cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7098233
title: Supplementary Material for: Impaired Skin Barrier Function and Downregulated Expression of Caspase-14 in Moderate to Severe Chronic Hand Eczema

description: <b><i>Aim:</i></b> To investigate whether the skin barrier function is impaired with regard to the pH value, water content, transepidermal water loss (TEWL), and the integrity of the stratum corneum, and whether the expression of caspase-14 is altered in moderate to severe chronic hand eczema (CHE). <b><i>Methods:</i></b> Thirty patients with moderate to severe CHE treated at our institute and 30 healthy volunteers were included in this study. The pH value, water content, TEWL, and the integrity of the stratum corneum were measured in all subjects. <b><i>Results:</i></b> Significantly increased pH value, decreased water content, elevated TEWL, and impaired integrity of the stratum corneum were observed in the lesional skin of CHE patients compared with the nonlesional skin of CHE patients and the normal skin of healthy volunteers. The expression of caspase-14 decreased in the lesional and nonlesional skin of CHE patients compared with the normal skin of healthy volunteers, especially prominent in the nonlesional skin. The mean optical density (OD) value of immunohistochemical staining for caspase-14 was significantly lower in the nonlesional skin than in the lesional skin and normal skin (<i>p</i> &lt; 0.01 for both). Although the mean OD value was lower in the lesional skin than in the normal skin, the difference was not statistically significant (<i>p</i> &gt; 0.05). <b><i>Conclusion:</i></b> Skin barrier dysfunction indeed occurs in CHE patients, which may be related to mechanisms associated with a downregulated expression of caspase-14.
DOI: 10.6084/m9.figshare.7098212
title: DEGs

description: DEGs for all comparisons<br>
DOI: 10.6084/m9.figshare.7098185
title: Supplemental table 3

description: supplemental table 3<br>
DOI: 10.6084/m9.figshare.7098212.v1
title: DEGs

description: DEGs for all comparisons<br>
DOI: 10.6084/m9.figshare.7098167
title: supplemental table 2

description: Supplemental table 2<br>
DOI: 10.6084/m9.figshare.7098185.v1
title: Supplemental table 3

description: supplemental table 3<br>
DOI: 10.6084/m9.figshare.7098140
title: Supplementary Material for: How to Define Acute Liver Failure Patients with Pre-Existing Liver Disease without Signs of Cirrhosis

description: <b><i>Background:</i></b> The definition of acute liver failure (ALF) usually implies no previous liver injury. Though, some patients admitted to liver transplantation centers with the diagnosis of ALF are obese or have diabetes. Elevated liver enzymes were not recorded previously, and no signs of cirrhosis or prior decompensation of the liver function were ever present. Still, these patients differ from the “typical” ALF-patient. <b><i>Goals:</i></b> In this study, we aimed to confirm acute-on-chronic-liver failure (AOCLF) in patients diagnosed with ALF and to identify possible differences between ALF and AOCLF. <b><i>Study:</i></b> Patients were retrospectively recruited from all patients admitted to the University Hospital Essen with diagnosis of ALF between 2008 and 2015. Data of 163 patients were evaluated, resulting in a reclassification of 32 patients as AOCLF (remaining ALF: 131). Demographic and clinical data as well as serum parameters, including cell death markers, were correlated with clinical outcome. <b><i>Results:</i></b> Patients with AOCLF were significantly older, had a higher body mass index (BMI), and were more often male. The cause for liver failure in these patients differed significantly from patients who had an actual ALF. Significant differences were also found for serum liver enzymes. Outcome of patients did not differ between AOCLF and ALF. Though, lower BMI and MELD and higher AST and GLDH were predictors for a beneficial outcome. <b><i>Conclusion:</i></b> AOCLF is still commonly misdiagnosed as ALF. While clinical outcome does not significantly differ between ALF and AOCLF, risk factors for adverse outcome may significantly differ between these entities.
DOI: 10.6084/m9.figshare.7098143
title: supplemetal table 1 CDE.docx

description: Supplemental table 1<br>
DOI: 10.6084/m9.figshare.7098167.v1
title: supplemental table 2

