cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6943802
title: Saquinavir plus methylprednisolone ameliorates experimental acute lung injury

description: Glucocorticoid insensitivity is an important barrier to the treatment of several inflammatory diseases, including acute lung injury (ALI). Saquinavir (SQV) is an inhibitor of the human immunodeficiency virus protease, and the therapeutic effects of SQV in ALI accompanied with glucocorticoid insensitivity have not been previously investigated. In this study, the effects of SQV on lipopolysaccharide (LPS)-mediated injury in human pulmonary microvascular endothelial cells (HPMECs), human type I alveolar epithelial cells (AT I), and alveolar macrophages were determined. In addition, the effects of SQV on an LPS-induced ALI model with or without methylprednisolone (MPS) were studied. In LPS-stimulated HPMECs, SQV treatment resulted in a decrease of high mobility group box 1 (HMGB1), phospho-NF-κB (p-NF-κB), and toll-like receptor 4 (TLR4), and an increase of VE-cadherin. Compared to MPS alone, MPS plus SQV attenuated the decrease of glucocorticoid receptor alpha (GRα) and IκBα in LPS-stimulated HPMECs. HMGB1, TLR4, and p-NF-κB expression were also lessened in LPS-stimulated alveolar macrophages with SQV treatment. In addition, SQV reduced the injury in human AT I with a decrease of HMGB1 and p-NF-κB, and with an increase of aquaporin 5 (AQP 5). SQV ameliorated the lung injury caused by LPS in rats with reductions in vascular permeability, myeloperoxidase activity (MPO) and histopathological scores, and with lowered HMGB1, TLR4, and p-NF-κB expression, but with enhanced VE-cadherin expression. By comparison, SQV plus MPS increased GRα and IκBα in lung tissues of rats with ALI. This study demonstrated that SQV prevented experimental ALI and improved glucocorticoid insensitivity by modulating the HMGB1/TLR4 pathway.
DOI: 10.6084/m9.figshare.6943847
title: Two independent grain-length mutants mapped to a single region on the long arm of chromosome 2 in rice

description: ABSTRACT Grain shape in rice is a key determinant of grain appearance, yield and market value, and thus has been widely studied. Rice mutant lines with long-grain phenotypes were previously isolated from an M2 population derived from mutagenized mature pollen grains that were treated with gamma-ray irradiation for a cultivar Ma85. To understand the genetic basis underlying the long-grain trait, two mutant lines, JF171 and JF178, were crossed with the short-grain parents JF222 and Samba, generating three F2 populations. Molecular marker-based genetic analysis was employed to detect the major QTLs that affected grain length, grain width, length-to-width ratio and grain weight. Based on the data obtained for the three populations, a joint major QTL for grain length was mapped to a 4.7 Mb region between the SSR makers RM263 and RM318 on the long arm of chromosome 2. The results suggested that the two independent mutations contained in JF171 and JF178 are likely due to alterations in the same genetic region. Furthermore, we developed a BC2F2 population using JF178 and Samba and narrowed the region to 0.6 Mb. The results of the current study will be helpful to reveal the genetic basis of the above long-grain mutant lines. In general, our results provide solid genetic data to identify the unknown gene that affects grain length by map-based cloning and practice marker-assisted breeding for long-grain rice cultivars.
DOI: 10.6084/m9.figshare.6943847.v1
title: Two independent grain-length mutants mapped to a single region on the long arm of chromosome 2 in rice

description: ABSTRACT Grain shape in rice is a key determinant of grain appearance, yield and market value, and thus has been widely studied. Rice mutant lines with long-grain phenotypes were previously isolated from an M2 population derived from mutagenized mature pollen grains that were treated with gamma-ray irradiation for a cultivar Ma85. To understand the genetic basis underlying the long-grain trait, two mutant lines, JF171 and JF178, were crossed with the short-grain parents JF222 and Samba, generating three F2 populations. Molecular marker-based genetic analysis was employed to detect the major QTLs that affected grain length, grain width, length-to-width ratio and grain weight. Based on the data obtained for the three populations, a joint major QTL for grain length was mapped to a 4.7 Mb region between the SSR makers RM263 and RM318 on the long arm of chromosome 2. The results suggested that the two independent mutations contained in JF171 and JF178 are likely due to alterations in the same genetic region. Furthermore, we developed a BC2F2 population using JF178 and Samba and narrowed the region to 0.6 Mb. The results of the current study will be helpful to reveal the genetic basis of the above long-grain mutant lines. In general, our results provide solid genetic data to identify the unknown gene that affects grain length by map-based cloning and practice marker-assisted breeding for long-grain rice cultivars.
DOI: 10.6084/m9.figshare.6943802.v1
title: Saquinavir plus methylprednisolone ameliorates experimental acute lung injury

