bluuebunny/crossref_metadata_2025 huggingface dataset:
Some Special Aspects of Liver Repair after Resection and Administration of Multipotent Stromal Cells in Experiment
Authors: Maiborodin Igor , Lushnikova Elena , Klinnikova Marina , Klochkova Swetlana
Published: January 2021

Changes in rat liver after resection and injection of autologous multipotent mesenchymal stromal cells of bone marrow origin (MSCs) transfected with the GFP gene and cell membranes stained with red-fluorescent lipophilic membrane dye were studied by light microscopy. It was found that after the introduction of MSCs into the damaged liver, their differentiation into any cells was not found. However, under the conditions of MSCs use, the number of neutrophils in the parenchyma normalizes earlier, and necrosis and hemorrhages disappear more quickly. It was concluded that the use of MSCs at liver resection for the rapid restoration of an organ is inappropriate, since the injected cells in vivo do not differentiate either into hepatocytes, into epithelial cells of bile capillaries, into endotheliocytes and pericytes of the vascular membranes, into fibroblasts of the scar or other connective tissue structures, or into any other cells present in the liver.
Development of Low-Viscosity and High-Performance Biobased Monobenzoxazine from Tyrosol and Furfurylamine
Authors: Wen Zhibin , Bonnaud Leïla , Mincheva Rosica , Dubois Philippe , Raquez Jean-Marie
Published: January 2021

This work details the scalable and solventless synthesis of a potential fully biobased monobenzoxazine resin derived from tyrosol and furfurylamine. The structure of the monomer was studied by nuclear magnetic resonance (NMR) spectroscopy and Fourier transform infrared (FTIR). The curing of the precursors was characterized by differential scanning calorimetry (DSC), rheological measurements, and thermogravimetric analysis (TGA). The properties of the resulting biobased polybenzoxazine were then determined by thermogravimetric analysis (TGA) and dynamic mechanical thermal analysis (DMA). A thermally stable resin was obtained with 5% and 10% weight-reduction-temperature (Td5 and Td10) values of 349 and 395 °C, respectively, and a char yield of 53%. Moreover, the low melting temperature, low viscosity, and excellent thermomechanical behavior make this fully biobased resin a promising candidate for coating applications.
Propolis and Organosilanes as Innovative Hybrid Modifiers in Wood-Based Polymer Composites
Authors: Odalanowska Majka , Woźniak Magdalena , Ratajczak Izabela , Zielińska Daria , Cofta Grzegorz , Borysiak Sławomir
Published: January 2021

The article presents characteristics of wood/polypropylene composites, where the wood was treated with propolis extract (EEP) and innovative propolis-silane formulations. Special interest in propolis for wood impregnation is due to its antimicrobial properties. One propolis-silane formulation (EEP-TEOS/VTMOS) consisted of EEP, tetraethyl orthosilicate (TEOS), and vinyltrimethoxysilane (VTMOS), while the other (EEP-TEOS/OTEOS) contained EEP, tetraethyl orthosilicate (TEOS), and octyltriethoxysilane (OTEOS). The treated wood fillers were characterized by Fourier transform infrared spectroscopy (FTIR), atomic absorption spectrometry (AAS), and X-ray diffraction (XRD), while the composites were investigated using differential scanning calorimetry (DSC), X-ray diffraction (XRD), and optical microscopy. The wood treated with EEP and propolis-silane formulations showed resistance against moulds, including Aspergillus niger, Chaetomium globosum, and Trichoderma viride. The chemical analyses confirmed presence of silanes and constituents of propolis in wood structure. In addition, treatment of wood with the propolis-silane formulations produced significant changes in nucleating abilities of wood in the polypropylene matrix, which was confirmed by an increase in crystallization temperature and crystal conversion, as well as a decrease in half-time of crystallization parameters compared to the untreated polymer matrix. In all the composites, the formation of a transcrystalline layer was observed, with the greatest rate recorded for the composite with the filler treated with EEP-TEOS/OTEOS. Moreover, impregnation of wood with propolis-silane formulations resulted in a considerable improvement of strength properties in the produced composites. A dependence was found between changes in the polymorphic structures of the polypropylene matrix and strength properties of composite materials. It needs to be stressed that to date literature sources have not reported on treatment of wood fillers using bifunctional modifiers providing a simultaneous effect of compatibility in the polymer-filler system or any protective effect against fungi.
Assembling Surface Linker Chemistry with Minimization of Non-Specific Adsorption on Biosensor Materials
Authors: Sheng Jack Chih-Chieh , De La Franier Brian , Thompson Michael
Published: January 2021

The operation of biosensors requires surfaces that are both highly specific towards the target analyte and that are minimally subject to fouling by species present in a biological fluid. In this work, we further examined the thiosulfonate-based linker in order to construct robust and durable self-assembling monolayers (SAMs) onto hydroxylated surfaces such as silica. These SAMs are capable of the chemoselective immobilization of thiol-containing probes (for analytes) under aqueous conditions in a single, straightforward, reliable, and coupling-free manner. The efficacy of the method was assessed through implementation as a biosensing interface for an ultra-high frequency acoustic wave device dedicated to the detection of avidin via attached biotin. Fouling was assessed via introduction of interfering bovine serum albumin (BSA), IgG antibody, or goat serum. Improvements were investigated systematically through the incorporation of an oligoethylene glycol backbone employed together with a self-assembling diluent without a functional distal group. This work demonstrates that the incorporation of a diluent of relatively short length is crucial for the reduction of fouling. Included in this work is a comparison of the surface attachment of the linker to Si3N4 and AlN, both materials used in sensor technology.
Acknowledgment to Reviewers of Machines in 2020
Authors:   Machines Editorial Office
Published: January 2021

