bluuebunny/crossref_metadata_2025 huggingface dataset:
Field Cage Assessment of Feeding Damage by Riptortus pedestris on Soybeans in China
Authors: Li Wenjing , Gao Yu , Hu Yinglu , Chen Juhong , Zhang Jinping , Shi Shusen
Published: March 2021

The bean bug, Riptortus pedestris, is a major pest of soybeans. In order to assess the critical stages of soybean damage by R. pedestris, we tested the damage to soybeans at different growth stages (R2, R4, and R6) caused by five densities of R. pedestris (1, 2, 3, 4, and 5) through a field cage experiment. The results show that the R4 stage was the most sensitive stage in terms of suffering R. pedestris injury damage, followed by the R6 stage and then the R2 stage. The number of stay green leaves was 7.04 per plant, the abortive pod rate of the soybeans was 56.36%, and the abortive seed rate of the soybeans was 46.69%. The dry weight of the soybeans was 14.20 g at the R4 stage; these values of R4 were significantly higher than at the R2 and R6 stages. However, the dry weight of soybean seed was 4.27 g and the nutrient transfer rate was 27.01% in the R4 stage; these values were significantly lower than in the R2 and R6 stages. The number of stay green leaves, abortive pod rates, and abortive seed rates were all increased significantly with increasing pest density at each stage of soybean growth. However, the nutrient transfer rate was significantly decreased with the increase in the pest density. Soybean nutrition factors changed after they suffered R. pedestris injury; the lipid content of the soybean seed decreased and the lipid content of the soybean plant increased compared to controls, when tested with a density of five R. pedestris in the R4 stage. These results will be beneficial to the future management of R. pedestris in soybean fields.
Managing Osteoporosis and Joint Damage in Patients with Rheumatoid Arthritis: An Overview
Authors: Tanaka Yoshiya
Published: March 2021

In rheumatoid arthritis, a representative systemic autoimmune disease, immune abnormality and accompanying persistent synovitis cause bone and cartilage destruction and systemic osteoporosis. Biologics targeting tumor necrosis factor, which plays a central role in the inflammatory process, and Janus kinase inhibitors have been introduced in the treatment of rheumatoid arthritis, making clinical remission a realistic treatment goal. These drugs can prevent structural damage to bone and cartilage. In addition, osteoporosis, caused by factors such as menopause, aging, immobility, and glucocorticoid use, can be treated with bisphosphonates and the anti-receptor activator of the nuclear factor-κB ligand antibody. An imbalance in the immune system in rheumatoid arthritis induces an imbalance in bone metabolism. However, osteoporosis and bone and cartilage destruction occur through totally different mechanisms. Understanding the mechanisms underlying osteoporosis and joint destruction in rheumatoid arthritis leads to improved care and the development of new treatments.
Insights into Macrophage/Monocyte-Endothelial Cell Crosstalk in the Liver: A Role for Trem-2
Authors: Coelho Inês , Duarte Nádia , Macedo Maria Paula , Penha-Gonçalves Carlos
Published: March 2021

Liver disease accounts for millions of deaths worldwide annually being a major cause of global morbidity. Hepatotoxic insults elicit a multilayered response involving tissue damage, inflammation, scar formation, and tissue regeneration. Liver cell populations act coordinately to maintain tissue homeostasis and providing a barrier to external aggressors. However, upon hepatic damage, this tight regulation is disrupted, leading to liver pathology which spans from simple steatosis to cirrhosis. Inflammation is a hallmark of liver pathology, where macrophages and endothelial cells are pivotal players in promoting and sustaining disease progression. Understanding the drivers and mediators of these interactions will provide valuable information on what may contribute to liver resilience against disease. Here, we summarize the current knowledge on the role of macrophages and liver sinusoidal endothelial cells (LSEC) in homeostasis and liver pathology. Moreover, we discuss the expanding body of evidence on cell-to-cell communication between these two cell compartments and present triggering receptor expressed on myeloid cells-2 (Trem-2) as a plausible mediator of this cellular interlink. This review consolidates relevant knowledge that might be useful to guide the pursue of successful therapeutic targets and pharmacological strategies for controlling liver pathogenesis.
The Effect of Wave-Induced Current and Coastal Structure on Sediment Transport at the Zengwen River Mouth
Authors: Pao Chun-Hung , Chen Jia-Lin , Su Shih-Feng , Huang Yu-Ching , Huang Wen-Hsin , Kuo Chien-Hung
Published: March 2021

