bluuebunny/crossref_metadata_2025 huggingface dataset:
miRNAs in Regulation of Tumor Microenvironment, Chemotherapy Resistance, Immunotherapy Modulation and miRNA Therapeutics in Cancer
Authors: Kousar Kousain , Ahmad Tahir , Abduh Maisa S. , Kanwal Balquees , Shah Syeda Saba , Naseer Faiza , Anjum Sadia
Published: November 2022

miRNAs are 20–22 long nucleotide non-coding ribonucleic acid molecules critical to the modulation of molecular pathways. Immune evasion and the establishment of a suitable tumor microenvironment are two major contributors that support tumor invasion and metastasis. Tumorigenic miRNAs support these two hallmarks by desensitizing important tumor-sensitive regulatory cells such as dendritic cells, M1 macrophages, and T helper cells towards tumors while supporting infiltration and proliferation of immune cells like Treg cells, tumor-associated M2 macrophages that promote self-tolerance and chronic inflammation. miRNAs have a significant role in enhancing the efficacies of immunotherapy treatments like checkpoint blockade therapy, adoptive T cell therapy, and oncolytic virotherapy in cancer. A clear understanding of the role of miRNA can help scientists to formulate better-targeted treatment modalities. miRNA therapeutics have emerged as diverse class of nucleic acid-based molecules that can suppress oncogenic miRNAs and promote the expression of tumor suppressor miRNAs.
Agomelatine, Ketamine and Vortioxetine Attenuate Energy Cell Metabolism—In Vitro Study
Authors: Ľupták Matej , Fišar Zdeněk , Hroudová Jana
Published: November 2022

This determination of the mitochondrial effect of pharmacologically different antidepressants (agomelatine, ketamine and vortioxetine) was evaluated and quantified in vitro in pig brain-isolated mitochondria. We measured the activity of mitochondrial complexes, citrate synthase, malate dehydrogenase and monoamine oxidase, and the mitochondrial respiratory rate. Total hydrogen peroxide production and ATP production were assayed. The most potent inhibitor of all mitochondrial complexes and complex I-linked respiration was vortioxetine. Agomelatine and ketamine inhibited only complex IV activity. None of the drugs affected complex II-linked respiration, citrate synthase or malate dehydrogenase activity. Hydrogen peroxide production was mildly increased by agomelatine, which might contribute to increased oxidative damage and adverse effects at high drug concentrations. Vortioxetine significantly reduced hydrogen peroxide concentrations, which might suggest antioxidant mechanism activation. All tested antidepressants were partial MAO-A inhibitors, which might contribute to their antidepressant effect. We observed vortioxetine-induced MAO-B inhibition, which might be linked to decreased hydrogen peroxide formation and contribute to its procognitive and neuroprotective effects. Mitochondrial dysfunction could be linked to the adverse effects of vortioxetine, as vortioxetine is the most potent inhibitor of mitochondrial complexes and complex I-linked respiration. Clarifying the molecular interaction between drugs and mitochondria is important to fully understand their mechanism of action and the connection between their mechanisms and their therapeutic and/or adverse effects.
Multiplex Analysis of Serum Cytokine Profiles in Systemic Lupus Erythematosus and Multiple Sclerosis
Authors: Melamud Mark M. , Ermakov Evgeny A. , Boiko Anastasiia S. , Kamaeva Daria A. , Sizikov Alexey E. , Ivanova Svetlana A. , Baulina Natalia M. , Favorova Olga O. , Nevinsky Georgy A. , Buneva Valentina N.
Published: November 2022

Changes in cytokine profiles and cytokine networks are known to be a hallmark of autoimmune diseases, including systemic lupus erythematosus (SLE) and multiple sclerosis (MS). However, cytokine profiles research studies are usually based on the analysis of a small number of cytokines and give conflicting results. In this work, we analyzed cytokine profiles of 41 analytes in patients with SLE and MS compared with healthy donors using multiplex immunoassay. The SLE group included treated patients, while the MS patients were drug-free. Levels of 11 cytokines, IL-1b, IL-1RA, IL-6, IL-9, IL-10, IL-15, MCP-1/CCL2, Fractalkine/CX3CL1, MIP-1a/CCL3, MIP-1b/CCL4, and TNFa, were increased, but sCD40L, PDGF-AA, and MDC/CCL22 levels were decreased in SLE patients. Thus, changes in the cytokine profile in SLE have been associated with the dysregulation of interleukins, TNF superfamily members, and chemokines. In the case of MS, levels of 10 cytokines, sCD40L, CCL2, CCL3, CCL22, PDGF-AA, PDGF-AB/BB, EGF, IL-8, TGF-a, and VEGF, decreased significantly compared to the control group. Therefore, cytokine network dysregulation in MS is characterized by abnormal levels of growth factors and chemokines. Cross-disorder analysis of cytokine levels in MS and SLE showed significant differences between 22 cytokines. Protein interaction network analysis showed that all significantly altered cytokines in both SLE and MS are functionally interconnected. Thus, MS and SLE may be associated with impaired functional relationships in the cytokine network. A cytokine correlation networks analysis revealed changes in correlation clusters in SLE and MS. These data expand the understanding of abnormal regulatory interactions in cytokine profiles associated with autoimmune diseases.
Added Value of Biophysics to Study Lipid-Driven Biological Processes: The Case of Surfactins, a Class of Natural Amphiphile Molecules
Authors: Gilliard Guillaume , Furlan Aurélien L. , Smeralda Willy , Pršić Jelena , Deleu Magali
Published: November 2022