Peer review is the driving force of journal development, and reviewers are gatekeepers who ensure that Machines maintains its standards for the high quality of its published papers [...]
Quantitative NMR as a Versatile Tool for the Reference Material Preparation
Authors: Choi Kihwan , Myoung Sangki , Seo Yejin , Ahn Sangdoo
Published: January 2021

The assessment of primary calibrator purity is critical for establishing traceability to the International System of Units (SI). Recently, quantitative nuclear magnetic resonance (qNMR) has been used as a purity determination method for reference material development, and many related measurement techniques have been designed to acquire accurate and reliable results. This review introduces the recent advances in these techniques (including multidimensional methods), focusing on the application of qNMR to reference material preparation.
Mathematical Calculation of Stray Losses in Transformer Tanks with a Stainless Steel Insert
Authors: Maximov Serguei , Corona-Sánchez Manuel A. , Olivares-Galvan Juan C. , Melgoza-Vazquez Enrique , Escarela-Perez Rafael , Jimenez-Mondragon Victor M.
Published: January 2021

At present it is claimed that all electrical energy systems operate with high values of efficiency and reliability. In electric power systems (EPS), electrical power and distribution transformers are responsible for transferring the electrical energy from power stations up to the load centers. Consequently, it is mandatory to design transformers that possess the highest efficiency and reliability possible. Considerable power losses and hotspots may exist in the bushing region of a transformer, where conductors pass through the tank. Most transformer tanks are made of low-carbon steel, for economical reasons, causing the induction of high eddy currents in the bushing regions. Using a non-magnetic insert in the transformer tank can reduce the eddy currents in the region and as a consequence avoid overheating. In this work, analytical formulations were developed to calculate the magnetic field distribution and the stray losses in the transformer region where bushings are mounted, considering a stainless steel insert (SSI) in the transformer tank. Previously, this problem had only been tackled with numerical models. Several cases were analyzed considering different non-magnetic insert sizes. Additionally, a numerical study using a two dimensional (2D) finite element (FE) axisymmetric model was carried out in order to validate the analytical results. The solved cases show a great concordance between models, obtaining relative errors between the solutions of less than two percent.
Weak Measurable Optimal Controls for the Problems of Bolza
Authors: Sánchez Licea Gerardo
Published: January 2021

Two sufficiency theorems for parametric and a nonparametric problems of Bolza in optimal control are derived. The dynamics of the problems are nonlinear, the initial and final states are free, and the main results can be applied when nonlinear mixed time-state-control inequality and equality constraints are presented. The deviation between admissible costs and optimal costs around the optimal control is estimated by functionals playing the role of the square of some norms.
Recognizing Human Races through Machine Learning—A Multi-Network, Multi-Features Study
Authors: Darabant Adrian Sergiu , Borza Diana , Danescu Radu
Published: January 2021

The human face holds a privileged position in multi-disciplinary research as it conveys much information—demographical attributes (age, race, gender, ethnicity), social signals, emotion expression, and so forth. Studies have shown that due to the distribution of ethnicity/race in training datasets, biometric algorithms suffer from “cross race effect”—their performance is better on subjects closer to the “country of origin” of the algorithm. The contributions of this paper are two-fold: (a) first, we gathered, annotated and made public a large-scale database of (over 175,000) facial images by automatically crawling the Internet for celebrities’ images belonging to various ethnicity/races, and (b) we trained and compared four state of the art convolutional neural networks on the problem of race and ethnicity classification. To the best of our knowledge, this is the largest, data-balanced, publicly-available face database annotated with race and ethnicity information. We also studied the impact of various face traits and image characteristics on the race/ethnicity deep learning classification methods and compared the obtained results with the ones extracted from psychological studies and anthropomorphic studies. Extensive tests were performed in order to determine the facial features to which the networks are sensitive to. These tests and a recognition rate of 96.64% on the problem of human race classification demonstrate the effectiveness of the proposed solution.
Recovering Density and Speed of Sound Coefficients in the 2D Hyperbolic System of Acoustic Equations of the First Order by a Finite Number of Observations
Authors: Klyuchinskiy Dmitriy , Novikov Nikita , Shishlenin Maxim
Published: January 2021

We consider the coefficient inverse problem for the first-order hyperbolic system, which describes the propagation of the 2D acoustic waves in a heterogeneous medium. We recover both the denstity of the medium and the speed of sound by using a finite number of data measurements. We use the second-order MUSCL-Hancock scheme to solve the direct and adjoint problems, and apply optimization scheme to the coefficient inverse problem. The obtained functional is minimized by using the gradient-based approach. We consider different variations of the method in order to obtain the better accuracy and stability of the appoach and present the results of numerical experiments.
Data Envelopment Analysis Approach to Energy-Saving Projects Selection in an Energy Service Company
Authors: Villa Gabriel , Lozano Sebastián , Redondo Sandra
Published: January 2021