The mechanisms that control estuarine sediment transport are complicated due to the interaction between riverine flows, tidal currents, waves, and wave-driven currents. In the past decade, severe seabed erosion and shoreline retreat along the sandy coast of western Taiwan have raised concerns regarding the sustainability of coastal structures. In this study, ADCPs (Acoustic Doppler Current Profiler) and turbidity meters were deployed at the mouth of the Zengwen river to obtain the time series and the spatial distribution of flow velocities and turbidity during the base flow and flood conditions. A nearshore circulation model, SHORECIRC, has been adapted into a hybrid finite-difference/finite-volume, TVD (Total Variation Diminishing)-type scheme and coupled with the wave-spectrum model Simulating Waves Nearshore (SWAN). Conventional finite-difference schemes often produce unphysical oscillations when modeling coastal processes with abrupt bathymetric changes at river mouths. In contrast, the TVD-type finite volume scheme allows for robust treatment of discontinuities through the shock-capturing mechanism. The model reproduces water levels, waves, currents observed at the mouth of the Zengwen River reasonably well. The simulated residual sediment transport patterns demonstrate that the transport process at the river mouth is dominated by the interaction of the bathymetry and wave-induced currents when the riverine discharge was kept in reservoirs. The offshore residual transport causes erosion at the northern part of the river mouth, and the onshore residual transport causes accretion in the ebb tidal shoals around the center of the river mouth. The simulated morphological evolution displays significant changes on shallower deltas. The location with significant sea bed changes is consistent with the spot in which severe erosion occurred in recent years. Further analysis of morphological evolution is also discussed to identify the role of coastal structures, for example, the extension of the newly constructed groins near the river mouth.
Diversity and N2O Production Potential of Fungi in an Oceanic Oxygen Minimum Zone
Authors: Peng Xuefeng , Valentine David L.
Published: March 2021

Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled 15N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N2O) production. Fungal communities evaluated by ITS2 sequencing were dominated by the phyla Basidiomycota and Ascomycota at most depths. However, the metagenome dataset showed that about one third of the fungal community belong to early-diverging phyla. Fungal N2O production rates peaked at the oxic–anoxic interface of the water column, and when integrated from the oxycline to the top of the anoxic depths, fungi accounted for 18–22% of total N2O production. Our findings highlight the limitation of ITS-based methods typically used to investigate terrestrial fungal diversity and indicate that fungi may play an active role in marine nitrogen cycling.
Comparison of Attitudes towards Roadside Vegetation Management across an Exurban Landscape
Authors: DiFalco Steven , Morzillo Anita
Published: March 2021

Exurban development is the fastest growing land use across the United States (US). Its prevalence on the East Coast is susceptible to natural disaster events such as hurricanes and nor’easters. However, the socio-ecological processes related to disaster mitigation within exurban areas remain understudied. Our objective was to integrate social and landscape data to compare resident attitudes towards utility roadside vegetation management across four areas in the state of Connecticut, US. We collected data from residents using two mail surveys completed in 2017 and 2019 (n = 1962). From the survey questions, three attitude variables measured perceptions of the utility vegetation management process, and tradeoffs between protecting trees and maintaining reliable power. Across all locations, respondents with more favorable attitudes toward vegetation management were more likely to have greater knowledge about trees, and beliefs that trees should be used for human benefit; land cover characteristics and sociodemographic variables were less strongly associated with attitudes scores. Respondents differed among study areas in their preferences for aesthetics of roadside trees and their basic beliefs regarding the importance of trees. The results suggested that social processes within the exurban landscapes are spatially heterogeneous. Therefore, local variation in residential preferences for vegetation management may influence support for natural disaster management policy.
Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology
Authors: Ge Huanhuan , Marchisio Mario Andrea
Published: March 2021

Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.
Modeling of Nonlinear Optical Phenomena in Host-Guest Systems Using Bond Fluctuation Monte Carlo Model: A Review
Authors: Mitus Antoni C. , Saphiannikova Marina , Radosz Wojciech , Toshchevikov Vladimir , Pawlik Grzegorz
Published: March 2021

We review the results of Monte Carlo studies of chosen nonlinear optical effects in host-guest systems, using methods based on the bond-fluctuation model (BFM) for a polymer matrix. In particular, we simulate the inscription of various types of diffraction gratings in degenerate two wave mixing (DTWM) experiments (surface relief gratings (SRG), gratings in polymers doped with azo-dye molecules and gratings in biopolymers), poling effects (electric field poling of dipolar molecules and all-optical poling) and photomechanical effect. All these processes are characterized in terms of parameters measured in experiments, such as diffraction efficiency, nonlinear susceptibilities, density profiles or loading parameters. Local free volume in the BFM matrix, characterized by probabilistic distributions and correlation functions, displays a complex mosaic-like structure of scale-free clusters, which are thought to be responsible for heterogeneous dynamics of nonlinear optical processes. The photoinduced dynamics of single azopolymer chains, studied in two and three dimensions, displays complex sub-diffusive, diffusive and super-diffusive dynamical regimes. A directly related mathematical model of SRG inscription, based on the continuous time random walk (CTRW) formalism, is formulated and studied. Theoretical part of the review is devoted to the justification of the a priori assumptions made in the BFM modeling of photoinduced motion of the azo-polymer chains.
The Analysis of the Morphology of the Saddle-Shaped Bronze Chips Briquettes Produced in the Roller Press
Authors: Bembenek Michał , Krawczyk Janusz , Frocisz Łukasz , Śleboda Tomasz
Published: March 2021

