bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana
Authors: Zhang Jingjing , Liu Ruiqi , Zhu Yanfeng , Gong Jiaxin , Yin Shuwei , Sun Peisen , Feng Hao , Wang Qi , Zhao Shuaijing , Wang Zhongyuan , Li Guanglin
Published: January 2020

Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.
Chimerization Enables Gene Synthesis and Lentiviral Delivery of Customizable TALE-Based Effectors
Authors: Fang Yongxing , Stroukov Wladislaw , Cathomen Toni , Mussolino Claudio
Published: January 2020

Designer effectors based on the DNA binding domain (DBD) of Xanthomonas transcription activator-like effectors (TALEs) are powerful sequence-specific tools with an excellent reputation for their specificity in editing the genome, transcriptome, and more recently the epigenome in multiple cellular systems. However, the repetitive structure of the TALE arrays composing the DBD impedes their generation as gene synthesis product and prevents the delivery of TALE-based genes using lentiviral vectors (LVs), a widely used system for human gene therapy. To overcome these limitations, we aimed at chimerizing the DNA sequence encoding for the TALE-DBDs by introducing sufficient diversity to facilitate both their gene synthesis and enable their lentiviral delivery. To this end, we replaced three out of 17 Xanthomonas TALE repeats with TALE-like units from the bacterium Burkholderia rhizoxinica. This was combined with extensive codon variation and specific amino acid substitutions throughout the DBD in order to maximize intra- and inter-repeat sequence variability. We demonstrate that chimerized TALEs can be easily generated using conventional Golden Gate cloning strategy or gene synthesis. Moreover, chimerization enabled the delivery of TALE-based designer nucleases, transcriptome and epigenome editors using lentiviral vectors. When delivered as plasmid DNA, chimerized TALEs targeting the CCR5 and CXCR4 loci showed comparable activities in human cells. However, lentiviral delivery of TALE-based transcriptional activators was only successful in the chimerized form. Similarly, delivery of a chimerized CXCR4-specific epigenome editor resulted in rapid silencing of endogenous CXCR4 expression. In conclusion, extensive codon variation and chimerization of TALE-based DBDs enables both the simplified generation and the lentiviral delivery of designer TALEs, and therefore facilitates the clinical application of these tools to precisely edit the genome, transcriptome and epigenome.
Gap Junctions in the Bone Marrow Lympho-Hematopoietic Stem Cell Niche, Leukemia Progression, and Chemoresistance
Authors: Singh Abhishek K. , Cancelas Jose A.
Published: January 2020

The crosstalk between hematopoietic stem cells (HSC) and bone marrow (BM) microenvironment is critical for homeostasis and hematopoietic regeneration in response to blood formation emergencies after injury, and has been associated with leukemia transformation and progression. Intercellular signals by the BM stromal cells in the form of cell-bound or secreted factors, or by physical interaction, regulate HSC localization, maintenance, and differentiation within increasingly defined BM HSC niches. Gap junctions (GJ) are comprised of arrays of membrane embedded channels formed by connexin proteins, and control crucial signaling functions, including the transfer of ions, small metabolites, and organelles to adjacent cells which affect intracellular mechanisms of signaling and autophagy. This review will discuss the role of GJ in both normal and leukemic hematopoiesis, and highlight some of the most novel approaches that may improve the efficacy of cytotoxic drugs. Connexin GJ channels exert both cell-intrinsic and cell-extrinsic effects on HSC and BM stromal cells, involved in regenerative hematopoiesis after myelosuppression, and represent an alternative system of cell communication through a combination of electrical and metabolic coupling as well as organelle transfer in the HSC niche. GJ intercellular communication (GJIC) in the HSC niche improves cellular bioenergetics, and rejuvenates damaged recipient cells. Unfortunately, they can also support leukemia proliferation and survival by creating leukemic niches that provide GJIC dependent energy sources and facilitate chemoresistance and relapse. The emergence of new strategies to disrupt self-reinforcing malignant niches and intercellular organelle exchange in leukemic niches, while at the same time conserving normal hematopoietic GJIC function, could synergize the effect of chemotherapy drugs in eradicating minimal residual disease. An improved understanding of the molecular basis of connexin regulation in normal and leukemic hematopoiesis is warranted for the re-establishment of normal hematopoiesis after chemotherapy.
TGFβ1 Regulates Human RANKL-Induced Osteoclastogenesis via Suppression of NFATc1 Expression
Authors: Tokunaga Tadahiro , Mokuda Sho , Kohno Hiroki , Yukawa Kazutoshi , Kuranobu Tatsuomi , Oi Katsuhiro , Yoshida Yusuke , Hirata Shintaro , Sugiyama Eiji
Published: January 2020

