bluuebunny/crossref_metadata_2025 huggingface dataset:
The Aberrant Expression of the Mesenchymal Variant of FGFR2 in the Epithelial Context Inhibits Autophagy
Authors: Nanni Monica , Ranieri Danilo , Persechino Flavia , Torrisi Maria Rosaria , Belleudi Francesca
Published: July 2019

Signaling of the epithelial splice variant of fibroblast growth factor receptor 2 (FGFR2b) triggers both differentiation and autophagy, while the aberrant expression of the mesenchymal FGFR2c isoform in epithelial cells induces impaired differentiation, epithelial mesenchymal transition (EMT) and tumorigenic features. Here we analyzed in the human keratinocyte cell line, as well as in primary cultured cells, the possible impact of FGFR2c forced expression on the autophagic process. Biochemical and quantitative immunofluorescence analysis, coupled to the use of autophagic flux sensors, specific substrate inhibitors or silencing approaches, showed that ectopic expression and the activation of FGFR2c inhibit the autophagosome formation and that AKT/MTOR is the downstream signaling mainly involved. Interestingly, the selective inhibition of AKT or MTOR substrates caused a reversion of the effects of FGFR2c on autophagy, which could also arise from the imbalance of the interplay between AKT/MTOR pathway and JNK1 signaling in favor of JNK1 activation, BCL-2 phosphorylation and possibly phagophore nucleation. Finally, silencing experiments of depletion of ESRP1, responsible for FGFR2 splicing and consequent FGFR2b expression, indicated that the switching from FGFR2b to FGFR2c isoform could represent the key event underlying the inhibition of the autophagic process in the epithelial context. Our results provide the first evidence of a negative impact of the out-of-context expression of FGFR2c on autophagy, suggesting a possible role of this receptor in the modulation of the recently proposed negative loop between autophagy and EMT during carcinogenesis.
Viroporins in the Influenza Virus
Authors: To Janet , Torres Jaume
Published: July 2019

Influenza is a highly contagious virus that causes seasonal epidemics and unpredictable pandemics. Four influenza virus types have been identified to date: A, B, C and D, with only A–C known to infect humans. Influenza A and B viruses are responsible for seasonal influenza epidemics in humans and are responsible for up to a billion flu infections annually. The M2 protein is present in all influenza types and belongs to the class of viroporins, i.e., small proteins that form ion channels that increase membrane permeability in virus-infected cells. In influenza A and B, AM2 and BM2 are predominantly proton channels, although they also show some permeability to monovalent cations. By contrast, M2 proteins in influenza C and D, CM2 and DM2, appear to be especially selective for chloride ions, with possibly some permeability to protons. These differences point to different biological roles for M2 in types A and B versus C and D, which is also reflected in their sequences. AM2 is by far the best characterized viroporin, where mechanistic details and rationale of its acid activation, proton selectivity, unidirectionality, and relative low conductance are beginning to be understood. The present review summarizes the biochemical and structural aspects of influenza viroporins and discusses the most relevant aspects of function, inhibition, and interaction with the host.
Static Fatigue of SiC Multifilament Tows at Temperatures up to 1200 °C in Air
Authors: Lamon Jacques
Published: July 2019

SiC-based fibers are sensitive to delayed failure under constant load at high temperatures in air. Static fatigue at intermediate temperatures < 800 °C was attributed to slow crack growth from flaws located at the surface of fibers, driven by the oxidation of free carbon at grain boundaries. The present paper examines the static fatigue behavior of SiC-based Hi-Nicalon fibers at high temperatures up to 1200 °C and Hi Nicalon S fibers at intermediate temperatures (500–800 °C). The degradation of stress- rupture time relation of multifilament tows with increasing temperature was investigated. Predictions of tow lifetime based on critical filament-based model of tow failure were compared to experimental stress-rupture time diagrams. Critical filaments are characterized by strength–probability relation. The critical filament-based model was found to describe satisfactorily the static fatigue behavior of fiber tows at these temperatures. The influence of various factors on lifetime as well as the origins of variability is analyzed.
Growth of GaN Thin Film on Amorphous Glass Substrate by Direct-Current Pulse Sputtering Deposition Technique
Authors: Liu Wei-Sheng , Chang Yu-Lin , Chen Hui-Yu
Published: July 2019