Project selection is a common problem for many companies. Specifically, it consists in identifying which projects should be selected with regard to their economic efficiency, i.e., the projects that maximise the profit they bring in while minimising the cost of the resources consumed. In this paper, we have focused our interest on energy service companies because of the importance of a convenient selection of their projects. In these types of companies, the attractiveness of a project depends on both the profit estimations obtained in simulations of the energy systems to be improved, as well as the probability that the project will be awarded (e.g., in local government bids, where typically several energy service companies compete to win the bid). We propose a new project selection method, especially tailored to energy service companies and based on centralised data envelopment analysis models with limited availability of the resources. This contrasts with all existing project selection methods and allows the proposed approach to make more efficient use of the limited resources. We have applied the model to a real-world case by selecting projects in a Spanish energy service company, showing the benefits of applying this approach, and comparing the results obtained with other data envelopment analysis project selection approaches.
Density Functional Theory (DFT)-Aided Structure Elucidation of Linear Diterpenes from the Irish Brown Seaweed Bifurcaria bifurcata
Authors: Smyrniotopoulos Vangelis , Firsova Daria , Fearnhead Howard , Grauso Laura , Mangoni Alfonso , Tasdemir Deniz
Published: January 2021

Brown alga Bifurcaria bifurcata is an extraordinarily rich source of linear (acylic) diterpenes with enormous structural diversity. As part of our interest into secondary metabolites of the Irish seaweeds, here we report four new acyclic diterpenes (1–4) and seven known terpenoids (5–11) from the CHCl3 extract of B. bifurcata. The planar structures of the new metabolites were elucidated by means of 1D and 2D NMR, HRMS, and FT-IR spectroscopy. Since linear diterpenes are highly flexible compounds, the assignment of their stereochemistry by conventional methods, e.g., NOESY NMR, is difficult. Therefore, we employed extensive quantum-mechanical prediction of NMR chemical shifts and optical rotation analyses to identify the relative and absolute configurations of the new compounds 1–4. Several compounds moderately inhibited the human breast cancer cell line (MDA-MB-231) with IC50 values ranging from 10.0 to 33.5 μg/mL. This study not only demonstrates the vast capacity of the Irish B. bifurcata to produce highly oxygenated linear diterpenoids, but also highlights the potential of new methodologies for assignment of their stereogenic centers.
Induction Chemotherapy for Primarily Unresectable Locally Advanced Pancreatic Adenocarcinoma—Who Will Benefit from a Secondary Resection?
Authors: Rosumeck Nathalie , Timmermann Lea , Klein Fritz , Bahra Marcus , Stintzig Sebastian , Malinka Thomas , Pelzer Uwe
Published: January 2021

Background and Objectives: An increasing number of patients (pts) with locally advanced pancreatic cancer (LAPC) are treated with an intensive neoadjuvant therapy to obtain a secondary curative resection. Only a certain number of patients benefit from this intention. The aim of this investigation was to identify prognostic factors which may predict a benefit for secondary resection. Materials and Methods: Survival time and clinicopathological data of pts with pancreatic cancer were prospective and consecutively collected in our Comprehensive Cancer Center Database. For this investigation, we screened for pts with primarily unresectable pancreatic cancer who underwent a secondary resection after receiving induction therapy in the time between March 2017 and May 2019. Results: 40 pts had a sufficient database to carry out a reliable analysis. The carbohydrate-antigen 19-9 (CA 19-9) level of the pts treated with induction therapy decreased by 44.7% from 4358.3 U/mL to 138.5 U/mL (p = 0.001). The local cancer extension was significantly reduced (p < 0.001), and the Eastern Cooperative Oncology Group (ECOG) performance status was lowered (p = 0.03). The median overall survival (mOS) was 20 months (95% CI: 17.2–22.9). Pts who showed a normal CA 19-9 level (<37 U/mL) at diagnosis and after neoadjuvant therapy or had a Body Mass Index (BMI) below 25 kg/m2 after chemotherapy had a significant prolonged overall survival (29 vs. 19 months, p = 0.02; 26 vs. 18 months, p = 0.04; 15 vs. 24 months, p = 0.01). Pts who still presented elevated CA 19-9 levels >400 U/mL after induction therapy did not profit from a secondary resection (24 vs. 7 months, p < 0.001). Nodal negativity as well as the performance of an adjuvant therapy lead to better mOS (25 vs. 15 months, p = 0.003; 10 vs. 25 months, p < 0.001). Conclusion: The pts in our investigation had different benefits from the multimodal treatment. We identified the CA 19-9 level at time of diagnosis and after neoadjuvant therapy as well as the preoperative BMI as predictive factors for overall survival. Furthermore, diagnostics of presurgical nodal status should gain more importance as nodal negativity is associated with better outcome.
Prognostic Utility of Circulating Growth Factors in Aortic Valve Stenosis: A Pilot Study
Authors: Hofmanis Juris , Tretjakovs Peteris , Svirskis Simons , Gersone Gita , Hofmane Dace , Rozenberga Ulla , Blumfelds Leons , Bahs Guntis , Lejnieks Aivars , Mackevics Vitolds
Published: January 2021

