bluuebunny/crossref_metadata_2025 huggingface dataset:
Engineering Hydrogels for the Development of Three-Dimensional In Vitro Models
Authors: Maji Somnath , Lee Hyungseok
Published: March 2022

The superiority of in vitro 3D cultures over conventional 2D cell cultures is well recognized by the scientific community for its relevance in mimicking the native tissue architecture and functionality. The recent paradigm shift in the field of tissue engineering toward the development of 3D in vitro models can be realized with its myriad of applications, including drug screening, developing alternative diagnostics, and regenerative medicine. Hydrogels are considered the most suitable biomaterial for developing an in vitro model owing to their similarity in features to the extracellular microenvironment of native tissue. In this review article, recent progress in the use of hydrogel-based biomaterial for the development of 3D in vitro biomimetic tissue models is highlighted. Discussions of hydrogel sources and the latest hybrid system with different combinations of biopolymers are also presented. The hydrogel crosslinking mechanism and design consideration are summarized, followed by different types of available hydrogel module systems along with recent microfabrication technologies. We also present the latest developments in engineering hydrogel-based 3D in vitro models targeting specific tissues. Finally, we discuss the challenges surrounding current in vitro platforms and 3D models in the light of future perspectives for an improved biomimetic in vitro organ system.
Modulation of Gut Microbiota Combined with Upregulation of Intestinal Tight Junction Explains Anti-Inflammatory Effect of Corylin on Colitis-Associated Cancer in Mice
Authors: Chang Zi-Yu , Liu Hsuan-Miao , Leu Yann-Lii , Hsu Chung-Hua , Lee Tzung-Yan
Published: March 2022

Inflammatory bowel disease (IBD) involves chronic inflammation, loss of epithelial integrity, and gastrointestinal microbiota dysbiosis, resulting in the development of a colon cancer known as colitis-associated colorectal cancer (CAC). In this study, we evaluated the effects of corylin in a mouse model of dextran sodium sulfate (DSS)-induced colitis. The results showed corylin could improved the survival rate and colon length, maintained body weight, and ameliorated the inflammatory response in the colon. Then, we further identified the possible antitumor effects after 30-day treatment of corylin on an azoxymethane (AOM)/DSS-induced CAC mouse model. Biomarkers associated with inflammation, the colon tissue barrier, macrophage polarization (CD11c, CCR7, CD163, and CD206), and microbiota dysbiosis were monitored in the AOM/DSS group versus corylin groups. Corylin downregulated pro-inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and IL-6) mRNA expression and inflammatory signaling-associated markers (TLR4, MyD88, AP-1, CD11b, and F4/80). In addition, a colon barrier experiment revealed that epithelial cell proliferation of the mucus layer (Lgr5, Cyclin D1, and Olfm4) was downregulated and tight junction proteins (claudin-1 and ZO-1) were upregulated. Furthermore, the Firmicutes/Bacteroidetes ratio changed with corylin intervention, and the microbial diversity and community richness of the AOM/DSS mice were improved by corylin. The comparative analysis of gut microbiota revealed that Bacteroidetes, Patescibacteria, Candidatus Saccharimonas, Erysipelatoclostridium, and Enterorhabdus were significantly increased but Firmicutes, Turicibacter, Romboutsia, and Blautia decreased after corylin treatment. Altogether, corylin administration showed cancer-ameliorating effects by reducing the risk of colitis-associated colon cancer via regulation of inflammation, carcinogenesis, and compositional change of gut microbiota. Therefore, corylin could be a novel, potential health-protective, natural agent against CAC.
Stereoselective Promiscuous Reactions Catalyzed by Lipases
Authors: Patti Angela , Sanfilippo Claudia
Published: March 2022

The ability of lipases to display activity beyond their physiological reactions, so-called “catalytic promiscuity”, has gained increasing interest in the last two decades as an important tool for expanding the application of these enzymes in organic synthesis. Some lipases have been shown to be effective in catalyzing a variety of C-C bond formation reactions and most of the investigations have been directed to the optimization of the products yield through a careful tuning of the experimental parameters. Despite the fact that new stereogenic carbons are formed in many of the tested reactions, the target products have been often obtained in racemic form and examples of an efficient asymmetric induction by the used lipases are quite limited. The aim of this review, mainly focused on those lipase-catalyzed promiscuous reactions in which optically active products have been obtained, is to offer a current state of art together with a perspective in this field of asymmetric synthesis.
Subcellular Distribution of Thyroid Hormone Receptor Beta in Ovarian Cancer
Authors: Heublein Sabine , Jeschke Udo , Sattler Cornelia , Kuhn Christina , Hester Anna , Czogalla Bastian , Trillsch Fabian , Mahner Sven , Mayr Doris , Schmoeckel Elisa , Ditsch Nina
Published: March 2022