We deposited 300-nm-thick GaN films on an amorphous glass substrate at a substrate temperature of 300 °C by using pulsed direct current (DC) sputtering. A ZnO buffer layer was utilized to improve the crystalline quality of the GaN films. Scanning electron microscopy results showed that the GaN thin films were grown along the c-axis and possessed a columnar structure. Atomic force microscopy results revealed that the GaN film deposited at a sputtering power of 75 W had the maximum grain size (24.1 nm). Room-temperature photoluminescence measurement of the GaN films indicated an ultraviolet near-band-edge emission at 365 nm and a Zn impurity energy transition level at 430 nm. In addition, X-ray diffraction conducted on the GaN films revealed a predominant (002) hexagonal wurtzite structure. The GaN film deposited at the sputtering power of 75 W demonstrated a high optical transmittance level of 88.5% in the wavelength range of 400–1100 nm. The material characteristics of the GaN films and ZnO buffer layer were studied using cross-sectional high-resolution transmission electron microscopy. The deposition of GaN films by using pulsed DC magnetron sputtering can result in high material quality and has high potential for realizing GaN-related optoelectronic devices on glass substrates.
Designing a Virtual Reality Platform to Facilitate Augmented Theatrical Experiences Based on Auralization
Authors: Lakka Eftychia , Malamos Athanasios G. , Pavlakis Konstantinos G. , Ware J. Andrew
Published: July 2019

In the last few years, the immersive theater has become a new trend for modern performances. Venues increasingly utilize widely available computer technologies, such as virtual/augmented reality and spatial sound, to help facilitate the realization of different ideas. Motivated by this current trend, a prototype platform has been developed that enables the design and implementation of an augmented theatrical experience based on spatial sound immersion. This paper describes the implementation of the platform and, through several use case scenarios, its evaluation. The paper concludes with a discussion of the results and offers some thoughts on future developments.
Dental Rehabilitation for Free Fibula Flap-Reconstructed Mandible with Scar Contracture: A Technical Note
Authors: Akashi Masaya , Matsumoto Kousuke , Takeda Daisuke , Yamashita Junya , Yatagai Nanae , Hashikawa Kazunobu , Komori Takahide
Published: July 2019

Dental rehabilitation with osseointegrated implants in reconstructed mandibles is a common procedure, but the technique still requires improvement, especially in its reliability and technical simplification. We herein report dental rehabilitation of a free fibula-reconstructed mandible with scar contracture. A vestibuloplasty technique with application of a polyglycolic acid (PGA) sheet is described. The implants were inserted into a viable fibula flap with severe scar contracture of the overlying epithelium resulting from vascular instability in skin paddle. Only the fibula periosteum was sutured after implant insertion; exposed surfaces were covered with a combination of PGA sheet and fibrin sealant. The area with PGA sheet coverage gradually healed with moderate contracture. The epithelium around the almost implants became immobilized. The implant-supported removable partial denture with custom titanium bar was acceptable. Dental rehabilitation is possible for reconstructed mandibles with severe scar contracture. Application of a PGA sheet may be useful for vestibuloplasty in patients with reconstructed mandibles.
Emotion Recognition from Skeletal Movements
Authors: Sapiński Tomasz , Kamińska Dorota , Pelikant Adam , Anbarjafari Gholamreza
Published: July 2019

Automatic emotion recognition has become an important trend in many artificial intelligence (AI) based applications and has been widely explored in recent years. Most research in the area of automated emotion recognition is based on facial expressions or speech signals. Although the influence of the emotional state on body movements is undeniable, this source of expression is still underestimated in automatic analysis. In this paper, we propose a novel method to recognise seven basic emotional states—namely, happy, sad, surprise, fear, anger, disgust and neutral—utilising body movement. We analyse motion capture data under seven basic emotional states recorded by professional actor/actresses using Microsoft Kinect v2 sensor. We propose a new representation of affective movements, based on sequences of body joints. The proposed algorithm creates a sequential model of affective movement based on low level features inferred from the spacial location and the orientation of joints within the tracked skeleton. In the experimental results, different deep neural networks were employed and compared to recognise the emotional state of the acquired motion sequences. The experimental results conducted in this work show the feasibility of automatic emotion recognition from sequences of body gestures, which can serve as an additional source of information in multimodal emotion recognition.
Unsteady Simulation of Ignition of Turbulent Reactive Swirling Flow of Novel Design of Solid-Fuel Ramjet Motor
Authors: Musa Omer , Chen Xiong , Li Yingkun , Li Weixuan , Liao Wenhe
Published: July 2019

