bluuebunny/crossref_metadata_2025 huggingface dataset:
Designing a Waterless Toilet Prototype for Reusable Energy Using a User-Centered Approach and Interviews
Authors: Lee Hyun-Kyung
Published: March 2019

User-oriented community engagement can reveal insights into ways of improving a community and solving complex public issues, such as natural resource scarcity. This study describes the early process of co-designing a novel, waterless toilet to respond to the water scarcity problem in the Republic of Korea. It presents how we designed a toilet focusing on three factors—a sanitization function, an ergonomic posture, and clean aesthetics—by conducting focus group interviews as part of a user engagement approach to understand what community users want from a toilet and ways of improving their toilet experiences. The results not only supported the development of an experiential service design project to raise community awareness of water scarcity but also supported scientists and engineers in experimenting with and developing new technologies by collaborating closely with designers.
Application of Sliding Rehabilitation Machine in Patients with Severe Cognitive Dysfunction after Stroke
Authors: Kim Ae Ryoung , Lee Yang-Soo
Published: March 2019

A sliding rehabilitation machine (SRM) allows closed kinetic chain exercises of the hip, knee, and ankle. This study aimed to explore the feasibility of SRM training when included in an intensive rehabilitation program for post-stroke patients with severe cognitive dysfunction. The study design is a retrospective analysis. Patients who were admitted for inpatient rehabilitation after stroke with subsequent severe cognitive dysfunction were enrolled. Training with the SRM was conducted twice a day from Monday to Friday during hospitalization for three to four weeks. The number of sessions and the occurrence of side effects were documented daily. The SRM’s inclination angle, Berg Balance Scale (BBS), manual muscle test (MMT), and Korean version of the Modified Barthel Index (K-MBI) were documented upon admission and discharge. In 30 patients, 1736 sessions were performed from a total of 1754 scheduled sessions of SRM training. The performance rate was 98.9%, and there were no serious side effects. Transient side effects such as dizziness, nausea, and knee pain were observed in a few cases. At discharge, patients showed improvement in the SRM inclination angle, BBS, MMT, and K-MBI. This study shows that the use of the SRM for intensive muscle strengthening is readily applicable to patients who have had a stroke with severe cognitive dysfunction.
The Virial Effect—Applications for SF6 and CH4 Thermal Plasmas
Authors: Harry Solo Andriniaina , Freton Pierre , Gonzalez Jean-Jacques
Published: March 2019

A tool based on the mass action law was developed to calculate plasma compositions and thermodynamic properties for pure gases and mixtures, assuming a local thermodynamic equilibrium for pressures of up to 300 bar. The collection of the data that was necessary for tool calculation was automated by another tool that was written using Python, and the formats for the model were adapted directly from the NIST and JANAF websites. In order to calculate the plasma compositions for high pressures, virial correction was introduced. The influences of the parameters that were chosen to calculate the Lennard–Jones (12-6) potential were studied. The results at high pressure show the importance of virial correction for low temperatures and the dependence of the dataset used. Experimental data are necessary to determine a good dataset, and to obtain interaction potential. However, the data available in the literature were not always provided, so they are not well-adapted to a large pressure range. Due to this lack, the formulation provided by L. I. Stiel and G. Thodos (Journal of Chemical and Engineering Data, vol. 7, 1962, p. 234–236) is a good alternative when the considered pressure is not close to the critical point. The results may depend strongly on the system studied: examples using SF6 and CH4 plasma compositions are given at high pressure.
Evaluating the Effects of Urbanization Evolution on Air Temperature Trends Using Nightlight Satellite Data
Authors: Paranunzio Roberta , Ceola Serena , Laio Francesco , Montanari Alberto
Published: March 2019

Confounding factors like urbanization and land-use change could introduce uncertainty to the estimation of global temperature trends related to climate change. In this work, we introduce a new way to investigate the nexus between temporal trends of temperature and urbanization data at the global scale in the period from 1992 to 2013. We analyze air temperature data recorded from more than 5000 weather stations worldwide and nightlight satellite measurements as a proxy for urbanization. By means of a range of statistical methods, our results quantify and outline that the temporal evolution of urbanization affects temperature trends at multiple spatial scales with significant differences at regional and continental scales. A statistically significant agreement in temperature and nightlight trends is detected, especially in low and middle-income regions, where urbanization is rapidly growing. Conversely, in continents such as Europe and North America, increases in temperature trends are typically detected along with non-significant nightlight trends.
Air Quality in Ningbo and Transport Trajectory Characteristics of Primary Pollutants in Autumn and Winter
Authors: Tu Xiaoping , Lu Yun , Yao Risheng , Zhu Jiamin
Published: March 2019