Background: Since the most well-known function of thyroid hormone receptors (TRs) relies on their ability to act as ligand-activated transcription factors, their subcellular localization has been recognized to be relevant for their biological meaning. The current study aimed to determine the prevalence and subcellular distribution of TR beta and TR beta-1 in ovarian cancer (OC). Methods: Tissue was collected from 153 patients that had undergone surgery due to OC at the Department of Obstetrics and Gynaecology of the Ludwig-Maximilians-University Munich. Immunohistochemistry detecting TR beta and TR beta-1 was performed. Staining signals were quantified and tested for association with clinico-pathological parameters including overall survival (OS). Results: The subcellular distribution of TR beta and TR beta-1 differed among histologic subtypes, grade and FIGO stage. TR beta positivity was strongly linked to shortened overall survival (p < 0.001). Strikingly, this shortened OS was mainly attributed to those cases showing complete (p = 0.005) or incomplete shift of TR beta to the cytoplasm (p < 0.001). Significance was lost in multivariate testing. Conclusions: Cytoplasmatic localization of TR beta was associated with reduced OS, at least in univariate analysis. Since TRs have long been supposed to mainly function via the regulation of gene transcription in the nucleus, cytoplasmatic shifting might be interpreted as a regulator of their activity.
Identification of a Tumor Cell Associated Type I IFN Resistance Gene Expression Signature of Human Melanoma, the Components of Which Have a Predictive Potential for Immunotherapy
Authors: Ladányi Andrea , Rásó Erzsébet , Barbai Tamás , Vízkeleti Laura , Puskás László G. , Kovács Szonja A. , Győrffy Balázs , Tímár József
Published: March 2022

We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in vitro (HT168-M1res), which was proven to be maintained in vivo in SCID mice. Comparing the mRNA profile of in vitro cultured HT168-M1res cells to its sensitive counterpart, we found 79 differentially expressed genes (DEGs). We found that only a 13-gene core of the DEGs was stable in vitro and only a 4-gene core was stable in vivo. Using an in silico cohort of IFN-treated melanoma tissues, we validated a differentially expressed 9-gene core of the DEGs. Furthermore, using an in silico cohort of immune checkpoint inhibitor (ICI)-treated melanoma tissues, we tested the predictive power of the DEGs for the response rate. Analysis of the top four upregulated and top four downregulated genes of the DEGs identified WFDC1, EFNA3, DDX10, and PTBP1 as predictive genes, and analysis of the “stable” genes of DEGs for predictive potential of ICI response revealed another 13 genes, out of which CDCA4, SOX4, DEK, and HSPA1B were identified as IFN-regulated genes. Interestingly, the IFN treatment associated genes and the ICI-therapy predictive genes overlapped by three genes: WFDC1, BCAN, and MT2A, suggesting a connection between the two biological processes.
Double-Stranded RNA Enhances Matrix Metalloproteinase-1 and -13 Expressions through TLR3-Dependent Activation of Transglutaminase 2 in Dermal Fibroblasts
Authors: Hong Ah-Young , Lee Seok-Jin , Lee Ki Baek , Shin Ji-Woong , Jeong Eui Man , Kim In-Gyu
Published: March 2022

UV-irradiation induces the secretion of double-stranded RNA (dsRNA) derived from damaged noncoding RNAs in keratinocytes, which enhance the expression of matrix metalloproteinases (MMP) in non-irradiated dermal fibroblasts, leading to dysregulation of extracellular matrix homeostasis. However, the signaling pathway responsible for dsRNA-induced MMP expression has not been fully understood. Transglutaminase 2 (TG2) is an enzyme that modifies substrate proteins by incorporating polyamine or crosslinking of proteins, thereby regulating their functions. In this study, we showed that TG2 mediates dsRNA-induced MMP-1 expression through NF-κB activation. Treatment of poly(I:C), a synthetic dsRNA analogue binding to toll-like receptor 3 (TLR3), generates ROS, which in turn activates TG2 in dermal fibroblast. Subsequently, TG2 activity enhances translocation of p65 into the nucleus, where it augments transcription of MMP. We confirmed these results by assessing the level of MMP expression in Tlr3−/−, TG2-knockdowned and Tgm2−/− dermal fibroblasts after poly(I:C)-treatment. Moreover, treatment with quercetin showed dose-dependent suppression of poly(I:C)-induced MMP expression. Furthermore, ex vivo cultured skin from Tgm2−/− mice exhibited a significantly reduced level of MMP mRNA compared with those from wild-type mice. Our results indicate that TG2 is a critical regulator in dsRNA-induced MMP expression, providing a new target and molecular basis for antioxidant therapy in preventing collagen degradation.
Reduction in Phosphoribulokinase Amount and Re-Routing Metabolism in Chlamydomonas reinhardtii CP12 Mutants
Authors: Gérard Cassy , Lebrun Régine , Lemesle Erwan , Avilan Luisana , Chang Kwang Suk , Jin EonSeon , Carrière Frédéric , Gontero Brigitte , Launay Hélène
Published: March 2022

The chloroplast protein CP12 is involved in the dark/light regulation of the Calvin–Benson–Bassham cycle, in particular, in the dark inhibition of two enzymes: glyceraldehyde−3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), but other functions related to stress have been proposed. We knocked out the unique CP12 gene to prevent its expression in Chlamydomonas reinhardtii (ΔCP12). The growth rates of both wild-type and ΔCP12 cells were nearly identical, as was the GAPDH protein abundance and activity in both cell lines. On the contrary, the abundance of PRK and its specific activity were significantly reduced in ΔCP12, as revealed by relative quantitative proteomics. Isolated PRK lost irreversibly its activity over-time in vitro, which was prevented in the presence of recombinant CP12 in a redox-independent manner. We have identified amino acid residues in the CP12 protein that are required for this new function preserving PRK activity. Numerous proteins involved in redox homeostasis and stress responses were more abundant and the expressions of various metabolic pathways were also increased or decreased in the absence of CP12. These results highlight CP12 as a moonlighting protein with additional functions beyond its well-known regulatory role in carbon metabolism.
Ceramides as Mediators of Oxidative Stress and Inflammation in Cardiometabolic Disease
Authors: Gaggini Melania , Ndreu Rudina , Michelucci Elena , Rocchiccioli Silvia , Vassalle Cristina
Published: March 2022