The role of membrane lipids is increasingly claimed to explain biological activities of natural amphiphile molecules. To decipher this role, biophysical studies with biomimetic membrane models are often helpful to obtain insights at the molecular and atomic levels. In this review, the added value of biophysics to study lipid-driven biological processes is illustrated using the case of surfactins, a class of natural lipopeptides produced by Bacillus sp. showing a broad range of biological activities. The mechanism of interaction of surfactins with biomimetic models showed to be dependent on the surfactins-to-lipid ratio with action as membrane disturber without membrane lysis at low and intermediate ratios and a membrane permeabilizing effect at higher ratios. These two mechanisms are relevant to explain surfactins’ biological activities occurring without membrane lysis, such as their antiviral and plant immunity-eliciting activities, and the one involving cell lysis, such as their antibacterial and hemolytic activities. In both biological and biophysical studies, influence of surfactin structure and membrane lipids on the mechanisms was observed with a similar trend. Hence, biomimetic models represent interesting tools to elucidate the biological mechanisms targeting membrane lipids and can contribute to the development of new molecules for pharmaceutical or agronomic applications.
Isotherm, Thermodynamics, and Kinetics of Methyl Orange Adsorption onto Magnetic Resin of Chitosan Microspheres
Authors: Yu Lina , Bi Jie , Song Yu , Wang Mingqing
Published: November 2022

Severe environmental pollution problems arising from toxic dyestuffs (e.g., methyl orange) are receiving increasing attention. Therefore, dyes’ safe removal has become a research hotspot. Among the many physical–chemical removal techniques, adsorption using renewable biological resources has proved to be more advantageous over others due to its effectiveness and economy. Chitosan is a natural, renewable biopolymer obtained by deactivated chitin. Thus, the magnetic resin of chitosan microspheres (MRCM), prepared by reversed-phase suspension cross-linking polymerization, was used to remove methyl orange from a solution in a batch adsorption system. The main results are as follows: (1) The results of physical and swelling properties of MRCM indicated that MRCM was a type of black spherical, porous, water-absorbing, and weak alkali exchange resin, and it had the ability to adsorb methyl orange when it was applied in solutions above pH 2.0. (2) In batch adsorption studies, the maximum adsorption capacity was obtained at pH 5; the adsorption equilibrium time was 140 min; and the maximum adsorption was reached at 450 mg/L initial concentration. (3) Among the three isotherm adsorption models, Langmuir achieved the best fit for the adsorption of methyl orange onto MRCM. (4) The adsorption thermodynamics indicated that the adsorption was spontaneous, with increasing enthalpy, and was driven by the entropy. (5) The pseudo-second-order kinetics equation was most suitable to describe the adsorption kinetics, and the adsorption kinetics was also controlled by the liquid–film diffusion dynamics. Consequently, MRCM with relatively higher methyl orange adsorption exhibited the great efficiency for methyl orange removal as an environment-friendly sorbent. Thus, the findings are useful for methyl orange pollution control in real-life wastewater treatment applications.
Fat Checking: Emerging Role of Lipids in Metabolism and Disease
Authors: Segatto Marco , Cutone Antimo , Pallottini Valentina
Published: November 2022

Lipids are hydrophobic molecules involved in a plethora of biological functions; for example, they are employed for the storage of energy, serve as essential constituents of cell membranes and participate in the assembly of bilayer configuration [...]
Effect of Sucrose Concentration on Rhaponticum carthamoides (Willd.) Iljin Transformed Root Biomass, Caffeoylquinic Acid Derivative, and Flavonoid Production
Authors: Skała Ewa , Olszewska Monika Anna , Makowczyńska Joanna , Kicel Agnieszka
Published: November 2022

