cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9767783.v1
title: High-throughput sequencing reveals biofluid exosomal miRNAs associated with immunity in pigs

description: Large numbers of miRNAs are found in biofluid exosomes. We isolated ~50–200 nm diameter exosomes from four types of porcine biofluid (urine, plasma, semen, and bile) using serial centrifugation and ultracentrifugation procedures. A total of 42.15 M raw data were generated from four small RNA libraries. This produced 40.17 M map-able sequences, of which we identified 204 conserved miRNAs, and 190 novel candidate miRNAs. Furthermore, we identified 34 miRNAs specifically expressed in only one library, all with well-characterized immune-related functions. A set of five universally abundant miRNAs (miR-148a-3p, miR-21-5p, let-7f-5p, let-7i-5p, and miR-99a-5p) across all four biofluids was also found. Function enrichment analysis revealed that the target genes of the five ubiquitous miRNAs are primarily involved in immune and RNA metabolic processes. In summary, our findings suggest that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system. High-throughput sequencing evidence indicates that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system.
DOI: 10.5281/zenodo.10677543
title: Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling

description: This repository contains the data for the paper "Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling".

Data schema is follows:

'n_obs': 1510295, 'n_vars': 6, 'obs': ['sample_id',         'cell_index',         'cell_type',         'graph_cluster',         'distance_Fat',         'distance_Trabecules',         'distance_Endothelium',         'perimeter',         'center_x',         'center_y',         'cell_type_community',         'nb_num_pixels_150_Endothelium',         'nb_num_pixels_150_Trabeculae',         'nb_num_pixels_150_Fat',         'nuclei_ratio',         'case_id',         'category',         'age_at_dx',         'm_f',         'CD71_mean_intensity',         'CD61_mean_intensity',         'CD117_mean_intensity',         'CD38_mean_intensity',         'CD34_mean_intensity',         'CD15_mean_intensity',         'chm',         'cell_area_um',         'age_group',         'gender',         'fat_to_cell_ratio',         'fat_to_cell_amount',         'organism_ontology_term_id',         'donor_id',         'disease_ontology_term_id',         'tissue_type',         'suspension_type',         'development_stage_ontology_term_id',         'sex_ontology_term_id',         'assay_ontology_term_id',         'tissue_ontology_term_id',         'self_reported_ethnicity_ontology_term_id',         'cell_type_ontology_term_id'], 'obsm': ['X_graph_nn_embeddings', 'X_pca', 'spatial'], 'uns': ['age_group_palette',         'cell_type_colors',         'cell_type_order',         'cell_type_palette',         'cytopenia_palette',         'dendrogram_graph_cluster',         'gender_palette',         'graph_cluster_palette',         'sample_order',         'staging_palette',         'tissue_type_palette',         'title'], 'var': ['gene_name_at_imaging']}

 

anndata.X contains mean intensity values per segmented cell contour
DOI: 10.5281/zenodo.10677544
title: Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling

description: This repository contains the data for the paper "Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling".

Data schema is follows:

'n_obs': 1510295, 'n_vars': 6, 'obs': ['sample_id',         'cell_index',         'cell_type',         'graph_cluster',         'distance_Fat',         'distance_Trabecules',         'distance_Endothelium',         'perimeter',         'center_x',         'center_y',         'cell_type_community',         'nb_num_pixels_150_Endothelium',         'nb_num_pixels_150_Trabeculae',         'nb_num_pixels_150_Fat',         'nuclei_ratio',         'case_id',         'category',         'age_at_dx',         'm_f',         'CD71_mean_intensity',         'CD61_mean_intensity',         'CD117_mean_intensity',         'CD38_mean_intensity',         'CD34_mean_intensity',         'CD15_mean_intensity',         'chm',         'cell_area_um',         'age_group',         'gender',         'fat_to_cell_ratio',         'fat_to_cell_amount',         'organism_ontology_term_id',         'donor_id',         'disease_ontology_term_id',         'tissue_type',         'suspension_type',         'development_stage_ontology_term_id',         'sex_ontology_term_id',         'assay_ontology_term_id',         'tissue_ontology_term_id',         'self_reported_ethnicity_ontology_term_id',         'cell_type_ontology_term_id'], 'obsm': ['X_graph_nn_embeddings', 'X_pca', 'spatial'], 'uns': ['age_group_palette',         'cell_type_colors',         'cell_type_order',         'cell_type_palette',         'cytopenia_palette',         'dendrogram_graph_cluster',         'gender_palette',         'graph_cluster_palette',         'sample_order',         'staging_palette',         'tissue_type_palette',         'title'], 'var': ['gene_name_at_imaging']}

 

anndata.X contains mean intensity values per segmented cell contour
DOI: 10.6084/m9.figshare.8194979
title: Transcriptional profiling of uterine leiomyoma rats treated by a traditional herb pair, Curcumae rhizoma and Sparganii rhizoma

description: The aim of this study was to elucidate the concise effects of a traditional herb pair, Curcumae rhizoma-Sparganii rhizoma (CRSR), on uterine leiomyoma (UL) by analyzing transcriptional profiling. The UL rat model was made by intramuscular injection of progesterone and gavage administration of diethylstilbestrol. From 11 weeks of the establishment of the model, rats of the UL+CRSR group were gavaged daily with CRSR (6.67 g/kg). The serum concentrations of progesterone (P) and estradiol (E2) were determined by radioimmunoassay, the uterine index was measured by caliper measurement, and the pathological status was observed by hematoxylin and eosin stain. Gene expression profiling was checked by NimbleGen Rat Gene Expression Microarrays. The results indicated that the uterine mass of UL+CRSR rats was significantly shrunk and serum P and E2 levels significantly reduced compared to UL animals and nearly to the level of normal rats. Results of microarrays displayed the extensive inhibition of CRSR upon the expression of proliferation and deposition of extracellular matrix (ECM)-related genes, and significantly regulated a wide range of metabolism disorders. Furthermore, CRSR extensively regulated key pathways of the UL process, such as MAPK, PPAR, Notch, and TGF-β/Smad. Regulation of the crucial pathways for the UL process and ECM metabolism may be the underlying mechanisms of CRSR treatment. Further studies will provide clear clues for effectively treating UL with CRSR.
DOI: 10.6084/m9.figshare.8194979.v1
title: Transcriptional profiling of uterine leiomyoma rats treated by a traditional herb pair, Curcumae rhizoma and Sparganii rhizoma

description: The aim of this study was to elucidate the concise effects of a traditional herb pair, Curcumae rhizoma-Sparganii rhizoma (CRSR), on uterine leiomyoma (UL) by analyzing transcriptional profiling. The UL rat model was made by intramuscular injection of progesterone and gavage administration of diethylstilbestrol. From 11 weeks of the establishment of the model, rats of the UL+CRSR group were gavaged daily with CRSR (6.67 g/kg). The serum concentrations of progesterone (P) and estradiol (E2) were determined by radioimmunoassay, the uterine index was measured by caliper measurement, and the pathological status was observed by hematoxylin and eosin stain. Gene expression profiling was checked by NimbleGen Rat Gene Expression Microarrays. The results indicated that the uterine mass of UL+CRSR rats was significantly shrunk and serum P and E2 levels significantly reduced compared to UL animals and nearly to the level of normal rats. Results of microarrays displayed the extensive inhibition of CRSR upon the expression of proliferation and deposition of extracellular matrix (ECM)-related genes, and significantly regulated a wide range of metabolism disorders. Furthermore, CRSR extensively regulated key pathways of the UL process, such as MAPK, PPAR, Notch, and TGF-β/Smad. Regulation of the crucial pathways for the UL process and ECM metabolism may be the underlying mechanisms of CRSR treatment. Further studies will provide clear clues for effectively treating UL with CRSR.
DOI: 10.6084/m9.figshare.7146419
title: Data File 2.csv

description: dispersion of the refractive indices of [EMIM][BrI2] measured at three different temperatures
DOI: 10.6084/m9.figshare.7146419.v1
title: Data File 2.csv

description: dispersion of the refractive indices of [EMIM][BrI2] measured at three different temperatures
DOI: 10.6084/m9.figshare.7146422
title: Data File 1.csv

description: dispersion of the refractive indices of six low index ionic liquids
DOI: 10.6084/m9.figshare.7146422.v1
title: Data File 1.csv

description: dispersion of the refractive indices of six low index ionic liquids
DOI: 10.6084/m9.figshare.7146425
title: Data File 4.csv