Osteoclasts are multinucleated giant cells responsible for bone resorption. Various mediators involved in osteoclast differentiation have been investigated as possible therapeutic targets for osteoporosis and rheumatoid arthritis (RA). Although transforming growth factor beta1 (TGFβ1) has been described as one such multifunctional cytokine essential for bone remodeling, its effect on osteoclastogenesis remains controversial. Therefore, we sought to examine the effect of TGFβ1 on osteoclast generation induced by receptor activator of nuclear factor (NF)-κB ligand (RANKL) in humans. Peripheral blood monocytes, isolated using magnetic bead sorting, were cultured with macrophage-colony stimulating factor (M-CSF) or RANKL with or without TGFβ1. Tartrate-resistant acid phosphatase (TRAP) staining, as well as bone resorption assays, revealed that TGFβ1 suppressed RANKL-mediated human osteoclast development. Real-time reverse transcription PCR and Western blotting revealed that TGFβ1 reduced the gene and protein expression of nuclear factor of activated T cells, cytoplasmic 1 (NFATc1), the master regulator of osteoclast differentiation, respectively. Luciferase assays indicated that TGFβ1 inhibited the NF-κB p65-stimulated promoter activity of NFATc1. Immunofluorescence analysis demonstrated that TGFβ1 abrogated RANKL-induced nuclear translocation of p65. Thus, TGFβ1 regulates human RANKL-induced osteoclastogenesis via downregulation of NFATc1 by blocking nuclear translocation of NF-κB, suggesting that TGFβ1 may be a potential therapeutic target for RA.
Halogen-Mediated Partial Oxidation of Polyvinyl Alcohol for Tissue Engineering Purposes
Authors: Barbon Silvia , Stocco Elena , Dalzoppo Daniele , Todros Silvia , Canale Antonio , Boscolo-Berto Rafael , Pavan Piero , Macchi Veronica , Grandi Claudio , De Caro Raffaele , Porzionato Andrea
Published: January 2020

Partial oxidation of polyvinyl alcohol (PVA) with potassium permanganate turned out to be an efficient method to fabricate smart scaffolds for tissue engineering, endowed with biodegradation and protein delivery capacity. This work considered for the first time the use of halogens (bromine, chlorine and iodine) as less aggressive agents than potassium permanganate to perform controlled PVA oxidation, in order to prevent degradation of polymer molecular size upon chemical modification. Oxidized PVA solutions were chemically characterized (i.e., dinitrophenylhydrazine assay, viscosity measurements, molecular size distribution) before preparing physically cross-linked hydrogels. Scaffolds were assessed for their mechanical properties and cell/tissue biocompatibiliy through cytotoxic extract test on IMR-90 fibroblasts and subcutaneous implantation into BALB/c mice. According to chemical investigations, bromine and iodine allowed for minor alteration of polymer molecular weight. Uniaxial tensile tests demonstrated that oxidized scaffolds had decreased mechanical resistance to deformation, suggesting tunable hydrogel stiffness. Finally, oxidized hydrogels exhibited high biocompatibility both in vitro and in vivo, resulting neither to be cytotoxic nor to elicit severe immunitary host reaction in comparison with atoxic PVA. In conclusion, PVA hydrogels oxidized by halogens were successfully fabricated in the effort of adapting polymer characteristics to specific tissue engineering applications.
Associative Interactions among Zinc, Apolipoprotein E, and Amyloid-β in the Amyloid Pathology
Authors: Oh Shin Bi , Kim Jung Ah , Park SuJi , Lee Joo-Yong
Published: January 2020

Zinc and apolipoprotein E (apoE) are reportedly involved in the pathology of Alzheimer’s disease. To investigate the associative interaction among zinc, apoE, and amyloid-β (Aβ) and its role in amyloid pathogenesis, we performed various biochemical and immunoreactive analyses using brain tissues of Tg2576 mice and synthetic Aβ and apoE peptides. On amyloid plaques or in brain lysates of Tg2576 mice, apoE and Aβ immunoreactivities increased after zinc chelation and were restored by its subsequent replacement. Zinc depletion dissociated apoE/Aβ complexes or larger-molecular sizes of Aβ oligomers/aggregates into smaller-molecular sizes of apoE and/or Aβ monomers/complexes. In the presence of zinc, synthetic apoE and/or Aβ peptides aggregated into larger-molecular sizes of oligomers or complexes. Endogenous proteases or plasmin in brain lysates degraded apoE and/or Aβ complexes, and their proteolytic activity increased with zinc depletion. These biochemical findings suggest that zinc associates with apoE and Aβ to encourage the formation of apoE/Aβ complexes or large aggregates, raising the deposition of zinc-rich amyloid plaques. In turn, the presence of abundant zinc around and within apoE/Aβ complexes may block the access or activity of Aβ-degrading antibodies or proteases. These results support the plausibility of chelation strategy aiming at reducing amyloid pathology in Alzheimer’s disease.
Effects of Elevated Root-Zone CO2 on Root Morphology and Nitrogen Metabolism Revealed by Physiological and Transcriptome Analysis in Oriental Melon Seedling Roots
Authors: Chen Xinyu , Yin Zepeng , Yin Yang , Xu Chuanqiang , Wang Wanxin , Liu Yiling , Li Tianlai
Published: January 2020

Rhizosphere CO2 is vital for crop growth, development, and productivity. However, the mechanisms of plants’ responses to root-zone CO2 are unclear. Oriental melons are sensitive to root-zone gas, often encountering high root-zone CO2 during cultivation. We investigated root growth and nitrogen metabolism in oriental melons under T1 (0.5%) and T2 (1.0%) root-zone CO2 concentrations using physiology and comparative transcriptome analysis. T1 and T2 increased root vigor and the nitrogen content in the short term. With increased treatment time and CO2 concentration, root inhibition increased, characterized by decreased root absorption, incomplete root cell structure, accelerated starch accumulation and hydrolysis, and cell aging. We identified 1280 and 1042 differentially expressed genes from T1 and T2, respectively, compared with 0.037% CO2-grown plants. Among them, 683 co-expressed genes are involved in stress resistance and nitrogen metabolism (enhanced phenylpropanoid biosynthesis, hormone signal transduction, glutathione metabolism, and starch and sucrose metabolism). Nitrogen metabolism gene expression, enzyme activity, and nitrogen content analyses showed that short-term elevated root-zone CO2 mainly regulated plant nitrogen metabolism post-transcriptionally, and directly inhibited it transcriptionally in the long term. These findings provided a basis for further investigation of nitrogen regulation by candidate genes in oriental melons under elevated root-zone CO2.
Lysosomal Abnormalities in Cardiovascular Disease
Authors: Chi Congwu , Riching Andrew S. , Song Kunhua
Published: January 2020

