cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25111334
title: Multi-omics and single-cell sequencing analyses reveal the potential significance of circadian pathways in cancer therapy

description: Circadian rhythm disturbance is an independent risk factor for cancer. However, few studies have been reported on circadian rhythm related genes (CRGs) in cancer, so it is important to further explore the impact of CRGs in pan-cancer. The Cancer Genome Atlas database was used to collect cancer-related data such as copy number variation, single nucleotide variants, methylation, and survival differences. Immunohistochemistry (IHC) was used to verify the expression of circadian rhythm hub genes. The circadian pathway scores (CRS) were calculated using single-sample gene enrichment analysis. TIMER and GEPIA databases were used for immune-cell integration and assessment. Single-cell sequencing data was used to evaluate the abundance of CRS in tumor microenvironment cells. In this study, we found that the expression of circadian pathway varies between tumors. CSNK1E was significantly up-regulated in most tumors and CRY2 was significantly down-regulated in most tumors. The protein interaction network suggested CRY2 as the core gene and IHC verified its significant low expression in KIRC. In addition, CRGs were found to be protective factors in most tumors and have the potential to act as specific immune markers in different tumors. CRS was significantly lower in abundance in most tumors. CRS was significantly associated with overall survival in tumor patients and associated with the expression of many immune cells in the tumor immune microenvironment. CRS is significantly associated with tumor mutational burden and microsatellite instability scores in most tumors and may serve as a potential immunotherapeutic marker. The circadian rhythm pathway may be a breakthrough point in regulating the tumor microenvironment meanwhile a suitable immunotherapy method in the future.
DOI: 10.6084/m9.figshare.25111334.v1
title: Multi-omics and single-cell sequencing analyses reveal the potential significance of circadian pathways in cancer therapy

description: Circadian rhythm disturbance is an independent risk factor for cancer. However, few studies have been reported on circadian rhythm related genes (CRGs) in cancer, so it is important to further explore the impact of CRGs in pan-cancer. The Cancer Genome Atlas database was used to collect cancer-related data such as copy number variation, single nucleotide variants, methylation, and survival differences. Immunohistochemistry (IHC) was used to verify the expression of circadian rhythm hub genes. The circadian pathway scores (CRS) were calculated using single-sample gene enrichment analysis. TIMER and GEPIA databases were used for immune-cell integration and assessment. Single-cell sequencing data was used to evaluate the abundance of CRS in tumor microenvironment cells. In this study, we found that the expression of circadian pathway varies between tumors. CSNK1E was significantly up-regulated in most tumors and CRY2 was significantly down-regulated in most tumors. The protein interaction network suggested CRY2 as the core gene and IHC verified its significant low expression in KIRC. In addition, CRGs were found to be protective factors in most tumors and have the potential to act as specific immune markers in different tumors. CRS was significantly lower in abundance in most tumors. CRS was significantly associated with overall survival in tumor patients and associated with the expression of many immune cells in the tumor immune microenvironment. CRS is significantly associated with tumor mutational burden and microsatellite instability scores in most tumors and may serve as a potential immunotherapeutic marker. The circadian rhythm pathway may be a breakthrough point in regulating the tumor microenvironment meanwhile a suitable immunotherapy method in the future.
DOI: 10.5281/zenodo.10686758
title: C-C chemokine receptor type 7 (CCR7) regulates hepatic CD8+ T cell homeostasis and response to acute liver injury - Nanostring gene expression data

description: Acute liver failure (ALF) is a rare but life-threatening condition, and drug-induced liver injury (DILI), particularly acetaminophen (APAP) toxicity, is the leading cause of ALF. Innate immune mechanisms further perpetuate liver injury, while the role of the adaptive immune system in DILI-related ALF is unclear. We analyzed liver tissue from two independent patient cohorts with ALF and identified hepatic T cell infiltration as a prominent feature in human ALF. CD8+ T cells were characterised by zonation towards necrotic regions and an activated gene expression signature. In murine APAP-induced liver injury, intravital microscopy revealed zonation of CD8+ but not CD4+ T cells at necrotic areas. Gene expression analysis exposed pregulated C-C chemokine receptor 7 (CCR7) and its ligand CCL21 in liver as well as a broadly activated phenotype of hepatic CD8+ T cells. In two mouse models of ALF, Ccr7-/- mice had significantly aggravated early-phase liver damage. Functionally, CCR7 was not involved in the recruitment of CD8+ T cells, but regulated their activation profile potentially via egress to lymphatics. Ccr7-/- CD8+ T cells were characterized by elevated expression of activation, effector, and exhaustion profiles.