Rhaponticum carthamoides (Willd.) Iljin is a rare, pharmacopoeial, and medicinal plant, endemic to Siberia and endangered due to the massive collection of raw material from the natural habitat. The aim of the current study was to estimate the effect of sucrose concentration (0–7%) on R. carthamoides transformed root growth and on caffeoylquinic acid derivative (CQA) and flavonoid production. Sucrose in higher concentrations may induce osmotic stress and thus may affect secondary metabolism in plants. It was revealed that sucrose concentration influenced R. carthamoides transformed root biomass and modified the phenolic compound metabolic pathway. However, the dynamics of both processes varied significantly. The optimal sucrose level was different for biomass accumulation and the biosynthesis of specialized metabolite. The highest dry weight of roots was achieved for 7% sucrose (31.17 g L−1 of dry weight), while 1% sucrose was found to be optimal for phenolic acid and flavonoid production. Considering the dry weight increase and metabolite accumulation, 3% sucrose was revealed to give optimal yields of CQAs (511.1 mg L−1) and flavonoids (38.9 mg L−1). Chlorogenic acid, 3,5-, 4,5-di-O-caffeoylquinic acids, 1,4,5-O-tricaffeoylquinic acid, and a tentatively-identified tricaffeoylquinic acid derivative 1 were found to be the most abundant specialized metabolites among the identified CQAs. Our findings indicate that R. carthamoides transformed roots may be an efficient source of CQA derivatives, with valuable health-promoting activities.
Inhibition of Calpain Attenuates Degeneration of Substantia Nigra Neurons in the Rotenone Rat Model of Parkinson’s Disease
Authors: Zaman Vandana , Drasites Kelsey P. , Myatich Ali , Shams Ramsha , Shields Donald C. , Matzelle Denise , Haque Azizul , Banik Narendra L.
Published: November 2022

In the central nervous system (CNS), calcium homeostasis is a critical determinant of neuronal survival. Calpain, a calcium-dependent neutral protease, is widely expressed in the brain, including substantia nigra (SN) dopaminergic (DA) neurons. Though calpain is implicated in human Parkinson’s disease (PD) and corresponding animal models, the roles of specific ubiquitous calpain isoforms in PD, calpain-1 and calpain-2, remain poorly understood. In this study, we found that both isoforms are activated in a nigrostriatal pathway with increased phosphorylated synuclein following the administration of rotenone in Lewis rats, but calpain isoforms played different roles in neuronal survival. Although increased expression of calpain-1 and calpain-2 were detected in the SN of rotenone-administered rats, calpain-1 expression was not altered significantly after treatment with calpain inhibitor (calpeptin); this correlated with neuronal survival. By contrast, increased calpain-2 expression in the SN of rotenone rats correlated with neuronal death, and calpeptin treatment significantly attenuated calpain-2 and neuronal death. Calpain inhibition by calpeptin prevented glial (astroglia/microglia) activation in rotenone-treated rats in vivo, promoted M2-type microglia, and protected neurons. These data suggest that enhanced expression of calpain-1 and calpain-2 in PD models differentially affects glial activation and neuronal survival; thus, the attenuation of calpain-2 may be important in reducing SN neuronal loss in PD.
The Role of Copper Homeostasis in Brain Disease
Authors: An Yumei , Li Sunao , Huang Xinqi , Chen Xueshi , Shan Haiyan , Zhang Mingyang
Published: November 2022

In the human body, copper is an important trace element and is a cofactor for several important enzymes involved in energy production, iron metabolism, neuropeptide activation, connective tissue synthesis, and neurotransmitter synthesis. Copper is also necessary for cellular processes, such as the regulation of intracellular signal transduction, catecholamine balance, myelination of neurons, and efficient synaptic transmission in the central nervous system. Copper is naturally present in some foods and is available as a dietary supplement. Only small amounts of copper are typically stored in the body and a large amount of copper is excreted through bile and urine. Given the critical role of copper in a breadth of cellular processes, local concentrations of copper and the cellular distribution of copper transporter proteins in the brain are important to maintain the steady state of the internal environment. The dysfunction of copper metabolism or regulatory pathways results in an imbalance in copper homeostasis in the brain, which can lead to a myriad of acute and chronic pathological effects on neurological function. It suggests a unique mechanism linking copper homeostasis and neuronal activation within the central nervous system. This article explores the relationship between impaired copper homeostasis and neuropathophysiological progress in brain diseases.
Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications
Authors: Arzumanian Viktoriia A. , Dolgalev Georgii V. , Kurbatov Ilya Y. , Kiseleva Olga I. , Poverennaya Ekaterina V.
Published: November 2022

The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
Electro-Elastic Modeling of Thermal Spin Transition in Diluted Spin-Crossover Single Crystals
Authors: Affes Karim , Singh Yogendra , Boukheddaden Kamel
Published: November 2022