This paper presents the results of the investigations of the properties of saddle-shaped copper alloy chips briquettes produced in a roller press. The physical and mechanical properties of the investigated briquettes were examined on their external surfaces as well as on their cross-sections. The density, chemical composition, microstructure analysis obtained with a 3D and scanning microscope, surface roughness and hardness of the obtained briquettes were investigated. The research proved the differentiation of the physical and mechanical properties of briquettes depending on the investigated area of their surface. The analysis of changes in the porosity of briquettes on their cross-section showed zones of various densification levels. This research expands the knowledge of the processes taking place during the compaction and consolidation of granular materials in roller presses as well as the knowledge concerning designing the geometry of forming tools.
Effect of Thermal Treatment and Erosion Aggressiveness on Resistance of S235JR Steel to Cavitation and Slurry
Authors: Krella Alicja K. , Zakrzewska Dominika E. , Buszko Marta H. , Marchewicz Artur
Published: March 2021

S235JR steel is used in many applications, but its resistance to the erosion processes has been poorly studied. To investigate this resistance, cavitation, and slurry erosion tests were conducted. These tests were carried out at different erosion intensities, i.e., different flow rates in the cavitation tunnel with a system of barricades and different rotational speeds in the slurry pot. The steel was tested as-received and after thermal treatment at 930 °C, which lowered the hardness of the steel. To better understand the degradation processes, in addition to mass loss measurements, surface roughness and hardness were measured. Along with increasing erosion intensity, the mass loss increased as well. However, the nature of the increase in mass loss, as well as the effect of steel hardness on this mass loss, was different for each of the erosion processes. In the cavitation erosion tests, the mass loss increased linearly with the increase in flow velocity, while in the slurry tests this relationship was polynomial, indicating a strong increase in mass losses with an increase in rotational speed. Cavitation erosion resulted in stronger and deeper strain hardening than slurry. Surface damage from cavitation erosion tests was mainly deep pits, voids, and cracks during the slurry tests, while flaking was the most significant damage.
Analytical Model of Two-Directional Cracking Shear-Friction Membrane for Finite Element Analysis of Reinforced Concrete
Authors: Mitchell Jeffrey P. , Cho Bum-Yean , Kim Yoo-Jae
Published: March 2021

There are a multitude of existing material models for the finite element analysis of cracked reinforced concrete that provide reduced shear stiffness but do not limit shear strength. In addition, typical models are not based on the actual physical behavior of shear transfer across cracks by shear friction recognized in the ACI 318 Building Code. A shear-friction model was recently proposed that was able to capture the recognized cracked concrete behavior by limiting shear strength as a yielding function in the reinforcement across the crack. However, the proposed model was formulated only for the specific case of one-directional cracking parallel to the applied shear force. This study proposed and generalized an orthogonal-cracking shear-friction model for finite element use. This was necessary for handling the analysis of complex structures and nonproportional loading cases present in real design and testing situations. This generalized model was formulated as a total strain-based model using the approximation that crack strains are equal to total strains, using the proportional load vector, constant vertical load, and modified Newton–Raphson method to improve the model’s overall accuracy.
Influence of Geometric and Manufacturing Parameters on the Compressive Behavior of 3D Printed Polymer Lattice Structures
Authors: Guerra Silva Rafael , Salinas Estay Cristóbal , Morales Pavez Gustavo , Zahr Viñuela Jorge , Torres María Josefina
Published: March 2021

Fused deposition modeling represents a flexible and relatively inexpensive alternative for the production of custom-made polymer lattices. However, its limited accuracy and resolution lead to geometric irregularities and poor mechanical properties when compared with the digital design. Although the link between geometric features and mechanical properties of lattices has been studied extensively, the role of manufacturing parameters has received little attention. Additionally, as the size of cells/struts nears the accuracy limit of the manufacturing process, the interaction between geometry and manufacturing parameters could be decisive. Hence, the influence of three geometric and two manufacturing parameters on the mechanical behavior was evaluated using a fractional factorial design of experiments. The compressive behavior of two miniature lattice structures, the truncated octahedron and cubic diamond, was evaluated, and multilinear regression models for the elastic modulus and plateau stress were developed. Cell size, unit cell type, and strut diameter had the largest impact on the mechanical properties, while the influence of feedstock material and layer thickness was very limited. Models based on factorial design, although limited in scope, could be an effective tool for the design of customized lattice structures.
Feasible Use of Recycled Concrete Aggregates with Alumina Waste in Road Construction
Authors: Cabrera Manuel , López-Alonso Mónica , Garach Laura , Alegre Javier , Ordoñez Javier , Agrela Francisco
Published: March 2021