In this data set, gene expression of sorted CD4+ or CD8+ T-cells from  liver leukocyte extracts of either WT or CCR7-knock-out mice that were either untreated or challenged with APAP was measured using the nCounter Mouse Immunology Kit.
DOI: 10.5281/zenodo.10686759
title: C-C chemokine receptor type 7 (CCR7) regulates hepatic CD8+ T cell homeostasis and response to acute liver injury - Nanostring gene expression data

description: Acute liver failure (ALF) is a rare but life-threatening condition, and drug-induced liver injury (DILI), particularly acetaminophen (APAP) toxicity, is the leading cause of ALF. Innate immune mechanisms further perpetuate liver injury, while the role of the adaptive immune system in DILI-related ALF is unclear. We analyzed liver tissue from two independent patient cohorts with ALF and identified hepatic T cell infiltration as a prominent feature in human ALF. CD8+ T cells were characterised by zonation towards necrotic regions and an activated gene expression signature. In murine APAP-induced liver injury, intravital microscopy revealed zonation of CD8+ but not CD4+ T cells at necrotic areas. Gene expression analysis exposed pregulated C-C chemokine receptor 7 (CCR7) and its ligand CCL21 in liver as well as a broadly activated phenotype of hepatic CD8+ T cells. In two mouse models of ALF, Ccr7-/- mice had significantly aggravated early-phase liver damage. Functionally, CCR7 was not involved in the recruitment of CD8+ T cells, but regulated their activation profile potentially via egress to lymphatics. Ccr7-/- CD8+ T cells were characterized by elevated expression of activation, effector, and exhaustion profiles.

In this data set, gene expression of sorted CD4+ or CD8+ T-cells from  liver leukocyte extracts of either WT or CCR7-knock-out mice that were either untreated or challenged with APAP was measured using the nCounter Mouse Immunology Kit.
DOI: 10.5281/zenodo.10461467
title: Postfabrication tuning of circular Bragg resonators for enhanced emitter-cavity coupling

description: Dataset for "Postfabrication tuning of circular Bragg resonators for enhanced emitter-cavity coupling"

ACS Photonics 2024, 11, 2, 596-603https://doi.org/10.1021/acsphotonics.3c01480Accepted: December 29, 2023Published: January 19, 2024

A description of the dataset is found in the readme.md file (markdown language).

Data reuse policyCite the corresponding publication properly in publications that reuse this data. Adaptions can only be shared under identical license terms. If possible, please inform the corresponding authors (first and last author).
DOI: 10.5281/zenodo.10461466
title: Postfabrication tuning of circular Bragg resonators for enhanced emitter-cavity coupling

description: Dataset for "Postfabrication tuning of circular Bragg resonators for enhanced emitter-cavity coupling"

ACS Photonics 2024, 11, 2, 596-603https://doi.org/10.1021/acsphotonics.3c01480Accepted: December 29, 2023Published: January 19, 2024

A description of the dataset is found in the readme.md file (markdown language).

Data reuse policyCite the corresponding publication properly in publications that reuse this data. Adaptions can only be shared under identical license terms. If possible, please inform the corresponding authors (first and last author).
DOI: 10.25402/pme.25256842
title: Five Genes Were Identified as Prognostic Markers for Colorectal Cancer through the Integration of GWAS and eQTL Data.- supplementary material

description: Table 1. Genes identified by SMR for colorectal cancer
DOI: 10.6084/m9.figshare.20318879
title: Comparing reactogenicity of COVID-19 vaccines: a systematic review and meta-analysis

description: A number of vaccines have now been developed against COVID-19. Differences in reactogenicity and safety profiles according to the vaccine technologies employed are becoming apparent from clinical trials. Five databases (Medline, EMBASE, Science Citation Index, Cochrane Central Register of Controlled Trials, London School of Hygiene and Tropical Medicine COVID-19 vaccine tracker) were searched for relevant randomized controlled trials between 1 January 2020 and 12 January 2022 according to predetermined criteria with no language limitations. Forty-two datasets were identified, with 20 vaccines using four different technologies (viral vector, inactivated, mRNA and protein sub-unit). Adults and adolescents over 12 years were included. Control groups used saline placebos, adjuvants, and comparator vaccines. The most consistently reported solicited adverse events were fever, fatigue, headache, pain at injection site, redness, and swelling. Both doses of mRNA vaccines, the second dose of protein subunit and the first dose of adenovirus vectored vaccines were the most reactogenic, while the inactivated vaccines were the least reactogenic. The different COVID-19 vaccines currently available appear to have distinct reactogenicity profiles, dependent on the vaccine technology employed. Awareness of these differences may allow targeted recommendations for specific populations. Greater standardization of methods for adverse event reporting will aid future research in this field.
DOI: 10.6084/m9.figshare.20318879.v1
title: Comparing reactogenicity of COVID-19 vaccines: a systematic review and meta-analysis

