bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle
Authors: Kim Minseok , Park Tansol , Jeong Jin Young , Baek Youlchang , Lee Hyun-Jeong
Published: April 2020

This study demonstrated the potential effects of the rumen microbiota on the deposition of intramuscular fat, known as marbling. Previous studies on fatty acid metabolism in beef cattle have mostly focused on biohydrogenating rumen bacteria, whereas those on the overall rumen microbiota—to understand their roles in marbling—have not been systematically performed. The rumen microbiota of 14 Korean beef cattle (Hanwoo), which showed similar carcass characteristics and blood metabolites but different marbling scores, were analyzed by 16S rRNA gene sequencing. The rumen samples were grouped into two extreme marbling score groups of host animals as follows: LMS, marbling score≤ 4 or HMS, marbling score ≥7. Species richness tended to be higher in the HMS group, whereas the overall microbiota differed between LMS and HMS groups. RFP12, Verrucomicrobia, Oscillospira, Porphyromonadaceae, and Paludibacter were differentially abundant in the HMS group, whereas Olsenella was abundant in the LMS group. Some marbling-associated bacterial taxa also contributed to the enrichment of two lipid metabolic pathways including “alpha-linolenic acid metabolism” and “fatty acid biosynthesis” in the HMS microbiome. Taxonomic drivers of fatty acid biosynthesis, particularly in the rumen microbiome of high-marbled meat, could thus be further studied to increase the intramuscular fat content.
A Survey of Dairy Cattle Behavior in Different Barns in Northern Italy
Authors: Lovarelli Daniela , Finzi Alberto , Mattachini Gabriele , Riva Elisabetta
Published: April 2020

Due to its increasing pressure on dairy cows, studies that investigate how to cope with heat stress are needed. The heat stress affects multiple aspects of cows’ lives, among which their behavior and welfare. In this study, a survey was carried out in eight farms located in Northern Italy to monitor and evaluate the environmental aspects of the barns and the behavioral responses of dairy cows. For one year, three periods were monitored: thermoneutral (T_S), hot (H_S) and cold (C_S) seasons. Temperature and relative humidity were measured by environmental sensors, and lying vs. standing time, number of lying bouts and their average duration were collected by accelerometers. The temperature-humidity index (THI) was quantified inside and outside of the barn. Results show that at the increase of the THI, behavioral adaptations occurred in all the farms, especially with a reduction of lying time and an increase of respiration rate. Four of the eight farms need interventions for improving the cows’ welfare. Here, environmental problems should be solved by introducing or improving the efficacy of the forced ventilation or by modifying the barn structure. Monitoring dairy barns with sensors and Precision Livestock Farming techniques can be helpful for future livestock farming to alert farmers on the need for their interventions to respond immediately to unwanted barn living conditions.
Correlating Volatile Lipid Oxidation Compounds with Consumer Sensory Data in Dairy Based Powders during Storage
Authors: Clarke Holly J. , O’Sullivan Maurice G. , Kerry Joseph P. , Kilcawley Kieran N.
Published: April 2020

Lipid oxidation (LO) is a recognised problem in dairy powders due to the formation of volatile odour compounds that can negatively impact sensory perception. Three commercial dairy powders, fat-filled whole milk powder (FFWMP), skim milk powder (SMP), and infant milk formula (IMF), stored under different conditions (21 °C, 37 °C, or 25 °C with 50% humidity), were evaluated by consumer acceptance studies, ranked descriptive sensory analysis, and LO volatile profiling using headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME GCMS) over 16 weeks. Significant (p = 0.001) differences in the concentration of LO compounds and sensory perception were evident between sample types in the different storage conditions. The sensory acceptance scores for FFWMP and SMP remained stable throughout storage in all conditions, despite the increased perception of some LO products. The IMF sample was perceived negatively in each storage condition and at each time point. Overall increases in hexanal, heptanal, and pentanal correlated with “painty”, “oxidised”, “cooked”, and “caramelised” attributes in all samples. The concentration of some LO volatiles in the IMF was far in excess of those in FFWMP and SMP. High levels of LO volatiles in IMF were presumably due to the addition of polyunsaturated fatty acids (PUFA) in the formulation.
Improvement of Anaerobic Digestion of Hydrolysed Corncob Waste by Organosolv Pretreatment for Biogas Production
Authors: Sulbarán-Rangel Belkis , Alarcón Aguirre Jaime Santiago , Breton-Deval Luz , del Real-Olvera Jorge , Gurubel Tun Kelly Joel
Published: April 2020

This paper describes an organosolv pretreatment of corncob waste to improve its anaerobic digestion for biogas production. Through a thermochemical process based on the use of ethanol and acetic acid, it was possible to separate the fractions of lignin, considered to be a natural inhibitor of anaerobic digestion processes. In addition, with this organosolv pretreatment, the available sugars in the carbohydrates present as monosaccharides, or simple sugars, were depolymerised, facilitating the digestion process. The obtained results include the chemical characterisation of the corncob, the hydrolysate, and the mixture with cow manure, finding that these substrates have potential to be used in anaerobic digestion. The total reducing sugars consumed were 96.8%, and total sugars were 85.75%. It was clearly observed that with the use of pretreatment with organosolv, the production of biogas was superior, because 484 NmL/gVS was obtained compared to the other reported treatments. It was also observed that adding the hydrolysate organosolv increased the production because the values of the control without hydrolysate were 120 NmL/gVS in the bottle experiment. When the experiment was scaled to the 5L reactor, the total volumes of biogas that were accumulated in 15 days of production were 5050 NmL/gVS and 1212 NmL/gVS with and without hydrolysate, respectively. This indicates that the organosolv pretreatment of corncob waste is effective in improving biogas production.
Glass-Ceramics Processed by Spark Plasma Sintering (SPS) for Optical Applications
Authors: Singarapu Babu , Galusek Dušan , Durán Alicia , Pascual María Jesús
Published: April 2020