description: Glucocorticoid insensitivity is an important barrier to the treatment of several inflammatory diseases, including acute lung injury (ALI). Saquinavir (SQV) is an inhibitor of the human immunodeficiency virus protease, and the therapeutic effects of SQV in ALI accompanied with glucocorticoid insensitivity have not been previously investigated. In this study, the effects of SQV on lipopolysaccharide (LPS)-mediated injury in human pulmonary microvascular endothelial cells (HPMECs), human type I alveolar epithelial cells (AT I), and alveolar macrophages were determined. In addition, the effects of SQV on an LPS-induced ALI model with or without methylprednisolone (MPS) were studied. In LPS-stimulated HPMECs, SQV treatment resulted in a decrease of high mobility group box 1 (HMGB1), phospho-NF-κB (p-NF-κB), and toll-like receptor 4 (TLR4), and an increase of VE-cadherin. Compared to MPS alone, MPS plus SQV attenuated the decrease of glucocorticoid receptor alpha (GRα) and IκBα in LPS-stimulated HPMECs. HMGB1, TLR4, and p-NF-κB expression were also lessened in LPS-stimulated alveolar macrophages with SQV treatment. In addition, SQV reduced the injury in human AT I with a decrease of HMGB1 and p-NF-κB, and with an increase of aquaporin 5 (AQP 5). SQV ameliorated the lung injury caused by LPS in rats with reductions in vascular permeability, myeloperoxidase activity (MPO) and histopathological scores, and with lowered HMGB1, TLR4, and p-NF-κB expression, but with enhanced VE-cadherin expression. By comparison, SQV plus MPS increased GRα and IκBα in lung tissues of rats with ALI. This study demonstrated that SQV prevented experimental ALI and improved glucocorticoid insensitivity by modulating the HMGB1/TLR4 pathway.
DOI: 10.6084/m9.figshare.6943832.v1
title: The Formation and Dynamic Evolution of Antiphase Domain Boundary in FeAl Alloy: Computational Simulation in Atomic Scale

description: The main objective of the present work is to build a model and analyze the dynamic evolution process of antiphase domain boundary (APDB) in FeAl alloy. The formation, evolution of APDB, long range order (LRO), the crystal structure transition, impact of temperature on LRO, are investigated. Comparisons with experiments proves that the model is competent for the dynamic investigation of APDB in microscopic scale and able to predict different boundary-types and their corresponding atoms distribution. The dynamic process shows that the initial distribution of premier micro domains determine the morphology of APDB. The morphological evolution of APDB significantly affects the quantity of APDB. The in situ observation shows that the crystal structure of a micro domain is altered by the APDB movement. The calculated LRO revealed that the atoms in Al-sublattice mainly contribute to the low order degree of FeAl at different temperatures.
DOI: 10.6084/m9.figshare.6943832
title: The Formation and Dynamic Evolution of Antiphase Domain Boundary in FeAl Alloy: Computational Simulation in Atomic Scale

description: The main objective of the present work is to build a model and analyze the dynamic evolution process of antiphase domain boundary (APDB) in FeAl alloy. The formation, evolution of APDB, long range order (LRO), the crystal structure transition, impact of temperature on LRO, are investigated. Comparisons with experiments proves that the model is competent for the dynamic investigation of APDB in microscopic scale and able to predict different boundary-types and their corresponding atoms distribution. The dynamic process shows that the initial distribution of premier micro domains determine the morphology of APDB. The morphological evolution of APDB significantly affects the quantity of APDB. The in situ observation shows that the crystal structure of a micro domain is altered by the APDB movement. The calculated LRO revealed that the atoms in Al-sublattice mainly contribute to the low order degree of FeAl at different temperatures.
DOI: 10.6084/m9.figshare.7992746.v1
title: Additional file 5: of Cognitive training for children and adolescents with fragile X syndrome: a randomized controlled trial of Cogmed