description: A number of vaccines have now been developed against COVID-19. Differences in reactogenicity and safety profiles according to the vaccine technologies employed are becoming apparent from clinical trials. Five databases (Medline, EMBASE, Science Citation Index, Cochrane Central Register of Controlled Trials, London School of Hygiene and Tropical Medicine COVID-19 vaccine tracker) were searched for relevant randomized controlled trials between 1 January 2020 and 12 January 2022 according to predetermined criteria with no language limitations. Forty-two datasets were identified, with 20 vaccines using four different technologies (viral vector, inactivated, mRNA and protein sub-unit). Adults and adolescents over 12 years were included. Control groups used saline placebos, adjuvants, and comparator vaccines. The most consistently reported solicited adverse events were fever, fatigue, headache, pain at injection site, redness, and swelling. Both doses of mRNA vaccines, the second dose of protein subunit and the first dose of adenovirus vectored vaccines were the most reactogenic, while the inactivated vaccines were the least reactogenic. The different COVID-19 vaccines currently available appear to have distinct reactogenicity profiles, dependent on the vaccine technology employed. Awareness of these differences may allow targeted recommendations for specific populations. Greater standardization of methods for adverse event reporting will aid future research in this field.
DOI: 10.6084/m9.figshare.25256848
title: Initial_aperture_field.xlsx

description: The initial aperture field follows a Gaussian distribution with a self-affine spatial correlation
DOI: 10.6084/m9.figshare.25256848.v1
title: Initial_aperture_field.xlsx

description: The initial aperture field follows a Gaussian distribution with a self-affine spatial correlation
DOI: 10.34740/kaggle/dsv/7669945
title: Test Dataset By Me
DOI: 10.13140/rg.2.2.34094.28484
title: Static-Eccentricity-Fault-Location-Diagnosis-in-Resolvers-Using-Siamese-Based-Few-Shot-Learning-master
DOI: 10.6084/m9.figshare.11930310
title: Methylophiopogonanone A, an Ophiopogon homoisoflavonoid, alleviates high-fat diet-induced hyperlipidemia: assessment of its potential mechanism

description: Methylophiopogonanone A (MO-A), a homoisoflavonoid extracted from Ophiopogon japonicus, has been shown to attenuate myocardial apoptosis and improve cerebral ischemia/reperfusion injury. However, the hypolipidemic effects remain unknown. This study was performed to investigate a potential hypolipidemic effect of MO-A in hyperlipidemia rats, as well as its underlying mechanism of action. A rat model of hyperlipidemia was induced by a high-fat diet (HFD). Animals were randomly divided into three groups (n=8/group): normal control group (NC), HFD group, and HFD+MO-A (10 mg·kg-1·d-1) treatment group. The effects of MO-A on serum lipids, body weight, activity of lipoprotein metabolism enzyme, and gene expression of lipid metabolism were evaluated in HFD-induced rats. In HFD-induced rats, pretreatment with MO-A decreased the body weight gain and reduced serum and hepatic lipid levels. In addition, pretreatment with MO-A improved the activities of lipoprotein lipase and hepatic lipase in serum and liver, down-regulated mRNA expression of acetyl CoA carboxylase and sterol regulatory element-binding protein 1c, and up-regulated mRNA expression of low-density lipoprotein receptor and peroxisome proliferator-activated receptor α in the liver. Our results indicated that MO-A showed strong ability to ameliorate the hyperlipidemia in HFD-induced rats. MO-A might be a potential candidate for prevention of overweight and dyslipidemia induced by HFD.
DOI: 10.6084/m9.figshare.11930310.v1
title: Methylophiopogonanone A, an Ophiopogon homoisoflavonoid, alleviates high-fat diet-induced hyperlipidemia: assessment of its potential mechanism