The management of different industrial by-products, such as recycled aggregates from construction and demolition waste and alumina by-products, as well as the reduction of landfill deposits by incorporating these products in a second life cycle, were the focus of this work. The aim of this study was to demonstrate the technical viability of using these waste and by-product as a material for road pavement base layers. For this purpose, a real-scale application was carried out, and the behavior of three types of materials, applied on a section of an experimental road under real vehicle traffic conditions, was studied and compared. Three materials were used in these sections applied in the road sub-bases. First, a control material composed of a type of artificial gravel was used to be compared with the rest of materials; the second material was composed of recycled aggregates, and the third was composed of a mix of recycled aggregates and alumina waste. The results concluded that the effectiveness of the sections built using recycled aggregates and alumina waste was very positive and similar those constructed using natural aggregates.
Effect of Air-Abraded Versus Laser-Fused Fluorapatite Glass-Ceramics on Shear Bond Strength of Repair Materials to Zirconia
Authors: Elraggal Alaaeldin , Silikas Nikolaos
Published: March 2021

Zirconia repair could be a feasible alternative option to total replacement in fractured zirconia-based restorations. Maximising the bond strength by enriching zirconia with fluorapatite glass-ceramics (FGC) powder has been addressed and compared to other surface treatments. Besides resin composite, other repair materials have been proposed and compared. Zirconia blocks received different surface treatments (A—sandblasting with tribochemical silica-coated alumina (CoJet). B—sandblasting with FGC powder (FGC), C—fluorapatite glass-ceramic coat+ neodymium-doped yttrium aluminum garnet laser irradiation (FGC + Nd: YAG), and D—no surface treatment). The surface roughness, topography, and crystallinity were investigated by a profilometer, scanning electron microscopy (SEM), and X-ray diffraction (XRD) analyses, respectively. For each surface treatment, three repair materials (feldspathic porcelain, lithium disilicate, and resin composite) were bonded to zirconia with 10, Methacryloyloxydecyl dihydrogen phosphate (MDP)–Monobond Plus/ Multilink Automix. Bonded specimens were thermocycled for 10,000 cycles and tested for shear bond strength (SBS) at a speed of 1 mm/min, followed by the analysis of the mode of failure. FGC + Nd: YAG laser group reported the highest surface roughness and monoclinic content compared to CoJet, FGC, and control groups. The highest mean SBS was found in FGC-blasted zirconia, followed by FGC + Nd: YAG laser and CoJet treated groups. However, the lowest SBS was found in control groups regardless of the repair material. Sandblasting zirconia with FGC powder increased SBS of resin to zirconia with lower monoclinic phase transformation compared to FGC + Nd: YAG or CoJet groups.
Tissue Level Changes after Maxillary Sinus Floor Elevation with Three Types of Calcium Phosphate Ceramics: A Radiological Study with a 5-Year Follow-Up
Authors: Bouwman Wilhelmus F. , Bravenboer Nathalie , ten Bruggenkate Christiaan M. , Eijsackers Francis A. , Stringa Najada , Schulten Engelbert A. J. M.
Published: March 2021

This study evaluates the radiological changes in tissue height after maxillary sinus floor elevation (MSFE) using three types of calcium phosphate ceramics over a period of up to 5 years after dental implant placement. In 163 patients, MSFE was performed. Three groups of patients were distinguished and treated based on the type of calcium phosphate ceramic used and radiologically evaluated: 40 patients with β-tricalcium phosphate (β-TCP), 76 patients with biphasic calcium phosphate (BCP) 20% hydroxyapatite (HA)-80% β-TCP, and 47 patients with BCP 60% HA-40% β-TCP. Radiological measurements were performed on panoramic radiographs at several time points up to 5 years after dental implant placement. After MSFE, a slow decrease in tissue height measured over time was seen in all three study groups. Resorption of the grafted bone substitutes was more prominent in β-TCP than in BCP ceramics with an HA component (60/40 and 20/80). Loss of tissue height after 5 years was lowest in BCP 60/40 and highest in β-TCP. This radiological study shows a predictable and comparable behavior of the slow decrease in tissue height over time for all three types of calcium phosphate ceramics used in MSFE. The fraction of HA in calcium phosphate ceramics and dental implant loading seems to be beneficial for tissue height maintenance after MSFE.
Special Issue: Structure, Properties and Applications of Polymeric Foams
Authors: Hejna Aleksander
Published: March 2021