Ceramides, composed of a sphingosine and a fatty acid, are bioactive lipid molecules involved in many key cellular pathways (e.g., apoptosis, oxidative stress and inflammation). There is much evidence on the relationship between ceramide species and cardiometabolic disease, especially in relationship with the onset and development of diabetes and acute and chronic coronary artery disease. This review reports available evidence on ceramide structure and generation, and discusses their role in cardiometabolic disease, as well as current translational chances and difficulties for ceramide application in the cardiometabolic clinical settings.
Non-Coding RNAs: Prevention, Diagnosis, and Treatment in Myocardial Ischemia–Reperfusion Injury
Authors: Marinescu Mihnea-Cosmin , Lazar Andrada-Luciana , Marta Monica Mihaela , Cozma Angela , Catana Cristina-Sorina
Published: March 2022

Recent knowledge concerning the role of non-coding RNAs (ncRNAs) in myocardial ischemia/reperfusion (I/R) injury provides new insight into their possible roles as specific biomarkers for early diagnosis, prognosis, and treatment. MicroRNAs (miRNAs) have fewer than 200 nucleotides, while long ncRNAs (lncRNAs) have more than 200 nucleotides. The three types of ncRNAs (miRNAs, lncRNAs, and circRNAs) act as signaling molecules strongly involved in cardiovascular disorders (CVD). I/R injury of the heart is the main CVD correlated with acute myocardial infarction (AMI), cardiac surgery, and transplantation. The expression levels of many ncRNAs and miRNAs are highly modified in the plasma of MI patients, and thus they have the potential to diagnose and treat MI. Cardiomyocyte and endothelial cell death is the major trigger for myocardial ischemia–reperfusion syndrome (MIRS). The cardioprotective effect of inflammasome activation in MIRS and the therapeutics targeting the reparative response could prevent progressive post-infarction heart failure. Moreover, the pharmacological and genetic modulation of these ncRNAs has the therapeutic potential to improve clinical outcomes in AMI patients.
Mechanism Underlying the Bypass of Apurinic/Pyrimidinic Site Analogs by Sulfolobus acidocaldarius DNA Polymerase IV
Authors: Huang Qin-Ying , Song Dong , Wang Wei-Wei , Peng Li , Chen Hai-Feng , Xiao Xiang , Liu Xi-Peng
Published: March 2022

The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with relatively low fidelity. The Y-family DNA polymerases are the main error-prone DNA polymerases, and they employ three mechanisms to perform TLS, including template-skipping, dNTP-stabilized misalignment, and misincorporation-misalignment. The bypass mechanism of the dinB homolog (Dbh), an archaeal Y-family DNA polymerase from Sulfolobus acidocaldarius, is unclear and needs to be confirmed. In this study, we show that the Dbh primarily uses template skipping accompanied by dNTP-stabilized misalignment to bypass AP site analogs, and the incorporation of the first nucleotide across the AP site is the most difficult. Furthermore, based on the reported crystal structures, we confirmed that three conserved residues (Y249, R333, and I295) in the little finger (LF) domain and residue K78 in the palm subdomain of the catalytic core domain are very important for TLS. These results deepen our understanding of how archaeal Y-family DNA polymerases deal with intracellular AP site damage and provide a biochemical basis for elucidating the intracellular function of these polymerases.
Functional Properties of Gelatin/Polyvinyl Alcohol Films Containing Black Cumin Cake Extract and Zinc Oxide Nanoparticles Produced via Casting Technique
Authors: Tymczewska Alicja , Furtado Bliss Ursula , Nowaczyk Jacek , Hrynkiewicz Katarzyna , Szydłowska-Czerniak Aleksandra
Published: March 2022

This study aimed to develop and characterize gelatin/polyvinyl alcohol (G/PVA) films loaded with black cumin cake extract (BCCE) and zinc oxide nanoparticles (ZnONPs). The BCCE was also applied for the green synthesis of ZnONPs with an average size of less than 100 nm. The active films were produced by a solvent-casting technique, and their physicochemical and antibacterial properties were investigated. Supplementation of G/PVA film in ZnONPs decreased the tensile strength (TS) from 2.97 MPa to 1.69 MPa. The addition of BCCE and ZnONPs increased the elongation at the break (EAB) of the enriched film by about 3%. The G/PVA/BCCE/ZnONPs film revealed the lowest water vapor permeability (WVP = 1.14 × 10−9 g·mm·Pa−1·h−1·mm−2) and the highest opacity (3.41 mm−1). The QUick, Easy, New, CHEap and Reproducible (QUENCHER) methodologies using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6- sulfonic acid) (ABTS) and cupric ion reducing antioxidant capacity (CUPRAC) were applied to measure antioxidant capacity (AC) of the prepared films. The incorporation of BCCE and ZnONPs into G/PVA films enhanced the AC by 8–144%. The films containing ZnONPs and a mixture of BCCE and ZnONPs inhibited the growth of three Gram-positive bacterial strains. These nanocomposite films with desired functional properties can be recommended to inhibit microbial spoilage and oxidative rancidity of packaged food.
Grainyhead-like (Grhl) Target Genes in Development and Cancer
Authors: Gasperoni Jemma G. , Fuller Jarrad N. , Darido Charbel , Wilanowski Tomasz , Dworkin Sebastian
Published: March 2022