This paper presents a review on the preparation of glass-ceramics (GCs) and, in particular, transparent GCs by the advanced processing technique of spark plasma sintering (SPS). SPS is an important approach to obtain from simple to complex nanostructured transparent GCs, full densification in a short time, and highly homogeneous materials for optical applications. The influence of the different processing parameters, such as temperature, pressure, sintering dwell time on the shrinkage rate, and final densification and transparency, are discussed and how this affects the glass material properties. Normally, transparent glass-ceramics are obtained by conventional melt-quenching, followed by thermal treatment. Additionally, the GC scan is produced by sintering and crystallization from glass powders. Hot pressing techniques (HP) in which the source of heating is high-frequency induction can be also applied to enhance this process. In the case of transparent ceramics and glass-ceramics, spark plasma sintering is a promising processing tool. It is possible to enhance the material properties in terms of its compactness, porosities, crystallization, keeping the size of the crystals in the nanometric scale. Moreover, the introduction of a high concentration of active gain media into the host matrix provides functional glass-ceramics systems with enhanced luminescence intensity through reducing non-radiative transitions like multi phonon relaxation (MPR) and cross relaxations (CR), thus providing longer lifetimes. More effort is needed to better understand the sintering mechanisms by SPS in transparent GC systems and optimize their final optical performance.
Predeployment of Transponders for Dynamic Lightpath Provisioning in Translucent Spectrally–Spatially Flexible Optical Networks
Authors: Walkowiak Krzysztof , Klinkowski Mirosław , Włodarczyk Adam , Kasprzak Andrzej
Published: April 2020

We consider a dynamic lightpath provisioning problem in translucent spectrally–spatially flexible optical networks (SS-FONs) in which flexible signal regeneration is achieved with transponders operating in back-to-back (B2B) configurations. In the analyzed scenario, an important aspect that has a significant impact on the network performance is the decision on placement of transponders that can be used for two purposes: transmitting/receiving (add/drop) of optical signals at the source/destination nodes and regeneration of the signals at some intermediate nodes. We propose a new algorithm called scaled average used regenerators (SAUR). The key idea of the SAUR method is based on a data analytics approach, i.e., the algorithm exploits information on network traffic characteristics and the applied dynamic routing algorithm to obtain additional knowledge for the decision on transponder placement. The numerical results obtained for two representative topologies highlight that the proposed SAUR method outperforms reference algorithms in terms of the amount of traffic that can be accepted in the network. In other words, placement of transponders yielded by the SAUR method allows to increase the SS-FON throughput using only the existing resources, i.e., the network operator does not have to invest in new devices or fibers.
Editorial for “Recent Advances in the Design of Structures with Passive Energy Dissipation Systems”
Authors: De Domenico Dario , Ricciardi Giuseppe , Zhang Ruifu
Published: April 2020

Civil engineering structures and infrastructures are inherently vulnerable to exceptional loads related to natural disasters, primarily earthquakes, tsunamis, strong winds, and floods [...]
XOR Multiplexing Technique for Nanocomputers
Authors: Yu Lianhua , Diao Ming , Chen Xiaobo , Cheng Xiaochun
Published: April 2020

In emerging nanotechnologies, due to the manufacturing process, a significant percentage of components may be faulty. In order to make systems based on unreliable nano-scale components reliable, it is necessary to design fault-tolerant architectures. This paper presents a novel fault-tolerant technique for nanocomputers, namely the XOR multiplexing technique. This hardware redundancy technique is based on a numerous duplication of faulty components. We analyze the error distributions of the XOR multiplexing unit and the error distributions of multiple stages of the XOR multiplexing system, then compare them to the NAND multiplexing unit and the NAND multiplexing multiple stages system, respectively. The simulation results show that XOR multiplexing is more reliable than NAND multiplexing. Bifurcation theory is used to analyze the fault-tolerant ability of the system and the results show that XOR multiplexing technique has a high fault-tolerant ability. Similarly to the NAND multiplexing technique, this fault-tolerant technique is a potentially effective fault tolerant technique for future nanoelectronics.
Method to Control the Deformation of Anti-Slide Piles in Zhenzilin Landslide
Authors: Wang Hao , Wang Peng , Qin Hongyu , Yue Jianwei , Zhang Jianwei
Published: April 2020

