cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12514178
title: Supplementary Material for: Neutral Lipid Storage Disease Associated with the <b><i>PNPLA2</i></b> Gene: Case Report and Literature Review

description: Mutations in the <i>PNPLA2</i> gene cause neutral lipid storage disease with myopathy (NLSDM) or triglyceride deposit cardiomyovasculopathy. We report a detailed case study of a 53-year-old man with NLSDM. The <i>PNPLA2</i> gene was analyzed according to the reported method. We summarized the clinical, laboratory, and genetic information of 56 patients, including our patient and 55 other reported patients with homozygous or compound heterozygous mutations in the <i>PNPLA2</i> gene. We found a novel homozygous mutation (c.194delC) in the <i>PNPLA2</i> gene that resulted in frameshift. The patient suffered from normal-tension glaucoma and pulmonary cysts, symptoms that are relatively common in the elderly but were not previously reported for this disease. Our summary confirmed that Jordan’s anomaly, polymorphonuclear leukocytes with lipid accumulation, was the most consistent finding of this disease. Because this disease is potentially treatable, our results may help rapid and correct diagnosis.
DOI: 10.6084/m9.figshare.12513986
title: Supplementary Material for: Investigation of the Relationship between MR-Based Supraclavicular Fat Fraction and Thyroid Hormones

description: <b><i>Purpose:</i></b> Brown adipose tissue (BAT) plays a potential role in energy and glucose metabolism in humans. Thyroid hormones (TH) are main regulators of BAT development and function. However, it remains unknown how the magnetic resonance (MR)-based proton density fat fraction (PDFF) of supraclavicular adipose tissue used as a surrogate marker for BAT presence relates to TH. Therefore, the purpose of this analysis was to investigate the relationship between supraclavicular PDFF and serum levels of TH. <b><i>Methods:</i></b> In total, 96 adult volunteers from a large cross-sectional study who underwent additional MR examination of the neck and pelvis were included in this analysis. Segmented PDFF maps of the supraclavicular and gluteal subcutaneous adipose tissue were generated. Delta PDFF was calculated as the difference between gluteal and supraclavicular PDFF and grouped as high (≥12%) or low (&lt;12%) based on the median and the clinical rationale of a high versus low probability of BAT being present. Thyroid-stimulating hormone (mIU/L), free triiodothyronine (FT3, pg/mL) and free thyroxine (FT4, ng/dL) levels were determined in blood samples. Body mass index (BMI) was calculated as weight (kg)/height (m)<sup>2</sup>. Statistical analyses included the use of paired samples <i>t</i>test, simple linear regression analysis and a multivariable linear regression analysis. <b><i>Results:</i></b> The median age of the subjects (77% female) was 33 years, BMI ranged from 17.2 to 43.1 kg/m<sup>2</sup>. Supraclavicular and gluteal PDFF differed significantly (76.5 ± 4.8 vs. 89.4 ± 3.5 %, <i>p</i> &lt; 0.01). Supraclavicular PDFF was associated with FT3 in subjects with high delta PDFF (<i>R</i><sup>2</sup> = 0.17, <i>p</i> &lt; 0.01), with higher FT3 being associated with lower supraclavicular PDFF (<i>y</i> = 85.2 + –3.6 <i>x</i>). In a multivariable linear regression analysis considering further potential prognostic factors, the interaction between the delta PDFF group and FT3 remained a predictor for supraclavicular PDFF (B = –4.65, <i>p</i> &lt; 0.01). <b><i>Discussion/Conclusions:</i></b> Supraclavicular PDFF corresponds to the presence of BAT. In the present analysis, supraclavicular PDFF is correlated with FT3 in subjects with high delta PDFF. Therefore, the present findings suggest that biologically active T3 may be involved in the development of supraclavicular BAT.
DOI: 10.6084/m9.figshare.12513779
title: Supplementary Material for: Up-Regulation of GATA4 Regulates Human Lens Epithelial Cell Function in Age-Related Cataract