The lysosome, a key organelle for cellular clearance, is associated with a wide variety of pathological conditions in humans. Lysosome function and its related pathways are particularly important for maintaining the health of the cardiovascular system. In this review, we highlighted studies that have improved our understanding of the connection between lysosome function and cardiovascular diseases with an emphasis on a recent breakthrough that characterized a unique autophagosome-lysosome fusion mechanism employed by cardiomyocytes through a lysosomal membrane protein LAMP-2B. This finding may impact the development of future therapeutic applications.
Resveratrol as Inducer of Autophagy, Pro-Survival, and Anti-Inflammatory Stimuli in Cultured Human RPE Cells
Authors: Josifovska Natasha , Albert Réka , Nagymihály Richárd , Lytvynchuk Lyubomyr , Moe Morten C. , Kaarniranta Kai , Veréb Zoltán J. , Petrovski Goran
Published: January 2020

Purpose: To investigate the mechanism by which resveratrol acts upon retinal pigment epithelial (RPE) cells and to characterize its effect upon autophagy, survival, and inflammation, with consequent implications to treatment for age-related macular degeneration (AMD). Methods: Cultured ARPE-19 cells were exposed to 10 and 50 μM resveratrol. Cell survival/death was determined by annexin-FITC/propidium iodide using flow cytometry, while autophagy was studied by detecting autophagic vacuoles formation (acridine orange and transmission electron microscopy), as well as LC3II/I ratio and p62 expression by Western blot. In addition, time-lapse confocal microscopy of a pDENDRA-LC3 expression vector was performed to detect autophagy in transfected ARPE-19 cells under the different treatment conditions. Inhibition of proteasomal and autophagy-lysosomal fusion was carried out by MG-132 and chloroquine, respectively, while induction of autophagy was achieved by rapamycin treatment. Detection of secreted cytokines by ARPE-19 cells using Human XL Cytokine Array was performed under oxidative stress (H2O2) and resveratrol treatments, respectively. Results: Resveratrol induced autophagy in ARPE-19 cells as determined by augmented presence of autophagic vacuoles, increased LC3II/I ratio and decreased p62 expression, as well as time-lapse confocal microscopy using pDENDRA-LC3 expression vector. Resveratrol acted similarly to proteasomal inhibition and downstream of mammalian target of rapamycin (mTOR), since upstream inhibition of autophagy by 3-methyladenine could not inhibit autophagy in ARPE-19 cells. Co-treatmeant by rapamycin and/or proteasome inhibition showed no additive effect upon autophagy induction. ARPE-19 cells treated by resveratrol showed lower cell death rate compared to untreated controls. Resveratrol induced a specific anti-inflammatory response in ARPE-19 cells. Conclusions: Resveratrol can induce autophagy, pro-survival, and anti-inflammatory stimuli in ARPE-19 cells, properties which could be plausible to formulate future treatment modalities for AMD.
Adenosine Suppresses Cholangiocarcinoma Cell Growth and Invasion in Equilibrative Nucleoside Transporters-Dependent Pathway
Authors: Lertsuwan Kornkamon , Phoaubon Supathra , Tasnawijitwong Nathapol , Lertsuwan Jomnarong
Published: January 2020

Cholangiocarcinoma (CCA) is a lethal disease with increasing incidence worldwide. Previous study showed that CCA was sensitive to adenosine. Thereby, molecular mechanisms of CCA inhibition by adenosine were examined in this study. Our results showed that adenosine inhibited CCA cells via an uptake of adenosine through equilibrative nucleoside transporters (ENTs), instead of activation of adenosine receptors. The inhibition of ENTs by NBTI caused the inhibitory effect of adenosine to subside, while adenosine receptor antagonists, caffeine and CGS-15943, failed to do so. Intracellular adenosine level was increased after adenosine treatment. Also, a conversion of adenosine to AMP by adenosine kinase is required in this inhibition. On the other hand, inosine, which is a metabolic product of adenosine has very little inhibitory effect on CCA cells. This indicates that a conversion of adenosine to inosine may reduce adenosine inhibitory effect. Furthermore, there was no specific correlation between level of proinflammatory proteins and CCA responses to adenosine. A metabolic stable analog of adenosine, 2Cl-adenosine, exerted higher inhibition on CCA cell growth. The disturbance in intracellular AMP level also led to an activation of 5′ AMP-activated protein kinase (AMPK). Accordingly, we proposed a novel adenosine-mediated cancer cell growth and invasion suppression via a receptor-independent mechanism in CCA.
GAI Functions in the Plant Response to Dehydration Stress in Arabidopsis thaliana
Authors: Wang Zhijuan , Liu Liu , Cheng Chunhong , Ren Ziyin , Xu Shimin , Li Xia
Published: January 2020