By using meteorology and pollution observation data from Zhejiang province, and data from the National Centers for Environmental Prediction’s Global Data Assimilation System from 1 June 2013, to 31 May 2016, we analyzed air quality characteristics in Ningbo and applied the HYSPLIT model to do backward trajectory clustering statistics for pollution cases of moderate, heavy and severe (henceforth referred to as moderate-and-above) levels. The results indicated that the percentage of moderate-and-above pollution was approximately 6%, which mostly occurred from November to February, with the primary pollutant being particulate matter with a diameter of ≤2.5 μm; Moderate-and-above pollution was mainly caused by pollutants from three types of trajectories (type mx, type 1, and type 2), with type 2 differing significantly from types 1 and mx. Type 2 occurred in stable boundary layers, whereas types mx and 1 occurred in unstable and conditionally unstable layers respectively. These three trajectory types were all related to cold air, but type 2 was weaker than the other two. Analysis of typical cases of various pollution types revealed that a heavy pollution outbreak was due to continuous superposition of pollutants. The input particles most likely originated from the northwest. The upstream situation was the focus of investigation to assist in local pollution forecasting.
The Volume-Regulated Anion Channel in Glioblastoma
Authors: Caramia Martino , Sforna Luigi , Franciolini Fabio , Catacuzzeno Luigi
Published: March 2019

Malignancy of glioblastoma multiforme (GBM), the most common and aggressive form of human brain tumor, strongly depends on its enhanced cell invasion and death evasion which make surgery and accompanying therapies highly ineffective. Several ion channels that regulate membrane potential, cytosolic Ca2+ concentration and cell volume in GBM cells play significant roles in sustaining these processes. Among them, the volume-regulated anion channel (VRAC), which mediates the swelling-activated chloride current (IClswell) and is highly expressed in GBM cells, arguably plays a major role. VRAC is primarily involved in reestablishing the original cell volume that may be lost under several physiopathological conditions, but also in sustaining the shape and cell volume changes needed for cell migration and proliferation. While experimentally VRAC is activated by exposing cells to hypotonic solutions that cause the increase of cell volume, in vivo it is thought to be controlled by several different stimuli and modulators. In this review we focus on our recent work showing that two conditions normally occurring in pathological GBM tissues, namely high serum levels and severe hypoxia, were both able to activate VRAC, and their activation was found to promote cell migration and resistance to cell death, both features enhancing GBM malignancy. Also, the fact that the signal transduction pathway leading to VRAC activation appears to involve GBM specific intracellular components, such as diacylglicerol kinase and phosphatidic acid, reportedly not involved in the activation of VRAC in healthy tissues, is a relevant finding. Based on these observations and the impact of VRAC in the physiopathology of GBM, targeting this channel or its intracellular regulators may represent an effective strategy to contrast this lethal tumor.
Ball Milling-Assisted Synthesis of Ultrasmall Ruthenium Phosphide for Efficient Hydrogen Evolution Reaction
Authors: Liu Xiaofei , Guo Yanglong , Zhan Wangcheng , Jin Tian (Leo)
Published: March 2019

The development of scalable hydrogen production technology to produce hydrogen economically and in an environmentally friendly way is particularly important. The hydrogen evolution reaction (HER) is a clean, renewable, and potentially cost-effective pathway to produce hydrogen, but it requires the use of a favorable electrocatalyst which can generate hydrogen with minimal overpotential for practical applications. Up to now, ruthenium phosphide Ru2P has been considered as a high-performance electrocatalyst for the HER. However, a tedious post-treatment method as well as large consumption of solvents in conventional solution-based synthesis still limits the scalable production of Ru2P electrocatalysts in practical applications. In this study, we report a facile and cost-effective strategy to controllably synthesize uniform ultrasmall Ru2P nanoparticles embedded in carbon for highly efficient HER. The key to our success lies in the use of a solid-state ball milling-assisted technique, which overcomes the drawbacks of the complicated post-treatment procedure and large solvent consumption compared with solution-based synthesis. The obtained electrocatalyst exhibits excellent Pt-like HER performance with a small overpotential of 36 mV at current density of 10 mA cm−2 in 1 M KOH, providing new opportunities for the fabrication of highly efficient HER electrocatalysts in real-world applications.
Application of Heterogeneous Catalytic Ozonation for Refractory Organics in Wastewater
Authors: Wang Bing , Zhang Huan , Wang Feifei , Xiong Xingaoyuan , Tian Kun , Sun Yubo , Yu Tingting
Published: March 2019

Catalytic ozonation is believed to belong to advanced oxidation processes (AOPs). Over the past decades, heterogeneous catalytic ozonation has received remarkable attention as an effective process for the degradation of refractory organics in wastewater, which can overcome some disadvantages of ozonation alone. Metal oxides, metals, and metal oxides supported on oxides, minerals modified with metals, and carbon materials are widely used as catalysts in heterogeneous catalytic ozonation processes due to their excellent catalytic ability. An understanding of the application can provide theoretical support for selecting suitable catalysts aimed at different kinds of wastewater to obtain higher pollutant removal efficiency. Therefore, the main objective of this review article is to provide a summary of the accomplishments concerning catalytic ozonation to point to the major directions for choosing the catalysts in catalytic ozonation in the future.
Sensors Based on Amino Group Surface-Modified CNTs
Authors: Boroznina Natalia , Zaporotskova Irina , Boroznin Sergey , Dryuchkov Evgeniy
Published: March 2019