Grainyhead-like (GRHL) factors are essential, highly conserved transcription factors (TFs) that regulate processes common to both natural cellular behaviours during embryogenesis, and de-regulation of growth and survival pathways in cancer. Serving to drive the transcription, and therefore activation of multiple co-ordinating pathways, the three GRHL family members (GRHL1-3) are a critical conduit for modulating the molecular landscape that guides cellular decision-making processes during proliferation, epithelial-mesenchymal transition (EMT) and migration. Animal models and in vitro approaches harbouring GRHL loss or gain-of-function are key research tools to understanding gene function, which gives confidence that resultant phenotypes and cellular behaviours may be translatable to humans. Critically, identifying and characterising the target genes to which these factors bind is also essential, as they allow us to discover and understand novel genetic pathways that could ultimately be used as targets for disease diagnosis, drug discovery and therapeutic strategies. GRHL1-3 and their transcriptional targets have been shown to drive comparable cellular processes in Drosophila, C. elegans, zebrafish and mice, and have recently also been implicated in the aetiology and/or progression of a number of human congenital disorders and cancers of epithelial origin. In this review, we will summarise the state of knowledge pertaining to the role of the GRHL family target genes in both development and cancer, primarily through understanding the genetic pathways transcriptionally regulated by these factors across disparate disease contexts.
Preliminary Design and Dynamic Response of Multi-Purpose Floating Offshore Wind Turbine Platform: Part 1
Authors: Alsubal Shamsan , Liew Mohd S. , Shawn Lim Eu
Published: March 2022

Floating offshore wind turbine foundations are based on platforms operated by the oil and gas industry. However, they are designed and optimized to meet the wind turbines’ operating criteria. Although Malaysia is considered a low-wind-speed country, there are some locations facing the South China Sea that are found to be feasible for wind energy harnessing. The average daily wind speed may reach up to 15 m/s. Therefore, designing a cost-effective platform that can operate in Malaysian waters which has less severe environmental conditions compared to the North Sea would be a prudent undertaking. In this study, a new design of a multi-purpose floating offshore wind turbine platform (Mocha-TLP) is presented. In addition, the dynamic response of the platform to wave loads was investigated using the Navier–Stokes code STAR CCM+ developed by CD-adapco. Moreover, free-oscillation tests were performed to determine the natural periods of the platform. Three approaching wave cases and two wave conditions (WC) were considered. The results show that the natural periods of the platforms were within the recommended range for pitch, roll, yaw, heave, sway and surge motions. The platform was stable in rotational motion within the three cases. However, it experienced a noticeable surge motion which was more critical with wave condition one (WC1) since the wavelength equalled the length of the structure. The dynamic response of the platform to wave loads wase minimal and within the operational requirements for wind turbines.
A Tracking Algorithm for Sparse and Dynamic Underwater Sensor Networks
Authors: Liu Haiming , Xu Bo , Liu Bin
Published: March 2022

An underwater sensor network (UWSN) has sparse and dynamic characteristics. In sparse and dynamic UWSNs, the traditional particle filter based on multi-rate consensus/fusion (CF/DPF) has the problems of a slow convergence rate and low filtering accuracy. To solve these problems, a tracking algorithm for sparse and dynamic UWSNs based on particle filter (TASD) is proposed. Firstly, the estimation results of a local particle filter are processed by a weighted average consensus filter (WACF). In this way, the reliability difference of state estimation between nodes in sparse and dynamic UWSN is reasonably eliminated. Secondly, a delayed update mechanism (DUM) is added to WACF, which effectively solves the problem of time synchronization between the two particle filters. Thirdly, under the condition of limited communication energy consumption, an alternating random scheme (ARS) is designed, which optimizes the mean square convergence rate of the fusion particle filter. Simulation results show that the proposed algorithm can be applied to maneuvering target tracking in sparse and dynamic UWSN effectively. Compared with the traditional method, it has higher tracking accuracy and faster convergence speed. The average estimation error of TASD is 91.3% lower than that of CF/DPF, and the weighted consensus tracking error of TASD is reduced by 85.6% compared with CF/DPF.
Making of Massoia Lactone-Loaded and Food-Grade Nanoemulsions and Their Bioactivities against a Pathogenic Yeast
Authors: Yuan Li , Zhang Hong-Qian , Chi Zhe , Liu Guang-Lei , Chi Zhen-Ming
Published: March 2022

Nanoemulsions (NEs) have been made for improving the delivery and disperse of bioactive compounds. In this study, it was found that the best ingredients for the stable Massoia lactone-loaded and food-grade NEs making were 560.0 µL of Tween-80, 240.0 µL of Span-80 and 200.0 µL of Massoia lactone. Then, 9.0 mL of distilled water was titrated into the mixture under continuous magnetic stirring (750 rotations min−1) with about 2 drops per second for 20 min. Finally, the system was treated by ultrasonication using an ultrasonic generator (180 W and 22 KHz) for 5 min. All the prepared particles with a mean droplet diameter of 43 nm were spherical, had uniform size distribution and were equally distributed in the Massoia lactone-loaded NEs. The obtained Massoia lactone-loaded nanoemulsions (NEs) were very stable without changes of the mean droplet diameter and polydispersity indexes (PDI) for over two months under different conditions. As with free Massoia lactone, Massoia lactone loaded in the NEs had high anti-fungal activity against Metschnikowia bicuspidate LIAO, a pathogenic yeast causing milky disease in the Chinese mitten crab by damaging its cell membrane and causing cellular necrosis. Massoia lactone loaded in the NEs also had the DPPH radical scavenging activity and the hydroxyl radical scavenging activity.
Research on the Dynamic Performance of a Novel Floating Offshore Wind Turbine Considering the Fully-Coupled-Effect of the System
Authors: Zhang Hongjian , Wang Hao , Cai Xin , Xie Jiaojie , Wang Yazhou , Zhang Ningchuan
Published: March 2022