description: Supplemental table 2<br>
DOI: 10.6084/m9.figshare.7098143.v1
title: supplemetal table 1 CDE.docx

description: Supplemental table 1<br>
DOI: 10.6084/m9.figshare.7098140.v1
title: Supplementary Material for: How to Define Acute Liver Failure Patients with Pre-Existing Liver Disease without Signs of Cirrhosis

description: <b><i>Background:</i></b> The definition of acute liver failure (ALF) usually implies no previous liver injury. Though, some patients admitted to liver transplantation centers with the diagnosis of ALF are obese or have diabetes. Elevated liver enzymes were not recorded previously, and no signs of cirrhosis or prior decompensation of the liver function were ever present. Still, these patients differ from the “typical” ALF-patient. <b><i>Goals:</i></b> In this study, we aimed to confirm acute-on-chronic-liver failure (AOCLF) in patients diagnosed with ALF and to identify possible differences between ALF and AOCLF. <b><i>Study:</i></b> Patients were retrospectively recruited from all patients admitted to the University Hospital Essen with diagnosis of ALF between 2008 and 2015. Data of 163 patients were evaluated, resulting in a reclassification of 32 patients as AOCLF (remaining ALF: 131). Demographic and clinical data as well as serum parameters, including cell death markers, were correlated with clinical outcome. <b><i>Results:</i></b> Patients with AOCLF were significantly older, had a higher body mass index (BMI), and were more often male. The cause for liver failure in these patients differed significantly from patients who had an actual ALF. Significant differences were also found for serum liver enzymes. Outcome of patients did not differ between AOCLF and ALF. Though, lower BMI and MELD and higher AST and GLDH were predictors for a beneficial outcome. <b><i>Conclusion:</i></b> AOCLF is still commonly misdiagnosed as ALF. While clinical outcome does not significantly differ between ALF and AOCLF, risk factors for adverse outcome may significantly differ between these entities.
DOI: 10.6084/m9.figshare.7098077
title: Supplementary Material for: Biochemical and Morphological Characterization of a Neurodevelopmental Disorder-Related Mono-ADP-Ribosylhydrolase, MACRO Domain Containing 2

description: MACRO Domain Containing 2 (MacroD2) is a neurodevelopmental disorder-related mono-ADP-ribosylhydrolase. Molecular features of this protein in neural tissues are largely unknown. In this study, we generated a specific antibody against MacroD2, and carried out expression and morphological analyses of the molecule during mouse brain development. In Western blotting, 2 MacroD2 isoforms with molecular masses of ∼70 and ∼75 kDa started to be expressed at embryonic day 16.5, reached the maximal level at postnatal day 8, and then gradually decreased through P30. In contrast, other isoforms with molecular masses of ∼110 and ∼140 kDa gradually increased during embryonic to postnatal development. In immunohistochemical analyses, MacroD2 was strongly detected in cortical neurons in layer II–V at P0 and P7, while the protein expression decreased significantly in the neurons at P30. Immunofluorescence analyses revealed that MacroD2 was mainly distributed in the soma and to a lesser extent in the axon and dendrite of immature primary cultured mouse hippocampal neurons. On the other hand, in the matured hippocampal neurons, while MacroD2 was detected in the soma, it displayed in dendrites a punctate distribution pattern with a partial colocalization with synaptic markers, synaptophysin, and PSD95. The obtained results indicate that MacroD2 is expressed and may have a physiological role in the central nervous system during brain development.
DOI: 10.6084/m9.figshare.7098002
title: Supplementary Material for: Early Loss of Forkhead Transcription Factor, O Subgroup, Member 1 Protein in the Development of Pancreatic Ductal Adenocarcinoma