DELLA (GAI/RGA/RGL1/RGL2/RGL3) proteins are key negative regulators in GA (gibberellin) signaling and are involved in regulating plant growth as a response to environmental stresses. It has been shown that the DELLA protein PROCERA (PRO) in tomato promotes drought tolerance, but its molecular mechanism remains unknown. Here, we showed that the gai-1 (gibberellin insensitive 1) mutant (generated from the gai-1 (Ler) allele (with a 17 amino acid deletion within the DELLA domain of GAI) by backcrossing gai-1 (Ler) with Col-0 three times), the gain-of-function mutant of GAI (GA INSENSITIVE) in Arabidopsis, increases drought tolerance. The stomatal density of the gai-1 mutant was increased but its stomatal aperture was decreased under abscisic acid (ABA) treatment conditions, suggesting that the drought tolerance of the gai-1 mutant is a complex trait. We further tested the interactions between DELLA proteins and ABF2 (abscisic acid (ABA)-responsive element (ABRE)-binding transcription factors) and found that there was a strong interaction between DELLA proteins and ABF2. Our results provide new insight into DELLA proteins and their role in drought stress tolerance.
Circadian Rhythms in Exudative Age-Related Macular Degeneration: The Key Role of the Canonical WNT/β-Catenin Pathway
Authors: Vallée Alexandre , Lecarpentier Yves , Vallée Rodolphe , Guillevin Rémy , Vallée Jean-Noël
Published: January 2020

Age-related macular degeneration (AMD) is considered as the main worldwide cause of blindness in elderly adults. Exudative AMD type represents 10 to 15% of macular degeneration cases, but is the main cause of vision loss and blindness. Circadian rhythm changes are associated with aging and could further accelerate it. However, the link between circadian rhythms and exudative AMD is not fully understood. Some evidence suggests that dysregulation of circadian functions could be manifestations of diseases or could be risk factors for the development of disease in elderly adults. Biological rhythms are complex systems interacting with the environment and control several physiological pathways. Recent findings have shown that the dysregulation of circadian rhythms is correlated with exudative AMD. One of the main pathways involved in exudative AMD is the canonical WNT/β-catenin pathway. Circadian clocks have a main role in some tissues by driving the circadian expression of genes involved in physiological and metabolic functions. In exudative AMD, the increase of the canonical WNT/β-catenin pathway is enhanced by the dysregulation of circadian rhythms. Exudative AMD progression is associated with major metabolic reprogramming, initiated by aberrant WNT/β-catenin pathway, of aerobic glycolysis. This review focuses on the interest of circadian rhythm dysregulation in exudative AMD through the aberrant upregulation of the canonical WNT/β-catenin pathway.
Reciprocal Regulatory Interaction between TRPV1 and Kinin B1 Receptor in a Rat Neuropathic Pain Model
Authors: Cernit Veronica , Sénécal Jacques , Othman Rahmeh , Couture Réjean
Published: January 2020

Kinins are mediators of pain and inflammation and evidence suggests that the inducible kinin B1 receptor (B1R) is involved in neuropathic pain (NP). This study investigates whether B1R and TRPV1 are colocalized on nociceptors and/or astrocytes to enable regulatory interaction either directly or through the cytokine pathway (IL-1β, TNF-α) in NP. Sprague Dawley rats were subjected to unilateral partial sciatic nerve ligation (PSNL) and treated from 14 to 21 days post-PSNL with antagonists of B1R (SSR240612, 10 mg·kg−1, i.p.) or TRPV1 (SB366791, 1 mg·kg−1, i.p.). The impact of these treatments was assessed on nociceptive behavior and mRNA expression of B1R, TRPV1, TNF-α, and IL-1β. Localization on primary sensory fibers, astrocytes, and microglia was determined by immunofluorescence in the lumbar spinal cord and dorsal root ganglion (DRG). Both antagonists suppressed PSNL-induced thermal hyperalgesia, but only SB366791 blunted mechanical and cold allodynia. SSR240612 reversed PSNL-induced enhanced protein and mRNA expression of B1R and TRPV1 mRNA levels in spinal cord while SB366791 further increased B1R mRNA/protein expression. B1R and TRPV1 were found in non-peptide sensory fibers and astrocytes, and colocalized in the spinal dorsal horn and DRG, notably with IL-1β on astrocytes. IL-1β mRNA further increased under B1R or TRPV1 antagonism. Data suggest that B1R and TRPV1 contribute to thermal hyperalgesia and play a distinctive role in allodynia associated with NP. Close interaction and reciprocal regulatory mechanism are suggested between B1R and TRPV1 on astrocytes and nociceptors in NP.
miR-21-KO Alleviates Alveolar Structural Remodeling and Inflammatory Signaling in Acute Lung Injury
Authors: Jansing Johanna Christine , Fiedler Jan , Pich Andreas , Viereck Janika , Thum Thomas , Mühlfeld Christian , Brandenberger Christina
Published: January 2020

