cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14278957.v1
title: AN ELECTROCHEMILUMINESCENCE SANDWICH BIOSENSOR FOR THE DETECTION OF LIPOPOLYSACCHARIDE

description: A novel electrochemiluminescence (ECL) biosensor for the determination of lipopolysaccharide (LPS), a biomarker of endotoxemia, was designed. The nanoprobe (Ru1@SiO2-peptide) with a specific peptide (CIGKLHSAGK) labeled with a carboxyl functionalized Ru@SiO2 (Ru1@SiO2) was prepared by the acylation reaction. The ECL peptide biosensor was obtained by the strong gold-sulfur bond between Au on the gold electrode (AuE) surface and thiol group in the peptide. In the present of LPS, the peptide on the ECL biosensor can capture effectively LPS and the LPS/peptide/AuE was fabricated. When the Ru1@SiO2-peptide nanoprobe was bound, a sandwich compound of Ru1@SiO2-peptide/LPS/peptide was formed, and Ru(bpy)32+, in the sandwich compound, will do the ECL performance. The effective ECL amplification of Ru1@SiO2 exhibited excellent analytical performance to LPS with a wide detection linear range of 1.0~500 ng mL-1 and the detection limit was 0.3 ng mL-1. The biosensor could provide an evaluate of LPS expression on the bacteria surface and guide a new path to the clinical analysis of LPS related diseases.
DOI: 10.6084/m9.figshare.6938168.v2
title: Expression of circular RNAs during C2C12 myoblast differentiation and prediction of coding potential based on the number of open reading frames and N6-methyladenosine motifs

description: The importance of circular RNAs (circRNAs) as regulators of muscle development and muscle-associated disorders is becoming increasingly apparent. To explore potential regulators of muscle differentiation, we determined the expression profiles of circRNAs of skeletal muscle C2C12 myoblasts and myotubes using microarray analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore circRNA functions. We also established competing endogenous RNA (ceRNA) networks using bioinformatics methods and predicted the coding potential of differentially expressed circRNAs. We found that 581 circRNAs were differentially regulated between C2C12 myoblasts and myotubes. Bioinformatics analysis suggested that the primary functions of the linear transcripts of the circRNAs were linked with organization of the cytoskeleton, calcium signaling, cell cycle, and metabolic pathways. ceRNA networks showed that the myogenic-specific genes myogenin, myocyte enhancer factor 2a, myosin heavy chain (Myh)-1, Myh7, and Myh7b could combine with 91 miRNAs and the top 30 upregulated circRNAs, forming 239 edges. According to the number of open reading frames and <i>N</i><sup>6</sup>-methyladenosine motifs, we identified 224 circRNAs with coding potential, and performed GO and KEGG analyses based on the linear counterparts of 75 circRNAs. We determined that the 75 circRNAs were related to regulation of the actin cytoskeleton and metabolic pathways. We established expression profiles of circRNAs during C2C12 myoblast differentiation and predicted the function of differentially expressed circRNAs, which might be involved in skeletal muscle development. Our study offers new insight into the functions of circRNAs in skeletal muscle growth and development.
DOI: 10.6084/m9.figshare.6938564
title: MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

description: MicroRNAs (miRNAs) are small non-coding RNAs with the potential as biomarkers for disease diagnosis, prognosis and therapy. In the era of big data and biomedical informatics, computer-aided biomarker discovery has become the current frontier. However, most of the computational models are highly dependent on specific prior knowledge and training-testing procedures, very few are mechanism-guided or evidence-based. To the best of our knowledge, untill now no general rules have been uncovered and applied to miRNA biomarker screening. In this study, we manually collected literature-reported cancer miRNA biomarkers and analyzed their regulatory patterns, including the regulatory modes, biological functions and evolutionary characteristics of their targets in the human miRNA-mRNA network. Two evidences were statistically detected and used to distinguish biomarker miRNAs from others. Based on these observations, we developed a novel bioinformatics model and software tool for miRNA biomarker discovery (http://sysbio.suda.edu.cn/MiRNA-BD/). In contrast to routine methods that focus on miRNA synergic functions, our method searches for vulnerable sites in the miRNA-mRNA network and considers the independent regulatory power of miRNAs, i.e., single-line regulations between miRNAs and mRNAs. The performance comparison demonstrates the generality and precision of our model, which identifies miRNA biomarkers for cancers as well as other complex diseases without training or specific prior knowledge.
DOI: 10.6084/m9.figshare.14278989
title: INSIGHT INTO THE EFFECTS OF BAY-SUBSTITUENTS ON STABLE PERYLENE DIIMIDE RADICAL ANION SALTS