This paper presents a numerical investigation of ignition and combustion stabilization of a novel design of a solid-fuel ramjet (SFRJ) motor with and without swirl flow. The proposed design includes two solid fuels, retaining the simple design of the classic SFRJ. Numerical simulations of unsteady, turbulent, reactive, and swirling flow coupled with solid-fuel pyrolysis have been performed using an in-house CFD solver. Experiments on SFRJ were conducted via a connected-pipe test facility to validate the developed code. Furthermore, the code was validated for chemical reactions, heat diffusion, and swirl flow by using benchmark test cases of shock-induced, semi-infinite plate, and dump combustor with swirl flow, respectively. Then, the proposed and classic designs were simulated for the same inflow conditions and configurations, and the results were analyzed and discussed. It is found that the mixing degree, reactant residence time, mass flux, ignition delay time, and regression rate improve when using the proposed design. Moreover, the proposed design reveals interesting observations of a new flame being created and merged with the main flame.
Performance Analysis of a Combined Solar-Assisted Heat Pump Heating System in Xi’an, China
Authors: Huan Chao , Li Shengteng , Wang Fenghao , Liu Lang , Zhao Yujiao , Wang Zhihua , Tao Pengfei
Published: July 2019

This study proposed a combined solar-assisted heat pump (SAHP) system that could operate in the serial mode or parallel mode. For this proposed system, a stable year-round operation could be achieved without the assistance of electric heating or low-temperature heat pump. By analyzing the heat balance equations, a correlation of the combined SAHP system for the two modes switched was obtained, which provided a theoretical basis for the optimal operation of this system. In addition, the performance of the proposed system applied in a university bathroom in Xi’an district was investigated using TRNSYS. The results illustrated that compared to the serial and parallel systems, the proposed system exhibited a good performance on energy efficiency. The annual average coefficient of performance (COP) of the proposed system was 5.7, obviously higher than those of the serial system and the parallel system, which were 3.3 and 4.3, respectively. Therefore, the results in this study could provide the theoretical guidance and reference for practical engineering design.
Modeling and Analysis of hHoneycomb—A Polyhex Inspired Reconfigurable Tiling Robot
Authors: Parween Rizuwana , Shi Yuyao , Parasuraman Karthikeyan , Vengadesh Ayyalusami , Sivanantham Vinu , Ghanta Sriharsha , Mohan Rajesh Elara
Published: July 2019

hHoneycomb, a self-reconfigurable cleaning robot, is designed based on tiling theory, to overcome the significant challenges experienced by the fixed morphology cleaning robot. It consists of four regular hexagonal units and the units are connected by a planar revolute joint which helps in reconfiguration. This platform attains six distinct configurations (bar, bee, arch, wave, worm, and pistol) and these configurations have circular arcs and irregular concave and convex boundary that would help in accessing various obstacles in the cleaning space. This work addresses the mechanical design, system-level modeling, reconfiguration of the platform via hinged joint mechanism, mobility of the platform, polyhex based tiling set, and power consumption during reconfiguration. The strength of the mechanical structure is studied based on the structural analysis of the system using finite element method. Based on the natural frequency and deformation pattern, the proposed design is validated and proven to overcome structural failure and system resonance. The kinematics formulation of the platform during locomotion and dynamics of each block during reconfiguration are derived. The robotic system is modeled in Simscape multibody toolbox of Matlab and the mobility of the platform is studied using the numerical simulation. Based on the real-time current consumption of each joint during reconfiguration, the energy efficient configuration and tiling set are addressed.
Train Operation Strategy Optimization Based on a Double-Population Genetic Particle Swarm Optimization Algorithm
Authors: Liu Kaiwei , Wang Xingcheng , Qu Zhihui
Published: July 2019