Floating offshore wind turbines (FOWTs) still face many challenges in improving platform stability. A fully submersible FOWT platform with inclined side columns is designed to tackle the current technical bottleneck of the FOWT platform, combining the structural characteristics of the semi-submersible and Spar platform. An integrated numerical model of FOWT is established considering the fully coupled effect, and the hydrodynamic performance of the novel FOWT, the semi-submersible FOWT, and the Spar FOWT are compared and analyzed under different wave incidence angles and wave frequencies, as well as the blade and tower dynamic response of the three FOWTs under the coupling effect of wind, wave, and current. The results show that the novel floating platform can significantly optimize the hydrodynamic performance and has a better recovery ability after being subjected to external loads. The novel floating platform can significantly reduce the heave peak and its corresponding wave frequency compared to the semi-submersible platform, reducing the possibility of heave resonance. FOWT operation should ensure positive wave inflow as far as possible to avoid excessive wave forces in the lateral direction. Both blade and tower dynamic response are affected by rotor rotation and tower vibration to varying degrees, while tower dynamic response is mainly affected by platform motion. This study suggests that the application of the novel FOWT concept is feasible and can be an alternative in offshore wind exploitation in deep water.
Minimal versus Intensive: How the Pruning Intensity Affects Occurrence of Grapevine Leaf Stripe Disease, Wood Integrity, and the Mycobiome in Grapevine Trunks
Authors: Kraus Christian , Rauch Carolin , Kalvelage Elisa Maria , Behrens Falk Hubertus , d’Aguiar Dagmar , Dubois Cornelia , Fischer Michael
Published: March 2022

Previous works on grapevine-trunk diseases indicate that minimal or non-pruning of the grapevine under certain circumstances can significantly reduce the risk of symptom expression. Nevertheless, knowledge of the mechanisms behind these observations are limited. Therefore, it was the aim of this study to investigate in more detail the effect of pruning intensity on the grapevine trunk by means of trunk integrity and the fungal community in the wood tissue. Two German vineyards partially trained in vertical-shoot position and semi-minimally pruned hedges were chosen for this survey due to the accessibility of multi-annual esca-monitoring data. The results revealed that only in one of the two vineyards was the incidence of external esca symptoms significantly reduced over a period of five years (2017–2021) by minimal pruning, which was up to 73.7% compared to intensive pruning. In both vineyards, the trunks of intensively pruned vines not only had more pruning wounds on the trunk (by 86.0% and 72.9%, respectively) than minimally pruned vines, but also exhibited a larger (by 19.3% and 14.7%, respectively) circumference of the trunk head. In addition, the percentage of white rot and necrosis in the trunks of esca-positive and esca-negative vines was analyzed and compared between the two pruning intensities; hereby, significant differences were only found for esca-negative ‘Dornfelder’ vines, in which the proportion of necrosis was higher for intensively pruned vines (23.0%) than for minimally pruned vines (11.5%). The fungal communities of the differently pruned vine trunks were mainly dominated by four genera, which are also associated with GTDs: Diplodia, Eutypa, Fomitiporia and Phaeomoniella. All in all, the fungal diversity and community composition did not differ between minimally and intensively pruned, esca-positive vines.
AMF Community Diversity Promotes Grapevine Growth Parameters under High Black Foot Disease Pressure
Authors: Moukarzel Romy , Ridgway Hayley J. , Liu Jing , Guerin-Laguette Alexis , Jones E. Eirian
Published: March 2022

Black foot disease is one of the main grapevine root diseases observed worldwide and is especially problematic in New Zealand. Arbuscular mycorrhizal fungi (AMF) have been shown to reduce infection and mitigate the effect of black foot disease on grapevine rootstocks. In contrast to prior studies, which have limited their focus to the effect of one, two or a combination of only a small number of AMF species, this study used whole AMF communities identified from 101-14, 5C and Schwarzmann rootstocks sampled from New Zealand vineyards. The effect of AMF on black foot disease was investigated in a ‘home’ and ‘away’ experiment using three commercial grapevine rootstocks. The study produced some evidence that AMF treatments lowered disease incidence at 5 cm and disease severity in vines by 40% to 50% compared to the vines inoculated with the pathogen only. This work also showed that the presence of high disease incidence may have limited the potential disease protective effect of AMF community. However, despite the high disease incidence and severity, AMF inoculation increased vine growth parameters by 60% to 80% compared to the vines inoculated with the pathogen only. This study is the first to provide an understanding on how young grapevine rootstocks inoculated with their ‘home’ and ‘away’ AMF communities would respond to challenge with a black foot pathogen species mixture. Further research is required to understand the mechanistic effect of AMF colonization on the increase of grapevine growth parameters under high black foot disease pressure.
Mineral and Organic Fertilizers Distinctly Affect Fungal Communities in the Crop Rhizosphere
Authors: Semenov Mikhail V. , Krasnov George S. , Semenov Vyacheslav M. , van Bruggen Ariena
Published: March 2022