Spin-crossover solids have been studied for many years for their promising applications as optical switches and reversible high-density memories for information storage. This study reports the effect of random metal dilution on the thermal and structural properties of a spin-crossover single crystal. The analysis is performed on a 2D rectangular lattice using an electro-elastic model. The lattice is made of sites that can switch thermally between the low-spin and high-spin states, accompanied by local volume changes. The model is solved by Monte Carlo simulations, running on the spin states and atomic positions of this compressible 2D lattice. A detailed analysis of metal dilution on the magneto-structural properties allows us to address the following issues: (i) at low dilution rates, the transition is of the first order; (ii) increasing the concentration of dopant results in a decrease in cooperativity and leads to gradual transformations above a threshold concentration, while incomplete spin transitions are obtained for big dopant sizes. The effects of the metal dilution on the spatiotemporal aspects of the spin transition along the thermal transition and on the low-temperature relaxation of the photo-induced metastable high-spin states are also studied. Significant changes in the organization of the spin states are observed for the thermal transition, where the single-domain nucleation caused by the long-range elastic interactions is replaced by a multi-droplet nucleation. As to the issue of the relaxation curves: their shape transforms from a sigmoidal shape, characteristic of strong cooperative systems, into stretched exponentials for high dilution rates, which is the signature of a disordered system.
Low-Dose IL-2 Attenuated Depression-like Behaviors and Pathological Changes through Restoring the Balances between IL-6 and TGF-β and between Th17 and Treg in a Chronic Stress-Induced Mouse Model of Depression
Authors: Huang Chengyi , Zhang Fucheng , Li Peng , Song Cai
Published: November 2022

Microglia activation, increased IL-6 and decreased TGF-β were found in depressed patients or in animal models of depression. IL-6 enhances T helper 17 cell differentiation, thereby causing an imbalance between Th17 and Treg cells, which induces neuroinflammation and neuronal dysfunction. However, whether imbalances between IL-6 and TGF-β and between Th17 and Treg occur in depression and whether depression can be improved upon restoring these imbalances are unknown. Treg promoter IL-2 (1500UI/0.1 mL/day) was used to treat a mouse model of depression induced by chronic unpredictable mild stress (CUMS). The behavior and concentrations of IL-6, TGF-β, Th17, IL-17A, IL-17Rc, Treg-related factors (helios and STAT5), astrocyte A1 phenotype S100β, microglia M1 phenotype Iba-1, indoleamine-2,3-dioxygenase (IDO) enzyme, corticosterone (CORT) and neurotransmitters were evaluated. When compared to controls, CUMS reduced sucrose preference, the number of entries into and the time spent in the open arms of the elevated plus maze and the exploration in the “open field”, while it increased the immobility time in tail suspension, which was ameliorated by IL-2 treatment. RoRα, S100β, IL-17A, IL-17Rc, IL-6, Iba-1, IDO enzyme and CORT concentrations were significantly increased, and Helios, FoxP3+, STAT5 and TGF-β were significantly decreased by CUMS, which were significantly attenuated by IL-2 when compared to the CUMS group. The NE, DA and 5-HT contents and those of their metabolites were decreased by CUMS, which returned to control levels after IL-2 treatment. The study demonstrated that imbalances between IL-6 and TGF-β and between Th17and Treg occurred in the hippocampus of the depression model. IL-2 attenuated depression- and anxiety-like behaviors and normalized the neurotransmitter concentration and the activity of the IDO enzyme, astrocytes and microglia through restoring both balances, but it did not decrease the CORT concentration.
Brca1 Is Regulated by the Transcription Factor Gata3, and Its Silencing Promotes Neural Differentiation in Retinal Neurons
Authors: Zhuang Jiejie , Chen Pei , Wu Yihui , Luo Qian , Wang Qiyun , Chen Shuilian , Chen Xi , Jiang Zihua , Qiu Jin , Li Yan , Yuan Zhaohui , Zhuang Jing
Published: November 2022

Previous studies have indicated that Brca1 (Breast cancer suppressor gene 1) plays an important role in neural development and degenerative diseases. However, the bioactivity and regulatory mechanism of Brca1 expression in retinal neurocytes remain unclear. In the present study, our data indicated that Brca1 maintains the state of neuronal precursor cells. Brca1 silencing induces differentiation in 661W cells. Nestin, a marker of precursor cells, was significantly decreased in parallel with Brca1 silencing in 661W cells, whereas Map2 (Microtubule associated protein 2), a marker of differentiated neurons, was significantly increased. Neurite outgrowth was increased by ~4.0-fold in Brca1-silenced cells. Moreover, DNA affinity purification assays and ChIP assays demonstrated that Gata3 (GATA binding protein 3) regulates Brca1 transcription in 661W cells. Silencing or overexpressing Gata3 could significantly regulate the expression of Brca1 and affect its promoter inducibility. Furthermore, the expression of Gata3 generally occurred in parallel with that of Brca1 in developing mouse retinas. Both Gata3 and Brca1 are expressed in the neonatal mouse retina but are developmentally silenced with age. Exogenous Gata3 significantly inhibited neural activity by decreasing synaptophysin and neurite outgrowth. Thus, this study demonstrated that Brca1 is transcriptionally regulated by Gata3. Brca1/Gata3 silencing is involved in neuronal differentiation and maturation.
Aberrant Cortical Layer Development of Brain Organoids Derived from Noonan Syndrome-iPSCs
Authors: Kim Bumsoo , Koh Yongjun , Do Hyunsu , Ju Younghee , Choi Jong Bin , Cho Gahyang , Yoo Han-Wook , Lee Beom Hee , Han Jinju , Park Jong-Eun , Han Yong-Mahn
Published: November 2022