description: <b><i>Purpose:</i></b> GATA4 has emerged as a novel regulator that plays a critical role in mediating senescence. However, the role of GATA4 in age-related cataract (ARC), the leading cause of visual impairment, requires further elucidation. <b><i>Methods:</i></b> GATA4 expression was measured by quantitative RT-PCR and capillary Western immunoassay (WES). The MTT assay, EdU assay, and rhodamine-123/Hoechst and calcein-AM/propidium iodide double staining were used to investigate the role of GATA4 in the viability, proliferation, and apoptosis of cultured human lens epithelial cells (HLECs). <b><i>Results:</i></b> HLECs were subjected to 3 different treatment models, including prolonged exposure to low-dose H<sub>2</sub>O<sub>2</sub>, UVB irradiation, and mild heating, to simulate senescence and apoptosis. GATA4 expression was significantly increased in these models in a time- and dose-dependent manner. Overexpression of GATA4 reduced cell viability, accelerated apoptosis development, and reduced the proliferation of HLECs. Furthermore, the expression of GATA4 from ARC was up-regulated at both mRNA and at protein level compared with clear lenses. <b><i>Conclusion:</i></b> GATA4 is up-regulated in all 3 models of HLECs in vitro and the cells from ARC lenses in vivo. Up-regulation of GATA4 mediates HLEC dysfunction. GATA4-mediated effects in HLECs would provide a novel insight into the pathogenesis of ARC.
DOI: 10.6084/m9.figshare.12513779.v1
title: Supplementary Material for: Up-Regulation of GATA4 Regulates Human Lens Epithelial Cell Function in Age-Related Cataract

description: <b><i>Purpose:</i></b> GATA4 has emerged as a novel regulator that plays a critical role in mediating senescence. However, the role of GATA4 in age-related cataract (ARC), the leading cause of visual impairment, requires further elucidation. <b><i>Methods:</i></b> GATA4 expression was measured by quantitative RT-PCR and capillary Western immunoassay (WES). The MTT assay, EdU assay, and rhodamine-123/Hoechst and calcein-AM/propidium iodide double staining were used to investigate the role of GATA4 in the viability, proliferation, and apoptosis of cultured human lens epithelial cells (HLECs). <b><i>Results:</i></b> HLECs were subjected to 3 different treatment models, including prolonged exposure to low-dose H<sub>2</sub>O<sub>2</sub>, UVB irradiation, and mild heating, to simulate senescence and apoptosis. GATA4 expression was significantly increased in these models in a time- and dose-dependent manner. Overexpression of GATA4 reduced cell viability, accelerated apoptosis development, and reduced the proliferation of HLECs. Furthermore, the expression of GATA4 from ARC was up-regulated at both mRNA and at protein level compared with clear lenses. <b><i>Conclusion:</i></b> GATA4 is up-regulated in all 3 models of HLECs in vitro and the cells from ARC lenses in vivo. Up-regulation of GATA4 mediates HLEC dysfunction. GATA4-mediated effects in HLECs would provide a novel insight into the pathogenesis of ARC.
DOI: 10.6084/m9.figshare.12514031.v1
title: Supplementary data for heavy duty truck thermal modelling

description: Supplementary data for the paper: Efect of glazing and paint optical properties on the air conditioning loads, fuel consumption and tailpipe emissions of heavy-duty trucks
DOI: 10.6084/m9.figshare.12513650
title: Supplementary Material for: Nomenclature for Kidney Function and Disease: Executive Summary and Glossary from a Kidney Disease: Improving Global Outcomes (KDIGO) Consensus Conference

description: Medicine
DOI: 10.6084/m9.figshare.12513695
title: Metadata record for: Disassembly-based bill of materials data for consumer electronic products

description: This dataset contains key characteristics about the data described in the Data Descriptor Disassembly-based bill of materials data for consumer electronic products. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12514031.v2
title: Supplementary data for heavy duty truck thermal modelling