This article discusses the possibility of the fabrication of a highly sensitive sensor based on single-walled carbon nanotubes surface modified with functional amino groups (-NH2). The sensor potential for detection of alkali (sodium, lithium, and potassium) metals was investigated. The results of computer simulation of the interaction process between the sensor and an arbitrary surface of the modified tube containing atoms of the studied metals are presented. The calculations were carried out within the framework of the density functional theory (DFT) method using the molecular cluster model. It has been proved that surface-modified ammonium carbon nanotubes show high sensitivity for the metal atoms under study.
Japanese Systems to Support Inclusive Education for Children Requiring Medical Care, Current Status of Such Support, and Related Challenges—Based on the Results of Surveys Involving Departments of Education Supporting their Enrollment in General Schools
Authors: Yamamoto Tomoko , Moriwaki Koichi
Published: March 2019

Based on the results of our surveys involving several municipal departments of education that support the enrollment of children requiring medical care in general schools, this report describes Japanese systems to support inclusive education for these children, the current status of such support, and related challenges. The municipal departments of education that systematically support inclusive education for children requiring medical care began to promote such education in their communities before the initiation of nationwide enrollment support for the children. In addition, their sections in charge of enrollment support also manage affairs related to human rights education, rather than general affairs for special support and education. Such a variation in the sections in charge resulted in differences in the purposes of support. Further nationwide surveys should be conducted to develop universal design principles and comprehensively support inclusive education for children requiring medical care.
Combustion Analysis of Homogeneous Charge Compression Ignition in a Motorcycle Engine Using a Dual-Fuel with Exhaust Gas Recirculation
Authors: Wu Yuh-Yih , Jang Ching-Tzan
Published: March 2019

Exhaust emissions from the large population of motorcycles are a major issue in Asian countries. The regulation of exhaust emissions is therefore becoming increasingly stringent, with those relating to nitrogen oxides (NOx) the most difficult to pass. The homogeneous charge compression ignition (HCCI) has special combustion characteristics and hence produces low NOx emissions and exhibits high thermal efficiency. This study developed an HCCI system for a 150 cc motorcycle engine. The target engine was modified using a dual-fuel of dimethyl ether (DME) and gasoline with exhaust gas recirculation (EGR). It was tested at 2000–4000 rpm and the analysis was focused on 2000 rpm. The DME was supplied continuously at an injection pressure of 1.5 kg/cm2. The gasoline injection rate was adjusted at a pressure of 2.5 kg/cm2. A brake-specific fuel consumption of <250 g/kW·h was achieved under a condition of air–fuel equivalence ratio (λ) < 2 and an EGR of 25%. The nitric oxide concentration was too low to measure. The brake mean effective pressure (BMEP) increased by 65.8% from 2.93 to 4.86 bar when the EGR was 0% to 25%. The combustion efficiency was close to 100% when the BMEP was >3 bar.
Agent-Based Modeling of a Thermal Energy Transition in the Built Environment
Authors: Nava Guerrero Graciela del Carmen , Korevaar Gijsbert , Hansen Helle Hvid , Lukszo Zofia
Published: March 2019

To reduce greenhouse gas emissions to 80% below 1990 levels by 2050, an energy transition is taking place in the European Union. Achieving these targets requires changes in the heating and cooling sector (H&C). Designing and implementing this energy transition is not trivial, as technology, actors, and institutions interact in complex ways. We provide an illustrative example of the development and use of an agent-based model (ABM) for thermal energy transitions in the built environment, from the perspective of sociotechnical systems (STS) and complex adaptive systems (CAS). In our illustrative example, we studied the transition of a simplified residential neighborhood to heating without natural gas. We used the ABM to explore socioeconomic conditions that could support the neighborhoods’ transition over 20 years while meeting the neighborhoods’ heat demand. Our illustrative example showed that through the use of STS, CAS, and an ABM, we can account for technology, actors, institutions, and their interactions while designing for thermal energy transitions in the built environment.
Multi-Level Open End Windings Multi-Motor Drives
Authors: Foti Salvatore , Testa Antonio , De Caro Salvatore , Scimone Tommaso , Scelba Giacomo , Scarcella Giuseppe
Published: March 2019

A multi-level open-end winding converter topology for multiple-motor drives is presented featuring a main multi-level inverter processing the power delivered to the motors and an active filter based on an auxiliary two-level inverter. The main inverter operates at the fundamental frequency in order to achieve low switching power losses, while the active filter is Pulse Width Modulation (PWM) operated to suitably shape the motor currents. The proposed configuration features less phase current distortion than conventional multi-level inverters operating at the fundamental frequency, while achieving a higher efficiency compared to PWM multi-level inverters. Experimental results confirm the effectiveness of such a configuration on both multiple motors-single converter and multiple motor-multiple converter drives.
Study of Generalized Interaction Wake Models Systems with ELM Variation for Off-Shore Wind Farms
Authors: Li Mingcan , Xiao Hanbin , Pan Lin , Xu Chengjun
Published: March 2019