Background and Objectives: Aortic valve stenosis (AS) develops with a pronounced local inflammatory response, where a variety of growth factors are involved in the process, and may have a pro-inflammatory and anti-inflammatory effect. The aim of our study was to elucidate whether circulating growth factors: growth differentiation factor 15 (GDF-15), angiopoietin-2 (Ang-2), vascular endothelial growth factor A (VEGF-A), fibroblast growth factor 2 (FGF-2), and fibroblast growth factor 21 (FGF-21) could be proposed as clinically relevant biomarkers to improve risk stratification in AS patients. Materials and Methods: AS patients were classified into three groups: 16 patients with mild AS stenosis; 19 with moderate and 11 with severe AS, and 30 subjects without AS (echocardiographically approved) were selected as a control group. GDF-15, Ang-2, VEGF-A, FGF-2, and FGF-21 were measured in plasma by the ELISA method. Results: GDF-15 levels differed significantly not only when comparing AS patients with control groups (p < 0.0001), but also a statistically significant difference was achieved when comparing AS patients at a mild degree stage with control individuals. We found a strong relationship of GDF-15 levels regarding AS severity degree (p < 0.0001). VEGF-A, FGF-2 and FGF-21 levels were significantly higher in AS patients than in controls, but relationships regarding the AS severity degree were weaker (p < 0.02). ROC analysis of the study growth factors showed that GDF-15 might serve as a specific and sensitive biomarker of AS stenosis (AUC = 0.75, p = 0.0002). FGF-21 correlated with GDF-15, Ang-2, and FGF-2, but it did not reach the level to serve as a clinically relevant biomarker of AS stenosis. Conclusions: AS is associated with significantly increased GDF-15, VEGF-A, FGF-2, and FGF-21 levels in plasma, but only GDF-15 shows a pronounced relationship regarding AS severity degree, and GDF-15 might serve as a specific and sensitive biomarker of AS stenosis.
Interface Quality Indices of Al–10Si–Mg Aluminum Alloy and Cr18–Ni10–Ti Stainless-Steel Bimetal Fabricated via Selective Laser Melting
Authors: Khaimovich Alexander , Erisov Yaroslav , Smelov Vitaliy , Agapovichev Anton , Petrov Ilia , Razhivin Vasilii , Bobrovskij Igor , Kokareva Viktoriya , Kuzin Alexander
Published: January 2021

Bimetallic materials are important in many industries (aerospace, medicine, etc.) since they allow the creation of constructions that combine specific functional properties, for example, low density (aluminum alloy) and high corrosion resistance (stainless steel), due to layering fabrication of the bimetallic joint. On the other hand, the difference in thermophysical properties of the dissimilar material layers leads to residual stresses, which cause deformation and destruction of such a bimetallic joint produced via the methods of surfacing or additive technologies. This article discusses the methods based on the gray relational analysis and generalized desirability function for the quality assessment of Al–10Si–Mg aluminum alloy and Cr18–Ni10–Ti stainless-steel bimetal fabricated via selective laser melting (SLM). There are four main parameters (quality indices) of the quality generalized assessment, which determine the degree of Al penetration into the steel substrate and Fe into the deposited layer, the difference in microhardness values on both sides of the interface boundary, and the resistance to mechanical destruction of the bimetallic joint. According to the results obtained, the best set of quality indices corresponds to the SLM technological modes with an energy density of 105 and 147 J/mm3. The greatest functionality of the bimetals is determined by the quality index associated with its strength. Therefore, methods of gray relational analysis and desirability function make it possible to form a generalized assessment for the bimetallic joint quality and, consequently, to select the best technological mode.
Multiphysics Modeling and Numerical Simulation in Computer-Aided Manufacturing Processes
Authors: Trzepieciński Tomasz , dell’Isola Francesco , Lemu Hirpa G.
Published: January 2021

The concept of Industry 4.0 is defined as a common term for technology and the concept of new digital tools to optimize the manufacturing process. Within this framework of modular smart factories, cyber-physical systems monitor physical processes creating a virtual copy of the physical world and making decentralized decisions. This article presents a review of the literature on virtual methods of computer-aided manufacturing processes. Numerical modeling is used to predict stress and temperature distribution, springback, material flow, and prediction of phase transformations, as well as for determining forming forces and the locations of potential wrinkling and cracking. The scope of the review has been limited to the last ten years, with an emphasis on the current state of knowledge. Intelligent production driven by the concept of Industry 4.0 and the demand for high-quality equipment in the aerospace and automotive industries forces the development of manufacturing techniques to progress towards intelligent manufacturing and ecological production. Multi-scale approaches that tend to move from macro- to micro- parameters become very important in numerical optimization programs. The software requirements for optimizing a fully coupled thermo-mechanical microstructure then increase rapidly. The highly advanced simulation programs based on our knowledge of physical and mechanical phenomena occurring in non-homogeneous materials allow a significant acceleration of the introduction of new products and the optimization of existing processes.
Towards Efficient Milling of Multi-Cavity Aeronautical Structural Parts Considering ACO-Based Optimal Tool Feed Position and Path
Authors: Xin Yupeng , Li Yuanheng , Li Wenhui , Wang Gangfeng
Published: January 2021