Anti-slide piles were used in the region of the Zhenzilin landslide in Sichuan, China. The horizontal displacement of these piles exceeds specifications. Deterioration in bedrock properties may cause deformation, thereby causing landslide destabilization. An approach was developed for the analysis of anti-slide pile in two bedrocks with different strengths below the slip surface. A relationship has been established between the modulus of subgrade reaction of the first weak bedrock and reasonable embedded length for landfill slopes with strata of various strengths. Furthermore, the influence of embedding length on deformation has been studied to determine the reasonable embedded length, which helps reduce deformation and ensure landslide stability. The results reveal that (1) at a constant embedded length, horizontal displacement increases with the thickness of the first soft bedrock, meanwhile the maximum shear force remains constant, and the bending moment first increases followed by subsequent decrease; (2) with an increase in the embedded length, horizontal displacement and the maximum shear force of the pile in the embedded bedrock decrease, whereas the bending moment increases; (3) the maximum internal forces and horizontal displacement increase with a decrease in the subgrade reaction modulus of the first weak rock; and (4) the reasonable embedded length of an anti-slide pile increases with a decrease in the subgrade reaction modulus of the first weak bedrock. The proposed approach can be employed to design anti-slide piles in similar landslide regions to control pile-head deformation.
Analysis of Undrained Seismic Behavior of Shallow Tunnels in Soft Clay Using Nonlinear Kinematic Hardening Model
Authors: Saleh Asheghabadi Mohsen , Cheng Xiaohui
Published: April 2020

In this study, a soil–tunnel model for clay under earthquake loading is analyzed, using finite element methods and a kinematic hardening model with the Von Mises failure criterion. The results are compared with those from the linear elastic–perfectly plastic Mohr–Coulomb model. The latter model does not consider the stiffness degradation caused by imposing cyclic loading and unloading to the soil, whereas the kinematic hardening model can simulate this stiffness degradation. The parameters of the kinematic hardening model are calibrated based on the results of experimental cyclic tests and finite element simulation. Here, two methods—one using data from cyclic shear tests, and the other a new method using undrained cyclic triaxial tests—are used to calibrate the parameters. The parameters investigated are the peak ground acceleration (PGA), tunnel lining thickness, tunnel shape, and tunnel embedment depth, all of which have an effect on the resistance of the shallow tunnel to the stresses and deformations caused by the surrounding clay soils. The results show that unlike traditional models, the nonlinear kinematic hardening model can predict the response reasonably well, and it is able to create the hysteresis loops and consider the soil stiffness degradation under the seismic loads.
Study on Residual Stress of Welded Hoop Structure
Authors: Ma Wenbo , Zhang Heng , Zhu Wei , Xu Fu , Yang Caiqian
Published: April 2020

Residual stress is inevitable during welding, which will greatly affect the reliability of the structure. The purpose of this paper was to study the residual stress of the hoop structure caused by the cooling shrinkage of the weld when the outer cylinder was wrapped and welded under the condition of the existing inner cylinder. In this paper, the “method of killing activating elements” of ANSYS was used to simulate the three-dimensional finite element of the hoop structure. In the case of applying interlayer friction, the welding-forming process and welding circumferential residual stress of the hoop structure were analyzed. The blind hole method was used to test the residual stress distribution of the hoop structure, and the test results were compared with the finite element simulation results to verify the reliability of the simulation calculation method and the reliability of the calculation results. Then, the influence factors of the maximum welding residual stress of the hoop structure were studied. The results show that the maximum residual stress of the outer plate surface of the hoop structure decreases with the increase of the welding energy, the thickness of the laminate, the width of the weld seam, the welding speed, and the radius of the container. Based on the results of numerical simulation, the ternary first-order equations of the maximum residual stress of the hoop structure with respect to the welding speed, the thickness of the laminate, and the width of the weld seam were established. Then, the optimal welding parameters were obtained by optimizing the equations, which provided an important basis for the safe use and optimal design of the welding hoop structure.
Tolerance Modeling and Analysis Considering Form Defects for Spaceborne Array Antenna
Authors: Sa Guodong , Liu Zhenyu , Qiu Chan , Tan Jianrong
Published: April 2020

Tolerance analysis is becoming increasingly important for tolerance design and optimization. When dealing with electromechanical products such as the array antenna, the form errors of the assembly must be considered. Traditional tolerance analysis with form errors relies on a double loop process, which is computationally expensive. A new tolerance analysis method is proposed in this paper, which can be achieved by a single loop process. First, a new tolerance modeling method considering form errors was proposed, it can represent the geometric error of a surface feature precisely. Then an effective sampling method was developed by introducing the variance separation method. An assembly simulation method was proposed to determine the final state of the whole assembly. Finally, the tolerance analysis was achieved based on the sufficient sample. The proposed analysis method was applied to an X-band spaceborne active-phased array antenna, numerical simulation results show the effectiveness of the method.
Low-Frequency Vibration and Radiation Performance of a Locally Resonant Plate Attached with Periodic Multiple Resonators
Authors: Qin Qi , Sheng Meiping , Guo Zhiwei
Published: April 2020

The low-frequency vibration and radiation performance of a locally resonant (LR) plate with periodic multiple resonators is studied in this paper, with both infinite and finite structure properties examined. For the finite cases, taking the LR plate attached with two periodic arrays of resonators as an example, the forced vibration response and the radiation efficiency are theoretically derived by adopting a general model with elastic boundary conditions. Through a comparison with the band structures calculated by the plane-wave-expansion method, it shows that the band gaps in the infinite LR plate are in good agreement with the vibration-attenuation bands in the finite LR plate, no matter what boundary conditions are applied to the latter. In contrast to the vibration reduction in the band gaps, the radiation efficiency of the finite LR plate is sharply increased in the band-gap frequency ranges. Furthermore, the acoustic power radiated from the finite LR plate can be seriously affected by its boundary conditions. For the LR plate with greater constraints, the acoustic power is reduced in the band-gap frequency ranges, while that from the one with fully free boundary conditions is increased. When further considering the damping loss factors of the resonators, the attenuation performance can be improved for both the vibration and radiation of the LR plate.
Japan and the “Transnational Cinema”
Authors: Martín Marcos P. Centeno , Morita Nori
Published: April 2020