Train operation strategy optimization is a multi-objective optimization problem affected by multiple conditions and parameters, and it is difficult to solve it by using general optimization methods. In this paper, the parallel structure and double-population strategy are used to improve the general optimization algorithm. One population evolves by genetic algorithm (GA), and the other population evolves by particle swarm optimization (PSO). In order to make these two populations complement each other, an immigrant strategy is proposed, which can give full play to the overall advantages of parallel structure. In addition, GA and PSO is also improved, respectively. For GA, its convergence speed is improved by adjusting the selection pressure adaptively based on the current iteration number. Elite retention strategy (ERS) is introduced into GA, so that the best individual in each iteration can be saved and enter the next iteration process. In addition, the opposition-based learning (OBL) can produce the opposition population to maintain the diversity of the population and avoid the algorithm falling into local convergence as much as possible. For PSO, linear decreasing inertia weight (LDIW) is presented to better balance the global search ability and local search ability. Both MATLAB simulation results and hardware-in-the-loop (HIL) simulation results show that the proposed double-population genetic particle swarm optimization (DP-GAPSO) algorithm can solve the train operation strategy optimization problem quickly and effectively.
Effect of Platform Motion on Aerodynamic Performance and Aeroelastic Behavior of Floating Offshore Wind Turbine Blades
Authors: Kim Youngjin , Kwon Oh Joon
Published: July 2019

In the present study, a numerical framework for predicting the aerodynamic performance and the aeroelastic behavior of floating offshore wind turbine rotor blades involving platform motion was developed. For this purpose, the aerodynamic and structural analyses were conducted simultaneously in a tightly coupled manner by exchanging the information about the aerodynamic loads and the elastic blade deformations at every time step. The elastic behavior of the turbine rotor blades was described by adopting a structural model based on the Euler-Bernoulli beam. The aerodynamic loads by the rotor blades were evaluated by adopting a blade element momentum theory. The numerical simulations were conducted when the platform of the wind turbine independently moves in each of the six degrees-of-freedom directions consisting of heave, sway, surge, roll, pitch, and yaw. It was observed that flexible blades exhibit complicated vibratory behaviors when they are excited by the aerodynamic, inertia, and gravitational forces simultaneously. It was found that the load variation caused by the platform surge or pitch motion has a significant influence on the flapwise and torsional deformations of the rotor blades. The torsional deformation mainly occurs in the nose-down direction, and results in a reduction of the aerodynamic loads. It was also found that the flapwise root bending moment is mainly influenced by the platform surge and pitch motions. On the other hand, the edgewise bending moment is mostly dictated by the gravitational force, but is not affected much by the platform motion.
Design and Analysis of a Novel Converter Topology for Photovoltaic Pumps Based on Switched Reluctance Motor
Authors: Zan Xiaoshu , Wu Ning , Xu Ruidong , Cui Mingliang , Jiang Zhikai , Ni Kai , Alkahtani Mohammed
Published: July 2019

In order to improve the performance of switched reluctance motor (SRM) systems for photovoltaic (PV) pumps, this paper introduces a new converter topology for SRM with controllable multiple power sources. Only simple switching components need to be added at the front end of the asymmetric half-bridge converter in this topology, which enables the control of multiple power sources. The new PV pump system has four operating modes, which are the PV panel driven mode, battery bank driven mode, dual-source driven mode, and battery charging mode. By adjusting the state of the front-end converter switch, the voltage tracking of PV panel can be achieved, providing a stable bus voltage for the SRM system. By controlling the battery bypass switch, the bus voltage of SRM system can be increased, thereby increasing the system power level. Simulations and experiments based on a four-phase 8/6 SRM demonstrate the effect of the novel converter proposed in this paper.
Effect of Irrelevant Variables on Faulty Wafer Detection in Semiconductor Manufacturing
Authors: Kim Dongil , Kang Seokho
Published: July 2019