The Special Issue “Structure, Properties and Applications of Polymeric Foams” aimed to gather the numerous reports associated with the different aspects of polymeric foams [...]
Transfer of Risk in Supply Chain Management with Joint Pricing and Inventory Decision Considering Shortages
Authors: Khan Irfanullah , Sarkar Biswajit
Published: March 2021

This study is the first to consider a distribution-free approach in a newsvendor model with a transfer of risk and back-ordering. Previously, in many articles, discrete demand is considered. In this model, we consider a newsvendor selling a single seasonal item with price-dependent stochastic demand. Competition in markets has forced the retailer and manufacturer to coordinate in decentralized supply chain management. A coordination contract is made between a retailer and manufacturer to overcome the randomness of demand for a short-life-cycle product. The retailer pays an additional amount per product to transfer the risk of unsold items. The manufacturer bears the cost of unsold products from the retailer. Shortages are allowed with back-ordering costs during the season. The distribution-free model is developed and solved with only available demand data of mean and standard deviation. Stackelberg’s game approach is used to calculate the optimal ordering quality and price. This model aims to maximize expected profit by optimizing unit selling price and ordered quantity through coordination. To illustrate that the model is robust, numerical experiment and sensitivity analyses are conducted for both decentralized and centralized supply chain management. For applicability of the model in the real-world business scenario, managerial insights are provided with sensitivity analysis.
Fixed-Point Theorems in Fuzzy Metric Spaces via Fuzzy F-Contraction
Authors: Huang Huaping , Carić Biljana , Došenović Tatjana , Rakić Dušan , Brdar Mirjana
Published: March 2021

The purpose of this paper is to introduce a new type of contraction called fuzzy F-contraction. As compared to the F-contraction in the existing literature, our fuzzy F-contraction is much simpler and more straightforward, since it contains only one condition—that is, the function F is strictly increasing. Moreover, some fixed-point theorems for fuzzy F-contraction are presented. Further, some examples are given to illustrate its validity and superiority. In addition, by applying a very significant lemma, we show that our proofs of most fixed-point theorems are shorter and more elegant than ones in the literature.
Poly- and Oligosaccharide Ulva sp. Fractions from Enzyme-Assisted Extraction Modulate the Metabolism of Extracellular Matrix in Human Skin Fibroblasts: Potential in Anti-Aging Dermo-Cosmetic Applications
Authors: Fournière Mathilde , Bedoux Gilles , Lebonvallet Nicolas , Leschiera Raphaël , Le Goff-Pain Claudie , Bourgougnon Nathalie , Latire Thomas
Published: March 2021

Ulva sp. is known to be a source of bioactive compounds such as ulvans, but their biological activity on human dermal fibroblast extracellular matrix (ECM) is poorly reported. In this work, the regulation of ECM has been investigated for the first time at both proteomic and transcriptomic levels in normal human skin dermal fibroblasts, after 48 h of incubation with poly- and oligosaccharide fractions from Ulva sp. obtained after enzyme-assisted extraction and depolymerization. Cell proliferation enhancement (up to +68%) without exhibiting any cytotoxic effect on fibroblasts was demonstrated at 50 and 1000 µg/mL by both fractions. At the proteomic level, polysaccharide fractions at 1000 µg/mL enhanced the most the synthesis of glycosaminoglycans (GAGs, up to +57%), total collagen, especially types I (up to +217%) and III, as well as the synthesis and activity of MMP-1 (Matrix Metalloproteinase-1, up to +309%). In contrast, oligosaccharide fractions had no effect on GAGs synthesis but exhibited similarities for collagens and MMP-1 regulation. At the transcriptomic level, the decrease of COL1A1 and COL1A2 expression, and increase of COL3A1 and MMP-1 expression, confirmed the modulation of ECM metabolism by both fractions. Our research emphasizes that poly- and oligosaccharide Ulva sp. fractions exhibit interesting biological activities and supports their potential use in the area of skin renewal for anti-aging dermo-cosmetic applications.
Influence of Ceramic Particles Character on Resulted Properties of Zinc-Hydroxyapatite/Monetite Composites
Authors: Hosová Klára , Pinc Jan , Školáková Andrea , Bartůněk Vilém , Veřtát Petr , Školáková Tereza , Průša Filip , Vojtěch Dalibor , Čapek Jaroslav
Published: March 2021