Since the Western “discovery” of Japanese cinema in the 1950s, there has been a tendency among both Film Studies and Japanese Studies scholars to draw on essentialist visions of Japanese Cinema, understating its uniqueness as a consequence of its isolation from the rest of the world [...]
Evaluation of Four Reanalysis Datasets against Radiosonde over Southwest Asia
Authors: Alghamdi Ali S.
Published: April 2020

Upper-air observational networks in Southwest Asia (SWA) are geographically sparse and reanalysis datasets (RDs) are a typical alternative. However, RDs can perform with varying degrees of quality and accuracy due to differences in assimilation schemes and input observations, among other factors. Geopotential height (gph), air temperature (tmp) and horizontal wind (U and V) modelled by the Japanese 55-year Reanalysis (JRA-55), the European Centre for Medium-Range Weather Forecasts Reanalysis Interim (ERA-I), the ERA fifth-generation (ERA-5), and the National Aeronautics and Space Administration (NASA) Modern Era Retrospective Analysis for Research and Applications version 2 (MERRA), are compared with radiosonde observations at three standard vertical levels (850, 500 and 300 hPa). Results showed that most RDs represent the general climatology, and ERA-5 tended to show the smallest agreements in most cases. RDs did not show consistent performance across seasons, variables, and pressure levels. RDs tended to conduct reasonable estimates over subregions with less complex topography. RDs showed better resampling performance at the upper and lower ends of sounding data distributions more frequently than around the means for most of the variables. This highlights the high potential usefulness of RDs in studying extremes over the region.
An Inter-Comparison of the Holiday Climate Index (HCI:Beach) and the Tourism Climate Index (TCI) to Explain Canadian Tourism Arrivals to the Caribbean
Authors: Rutty Michelle , Scott Daniel , Matthews Lindsay , Burrowes Ravidya , Trotman Adrian , Mahon Roché , Charles Amanda
Published: April 2020

Through an empirical investigation of the historical relationship between the destination climate and tourist arrivals in the Caribbean, this study presents the first revealed preference evaluation of a climate index informed by tourists’ stated climatic preferences for coastal-beach tourism (i.e., a sun-sand-surf or 3S travel market). The goal of this multi-organization collaboration was to examine the potential application of a newly designed climate index—the Holiday Climate Index (HCI):Beach—for three Caribbean destinations (Antigua and Barbuda, Barbados, Saint Lucia). This paper provides an overview of the evolution of climate indices, including the development of the (HCI):Beach. To test the validity of climate indices for a beach travel market, daily climate ratings based on outputs from the Tourism Climate Index and the HCI were correlated with monthly arrivals data from Canada (a key source market) at an island destination scale. The results underscore the strength of the new index, with each destination scoring consistently higher using the HCI:Beach, including a stronger relationship (R2) between index scores and tourist arrivals. These findings demonstrate the value of combining stated and revealed preference methodologies to predict tourism demand and highlight opportunities for future research.
The Microphysical Properties of a Sea-Fog Event along the West Coast of the Yellow Sea in Spring
Authors: Wang Shengkai , Yi Li , Zhang Suping , Shi Xiaomeng , Chen Xianyao
Published: April 2020

The microphysics and visibility of a sea-fog event were measured at the Qingdao Meteorological Station (QDMS) (120°19′ E, 36°04′ N) from 5 April to 8 April 2017. The two foggy periods with low visibility (<200 m) lasted 31 h together. The mean value of the average liquid water content (LWC) was 0.057 g m−3, and the mean value of the number concentration (NUM) was 64.4 cm−3. We found that although large droplets only constituted a small portion of the total number of the concentration; they contributed the majority of the LWC and therefore determined ~76% of total extinction of the visibility. The observed droplet-size distribution (DSD) exhibited a new bimodal Gaussian (G-exponential) distribution function, rather than the well-accepted Gamma distribution. This work suggests a new distribution function to describe fog DSD, which may help to improve the microphysical parameterization for the Yellow Sea fog numerical forecasting.
Generalized Briot-Bouquet Differential Equation Based on New Differential Operator with Complex Connections
Authors: Ibrahim Rabha W. , Elobaid Rafida M. , Obaiys Suzan J.
Published: April 2020

A class of Briot–Bouquet differential equations is a magnificent part of investigating the geometric behaviors of analytic functions, using the subordination and superordination concepts. In this work, we aim to formulate a new differential operator with complex connections (coefficients) in the open unit disk and generalize a class of Briot–Bouquet differential equations (BBDEs). We study and generalize new classes of analytic functions based on the new differential operator. Consequently, we define a linear operator with applications.
Ready to Use Therapeutical Beverages: Focus on Functional Beverages Containing Probiotics, Prebiotics and Synbiotics
Authors: Nazhand Amirhossein , Souto Eliana B. , Lucarini Massimo , Souto Selma B. , Durazzo Alessandra , Santini Antonello
Published: April 2020