Noonan syndrome (NS) is a genetic disorder mainly caused by gain-of-function mutations in Src homology region 2-containing protein tyrosine phosphatase 2 (SHP2). Although diverse neurological manifestations are commonly diagnosed in NS patients, the mechanisms as to how SHP2 mutations induce the neurodevelopmental defects associated with NS remain elusive. Here, we report that cortical organoids (NS-COs) derived from NS-induced pluripotent stem cells (iPSCs) exhibit developmental abnormalities, especially in excitatory neurons (ENs). Although NS-COs develop normally in their appearance, single-cell transcriptomic analysis revealed an increase in the EN population and overexpression of cortical layer markers in NS-COs. Surprisingly, the EN subpopulation co-expressing the upper layer marker SATB2 and the deep layer maker CTIP2 was enriched in NS-COs during cortical development. In parallel with the developmental disruptions, NS-COs also exhibited reduced synaptic connectivity. Collectively, our findings suggest that perturbed cortical layer identity and impeded neuronal connectivity contribute to the neurological manifestations of NS.
Nanoparticles for Antimicrobial Agents Delivery—An Up-to-Date Review
Authors: Mercan Doina-Antonia , Niculescu Adelina-Gabriela , Grumezescu Alexandru Mihai
Published: November 2022

Infectious diseases constitute an increasing threat to public health and medical systems worldwide. Particularly, the emergence of multidrug-resistant pathogens has left the pharmaceutical arsenal unarmed to fight against such severe microbial infections. Thus, the context has called for a paradigm shift in managing bacterial, fungal, viral, and parasitic infections, leading to the collision of medicine with nanotechnology. As a result, renewed research interest has been noted in utilizing various nanoparticles as drug delivery vehicles, aiming to overcome the limitations of current treatment options. In more detail, numerous studies have loaded natural and synthetic antimicrobial agents into different inorganic, lipid, and polymeric-based nanomaterials and tested them against clinically relevant pathogens. In this respect, this paper reviews the most recently reported successfully fabricated nanoformulations that demonstrated a great potential against bacteria, fungi, viruses, and parasites of interest for human medicine.
Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex
Authors: Hu Zheyao , Marti Jordi
Published: November 2022

KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.
Ni Nanoparticles Stabilized by Hyperbranched Polymer: Does the Architecture of the Polymer Affect the Nanoparticle Characteristics and Their Performance in Catalysis?
Authors: Sorokina Svetlana A. , Kuchkina Nina V. , Ezernitskaya Mariam G. , Bykov Alexey V. , Vasiliev Alexander L. , Efimov Nikolay N. , Shifrina Zinaida B.
Published: November 2022

Heat-up and hot-injection methods were employed to synthesize Ni nanoparticles (NPs) with narrow size distribution in the presence of hyperbranched pyridylphenylene polymer (PPP) as a stabilizing agent. It was shown that depending on the synthetic method, Ni NPs were formed either in a cross-linked polymer network or stabilized by a soluble hyperbranched polymer. Ni NPs were characterized by a combination of transmission electron microscopy (TEM), scanning TEM, thermogravimetric analysis, powder X-ray diffraction, X-ray photoelectron spectroscopy, energy dispersive X-ray analysis, and magnetic measurements. The architecture of polymer support was found to significantly effect Ni NPs characteristics and behavior. The Ni NPs demonstrated a high catalytic activity in a model Suzuki–Miyaura cross-coupling reaction. No significant drop in activity was observed upon repeated use after magnetic separation in five consecutive catalytic cycles. We believe that hyperbranched PPP can serve as universal platform for the controllable synthesis of Ni NPs, acting as highly active and stable catalysts.
Genome-Wide Identification and Expression Patterns of AcSWEET Family in Pineapple and AcSWEET11 Mediated Sugar Accumulation
Authors: Lin Wenqiu , Pu Yue , Liu Shenghui , Wu Qingsong , Yao Yanli , Yang Yumei , Zhang Xiumei , Sun Weisheng
Published: November 2022