description: <b><i>Objectives:</i></b> Forkhead transcription factor, O subgroup, member 1 (FOXO1) is a regulatory protein that plays an essential role in cellular homeostasis. A biological function as a tumor suppressor has been proposed. Here, we examined FOXO1 expression in human pancreatic ductal adenocarcinoma (PDAC) and its precursor lesions. <b><i>Methods:</i></b> We immunohistochemically labeled tissue samples from 47 patients with PDAC for FOXO1 protein. In addition, we extracted data from the Cancer Genome Atlas and the Cancer Cell Line Encyclopedia and studied a potential association with well-established genetic variants. A publicly available microarray dataset of 102 PDAC samples was used to explore the influence of <i>FOXO1</i> expression on patients’ clinical outcome. <b><i>Results:</i></b> Normal ductal epithelium universally expressed nuclear and cytoplasmic FOXO1. Reduced expression was observed in PanIN lesions and PDAC of all cases. Analysis of several datasets showed that the <i>FOXO1</i> gene transcript levels do not correlate with <i>KRAS</i>, <i>TP53</i>, <i>SMAD4</i>, or <i>CDKN2A</i> mutation status, but positively correlate with patients’ outcomes. <b><i>Conclusions:</i></b> Loss of FOXO1 protein is identified as an early event during PDAC development and may be independent of the top 4 mutated cancer genes. Because of its strong expression in normal ductal cells, immunohistochemical detection of FOXO1 can function as a valuable test to establish the diagnosis of transformation and malignancy in pancreatic tissues.
DOI: 10.6084/m9.figshare.7097972
title: Supplementary Material for: Treatment Effects in Retinal Angiomatous Proliferation Imaged with OCT Angiography

description: <b><i>Purpose:</i></b> This prospective case series is aimed at exploring optical coherence tomographic angiography (OCT-A) as a treatment monitoring tool in patients treated for retinal angiomatous proliferation (RAP). <b><i>Methods:</i></b> Twelve treatment-naïve RAP patients were included, with a median age of 79 years (range 65–90). Patients were imaged with an experimental 1,040-nm swept-source phase-resolved OCT-A instrument before and after treatment. Treatment consisted of either intravitreal bevacizumab or triamcinolone injections with or without photodynamic therapy (PDT). Abnormal blood flow after treatment was graded as increased, unchanged, decreased, or resolved. <b><i>Results:</i></b> OCT-A images before and after treatment could be obtained in 9 patients. The median follow-up period was 10 weeks (range 5–19). After various treatments, the RAP lesion resolved in 7 patients, in 1 patient the OCT-A depicted decreased flow in the lesion, and 1 patient showed unchanged abnormal blood flow. Monotherapy with intravitreal bevacizumab injections resolved RAP in 1 out of 2 patients. Combined therapy of bevacizumab with PDT resolved RAP in 6 out of 7 patients. <b><i>Conclusions:</i></b> OCT-A visualized resolution of abnormal blood flow in 7 out of 9 RAP patients after various short-term treatment sequences. OCT-A may become an important noninvasive monitoring tool for optimizing treatment strategies in RAP patients.
DOI: 10.6084/m9.figshare.7097993
title: Supplementary Material for: Copy Number Alterations with Prognostic Potential in Clear Cell Renal Cell Carcinoma

description: <b><i>Objectives:</i></b> To detect chromosomal aberrations in a genome-wide manner with potential value for prognosis in groups of patients with different histopathological grading in clear cell renal carcinoma (ccRCC). <b><i>Material and Methods:</i></b> We performed a copy number alteration analysis using the Affymetrix platform and SNP 6.0 mapping arrays with samples from 48 ccRCC-patients. The data analysis was done using 3 different Software Platforms: Affymetrix Genotyping Console (version 4.1.3.840) and 2 open-source packages for validation: PennCNV and PICNIC. <b><i>Results:</i></b> Consistent changes were found to divide the tumors into 4 groups: first group showed typical losses on 3p, second group losses on 3p plus gains on 5q, third group gains on chromosome 7 plus losses on chromosome 8; fourth group did not show any major changes. We selected the affected genes with the highest consistency and identified 13 different genes mapping in the SNP 6.0 results and Kyoto Encyclopedia of Genes and Genomes. Remarkable for further consideration were the phosphatidylinositol 3-kinase pathway, BRAF, MET, EGLN1; growth factors, for example, HGF, PGF and TGFB2. <b><i>Conclusion:</i></b> A multimodal approach with a well-defined workflow for detecting genomic aberrations by using array technologies and comparing the findings with different comprehensive databases may provide insights into functional tumor processes and help to identify potential new targets for more individualized future treatment.
DOI: 10.6084/m9.figshare.7097993.v1
title: Supplementary Material for: Copy Number Alterations with Prognostic Potential in Clear Cell Renal Cell Carcinoma