Acute lung injury (ALI) is characterized by enhanced permeability of the air–blood barrier, pulmonary edema, and hypoxemia. MicroRNA-21 (miR-21) was shown to be involved in pulmonary remodeling and the pathology of ALI, and we hypothesized that miR-21 knock-out (KO) reduces injury and remodeling in ALI. ALI was induced in miR-21 KO and C57BL/6N (wildtype, WT) mice by an intranasal administration of 75 µg lipopolysaccharide (LPS) in saline (n = 10 per group). The control mice received saline alone (n = 7 per group). After 24 h, lung function was measured. The lungs were then excised for proteomics, cytokine, and stereological analysis to address inflammatory signaling and structural damage. LPS exposure induced ALI in both strains, however, only WT mice showed increased tissue resistance and septal thickening upon LPS treatment. Septal alterations due to LPS exposure in WT mice consisted of an increase in extracellular matrix (ECM), including collagen fibrils, elastic fibers, and amorphous ECM. Proteomics analysis revealed that the inflammatory response was dampened in miR-21 KO mice with reduced platelet and neutrophil activation compared with WT mice. The WT mice showed more functional and structural changes and inflammatory signaling in ALI than miR-21 KO mice, confirming the hypothesis that miR-21 KO reduces the development of pathological changes in ALI.
Research on Optimization Method of VR Task Scenario Resources Driven by User Cognitive Needs
Authors: Fu Qianwen , Lv Jian , Zhao Zeyu , Yue Di
Published: January 2020

Research was performed in order to improve the efficiency of a user’s access to information and the interactive experience of task selection in a virtual reality (VR) system, reduce the level of a user’s cognitive load, and improve the efficiency of designers in building a VR system. On the basis of user behavior cognition-system resource mapping, a task scenario resource optimization method for VR system based on quality function deployment-convolution neural network (QFD-CNN) was proposed. Firstly, under the guidance of user behavior cognition, the characteristics of multi-channel information resources in a VR system were analyzed, and the correlation matrix of the VR system scenario resource characteristics was constructed based on the design criteria of human–computer interaction, cognition, and low-load demand. Secondly, analytic hierarchy process (AHP)-QFD combined with evaluation matrix is used to output the priority ranking of VR system resource characteristics. Then, the VR system task scenario cognitive load experiment is carried out on users, and the CNN input set and output set data are collected through the experiment, in order to build a CNN system and predict the user cognitive load and satisfaction in the human–computer interaction in the VR system. Finally, combined with the task information interface of a VR system in a smart city, the application research of the system resource feature optimization method under multi-channel cognition is carried out. The results show that the test coefficient CR value of the AHP-QFD model based on cognitive load is less than 0.1, and the MSE of CNN prediction model network is 0.004247, which proves the effectiveness of this model. According to the requirements of the same design task in a VR system, by comparing the scheme formed by the traditional design process with the scheme optimized by the method in this paper, the results show that the user has a lower cognitive load and better task operation experience when interacting with the latter scheme, so the optimization method studied in this paper can provide a reference for the system construction of virtual reality.
Delphi Method Supported by Forecasting Software
Authors: Lawnik Marcin , Banasik Arkadiusz
Published: January 2020

The Delphi method is one of the basic tools for forecasting values in various types of issues. It uses the knowledge of experts, which is properly aggregated (e.g., in the form of descriptive statistics measures) and returns to the previous group of experts again, thus starting the next round of forecasting. The multi-stage prediction under the Delphi method allows for better stabilization of the results, which is extremely important in the process of forecasting. Experts in the forecasting process often have access to time series forecasting software but do not necessarily use it. Therefore, it seems advisable to add to the aggregate the value obtained using forecasting software. The advantage of this approach is in saving the time and costs of obtaining a forecast. That should be understood as a smaller burden on data analysts and the value of their work. According to the above mentioned key factors, the main contribution of the article is the use of a virtual expert in the form of a computer-enhanced mathematical tool, i.e., a programming library for a forecasting time series. The chosen software tool is the Prophet library—a Facebook tool that can be used in Python or R programming languages.
Formal Ontologies in Information Systems Development: A Systematic Review
Authors: Husáková Martina , Bureš Vladimír
Published: January 2020

Computational ontologies are machine-processable structures which represent particular domains of interest. They integrate knowledge which can be used by humans or machines for decision making and problem solving. The main aim of this systematic review is to investigate the role of formal ontologies in information systems development, i.e., how these graphs-based structures can be beneficial during the analysis and design of the information systems. Specific online databases were used to identify studies focused on the interconnections between ontologies and systems engineering. One-hundred eighty-seven studies were found during the first phase of the investigation. Twenty-seven studies were examined after the elimination of duplicate and irrelevant documents. Mind mapping was substantially helpful in organising the basic ideas and in identifying five thematic groups that show the main roles of formal ontologies in information systems development. Formal ontologies are mainly used in the interoperability of information systems, human resource management, domain knowledge representation, the involvement of semantics in unified modelling language (UML)-based modelling, and the management of programming code and documentation. We explain the main ideas in the reviewed studies and suggest possible extensions to this research.
Application of Ground Penetrating Radar to Estimate Subgrade Soil Density
Authors: Abdelmawla Ahmad , Kim S. Sonny
Published: January 2020