Machine learning has been applied successfully for faulty wafer detection tasks in semiconductor manufacturing. For the tasks, prediction models are built with prior data to predict the quality of future wafers as a function of their precedent process parameters and measurements. In real-world problems, it is common for the data to have a portion of input variables that are irrelevant to the prediction of an output variable. The inclusion of many irrelevant variables negatively affects the performance of prediction models. Typically, prediction models learned by different learning algorithms exhibit different sensitivities with regard to irrelevant variables. Algorithms with low sensitivities are preferred as a first trial for building prediction models, whereas a variable selection procedure is necessarily considered for highly sensitive algorithms. In this study, we investigate the effect of irrelevant variables on three well-known representative learning algorithms that can be applied to both classification and regression tasks: artificial neural network, decision tree (DT), and k-nearest neighbors (k-NN). We analyze the characteristics of these learning algorithms in the presence of irrelevant variables with different model complexity settings. An empirical analysis is performed using real-world datasets collected from a semiconductor manufacturer to examine how the number of irrelevant variables affects the behavior of prediction models trained with different learning algorithms and model complexity settings. The results indicate that the prediction accuracy of k-NN is highly degraded, whereas DT demonstrates the highest robustness in the presence of many irrelevant variables. In addition, a higher model complexity of learning algorithms leads to a higher sensitivity to irrelevant variables.
S-GoSV: Framework for Generating Secure IEC 61850 GOOSE and Sample Value Messages
Authors: Farooq Shaik Mullapathi , Hussain S.M. Suhail , Ustun Taha Selim
Published: July 2019

Standardized communication plays an important role in substation automation system (SAS). IEC 61850 is a de-facto standard in SAS. It facilitates smooth communication between different devices located in the substation by achieving interoperability. Generic Object-Oriented Substation Event (GOOSE) and Sample Value (SV) messages developed according to IEC 61850 enable efficient monitoring and operation control of SAS. IEC 61850 is very popular due to its flexible and robust modeling. As the number of critical infrastructures that employed IEC 61850 increases, it is important to study cybersecurity aspects as well. To this end, this paper develops a software framework, S-GoSV (Secure GOOSE and SV), that generates custom GOOSE and Sample Value messages. Furthermore, security features are added to protect them from different security attacks within a substation. IEC 62351-6 specifies digital signatures to achieve node authentication and messages integrity. Therefore, S-GoSV implements RSASSA-PKCS1-v1_5 digital signature algorithm based on RFC 2313. Performance studies show that digital signature algorithms based on RSA signing and verification take long times and do not conform to timing requirements stipulated by IEC 61850 for power system communication. To address this, Message Authentication Code (MAC) based digital signature algorithm, Keyed Hash-Message Authentication Code- Secure Hash Algorithm (HMAC-SHA256), is additionally implemented in S-GoSV framework for securing GOOSE messages.
Effects of Five Growing Media and Two Fertilizer Levels on Polybag—Raised Camden Whitegum (Eucalyptus benthamii Maiden & Cambage) Seedling Morphology and Drought Hardiness
Authors: Shalizi Mohammad Nasir , Goldfarb Barry , Burney Owen Thomas , Shear Theodore Henry
Published: June 2019

In developing countries, tree seedlings are often produced in polybags filled with mixtures of locally available materials. Seedling growth and quality can be affected by the type and amount of these substrates used in the mixture. Differences in seedling growth and quality can also be significantly affected when fertilization is employed during the nursery growing period. In this study, we assessed the effects of five different growing media and two fertilization regimes on nursery growth, seedling morphology and early post-planting response to drought of Eucalyptus benthamii (Maiden & Cambage) seedlings. First, we evaluated the effects of each media by fertilizer treatment combination on morphological attributes during a nursery growing period. Seedlings raised in fertilized media without rice hulls yielded higher growth, root dry mass, shoot dry mass, total dry mass, Dickson quality index (DQI) scores, and number of first order lateral roots (FOLRs). Root to shoot ratio (R:S ratio) was, however, greater in non-fertilized media that contained rice hulls. We then conducted a simulated outplanting and drought hardiness experiment, in which seedlings were planted in 13.2 L containers and irrigated for one month, followed by the imposition of drought stress. Seedlings in fertilized media composed of sand, topsoil and compost showed greater growth than those in rice hull-containing media, during the irrigation phase. With the discontinuation of irrigation and prevention of precipitation reaching the seedlings, seedlings grown in non-fertilized media containing rice hulls survived longer than those in other media. There were no large differences in survival among other media or between fertilized and other non-fertilized seedlings. Seedling total size and shoot height at the time of planting played a major role in survival. Smaller seedlings with smaller shoot sizes and greater R:S ratios survived longer. This study demonstrates that growing media and fertilization can be manipulated to affect seedling morphology in the nursery and, ultimately, seedling performance and survival under water stressed conditions.
Does Land Use Change Affect Green Space Water Use? An Analysis of the Haihe River Basin
Authors: Zhao Yu , Zhang Xuanchang , Bai Yang , Mi Feng
Published: June 2019

Research Highlights: Land use/cover change (LUCC) has an impact on the water use efficiency (WUE) of green space in the Haihe River Basin. Background and Objectives: The Haihe River Basin has historically been one of the most water-stressed basins in China. With the increase in green space and economic development, land use and water use in the Haihe River Basin have changed significantly. In order to contribute to the sustainable development of basin water management, the impacts of LUCC on the WUE of the Haihe River Basin were assessed with the goal to support decision makers with regard to water resources planning and watershed management. Materials and Methods: (1) Moderate Resolution Imaging Spectroradiometer (MODIS) data and land use data were used to produce land use/land cover and other related maps. (2) The WUE equation was used to calculate the green space WUE. (3) The contribution rates of changes in land use were assessed to illustrate how LUCC affected green space WUE. Results: (1) Artificial surfaces increased and large areas of farmland were converted to non-agricultural use, accompanied by the addition of green space. (2) Green space WUE increased significantly from 2005 to 2015. The average annual WUE exhibited a relatively uniform spatial distribution in the Haihe River Basin. Except for the central area of urban land, the WUE of most areas exhibited an increasing trend. (3) The impact of LUCC on WUE was mainly a result from the conversion of farmland and artificial surfaces and the increase in green space. Ecological restoration and crop adjustment contributed greatly to the improvement in green space WUE in the basin. Conclusions: Green space WUE of the Haihe River Basin was significantly affected by LUCC and there is room for improvement in the WUE of green spaces in the basin. The paper concludes with recommendations for further research to assist in planning for green space to promote sustainable development related to land use and water management.
Response of Oak and Maple Seed Germination and Seedling Growth to Different Manganese Fertilizers in a Cultured Substratum
Authors: Mai Kaile , Williams Roger A.
Published: July 2019

Oak regeneration failures have been causing a slow decline in the occurrence of oak forest ecosystems in eastern North America. Accordingly, our study sought to determine a means of creating more vigorous and competitive oak seedlings by the addition of manganese (Mn) fertilizers. Seeds of northern red oak (Quercus rubra L.), chestnut oak (Quercus prinus L.), and red maple (Acer rubrum L.), one of oak’s major competitors in North America oak forest ecosystems, were sown in 0.7 liter pots that contained a growing medium mixture of peat moss, perlite, and sand in a ratio of 2:1:2, and germinated in a greenhouse. Three different chemical compound Mn fertilizer treatments—manganese chloride (0.16 mg L−1 Mn, MnCl2·4H2O), nanoparticle manganese in the form of manganese hydroxide (0.01 mg/L Mn, nanoparticle Mn(OH)2), and manganese hydroxide (0.01 mg L−1 Mn, Mn(OH)2)—and a treatment of Hoagland solution were applied to the planted seed. These treatments were compared to a control consisting of water, and treatments were applied twice a week over a 12 week period. Germination rates and seedling growth were measured over this period of time. At the end of 12 weeks seedlings were harvested, separated into roots, stem, and foliage for the purpose of biomass and nutrient analysis by seedling component. Northern red oak displayed a 100% germination success rate with MnCl2·4H2O and Mn(OH)2 treatments, while red maple germination was reduced with the MnCl2·4H2O and nanoparticle Mn(OH)2 treatments with only a 32% and 24% germination rate, respectively. The MnCl2·4H2O treatment produced the largest overall seedling size (basal diameter squared times the seedling height) of red maple with a 191.6% increase; however, the MnCl2·4H2O treatment produced the largest overall seedling size (basal diameter squared times the seedling height) of northern red oak and chestnut oak with an increase of 503.7% and 339.5%, respectively. The greatest increase in overall seedling size for northern red oak was with the Mn(OH)2 treatment at 507.2%, and 601.2% for chestnut oak with the nanoparticle Mn(OH)2 treatment. MnCl2·4H2O treatment significantly increased the oak foliar nitrogen (N) content. It appears that the application of Mn fertilizer can increase the germination and growth of these oak species while suppressing or having a lesser effect on red maple, thus creating a competitive advantage for oak over its competitor.
Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation
Authors: Feng Huili , Guo Jiahuan , Wang Weifeng , Song Xinzhang , Yu Shuiqiang
Published: July 2019

