Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatocyte steatosis increases the expression of adhesion molecules in endothelial cells

Abstract Background: Non-alcoholic fatty liver disease is considered a hepatic manifestation of the metabolic syndrome. It is associated with endothelial dysfunction as an early event of generalized atherosclerosis. However, it is unclear whether steatotic hepatocytes influence endothelial function directly. Objective: Explore the influence of hepatocyte steatosis on the function of endothelial cells. Methods: Oleic and palmitic acid (2:1 mixture, final concentration: 1 mM for 24 hours) was used to induce a normal adult hepatocyte strain (L-02) for transformation into steatosis cells. This was followed by oil red O staining and transmission electron microscopy (TEM) for verification. The culture solution of steatotic L-02 cells was filtered and collected, and added into the culture substrate of human umbilical vein endothelial cells (HUVECs). The expression of vascular cellular adhesion molecule -1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and E-selectin in HUVECs was detected by real-time polymerase chain reaction and Western blot assays. The apoptosis and proliferation of HUVECs was determined using flow cytometry. The experimental results were compared with the controls. Results: Oil red O staining and microscopic observation showed that the cytoplasm of induced L-02 cells contained a large amount of red lipid droplets. TEM results showed that the cytoplasm had lipid accumulation, swelling mitochondria, fewer cristae, and reduced number of rough endoplasmic reticula accompanied with degranulation. However, these changes were not observed in normal L-02 cells. As to the group of HUVECs treated by the filtrate of steatosis L-02 cells, the mRNA and protein expression of VCAM-1, ICAM-1, and E-selectin was higher than that in the control group. The difference was statistically significant (p <0.01). No significant difference was found when HUVECs apoptosis and proliferation were assessed by flow cytometry. Conclusion: Secretion from steatotic hepatocytes could boost the expression of VCAM-1, ICAM-1, and E-selectin in endothelial cells, indicating that hepatocyte steatosis could induce endothelial cell dysfunction. The proliferation and apoptosis of endothelial cells did not change, suggesting that hepatocyte steatosis had no influence on the viability of endothelial cells under this condition.
Staying Home or Moving Away? The Effect of Restructuring on Employment in Multinational Enterprises

This paper analyzes the geographic dispersion of employment restructuring in multinational enterprises, where we distinguish between headquarters and geographically dispersed affiliates. To this end, we use data of 255 Belgian parents and 1,887 affiliates between 1996 and 2005. We show that for multinational enterprises that restructure headquarters have superior employment performance than their affiliates. This effect seems t be stronger for vertically integrated firms, which is consistent with theories of imperfect information and increased agency costs. We also show that proximity matters: restructuring hurts the most the further the affiliate is located from the headquarter. This effect is consistent with the monitoring difficulties that are associated with vertical FDI firms and with the role of social network effects.
Feasibility Assessment of Using the KIP System to Achieve an Energy-Savings Potential for an Electronic Marquee

Conventional electronic marquees continue to consume energy even without a human presence. The purpose of this study is to assess energy-savings potential via the installation of the Kinect and IP Power integrated system (KIP) on an electronic marquee; this system will transfer the consumption data for total electricity to electricity-monitoring software (EZ-HD) using a smart meter (EZ-RE) and the ZigBee USB Dongle. An experiment was conducted at one school entrance for two periods during 10 school months, and it was found that the hourly electricity consumption rate for the original electronic marquee system was 1.25 kWh. After the KIP system was installed, the electronic marquee was activated only during human presence, and the hourly electricity consumption rate was 0.97 kWh, providing an average electricity savings rate of 22.4%. The results suggest that the KIP system can help to reduce the consumption of electricity for electronic marquees. Compared to infrared sensor parts used in the past as power switches for electronic equipment, the advantage of the KIP system is that it can distinguish a human presence and would not be interfered by moving objects or animals. In addition, the KIP system has a wider detection range and allows the users to program and detect different electricitysaving contexts and configurations for electronic equipment in different venues according to their individual needs. Therefore, through this test and assessment, we suggest that it is feasible to apply the KIP system in automatic lighting devices, televisions, air conditioners, or security monitoring systems.
Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions

Computer-aided drug discovery is an essential component of modern drug development. Therein, deep learning has become an important tool for rapid screening of billions of molecules in silico for potential hits containing desired chemical features. Despite its importance, substantial challenges persist in training these models, such as severe class imbalance, high decision thresholds, and lack of ground truth labels in some datasets. In this work we argue in favor of directly optimizing the receiver operating characteristic (ROC) in such cases, due to its robustness to class imbalance, its ability to compromise over different decision thresholds, certain freedom to influence the relative weights in this compromise, fidelity to typical benchmarking measures, and equivalence to positive/unlabeled learning. We also propose new training schemes (coherent mini-batch arrangement, and usage of out-of-batch samples) for cost functions based on the ROC, as well as a cost function based on the logAUC metric that facilitates early enrichment (i.e. improves performance at high decision thresholds, as often desired when synthesizing predicted hit compounds). We demonstrate that these approaches outperform standard deep learning approaches on a series of PubChem high-throughput screening datasets that represent realistic and diverse drug discovery campaigns on major drug target families.
Nonlinear Control of Quadrotor for Point Tracking: Actual Implementation and Experimental Tests