description: dispersion of the refractive indices of [EMIM][BrI2] measured at different angles of incidence at 20°C
DOI: 10.6084/m9.figshare.7146425.v1
title: Data File 4.csv

description: dispersion of the refractive indices of [EMIM][BrI2] measured at different angles of incidence at 20°C
DOI: 10.6084/m9.figshare.7146428
title: Data File 3.csv

description: dispersion of the refractive index of [EMIM][I5] at 20°C
DOI: 10.6084/m9.figshare.7146428.v1
title: Data File 3.csv

description: dispersion of the refractive index of [EMIM][I5] at 20°C
DOI: 10.6084/m9.figshare.8195054
title: Electrochemiluminescence Detection of Silver Ion Based on Trigeminal Structure of DNA

description: A novel electrochemiluminescence (ECL) biosensor for highly sensitive and selective detection of Ag+ is developed based on the sensitive “turn-on” structure-switching trigeminal structure of deoxyribonucleic acid (DNA-TS). DNA-TS consists of three oligonucleotides hybridized to form three double-stranded DNA like Y-shaped DNA structure. The formation of DNA-TS makes the ECL sign Ru(bpy)2(mcbpy-O-Su-ester)(PF6)2 of reporter probe approach to the electrode surface and thus increase the ECL signal intensity. The “signal-on” ECL biosensor could detect Ag+ concentration in the range from 1.0 × 10-11 to 3.2 × 10-9 mol L-1, and the limit of detection is 3.0 × 10-12 mol L-1. The strategy is sensitive and rapid. This approach could be extended to the design of sensors for other desired heavy metal ions as well. Such ECL sensors are promising for sensitive detection of other heavy metal ions.
DOI: 10.6084/m9.figshare.8195054.v1
title: Electrochemiluminescence Detection of Silver Ion Based on Trigeminal Structure of DNA

description: A novel electrochemiluminescence (ECL) biosensor for highly sensitive and selective detection of Ag+ is developed based on the sensitive “turn-on” structure-switching trigeminal structure of deoxyribonucleic acid (DNA-TS). DNA-TS consists of three oligonucleotides hybridized to form three double-stranded DNA like Y-shaped DNA structure. The formation of DNA-TS makes the ECL sign Ru(bpy)2(mcbpy-O-Su-ester)(PF6)2 of reporter probe approach to the electrode surface and thus increase the ECL signal intensity. The “signal-on” ECL biosensor could detect Ag+ concentration in the range from 1.0 × 10-11 to 3.2 × 10-9 mol L-1, and the limit of detection is 3.0 × 10-12 mol L-1. The strategy is sensitive and rapid. This approach could be extended to the design of sensors for other desired heavy metal ions as well. Such ECL sensors are promising for sensitive detection of other heavy metal ions.
DOI: 10.6084/m9.figshare.7146560
title: Study of biological up-flow roughing filters designed for drinking water pretreatment in rural areas: using ceramic media as filter material

description: Roughing filters have been successfully employed as a pretreatment method in rural water supply, but few studies have reported the performance of up-flow roughing filters (URFs) packed with ceramic media. In this study, two pilot-scale URFs filled with ceramic media were designed. Filter performance, height profiles and head loss development were fully investigated. The average DOC, UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and total bacterial counts removal efficiencies of filters were found to be close to 8%, 10%, 70% and 0.6 log (75%), respectively. Both filters could remove about 60–90% of turbidity with influent turbidity ranging from 1 to 500 NTU and high removal efficiencies (∼60%) were achieved when influent turbidity was lower than 2.5 NTU at a hydraulic load up to 2 m h<sup>−1</sup>. Height profiles revealed that UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and turbidity were primarily removed in the former part of filter columns and that the separated solids stored within 20 cm of ceramic media layer above the bottom contributed to over 90% of total head loss. Filter run times were estimated to be around 60–80 days with a maximum head loss of 30 cm and an average influent turbidity of 10 NTU. The results indicated that the two URFs, combining low-cost operation and simple maintenance with good performance, were well suited to small waterworks in rural areas.
DOI: 10.6084/m9.figshare.7146560.v2
title: Study of biological up-flow roughing filters designed for drinking water pretreatment in rural areas: using ceramic media as filter material