description: <b><i>Objectives:</i></b> To detect chromosomal aberrations in a genome-wide manner with potential value for prognosis in groups of patients with different histopathological grading in clear cell renal carcinoma (ccRCC). <b><i>Material and Methods:</i></b> We performed a copy number alteration analysis using the Affymetrix platform and SNP 6.0 mapping arrays with samples from 48 ccRCC-patients. The data analysis was done using 3 different Software Platforms: Affymetrix Genotyping Console (version 4.1.3.840) and 2 open-source packages for validation: PennCNV and PICNIC. <b><i>Results:</i></b> Consistent changes were found to divide the tumors into 4 groups: first group showed typical losses on 3p, second group losses on 3p plus gains on 5q, third group gains on chromosome 7 plus losses on chromosome 8; fourth group did not show any major changes. We selected the affected genes with the highest consistency and identified 13 different genes mapping in the SNP 6.0 results and Kyoto Encyclopedia of Genes and Genomes. Remarkable for further consideration were the phosphatidylinositol 3-kinase pathway, BRAF, MET, EGLN1; growth factors, for example, HGF, PGF and TGFB2. <b><i>Conclusion:</i></b> A multimodal approach with a well-defined workflow for detecting genomic aberrations by using array technologies and comparing the findings with different comprehensive databases may provide insights into functional tumor processes and help to identify potential new targets for more individualized future treatment.
DOI: 10.6084/m9.figshare.7097969
title: Data from: Ontogenetic shifts in plant ecological strategies

description: <b>Dataset - Dayrell RLC; Arruda AJ; Pierce S; Negreiros D; Meyer PB; Lambers H; Silveira FAO (2018) Ontogenetic shifts in plant ecological strategies. </b><i>Functional Ecology</i><b></b>
DOI: 10.6084/m9.figshare.7097972.v1
title: Supplementary Material for: Treatment Effects in Retinal Angiomatous Proliferation Imaged with OCT Angiography

description: <b><i>Purpose:</i></b> This prospective case series is aimed at exploring optical coherence tomographic angiography (OCT-A) as a treatment monitoring tool in patients treated for retinal angiomatous proliferation (RAP). <b><i>Methods:</i></b> Twelve treatment-naïve RAP patients were included, with a median age of 79 years (range 65–90). Patients were imaged with an experimental 1,040-nm swept-source phase-resolved OCT-A instrument before and after treatment. Treatment consisted of either intravitreal bevacizumab or triamcinolone injections with or without photodynamic therapy (PDT). Abnormal blood flow after treatment was graded as increased, unchanged, decreased, or resolved. <b><i>Results:</i></b> OCT-A images before and after treatment could be obtained in 9 patients. The median follow-up period was 10 weeks (range 5–19). After various treatments, the RAP lesion resolved in 7 patients, in 1 patient the OCT-A depicted decreased flow in the lesion, and 1 patient showed unchanged abnormal blood flow. Monotherapy with intravitreal bevacizumab injections resolved RAP in 1 out of 2 patients. Combined therapy of bevacizumab with PDT resolved RAP in 6 out of 7 patients. <b><i>Conclusions:</i></b> OCT-A visualized resolution of abnormal blood flow in 7 out of 9 RAP patients after various short-term treatment sequences. OCT-A may become an important noninvasive monitoring tool for optimizing treatment strategies in RAP patients.
DOI: 10.6084/m9.figshare.7097969.v2
title: Data from: Ontogenetic shifts in plant ecological strategies

description: <b>Dataset - Dayrell RLC; Arruda AJ; Pierce S; Negreiros D; Meyer PB; Lambers H; Silveira FAO (2018) Ontogenetic shifts in plant ecological strategies. </b><i>Functional Ecology</i><b></b>
DOI: 10.6084/m9.figshare.7097969.v1
title: Original data - Dayrell et al. - Functional Ecology

description: <b>Dataset - Dayrell RLC; Arruda AJ; Pierce S; Negreiros D; Meyer PB; Lambers H; Silveira FAO (2018) Ontogenetic shifts in plant ecological strategies. </b><i>Functional Ecology</i><b></b>
DOI: 10.6084/m9.figshare.7097879
title: MRIQC WebAPI - Database snapshot