This paper reports a novel frandsen generalized wake model and its variation model-frandsen generalized normal distribution wake model for off-shore wind farms. Two different new wake models in off-shore wind farms have been studied comparatively. Their characteristics have been analyzed through mathematical modeling and derivation. Meanwhile, simulation experiments show that the proposed two new wake models have different properties. Furthermore, the distributions of wind speed and wind direction are modeled by the statistical methods and Extreme Learning Machine through the off-shore wind farms of Yangshan Deepwater Harbor in the Port of Shanghai, China. In addition, the data of wind energy are provided to verify and test the correctness and effectiveness of the proposed two models. Wind power has been demonstrated by wind rose and wind resources with real-time data. These techniques contribute to enhance planning, utilization and exploitation for wind power of off-shore wind farms.
An Optimum Enthalpy Approach for Melting and Solidification with Volume Change
Authors: Faden Moritz , König-Haagen Andreas , Brüggemann Dieter
Published: March 2019

Classical numerical methods for solving solid–liquid phase change assume a constant density upon melting or solidification and are not efficient when applied to phase change with volume expansion or shrinkage. However, solid–liquid phase change is accompanied by a volume change and an appropriate numerical method must take this into account. Therefore, an efficient algorithm for solid–liquid phase change with a density change is presented. Its performance for a one-dimensional solidification problem and for the quasi two-dimensional melting of octadecane in a cubic cavity was tested. The new algorithm requires less than 1/9 of the iterations compared to the source based method in one dimension and less than 1/7 in two dimensions. Moreover, the new method is validated against PIV measurements from the literature. A conjugate heat transfer simulation, which includes parts of the experimental setup, shows that parasitic heat fluxes can significantly alter the shape of the phase front near the bottom wall.
Cyber Security Threat Modeling for Supply Chain Organizational Environments
Authors: Yeboah-Ofori Abel , Islam Shareeful
Published: March 2019

Cyber security in a supply chain (SC) provides an organization the secure network facilities to meet its overall business objectives. The integration of technologies has improved business processes, increased production speed, and reduced distribution costs. However, the increased interdependencies among various supply chain stakeholders have brought many challenges including lack of third party audit mechanisms and cascading cyber threats. This has led to attacks such as the manipulation of the design specifications, alterations, and manipulation during distribution. The aim of this paper is to investigate and understand supply chain threats. In particular, the paper contributes towards modeling and analyzing CSC attacks and cyber threat reporting among supply chain stakeholders. We consider concepts such as goal, actor, attack, TTP, and threat actor relevant to the supply chain, threat model, and requirements domain, and modeled the attack using the widely known STIX threat model. The proposed model was analyzed using a running example of a smart grid case study and an algorithm to model the attack. A discrete probability method for calculating the conditional probabilities was used to determine the attack propagation and cascading effects, and the results showed that our approach effectively analyzed the threats. We have recommended a list of CSC controls to improve the overall security of the studied organization.
A Cache Placement Strategy with Energy Consumption Optimization in Information-Centric Networking
Authors: Zheng Xin , Wang Gaocai , Zhao Qifei
Published: March 2019

With the rapid development of cloud computing, big data, and Internet of Things, Information-Centric Networking (ICN) has become a novel hotspot in the field of future Internet architecture, and new problems have appeared. In particular, more researchers consider information naming, delivery, mobility, and security in ICN. In this paper, we mainly focus on the cache placement strategy and network performance of ICN, and propose a cache placement strategy with energy consumption optimization. In order to optimize the energy consumption of the ICN, the best cache placement node is selected from the view of users. First of all, the distance sequence of different nodes arriving at each user is obtained in terms of detection results of network distribution channels, and the corresponding energy consumption of information distribution is obtained from the distance sequence. Secondly, the reward function of the cache node is derived using two factors of energy consumption, which includes the additional energy consumed by the change of the cache node and the energy consumption of the content distribution. Finally, we construct the optimal stopping theory problem to solve the maximum expected energy saving. In simulations, we give the comparison results of energy savings, caching benefit, and delivery success rate. The results show that the strategy proposed by this paper has higher delivery success rate and lower energy consumption than other strategies.
Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains
Authors: Oldach Phoebe , Nieduszynski Conrad A.
Published: March 2019

3D genome organization is strongly predictive of DNA replication timing in mammalian cells. This work tested the extent to which loop-based genome architecture acts as a regulatory unit of replication timing by using an auxin-inducible system for acute cohesin ablation. Cohesin ablation in a population of cells in asynchronous culture was shown not to disrupt patterns of replication timing as assayed by replication sequencing (RepliSeq) or BrdU-focus microscopy. Furthermore, cohesin ablation prior to S phase entry in synchronized cells was similarly shown to not impact replication timing patterns. These results suggest that cohesin-mediated genome architecture is not required for the execution of replication timing patterns in S phase, nor for the establishment of replication timing domains in G1.
The Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Is Critical for Abiotic Stress Response in Wheat
Authors: Li Xixi , Wei Wenjie , Li Fangfang , Zhang Lin , Deng Xia , Liu Ying , Yang Shushen
Published: March 2019