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.
A Dynamic Application-Partitioning Algorithm with Improved Offloading Mechanism for Fog Cloud Networks
Authors: Abro Adeel , Deng Zhongliang , Memon Kamran Ali , Laghari Asif Ali , Mohammadani Khalid Hussain , ul Ain Noor
Published: June 2019

This paper aims to propose a new fog cloud architecture that performs a joint energy-efficient task assignment (JEETA). The proposed JEETA architecture utilizes the dynamic application-partitioning algorithm (DAPTS), a novel algorithm that efficiently decides and switches the task to be offloaded or not in heterogeneous environments with minimal energy consumption. The proposed scheme outperforms baseline approaches such as MAUI, Think Air and Clone Cloud in many performance aspects. Results show that for the execution of 1000 Tasks on fog, mobile offloaded nodes, JEETA consumes the leas, i.e., 23% of the total energy whereas other baseline approaches consume in between 50–100% of the total energy. Results are validated via real test-bed experiments and trice are driven efficient simulations.
Meshless Modeling of Flow Dispersion and Progressive Piping in Poroelastic Levees
Authors: Khoury Anthony , Divo Eduardo , Kassab Alain , Kakuturu Sai , Reddi Lakshmi
Published: July 2019

Performance data on earth dams and levees continue to indicate that piping is one of the major causes of failure. Current criteria for prevention of piping in earth dams and levees have remained largely empirical. This paper aims at developing a mechanistic understanding of the conditions necessary to prevent piping and to enhance the likelihood of self-healing of cracks in levees subjected to hydrodynamic loading from astronomical and meteorological (including hurricane storm surge-induced) forces. Systematic experimental investigations are performed to evaluate erosion in finite-length cracks as a result of transient hydrodynamic loading. Here, a novel application of the localized collocation meshless method (LCMM) to the hydrodynamic and poroelastic problem is introduced to arrive at high-fidelity field solutions. Results from the LCMM numerical simulations are designed to be used as an input, along with the soil and erosion parameters obtained experimentally, to characterize progressive piping.
Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus
Authors: Durante-Rodríguez Gonzalo , Gutiérrez-del-Arroyo Paloma , Vélez Marisela , Díaz Eduardo , Carmona Manuel
Published: June 2019

The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the PN promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the PN promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the PN promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the PN promoter in the form of four dimers, two of them binding to OR1. The BzdR/PN complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains.
Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds
Authors: Grilz-Seger Gertrud , Neuditschko Markus , Ricard Anne , Velie Brandon , Lindgren Gabriella , Mesarič Matjaz , Cotman Marko , Horna Michaela , Dobretsberger Max , Brem Gottfried , Druml Thomas
Published: June 2019

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) and gait patterns (DMRT3), several putative target genes related to embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle morphogenesis (KRT25, KRT27, INTU) and autophagy (RALB) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (UVSSA, STXBP4, COX11, HLF, MMD).
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
Authors: Ferrante Maria Immacolata , Entrambasaguas Laura , Johansson Mathias , Töpel Mats , Kremp Anke , Montresor Marina , Godhe Anna
Published: June 2019

Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual phase of the centric planktonic diatom Skeletonema marinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschia multistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets.
Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa
Authors: Li Feng , Guo Xuhu , Liu Jianxia , Zhou Feng , Liu Wenying , Wu Juan , Zhang Hongli , Cao Huifen , Su Huanzhen , Wen Riyu
Published: July 2019

The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon–intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa’s strong salinity tolerance.
Global Dynamics in Protein Disorder during Maize Seed Development
Authors: Zamora-Briseño Jesús Alejandro , Pereira-Santana Alejandro , Reyes-Hernández Sandi Julissa , Castaño Enrique , Rodríguez-Zapata Luis Carlos
Published: July 2019

Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
An Assessment of Chinese Pathways to Implement the UN Sustainable Development Goal-11 (SDG-11)—A Case Study of the Yangtze River Delta Urban Agglomeration
Authors: Xu Xueyan , Gao Jun , Zhang Zhonghao , Fu Jing
Published: June 2019

Urban sustainability is a crucial part of the United Nations (UN) Sustainable Development Goals (SDGs) and one of the core objectives of China’s national strategy to promote new urbanization and achieve integration in the Yangtze River Delta (YRD). This paper mainly focused on the 11th SDG, which is a universal call to make cities and human settlements inclusive, safe, resilient and sustainable. The full permutation polygon synthetic indicator (FPPSI) method was applied to synthetically evaluate the sustainable level of 26 cities in the YRD urban agglomeration from 2007 to 2016. The results showed that: (1) the synthesis indicators were increasing year by year, which implied that the sustainable development of the YRD has shown obvious progress in recent years. However, each city faced its own challenges to achieving the sustainable development goals. The sustainability level for the majority of cities was restricted by obstacles such as the per capita green area, air quality and commercial housing sales area; (2) Among the 26 cities, small and medium-sized cities were subject to the traditional strong sustainability indicators while large and mega cities were more affected by weak sustainability indicators; (3) Spatial differences were found for the overall sustainable development level of the YRD. The diffusion and assembly effect among cities had not yet been formed; however, the strong spillover effect of developed cities might influence the ability of other cities to achieve sustainable development goals in many aspects of the environment, economy and society. The results suggest the need for a stronger focus on improving regional developing patterns and strengthening coordination in the process of achieving the sustainable development goal of urban agglomeration in the YRD. Furthermore, according to the conditions of different cities, integrated policies are required to address all aspects of sustainability and to avoid unintended consequences.
The Prevalence of Cigarette and E-cigarette Smoking Among Students in Central and Eastern Europe—Results of the YUPESS Study
Authors: Brożek Grzegorz Marek , Jankowski Mateusz , Lawson Joshua Allan , Shpakou Andrei , Poznański Michał , Zielonka Tadeusz Maria , Klimatckaia Ludmila , Loginovich Yelena , Rachel Marta , Gereová Justína , Golonko Justyna , Naumau Ihar , Kornicki Kamil , Pepłowska Paulina , Kovalevskiy Valeriy , Raskiliene Asta , Bielewicz Krzysztof , Krištúfková Zuzana , Mróz Robert , Majek Paulina , Lubanski Jakub , Kaleta Dorota , Pinkas Jarosław , Zejda Jan Eugeniusz
Published: June 2019

Electronic cigarettes (e-cigarettes) are an alternative to traditional tobacco cigarette smoking. The aim of this study was to assess the prevalence of cigarette smoking and e-cigarette use among university students from Central and Eastern Europe and to investigate personal characteristics associated with cigarette and e-cigarette smoking. A questionnaire-based cross-sectional survey was performed between 2017–2018 among university students in five European countries: Belarus, Lithuania, Poland, Russia, and Slovakia. The questionnaire included 46 questions related to the frequency and habits of traditional cigarettes and e-cigarettes use. Completed questionnaires were obtained from 14,352 students (8800 medical; aged 20.9 ± 2.4 years) with an overall response rate of 72.2%. Two-thirds of the respondents had smoked a traditional tobacco cigarette and 43.7% had used an e-cigarette. Overall current smoking status included 12.3% traditional cigarette smokers, 1.1% e-cigarette users, and 1.8% were dual users with the remainder being non-smokers. Smoking status differed between the research centres (p < 0.001). Females were less likely to try either cigarettes (OR = 0.83) or e-cigarettes (OR = 0.62) and were less likely to be current cigarette (OR = 0.64), e-cigarette (OR = 0.34), or dual users (OR = 0.33) than males. Perception of e-cigarettes significantly differed between smokers and non-smokers (p < 0.001). Among university students, cigarettes are more popular than e-cigarettes.
Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses
Authors: Wan Yu , Ruan Xiaohong , Wang Jie , Shi Xiaojun
Published: June 2019

Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NOx--N in the sediment, NH4+-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.