Ground penetrating radar (GPR) technology has been widely used in pavement assessment over the last decade. Assessing the subgrade condition and monitoring its temporal variation provide valuable information regarding changes associated with pavement deterioration, allowing for the beneficial prediction of future road maintenance. This paper presents a method to estimate the density and water content of prepared subgrade soils of highly plastic silt using a 2 GHz GPR scan system and a simple exponential model. A bulk density prediction model was developed based on electromagnetic mixing theory to back calculate subgrade soils density. The model developed determines the soil’s dielectric constant, considering dielectric and volumetric properties of the three major components of soil: air, water, and solid particles. A series of laboratory tests was conducted on six (6) soil samples at various density levels to validate the newly developed model. For validation purposes, sand cone and dynamic cone penetration (DCP) tests were performed and compared with the estimated soils strength from GPR data. The results show that the prediction of soils density and stiffness using nondestructive technology helps efficiently forecast not only pavement deterioration, but potential risks to the subsurface pavement structure with all the advances of time saving using air coupled GPR antenna mounted on a moving vehicle.
Sarcopenic Obesity Predicts Early Attrition in Treatment-Seeking Patients with Obesity: A Longitudinal Pilot Study
Authors: Kreidieh Dima , Itani Leila , Tannir Hana , El Masri Dana , El Ghoch Marwan
Published: January 2020

Attrition is a major cause of failure in obesity treatment, which is still not fully understood. The identification of factors related to this outcome is of clinical relevance. We aimed to assess the relationship between sarcopenic obesity (SO) and early attrition. Early attrition was assessed at six months, and two groups of patients were selected from a large cohort of participants with overweight or obesity enrolled at the Outpatient Clinic of the Department of Nutrition and Dietetics at Beirut Arab University (Lebanon). Body composition was measured using a bioimpedance analyser (Tanita BC-418) and participants at baseline were categorized as having or not having SO. The “dropout group” included 72 participants (cases) compared to 31 participants (controls) in the “completer group”, with the former displaying a higher prevalence of SO than the latter (51.0% vs. 25.8%; p = 0.016). In the same direction, Poisson regression analysis showed that SO increased the relative risk of dropout by nearly 150% (RR = 1.45; 95% CI = 1.10–1.89; p = 0.007) after adjustment for age, gender, body mass index (BMI), age at first dieting, sedentary habits and weight-loss expectation. In conclusion, in a “real-world” outpatient clinical setting, the presence of SO at baseline increases the risk of dropout at six months. New directions of future research should be focused on identifying new strategies to reduce the attrition rate in this population.
Cardiac Autonomic Dysfunction in Multiple Sclerosis: A Systematic Review of Current Knowledge and Impact of Immunotherapies
Authors: Findling Oliver , Hauer Larissa , Pezawas Thomas , Rommer Paulus S. , Struhal Walter , Sellner Johann
Published: January 2020

Cardiac autonomic dysfunction (CAD) has been reported in patients with multiple sclerosis (MS). This systematic review summarizes the evidence for the types and prevalence of CAD in MS patients, as well as its association with MS type, disease characteristics, fatigue and immunotherapies used to treat MS. The analysis revealed that CAD is correlated with pathophysiological processes of MS, can trigger serious cardiovascular complications that may reduce life expectancy, and may have implications for treatment with immunotherapies, especially fingolimod. Numerous mainly small case–control or cohort studies have reported various measures of CAD (particularly heart rate variation) in MS patients, showing higher rates of abnormality versus controls. A smaller number of studies have reported on cardiac autonomic symptoms in MS, including orthostatic intolerance/dizziness in around 50% of patients. CAD also appears to be associated with disease duration and to be more common in progressive than relapsing–remitting MS. However, although a substantial evidence base suggests that assessing CAD in people with MS may be important, standardised methods to evaluate CAD in these patients have not yet been established. In addition, no studies have yet looked at whether treating CAD can reduce the burden of MS symptoms, disease activity or the rate of progression.
Pharmacological Inhibition of Spermine Oxidase Reduces Neurodegeneration and Improves Retinal Function in Diabetic Mice
Authors: Liu Fang , Saul Alan B. , Pichavaram Prahalathan , Xu Zhimin , Rudraraju Madhuri , Somanath Payaningal R. , Smith Sylvia B. , Caldwell Ruth B. , Narayanan S. Priya
Published: January 2020

Diabetic retinopathy (DR) is a significant cause of blindness in working-age adults worldwide. Lack of effective strategies to prevent or reduce vision loss is a major problem. Since the degeneration of retinal neurons is an early event in the diabetic retina, studies to characterize the molecular mechanisms of diabetes-induced retinal neuronal damage and dysfunction are of high significance. We have demonstrated that spermine oxidase (SMOX), a mediator of polyamine oxidation is critically involved in causing neurovascular damage in the retina. The involvement of SMOX in diabetes-induced retinal neuronal damage is completely unknown. Utilizing the streptozotocin-induced mouse model of diabetes, the impact of the SMOX inhibitor, MDL 72527, on neuronal damage and dysfunction in the diabetic retina was investigated. Retinal function was assessed by electroretinography (ERG) and retinal architecture was evaluated using spectral domain-optical coherence tomography. Retinal cryosections were prepared for immunolabeling of inner retinal neurons and retinal lysates were used for Western blotting. We observed a marked decrease in retinal function in diabetic mice compared to the non-diabetic controls. Treatment with MDL 72527 significantly improved the ERG responses in diabetic retinas. Diabetes-induced retinal thinning was also inhibited by the MDL 72527 treatment. Our analysis further showed that diabetes-induced retinal ganglion cell damage and neurodegeneration were markedly attenuated by MDL 72527 treatment. These results strongly implicate SMOX in diabetes-induced retinal neurodegeneration and visual dysfunction.
Comprehensive Evaluation of the Biological Properties of Surface-Modified Titanium Alloy Implants
Authors: Piszczek Piotr , Radtke Aleksandra , Ehlert Michalina , Jędrzejewski Tomasz , Sznarkowska Alicja , Sadowska Beata , Bartmański Michał , Erdoğan Yaşar Kemal , Ercan Batur , Jedrzejczyk Waldemar
Published: January 2020