description: Roughing filters have been successfully employed as a pretreatment method in rural water supply, but few studies have reported the performance of up-flow roughing filters (URFs) packed with ceramic media. In this study, two pilot-scale URFs filled with ceramic media were designed. Filter performance, height profiles and head loss development were fully investigated. The average DOC, UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and total bacterial counts removal efficiencies of filters were found to be close to 8%, 10%, 70% and 0.6 log (75%), respectively. Both filters could remove about 60–90% of turbidity with influent turbidity ranging from 1 to 500 NTU and high removal efficiencies (∼60%) were achieved when influent turbidity was lower than 2.5 NTU at a hydraulic load up to 2 m h<sup>−1</sup>. Height profiles revealed that UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and turbidity were primarily removed in the former part of filter columns and that the separated solids stored within 20 cm of ceramic media layer above the bottom contributed to over 90% of total head loss. Filter run times were estimated to be around 60–80 days with a maximum head loss of 30 cm and an average influent turbidity of 10 NTU. The results indicated that the two URFs, combining low-cost operation and simple maintenance with good performance, were well suited to small waterworks in rural areas.
DOI: 10.6084/m9.figshare.7146560.v1
title: Study of biological up-flow roughing filters designed for drinking water pretreatment in rural areas: Using ceramic media as filter material

description: Roughing filters have been successfully employed as a pretreatment method in rural water supply, but few studies have reported the performance of up-flow roughing filters (URFs) packed with ceramic media. In this study, two pilot-scale URFs filled with ceramic media were designed. Filter performance, height profiles and head loss development were fully investigated. The average DOC, UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and total bacterial counts removal efficiencies of filters were found to be close to 8%, 10%, 70% and 0.6 log (75%), respectively. Both filters could remove about 60-90% of turbidity with influent turbidity ranging from 1-500 NTU and high removal efficiencies (∼60%) were achieved when influent turbidity was lower than 2.5 NTU at a hydraulic load up to 2 m h<sup>-1</sup>. Height profiles revealed that UV<sub>254</sub> absorbance, NH<sub>4</sub><sup>+</sup>-N and turbidity were primarily removed in the former part of filter columns and that the separated solids stored within 20 cm of ceramic media layer above the bottom contributed to over 90% of total head loss. Filter run times were estimated to be around 60-80 days with a maximum head loss of 30 cm and an average influent turbidity of 10 NTU. The results indicated that the two URFs, combining low-cost operation and simple maintenance with good performance, were well suited to small waterworks in rural areas.
DOI: 10.6084/m9.figshare.8195138
title: Role of Adiponectin in prostate cancer

description: ABSTRACT Obesity is defined as a chronic and excessive growth of adipose tissue. It has been associated with a high risk for development and progression of obesity-associated malignancies, while adipokines may mediate this association. Adiponectin is an adipose tissue-derived adipokines, with significant anti-diabetic, anti-inflammatory, anti-atherosclerotic and anti-proliferative properties. Plasma adiponectin levels are decreased in obese individuals, and this feature is closely correlated with development of several metabolic, immunological and neoplastic diseases. Recent studies have shown that prostate cancer patients have lower serum adiponectin levels and decreased expression of adiponectin receptors in tumor tissues, which suggests plasma adiponectin level is a risk factor for prostate cancer. Furthermore, exogenous adiponectin has exhibited therapeutic potential in animal models. In this review, we focus on the potential role of adiponectin and the underlying mechanism of adiponectin in the development and progression of prostate cancer. Exploring the signaling pathways linking adiponectin with tumorigenesis might provide a potential target for therapy.
DOI: 10.6084/m9.figshare.8195138.v1
title: Role of Adiponectin in prostate cancer

description: ABSTRACT Obesity is defined as a chronic and excessive growth of adipose tissue. It has been associated with a high risk for development and progression of obesity-associated malignancies, while adipokines may mediate this association. Adiponectin is an adipose tissue-derived adipokines, with significant anti-diabetic, anti-inflammatory, anti-atherosclerotic and anti-proliferative properties. Plasma adiponectin levels are decreased in obese individuals, and this feature is closely correlated with development of several metabolic, immunological and neoplastic diseases. Recent studies have shown that prostate cancer patients have lower serum adiponectin levels and decreased expression of adiponectin receptors in tumor tissues, which suggests plasma adiponectin level is a risk factor for prostate cancer. Furthermore, exogenous adiponectin has exhibited therapeutic potential in animal models. In this review, we focus on the potential role of adiponectin and the underlying mechanism of adiponectin in the development and progression of prostate cancer. Exploring the signaling pathways linking adiponectin with tumorigenesis might provide a potential target for therapy.
DOI: 10.6084/m9.figshare.19729480
title: Predicting short-term PM2.5 concentrations at fine temporal resolutions using a multi-branch temporal graph convolutional neural network