Cavities are typical features in aeronautical structural parts and molds. For high-speed milling of multi-cavity parts, a reasonable processing sequence planning can significantly affect the machining accuracy and efficiency. This paper proposes an improved continuous peripheral milling method for multi-cavity based on ant colony optimization algorithm (ACO). Firstly, by analyzing the mathematical model of cavity corner milling process, the geometric center of the corner is selected as the initial tool feed position. Subsequently, the tool path is globally optimized through ant colony dissemination and pheromone perception for path solution of multi-cavity milling. With the advantages of ant colony parallel search and pheromone positive feedback, the searching efficiency of the global shortest processing path is effectively improved. Finally, the milling programming of an aeronautical structural part is taken as a sample to verify the effectiveness of the proposed methodology. Compared with zigzag milling and genetic algorithm (GA)-based peripheral milling modes in the computer aided manufacturing (CAM) software, the results show that the ACO-based methodology can shorten the milling time of a sample part by more than 13%.
Chronic Active Epstein–Barr Virus Infection: The Elucidation of the Pathophysiology and the Development of Therapeutic Methods
Authors: Arai Ayako
Published: January 2021

Chronic active Epstein–Barr virus infection (CAEBV) is a disease where Epstein–Barr virus (EBV)-infected T- or NK-cells are activated and proliferate clonally. The symptoms of this dual-faced disease include systemic inflammation and multiple organ failures caused by the invasion of infected cells: inflammation and neoplasm. At present, the only effective treatment strategy to eradicate EBV-infected cells is allogeneic stem cell transplantation. Lately, the investigation into the disease’s pathogenic mechanism and pathophysiology has been advancing. In this review, I will evaluate the new definition in the 2017 WHO classification, present the advancements in the study of CAEBV, and unfold the future direction.
Listeria monocytogenes Biofilms in the Food Industry: Is the Current Hygiene Program Sufficient to Combat the Persistence of the Pathogen?
Authors: Mazaheri Tina , Cervantes-Huamán Brayan R. H. , Bermúdez-Capdevila Maria , Ripolles-Avila Carolina , Rodríguez-Jerez José Juan
Published: January 2021

Biofilms contain microbial cells which are protected by a self-produced matrix and they firmly attach themselves to many different food industry surfaces. Due to this protection, microorganisms within biofilms are much more difficult to eradicate and therefore to control than suspended cells. A bacterium that tends to produce these structures and persist in food processing plants is Listeria monocytogenes. To this effect, many attempts have been made to develop control strategies to be applied in the food industry, although there seems to be no clear direction on how to manage the risk the bacteria poses. There is no standardized protocol that is applied equally to all food sectors, so the strategies for the control of this pathogen depend on the type of surface, the nature of the product, the conditions of the food industry environment, and indeed the budget. The food industry performs different preventive and corrective measures on possible L. monocytogenes-contaminated surfaces. However, a critical evaluation of the sanitization methods applied must be performed to discern whether the treatment can be effective in the long-term. This review will focus on currently used strategies to eliminate biofilms and control their formation in processing facilities in different food sectors (i.e., dairy, meat, fish, chilled vegetables, and ready-to-eat products). The technologies employed for their control will be exemplified and discussed with the objective of understanding how L. monocytogenes can be improved through food safety management systems.
Microbiome Signatures in a Fast- and Slow-Progressing Gastric Cancer Murine Model and Their Contribution to Gastric Carcinogenesis
Authors: Bali Prerna , Coker Joanna , Lozano-Pope Ivonne , Zengler Karsten , Obonyo Marygorret
Published: January 2021

Gastric cancer is the third most common cause of death from cancer in the world and infection with Helicobacterpylori (H. pylori) is the main cause of gastric cancer. In addition to Helicobacter infection, the overall stomach microbiota has recently emerged as a potential factor in gastric cancer progression. Previously we had established that mice deficient in myeloid differentiation primary response gene 88 (MyD88, Myd88−/−) rapidly progressed to neoplasia when infected with H. felis. Thus, in order to assess the role of the microbiota in this fast-progressing gastric cancer model we investigated changes of the gastric microbiome in mice with different genotypic backgrounds: wild type (WT), MyD88-deficient (Myd88−/−), mice deficient in the Toll/interleukin-1 receptor (TIR) domain-containing adaptor-inducing interferon-β (TRIF, TrifLps2), and MyD88- and TRIF-deficient (Myd88−/−/TrifLps2, double knockout (DKO)) mice. We compared changes in alpha diversity, beta diversity, relative abundance, and log-fold differential of relative abundance ratios in uninfected and Helicobacter infected mice and studied their correlations with disease progression to gastric cancer in situ. We observed an overall reduction in microbial diversity post-infection with H. felis across all genotypes. Campylobacterales were observed in all infected mice, with marked reduction in abundance at 3 and 6 months in Myd88−/− mice. A sharp increase in Lactobacillales in infected Myd88−/− and DKO mice at 3 and 6 months was observed as compared to TrifLps2 and WT mice, hinting at a possible role of these bacteria in gastric cancer progression. This was further reinforced upon comparison of Lactobacillales log-fold differentials with histological data, indicating that Lactobacillales are closely associated with Helicobacter infection and gastric cancer progression. Our study suggests that differences in genotypes could influence the stomach microbiome and make it more susceptible to the development of gastric cancer upon Helicobacter infection. Additionally, increase in Lactobacillales could contribute to faster development of gastric cancer and might serve as a potential biomarker for the fast progressing form of gastric cancer.
Core and Accessory Genome Analysis of Vibrio mimicus
Authors: Guardiola-Avila Iliana , Sánchez-Busó Leonor , Acedo-Félix Evelia , Gomez-Gil Bruno , Zúñiga-Cabrera Manuel , González-Candelas Fernando , Noriega-Orozco Lorena
Published: January 2021