description: Table S4. Participant and parent characteristics by “improved”* vs. “non-improved” within the adaptive group. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12186327
title: Additional file 5 of Machine learning-selected variables associated with CD4 T cell recovery under antiretroviral therapy in very advanced HIV infection

description: Additional file 5.
DOI: 10.6084/m9.figshare.8987225.v1
title: A Comparative Study of Perventricular and Percutaneous Device Closure Treatments for Isolated Ventricular Septal Defect: A Chinese Single-Institution Experience

description: Abstract Objectives: To compare the advantages and disadvantages of perventricular and percutaneous procedures for treating isolated ventricular septal defect (VSD). Methods: A total of 572 patients with isolated VSD were selected in our hospital between January 2015 and December 2016. The patients’ median age and weight were five years (1-26 years) and 29 kg (9-55 kg), respectively. The median diameter of VSD was 6.0 mm (5-10 mm). Patients were divided into two groups. In group A, perventricular device closure was performed in 427 patients; in group B, 145 patients underwent percutaneous device closure. Results: Four hundred twelve patients in group A and 135 patients in group B underwent successful closure. The total occlusion rate was 98.5% (immediately) and 99.5% (3-month follow-up) in group A, which were not significantly different from those in group B (97.7% and 100%, respectively). Patients in group A had longer intensive care unit (ICU) stay than those in group B, but patients in group B experienced significantly longer operative times than those in group A. The follow-up period ranged from 8 months to 1.5 year (median, 1 year). During the follow-up period, late-onset complete atrioventricular block occurred in two patients. No other serious complications were noted in the remaining patients. Conclusion: Both procedures are safe and effective treatments for isolated VSD. The percutaneous procedure has obvious advantages of shorter ICU stay and less trauma than the perventricular procedure. However, the perventricular procedure is simpler to execute, results in a shorter operative time, and avoids X-ray exposure.
DOI: 10.6084/m9.figshare.8987225
title: A Comparative Study of Perventricular and Percutaneous Device Closure Treatments for Isolated Ventricular Septal Defect: A Chinese Single-Institution Experience

description: Abstract Objectives: To compare the advantages and disadvantages of perventricular and percutaneous procedures for treating isolated ventricular septal defect (VSD). Methods: A total of 572 patients with isolated VSD were selected in our hospital between January 2015 and December 2016. The patients’ median age and weight were five years (1-26 years) and 29 kg (9-55 kg), respectively. The median diameter of VSD was 6.0 mm (5-10 mm). Patients were divided into two groups. In group A, perventricular device closure was performed in 427 patients; in group B, 145 patients underwent percutaneous device closure. Results: Four hundred twelve patients in group A and 135 patients in group B underwent successful closure. The total occlusion rate was 98.5% (immediately) and 99.5% (3-month follow-up) in group A, which were not significantly different from those in group B (97.7% and 100%, respectively). Patients in group A had longer intensive care unit (ICU) stay than those in group B, but patients in group B experienced significantly longer operative times than those in group A. The follow-up period ranged from 8 months to 1.5 year (median, 1 year). During the follow-up period, late-onset complete atrioventricular block occurred in two patients. No other serious complications were noted in the remaining patients. Conclusion: Both procedures are safe and effective treatments for isolated VSD. The percutaneous procedure has obvious advantages of shorter ICU stay and less trauma than the perventricular procedure. However, the perventricular procedure is simpler to execute, results in a shorter operative time, and avoids X-ray exposure.
DOI: 10.6084/m9.figshare.11662884
title: Structural characterization and anticancer activity on osteosarcoma of Zn(II) coordination polymer