Pineapple (Ananas comosus L.) is an important fruit crop in tropical regions, and it requires efficient sugar allocation during fruit development. Sugars Will Eventually be Exported Transporters (SWEETs) are a group of novel sugar transporters which play critical roles in seed and fruit development. However, the function of AcSWEETs remains unknown in the sugar accumulation. Herein, 17 AcSWEETs were isolated and unevenly located in 11 chromosomes. Analysis of a phylogenetic tree indicated that 17 genes were classified into four clades, and the majority of AcSWEETs in each clade shared similar conserved motifs and gene structures. Tissue-specific gene expression showed that expression profiles of AcSWEETs displayed differences in different tissues and five AcSWEETs were strongly expressed during fruit development. AcSWEET11 was highly expressed in the stage of mature fruits in ‘Tainong16’ and ‘Comte de paris’, which indicates that AcSWEET11 was important to fruit development. Subcellular localization analysis showed that AcSWEET11 was located in the cell membrane. Notably, overexpression of AcSWEET11 could improve sugar accumulation in pineapple callus and transgenic tomato, which suggests that AcSWEET11 might positively contribute to sugar accumulation in pineapple fruit development. These results may provide insights to enhance sugar accumulation in fruit, thus improving pineapple quality in the future.
Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic
Authors: Shemesh-Mayer Einat , Faigenboim Adi , Ben Michael Tomer E. , Kamenetsky-Goldstein Rina
Published: November 2022

Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not found at the transcriptome level. Functions of TFL-like genes were reduced and replaced by FT-like homologs, whereas homologs of MFT-like genes were not found. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their role in garlic florogenesis. It is not yet clear whether AsLFY1 acts alone as the “pioneer transcription factor” or AsLFY2 also provides these functions. The presence of several orthologs of flowering genes that differ in their expression and co-expression network advocates ongoing evolution in the garlic genome and diversification of gene functions. We propose that the process of fertility deprivation in garlic cultivars is based on the loss of transcriptional functions of the specific genes.
The Association of Patent Ductus Arteriosus with Inflammation: A Narrative Review of the Role of Inflammatory Biomarkers and Treatment Strategy in Premature Infants
Authors: Wei Yu-Jen , Hsu Rosie , Lin Yung-Chieh , Wong Tak-Wah , Kan Chung-Dann , Wang Jieh-Neng
Published: November 2022

Patent ductus arteriosus (PDA) is a common cardiovascular complication that complicates clinical care in the intensive care of premature infants. Prenatal and postnatal infections and the inflammation process can contribute to PDA, and intrauterine inflammation is a known risk factor of PDA. A variety of inflammatory biomarkers have been reported to be associated with PDA. Chorioamnionitis induces the fetal inflammatory process via several cytokines that have been reported to be associated with the presence of PDA and may have a role in the vascular remodeling process or vessel dilation of the ductus. On the other hand, anti-inflammatory agents, such as antenatal steroids, decrease PDA incidence and severity in patients born to those with chorioamnionitis. Proinflammatory cytokines, which are expressed more significantly in preterm neonates and chorioamnionitis, are associated with the presence of PDA. In this review, we focus on the pathogenesis of PDA in preterm infants and the role of biomarkers associated with the perinatal inflammatory process.
Mitochondrial Respiratory Chain Supercomplexes: From Structure to Function
Authors: Guan Shuting , Zhao Li , Peng Ruiyun
Published: November 2022

Mitochondrial oxidative phospho rylation, the center of cellular metabolism, is pivotal for the energy production in eukaryotes. Mitochondrial oxidative phosphorylation relies on the mitochondrial respiratory chain, which consists of four main enzyme complexes and two mobile electron carriers. Mitochondrial enzyme complexes also assemble into respiratory chain supercomplexes (SCs) through specific interactions. The SCs not only have respiratory functions but also improve the efficiency of electron transfer and reduce the production of reactive oxygen species (ROS). Impaired assembly of SCs is closely related to various diseases, especially neurodegenerative diseases. Therefore, SCs play important roles in improving the efficiency of the mitochondrial respiratory chain, as well as maintaining the homeostasis of cellular metabolism. Here, we review the structure, assembly, and functions of SCs, as well as the relationship between mitochondrial SCs and diseases.
Four New Species and New Records of Orbilia from China Based on Molecular and Morphological Data
Authors: Ou Xiao-Yun , Shao Yuan-Yuan , Zheng Hai-Fu , Liu Bin
Published: November 2022

This study reports four new species and three new record species of Orbiliaceous fungi from China. Orbilia baisensis, O. hanzhongensis, O. nanningensis and O. pinea are described as new species and O. crenatomarginata, O. vinosa and O. vitalbae are described as new record species. All the studied species were identified by morphological characteristics and phylogenetic analysis of internal transcribed spacer (ITS) and large subunit (LSU) sequences. Four new species are described based on their sexual and asexual states, and their differences with the close relatives were compared and discussed.
Numerical Simulation of Dry Ice Compaction Process: Comparison of the Mohr–Coulomb Model with the Experimental Results
Authors: Berdychowski Maciej , Górecki Jan , Wałęsa Krzysztof
Published: November 2022