description: Supplementary data for the paper: Efect of glazing and paint optical properties on the air conditioning loads, fuel consumption and tailpipe emissions of heavy-duty trucks
DOI: 10.6084/m9.figshare.12513695.v1
title: Metadata record for: Disassembly-based bill of materials data for consumer electronic products

description: This dataset contains key characteristics about the data described in the Data Descriptor Disassembly-based bill of materials data for consumer electronic products. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12512963
title: Soluble urokinase plasminogen activator receptor as a long-term prognostic biomarker in acute coronary syndromes

description: <b>Purpose:</b> The aim of our study was to analyse the long-term prognostic value of soluble urokinase plasminogen activator receptor (suPAR) in the setting of an acute coronary syndrome (ACS). <b>Methods:</b> We included 340 patients with an ACS who underwent coronary angiography and plasma suPAR concentration was measured. Patients were classified into low suPAR concentrations (&lt;2.6 ng/mL) and high suPAR concentrations (≥2.6 ng/mL) and long-term events were evaluated. suPAR prognostic value was assessed beyond a clinical model that included age, GRACE score, estimated glomerular filtration rate, cardiac troponin-I peak and left ventricular ejection fraction &lt;40%. <b>Results:</b> Higher suPAR concentrations were associated with an increased prevalence of cardiovascular risk factors. After multivariate adjustment, suPAR ≥2.6 ng/mL were independently associated with an increased risk of all-cause death (HR 2.3; 95%CI 1.2–4.4; <i>p</i> = .017), major adverse cardiovascular events (MACE) (HR 1.7; 95%CI 1.1–2.5; <i>p</i> = .020) and heart failure (HR 4.1; 95%CI 1.3–12.6; <i>p</i> = .015), but not with myocardial infarction. For long-term all-cause death significant improvement of reclassification and discrimination were seen after addition of suPAR to a clinical model. <b>Conclusions:</b> In the setting of an ACS, suPAR is associated with long-term all-cause death, heart failure and MACE, and provides incremental prognostic value beyond traditional risks factors.
DOI: 10.6084/m9.figshare.12512714
title: Clustering-based binarization methods applied to the crow search algorithm for 0_1 combinatorial problems.pdf

description: results
DOI: 10.26180/5eec6125bf4e5
title: Conspecific cues suppress metabolic rate.xlsx

description: We used sessile marine invertebrates to test how food availability interacts with oxygen availability, water flow and chemical cues to affect metabolic rate. Mass is weight of colony (g)VO2 is oxygen consumption rate (mL O2/h)Avg_Loph is the average number of extruded lophophoresTreatment_order is the order colonies were exposed to the control treatment in Experiment 4
DOI: 10.6084/m9.figshare.12512672
title: Supplementary Material for: White Tea Reduced Bone Loss by Suppressing the TRAP/CTX Pathway in Ovariectomy-Induced Osteoporosis Model Rats

description: Osteoporosis is an important skeletal disease characterized by bone weakness and high risk of fracture in postmenopausal women. Tea consumption is known to play an important role in the prevention or alleviation of osteoporosis. However, the therapeutic effects of aqueous extracts of white tea (WT) have not been evaluated in osteoporosis rat models. The aim of this study was to investigate the potential anti-osteoporotic role of WT in ovariectomized (OVX) rats. WT was given orally at 0.5% w/v doses for 12 weeks in OVX rats. Biochemical parameters in blood samples, bone tartrate-resistant acid phosphatase (TRAP), C-terminal telopeptide of type 1 collagen (CTX) and estradiol levels were evaluated. Bone mineral density and bone mineral content values were measured in the left femur. In addition to histopathological examination, osteolcalcin, osteopontin and TUNEL levels were determined. OVX group data demonstrated that bone loss occurred by thinning of the metaphyseal growth plates of the femur. Similarly, the levels of TRAP and CTX, markers of osteoclastic activity, were found to be high concurrently with a decrease in femoral bone mineral density. In addition, increased osteolcalcin and osteopontin levels were present in the metaphyseal growth zones. On the other hand, while TRAP and CTX levels were suppressed in the OVX-WT group, bone mineral content increased. In ad­dition, TUNEL, osteocalcin and osteopontin positivity decreased in the right femoral metaphysis growth zones, proliferating zone and resting zone cells. These results showed that chronic WT consumption has a protective effect by reducing bone resorption in OVX-induced osteoporotic rats.
DOI: 10.6084/m9.figshare.12512714.v2
title: Clustering-based binarization methods applied to the crow search algorithm for 0_1 combinatorial problems.pdf