Fungi represent a diverse group of organisms that play an essential role in maintaining soil health and ecosystem functioning. Plant root exudates form nutrient-rich niches that harbor specific fungal communities, or so-called rhizosphere mycobiomes. The long-term application of fertilizers supplies the soil with nutrients that may override the plant-related effects on rhizosphere fungal communities. Here, we assessed the effect of contrasting fertilization regimes on the composition, diversity, and abundance of bulk soil and rhizosphere mycobiomes of potato, white mustard, and maize under NPK (mineral fertilizers) or fresh cattle manure (organic fertilizers). Mineral and organic fertilizers led to distinct fungal communities in the rhizospheres of all studied crops, and the plant-related effects on the mycobiome were overridden by the effect of fertilization. The abundances of Ascomycota and Olpidiomycota were higher under manure, while the abundances of Basidiomycota and Monoblepharomycota increased under NPK. Manure input strongly increased fungal abundance but decreased fungal diversity and the total number of species. NPK had a slight effect on fungal diversity, but significantly increased the relative abundances of fungal phytopathogens, such as Alternaria and Fusarium. Our study shows that that potential plant species effects on the abundance and diversity of the rhizosphere mycobiomes are governed by long-term fertilization. Fertilization management could therefore be used to manipulate rhizosphere fungal communities and soilborne pathogen suppressiveness.
MHD Hybrid Nanofluid Mixed Convection Heat Transfer and Entropy Generation in a 3-D Triangular Porous Cavity with Zigzag Wall and Rotating Cylinder
Authors: Abderrahmane Aissa , Qasem Naef A. A. , Younis Obai , Marzouki Riadh , Mourad Abed , Shah Nehad Ali , Chung Jae Dong
Published: March 2022

The purpose of this work was to conduct a numerical examination of mixed convective heat transfer in a three-dimensional triangular enclosure with a revolving circular cylinder in the cavity’s center. Numerical simulations of the hybrid Fe3O4/MWCNT-water nanofluid are performed using the finite element approach (FEM). The simulation is carried out for a range of parameter values, including the Darcy number (between 10−5 and 10−2), the Hartmann number (between 0 and 100), the angular speed of the rotation (between −500 and 1000), and the number of zigzags. The stream function, isotherms, and isentropic contours illustrate the impact of many parameters on motion, heat transfer, and entropy formation. The findings indicate that for enhancing the heat transfer rates of hybrid nanofluid in a three-dimensional triangular porous cavity fitted with a rotating cylinder and subjected to a magnetic field, Darcy number > 10−3, Hartmann number < 0, one zigzag on the hot surface, and rotation speed >500 in flow direction are recommended.
Grazing and Symmetry-Breaking Bifurcations Induced Oscillations in a Switched System Composed of Duffing and van der Pol Oscillators
Authors: Zhang Chun , Tang Qiaoxia , Wang Zhixiang
Published: March 2022

By introducing a switching scheme related to the state and time, a typical switched model alternating between a Duffing oscillator and van der Pol oscillator is established to explore the typical dynamical behaviors as well as the mechanism of the switched system. Shooting methods to locate the limit cycle and specify bifurcation sets are described by defining an appropriate Poincaré map. Different types of multiple-Focus/Cycle and single-Focus/Cycle period oscillations in the system can be observed. Symmetry-breaking, period-doubling, and grazing bifurcation curves are obtained in the plane of bifurcation parameters, dividing the parameters plane into several regions corresponding to different kinds of oscillations. Meanwhile, based on the numerical simulation and bifurcation analysis, the mechanisms of several typical dynamical behaviors observed in different regions are presented.
Anti-Osteoclastogenic and Antibacterial Effects of Chlorinated Polyketides from the Beibu Gulf Coral-Derived Fungus Aspergillus unguis GXIMD 02505
Authors: Zhang Yanting , Li Zhichao , Huang Bingyao , Liu Kai , Peng Shuai , Liu Xinming , Gao Chenghai , Liu Yonghong , Tan Yanhui , Luo Xiaowei
Published: March 2022

One new depsidone derivative, aspergillusidone H (3), along with seven known biosynthetically related chlorinated polyketides, were obtained from the Beibu Gulf coral-derived fungus Aspergillus unguis GXIMD 02505. Their structures were determined by comprehensive physicochemical and spectroscopic data interpretation. Notably, the X-ray crystal structure of 2 and the previously unknown absolute configuration of 8, assigned by ECD calculations, are described here for the first time. Compounds 1–5, 7 and 8 exhibited inhibition of lipopolysaccharide (LPS)-induced NF-κB in RAW 264.7 macrophages at 20 μM. In addition, the two potent inhibitors (2 and 7) dose-dependently suppressed RANKL-induced osteoclast differentiation without any evidence of cytotoxicity in bone marrow macrophages cells (BMMs). This is the first report of osteoclastogenesis inhibitory activity for the metabolites of these kinds. Besides, compounds 1, 2, 4, and 6–8 showed inhibitory activity against marine biofilm-forming bacteria, methicillin-resistant Staphylococcus aureus, Microbulbifer variabilis, Marinobacterium jannaschii, and Vibrio pelagius, with their MIC values ranging from 2 to 64 μg/mL. These findings provide a basis for further development of chlorinated polyketides as potential inhibitors of osteoclast differentiation and/or for use as anti-fouling agents.
Immunomodulatory and Antitumoral Activity of Gold Nanoparticles Synthesized by Red Algae Aqueous Extracts
Authors: González-Ballesteros Noelia , Diego-González Lara , Lastra-Valdor Mariano , Grimaldi Maria , Cavazza Antonella , Bigi Franca , Rodríguez-Argüelles M. Carmen , Simón-Vázquez Rosana
Published: March 2022