Vibrio mimicus is an emerging pathogen, mainly associated with contaminated seafood consumption. However, little is known about its evolution, biodiversity, and pathogenic potential. This study analyzes the pan-, core, and accessory genomes of nine V. mimicus strains. The core genome yielded 2424 genes in chromosome I (ChI) and 822 genes in chromosome II (ChII), with an accessory genome comprising an average of 10.9% of the whole genome for ChI and 29% for ChII. Core genome phylogenetic trees were obtained, and V. mimicus ATCC-33654 strain was the closest to the outgroup in both chromosomes. Additionally, a phylogenetic study of eight conserved genes (ftsZ, gapA, gyrB, topA, rpoA, recA, mreB, and pyrH), including Vibrio cholerae, Vibrio parilis, Vibrio metoecus, and Vibrio caribbenthicus, clearly showed clade differentiation. The main virulence genes found in ChI corresponded with type I secretion proteins, extracellular components, flagellar proteins, and potential regulators, while, in ChII, the main categories were type-I secretion proteins, chemotaxis proteins, and antibiotic resistance proteins. The accessory genome was characterized by the presence of mobile elements and toxin encoding genes in both chromosomes. Based on the genome atlas, it was possible to characterize differential regions between strains. The pan-genome of V. mimicus encompassed 3539 genes for ChI and 2355 genes for ChII. These results give us an insight into the virulence and gene content of V. mimicus, as well as constitute the first approach to its diversity.
Identification of an Acidic Amino Acid Permease Involved in d-Aspartate Uptake in the Yeast Cryptococcus humicola
Authors: Imanishi Daiki , Kera Yoshio , Takahashi Shouji
Published: January 2021

d-aspartate oxidase (DDO) catalyzes the oxidative deamination of acidic d-amino acids, and its production is induced by d-Asp in several eukaryotes. The yeast Cryptococcus humicola strain UJ1 produces large amounts of DDO (ChDDO) only in the presence of d-Asp. In this study, we analyzed the relationship between d-Asp uptake by an amino acid permease (Aap) and the inducible expression of ChDDO. We identified two acidic Aap homologs, named “ChAap4 and ChAap5,” in the yeast genome sequence. ChAAP4 deletion resulted in partial growth defects on d-Asp as well as l-Asp, l-Glu, and l-Phe at pH 7, whereas ChAAP5 deletion caused partial growth defects on l-Phe and l-Lys, suggesting that ChAap4 might participate in d-Asp uptake as an acidic Aap. Interestingly, the growth of the Chaap4 strain on d- or l-Asp was completely abolished at pH 10, suggesting that ChAap4 is the only Aap responsible for d- and l-Asp uptake under high alkaline conditions. In addition, ChAAP4 deletion significantly decreased the induction of DDO activity and ChDDO transcription in the presence of d-Asp. This study revealed that d-Asp uptake by ChAap4 might be involved in the induction of ChDDO expression by d-Asp.
Detection and Potential Virulence of Viable but Non-Culturable (VBNC) Listeria monocytogenes: A Review
Authors: Wideman Nathan E. , Oliver James D. , Crandall Philip Glen , Jarvis Nathan A.
Published: January 2021

The detection, enumeration, and virulence potential of viable but non-culturable (VBNC) pathogens continues to be a topic of discussion. While there is a lack of definitive evidence that VBNC Listeria monocytogenes (Lm) pose a public health risk, recent studies suggest that Lm in its VBNC state remains virulent. VBNC bacteria cannot be enumerated by traditional plating methods, so the results from routine Lm testing may not demonstrate a sample’s true hazard to public health. We suggest that supplementing routine Lm testing methods with methods designed to enumerate VBNC cells may more accurately represent the true level of risk. This review summarizes five methods for enumerating VNBC Lm: Live/Dead BacLightTM staining, ethidium monoazide and propidium monoazide-stained real-time polymerase chain reaction (EMA- and PMA-PCR), direct viable count (DVC), 5-cyano-2,3-ditolyl tetrazolium chloride-4′,6-diamidino-2-phenylindole (CTC-DAPI) double staining, and carboxy-fluorescein diacetate (CDFA) staining. Of these five supplementary methods, the Live/Dead BacLightTM staining and CFDA-DVC staining currently appear to be the most accurate for VBNC Lm enumeration. In addition, the impact of the VBNC state on the virulence of Lm is reviewed. Widespread use of these supplemental methods would provide supporting data to identify the conditions under which Lm can revert from its VBNC state into an actively multiplying state and help identify the environmental triggers that can cause Lm to become virulent. Highlights: Rationale for testing for all viable Listeria (Lm) is presented. Routine environmental sampling and plating methods may miss viable Lm cells. An overview and comparison of available VBNC testing methods is given. There is a need for resuscitation techniques to recover Lm from VBNC. A review of testing results for post VBNC virulence is compared
Effects of Radiation Intensity, Mineral Matrix, and Pre-Irradiation on the Bacterial Resistance to Gamma Irradiation under Low Temperature Conditions
Authors: Cheptsov Vladimir S. , Belov Andrey A. , Vorobyova Elena A. , Pavlov Anatoli K. , Lomasov Vladimir N.
Published: January 2021