Plastidial glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GAPCp) are ubiquitous proteins that play pivotal roles in plant metabolism and are involved in stress response. However, the mechanism of GAPCp’s function in plant stress resistance process remains unclear. Here we isolated, identified, and characterized the TaGAPCp1 gene from Chinese Spring wheat for further investigation. Subcellular localization assay indicated that the TaGAPCp1 protein was localized in the plastid of tobacco (Nicotiana tobacum) protoplast. In addition, quantitative real-time PCR (qRT-PCR) unraveled that the expression of TaGAPCp1 (GenBank: MF477938.1) was evidently induced by osmotic stress and abscisic acid (ABA). This experiment also screened its interaction protein, cytochrome b6-f complex iron sulfite subunit (Cyt b6f), from the wheat cDNA library using TaGAPCp1 protein as a bait via the yeast two-hybrid system (Y2H) and the interaction between Cyt b6f and TaGAPCp1 was verified by bimolecular fluorescence complementation assay (BiFC). Moreover, H2O2 could also be used as a signal molecule to participate in the process of Cyt b6f response to abiotic stress. Subsequently, we found that the chlorophyll content in OE-TaGAPCp1 plants was significantly higher than that in wild type (WT) plants. In conclusion, our data revealed that TaGAPCp1 plays an important role in abiotic stress response in wheat and this stress resistance process may be completed by H2O2-mediated ABA signaling pathway.
Endothelial Progenitor Cells as Pathogenetic and Diagnostic Factors, and Potential Targets for GLP-1 in Combination with Metabolic Syndrome and Chronic Obstructive Pulmonary Disease
Authors: Skurikhin Evgenii , Pershina Olga , Pakhomova Angelina , Pan Edgar , Krupin Vyacheslav , Ermakova Natalia , Vaizova Olga , Pozdeeva Anna , Zhukova Mariia , Skurikhina Viktoriia , Grimm Wolf-Dieter , Dygai Alexander
Published: March 2019

In clinical practice, there are patients with a combination of metabolic syndrome (MS) and chronic obstructive pulmonary disease (COPD). The pathological mechanisms linking MS and COPD are largely unknown. It remains unclear whether the effect of MS (possible obesity) has a major impact on the progression of COPD. This complicates the development of effective approaches for the treatment of patients with a diagnosis of MS and COPD. Experiments were performed on female C57BL/6 mice. Introduction of monosodium glutamate and extract of cigarette smoke was modeled to simulate the combined pathology of lipid disorders and emphysema. Biological effects of glucagon-like peptide 1 (GLP-1) and GLP-1 on endothelial progenitor cells (EPC) in vitro and in vivo were evaluated. Histological, immunohistochemical methods, biochemical methods, cytometric analysis of markers identifying EPC were used in the study. The CD31+ endothelial cells in vitro evaluation was produced by Flow Cytometry and Image Processing of each well with a Cytation™ 3. GLP-1 reduces the area of emphysema and increases the number of CD31+ endothelial cells in the lungs of mice in conditions of dyslipidemia and damage to alveolar tissue of cigarette smoke extract. The regenerative effects of GLP-1 are caused by a decrease in inflammation, a positive effect on lipid metabolism and glucose metabolism. EPC are proposed as pathogenetic and diagnostic markers of endothelial disorders in combination of MS with COPD. Based on GLP-1, it is proposed to create a drug to stimulate the regeneration of endothelium damaged in MS and COPD.
Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust
Authors: Zhang Hong , Fu Ying , Guo Huan , Zhang Lu , Wang Changyou , Song Weining , Yan Zhaogui , Wang Yajuan , Ji Wanquan
Published: March 2019

Stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is an important fungal foliar disease of wheat (Triticum aestivum). To study the mechanism underlying the defense of wheat to Pst, we used the next-generation sequencing and isobaric tags for relative and absolute quantification (iTRAQ) technologies to generate transcriptomic and proteomic profiles of seedling leaves at different stages under conditions of pathogen stress. By conducting comparative proteomic analysis using iTRAQ, we identified 2050, 2190, and 2258 differentially accumulated protein species at 24, 48, and 72 h post-inoculation (hpi). Using pairwise comparisons and weighted gene co-expression network analysis (WGCNA) of the transcriptome, we identified a stress stage-specific module enriching in transcription regulator genes. The homologs of several regulators, including splicing and transcription factors, were similarly identified as hub genes operating in the Pst-induced response network. Moreover, the Hsp70 protein were predicted as a key point in protein–protein interaction (PPI) networks from STRING database. Taking the genetics resistance gene locus into consideration, we identified 32 induced proteins in chromosome 1BS as potential candidates involved in Pst resistance. This study indicated that the transcriptional regulation model plays an important role in activating resistance-related genes in wheat responding to Pst stress.
Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds
Authors: Wang Jing , Ren Qiaoling , Hua Liushuai , Chen Junfeng , Zhang Jiaqing , Bai Hongjie , Li Haili , Xu Bin , Shi Zhihai , Cao Hai , Xing Baosong , Bai Xianxiao
Published: March 2019

Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc × (Landrace × Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and | log2FoldChange | >1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.
Hierarchical Clustering Approach for Selecting Representative Skylines
Authors: Battulga Lkhagvadorj , Nasridinov Aziz
Published: March 2019

Recently, the skyline query has attracted interest in a wide range of applications from recommendation systems to computer networks. The skyline query is useful to obtain the dominant data points from the given dataset. In the low-dimensional dataset, the skyline query may return a small number of skyline points. However, as the dimensionality of the dataset increases, the number of skyline points also increases. In other words, depending on the data distribution and dimensionality, most of the data points may become skyline points. With the emergence of big data applications, where the data distribution and dimensionality are a significant problem, obtaining representative skyline points among resulting skyline points is necessary. There have been several methods that focused on extracting representative skyline points with various success. However, existing methods have a problem of re-computation when the global threshold changes. Moreover, in certain cases, the resulting representative skyline points may not satisfy a user with multiple preferences. Thus, in this paper, we propose a new representative skyline query processing method, called representative skyline cluster (RSC), which solves the problems of the existing methods. Our method utilizes the hierarchical agglomerative clustering method to find the exact representative skyline points, which enable us to reduce the re-computation time significantly. We show the superiority of our proposed method over the existing state-of-the-art methods with various types of experiments.
Word Sense Disambiguation Studio: A Flexible System for WSD Feature Extraction
Authors: Agre Gennady , Petrov Daniel , Keskinova Simona
Published: March 2019

The paper presents a flexible system for extracting features and creating training and test examples for solving the all-words sense disambiguation (WSD) task. The system allows integrating word and sense embeddings as part of an example description. The system possesses two unique features distinguishing it from all similar WSD systems—the ability to construct a special compressed representation for word embeddings and the ability to construct training and test sets of examples with different data granularity. The first feature allows generation of data sets with quite small dimensionality, which can be used for training highly accurate classifiers of different types. The second feature allows generating sets of examples that can be used for training classifiers specialized in disambiguating a concrete word, words belonging to the same part-of-speech (POS) category or all open class words. Intensive experimentation has shown that classifiers trained on examples created by the system outperform the standard baselines for measuring the behaviour of all-words WSD classifiers.
Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study
Authors: Sheu Chau-Chyun , Chang Wei-An , Tsai Ming-Ju , Liao Ssu-Hui , Chong Inn-Wen , Kuo Po-Lin
Published: March 2019

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease. Therapeutic options for IPF remain limited. Nintedanib, a tyrosine kinase inhibitor approved for IPF treatment, is known to inhibit fibroblasts proliferation, migration and transformation to myofibroblasts. However, how nintedanib changes gene regulations in IPF has never been systematically investigated. We conducted a next-generation sequencing and bioinformatics study to evaluate the changes of mRNA and miRNA profiles in IPF fibroblasts treated with 2 µM and 4 µM nintedanib, compared to those without treatment. We identified 157 upregulated and 151 downregulated genes and used STRING and DAVID databases for analysis of protein–protein interactions, biological pathways, and molecular functions. We found strong protein–protein interactions within these dysregulated genes, mostly involved in the pathways of cell cycle and mitotic cell cycle. We also discovered 13 potential miRNA–mRNA interactions associated with nintedanib treatment. After validation using miRDB, TargetScan, and RT-qPCR, we identified 4 downregulated genes (DDX11, E2F1, NPTX1, and PLXNA4) which might be repressed by the upregulated hsa-miR-486-3p. According to the proposed functions of DDX11, E2F1, and PLXNA4 reported in previous studies, these gene expression changes together might contribute to decreased proliferation of fibroblasts and decreased angiogenesis in the microenvironment of IPF. Our findings need further studies to confirm.
Exposure to a Standardized Catastrophic Scenario in Virtual Reality or a Personalized Scenario in Imagination for Generalized Anxiety Disorder
Authors: Guitard Tanya , Bouchard Stéphane , Bélanger Claude , Berthiaume Maxine
Published: March 2019

The cognitive behavioral treatment of generalized anxiety disorder (GAD) often involves exposing patients to a catastrophic scenario depicting their most feared worry. The aim of this study was to examine whether a standardized scenario recreated in virtual reality (VR) would elicit anxiety and negative affect and how it compared to the traditional method of imagining a personalized catastrophic scenario. A sample of 28 participants were first exposed to a neutral non-catastrophic scenario and then to a personalized scenario in imagination or a standardized virtual scenario presented in a counterbalanced order. The participants completed questionnaires before and after each immersion. The results suggest that the standardized virtual scenario induced significant anxiety. No difference was found when comparing exposure to the standardized scenario in VR and exposure to the personalized scenario in imagination. These findings were specific to anxiety and not to the broader measure of negative affect. Individual differences in susceptibility to feel present in VR was a significant predictor of increase in anxiety and negative affect. Future research could use these scenarios to conduct a randomized control trial to test the efficacy and cost/benefits of using VR in the treatment of GAD.
Concerns and Expectations of Risk-Reducing Surgery in Women with Hereditary Breast and Ovarian Cancer Syndrome
Authors: Modaffari Paola , Ponzone Riccardo , Ferrari Alberta , Cipullo Isabella , Liberale Viola , D’Alonzo Marta , Maggiorotto Furio , Biglia Nicoletta
Published: March 2019