This study reports on the green and cost-efficient synthesis of gold nanoparticles from three different red algae extracts. The nanoparticles synthesized were fully characterized by UV-Vis spectroscopy, HRTEM, and Z-potential. Relevant components occurring in the extracts, such as polysaccharides or phenolic content, were assessed by analytical techniques such as spectrophotometric assays and liquid chromatography. Finally, the antioxidant, antitumoral, and anti-inflammatory potential of both the extracts and the gold nanoparticles synthesized were analyzed in order to determine a possible synergistic effect on the nanoparticles. The results obtained confirmed the obtainment of gold nanoparticles with significant potential as immunotherapeutic agents. The therapeutic potential of these nanoparticles could be higher than that of inert gold nanoparticles loaded with bioactive molecules since the former would allow for higher accumulation into the targeted tissue.
Early Transcriptional Changes in the Midgut of Ornithodoros moubata after Feeding and Infection with Borrelia duttonii
Authors: Schäfer Mandy , Pfaff Florian , Höper Dirk , Silaghi Cornelia
Published: March 2022

Studies on tick-pathogen-host interactions are helping to identify candidates for vaccines against ticks and tick-borne diseases and to discover potent bioactive tick molecules. The tick midgut is the main tissue involved in blood feeding and, moreover, the first organ to have contact with pathogens ingested through the blood meal. As little is known about the molecular biology of feeding and tick defence mechanisms against microorganisms, but important for understanding vector-pathogen interactions, we explored the early transcriptional changes in the midgut of Ornithodoros moubata after feeding and in response to challenge with the relapsing-fever spirochete Borrelia duttonii using the Ion S5XL platform. Besides transcripts with metabolic function and immune-related transcripts we discovered numerous putative and uncharacterized protein sequences. Overall, our analyses support previous studies and provides a valuable reference database for further functional proteomic analysis of midgut proteins of O. moubata.
Host Environment Shapes S. aureus Social Behavior as Revealed by Microscopy Pattern Formation and Dynamic Aggregation Analysis
Authors: Rivera-Yoshida Natsuko , Bottagisio Marta , Attanasi Davide , Savadori Paolo , De Vecchi Elena , Bidossi Alessandro , Franci Alessio
Published: March 2022

Understanding how bacteria adapt their social behavior to environmental changes is of crucial importance from both biological and clinical perspectives. Staphylococcus aureus is among the most common infecting agents in orthopedics, but its recalcitrance to the immune system and to antimicrobial treatments in the physiological microenvironment are still poorly understood. By means of optical and confocal microscopy, image pattern analysis, and mathematical modeling, we show that planktonic biofilm-like aggregates and sessile biofilm lifestyles are two co-existing and interacting phases of the same environmentally adaptive developmental process and that they exhibit substantial differences when S. aureus is grown in physiological fluids instead of common lab media. Physicochemical properties of the physiological microenvironment are proposed to be the key determinants of these differences. Besides providing a new tool for biofilm phenotypic analysis, our results suggest new insights into the social behavior of S. aureus in physiological conditions and highlight the inadequacy of commonly used lab media for both biological and clinical studies of bacterial development.
Impact of Phosphorylcholine Expression on the Adherence and Invasion of Streptococcus pyogenes to Epithelial Cells
Authors: Iuchi Hiroyuki , Ohori Junichiro , Matsuzaki Hisahiro , Tokushige Takeshi , Toge Sakiko , Yamashita Masaru
Published: March 2022

Phosphorylcholine (PC) is a structural component of various pathogens and is involved in bacterial adhesion via the platelet-activating factor receptor (PAF-R). In this study, we investigated how PC expression affects cell adhesion and invasion of Streptococcus pyogenes (S. pyogenes). Eight clinical strains of S. pyogenes were cultured, and PC expression was measured using fluorescence-activated cell sorting. Bacterial adherence and invasion were examined using Detroit 562 cells. An anti-PC-specific monoclonal antibody (TEPC-15) was used to inhibit bacterial PC, and a PAF-R antagonist (ABT-491) was used to inhibit cellular PAF-R. The emm gene was amplified by the polymerase chain reaction with the standard primers. The level of PC expressed on the S. pyogenes surfaces differed in each strain and differed even in the same emm genotype. Adherence assay experiments showed a significant negative correlation between TEPC-15 and ABT-491 inhibitory effects and PC expression in S. pyogenes. Similarly, intracellular invasion assay experiments showed a significant negative correlation between TEPC-15 and ABT-491 inhibitory effects and PC expression in S. pyogenes. This study suggests that S. pyogenes is involved in cell adhesion and invasion by PC.
Correction: Orita et al. Biosynthesis of Polyhydroxyalkanoate Terpolymer from Methanol via the Reverse β-Oxidation Pathway in the Presence of Lanthanide. Microorganisms 2022, 10, 184
Authors: Orita Izumi , Unno Gento , Kato Risa , Fukui Toshiaki
Published: March 2022