An increasing interest in the fabrication of implants made of titanium and its alloys results from their capacity to be integrated into the bone system. This integration is facilitated by different modifications of the implant surface. Here, we assessed the bioactivity of amorphous titania nanoporous and nanotubular coatings (TNTs), produced by electrochemical oxidation of Ti6Al4V orthopedic implants’ surface. The chemical composition and microstructure of TNT layers was analyzed by X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). To increase their antimicrobial activity, TNT coatings were enriched with silver nanoparticles (AgNPs) with the chemical vapor deposition (CVD) method and tested against various bacterial and fungal strains for their ability to form a biofilm. The biointegrity and anti-inflammatory properties of these layers were assessed with the use of fibroblast, osteoblast, and macrophage cell lines. To assess and exclude potential genotoxicity issues of the fabricated systems, a mutation reversal test was performed (Ames Assay MPF, OECD TG 471), showing that none of the TNT coatings released mutagenic substances in long-term incubation experiments. The thorough analysis performed in this study indicates that the TNT5 and TNT5/AgNPs coatings (TNT5—the layer obtained upon applying a 5 V potential) present the most suitable physicochemical and biological properties for their potential use in the fabrication of implants for orthopedics. For this reason, their mechanical properties were measured to obtain full system characteristics.
Activated Clotting Time Monitoring during Atrial Fibrillation Catheter Ablation: Does the Anticoagulant Matter?
Authors: Martin Anne-Céline , Kyheng Maeva , Foissaud Vincent , Duhamel Alain , Marijon Eloi , Susen Sophie , Godier Anne
Published: January 2020

Atrial fibrillation (AF) catheter ablation is performed in patients receiving direct oral anticoagulants (DOACs) with intra-procedural unfractionated heparin (UFH) administration to achieve activated clotting time (ACT) at 300 s, as for vitamin K antagonist (VKA). We determined whether ACT monitoring might be transposed from VKA to DOAC-treated patients. Blood was taken from 124 patients receiving uninterrupted dabigatran, rivaroxaban, apixaban, or VKA or being untreated. DOAC concentration or INR (VKA) were measured. ACT was determined at baseline, and after spiking with UFH doses equivalent to 1000, 2500, 5000 and 10000 IU in vivo. At baseline, anticoagulants prolonged ACT differently, ACT was longer with dabigatran and shorter with apixaban despite similar concentrations. ACT strongly correlated with INR and dabigatran concentration, but not with apixaban or rivaroxaban concentrations. Moreover, UFH effects on ACT prolongation depended on the anticoagulant: dose-response curves in samples with VKA and dabigatran were parallel whereas ACT prolongation in response to UFH was significantly smaller with rivaroxaban and especially apixaban. Therefore, UFH to achieve ACT at 300 s might be transposed from VKA to uninterrupted dabigatran-treated patients but not to patients receiving FXa-inhibitors, especially apixaban. Targeting 300 s might expose to UFH overdosing and bleeding, questioning the current anticoagulation strategy.
Biomarker-Based Preoperative Risk Stratification for Patients Undergoing Non-Cardiac Surgery
Authors: Yurttas Timur , Hidvegi Reka , Filipovic Miodrag
Published: January 2020

Perioperative morbidity and mortality remains a substantial problem and is strongly associated with patients’ cardiac comorbidities. Guidelines for the cardiovascular assessment and management of patients at risk of cardiac issues while undergoing non-cardiac surgery are traditionally based on the exclusion of active or unstable cardiac conditions, determination of the risk of surgery, the functional capacity of the patient, and the presence of cardiac risk factors. In the last two decades, strong evidence showed an association between cardiac biomarkers and adverse cardiac events, with newer guidelines incorporating this knowledge. This review describes a biomarker-based risk-stratification pathway and discusses potential treatment strategies for patients suffering from postoperative myocardial injury or infarction.
Structural Health Monitoring for Advanced Composite Structures: A Review
Authors: Güemes Alfredo , Fernandez-Lopez Antonio , Pozo Angel Renato , Sierra-Pérez Julián
Published: January 2020

Condition-based maintenance refers to the installation of permanent sensors on a structure/system. By means of early fault detection, severe damage can be avoided, allowing efficient timing of maintenance works and avoiding unnecessary inspections at the same time. These are the goals for structural health monitoring (SHM). The changes caused by incipient damage on raw data collected by sensors are quite small, and are usually contaminated by noise and varying environmental factors, so the algorithms used to extract information from sensor data need to focus on sensitive damage features. The developments of SHM techniques over the last 20 years have been more related to algorithm improvements than to sensor progress, which essentially have been maintained without major conceptual changes (with regards to accelerometers, piezoelectric wafers, and fiber optic sensors). The main different SHM systems (vibration methods, strain-based fiber optics methods, guided waves, acoustic emission, and nanoparticle-doped resins) are reviewed, and the main issues to be solved are identified. Reliability is the key question, and can only be demonstrated through a probability of detection (POD) analysis. Attention has only been paid to this issue over the last ten years, but now it is a growing trend. Simulation of the SHM system is needed in order to reduce the number of experiments.
Microbial Colonization in Marine Environments: Overview of Current Knowledge and Emerging Research Topics
Authors: Caruso Gabriella
Published: January 2020