Zinc and its alloys seem to be promising candidates for biodegradable applications. Those materials are often modified by other elements or compounds in order to enhance their properties. The combination of zinc and apatites is challenging for several reasons. However, the advantages connected with the biological aspects suggest the need for further research into such materials. In this study, three zinc-based composites with 4 and 8 wt. % of nanohydroxyapatite or nanomonetite (Zn-4MO, Zn-4HA, Zn-8HA) were prepared by sintering and subsequent extrusion. Materials prepared in this way were characterized from the microstructural, mechanical and corrosion point of view. The obtained results showed a significant influence of particle character (amount and morphology) on the strength and ductility of the prepared materials. In case of Zn-4MO, the presence of monetite significantly increased the ductility compared with the other materials. In addition, the increment of the degradation rate caused by the presence of monetite was observed as well. All obtained results pointed out to significant advantages of monetite for the preparation of Zn-apatite composites compared with hydroxyapatite.
The Importance of Objective Stool Classification in Fecal 1H-NMR Metabolomics: Exponential Increase in Stool Crosslinking Is Mirrored in Systemic Inflammation and Associated to Fecal Acetate and Methionine
Authors: Deutsch Leon , Stres Blaz
Published: March 2021

Past studies strongly connected stool consistency—as measured by Bristol Stool Scale (BSS)—with microbial gene richness and intestinal inflammation, colonic transit time and metabolome characteristics that are of clinical relevance in numerous gastro intestinal conditions. While retention time, defecation rate, BSS but not water activity have been shown to account for BSS-associated inflammatory effects, the potential correlation with the strength of a gel in the context of intestinal forces, abrasion, mucus imprinting, fecal pore clogging remains unexplored as a shaping factor for intestinal inflammation and has yet to be determined. Our study introduced a minimal pressure approach (MP) by probe indentation as measure of stool material crosslinking in fecal samples. Results reported here were obtained from 170 samples collected in two independent projects, including males and females, covering a wide span of moisture contents and BSS. MP values increased exponentially with increasing consistency (i.e., lower BSS) and enabled stratification of samples exhibiting mixed BSS classes. A trade-off between lowest MP and highest dry matter content delineated the span of intermediate healthy density of gel crosslinks. The crossectional transects identified fecal surface layers with exceptionally high MP and of <5 mm thickness followed by internal structures with an order of magnitude lower MP, characteristic of healthy stool consistency. The MP and BSS values reported in this study were coupled to reanalysis of the PlanHab data and fecal 1H-NMR metabolomes reported before. The exponential association between stool consistency and MP determined in this study was mirrored in the elevated intestinal and also systemic inflammation and other detrimental physiological deconditioning effects observed in the PlanHab participants reported before. The MP approach described in this study can be used to better understand fecal hardness and its relationships to human health as it provides a simple, fine scale and objective stool classification approach for the characterization of the exact sampling locations in future microbiome and metabolome studies.
Electrochemical Sensor for Determination of Various Phenolic Compounds in Wine Samples Using Fe3O4 Nanoparticles Modified Carbon Paste Electrode
Authors: Pwavodi Pwadubashiyi C. , Ozyurt Vasfiye H. , Asir Suleyman , Ozsoz Mehmet
Published: March 2021

Phenolic compounds contain classes of flavonoids and non-flavonoids, which occur naturally as secondary metabolites in plants. These compounds, when consumed in food substances, improve human health because of their antioxidant properties against oxidative damage diseases. In this study, an electrochemical sensor was developed using a carbon paste electrode (CPE) modified with Fe3O4 nanoparticles (MCPE) for the electrosensitive determination of sinapic acid, syringic acid, and rutin. The characterization techniques adapted for CPE, MCPE electrodes, and the solution interface were cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). Scan rate and pH were the parameters subjected to optimization studies for the determination of phenolic compounds. The incorporation of Fe3O4 nanoparticles to the CPE as a sensor showed excellent sensitivity, selectivity, repeatability, reproducibility, stability, and low preparation cost. The limits of detection (LOD) obtained were 2.2 × 10−7 M for sinapic acid, 2.6 × 10−7 M for syringic acid, and 0.8 × 10−7 M for rutin, respectively. The fabricated electrochemical sensor was applied to determine phenolic compounds in real samples of red and white wine.
Recognizing the Benefits of Pre-/Probiotics in Metabolic Syndrome and Type 2 Diabetes Mellitus Considering the Influence of Akkermansia muciniphila as a Key Gut Bacterium
Authors: Corb Aron Raluca Anca , Abid Areha , Vesa Cosmin Mihai , Nechifor Aurelia Cristina , Behl Tapan , Ghitea Timea Claudia , Munteanu Mihai Alexandru , Fratila Ovidiu , Andronie-Cioara Felicia Liana , Toma Mirela Marioara , Bungau Simona
Published: March 2021

Metabolic syndrome (MetS) and type 2 diabetes mellitus (T2DM) are diseases that can be influenced by the structure of gut microbiota, whose improvement is often neglected in metabolic pathology. This review highlights the following main aspects: the relationship between probiotics/gut microbes with the pathogenesis of MetS, the particular positive roles of Akkermansia muciniphila supplementation in the onset of MetS, and the interaction between dietary polyphenols (prebiotics) with gut microbiota. Therefore, an extensive and in-depth analysis of the often-neglected correlation between gut microbiota and chronic metabolic diseases was conducted, considering that this topic continues to fascinate and stimulate researchers through the discovery of novel strains and their beneficial properties.
Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up?
Authors: Tehfe Ali , Roseshter Talia , Wei Yulong , Xia Xuhua
Published: March 2021