The growing global interest in functional foods containing nutrients capable of adding possible beneficial health effects is rapidly increasing both interest and consumer demand. In particular, functionalized beverages for their potential positive effect on health e.g., decreasing cholesterol level, lowering sugar, high fiber content, ability to enhance the immune system, and help digestion, have recently received special attention. Among the different beverages available on the market, probiotic dairy and non-dairy products have attracted much attention because of their affordable cost and their numerous therapeutic activities. Fermented milk and yogurt are currently worth €46 billion, with 77% of the market reported in Europe, North America, and Asia. Consumption of dairy beverages has some limitations due for example to lactose intolerance and allergy to milk proteins, thereby leading consumers to use non-dairy beverages such as fruit, grains, and vegetable juices to add probiotics to diet as well as driving the manufacturers to food matrices-based beverages containing probiotic cultures. The purpose of this review article is to evaluate the therapeutic performance and properties of dairy and non-dairy beverages in terms of probiotic, prebiotic, and synbiotic activities.
Whole Organism Model to Study Molecular Mechanisms of Differentiation and Dedifferentiation
Authors: Anwar Areeba , Siddiqui Ruqaiyyah , Khan Naveed Ahmed
Published: April 2020

Cancer recurrence has remained a significant challenge, despite advances in therapeutic approaches. In part, this is due to our incomplete understanding of the biology of cancer stem cells and the underlying molecular mechanisms. The phenomenon of differentiation and dedifferentiation (phenotypic switching) is not only unique to stem cells but it is also observed in several other organisms, as well as evolutionary-related microbes. Here, we propose the use of a primitive eukaryotic unicellular organism, Acanthamoeba castellanii, as a model to study the molecular mechanisms of cellular differentiation and dedifferentiation.
Overexpression of T-bet, GATA-3 and TGF-ß Induces IFN-γ, IL-4/13A, and IL-17A Expression in Atlantic Salmon
Authors: Slettjord Tiril H. , Sekkenes Hege J. , Chi Heng , Bøgwald Jarl , Swain Trilochan , Dalmo Roy A. , Kumari Swain Jaya
Published: April 2020

The overexpression of GATA-3, T-bet and TGF-ß may theoretically induce IL-4/A, IFN-γ and IL-17A expression, respectively. Whether this also applies to fish is not yet known. The plasmid vectors encoding reporter gene (RFP)-tagged T-bet, GATA-3 and TGF-ß were used as overexpression tools, transfected into cells or injected intramuscularly to monitor the expression of IFN-γ, IL-4/13A and IL-17A. In addition, the fish were either experimentally challenged with Vibrio anguillarum (VA group) or Piscirickettsia salmonis (PS group). The reporter gene (RFP) inserted upstream of the GATA-3, T-bet and TGF-ß genes, was observed in muscle cell nuclei and in inflammatory cells after intramuscular (i.m.) injection. PS group: following the injection of GATA-3 and T-bet-encoding plasmids, the expression of GATA-3 and T-bet was high at the injection site. The spleen expression of IFN-γ, following the injection of a T-bet-encoding plasmid, was significantly higher on day 2. VA group: The T-bet and GATA-3-overexpressing fish expressed high T-bet and GATA-3 mRNA levels in the muscles and on day 4 post-challenge. The expression of TGF-ß in the muscles of fish injected with TGF-ß-encoding plasmids was significantly higher on days 7 (8 days pre-challenge) and 19 (4 days after challenge). The protective effects of the overexpression of T-bet, GATA-3 and TGF-ß on both bacterial infections were negligible.
LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method
Authors: Yan Tongmeng , Hu Kua , Ren Fei , Jiang Zhihong
Published: April 2020

Transfer RNAs (tRNAs) are the most heavily modified RNA species in life entities. Post-transcriptional modifications severely impact the structure and function of tRNAs. To date, hundreds of modifications have been identified in tRNAs, mainly from microorganisms and animals. However, tRNAs in plant roots or tubers that have been widely used for food and medical purpose for centuries are rarely studied because isolation of RNA from plants still remains a challenge. In this paper, a polysaccharase-aided RNA isolation (PARI) method for extraction of high-quality RNA from plants containing large quantities of polysaccharides is developed. This method presents a new strategy of “digesting” polysaccharides that is completely different from the conventional method of “dissolving” the contaminants. By using this method, RNA of high integrity and purity were successfully extracted from ginseng roots because polysaccharide contaminations were removed efficiently with α-amylase digestion. Ginseng tRNAs were first sequenced by NGS and a total of 41 iso acceptors were identified. ChloroplastictRNAGly(GCC) in ginseng root was purified and four modified nucleosides, including m7G, D, T, and Ψ, were identified by LC-MS/MS. The results also revealed that the m7G occurs at a novel position 18, which may be related to the deformation of D-loop. PARI is the first enzyme-assisted technique for RNA isolation from plants, which could fundamentally solve the problem of polysaccharide contaminations. By using the PARI method, more individual tRNAs could be isolated easily from polysaccharide-rich plant tissues, which would have a positive impact on the feasibility of research on structure and function of tRNA in plants.
Physicochemical Characterisation of KEIF—The Intrinsically Disordered N-Terminal Region of Magnesium Transporter A
Authors: Jephthah Stéphanie , Månsson Linda K. , Belić Domagoj , Morth Jens Preben , Skepö Marie
Published: April 2020