In this paper, a nonlinear control scheme along with its simulation and experimental results for a quadrotor are presented. It is not easy to control the quadrotor because the dynamics of quadrotor, which is obtained via the Euler-Lagrangian approach, has the features of underactuated, strongly coupled terms, uncertainty, and multiinput/multioutput. We propose a new nonlinear controller by using a backstepping-like feedback linearization method to control and stabilize the quadrotor. The designed controller is divided into three subcontrollers which are called attitude controller, altitude controller, and position controller. Stability of the designed controller is verified by the Lyapunov stability theorem. Detailed hardware parameters and experimental setups to implement the proposed nonlinear control algorithms are presented. The validity of proposed control scheme is demonstrated by simulations under different simulation scenarios. Experimental results show that the proposed controller is able to carry out the tasks of taking off, hovering, and positioning.
Hepatoprotective Effects of Kaempferol-3-O-α-l-Arabinopyranosyl-7-O-α-l-Rhamnopyranoside on d-Galactosamine and Lipopolysaccharide Caused Hepatic Failure in Mice

Fulminant hepatic failure (FHF), associated with high mortality, is characterized by extensive death of hepatocytes and hepatic dysfunction. There is no effective treatment for FHF. Several studies have indicated that flavonoids can protect the liver from different factor-induced injury. Previously, we found that the extracts of Elaeagnus mollis leaves had favorable protective effects on acute liver injury. However, the role and mechanisms behind that was elusive. This study examined the hepatoprotective mechanisms of kaempferol-3-O-α-l-arabinopyranosyl-7-O-α-l-rhamnopyra-noside (KAR), a major flavonol glycoside of E. mollis, against d-galactosamine (GalN) and lipopolysaccharide (LPS)-induced hepatic failure. KAR reduces the mouse mortality, protects the normal liver structure, inhibits the serum aspartate aminotransferase (AST) and alamine aminotransferase (ALT) activity and decreases the production of malondialdehyde (MDA) and reactive oxygen species (ROS) and inflammatory cytokines, TNF-α, IL-6, and IL-1β. Furthermore, KAR inhibits the apoptosis of hepatocytes and reduces the expression of TLR4 and NF-κB signaling pathway-related proteins induced by GalN/LPS treatment. These findings suggest that the anti-oxidative, anti-inflammatory, and anti-apoptotic effects of KAR on GalN/LPS-induced acute liver injury were performed through down-regulating the activity of the TLR4 and NF-κB signaling pathways.
An Updated Overview of Low Back Pain Management in Primary Care

Currently, guidelines for lower back pain (LBP) treatment are needed. We reviewed the current guidelines and high-quality articles to confirm the LBP guidelines for the Korean Society of Spine Surgery. We searched available databases for high-quality articles in English on LBP published from 2000 to the present year. Literature searches using these guidelines included studies from MEDLINE, the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and Embase. We analyzed a total of 132 randomized clinical trials, 116 systematic reviews, 9 meta-analyses, and 4 clinical guideline reviews. We adopted the SIGN checklist for the assessment of article quality. Data were subsequently abstracted by a reviewer and verified. Many treatment options exist for LBP, with a variety of recommendation grades. We assessed the recommendation grade for general behavior, pharmacological therapy, psychological therapy, and specific exercises. This information should be helpful to physicians in the treatment of LBP patients.
Editorial: Next-Generation Sequencing of Human Antibody Repertoires for Exploring B-cell Landscape, Antibody Discovery and Vaccine Development

Citation: Prabakaran P, Glanville J and Ippolito GC (2020) Editorial: Next-Generation Sequencing of Human Antibody Repertoires for Exploring B-cell Landscape, Antibody Discovery and Vaccine Development. Front. Immunol. 11:1344. doi: 10.3389/fimmu.2020. 01344 Editorial: Next-Generation Sequencing of Human Antibody Repertoires for Exploring B-cell Landscape, Antibody Discovery and Vaccine Development
Structure and mechanism of E. coli RNA 2′,3′-cyclic phosphodiesterase