Microbial biofilms are biological structures composed of surface-attached microbial communities embedded in an extracellular polymeric matrix. In aquatic environments, the microbial colonization of submerged surfaces is a complex process involving several factors, related to both environmental conditions and to the physical-chemical nature of the substrates. Several studies have addressed this issue; however, more research is still needed on microbial biofilms in marine ecosystems. After a brief report on environmental drivers of biofilm formation, this study reviews current knowledge of microbial community attached to artificial substrates, as obtained by experiments performed on several material types deployed in temperate and extreme polar marine ecosystems. Depending on the substrate, different microbial communities were found, sometimes highlighting the occurrence of species-specificity. Future research challenges and concluding remarks are also considered. Emphasis is given to future perspectives in biofilm studies and their potential applications, related to biofouling prevention (such as cell-to-cell communication by quorum sensing or improved knowledge of drivers/signals affecting biological settlement) as well as to the potential use of microbial biofilms as sentinels of environmental changes and new candidates for bioremediation purposes.
Improved Calculation of Nonlinear Near-Bed Wave Orbital Velocity in Shallow Water: Validation against Laboratory and Field Data
Authors: Nam Pham Thanh , Staneva Joanna , Thao Nguyen Thi , Larson Magnus
Published: January 2020

A new parameterization for calculating the nonlinear near-bed wave orbital velocity in the shallow water was presented. The equations proposed by Isobe and Horikawa (1982) were modified in order to achieve more accurate predictions of the peak orbital velocities. Based on field data from Egmond Beach in the Netherlands, the correction coefficient and maximum skewness were determined as functions of the Ursell number. The obtained equations were validated against measurements from Egmond Beach, and with laboratory data from small-scale wave flume experiments at Delft University of Technology and from large-scale wave flume experiments at Delft Hydraulics. Inter-comparisons with other previously developed parameterizations were also carried out. The model simulations by the present study were in good agreement with the measurements and have been improved compared to the previous ones. For Egmond Beach, the root-mean-square errors for the peak onshore (uc) and offshore (ut) orbital velocities were approximately 21%. The relative biases were small, approximately 0.013 for uc and −0.068 for ut. The coefficient of determination was in the range between 0.64 and 0.68. For laboratory experiments, the root-mean-square errors in a range of 7.2%–24% for uc, and 7.9%–15% for ut.
A Novel Random Access Algorithm for Very High Frequency Data Exchange (VDE)
Authors: Jiang Yi , Zheng Yang , Wang Junsen
Published: January 2020

VHF Data Exchange System (VDES) is considered as an important component of the future maritime communication system by the International Maritime Organization (IMO). On the basis of the existing Automatic Identification System (AIS), VDES adds the other two higher capacity subsystems: Application Specific Message (ASM) and VHF Data Exchange (VDE). The Random Access Channel (RACH) of VDE was first introduced in the International Telecommunication Union (ITU) Recommendation M.2092-0. As the slot planning principle of RACH in VDE is by interval, which is significantly different from the continuous slot map for access algorithms in AIS, the existing slot access algorithms cannot meet the requirements of VDE. The simulation results show that the VDE slot map can reduce the normalized throughput of the existing algorithm by 39%. A novel random access algorithm called Adaptive Traffic Load Contention Resolution Diversity Slotted ALOHA (ATL-CRDSA) is proposed in this paper. The algorithm combines the load control strategy and contention resolution scheme to overcome the challenges of the new RACH of VDE. Simulation results show that ATL-CRDSA has remarkable improvement on RACH, making it very efficient and providing low latency of the packets. The insights gained from this study may be of assistance to the Media Access Control (MAC) layer design for upcoming versions of VDES standard.
Laponites® for the Recovery of 133Cs, 59Co, and 88Sr from Aqueous Solutions and Subsequent Storage: Impact of Grafted Silane Loads
Authors: Thiebault Thomas , Brendlé Jocelyne , Augé Grégoire , Limousy Lionel
Published: January 2020

In this study, silylated Laponites® (LAP) were synthetized with various loads of 3-aminopropyltriethoxysilane (APTES) to evaluate their adsorption properties of 133Cs, 59Co, and 88Sr during single-solute and competitive experiments. The increase in the initial load of APTES increased the adsorbed amount of APTES in the resulted grafted clay. The characterization of LAP-APTES exhibited a covalent binding between APTES and LAP and emphasized the adsorption sites of APTES for each tested load. In comparison with raw LAP, LAP-APTES displayed significantly higher adsorption properties of Co2+, Cs+, and Sr2+. The competitive adsorption of these three contaminants provides a deeper understanding of the affinity between adsorbate and adsorbent. Therefore, Co2+ displayed a strong and specific adsorption onto LAP-APTES. Except for Cs+, the adsorption capacity was improved with increasing the load of APTES. Finally, the desorption behavior of the three contaminants was tested in saline solutions. Cs+ and Sr2+ were significantly released especially by inorganic cations displaying the same valence. Conversely, desorption of Co2+ was very low whatever the saline solution. LAP-APTES, therefore, presented suitable adsorption properties for the removal of radionuclides especially for Co2+, making this material suitable to improve the decontamination of radioactive wastewaters.