How to reduce consumption of energy in manufacturing has become a topical issue nowadays. Certain manufacturing processes are known for being highly energy-intensive and compression of materials belongs to this group. This article presents the simulation of the process of compression of dry ice snow with the use of the Mohr–Coulomb model. Two simulation variants were considered in this research. In the first one, constant input parameters were used and in the second one, the input parameters were variable, depending on the changing density of the compressed material. The experimental data were compared with the predicted values to find that the model using constant input parameters was inferior as regards to the goodness of fit. On the other hand, the model with variable input parameters was less accurate in predicting the maximum compression force acting in the process. The last section of this article deals with simulations performed with the Drucker–Prager Cap and modified Cam-Clay models. Finally, it was concluded that the Mohr–Coulomb model yields a more accurate representation of the compression process while requiring less information on the variation of the material parameters.
Computer Modelling of Energy Structure of Yb3+ and Lu3+ Doped LaF3 Crystals
Authors: Chornodolskyy Yaroslav , Karnaushenko Vladyslav , Selech Jaroslaw , Vistovskyy Vitaliy , Demkiv Taras , Przystupa Krzysztof , Syrotyuk Stepan , Voloshinovskii Anatolii
Published: November 2022

The energy band structure, as well as partial and total densities of states have been calculated for LaF3:Yb and LaF3:Lu crystals within density functional theory using the projector augmented wave method and Hubbard corrections (DFT + U). The influence of geometric optimization on the results of energy band calculations of LaF3:Ln crystals (Ln = Yb, Lu) was analysed and the absence of relaxation procedure is confirmed to negatively influence the energy position of states, and the variability between obtained results of different optimization algorithms are within the calculation accuracy. The top of the valence band of LaF3 is confirmed to be formed by the 2pF--states and the bottom of the conduction band is formed by the 5d-states of La3+. The positions of the 4f-states and 5d-states of activator ions in LaF3 were studied. It is shown that the 4f-states of Yb3+ are slightly above the top of the valence band and the 4f-states of Lu3+ to be 3.5 eV below the top of the valence band. The energy levels of the 5d states of the impurities are energetically close to the bottom of the LaF3 conduction band. The calculated band gap of 9.6 eV for LaF3 is in a good agreement with the experimental result and is not affected by impurity ions.
Electrostatic Analysis of Bioactivity of Ti-6Al-4V Hydrophilic Surface with Laser Textured Micro-Square Convexes
Authors: Li Si , Jin Yangyang , Bai Shaoxian , Yang Jing
Published: November 2022

At solid-liquid interfaces, charged particles within the electric double layer (EDL) are acted on by the electrostatic force, which may affect cell absorption and surface wettability. In this study, a model of the electrostatic force and surface tension of textured surfaces was presented. Then, the growth and adhesion of Murine osteoblasts (MC3T3-E1) cells on laser-ablated micro-square-textured Ti-6Al-4V surfaces were studied to demonstrate the use of a laser-processed texture to effectively improve bioactivity. Three different micro-square-textured hydrophilic surfaces, presenting lower contact angles of 19°, 22.5°, and 31.75° compared with that of a smooth surface (56.5°), were fabricated using a fiber-optic laser. Cellular morphology and initial cell attachment were analyzed by field emission scanning electron microscopy (SEM) and fluorescence microscopy, respectively. The results show that the electrostatic force not only made the textured surface more hydrophilic but also made the cells tend to adhere to the edges and corners of the protruding convexes. Cell morphology analysis also showed that cells would prefer to grow at the edges and corners of each micro-square convex protrusion. The laser-treated surfaces were more conducive to rapid cell growth and adhesion, and cells were preferentially attached on the hydrophilic-textured surfaces. Electrostatic force may be an important factor in effectively improving the bioactivity of Ti-6Al-4V surfaces, and the presence of more surface grooves would be more conducive to improving the bioactivity of cells.
Systematic Evaluation of Permeability of Concrete Incorporating Coconut Shell as Replacement of Fine Aggregate
Authors: Mhaya Akram M. , Algaifi Hassan Amer , Shahidan Shahiron , Zuki Sharifah Salwa Mohd , Azmi Mohamad Azim Mohammad , Ibrahim Mohd Haziman Wan , Huseien Ghasan Fahim
Published: November 2022