2H (two-histidine) phosphoesterase enzymes are distributed widely in all domains of life and are implicated in diverse RNA and nucleotide transactions, including the transesterification and hydrolysis of cyclic phosphates. Here we report a biochemical and structural characterization of the Escherichia coli 2H protein YapD, which was identified originally as a reversible transesterifying “nuclease/ligase” at RNA 2′,5′-phosphodiesters. We find that YapD is an “end healing” cyclic phosphodiesterase (CPDase) enzyme that hydrolyzes an HORNA>p substrate with a 2′,3′-cyclic phosphodiester to a HORNAp product with a 2′-phosphomonoester terminus, without concomitant end joining. Thus we rename this enzyme ThpR (two-histidine 2′,3′-cyclic phosphodiesterase acting on RNA). The 2.0 Å crystal structure of ThpR in a product complex with 2′-AMP highlights the roles of extended histidine-containing motifs 43HxTxxF48 and 125HxTxxR130 in the CPDase reaction. His43-Nε makes a hydrogen bond with the ribose O3′ leaving group, thereby implicating His43 as a general acid catalyst. His125-Nε coordinates the O1P oxygen of the AMP 2′-phosphate (inferred from geometry to derive from the attacking water nucleophile), pointing to His125 as a general base catalyst. Arg130 makes bidentate contact with the AMP 2′-phosphate, suggesting a role in transition-state stabilization. Consistent with these inferences, changing His43, His125, or Arg130 to alanine effaced the CPDase activity of ThpR. Phe48 makes a π–π stack on the adenine nucleobase. Mutating Phe28 to alanine slowed the CPDase by an order of magnitude. The tertiary structure and extended active site motifs of ThpR are conserved in a subfamily of bacterial and archaeal 2H enzymes.
Development and Application of a Program for Reinforcing Global Health Competencies in University Nursing Students

Purpose: With globalization, the importance of global health is being stressed. Although nurses are indispensable healthcare professionals, programs to develop nurses with global health competencies and relevant studies are rare. Accordingly, this study was designed to develop a program to increase global health competencies and global leadership in nursing students and test its effect. Methods: A single group pre- and post-test study design was used. A 13-weeks program was developed and implemented with 204 students. Data were analyzed using paired t-test. The program to promote global health competencies was designed to improve nursing students' knowledge of global health, global leadership, global health competencies, critical thinking ability, and student-student partnership. Results: Global health competencies (t = −19.96, p < 0.001), self-assessed global leadership (t = −7.67, p < 0.001), and critical thinking ability (t = −7.67, p < 0.001) all significantly increased. Discussion: The study findings of increased global health competencies and global leadership in nursing students after participation in the program indicated ways in which global health competencies of nurses need to be developed. Therefore, the following aspects should be considered. First, nursing educators should understand the need and importance of global health education and accordingly, current nursing curriculums should be revised to include courses about global health. A systematic course of studies about global health should be developed and implemented based on discussions among experts and researchers. Second, as future health care professionals, nursing students should take an interest in global health problems and recognize various issues that need to be solved beyond borders between countries. To develop global health competencies, various efforts and systematic curriculum revisions are necessary.
Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer

Gastric cancer (GC) is the fourth most common malignant tumor. The mechanism underlying GC occurrence and development remains unclear. Previous studies have indicated that long non-coding RNAs (lncRNAs) are significantly associated with gastric cancer, but a systematic understanding of the role of lncRNAs in gastric cancer is lacking. In recent years, with the development of next-generation sequencing technology, tens of thousands of lncRNAs have been discovered. However, a large number of unannotated lncRNAs remain unidentified in different tissues, including potential gastric cancer-related lncRNAs. In this study, RNA sequencing (RNA-seq) data from 16 samples of eight gastric cancer patients were obtained and analyzed. A total of 1,854 previously unannotated lncRNAs were identified by ab initio assembly, and 520 differentially expressed lncRNAs were validated in the TCGA expression dataset. Methylation and copy number variation (CNV) array data from the same sample were integrated in the analysis. Changes in DNA methylation levels and CNVs may be responsible for the differential expression of 91 lncRNAs. Differentially expressed lncRNAs were enriched in coexpressed clusters of genes related to functions such as cell signaling, cell cycle, immune response, metabolic processes, angiogenesis, and regulation of retinoic acid (RA) receptors. Finally, a differentially expressed lncRNA, AC004510.3, was identified as a potential biomarker for the prediction of the overall survival of gastric cancer patients.
Efficient parallel algorithms for betweenness- and closeness-centrality in dynamic graphs