description:   
The compressed package (study code.zip) contains the code files implemented by an under review paper ("Predicting short-term PM2.5 concentrations at fine temporal resolutions using a multi-branch temporal graph convolutional neural network").
<br>
Among the study code.zip, main.py is the model code based on a multi-branch temporal graph convolutional neural network. tgcn.py is the temporal graph convolutional network. utils.py contains some functions of graph convolution process. input_data.py is data processing.
<br>
The zip file (study data.zip) provides an example of air quality data including PM2.5 concentrations and some meteorological data. input_data.zip also contains a N by N adjacency matrix, which describes the spatial relationship between air quality monitoring stations.
DOI: 10.57702/eyff90ic
title: perez-alvarez-2018-1
DOI: 10.6084/m9.figshare.7256006
title: Analyzing the association between aortic regurgitation and atherosclerosis: is pulse pressure a cause of atherosclerosis?

description: If pulse pressure, one of the mechanical stresses, is a risk factor for atherosclerotic cardiovascular disease, then atherosclerosis should be progressive in aortic regurgitation which is a representative disease with increased pulse pressure. This cross-sectional study included 1,149 patients. We examined the influence of aortic regurgitation on maximum intima-media thickness or brachial-ankle pulse wave velocity. The degree of aortic regurgitation was classified into 4 grades by color Doppler examination. There were 177 patients with aortic regurgitation. Pulse pressure was significantly higher in patients with aortic regurgitation than in those without it. On multiple regression analysis, aortic regurgitation was not found to be a significant independent variable for maximum intima-media thickness [standard partial regression coefficient: aortic regurgitation = grade 1, 0.011, P = 0.7635; aortic regurgitation ≥ grade 2, −0.034, P = 0.3289] and brachial-ankle pulse wave velocity [standard partial regression coefficient: aortic regurgitation = grade1, −0.043, P = 0.1197; aortic regurgitation ≥ grade2, 0.002, P = 0.9358] after adjusting for age, sex, body mass index, presence or absence of cardiovascular disease, antihypertensive treatment, diabetes, dyslipidemia, and smoking. These results found no causal association between aortic regurgitation and atherosclerosis, and were a contradiction to the opinion that pulse pressure was a risk factor of atherosclerosis.
DOI: 10.6084/m9.figshare.7256006.v1
title: Analyzing the association between aortic regurgitation and atherosclerosis: is pulse pressure a cause of atherosclerosis?

description: If pulse pressure, one of the mechanical stresses, is a risk factor for atherosclerotic cardiovascular disease, then atherosclerosis should be progressive in aortic regurgitation which is a representative disease with increased pulse pressure. This cross-sectional study included 1,149 patients. We examined the influence of aortic regurgitation on maximum intima-media thickness or brachial-ankle pulse wave velocity. The degree of aortic regurgitation was classified into 4 grades by color Doppler examination. There were 177 patients with aortic regurgitation. Pulse pressure was significantly higher in patients with aortic regurgitation than in those without it. On multiple regression analysis, aortic regurgitation was not found to be a significant independent variable for maximum intima-media thickness [standard partial regression coefficient: aortic regurgitation = grade 1, 0.011, P = 0.7635; aortic regurgitation ≥ grade 2, −0.034, P = 0.3289] and brachial-ankle pulse wave velocity [standard partial regression coefficient: aortic regurgitation = grade1, −0.043, P = 0.1197; aortic regurgitation ≥ grade2, 0.002, P = 0.9358] after adjusting for age, sex, body mass index, presence or absence of cardiovascular disease, antihypertensive treatment, diabetes, dyslipidemia, and smoking. These results found no causal association between aortic regurgitation and atherosclerosis, and were a contradiction to the opinion that pulse pressure was a risk factor of atherosclerosis.