description: Methylophiopogonanone A (MO-A), a homoisoflavonoid extracted from Ophiopogon japonicus, has been shown to attenuate myocardial apoptosis and improve cerebral ischemia/reperfusion injury. However, the hypolipidemic effects remain unknown. This study was performed to investigate a potential hypolipidemic effect of MO-A in hyperlipidemia rats, as well as its underlying mechanism of action. A rat model of hyperlipidemia was induced by a high-fat diet (HFD). Animals were randomly divided into three groups (n=8/group): normal control group (NC), HFD group, and HFD+MO-A (10 mg·kg-1·d-1) treatment group. The effects of MO-A on serum lipids, body weight, activity of lipoprotein metabolism enzyme, and gene expression of lipid metabolism were evaluated in HFD-induced rats. In HFD-induced rats, pretreatment with MO-A decreased the body weight gain and reduced serum and hepatic lipid levels. In addition, pretreatment with MO-A improved the activities of lipoprotein lipase and hepatic lipase in serum and liver, down-regulated mRNA expression of acetyl CoA carboxylase and sterol regulatory element-binding protein 1c, and up-regulated mRNA expression of low-density lipoprotein receptor and peroxisome proliferator-activated receptor α in the liver. Our results indicated that MO-A showed strong ability to ameliorate the hyperlipidemia in HFD-induced rats. MO-A might be a potential candidate for prevention of overweight and dyslipidemia induced by HFD.
DOI: 10.6084/m9.figshare.13568234
title: ANN training Data

description: Centerline based representation of CFD-based aortic hemodynamics for clinical and synthetic cases. This data includes centerline coordinates, local radii and local, average values of static pressure, wall shear stress, secondary flow degree and specific kinetic energy.<br>DISCLAIMER: The data/software provided here comes from a publicly funded project and cannot be used for commercial purposes. The terms and conditions of CC BY-NC apply.<br>
DOI: 10.5281/zenodo.10686697
title: Role of Preoperative Ultrasound Shear-Wave Elastography and Radiofrequency-Based Arterial Wall Tracking in Assessing the Vulnerability of Carotid Plaques Preliminary Results

description: Mazzaccaro D, Giannetta M, Fancoli F, Matrone G, Curcio N, Conti M, Righini P, Nano G. Role of Preoperative Ultrasound Shear-Wave Elastography and Radiofrequency-Based Arterial Wall Tracking in Assessing the Vulnerability of Carotid Plaques: Preliminary Results. Diagnostics (Basel). 2023 Feb 20;13(4):805. doi: 10.3390/diagnostics13040805. PMID: 36832293; PMCID: PMC9955800.

Abstract



We aimed at evaluating the ability of point shear-wave elastography (pSWE) and of a radiofrequency (RF) echo-tracking-based method in preoperatively assessing the vulnerability of the carotid plaque in patients undergoing carotid endarterectomy (CEA) for significant asymptomatic stenosis. All patients who underwent CEA from 03/2021 to 03/2022 performed a preoperative pSWE and an RF echo-based wall evaluation of arterial stiffness using an Esaote MyLab ultrasound system (EsaoteTM, Genova, Italy) with dedicated software. The data derived from these evaluations (Young's modulus (YM), augmentation index (AIx), pulse-wave velocity (PWV)) were correlated with the outcome of the analysis of the plaque removed during the surgery. Data were analyzed on 63 patients (33 vulnerable and 30 stable plaques). In stable plaques, YM was significantly higher than in vulnerable plaques (49.6 + 8.1 kPa vs. 24.6 + 4.3 kPa, p = 0.009). AIx also tended to be slightly higher in stable plaques, even if it was not statistically significant (10.4 + 0.9% vs. 7.7 + 0.9%, p = 0.16). The PWV was similar (12.2 + 0.9 m/s for stable plaques vs. 10.6 + 0.5 m/s for vulnerable plaques, p = 0.16). For YM, values >34 kPa had a sensitivity of 50% and a specificity of 73.3% in predicting plaque nonvulnerability (area under the curve = 0.66). Preoperative measurement of YM by means of pSWE could be a noninvasive and easily applicable tool for assessing the preoperative risk of plaque vulnerability in asymptomatic patients who are candidates for CEA.
DOI: 10.5281/zenodo.10686698
title: Role of Preoperative Ultrasound Shear-Wave Elastography and Radiofrequency-Based Arterial Wall Tracking in Assessing the Vulnerability of Carotid Plaques Preliminary Results

description: Mazzaccaro D, Giannetta M, Fancoli F, Matrone G, Curcio N, Conti M, Righini P, Nano G. Role of Preoperative Ultrasound Shear-Wave Elastography and Radiofrequency-Based Arterial Wall Tracking in Assessing the Vulnerability of Carotid Plaques: Preliminary Results. Diagnostics (Basel). 2023 Feb 20;13(4):805. doi: 10.3390/diagnostics13040805. PMID: 36832293; PMCID: PMC9955800.

