cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14357504
title: High-Dimensional Elliptical Sliced Inverse Regression in Non-Gaussian Distributions

description: Sliced inverse regression (SIR) is the most widely used sufficient dimension reduction method due to its simplicity, generality and computational efficiency. However, when the distribution of covariates deviates from multivariate normal distribution, the estimation efficiency of SIR gets rather low, and the SIR estimator may be inconsistent and misleading, especially in the high-dimensional setting. In this article, we propose a robust alternative to SIR—called elliptical sliced inverse regression (ESIR), to analysis high-dimensional, elliptically distributed data. There are wide applications of elliptically distributed data, especially in finance and economics where the distribution of the data is often heavy-tailed. To tackle the heavy-tailed elliptically distributed covariates, we novelly use the multivariate Kendall’s tau matrix in a framework of generalized eigenvalue problem in sufficient dimension reduction. Methodologically, we present a practical algorithm for our method. Theoretically, we investigate the asymptotic behavior of the ESIR estimator under the high-dimensional setting. Extensive simulation results show ESIR significantly improves the estimation efficiency in heavy-tailed scenarios, compared with other robust SIR methods. Analysis of the Istanbul stock exchange dataset also demonstrates the effectiveness of our proposed method. Moreover, ESIR can be easily extended to other sufficient dimension reduction methods and applied to nonelliptical heavy-tailed distributions.
DOI: 10.6084/m9.figshare.14357504.v2
title: High-Dimensional Elliptical Sliced Inverse Regression in Non-Gaussian Distributions

description: Sliced inverse regression (SIR) is the most widely used sufficient dimension reduction method due to its simplicity, generality and computational efficiency. However, when the distribution of covariates deviates from multivariate normal distribution, the estimation efficiency of SIR gets rather low, and the SIR estimator may be inconsistent and misleading, especially in the high-dimensional setting. In this article, we propose a robust alternative to SIR—called elliptical sliced inverse regression (ESIR), to analysis high-dimensional, elliptically distributed data. There are wide applications of elliptically distributed data, especially in finance and economics where the distribution of the data is often heavy-tailed. To tackle the heavy-tailed elliptically distributed covariates, we novelly use the multivariate Kendall’s tau matrix in a framework of generalized eigenvalue problem in sufficient dimension reduction. Methodologically, we present a practical algorithm for our method. Theoretically, we investigate the asymptotic behavior of the ESIR estimator under the high-dimensional setting. Extensive simulation results show ESIR significantly improves the estimation efficiency in heavy-tailed scenarios, compared with other robust SIR methods. Analysis of the Istanbul stock exchange dataset also demonstrates the effectiveness of our proposed method. Moreover, ESIR can be easily extended to other sufficient dimension reduction methods and applied to nonelliptical heavy-tailed distributions.
DOI: 10.6084/m9.figshare.14357672
title: Inoculation with arbuscular mycorrhizal fungus modulates defense-related genes expression in banana seedlings susceptible to wilt disease

description: Banana as an important economic crop worldwide, often suffers from serious damage caused by <i>Fusarium oxysporum</i> f. sp. <i>Cubense</i>. Arbuscular mycorrhizal (AM) fungi have been considered as one of the promising plant biocontrol agents in preventing from root pathogens. This study examined the effect of AM fungal inoculation on plant growth and differential expressions of growth- and defense-related genes in banana seedlings. Tissue-cultured seedlings of Brazilian banana (<i>Musa acuminate</i> Cavendish cv. Brail) were inoculated with AM fungus (<i>Rhizophagus irregularis</i>, Ri), and developed good mycorrhizal symbiosis from 4 to 11 weeks after inoculation with an infection rate up to 71.7% of the roots system. Microbial abundance revealed that Ri abundance in banana roots was 1.85×10<sup>6</sup> copies/ml at 11 weeks after inoculaiton. Inoculation improved plant dry weights by 47.5, 124, and 129% for stem, leaf, and the whole plant, respectively, during phosphate depletion. Among a total of 1411 differentially expressed genes (DEGs) obtained from the transcriptome data analysis, genes related to plant resistance (e.g. POD, PAL, PYR, and HBP-1b) and those related to plant growth (e.g. IAA, GH3, SAUR, and ARR8) were up-regulated in AM plants. This study demonstrates that AM fungus effectively promoted the growth of banana plants and induced defense-related genes which could help suppress wilt disease. The outcomes of this study form a basis for further study on the mechanism of banana disease resistance induced by AM fungi.
DOI: 10.6084/m9.figshare.14357672.v1
title: Inoculation with arbuscular mycorrhizal fungus modulates defense-related genes expression in banana seedlings susceptible to wilt disease