description: In previous work, the facile method to prepare perylene diimide radical anion salt by alkali treatment was reported. However, the effects of structure on synthetic process of perylene diimide radical anion salt, and the difference of response to Cu 2+ are not thoroughly understood. In this work, two bay-substituted perylene diimide derivatives radical anion salts have been synthesized and characterized in order to study the influence of the bay-substituted groups on the formation condition of the corresponding radical anion salt, and the sensitivity to Cu 2+. The result indicates that the perylene diimide with electron-donating groups (-O-Ph) at bay position was much easier to get the air-stable radical anion salts and had higher sensitivity to Cu 2+ compared to the perylene diimide with electron-withdrawing groups (-Br) at bay position.
DOI: 10.6084/m9.figshare.16893007
title: Additional file 10 of A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

description: Additional file 10: Table S9. Genomic regions associated with environmental factors related to temperature, precipitation, and altitude.
DOI: 10.6084/m9.figshare.6938849.v1
title: Additional file 1: of Breast cancer in postmenopausal women is associated with an altered gut metagenome

description: Table S1. Generated data of the four groups. Table S2. Distribution of the samples of the four groups in the two enterotypes. Table S3. Relative abundance of the different species between premenopausal breast cancer patients and premenopausal healthy controls. Table S4. Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls. Table S5. PERMANOVA analysis was performed to assess effects of different phenotypes on gene profile. Table S6. The optimal species markers in the classification of postmenopausal breast cancer patients and postmenopausal healthy controls. Table S7. The abundance of Pathogen-Host Interactions (PHI) gene coding for diseases in postmenopausal breast cancer patients and postmenopausal healthy controls. Table S8. The virulence factor in samples of postmenopausal breast cancer patients and postmenopausal healthy controls. Table S9. Relative abundance of the different KEGG modules between premenopausal breast cancer patients and premenopausal healthy controls. Table S10. Relative abundance of the different KEGG modules between postmenopausal breast cancer patients and postmenopausal healthy controls. Table S11. Differentially enriched genes which annotated to butanoate metabolism pathways between postmenopausal breast cancer patients and postmenopausal healthy controls. Table S12. Relative abundance of the species of all the samples. Table S13. The species counts of all the samples. (XLS 2530 kb)
DOI: 10.6084/m9.figshare.14279084
title: RAPID DETECTION OF VITAMIN C CONTENT IN FRUITS AND VEGETABLES USING A DIGITAL CAMERA AND COLOR REACTION

description: In this study, we propose a novel method to determine the vitamin C content in fruits and vegetables. The proposed method exploits the image and data processing abilities of computers by coupling a digital camera and a color reaction. An image acquisition device was developed to collect the image information of the solution to be measured after the color reaction. The corresponding RGB and Lab color components were obtained by an image analysis software. Further, the standard curves of the vitamin C concentration and color component were established by nonlinear, linear, and multivariate data fitting. The detection range was 0.81-20.00 µg mL-1 (R2 = 0.9994), LOD was 0.24 µg mL-1, LOQ was 0.81 µg mL-1, accuracy was 98.95%, and precision was determined with an RSD of 0.73%. A comparison of the results confirmed that the proposed method’s accuracy was higher than that of the spectrophotometric method. The proposed method has a simple design and facilitates easy operation, and the cost of the equipment is only US$ 31.43. Therefore, it can replace the traditional spectrophotometric method for the determination of vitamin C content in fruits and vegetables and is highly applicable in the food, chemical, and medical fields.
DOI: 10.6084/m9.figshare.14278286.v1
title: Winter cover crops effects on soil microbial characteristics in sandy areas of Northern Shaanxi, China

description: ABSTRACT In sandy areas of Northern Shaanxi, after potato harvest, there are large areas of soil exposed to wind erosion from winter to spring, leading to degradation of soil quality. Planting cover crops in fallow fields is considered effective to improve soil biological properties; however, there is scarce study on the effect of winter cover crops on fallow soils in this region. In the study lasting from 2017 to 2019, four winter cover crops, i.e., alfalfa (AC), sweetclover (SC), winter wheat (WC), and ryegrass (RC), as well as bare land (CK), were used to study the effect of winter cover crops on soil microbial characteristics. The experiment showed that the soils in AC treatment had the highest values of microbial biomass N (MBN) content, dehydrogenase and urease activities, bacteria colonies, and Shannon and Richness indices. The soils in SC treatment had the maximum values of microbial biomass C (MBC) content, protease activity, fungi colonies, and Simpson index. Under AC and SC treatments, microbial communities in soil showed the highest percentage of carbon source utilization for amino acids, carbohydrates, and amines. Alfalfa and sweetclover as cover crops were helpful to improve the activity and diversity of soil microorganisms, exerting a positive effect on soil quality. This finding is of great significance for improving the methods of mitigating soil degradation in winter fallow fields of Northern Shaanxi, China.
DOI: 10.6084/m9.figshare.14278957
title: AN ELECTROCHEMILUMINESCENCE SANDWICH BIOSENSOR FOR THE DETECTION OF LIPOPOLYSACCHARIDE

description: A novel electrochemiluminescence (ECL) biosensor for the determination of lipopolysaccharide (LPS), a biomarker of endotoxemia, was designed. The nanoprobe (Ru1@SiO2-peptide) with a specific peptide (CIGKLHSAGK) labeled with a carboxyl functionalized Ru@SiO2 (Ru1@SiO2) was prepared by the acylation reaction. The ECL peptide biosensor was obtained by the strong gold-sulfur bond between Au on the gold electrode (AuE) surface and thiol group in the peptide. In the present of LPS, the peptide on the ECL biosensor can capture effectively LPS and the LPS/peptide/AuE was fabricated. When the Ru1@SiO2-peptide nanoprobe was bound, a sandwich compound of Ru1@SiO2-peptide/LPS/peptide was formed, and Ru(bpy)32+, in the sandwich compound, will do the ECL performance. The effective ECL amplification of Ru1@SiO2 exhibited excellent analytical performance to LPS with a wide detection linear range of 1.0~500 ng mL-1 and the detection limit was 0.3 ng mL-1. The biosensor could provide an evaluate of LPS expression on the bacteria surface and guide a new path to the clinical analysis of LPS related diseases.
DOI: 10.6084/m9.figshare.21087258.v1
title: Additional file 10 of Overexpression of cotton GhNAC072 gene enhances drought and salt stress tolerance in transgenic Arabidopsis

description: Additional file 10: Supplementary Table S6. Data for relative expression of transgenic and wildtype during drought and salt stress treatment.
DOI: 10.6084/m9.figshare.21087279.v1
title: Additional file 7 of Overexpression of cotton GhNAC072 gene enhances drought and salt stress tolerance in transgenic Arabidopsis

description: Additional file 7: Supplementary Table S3. Data for germination rate, and root length of transgenic and wildtype during drought and salt stress treatment.
DOI: 10.6084/m9.figshare.6938564.v1
title: MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

description: MicroRNAs (miRNAs) are small non-coding RNAs with the potential as biomarkers for disease diagnosis, prognosis and therapy. In the era of big data and biomedical informatics, computer-aided biomarker discovery has become the current frontier. However, most of the computational models are highly dependent on specific prior knowledge and training-testing procedures, very few are mechanism-guided or evidence-based. To the best of our knowledge, untill now no general rules have been uncovered and applied to miRNA biomarker screening. In this study, we manually collected literature-reported cancer miRNA biomarkers and analyzed their regulatory patterns, including the regulatory modes, biological functions and evolutionary characteristics of their targets in the human miRNA-mRNA network. Two evidences were statistically detected and used to distinguish biomarker miRNAs from others. Based on these observations, we developed a novel bioinformatics model and software tool for miRNA biomarker discovery (http://sysbio.suda.edu.cn/MiRNA-BD/). In contrast to routine methods that focus on miRNA synergic functions, our method searches for vulnerable sites in the miRNA-mRNA network and considers the independent regulatory power of miRNAs, i.e., single-line regulations between miRNAs and mRNAs. The performance comparison demonstrates the generality and precision of our model, which identifies miRNA biomarkers for cancers as well as other complex diseases without training or specific prior knowledge.
DOI: 10.6084/m9.figshare.14278900
title: VIBRATIONAL SPECTROSCOPIC INVESTIGATION AND MOLECULAR STRUCTURE OF A 5α-REDUCTASE INHIBITOR: FINASTERIDE

description: By way of Density Functional Theory (DFT)-based computational methods with commercially available software, the computational work of which about the molecular properties, the vibrational modes and vibrational frequencies of finasteride were accomplished for the first time. In order to gain a deeper and more thorough understanding of the molecular structure and infrared spectrum of finasteride, the equilibrium geometry harmonic vibrational frequencies and geometric parameters (bond lengths, bond angles and dihedral angles) were calculated by Generalized Gradient Approximations (GGAs) with five different density functional methods (PBE, RPBE, HCTH, PW91 and BLYP), using Material Studio 8.0 program. Theoretical vibrational frequencies and theoretical optimized geometric parameters were compared with the corresponding experimental data, which concluded that the GGA/PW91 method were shown to be in a good agreement with the results of experiment. In addition, the highest occupied molecular orbital (HOMO) energies, the lowest unoccupied molecular orbital (LUMO) energies and electron density isosurface calculations were done with an aim at a better understanding of the stability and reactivity of the molecule, indicating that the alkene and lactam conjugated system on the ring A is more likely to interact with other species. And, the atomic charge distribution was also calculated to understand the charge effect caused by electronegative atoms, which shows that the possible active-sites in chemical reactions are N1 and O1.
DOI: 10.6084/m9.figshare.14278841
title: THEORETICAL CALCULATIONS ABOUT THE THERMAL STABILITY AND DETONATION CHARACTER OF NITRAMINO-SUBSTITUTED PYRROLE

description: A series of nitramino-derivatives of pyrrole were designed through introducing the nitramino group into pyrrole ring to look for high-energy-density compounds. The molecular stabilities are explored thoroughly based on the calculated heats of formation, bond dissociation energy, and bond order at the B3PW91/6-311+G(d,p) level. The results indicated that the molecules designed in this paper have enough stability not only thermally but also kinetically. To evaluate the potential application as high-energy-density compounds, the detonation velocity and detonation pressure are calculated by using the Kamlet-Jacobs equation. Based on the calculation both of stability and detonation characters, four nitramino-derivatives of pyrrole (D1: 2,3-trinitramino-1H-pyrrole, D2: 2,3,4-trinitramino-1H-pyrrole, D3: 2,3,5-trinitramino-1H- pyrrole and E: 2,3,4,5- tetranitramino- 1H-pyrrole) are screened out as potential high-energy-density molecules for further study.
DOI: 10.6084/m9.figshare.16893007.v1
title: Additional file 10 of A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

description: Additional file 10: Table S9. Genomic regions associated with environmental factors related to temperature, precipitation, and altitude.
DOI: 10.5281/zenodo.10638885
title: Repository of hyperspectral images for image registration

description: This repository contains hyperspectral scenes used to test registration algorithms.

The images are in two formats: MATLAB and RAW. A colour composition of these images, in PNG, is also available in the folders.

In the RAW format, the hyperspectral data is stored as 32-bit signed integers. The pixels of each band are stored continuously (first band, second band...). A binary header of three integers (12 bytes) with the dimensions of the data (width, height, bands) is also included in the file. The images have to be extracted using 7z x file.raw.7z

This format can be displayed with the linux program imagevis3d or with HypeRvieW.

More information can be found in the README file and at https://gitlab.citius.usc.es/hiperespectral/RegistrationRepository
DOI: 10.5281/zenodo.10638886
title: Repository of hyperspectral images for image registration

description: This repository contains hyperspectral scenes used to test registration algorithms.

The images are in two formats: MATLAB and RAW. A colour composition of these images, in PNG, is also available in the folders.

In the RAW format, the hyperspectral data is stored as 32-bit signed integers. The pixels of each band are stored continuously (first band, second band...). A binary header of three integers (12 bytes) with the dimensions of the data (width, height, bands) is also included in the file. The images have to be extracted using 7z x file.raw.7z

This format can be displayed with the linux program imagevis3d or with HypeRvieW.

More information can be found in the README file and at https://gitlab.citius.usc.es/hiperespectral/RegistrationRepository
DOI: 10.25549/usctheses-c89-144031
title: Equity. Diversity. Inclusion: the future of women in S.T.E.M [pdf]
DOI: 10.25549/usctheses-c89-142104
title: Unsung III
DOI: 10.6084/m9.figshare.16900926.v1
title: Additional file 10 of Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

description: Additional file 10: Table S10. The quantitative distribution of cis-acting elements in the promoter region of BpJMJ gene family.
DOI: 10.6084/m9.figshare.16900941
title: Additional file 15 of Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

description: Additional file 15: Table S15. The Newick file obtained from MEGA software for constructing the phylogenetic tree.
DOI: 10.6084/m9.figshare.16900935.v1
title: Additional file 13 of Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

description: Additional file 13: Table S13. JHDM gene distribution among Birch, Maize, Arabidopsis and Rice.
DOI: 10.6084/m9.figshare.16900944
title: Additional file 16 of Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

description: Additional file 16: Table S16. The primers for qRT-PCR used in this study.
DOI: 10.6084/m9.figshare.16900944.v1
title: Additional file 16 of Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

description: Additional file 16: Table S16. The primers for qRT-PCR used in this study.
DOI: 10.6084/m9.figshare.17000071
title: Bankruptcy

description: This dataset includes
stata sintax: Sintax of November 22 version.docx
stata data: FILING BBDD2.dta
DOI: 10.6084/m9.figshare.17000071.v7
title: Bankruptcy

description: This dataset includes
stata sintax: Sintax of November 22 version.docx
stata data: FILING BBDD2.dta
DOI: 10.6084/m9.figshare.17000071.v8
title: Bankruptcy

description: This dataset includes
stata sintax: Sintax of November 22 version.docx
stata data: FILING BBDD2.dta
DOI: 10.6084/m9.figshare.16899998.v2
title: Generalized Factor Model for Ultra-High Dimensional Correlated Variables with Mixed Types

description: As high-dimensional data measured with mixed-type variables gradually become prevalent, it is particularly appealing to represent those mixed-type high-dimensional data using a much smaller set of so-called factors. Due to the limitation of the existing methods for factor analysis that deal with only continuous variables, in this article, we develop a generalized factor model, a corresponding algorithm and theory for ultra-high dimensional mixed types of variables where both the sample size <i>n</i> and variable dimension <i>p</i> could diverge to infinity. Specifically, to solve the computational problem arising from the non-linearity and mixed types, we develop a two-step algorithm so that each update can be carried out in parallel across variables and samples by using an existing package. Theoretically, we establish the rate of convergence for the estimators of factors and loadings in the presence of nonlinear structure accompanied with mixed-type variables when both <i>n</i> and <i>p</i> diverge to infinity. Moreover, since the correct specification of the number of factors is crucial to both the theoretical and the empirical validity of factor models, we also develop a criterion based on a penalized loss to consistently estimate the number of factors under the framework of a generalized factor model. To demonstrate the advantages of the proposed method over the existing ones, we conducted extensive simulation studies and also applied it to the analysis of the NFBC1966 dataset and a cardiac arrhythmia dataset, resulting in more predictive and interpretable estimators for loadings and factors than the existing factor model.