Magnesium transporter A (MgtA) is an active transporter responsible for importing magnesium ions into the cytoplasm of prokaryotic cells. This study focuses on the peptide corresponding to the intrinsically disordered N-terminal region of MgtA, referred to as KEIF. Primary-structure and bioinformatic analyses were performed, followed by studies of the undisturbed single chain using a combination of techniques including small-angle X-ray scattering, circular dichroism spectroscopy, and atomistic molecular-dynamics simulations. Moreover, interactions with large unilamellar vesicles were investigated by using dynamic light scattering, laser Doppler velocimetry, cryogenic transmission electron microscopy, and circular dichroism spectroscopy. KEIF was confirmed to be intrinsically disordered in aqueous solution, although extended and containing little β-structure and possibly PPII structure. An increase of helical content was observed in organic solvent, and a similar effect was also seen in aqueous solution containing anionic vesicles. Interactions of cationic KEIF with anionic vesicles led to the hypothesis that KEIF adsorbs to the vesicle surface through electrostatic and entropic driving forces. Considering this, there is a possibility that the biological role of KEIF is to anchor MgtA in the cell membrane, although further investigation is needed to confirm this hypothesis.
Machine Learning Approaches for Quality Assessment of Protein Structures
Authors: Chen Jiarui , Siu Shirley W. I.
Published: April 2020

Protein structures play a very important role in biomedical research, especially in drug discovery and design, which require accurate protein structures in advance. However, experimental determinations of protein structure are prohibitively costly and time-consuming, and computational predictions of protein structures have not been perfected. Methods that assess the quality of protein models can help in selecting the most accurate candidates for further work. Driven by this demand, many structural bioinformatics laboratories have developed methods for estimating model accuracy (EMA). In recent years, EMA by machine learning (ML) have consistently ranked among the top-performing methods in the community-wide CASP challenge. Accordingly, we systematically review all the major ML-based EMA methods developed within the past ten years. The methods are grouped by their employed ML approach—support vector machine, artificial neural networks, ensemble learning, or Bayesian learning—and their significances are discussed from a methodology viewpoint. To orient the reader, we also briefly describe the background of EMA, including the CASP challenge and its evaluation metrics, and introduce the major ML/DL techniques. Overall, this review provides an introductory guide to modern research on protein quality assessment and directions for future research in this area.
RETRACTED: Liu et al. Ailanthone Induces Cell Cycle Arrest and Apoptosis in Melanoma B16 and A375 Cells. Biomolecules 2019, 9, 275
Authors:   Biomolecules Editorial Office
Published: April 2020

The Editorial Office and the authors have taken the decision to retract the published article [...]
Immunogenicity and Protective Effect of a Virus-Like Particle Containing the SAG1 Antigen of Toxoplasma gondii as a Potential Vaccine Candidate for Toxoplasmosis
Authors: Choi Won Hyung , Park Ji Sun
Published: April 2020

This study was carried out to evaluate the vaccination effect of a virus-like particle (VLP) including the surface antigen 1 (SAG1) of Toxoplasma gondii as a potential vaccine for toxoplasmosis. The SAG1 virus-like particles (SAG1-VLPs) were expressed by Sf9 cells, and their expression was confirmed through cloning, RT-PCR analysis, and western blot method. The immunogenicity and vaccine efficacy of SAG1-VLPs were assessed by the antibody response, cytokine analysis, neutralization activity, splenocyte assay, and survival rates through a mouse model. In particular, IgG, IgG1, IgG2a, and IgA were markedly increased after immunization, and the survival rates of T. gondii were strongly inhibited by the immunized sera. Furthermore, the immunization of SAG1-VLPs effectively decreased the production of specific cytokines, such as IL-1β, IL-6, TNF-α, and IFN-γ, after parasite infection. In particular, the immunized group showed strong activity and viability compared with the non-immunized infection group, and their survival rate was 75%. These results demonstrate that SAG1-VLP not only has the immunogenicity to block T. gondii infection by effectively inducing the generation of specific antibodies against T. gondii, but is also an effective antigen delivery system for preventing toxoplasmosis. This study indicates that SAG1-VLP can be effectively utilized as a promising vaccine candidate for preventing or inhibiting T. gondii infection.
Structure and Frictional Properties of the Leg Joint of the Beetle Pachnoda marginata (Scarabaeidae, Cetoniinae) as an Inspiration for Technical Joints
Authors: Vagts Steffen , Schlattmann Josef , Kovalev Alexander , Gorb Stanislav N.
Published: April 2020

The efficient locomotion of insects is not only inspiring for control algorithms but also promises innovations for the reduction of friction in joints. After previous analysis of the leg kinematics and the topological characterization of the contacting joint surfaces in the beetle Pachnoda marginata, in the present paper, we report on the measurement of the coefficient of friction within the leg joints exhibiting an anisotropic frictional behavior in different sliding directions. In addition, the simulation of the mechanical behavior of a single microstructural element helped us to understand the interactions between the contact parts of this tribological system. These findings were partly transferred to a technical contact pair which is typical for such an application as joint connectors in the automotive field. This innovation helped to reduce the coefficient of friction under dry sliding conditions up to 17%.
Dexamethasone Attenuates X-Ray-Induced Activation of the Autotaxin-Lysophosphatidate-Inflammatory Cycle in Breast Tissue and Subsequent Breast Fibrosis
Authors: Meng Guanmin , Wuest Melinda , Tang Xiaoyun , Dufour Jennifer , McMullen Todd P.W. , Wuest Frank , Murray David , Brindley David N.
Published: April 2020