HAC1 encodes a key transcription factor that transmits the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus and regulates downstream UPR genes in Saccharomyces cerevisiae. In response to the accumulation of unfolded proteins in the ER, Ire1p oligomers splice HAC1 pre-mRNA (HAC1u) via a non-conventional process and allow the spliced HAC1 (HAC1i) to be translated efficiently. However, leaky splicing and translation of HAC1u may occur in non-UPR cells to induce undesirable UPR. To control accidental UPR activation, multiple fail-safe mechanisms have been proposed to prevent leaky HAC1 splicing and translation and to facilitate rapid degradation of translated Hac1up and Hac1ip. Among proposed regulatory mechanisms is a degron sequence encoded at the 5′ end of the HAC1 intron that silences Hac1up expression. To investigate the necessity of an intron-encoded degron sequence that specifically targets Hac1up for degradation, we employed publicly available transcriptomic data to quantify leaky HAC1 splicing and translation in UPR-induced and non-UPR cells. As expected, we found that HAC1u is only efficiently spliced into HAC1i and efficiently translated into Hac1ip in UPR-induced cells. However, our analysis of ribosome profiling data confirmed frequent occurrence of leaky translation of HAC1u regardless of UPR induction, demonstrating the inability of translation fail-safe to completely inhibit Hac1up production. Additionally, among 32 yeast HAC1 surveyed, the degron sequence is highly conserved by Saccharomyces yeast but is poorly conserved by all other yeast species. Nevertheless, the degron sequence is the most conserved HAC1 intron segment in yeasts. These results suggest that the degron sequence may indeed play an important role in mitigating the accumulation of Hac1up to prevent accidental UPR activation in the Saccharomyces yeast.
Genetic Markers of Genome Rearrangements in Helicobacter pylori
Authors: Noureen Mehwish , Kawashima Takeshi , Arita Masanori
Published: March 2021

Helicobacter pylori exhibits a diverse genomic structure with high mutation and recombination rates. Various genetic elements function as drivers of this genomic diversity including genome rearrangements. Identifying the association of these elements with rearrangements can pave the way to understand its genome evolution. We analyzed the order of orthologous genes among 72 publicly available complete genomes to identify large genome rearrangements, and rearrangement breakpoints were compared with the positions of insertion sequences, genomic islands, and restriction modification genes. Comparison of the shared inversions revealed the conserved genomic elements across strains from different geographical locations. Some were region-specific and others were global, indicating that highly shared rearrangements and their markers were more ancestral than strain—or region—specific ones. The locations of genomic islands were an important factor for the occurrence of the rearrangements. Comparative genomics helps to evaluate the conservation of various elements contributing to the diversity across genomes.
Novel Donepezil–Arylsulfonamide Hybrids as Multitarget-Directed Ligands for Potential Treatment of Alzheimer’s Disease
Authors: Queda Fausto , Calò Sonia , Gwizdala Karolina , Magalhães João D. , Cardoso Sandra M. , Chaves Sílvia , Piemontese Luca , Santos M. Amélia
Published: March 2021

Alzheimer’s disease (AD) is one of the most devastating neurodegenerative disorders, characterized by multiple pathological features. Therefore, multi-target drug discovery has been one of the most active fields searching for new effective anti-AD therapies. Herein, a series of hybrid compounds are reported which were designed and developed by combining an aryl-sulfonamide function with a benzyl-piperidine moiety, the pharmacophore of donepezil (a current anti-AD acetylcholinesterase AChE inhibitor drug) or its benzyl-piperazine analogue. The in vitro results indicate that some of these hybrids achieve optimized activity towards two main AD targets, by displaying excellent AChE inhibitory potencies, as well as the capability to prevent amyloid-β (Aβ) aggregation. Some of these hybrids also prevented Aβ-induced cell toxicity. Significantly, drug-like properties were predicted, including for blood-brain permeability. Compound 9 emerged as a promising multi-target lead compound (AChE inhibition (IC50 1.6 μM); Aβ aggregation inhibition 60.7%). Overall, this family of hybrids is worthy of further exploration, due to the wide biological activity of sulfonamides.
PepFun: Open Source Protocols for Peptide-Related Computational Analysis
Authors: Ochoa Rodrigo , Cossio Pilar
Published: March 2021

Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease.
Growth Restriction of Rhizoctonia solani via Breakage of Intracellular Organelles Using Crude Extracts of Gallnut and Clove
Authors: Wang Jian , Hu Xianfeng , Yang Chenglong , Wu Xiaomao , Li Rongyu , Li Ming
Published: March 2021