The authors wish to make the following corrections to this paper [...]
Trends in Microbial Community Composition and Function by Soil Depth
Authors: Naylor Dan , McClure Ryan , Jansson Janet
Published: March 2022

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
An Empirical Performance Analysis of the Speak Correct Computerized Interface
Authors: Jambi Kamal , Al-Barhamtoshy Hassanin , Al-Jedaibi Wajdi , Rashwan Mohsen , Abdou Sherif
Published: March 2022

The way in which people speak reveals a lot about where they are from, where they were raised, and also where they have recently lived. When communicating in a foreign language or second language, accents from one’s first language are likely to emerge, giving an individual a ‘strange’ accent. This is a great and challenging problem. Not particularly, because it is a part of one’s personality that they do not have to give up. It is only challenging when pronunciation causes a disruption in communication between an individual and the individuals with whom they are speaking. Making oneself understandable is the goal of perfecting English pronunciations. Many people require their pronunciation to be perfect, such as those individuals working in the healthcare industry, where it is rather critical that each term be read precisely. Speak Correct offers each of its users a service that assists them with any English pronunciation concerns that may arise. Some of the pronunciation improvements will only apply to a specific customer’s dictionary; however, in some cases, the modifications can be applied to the standard dictionary as well, benefiting our whole customer base. Speak Correct is a computerized linguist interface that can assist its users in many different places around the world with their English pronunciation issues due to Saudi or Egyptian accents. In this study, the authors carry out an empirical investigation of the Speak Correct computerized interface to assess its performance. The results of this research reveal that Speak Correct is highly effective at delivering pronunciation correction.
A New Electric Field Mill Network to Estimate Temporal Variation of Simplified Charge Model in an Isolated Thundercloud
Authors: Yamashita Kozo , Fujisaka Hironobu , Iwasaki Hiroyuki , Kanno Kakeru , Hayakawa Masashi
Published: March 2022

The gross charge distribution in an electrified cloud has already been estimated by polarity distribution of the electrostatic field on the ground surface. While either a dipole or a tripole charge structure is commonly accepted, the increase–decrease and motion of each point charge in those models are both still unclear. This paper presents a new network of electric field mills for multipoint electrostatic measurement to evaluate the temporal variations of a simple cloud charge model with second-scale resolution. Details of our newly developed equipment are described, with an emphasis on its advantages. This network was deployed in the north Kanto area of Japan and operated during the summer season in 2020. In order to simplify the relationship between cloud charge positions and the horizontal distribution of the measured electrostatic field, an isolated thundercloud is focused on. As an initial analysis, a negative point charge model is applied to an isolated cloud observed on 27 August 2020. The quantity and height of the point charge were estimated as being approximately −20 C and 7 km, respectively. The calculated charge location is generally coincident with the C-band radar echo regions. Significant correspondence is demonstrated between the intensity distribution of the electrostatic fields measured at seven sites and that calculated with estimated point charge. This result indicates the possibility to determine the amounts and positions of cloud charges inside the dipole charge structure based on multipoint measurement of the electrostatic field.
Study of Different Deep Learning Methods for Coronavirus (COVID-19) Pandemic: Taxonomy, Survey and Insights
Authors: Awassa Lamia , Jdey Imen , Dhahri Habib , Hcini Ghazala , Mahmood Awais , Othman Esam , Haneef Muhammad
Published: March 2022

COVID-19 has evolved into one of the most severe and acute illnesses. The number of deaths continues to climb despite the development of vaccines and new strains of the virus have appeared. The early and precise recognition of COVID-19 are key in viably treating patients and containing the pandemic on the whole. Deep learning technology has been shown to be a significant tool in diagnosing COVID-19 and in assisting radiologists to detect anomalies and numerous diseases during this epidemic. This research seeks to provide an overview of novel deep learning-based applications for medical imaging modalities, computer tomography (CT) and chest X-rays (CXR), for the detection and classification COVID-19. First, we give an overview of the taxonomy of medical imaging and present a summary of types of deep learning (DL) methods. Then, utilizing deep learning techniques, we present an overview of systems created for COVID-19 detection and classification. We also give a rundown of the most well-known databases used to train these networks. Finally, we explore the challenges of using deep learning algorithms to detect COVID-19, as well as future research prospects in this field.
Transmission Line Vibration Damper Detection Using Deep Neural Networks Based on UAV Remote Sensing Image
Authors: Chen Wenxiang , Li Yingna , Zhao Zhengang
Published: March 2022

Vibration dampers can greatly eliminate the galloping phenomenon of overhead transmission wires caused by wind. The detection of vibration dampers based on visual technology is an important issue. The current vibration damper detection work is mainly carried out manually. In view of the above situation, this article proposes a vibration damper detection model named DamperYOLO based on the one-stage framework in object detection. DamperYOLO first uses a Canny operator to smooth the overexposed points of the input image and extract edge features, then selectees ResNet101 as the backbone of the framework to improve the detection speed, and finally injects edge features into backbone through an attention mechanism. At the same time, an FPN-based feature fusion network is used to provide feature maps of multiple resolutions. In addition, we built a vibration damper detection dataset named DamperDetSet based on UAV cruise images. Multiple sets of experiments on self-built DamperDetSet dataset prove that our model reaches state-of-the-art level in terms of accuracy and test speed and meets the standard of real-time output of high-accuracy test results.