description: Banana as an important economic crop worldwide, often suffers from serious damage caused by <i>Fusarium oxysporum</i> f. sp. <i>Cubense</i>. Arbuscular mycorrhizal (AM) fungi have been considered as one of the promising plant biocontrol agents in preventing from root pathogens. This study examined the effect of AM fungal inoculation on plant growth and differential expressions of growth- and defense-related genes in banana seedlings. Tissue-cultured seedlings of Brazilian banana (<i>Musa acuminate</i> Cavendish cv. Brail) were inoculated with AM fungus (<i>Rhizophagus irregularis</i>, Ri), and developed good mycorrhizal symbiosis from 4 to 11 weeks after inoculation with an infection rate up to 71.7% of the roots system. Microbial abundance revealed that Ri abundance in banana roots was 1.85×106 copies/ml at 11 weeks after inoculaiton. Inoculation improved plant dry weights by 47.5, 124, and 129% for stem, leaf, and the whole plant, respectively, during phosphate depletion. Among a total of 1411 differentially expressed genes (DEGs) obtained from the transcriptome data analysis, genes related to plant resistance (e.g. POD, PAL, PYR, and HBP-1b) and those related to plant growth (e.g. IAA, GH3, SAUR, and ARR8) were up-regulated in AM plants. This study demonstrates that AM fungus effectively promoted the growth of banana plants and induced defense-related genes which could help suppress wilt disease. The outcomes of this study form a basis for further study on the mechanism of banana disease resistance induced by AM fungi.
DOI: 10.6084/m9.figshare.14357672.v2
title: Inoculation with arbuscular mycorrhizal fungus modulates defense-related genes expression in banana seedlings susceptible to wilt disease

description: Banana as an important economic crop worldwide, often suffers from serious damage caused by <i>Fusarium oxysporum</i> f. sp. <i>Cubense</i>. Arbuscular mycorrhizal (AM) fungi have been considered as one of the promising plant biocontrol agents in preventing from root pathogens. This study examined the effect of AM fungal inoculation on plant growth and differential expressions of growth- and defense-related genes in banana seedlings. Tissue-cultured seedlings of Brazilian banana (<i>Musa acuminate</i> Cavendish cv. Brail) were inoculated with AM fungus (<i>Rhizophagus irregularis</i>, Ri), and developed good mycorrhizal symbiosis from 4 to 11 weeks after inoculation with an infection rate up to 71.7% of the roots system. Microbial abundance revealed that Ri abundance in banana roots was 1.85×10<sup>6</sup> copies/ml at 11 weeks after inoculaiton. Inoculation improved plant dry weights by 47.5, 124, and 129% for stem, leaf, and the whole plant, respectively, during phosphate depletion. Among a total of 1411 differentially expressed genes (DEGs) obtained from the transcriptome data analysis, genes related to plant resistance (e.g. POD, PAL, PYR, and HBP-1b) and those related to plant growth (e.g. IAA, GH3, SAUR, and ARR8) were up-regulated in AM plants. This study demonstrates that AM fungus effectively promoted the growth of banana plants and induced defense-related genes which could help suppress wilt disease. The outcomes of this study form a basis for further study on the mechanism of banana disease resistance induced by AM fungi.
DOI: 10.6084/m9.figshare.7017248.v1
title: Leukocyte telomere length and epigenetic-based mortality risk score: associations with all-cause mortality among older adults