Plant diseases reduce crop yield and quality, hampering the development of agriculture. Fungicides, which restrict chemical synthesis in fungi, are the strongest controls for plant diseases. However, the harmful effects on the environment due to continued and uncontrolled utilization of fungicides have become a major challenge in recent years. Plant-sourced fungicides are a class of plant antibacterial substances or compounds that induce plant defenses. They can kill or inhibit the growth of target pathogens efficiently with no or low toxicity, they degrade readily, and do not prompt development of resistance, which has led to their widespread use. In this study, the growth inhibition effect of 24 plant-sourced ethanol extracts on rice sprigs was studied. Ethanol extract of gallnuts and cloves inhibited the growth of bacteria by up to 100%. Indoor toxicity measurement results showed that the gallnut and glove constituents inhibition reached 39.23 μg/mL and 18.82 μg/mL, respectively. Extract treated rice sprigs were dry and wrinkled. Gallnut caused intracellular swelling and breakage of mitochondria, disintegration of nuclei, aggregation of protoplasts, and complete degradation of organelles in hyphae and aggregation of cellular contents. Protection of Rhizoctonia solani viability reached 46.8% for gallnut and 37.88% for clove in water emulsions of 1000 μg/mL gallnut and clove in the presence of 0.1% Tween 80. The protection by gallnut was significantly stronger than that of clove. The data could inform the choice of plant-sourced fungicides for the comprehensive treatment of rice sprig disease. The studied extract effectively protected rice sprigs and could be a suitable alternative to commercially available chemical fungicides. Further optimized field trials are needed to effectively sterilize rice paddies.
Does the Phytochemical Diversity of Wild Plants Like the Erythrophleum genus Correlate with Geographical Origin?
Authors: Delporte Cédric , Noret Nausicaa , Vanhaverbeke Cécile , Hardy Olivier J. , Martin Jean-François , Tremblay-Franco Marie , Touboul David , Gorel Anais , Faes Marie , Stévigny Caroline , Van Antwerpen Pierre , Souard Florence
Published: March 2021

Secondary metabolites are essential for plant survival and reproduction. Wild undomesticated and tropical plants are expected to harbor highly diverse metabolomes. We investigated the metabolomic diversity of two morphologically similar trees of tropical Africa, Erythrophleum suaveolens and E. ivorense, known for particular secondary metabolites named the cassaine-type diterpenoids. To assess how the metabolome varies between and within species, we sampled leaves from individuals of different geographic origins but grown from seeds in a common garden in Cameroon. Metabolites were analyzed using reversed phase LC-HRMS(/MS). Data were interpreted by untargeted metabolomics and molecular networks based on MS/MS data. Multivariate analyses enabled us to cluster samples based on species but also on geographic origins. We identified the structures of 28 cassaine-type diterpenoids among which 19 were new, 10 were largely specific to E. ivorense and five to E. suaveolens. Our results showed that the metabolome allows an unequivocal distinction of morphologically-close species, suggesting the potential of metabolite fingerprinting for these species. Plant geographic origin had a significant influence on relative concentrations of metabolites with variations up to eight (suaveolens) and 30 times (ivorense) between origins of the same species. This shows that the metabolome is strongly influenced by the geographical origin of plants (i.e., genetic factors).
The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4
Authors: Šebela Marek , Raus Martin , Ondřej Vladan , Hašler Petr
Published: March 2021

The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10−5 M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).
Synthesis and Structure–Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research
Authors: Yoo Minjin , Park Tae Hyun , Yoo Miyoun , Kim Yeongrin , Lee Joo-Youn , Lee Kyu Myung , Ryu Seong Eon , Lee Byung Il , Jung Kwan-Young , Park Chi Hoon
Published: March 2021

Epigenetic regulation is known to play a key role in progression of anti-cancer therapeutics. Lysine acetylation is an important mechanism in controlling gene expression. There has been increasing interest in bromodomain owing to its ability to modulate transcription of various genes as an epigenetic ‘reader.’ Herein, we report the design, synthesis, and X-ray studies of novel aristoyagonine (benzo[6,7]oxepino[4,3,2-cd]isoindol-2(1H)-one) derivatives and investigate their inhibitory effect against Brd4 bromodomain. Five compounds 8ab, 8bc, 8bd, 8be, and 8bf have been discovered with high binding affinity over the Brd4 protein. Co-crystal structures of these five inhibitors with human Brd4 bromodomain demonstrated that it has a key binding mode occupying the hydrophobic pocket, which is known to be the acetylated lysine binding site. These novel Brd4 bromodomain inhibitors demonstrated impressive inhibitory activity and mode of action for the treatment of cancer diseases.