We recently showed that radiation-induced DNA damage in breast adipose tissue increases autotaxin secretion, production of lysophosphatidate (LPA) and expression of LPA1/2 receptors. We also established that dexamethasone decreases autotaxin production and LPA signaling in non-irradiated adipose tissue. In the present study, we showed that dexamethasone attenuated the radiation-induced increases in autotaxin activity and the concentrations of inflammatory mediators in cultured human adipose tissue. We also exposed a breast fat pad in mice to three daily 7.5 Gy fractions of X-rays. Dexamethasone attenuated radiation-induced increases in autotaxin activity in plasma and mammary adipose tissue and LPA1 receptor levels in adipose tissue after 48 h. DEX treatment during five daily fractions of 7.5 Gy attenuated fibrosis by ~70% in the mammary fat pad and underlying lungs at 7 weeks after radiotherapy. This was accompanied by decreases in CXCL2, active TGF-β1, CTGF and Nrf2 at 7 weeks in adipose tissue of dexamethasone-treated mice. Autotaxin was located at the sites of fibrosis in breast tissue and in the underlying lungs. Consequently, our work supports the premise that increased autotaxin production and lysophosphatidate signaling contribute to radiotherapy-induced breast fibrosis and that dexamethasone attenuated the development of fibrosis in part by blocking this process.
Ultraweak Photon Emissions as a Non-Invasive, Early-Malignancy Detection Tool: An In Vitro and In Vivo Study
Authors: Murugan Nirosha J. , Persinger Michael A. , Karbowski Lukasz M. , Dotta Blake T.
Published: April 2020

Early detection of cancer improves treatment options and increases survival. Building upon previous demonstrations that ultraweak photon emissions (UPE) could be measured to detect cancers, we designed an early detection protocol to test malignancy in both in vitro and in vivo systems. Photons were measured for 100 s from plates containing ~1 million malignant or non-malignant cells from 13 different types of human and mouse cell lines. Tumor cells displayed increased photon emissions compared to non-malignant cells. Examining the standardized Spectral Power Density (SPD) configurations for flux densities between 0.1 and 25 Hz (Δf = 0.01 Hz) yielded 90% discriminant accuracy. The emission profiles of mice that had been injected with melanoma cells could be differentiated from a non-malignant reference groups as early as 24 h post-injection. The peak SPD associated with photon emissions was ~20 Hz for both malignant cell cultures and mice with growing tumors. These results extend the original suggestion by Takeda and his colleagues (2004) published in this journal concerning the potential diagnostic value of UPEs for assessing proliferations of carcinoma cells. The specificity of the spectral profile in the 20 Hz range may be relevant to the consistent efficacy reported by several authors that weak magnetic field pulsations within this frequency range can diminish the growth of malignant cells in culture and tumor weights in mice.
P66Shc: A Pleiotropic Regulator of B Cell Trafficking and a Gatekeeper in Chronic Lymphocytic Leukemia
Authors: Patrussi Laura , Capitani Nagaja , Baldari Cosima T.
Published: April 2020

Neoplastic B cells from chronic lymphocytic leukemia patients (CLL) have a profound deficiency in the expression of p66Shc, an adaptor protein with pro-apoptotic and pro-oxidant activities. This defect results in leukemic B cell resistance to apoptosis and additionally impinges on the balance between chemokine receptors that control B cell homing to secondary lymphoid organs and the sphingosine phosphate receptor S1PR1 that controls their egress therefrom, thereby favoring leukemic B cell accumulation in the pro-survival lymphoid niche. Ablation of the gene encoding p66Shc in the Eµ-TCL1 mouse model of human CLL enhances leukemogenesis and promotes leukemic cell invasiveness in both nodal and extranodal organs, providing in vivo evidence of the pathogenic role of the p66Shc defect in CLL pathogenesis. Here we present an overview of the functions of p66Shc in B lymphocytes, with a specific focus on the multiple mechanisms exploited by p66Shc to control B cell trafficking and the abnormalities in this process caused by p66Shc deficiency in CLL.
Expansion of Circulating Tumor Cells from Patients with Locally Advanced Pancreatic Cancer Enable Patient Derived Xenografts and Functional Studies for Personalized Medicine
Authors: Rivera-Báez Lianette , Lohse Ines , Lin Eric , Raghavan Shreya , Owen Sarah , Harouaka Ramdane , Herman Kirk , Mehta Geeta , Lawrence Theodore S. , Morgan Meredith A. , Cuneo Kyle C. , Nagrath Sunitha
Published: April 2020