description: In this work, by employment of a rod-like ligand 4,4′-bis(imidazol-1-yl)-biphenyl (bibp) as the building block, a new Zn(II)-containing coordination polymer with the chemical formula of {[Zn<sub>2</sub>(HCO<sub>2</sub>)<sub>3</sub>(bibp)<sub>2</sub>](HCO<sub>2</sub>)<sub>3</sub>·2H<sub>2</sub>O} (<b>1</b>) has been successfully prepared by the reaction of Zn(II) salts and the bibp ligand in a mixed solvent of DMF and water. Furthermore, we use the grinding method to downsize the complex <b>1</b> to nano-region. To evaluate the anti-cancer activity of the synthetic compound, the Annexin V-FITC/PI assay in flow cytometry was performed to detect the apoptosis of human osteosarcoma cells, and the following mechanism exploration was performed by DCFH-DA detection assay for ROS measurement.
DOI: 10.6084/m9.figshare.11662884.v1
title: Structural characterization and anticancer activity on osteosarcoma of Zn(II) coordination polymer

description: In this work, by employment of a rod-like ligand 4,4′-bis(imidazol-1-yl)-biphenyl (bibp) as the building block, a new Zn(II)-containing coordination polymer with the chemical formula of {[Zn<sub>2</sub>(HCO<sub>2</sub>)<sub>3</sub>(bibp)<sub>2</sub>](HCO<sub>2</sub>)<sub>3</sub>·2H<sub>2</sub>O} (<b>1</b>) has been successfully prepared by the reaction of Zn(II) salts and the bibp ligand in a mixed solvent of DMF and water. Furthermore, we use the grinding method to downsize the complex <b>1</b> to nano-region. To evaluate the anti-cancer activity of the synthetic compound, the Annexin V-FITC/PI assay in flow cytometry was performed to detect the apoptosis of human osteosarcoma cells, and the following mechanism exploration was performed by DCFH-DA detection assay for ROS measurement.
DOI: 10.6084/m9.figshare.23721223.v1
title: Value Enhancement of Reinforcement Learning via Efficient and Robust Trust Region Optimization

description: Reinforcement learning (RL) is a powerful machine learning technique that enables an intelligent agent to learn an optimal policy that maximizes the cumulative rewards in sequential decision making. Most of methods in the existing literature are developed in <i>online</i> settings where the data are easy to collect or simulate. Motivated by high stake domains such as mobile health studies with limited and pre-collected data, in this paper, we study <i>offline</i> reinforcement learning methods. To efficiently use these datasets for policy optimization, we propose a novel value enhancement method to improve the performance of a given initial policy computed by existing state-of-the-art RL algorithms. Specifically, when the initial policy is not consistent, our method will output a policy whose value is no worse and often better than that of the initial policy. When the initial policy is consistent, under some mild conditions, our method will yield a policy whose value converges to the optimal one at a faster rate than the initial policy, achieving the desired “value enhancement” property. The proposed method is generally applicable to any parametrized policy that belongs to certain pre-specified function class (e.g., deep neural networks). Extensive numerical studies are conducted to demonstrate the superior performance of our method.
DOI: 10.6084/m9.figshare.7992890
title: The effect of temporal sampling intervals on typical human mobility indicators obtained from mobile phone location data

description: Mobile phone location data have been extensively used to understand human mobility patterns through the employment of mobility indicators. The temporal sampling interval (TSI), which is measured by the temporal interval between consecutive records, determines how well such data can describe human activities and influence the values of human mobility indicators. However, systematic investigations of how the TSI affects human mobility indicators remain scarce, and characterizing those relationships is a fundamental research question for many related studies. This study uses a mobile phone location dataset containing 19,370 intensively sampled individual trajectories (TSI &lt; 5 minutes) to systematically assess the impacts of the TSI on four typical mobility indicators that describe human mobility patterns from different aspects, which are movement entropy, radius of gyration, eccentricity, and daily travel frequency. We find that different TSIs have complex impacts on the values of different mobility indicators. Specifically, (1) coarser TSIs tend to underestimate the values of the four selected indicators with different degrees; (2) the degrees of underestimation vary significantly among users for eccentricity and daily travel frequency but exhibit high inter-user consistency for radius of gyration and movement entropy. The above findings can help better understand the variations among human mobility studies.
DOI: 10.6084/m9.figshare.7992890.v1
title: The effect of temporal sampling intervals on typical human mobility indicators obtained from mobile phone location data