Finding the centrality measures of nodes in a graph is a problem of fundamental importance due to various applications from social networks, biological networks, and transportation networks. Given the large size of such graphs, it is natural to use parallelism as a recourse. There have been several studies that show how to compute the various centrality measures of nodes in a graph on parallel architectures, including multi-core systems and GPUs. However, as these graphs evolve and change, it is pertinent to study how to update the centrality measures on changes to the underlying graph. In this paper, we show novel parallel algorithms for updating the betweenness- and closeness-centrality values of nodes in a dynamic graph. Our algorithms process a batch of updates in parallel by extending the approach of handling a single update for betweenness-and closeness-centrality by Jamour et al. [16] and Sariyüce et al. [27], respectively. Besides, our algorithms incorporate mechanisms to exploit the structural properties of graphs for enhanced performance. We implement our algorithms on two parallel architectures: an Intel 24-core CPU and an Nvidia Tesla V100 GPU. To the best of our knowledge, we are the first to show GPU algorithms for the above two problems. We conduct detailed experiments to study the impact of various parameters associated with our algorithms and their implementation. Our results on a collection of real-world graphs indicate that our algorithms achieve a significant speedup over corresponding state-of-the-art algorithms.
High-Throughput Screen for Cell Wall Synthesis Network Module in Mycobacterium tuberculosis Based on Integrated Bioinformatics Strategy

Background Mycobacterium tuberculosis is one of the deadliest pathogens in humans. Co-infection of M. tuberculosis with HIV and the emergence of multi-drug-resistant tuberculosis (TB) constitute a serious global threat. However, no effective anti-TB drugs are available, with the exception of first-line drugs such as isoniazid. The cell wall of M. tuberculosis, which is primarily responsible for the lack of effective anti-TB drugs and the escape of the bacteria from host immunity, is an important drug target. The core components of the cell wall of M. tuberculosis are peptidoglycan, arabinogalactan, and mycotic acid. However, the functional genome and metabolic regulation pathways for the M. tuberculosis cell wall are still unknown. In this study, we used the biclustering algorithm integrated into cMonkey, sequence alignment, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other bioinformatics methods to scan the whole genome of M. tuberculosis as well as to identify and statistically analyze the genes related to the synthesis of the M. tuberculosis cell wall. Method We performed high-throughput genome-wide screening for M. tuberculosis using Biocarta, KEGG, National Cancer Institute Pathway Interaction Database (NCI-PID), HumanCyc, and Reactome. We then used the Database of Origin and Registration (DOOR) established in our laboratory to classify the collection of operons for M. tuberculosis cell wall synthetic genes. We used the cMonkey double clustering algorithm to perform clustering analysis on the gene expression profile of M. tuberculosis for cell wall synthesis. Finally, we visualized the results using Cytoscape. Result and Conclusion Through bioinformatics and statistical analyses, we identified 893 M. tuberculosis H37Rv cell wall synthesis genes, distributed in 20 pathways, involved in 46 different functions related to cell wall synthesis, and clustered in 386 modules. We identified important pivotal genes and proteins in the cell wall synthesis pathway such as murA, a class of operons containing genes involved in cell wall synthesis such as ID6951, and a class of operons indispensable for the survival of the bacteria. In addition, we found 41 co-regulatory modules for cell wall synthesis and five co-expression networks of molecular complexes involved in peptidoglycan biosynthesis, membrane transporter synthesis, and other cell wall processes.
Deployable mechanisms for distributed denial-of-service (DDoS) attack mitigation

報告番号: 甲26232 ; 学位授与年月日: 2010-03-24 ; 学位の種別: 課程博士 ; 学位の種類: 博士(学際情報学) ; 学位記番号: 博学情第36号 ; 研究科・専攻: 学際情報学府学際情報学専攻
Integrated navigation and self alignment using Square Root Unscented Kalman filtering

GPS and INS integration is attracting researchers for decades. Advent of MEMS inertial sensors and low cost GPS receivers extended the use of this technology to airborne /ground vehicle navigation, mining, surveillance and robotics. Complementary characteristics of GPS and INS with Kalman filter can overcome the problem of huge INS drifts, GPS outages, dense urban multipath effects and other individual problems associated with these sensors. Extended Kalman filter (EKF) needs linearized system and measurement models, hence performs Jacobian or Hessian matrix evaluation on each time step. If small angle error assumption does not hold and system nonlinearity and large initial attitude errors are an issue Unscented Kalman Filter (UKF) is preferred over EKF. Although UKF does not evaluate Jacobian but it has a problem of Cholesky matrix factorization which is an unstable operation and leads towards divergence. Square Root Unscented Filters (SRUKF) solves this particular problem but still cannot work with non Gaussian noises A very few people have utilized Square Root Unscented Kalman filter in navigation application so far. This research explores use of different configuration of UKF like Central Difference UKF (CDUKF) along with SRUKF and SRCDUKF in the presence of large initial attitude errors, GPS outages and increased levels of noise. A Square Root Unscented Particle filter (SRUPF) is tested with ZUPT technique and in flight alignment to overcome non Gaussian noises. All the filters are tested on navigation grade sensors in loosely coupled mode. Trajectories of up to one hour duration are utilized to evaluate performance. CDUKF was found best in computation time and accuracy. This filter is found more stable towards increased level of noise.