description: results
DOI: 10.6084/m9.figshare.12512360
title: A novel multi-stage ensemble model with enhanced outlier adaptation for credit scoring

description: Nine datasets from the UC Irvine (UCI) machine learning repository, i.e., the Australian, Japanese, German (Asuncion & Newman, 2007), Taiwan (Yeh & Lien, 2009) and Polish credit datasets (Zięba et al., 2016) were adopted for the current study. The Polish credit datasets contain five datasets distinguished five classification cases that depend on the forecasting period (e.g., the Polish 1, the Polish 2, the Polish 3, the Polish 4 and the Polish 5). AER credit dataset (Greene, 2003), which is a credit card dataset for econometric analysis. Creator dataset, which is published in 2019 by a Chinese digital government services provider named Creator Information Technology Co., Ltd[1]. The Creator dataset contains the property rights, financial statements, and basic company information of 35960 Chinese companies. <br> [1] http://www.chinacreator.com/cn/
DOI: 10.6084/m9.figshare.12512714.v1
title: Clustering-based binarization methods applied to the crow search algorithm for 0_1 combinatorial problems.pdf

description: results
DOI: 10.6084/m9.figshare.12511622
title: Hirsch_GMI discordance supplemental data.docx

description: Supplemental data
DOI: 10.6084/m9.figshare.12511550
title: Additional file 9 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 9. Pathway analysis using KEGG pathway for the tumor-tumor comparison.
DOI: 10.6084/m9.figshare.12511544
title: Additional file 7 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 7. Pathway analysis using KEGG pathway for the tumor-normal comparison.
DOI: 10.6084/m9.figshare.12511547
title: Additional file 8 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 8. Pathway analysis using GO for the tumor-tumor comparison.
DOI: 10.6084/m9.figshare.12511550.v1
title: Additional file 9 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 9. Pathway analysis using KEGG pathway for the tumor-tumor comparison.
DOI: 10.6084/m9.figshare.12511622.v1
title: Hirsch_GMI discordance supplemental data.docx

description: Supplemental data
DOI: 10.6084/m9.figshare.12511541
title: Additional file 6 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 6. Pathway analysis using gene ontology (GO) for the tumor-normal comparison.
DOI: 10.6084/m9.figshare.12511538
title: Additional file 5 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 5. Differential gene expression of the clusters compared to normal adjacent tissues. Differential gene expression analysis using DESeq are shown along with p-values and log2 fold change.
DOI: 10.6084/m9.figshare.12511541.v1
title: Additional file 6 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 6. Pathway analysis using gene ontology (GO) for the tumor-normal comparison.
DOI: 10.6084/m9.figshare.12511544.v1
title: Additional file 7 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 7. Pathway analysis using KEGG pathway for the tumor-normal comparison.
DOI: 10.6084/m9.figshare.12511547.v1
title: Additional file 8 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 8. Pathway analysis using GO for the tumor-tumor comparison.
DOI: 10.6084/m9.figshare.12511529
title: Additional file 2 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 2. List of immune genes. The file contains a list of 2000 immune gene collected from MSigDB and from other publications.
DOI: 10.6084/m9.figshare.12511535
title: Additional file 4 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 4. Immune cell abundance for each patient in the 8 clusters. The abundance of immune cells was identified using CIBESORT for the patients in the identified clusters.
DOI: 10.6084/m9.figshare.12511526
title: Additional file 2 of Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis

description: Code to reproduce analyses. This file provides the code to reproduce all analyses discussed in this report in the open-source software R. All materials are made available in the open-science-framework repository: https://osf.io/spb37/.
DOI: 10.6084/m9.figshare.12511529.v1
title: Additional file 2 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 2. List of immune genes. The file contains a list of 2000 immune gene collected from MSigDB and from other publications.
DOI: 10.6084/m9.figshare.12511532
title: Additional file 3 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 3. The identified immune evasion clusters. This file shows for every cluster the list of patients and their corresponding levels of gene expression for all the investigated immune genes.
DOI: 10.6084/m9.figshare.12511532.v1
title: Additional file 3 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 3. The identified immune evasion clusters. This file shows for every cluster the list of patients and their corresponding levels of gene expression for all the investigated immune genes.
DOI: 10.6084/m9.figshare.12511535.v1
title: Additional file 4 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 4. Immune cell abundance for each patient in the 8 clusters. The abundance of immune cells was identified using CIBESORT for the patients in the identified clusters.
DOI: 10.6084/m9.figshare.12511538.v1
title: Additional file 5 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 5. Differential gene expression of the clusters compared to normal adjacent tissues. Differential gene expression analysis using DESeq are shown along with p-values and log2 fold change.
DOI: 10.6084/m9.figshare.12511514
title: Additional file 11 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 11. Statistical analysis of immune cells. The differential abundance of cells between the clusters and normal tissue samples was done using pairwise T-test in R.
DOI: 10.6084/m9.figshare.12511517
title: Additional file 12 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 12. The identified biomarkers and their functions. The identified biomarkers from the decision tree and their functions are shown in this file
DOI: 10.6084/m9.figshare.12511523
title: Additional file 1 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 1. Prostate cancer immunotherapy clinical trials. This file contains combination and mono-immunotherapies in clinical trial.
DOI: 10.6084/m9.figshare.12511511
title: Additional file 10 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 10. Differential gene expression for the analysis of the cancer-immunity pathway. The genes important for each step of the cancer immunity pathway were organized for the identification of the IEMs in each cluster.
DOI: 10.6084/m9.figshare.12511514.v1
title: Additional file 11 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 11. Statistical analysis of immune cells. The differential abundance of cells between the clusters and normal tissue samples was done using pairwise T-test in R.
DOI: 10.6084/m9.figshare.12511517.v1
title: Additional file 12 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 12. The identified biomarkers and their functions. The identified biomarkers from the decision tree and their functions are shown in this file
DOI: 10.6084/m9.figshare.12511523.v1
title: Additional file 1 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 1. Prostate cancer immunotherapy clinical trials. This file contains combination and mono-immunotherapies in clinical trial.
DOI: 10.6084/m9.figshare.12511526.v1
title: Additional file 2 of Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis

description: Code to reproduce analyses. This file provides the code to reproduce all analyses discussed in this report in the open-source software R. All materials are made available in the open-science-framework repository: https://osf.io/spb37/.
DOI: 10.6084/m9.figshare.12511511.v1
title: Additional file 10 of Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy

description: Additional file 10. Differential gene expression for the analysis of the cancer-immunity pathway. The genes important for each step of the cancer immunity pathway were organized for the identification of the IEMs in each cluster.
DOI: 10.6084/m9.figshare.12511460
title: Additional file 5 of Dried fruit pomace inclusion in poultry diet: growth performance, intestinal morphology and physiology

description: Additional file 5. Raw data of genera detected in broiler chickens fed experimental diets.
DOI: 10.6084/m9.figshare.12511457
title: Additional file 4 of Dried fruit pomace inclusion in poultry diet: growth performance, intestinal morphology and physiology

description: Additional file 4. Raw data of phyla detected in broiler chickens fed experimental diets.
DOI: 10.6084/m9.figshare.12511460.v1
title: Additional file 5 of Dried fruit pomace inclusion in poultry diet: growth performance, intestinal morphology and physiology

description: Additional file 5. Raw data of genera detected in broiler chickens fed experimental diets.