Ionizing radiation is one of the main factors limiting the survival of microorganisms in extraterrestrial conditions. The survivability of microorganisms under irradiation depends significantly on the conditions, in which the irradiation occurs. In particular, temperature, pressure, oxygen and water concentrations are of great influence. However, the influence of factors such as the radiation intensity (in low-temperature conditions) and the type of mineral matrix, in which microorganisms are located, has been practically unstudied. It has been shown that the radioresistance of bacteria can increase after their exposure to sublethal doses and subsequent repair of damage under favorable conditions, however, such studies are also few and the influence of other factors of extraterrestrial space (temperature, pressure) was not studied in them. The viability of bacteria Arthrobacter polychromogenes, Kocuria rosea and Xanthomonas sp. after irradiation with gamma radiation at a dose of 1 kGy under conditions of low pressure (1 Torr) and low temperature (−50 °C) at different radiation intensities (4 vs. 0.8 kGy/h) with immobilization of bacteria on various mineral matrices (montmorillonite vs. analogue of lunar dust) has been studied. Native, previously non-irradiated strains, and strains that were previously irradiated with gamma radiation and subjected to 10 passages of cultivation on solid media were irradiated. The number of survived cells was determined by culturing on a solid medium. It has been shown that the radioresistance of bacteria depends significantly on the type of mineral matrix, on which they are immobilized, wherein montmorillonite contributes to an increased survivability in comparison with a silicate matrix. Survivability of the studied bacteria was found to increase with decreasing radiation intensity, despite the impossibility of active reparation processes under experimental conditions. Considering the low intensity of radiation on various space objects in comparison with radiobiological experiments, this suggests a longer preservation of the viable microorganisms outside the Earth than is commonly believed. An increase in bacterial radioresistance was revealed even after one cycle of irradiation of the strains and their subsequent cultivation under favourable conditions. This indicates the possibility of hypothetical microorganisms on Mars increasing their radioresistance.
Fecal Microbiota Transplant from Human to Mice Gives Insights into the Role of the Gut Microbiota in Non-Alcoholic Fatty Liver Disease (NAFLD)
Authors: Burz Sebastian D. , Monnoye Magali , Philippe Catherine , Farin William , Ratziu Vlad , Strozzi Francesco , Paillarse Jean-Michel , Chêne Laurent , Blottière Hervé M. , Gérard Philippe
Published: January 2021

Non-alcoholic fatty liver diseases (NAFLD) are associated with changes in the composition and metabolic activities of the gut microbiota. However, the causal role played by the gut microbiota in individual susceptibility to NAFLD and particularly at its early stage is still unclear. In this context, we transplanted the microbiota from a patient with fatty liver (NAFL) and from a healthy individual to two groups of mice. We first showed that the microbiota composition in recipient mice resembled the microbiota composition of their respective human donor. Following administration of a high-fructose, high-fat diet, mice that received the human NAFL microbiota (NAFLR) gained more weight and had a higher liver triglycerides level and higher plasma LDL cholesterol than mice that received the human healthy microbiota (HR). Metabolomic analyses revealed that it was associated with lower and higher plasma levels of glycine and 3-Indolepropionic acid in NAFLR mice, respectively. Moreover, several bacterial genera and OTUs were identified as differently represented in the NAFLR and HR microbiota and therefore potentially responsible for the different phenotypes observed. Altogether, our results confirm that the gut bacteria play a role in obesity and steatosis development and that targeting the gut microbiota may be a preventive or therapeutic strategy in NAFLD management.
Production Optimization, Structural Analysis, and Prebiotic- and Anti-Inflammatory Effects of Gluco-Oligosaccharides Produced by Leuconostoc lactis SBC001
Authors: Kim Minhui , Jang Jae-Kweon , Park Young-Seo
Published: January 2021