Hereditary Breast and Ovarian Cancer syndrome (HBOC) carriers face complex decisions, which might affect their fertility and body image. Using an anonymous 40-items questionnaire we evaluated the expectations and concerns about Risk-Reducing Surgery (RRS) in 204 carriers. Participants are well-informed about the options to manage cancer risk, and women with previous cancer are more concerned with screening failure. Satisfaction with RR Mastectomy is high, even if many carriers are unsatisfied with reconstructed breast feel and nipple-areola complex tactile sensation and those with previous breast cancer report a change in their sexual habits. The decrease of libido and vaginal dryness are the most complained symptoms after RR Salpingo-Oophorectomy. Nevertheless, most carriers would choose RRS again, due to cancer risk or screening-related stress reduction. Women who deferred RRS are more afraid of menopausal symptoms and cancer risk than those who had undergone or declined surgery. Women who declined RRS feel well-informed and trust screening procedures. In conclusion, HBOC carriers consider themselves well-informed and able to choose the best option for their condition, would choose RRS again because of cancer risk and screening-related stress reduction, and those who delay RRS face a higher preoperative level of concern and need support.
How Far Does the European Union Reach? Foreign Land Acquisitions and the Boundaries of Political Communities
Authors: Menge Torsten
Published: March 2019

The recent global surge in large-scale foreign land acquisitions marks a radical transformation of the global economic and political landscape. Since land that attracts capital often becomes the site of expulsions and displacement, it also leads to new forms of migration. In this paper, I explore this connection from the perspective of a political philosopher. I argue that changes in global land governance unsettle the congruence of political community and bounded territory that we often take for granted. As a case study, I discuss the European Union’s Renewable Energy Directive as a significant driver of foreign land acquisitions. Using its global power, the European Union (EU) is effectively governing land far outside of its international borders and with it the people who live on this land or are expelled from it. As a result, EU citizens ought to consider such people fellow members of their political community. This has implications for normative debates about immigration and, in particular, for arguments that appeal to collective self-determination to justify a right of political communities to exclude newcomers. The political community to which EU citizens belong reaches far beyond the EU’s official borders.
Novel Bi-Functional 14-mer Peptides with Both Ovarian Carcinoma Cells Targeting and Magnetic Fe3O4 Nanoparticles Affinity
Authors: Li Yueting , Yin Guangfu , Pu Ximing , Chen Xianchun , Liao Xiaoming , Huang Zhongbing
Published: March 2019

Fe3O4 magnetic nanoparticles (Fe3O4-MNPs) have attracted much interest for their potential medical applications due to their desirable magnetic properties. However, their potential cytotoxicity, high RES clearance in circulation, and nonspecific distribution in tissue might be the main obstacles in practice. In the present study, a novel bi-functional 14-mer peptide with both ovarian carcinoma cells targeting and magnetic Fe3O4 nanoparticles affinity was designed and synthesized, and then a facile and effective modification method was developed to bestow the Fe3O4-MNPs with tumor-targeting capability via modification, using the bi-functional peptides. First, on the basis of a tumor-targeting 7-mer peptide QQTNWSL (Q-L) and another Fe3O4-MNPs-targeting 7-mer peptide TVNFKLY (T-Y)—screened by phage-displayed peptide libraries—two bi-functional 14-mer peptides sequenced as LSWNTQQ-YLKFNVT (abbreviated as LQ-YT) and QQTNWSL-YLKFNVT (QL-YT) were synthesized through combining the Q-L peptide and T-Y peptide in predetermined configurations. Their specificity for bonding with A2780 tumor cells and affinity for Fe3O4-MNPs were verified. Then the bi-functional 14-mer peptides were applied to modify the Fe3O4-MNPs. Results showed that both bi-functional 14-mer peptides could be conjugated to the Fe3O4-MNPs surface with high affinity. Immunofluorescence and Prussian blue staining assays indicated that the LQ-YT-modified Fe3O4-MNPs could specifically bond to A2780 tumor cells. In addition to our findings suggesting that more β-turns and random coils are conducive to increasing polypeptide surface area for binding and exposing the target group and bonding sites on LQ-YT to external targets, we demonstrated that the bi-functional 14-mer peptide has affinity for Fe3O4-MNPs, and that Fe3O4-MNPs, which was modified with a 14-mer peptide, could be bestowed with a targeting affinity for ovarian carcinoma cells.
Development of a Mucoadhesive and an in Situ Gelling Formulation Based on κ-Carrageenan for Application on Oral Mucosa and Esophagus Walls. II. Loading of a Bioactive Hydroalcoholic Extract
Authors: Vigani Barbara , Rossi Silvia , Gentile Matteo , Sandri Giuseppina , Bonferoni Maria Cristina , Cavalloro Valeria , Martino Emanuela , Collina Simona , Ferrari Franca
Published: March 2019