description: Database snapshot associated to "Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines" (2018).
DOI: 10.6084/m9.figshare.7097879.v1
title: MRIQC WebAPI - Database dump

description: Database dump associated to "Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines" (2018).
DOI: 10.6084/m9.figshare.7097879.v2
title: MRIQC WebAPI - Database dump

description: Database dump associated to "Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines" (2018).
DOI: 10.6084/m9.figshare.7097777
title: data2018GL080157.zip

description: This is a data repository for the journal article named "The rings of Jupiter as seen by the Electron and Proton Radiation belt Model Salammbô", to be published in the journal "Geophysical Research Letters".<br>
DOI: 10.6084/m9.figshare.7097777.v1
title: data2018GL080157.zip

description: This is a data repository for the journal article named "The rings of Jupiter as seen by the Electron and Proton Radiation belt Model Salammbô", to be published in the journal "Geophysical Research Letters".<br>
DOI: 10.6084/m9.figshare.7097762
title: Supplementary Material for: Hepatocyte Growth Factor Facilitates Esophageal Mucosal Repair and Inhibits the Submucosal Fibrosis in a Rat Model of Esophageal Ulcer

description: <b><i>Background/Aims:</i></b> Esophageal mucosal damage often causes scar tissue, leading to refractory stricture. The aim of this study was to clarify the effect of hepatocyte growth factor (HGF) on esophageal mucosal repair and fibrosis leading to stricture in a rat model of esophageal ulcer. <b><i>Methods:</i></b> Esophageal ulcers were induced in rats by topical exposure of the lower esophageal serosa to acetic acid, followed by intraperitoneal administration of HGF (200 µg/day) using an osmotic pump for 7 days. The effect of HGF on esophageal mucosal injury was investigated macroscopically and microscopically. The effect of HGF on epithelial cell proliferation and the expression of genes closely associated with the development of fibrosis were also examined. <b><i>Results:</i></b> The administration of HGF for 7 days led to a significant reduction in the ulcerative area and enhanced the proliferation of esophageal epithelial cells. HGF treatment significantly decreased the fibrosis, and subsequently attenuated not only the foreshortening but also the narrowing of the esophagus. The expression levels of <i>tissue inhibitor of metalloproteinase (TIMP)-1</i>, <i>-2</i>, and <i>matrix metalloproteinase (MMP)-2</i>, <i>-9</i> were significantly decreased among rats treated with HGF. <b><i>Conclusion:</i></b> HGF facilitates the repair of esophageal mucosal injury and may also ameliorate the esophageal fibrosis, possibly through enhanced re-epithelization.
DOI: 10.15131/shef.data.7097744
title: Data for Tagliapietra, L., Modenese, L., Reggiani, M., Ceseracciu, E., Mazzà, C., Validation of a model-based inverse kinematics approach based on wearable inertial sensors Computer Methods in Biomechanics and Biomedical Engineering

description: This dataset contains all the results presented in the linked paper. Data are organized as follow:- Framework_01 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - robot: contains the joint angles recorded from the robot encorders, thus they can be considered the ground of truth- Framework_02 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - mb-ik: contains the joint angles (in degrees) estimated from the marker based inverse kinematics, the gold-standard in human motion analysis. Therefore, they are used as reference values.- Framework_03 : same as Framework 02.
DOI: 10.15131/shef.data.7097744.v1
title: Data for Tagliapietra, L., Modenese, L., Reggiani, M., Ceseracciu, E., Mazzà, C., Validation of a model-based inverse kinematics approach based on wearable inertial sensors Computer Methods in Biomechanics and Biomedical Engineering

description: This dataset contains all the results presented in the linked paper. Data are organized as follow:- Framework_01 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - robot: contains the joint angles recorded from the robot encorders, thus they can be considered the ground of truth- Framework_02 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - mb-ik: contains the joint angles (in degrees) estimated from the marker based inverse kinematics, the gold-standard in human motion analysis. Therefore, they are used as reference values.- Framework_03 : same as Framework 02.