description: Telomere length (TL) has been established as a biomarker of aging and aging-related health outcomes, but showed only a weak or inconsistent association with all-cause mortality in previous epidemiological studies. Recently, an epigenetic ‘mortality risk score’ (MS) based on whole blood DNA methylation at 10 mortality-related CpG sites has been demonstrated to be strongly related to all-cause mortality at the population level. This study aimed to address the association between TL and this MS, and to assess and compare their associations with all-cause mortality. The MS was derived from the DNA methylation profiles measured by Illumina Human Methylation450K Beadchip and TL was measured by quantitative PCR at baseline among 1517 participants aged 50–75 of the German ESTHER cohort study. In cross-sectional bi- and multivariable analyses, the MS was strongly associated and showed monotonic dose-response relationships with TL (<i>p</i>-values &lt;0.05). However, only the MS but not TL was associated with all-cause mortality during a median follow-up of 12.5 years. After controlling for potential covariates and TL, hazard ratios (95% CI) for all-cause mortality for low, moderate and high levels of the MS defined by 1, 2–5 and &gt;5 CpG sites with aberrant methylation were 2.24 (1.13–4.41), 3.31 (1.76–6.22) and 6.33 (3.22–12.41) compared to a MS of 0, respectively. Our investigation shows that the epigenetic-based MS is strongly associated with TL, a broadly accepted aging biomarker, and at the same time shows much stronger associations with all-cause mortality than the latter.
DOI: 10.6084/m9.figshare.14357504.v1
title: High-Dimensional Elliptical Sliced Inverse Regression in non-Gaussian Distributions

description: Sliced Inverse Regression (SIR) is the most widely-used sufficient dimension reduction method due to its simplicity, generality and computational efficiency. However, when the distribution of covariates deviates from multivariate normal distribution, the estimation efficiency of SIR gets rather low, and the SIR estimator may be inconsistent and misleading, especially in the high-dimensional setting. In this paper, we propose a robust alternative to SIR - called Elliptical Sliced Inverse Regression (ESIR), to analysis high-dimensional, elliptically distributed data. There are wide applications of elliptically distributed data, especially in finance and economics where the distribution of the data is often heavy-tailed. To tackle the heavy-tailed elliptically distributed covariates, we novelly utilize the multivariate Kendall’s tau matrix in a framework of generalized eigenvalue problem in sufficient dimension reduction. Methodologically, we present a practical algorithm for our method. Theoretically, we investigate the asymptotic behavior of the ESIR estimator under the high-dimensional setting. Extensive simulation results show ESIR significantly improves the estimation efficiency in heavy-tailed scenarios, compared with other robust SIR methods. Analysis of the Istanbul stock exchange data set also demonstrates the effectiveness of our proposed method. Moreover, ESIR can be easily extended to other sufficient dimension reduction methods and applied to non-elliptical heavy-tailed distributions.
DOI: 10.6084/m9.figshare.23258805.v1
title: Additional file 2 of Analysis of the utilization value of different tissues of Taxus×Media based on metabolomics and antioxidant activity

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.13297329
title: Additional file 2 of Ultrasound shear wave elastography for assessing diaphragm function in mechanically ventilated patients: a breath-by-breath analysis

description: Additional file 2. Figure S2: Individual correlation coefficients between changes in transdiaphragmatic pressure (ΔPdi) and changes in diaphragm shear modulus (SMdi) can be found at the following link: https://figshare.com/s/c0f06ddf34d5a784ccb5 .
DOI: 10.6084/m9.figshare.7542947.v1
title: Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum

description: Ultracentrifugation remains the gold standard for isolation of small extracellular vesicles (sEV), particularly for cancer applications. The objective of this study was to determine if a widely used ultracentrifugation protocol for isolation of serum sEV could be modified to reduce the number of ultracentrifugation cycles and increase efficiency, while maintaining equal or better sample purity and yield. Serum was obtained from two healthy subjects. sEVs were isolated from 1 mL aliquots using three different ultracentrifugation protocols. Co-isolation of RNA carrier protein was assessed by performing Western blots for ApoA-I, ApoB, and Ago2. Small RNA-sequencing was performed on the sEV isolates, and differential detection of small ncRNA was compared across isolation protocols. Reduction from three- to two-ultracentrifuge cycles with no sucrose cushion resulted in a much higher sEV yield but also had the highest levels of lipoprotein and Ago2 contamination. However, the two-ultracentrifugation cycle protocol that incorporated a 30% sucrose cushion into the first cycle resulted in slightly higher sEV yields with lower levels of protein contamination compared to the lengthier three-ultracentrifugation cycle approach, therefore presenting a more efficient alternative approach for isolation of serum sEVs. It was also notable that there were some differences in sEV ncRNA cargo according to protocol, although it was less than expected given the differences in co-isolated RNA carrier proteins. Our results suggest that use of the modified serum sEV isolation protocol with two ultracentrifugation cycles and incorporating a 30% sucrose cushion offers a more efficient approach in terms of efficiency and purity.
DOI: 10.5281/zenodo.10654102
title: Dataset for Adversarial Machine Learning in Industry: A Systematic Literature Review

description: This Excel file contains meta-data about collected white literature, applied inclusion/exclusion criteria, and an overview of the Rigor and Relevance Scores of the identified articles.
DOI: 10.5281/zenodo.10654103
title: Dataset for Adversarial Machine Learning in Industry: A Systematic Literature Review

description: This Excel file contains meta-data about collected white literature, applied inclusion/exclusion criteria, and an overview of the Rigor and Relevance Scores of the identified articles.
DOI: 10.6084/m9.figshare.13297285.v1
title: Additional file 4 of Identification of the anti-breast cancer targets of triterpenoids in Liquidambaris Fructus and the hints for its traditional applications

description: Additional file 4. Predicted targets of LF triterpenoids and therapeutic targets of breast cancer.
DOI: 10.6084/m9.figshare.19076388
title: Additional file 1 of Identification of a novel HOOK3-FGFR1 fusion gene involved in activation of the NF-kappaB pathway

description: Additional file 1: Table S1. Clinical and laboratory characteristics of the 20 MDS patients. Table S2. A panel of 38 commonly mutated genes in myeloid hematologic malignancies. Table S3. Mutations detected by the target panel or WES in the MDS patients. Table S4. Gene fusions detected by STAR-Fusion in the 20 MDS patients. Table S5. Differentially expressed genes from the comparison between the HOOK3-FGFR1 positive patient and healthy donors
DOI: 10.6084/m9.figshare.19076388.v1
title: Additional file 1 of Identification of a novel HOOK3-FGFR1 fusion gene involved in activation of the NF-kappaB pathway

description: Additional file 1: Table S1. Clinical and laboratory characteristics of the 20 MDS patients. Table S2. A panel of 38 commonly mutated genes in myeloid hematologic malignancies. Table S3. Mutations detected by the target panel or WES in the MDS patients. Table S4. Gene fusions detected by STAR-Fusion in the 20 MDS patients. Table S5. Differentially expressed genes from the comparison between the HOOK3-FGFR1 positive patient and healthy donors
DOI: 10.17636/10194013
title: Replication package for 'Entry Barriers and Growth: The Role of Endogenous Market Structure'
DOI: 10.6084/m9.figshare.14880975
title: Additional file 2 of Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

description: Additional file 2. Supplementary Tables -Tables S1-S31.
DOI: 10.6084/m9.figshare.20648133.v1
title: Additional file 4 of Combining metabolome and clinical indicators with machine learning provides some promising diagnostic markers to precisely detect smear-positive/negative pulmonary tuberculosis

description: Additional file 4. Detailed information of the 79 DAMs between the SNPT patients and controls.
DOI: 10.5281/zenodo.10654142
title: soil moisture and rainfall data, soil moisture probability distribution code (R software)
DOI: 10.5281/zenodo.10654143
title: soil moisture and rainfall data, soil moisture probability distribution code (R software)
DOI: 10.6084/m9.figshare.20648136.v1
title: Additional file 5 of Combining metabolome and clinical indicators with machine learning provides some promising diagnostic markers to precisely detect smear-positive/negative pulmonary tuberculosis

description: Additional file 5. Detailed information of the 33 DAMs between the SPPT and SNPT patients.
DOI: 10.6084/m9.figshare.19076577
title: Electro-optical response of polymer-dispersed liquid crystals doped with <i>γ</i>-Fe<sub>2</sub>O<sub>3</sub> nanoparticles

description: In this paper, the microstructures of the dilute magnetic PDLC films, doped with low concentrations of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles, have hardly changed, but their electric-optical responses have distinctly changed. The experimental results show that the threshold voltage and hysteresis decreased with the increasing concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. Furthermore, at the relatively low concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles (samples (0) and (1) according to <i>ϕ<sub>m</sub></i> of 0 and 0.11%), the reciprocity of the rise time increased nonlinearly with the increasing square of the applied voltage. However, at the relatively high concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles (samples (2) according to <i>ϕ<sub>m</sub></i> = 0.15%), the reciprocity of the rise time increased linearly with the square of the applied voltage. Moreover, the reciprocity of the decay time was independent of the applied voltage and decreased with increasing the concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. These characteristics are due to the adsorption of free ions by γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. As a result, the interfacial interaction between liquid crystal droplets and the polymer matrix decreased, and the effective electric field inside the liquid crystal droplets increased.
DOI: 10.6084/m9.figshare.19076577.v1
title: Electro-optical response of polymer-dispersed liquid crystals doped with <i>γ</i>-Fe<sub>2</sub>O<sub>3</sub> nanoparticles

description: In this paper, the microstructures of the dilute magnetic PDLC films, doped with low concentrations of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles, have hardly changed, but their electric-optical responses have distinctly changed. The experimental results show that the threshold voltage and hysteresis decreased with the increasing concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. Furthermore, at the relatively low concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles (samples (0) and (1) according to <i>ϕ<sub>m</sub></i> of 0 and 0.11%), the reciprocity of the rise time increased nonlinearly with the increasing square of the applied voltage. However, at the relatively high concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles (samples (2) according to <i>ϕ<sub>m</sub></i> = 0.15%), the reciprocity of the rise time increased linearly with the square of the applied voltage. Moreover, the reciprocity of the decay time was independent of the applied voltage and decreased with increasing the concentration of γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. These characteristics are due to the adsorption of free ions by γ-Fe<sub>2</sub>O<sub>3</sub> nanoparticles. As a result, the interfacial interaction between liquid crystal droplets and the polymer matrix decreased, and the effective electric field inside the liquid crystal droplets increased.
DOI: 10.6084/m9.figshare.24975378
title: Supplemental Tables for Whole-Genome Sequences of <i>Campylobacter coli </i>and <i>Campylobacter jejuni</i> Isolates from Rhesus Macaques (<i>Macaca mulatta</i>) with and without Intestinal Disease

description: <i>Campylobacter jejuni </i>and <i>Campylobacter coli</i> infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (<i>Macaca mulatta</i>). A collection of 8 <i>C. jejuni </i>isolates and 103 <i>C. coli </i>isolates was obtained from rhesus macaques with and without intestinal disease and whole genome sequencing was performed. The supplemental data files for these isolates are provided in two tables here.
DOI: 10.6084/m9.figshare.24975378.v1
title: Supplemental Tables for Whole-Genome Sequences of <i>Campylobacter coli </i>and <i>Campylobacter jejuni</i> Isolates from Rhesus Macaques (<i>Macaca mulatta</i>) with and without Intestinal Disease

description: <i>Campylobacter jejuni </i>and <i>Campylobacter coli</i> infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (<i>Macaca mulatta</i>). A collection of 8 <i>C. jejuni </i>isolates and 103 <i>C. coli </i>isolates was obtained from rhesus macaques with and without intestinal disease and whole genome sequencing was performed. The supplemental data files for these isolates are provided in two tables here.
DOI: 10.6084/m9.figshare.24975378.v2
title: Supplemental Tables for Whole-Genome Sequences of <i>Campylobacter coli </i>and <i>Campylobacter jejuni</i> Isolates from Rhesus Macaques (<i>Macaca mulatta</i>) with and without Intestinal Disease

description: <i>Campylobacter jejuni </i>and <i>Campylobacter coli</i> infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (<i>Macaca mulatta</i>). A collection of 8 <i>C. jejuni </i>isolates and 103 <i>C. coli </i>isolates was obtained from rhesus macaques with and without intestinal disease and whole genome sequencing was performed. The supplemental data files for these isolates are provided in two tables here.
DOI: 10.6084/m9.figshare.21506849.v1
title: Additional file 3 of Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood–brain barrier microvessels

description: Additional file 3. Summary of tight junction dynamics data.