The aim of the present work was to load a Hibiscus sabdariffa (HS) hydroalcoholic extract into in situ gelling formulations for the treatment of oral mucositis and esophagitis. Such formulations, selected as the most promising options in a previous work of ours, were composed by κ-carrageenan (κ-CG), a sulfated marine polymer able to gelify in presence of saliva ions, hydroxypropyl cellulose (HPC), used as mucoadhesive agent, and CaCl2, salt able to enhance the interaction κ-CG/saliva ions. HS extract, which is rich in phytochemicals such as polyphenols, polysaccharides and organic acids, was selected due to its antioxidant and anti-inflammatory properties. For HS extraction, three different methodologies (maceration, Ultrasound Assisted Extraction (UAE) and Microwave Assisted Extraction (MAE)) were compared in terms of extraction yield and extract antioxidant activity, revealing that MAE was the best procedure. Rheological and mucoadhesive properties of HS-loaded formulations were investigated. Such formulations were characterized by a low viscosity at 25 °C, guaranteeing an easy administration, a proper in situ gelation behavior and marked elastic and mucoadhesive properties at 37 °C, functional to a protective action towards the damaged mucosa. Finally, the biocompatibility and the proliferative effect of HS-loaded formulations, as well as their antioxidant and anti-inflammatory properties, were proved in vitro on human dermal fibroblasts.
Metabolomics and Communication Skills Development in Children; Evidence from the Ages and Stages Questionnaire
Authors: Kelly Rachel S. , Boulin Adrianna , Laranjo Nancy , Lee-Sarwar Kathleen , Chu Su H. , Yadama Aishwarya P. , Carey Vincent , Litonjua Augusto A. , Lasky-Su Jessica , Weiss Scott T.
Published: March 2019

We hypothesized metabolomic profiling could be utilized to identify children who scored poorly on the communication component of the Ages and Stages Questionnaire (ASQ); which assesses development in childhood, and to provide candidate biomarkers for autism spectrum disorders (ASD). In a population of three-year-old children, 15 plasma metabolites, were significantly (p < 0.05) different between children who were categorized as having communication skills that were “on schedule” (n = 365 (90.6%)) as compared to those “requiring further monitoring/evaluation” (n = 38 (9.4%)) according to multivariable regression models. Five of these metabolites, including three endocannabinoids, were also dysregulated at age one (n = 204 “on schedule”, n = 24 “further monitoring/evaluation”) in the same children. Stool metabolomic profiling identified 11 significant metabolites. Both the plasma and stool results implicated a role for tryptophan and tyrosine metabolism; in particular, higher levels of N-formylanthranilic acid were associated with an improved communication score in both biosample types. A model based on the significant plasma metabolites demonstrated high sensitivity (88.9%) and specificity (84.5%) for the prediction of autism by age 8. These results provide evidence that ASQ communication score and metabolomic profiling of plasma and/or stool may provide alternative approaches for early diagnosis of ASD, as well as insights into the pathobiology of these conditions.
A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics
Authors: Considine Elizabeth C. , Salek Reza M.
Published: March 2019

Despite the proposal of minimum reporting guidelines for metabolomics over a decade ago, reporting on the data analysis step in metabolomics studies has been shown to be unclear and incomplete. Major omissions and a lack of logical flow render the data analysis’ sections in metabolomics studies impossible to follow, and therefore replicate or even imitate. Here, we propose possible reasons why the original reporting guidelines have had poor adherence and present an approach to improve their uptake. We present in this paper an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pre-treatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al). These minimum requirements are presented in the format of a questionnaire checklist in an R markdown template file. The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would be open to user feedback, modification and updating by the metabolomics community via GitHub.
An UPLC-MS/MS Assay to Measure Glutathione as Marker for Oxidative Stress in Cultured Cells
Authors: Herzog Katharina , IJlst Lodewijk , van Cruchten Arno G. , van Roermund Carlo W.T. , Kulik Wim , Wanders Ronald J. A. , Waterham Hans R.
Published: March 2019

Oxidative stress plays a role in the onset and progression of a number of diseases, such as Alzheimer’s disease, diabetes and cancer, as well as ageing. Oxidative stress is caused by an increased production of reactive oxygen species and reduced antioxidant activity, resulting in the oxidation of glutathione. The ratio of reduced to oxidised glutathione is often used as a marker of the redox state in the cell. Whereas a variety of methods have been developed to measure glutathione in blood samples, methods to measure glutathione in cultured cells are scarce. Here we present a protocol to measure glutathione levels in cultured human and yeast cells using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS).