541181
title: Supplementary Material for: Clinical Characteristics and Prognosis of Pregnancy-Associated Breast Cancer: Poor Survival of Luminal B Subtype

description: <b><i>Background:</i></b> Pregnancy-associated breast cancer (PABC) is rare and is generally defined as breast cancer diagnosed during pregnancy or within 1 year of delivery. The average ages of marriage and childbearing are increasing, and PABC is expected to also increase. This study is intended to increase understanding of the characteristics of PABC. <b><i>Methods:</i></b> A database of 2,810 patients with breast cancer diagnosed when they were less than 40 years of age was reviewed. The clinicopathological factors and survival of PABC (40 patients) were compared to those of patients with young breast cancer (YBC, non-pregnant or over 12 months after delivery; 2,770 patients). <b><i>Results:</i></b> PABC had significantly lower estrogen receptor (ER) and progesterone receptor (PR) expression (ER-positive 50.0%, PR-positive 45.0%) and higher HER2 overexpression (38.5%) than YBC. The most common subtype of PABC was triple-negative breast cancer (TNBC; 35.9%), and luminal A subtype represented only 7.7% of cases. In univariate analysis, PABC had significantly worse disease-free survival (DFS) and breast cancer-specific survival (BCSS) compared to YBC. In multivariate analysis, PABC was associated with worse BCSS (HR 4.0, 95% CI 1.2–12.9, <i>p</i> = 0.019) and survival, but there was no difference in DFS between PABC and YBC. In subgroup analysis by subtype, luminal B subtype of PABC showed worse DFS (HR 3.5; 95% CI 1.1–11.2, <i>p</i> = 0.039) and BCSS (HR 10.2, 95% CI 1.2–87.1, <i>p</i> = 0.035), especially with high Ki67. However, no differences were demonstrated in other subtypes. <b><i>Conclusion:</i></b> In this study, PABC showed lower expression of ER/PR, higher overexpression of HER2, fewer luminal A subtype, and more TNBC subtype compared to YBC. PABC had worse BCSS, especially luminal B subtype, compared to YBC.