Abstract



We aimed at evaluating the ability of point shear-wave elastography (pSWE) and of a radiofrequency (RF) echo-tracking-based method in preoperatively assessing the vulnerability of the carotid plaque in patients undergoing carotid endarterectomy (CEA) for significant asymptomatic stenosis. All patients who underwent CEA from 03/2021 to 03/2022 performed a preoperative pSWE and an RF echo-based wall evaluation of arterial stiffness using an Esaote MyLab ultrasound system (EsaoteTM, Genova, Italy) with dedicated software. The data derived from these evaluations (Young's modulus (YM), augmentation index (AIx), pulse-wave velocity (PWV)) were correlated with the outcome of the analysis of the plaque removed during the surgery. Data were analyzed on 63 patients (33 vulnerable and 30 stable plaques). In stable plaques, YM was significantly higher than in vulnerable plaques (49.6 + 8.1 kPa vs. 24.6 + 4.3 kPa, p = 0.009). AIx also tended to be slightly higher in stable plaques, even if it was not statistically significant (10.4 + 0.9% vs. 7.7 + 0.9%, p = 0.16). The PWV was similar (12.2 + 0.9 m/s for stable plaques vs. 10.6 + 0.5 m/s for vulnerable plaques, p = 0.16). For YM, values >34 kPa had a sensitivity of 50% and a specificity of 73.3% in predicting plaque nonvulnerability (area under the curve = 0.66). Preoperative measurement of YM by means of pSWE could be a noninvasive and easily applicable tool for assessing the preoperative risk of plaque vulnerability in asymptomatic patients who are candidates for CEA.
DOI: 10.5281/zenodo.10686857
title: Original data and images from Adipocytederived exosomes
DOI: 10.5281/zenodo.10686858
title: Original data and images from Adipocytederived exosomes
DOI: 10.6084/m9.figshare.11406108
title: MOESM2 of Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

description: Additional file 2: Table S4. ConFindr results from analysis of 10,000 Listeria monocytogenes, Salmonella enterica, and Escherichia coli fastq datasets. (XLS 7913 kb)
DOI: 10.21227/9chd-ng79
title: DeepCoAST Dataset

description: Our DeepCoAST dataset specifically explores the vulnerabilities of various traffic-splitting Website Fingerprinting (WF) Defenses, such as TrafficSliver, HyWF, and CoMPS. Our dataset comprises defended traces generated from the BigEnough dataset, which includes Tor cell trace instances of 95 websites, each represented by 200 instances collected under the standard browser security level. We simulated the traffic-splitting defenses assuming there are two split traces from the vanilla trace. Additionally, we set four configurations for TrafficSliver, adjusting the number of Tor cells and path selection probabilities to simulate realistic network conditions. We set one configuration for HyWF and CoMPS, and all configurations follow the parameters from the papers. We created the train and test dataset by extracting the various features such as Direction, Tik-Tok, ICD, ICDS, and 1-D TAM mentioned in our paper. Our dataset offers a comprehensive basis for evaluating traffic-splitting WF defenses.
DOI: 10.5281/zenodo.10686751
title: MRI Neonatal Lung Segmentation and 3D Morphologic Features

description: We developed an ensemble of deep convolutional neural networks (2D-UNets) to perform automated neonatal lung segmentation from MRI sequences. A three-dimensional reconstruction is used to calculate MRI features for lung volume, shape, pixel intensity, and surface.

In addition, ML Models for severity prediction of Bronchopulmonary Dysplasia (BPD) are implemented as an applied example of the use of MRI lung volumetric features for disease prognosis.

This dataset comprises:



Three pretrained 2D-UNet Models for Neonatal MRI Lung Segmentation.

Resulting performances and features per MRI-sequence.


See Publication:

Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease (2023)

https://doi.org/10.1148/ryai.220239
DOI: 10.5281/zenodo.7092360
title: MRI Neonatal Lung Segmentation and 3D Morphologic Features

description: We developed an ensemble of deep convolutional neural networks (2D-UNets) to perform automated neonatal lung segmentation from MRI sequences. A three-dimensional reconstruction is used to calculate MRI features for lung volume, shape, pixel intensity, and surface.

In addition, ML Models for severity prediction of Bronchopulmonary Dysplasia (BPD) are implemented as an applied example of the use of MRI lung volumetric features for disease prognosis.

This dataset comprises:



Three pretrained 2D-UNet Models for Neonatal MRI Lung Segmentation.

Resulting performances and features per MRI-sequence.


See Publication:

Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease (2023)

https://doi.org/10.1148/ryai.220239