description: Mobile phone location data have been extensively used to understand human mobility patterns through the employment of mobility indicators. The temporal sampling interval (TSI), which is measured by the temporal interval between consecutive records, determines how well such data can describe human activities and influence the values of human mobility indicators. However, systematic investigations of how the TSI affects human mobility indicators remain scarce, and characterizing those relationships is a fundamental research question for many related studies. This study uses a mobile phone location dataset containing 19,370 intensively sampled individual trajectories (TSI &lt; 5 minutes) to systematically assess the impacts of the TSI on four typical mobility indicators that describe human mobility patterns from different aspects, which are movement entropy, radius of gyration, eccentricity, and daily travel frequency. We find that different TSIs have complex impacts on the values of different mobility indicators. Specifically, (1) coarser TSIs tend to underestimate the values of the four selected indicators with different degrees; (2) the degrees of underestimation vary significantly among users for eccentricity and daily travel frequency but exhibit high inter-user consistency for radius of gyration and movement entropy. The above findings can help better understand the variations among human mobility studies.
DOI: 10.6084/m9.figshare.7992749
title: Additional file 6: of Cognitive training for children and adolescents with fragile X syndrome: a randomized controlled trial of Cogmed

description: Table S5. Participant and parent characteristics by “improved”* vs. “non-improved” within the non-adaptive group. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9565826
title: Additional file 1: of Aberrantly hypermethylated tumor suppressor genes were identified in oral squamous cell carcinoma (OSCC)

description: Figure S1. Correlation between transcriptional expression by qRT-PCR and the promoter hypermethylation of tumor suppressor genes by MSP analysis in OSCC cell lines. Related to Fig.Â 1a. Figure S2. Protein expression levels of TFPI2, SOX17, and GATA4 in additional set of primary OSCC tumors and normal oral mucosa. Related to Fig.Â 5. (PPTM 3917 kb)
DOI: 10.6084/m9.figshare.9565826.v1
title: Additional file 1: of Aberrantly hypermethylated tumor suppressor genes were identified in oral squamous cell carcinoma (OSCC)

description: Figure S1. Correlation between transcriptional expression by qRT-PCR and the promoter hypermethylation of tumor suppressor genes by MSP analysis in OSCC cell lines. Related to Fig.Â 1a. Figure S2. Protein expression levels of TFPI2, SOX17, and GATA4 in additional set of primary OSCC tumors and normal oral mucosa. Related to Fig.Â 5. (PPTM 3917 kb)
DOI: 10.6084/m9.figshare.9565829
title: Additional file 11: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S5. Primers used in this study. (XLS 20 kb)
DOI: 10.6084/m9.figshare.9565829.v1
title: Additional file 11: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S5. Primers used in this study. (XLS 20 kb)
DOI: 10.22002/424df-j9d14
title: Representative data of the South Pole DAS array for firn structure characterization

description: Active_Shots_StackedSP1_ID241-316.npy: Active shots data. 8225 DAS channels, 500 Hz sampling frequency.
Cross_Correlation_T.npy: Cross-correlation functions of the T component with the geophone located closest to the South Pole as a virtual source. 12 geophones colocated with the DAS cable, 100 Hz sampling frequency.
DOI: 10.6084/m9.figshare.9565853
title: Additional file 5: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S1. Similarities (%) between surface polysaccharide biosynthesis genes of E. alkalisoli YIC4027 and three E. fredii strains. (XLS 288 kb)
DOI: 10.6084/m9.figshare.9565853.v1
title: Additional file 5: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S1. Similarities (%) between surface polysaccharide biosynthesis genes of E. alkalisoli YIC4027 and three E. fredii strains. (XLS 288 kb)
DOI: 10.6084/m9.figshare.9565859
title: Additional file 6: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S2. Identified tts box sequences of E. alkalisoli YIC4027. Selected tts box sequences of E. fredii strains (NGR234, USDA257 and HH103) are shown for comparison. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9565859.v1
title: Additional file 6: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S2. Identified tts box sequences of E. alkalisoli YIC4027. Selected tts box sequences of E. fredii strains (NGR234, USDA257 and HH103) are shown for comparison. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9565865
title: Additional file 7: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S3. Genes involved in salt-alkali tolerance in E. alkalisoli YIC4027. (XLS 273 kb)
DOI: 10.6084/m9.figshare.9565865.v1
title: Additional file 7: of The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations

description: Table S3. Genes involved in salt-alkali tolerance in E. alkalisoli YIC4027. (XLS 273 kb)