Improvement in pancreatic cancer treatment represents an urgent medical goal that has been hampered by the lack of predictive biomarkers. Circulating Tumor Cells (CTCs) may be able to overcome this issue by allowing the monitoring of therapeutic response and tumor aggressiveness through ex vivo expansion. The successful expansion of CTCs is challenging, due to their low numbers in blood and the high abundance of blood cells. Here, we explored the utility of pancreatic CTC cultures as a preclinical model for treatment response. CTCs were isolated from ten patients with locally advanced pancreatic cancer using the Labyrinth, a biomarker independent, size based, inertial microfluidic separation device. Three patient-derived CTC samples were successfully expanded in adherent and spheroid cultures. Molecular and functional characterization was performed on the expanded CTC lines. CTC lines exhibited KRAS mutations, consistent with pancreatic cancers. Additionally, we evaluated take rate and metastatic potential in vivo and examined the utility of CTC lines for cytotoxicity assays. Patient derived expanded CTCs successfully generated patient derived xenograft (PDX) models with a 100% take rate. Our results demonstrate that CTC cultures are possible and provide a valuable resource for translational pancreatic cancer research, while also providing meaningful insight into the development of distant metastasis, as well as treatment resistance.
Contribution of Macrophages and T Cells in Skeletal Metastasis
Authors: Mendoza-Reinoso Veronica , McCauley Laurie K. , Fournier Pierrick G.J.
Published: April 2020

Bone is a common site for metastases with a local microenvironment that is highly conducive for tumor establishment and growth. The bone marrow is replete with myeloid and lymphoid linage cells that provide a fertile niche for metastatic cancer cells promoting their survival and growth. Here, we discuss the role of macrophages and T cells in pro- and anti-tumoral mechanisms, their interaction to support cancer cell growth, and their contribution to the development of skeletal metastases. Importantly, immunotherapeutic strategies targeting macrophages and T cells in cancer are also discussed in this review as they represent a great promise for patients suffering from incurable bone metastases.
Preparation of CdS Nanoparticles-TiO2 Nanorod Hererojunction and Their High-Performance Photocatalytic Activity
Authors: Song Jianhua , Zeng Dedong , Xie Yu , Zhang Fayun , Rao Shenli , Wang Fahui , Zhao Jinsheng , Zhang Jinbing , Wang Lei
Published: April 2020

As a new and emerging technology, photocatalytic oxidation is widely used in the fields of sewage treatment and organic pollution control. In this study, CdS nanoparticles were prepared at room temperature by an innovative preparation method, then TiO2 nanorod–CdS nanoparticle heterojunction photocatalysts were prepared using the solvothermal method, with TiCl3 used as the precursor for TiO2 nanorods. This study mainly took advantage of the small size of the CdS nanoparticles in combination with TiO2 nanorods, and the resultant heterojunctions had large specific surface areas, thereby increasing the contact area between the catalysts and the contaminants. In addition, due to the lower band gap energy (2.4 eV) of CdS, the photo response range of the heterojunction photocatalysts was also increased. In an experimental study, through photocatalytic performance tests of the catalysts with different weight ratios, it was found that the TiO2(40%)@CdS composite had the best photocatalytic performance and the highest catalytic rate. BET, SEM, and other tests showed that the specific surface area of the TiO2(40%)@CdS composite was the largest. TiO2 nanorods and CdS particles were uniformly distributed in the composite, and the optical response range was extended to the visible light region.
Advances in Designing Au Nanoparticles for Catalytic Epoxidation of Propylene with H2 and O2
Authors: Nguyen Van-Huy , Nguyen Ba-Son , Hu Chechia , Sharma Ajit , Vo Dai-Viet N. , Jin Zhong , Shokouhimehr Mohammadreza , Jang Ho Won , Kim Soo Young , Le Quyet Van
Published: April 2020

Au nanoparticles, which can be used in various industrial and environmental applications, have drawn substantial research interest. In this review, a comprehensive background and some insights are provided regarding recent studies concerning the use of Au nanoparticles for catalytic propylene epoxidation with H2 and O2. Over the last two decades, substantial progress has been made toward the efficient production of propylene oxide (PO); this includes the design of highly dispersed Au catalysts on Ti-modified mesoporous silica supports, the optimization of catalytic epoxidation, and the determination of the mechanisms and reaction pathways of epoxidation. Particularly, the critical roles of catalyst synthesis, the types of material support, Au nanoparticle sizes, and the dispersion amounts of Au nanoparticles are emphasized in this review. In future studies, novel, practical, robust, and highly PO-selective Au nanoparticle catalyst systems are expected to be continually designed for the enhanced catalytic epoxidation of propylene.
Palladium and Copper Catalyzed Sonogashira cross Coupling an Excellent Methodology for C-C Bond Formation over 17 Years: A Review
Authors: Kanwal Iram , Mujahid Aqsa , Rasool Nasir , Rizwan Komal , Malik Ayesha , Ahmad Gulraiz , Shah Syed Adnan Ali , Rashid Umer , Nasir Nadiah Mad
Published: April 2020

Sonogashira coupling involves coupling of vinyl/aryl halides with terminal acetylenes catalyzed by transition metals, especially palladium and copper. This is a well known reaction in organic synthesis and plays a role in sp2-sp C-C bond formations. This cross coupling was used in synthesis of natural products, biologically active molecules, heterocycles, dendrimers, conjugated polymers and organic complexes. This review paper focuses on developments in the palladium and copper catalyzed Sonogashira cross coupling achieved in recent years concerning substrates, different catalyst systems and reaction conditions.