Leuconostoc lactis SBC001, isolated from chive, produces glucansucrase and synthesizes oligosaccharides through its enzymatic activity. This study was conducted to optimize oligosaccharide production using response surface methodology, analyze the structure of purified oligosaccharides, and investigate the prebiotic effect on 24 bacterial and yeast strains and the anti-inflammatory activity using RAW 264.7 macrophage cells. The optimal conditions for oligosaccharide production were a culture temperature of 30 °C and sucrose and maltose concentrations of 9.6% and 7.4%, respectively. Based on 1H-NMR spectroscopic study, the oligosaccharides were identified as gluco-oligosaccharides that consisted of 23.63% α-1,4 glycosidic linkages and 76.37% α-1,6 glycosidic linkages with an average molecular weight of 1137 Da. The oligosaccharides promoted the growth of bacterial and yeast strains, including Lactobacillus plantarum, L. paracasei, L. johnsonii, Leuconostoc mesenteroides, L. rhamnosus, and Saccharomyces cerevisiae. When lipopolysaccharide-stimulated RAW 264.7 cells were treated with the oligosaccharides, the production of nitric oxide was decreased; the expression of inducible nitric oxide synthase, tumor necrosis factor-α, interleukin (IL)-1β, IL-6, and IL-10 was suppressed; and the nuclear factor-kappa B signaling pathway was inhibited. In conclusion, the gluco-oligosaccharides obtained from Leu. lactis SBC001 exhibited a prebiotic effect on six bacterial and yeast strains and anti-inflammatory activity in RAW 264.7 macrophage cells.
Study on Bacteria Isolates and Antimicrobial Resistance in Wildlife in Sicily, Southern Italy
Authors: Gambino Delia , Vicari Domenico , Vitale Maria , Schirò Giorgia , Mira Francesco , Giglia Maria La , Riccardi Alessandra , Gentile Antonino , Giardina Susanna , Carrozzo Anna , Cumbo Valentina , Lastra Antonio , Gargano Valeria
Published: January 2021

Wild environments and wildlife can be reservoirs of pathogens and antibiotic resistance. Various studies have reported the presence of zoonotic bacteria, resistant strains, and genetic elements that determine antibiotic resistance in wild animals, especially near urban centers or agricultural and zootechnical activities. The purpose of this study was the analysis, by cultural and molecular methods, of bacteria isolated from wild animals in Sicily, Italy, regarding their susceptibility profile to antibiotics and the presence of antibiotic resistance genes. Bacteriological analyses were conducted on 368 wild animals, leading to the isolation of 222 bacterial strains identified by biochemical tests and 16S rRNA sequencing. The most isolated species was Escherichia coli, followed by Clostridium perfringens and Citrobacter freundii. Antibiograms and the determination of resistance genes showed a reduced spread of bacteria carrying antibiotic resistance among wild animals in Sicily. However, since several wild animals are becoming increasingly close to residential areas, it is important to monitor their health status and to perform microbiological analyses following a One Health approach.
Modulating Protein–Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples
Authors: González-Muñiz Rosario , Bonache María Ángeles , Pérez de Vega María Jesús
Published: January 2021

Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein–protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
Formulation of Quaternized Aminated Chitosan Nanoparticles for Efficient Encapsulation and Slow Release of Curcumin
Authors: Omer Ahmed M. , Ziora Zyta M. , Tamer Tamer M. , Khalifa Randa E. , Hassan Mohamed A. , Mohy-Eldin Mohamed S. , Blaskovich Mark A. T.
Published: January 2021

An effective drug nanocarrier was developed on the basis of a quaternized aminated chitosan (Q-AmCs) derivative for the efficient encapsulation and slow release of the curcumin (Cur)-drug. A simple ionic gelation method was conducted to formulate Q-AmCs nanoparticles (NPs), using different ratios of sodium tripolyphosphate (TPP) as an ionic crosslinker. Various characterization tools were employed to investigate the structure, surface morphology, and thermal properties of the formulated nanoparticles. The formulated Q-AmCs NPs displayed a smaller particle size of 162 ± 9.10 nm, and higher surface positive charges, with a maximum potential of +48.3 mV, compared to native aminated chitosan (AmCs) NPs (231 ± 7.14 nm, +32.8 mV). The Cur-drug encapsulation efficiency was greatly improved and reached a maximum value of 94.4 ± 0.91%, compared to 75.0 ± 1.13% for AmCs NPs. Moreover, the in vitro Cur-release profile was investigated under the conditions of simulated gastric fluid [SGF; pH 1.2] and simulated colon fluid [SCF; pH 7.4]. For Q-AmCs NPs, the Cur-release rate was meaningfully decreased, and recorded a cumulative release value of 54.0% at pH 7.4, compared to 73.0% for AmCs NPs. The formulated nanoparticles exhibited acceptable biocompatibility and biodegradability. These findings emphasize that Q-AmCs NPs have an outstanding potential for the delivery and slow release of anticancer drugs.
A Review: Halogenated Compounds from Marine Fungi
Authors: Wang Cong , Lu Huanyun , Lan Jianzhou , Zaman KH , Cao Shugeng
Published: January 2021

Marine fungi produce many halogenated metabolites with a variety of structures, from acyclic entities with a simple linear chain to multifaceted polycyclic molecules. Over the past few decades, their pharmaceutical and medical application have been explored and still the door is kept open due to the need of new drugs from relatively underexplored sources. Biological properties of halogenated compounds such as anticancer, antiviral, antibacterial, anti-inflammatory, antifungal, antifouling, and insecticidal activity have been investigated. This review describes the chemical structures and biological activities of 217 halogenated compounds derived mainly from Penicillium and Aspergillus marine fungal strains reported from 1994 to 2019.