The concern about coconut shell disposal and natural fine aggregate depletion has prompted researchers to utilize coconut shell as aggregate in recent years. However, the majority of the present literature has focused on utilizing coconut shell as a coarse aggregate replacement in concrete via the traditional method. In this study, concrete incorporating coconut shell as a fine aggregate replacement (10–100%) was evaluated using permeability and water absorption tests in a systematic way. The response surface methodology (RSM) was first used to design the experimental works. In addition, an artificial neural network (ANN) and genetic expression programming (GEP) were also taken into account to mathematically predict the permeability and water absorption. Based on both experimental and theoretical modeling, three scenarios were observed. In the first scenario, high quality concrete was achieved when the replacement percentage of sand by coconut shell ranged from 0% to 10%. This is because both the permeability and water absorption were less than 1.5 × 10−11 m and 5%, respectively. In the second scenario, an acceptable and reasonable low permeability (less than 2.7 × 10−11 m/s) and water absorption (less than 6.7%) were also obtained when the replacement percentage increased up to 60%. In contrast, the high content coconut shell, such as 90% and 100%, developed concrete with a high permeability and water absorption and was defined in the third scenario. It was also inferred that both the experimental and mathematical models (ANN, GEP, and RSM) have consistent and accurate results. The correlation statistics indicators (R2) were greater than 0.94 and the error was less than 0.3, indicating a strong correlation and minimum error. In conclusion, coconut shell could act as a good alternative material to produce cleaner concrete with an optimum value of 50% as a fine aggregate replacement.
Imperfections Formation in Thin Layers of NiTi Triply Periodic Minimal Surface Lattices Fabricated Using Laser Powder Bed Fusion
Authors: Hussain Shahadat , Alagha Ali N. , Zaki Wael
Published: November 2022

In this paper, thin layers of NiTi shape memory alloy (SMA) triply periodic minimal surface lattices (TPMS) are fabricated using laser powder bed fusion (LPBF), considering different laser scanning strategies and relative densities. The obtained architected samples are studied using experimental methods to characterize their microstructural features, including the formation of cracks and balling imperfections. It is observed that balling is not only affected by the parameters of the fabrication process but also by structural characteristics, including the effective densities of the fabricated samples. In particular, it is reported here that higher densities of the TPMS geometries considered are generally associated with increased dimensions of balling imperfections. Moreover, scanning strategies at 45° angle with respect to the principal axes of the samples resulted in increased balling.
Structure, Properties, and Corrosion Behavior of Ti-Rich TiZrNbTa Medium-Entropy Alloys with β+α″+α′ for Biomedical Application
Authors: Wong Ka-Kin , Hsu Hsueh-Chuan , Wu Shih-Ching , Hung Tun-Li , Ho Wen-Fu
Published: November 2022

Five Ti-rich β+α″+α′ Ti–Zr–Nb–Ta biomedical medium-entropy alloys with excellent mechanical properties and corrosion resistance were developed by considering thermodynamic parameters and using the valence electron concentration formula. The results of this study demonstrated that the traditional valence electron concentration formula for predicting phases is not entirely applicable to medium-entropy alloys. All solution-treated samples with homogeneous compositions were obtained at a low temperature (900 °C) and within a short period (20 min). All solution-treated samples exhibited low elastic moduli ranging from 49 to 57 GPa, which were significantly lower than those of high-entropy alloys with β phase. Solution-treated Ti65–Zr29–Nb3–Ta3 exhibited an ultra-high bending strength (1102 MPa), an elastic recovery angle (>30°), and an ultra-low elastic modulus (49 GPa), which are attributed to its α″ volume fraction as high as more than 60%. The pitting potentials of all samples were higher than 1.8 V, and their corrosion current densities were lower than 10–5 A/cm3 in artificially simulated body fluid at 37 °C. The surface oxide layers on Ti65–Zr29–Nb3–Ta3 comprised TiO2, ZrO2, Nb2O5, and Ta2O5 (as discovered through X-ray photoelectron spectroscopy) and provided the alloy with excellent corrosion and pitting resistance.
Supportless Lattice Structure for Additive Manufacturing of Functional Products and the Evaluation of Its Mechanical Property at Variable Strain Rates
Authors: Prajapati Mayur Jiyalal , Bhat Chinmai , Kumar Ajeet , Verma Saurav , Lin Shang-Chih , Jeng Jeng-Ywan
Published: November 2022

This study proposes an innovative design solution based on the design for additive manufacturing (DfAM) and post-process for manufacturing industrial-grade products by reducing additive manufacturing (AM) time and improving production agility. The design of the supportless open cell Sea Urchin lattice structure is analyzed using DfAM for material extrusion (MEX) process to print support free in any direction. The open cell is converted into a global closed cell to entrap secondary foam material. The lattice structure is 3D printed with Polyethylene terephthalate glycol (PETG) material and is filled with foam using the Hybrid MEX process. Foam-filling improves the lattice structure’s energy absorption and crash force efficiency when tested at different strain rates. An industrial case study demonstrates the importance and application of this lightweight and tough design to meet the challenging current and future mass customization market. A consumer-based industrial scenario is chosen wherein an innovative 3D-printed universal puck accommodates different shapes of products across the supply line. The pucks are prone to collisions on the supply line, generating shock loads and hazardous noise. The results show that support-free global closed-cell lattice structures filled with foam improve energy absorption at a high strain rate and enhance the functional requirement of noise reduction during the collision.
Structural, Magnetic, and Electrical Properties of CoFe2O4 Nanostructures Synthesized Using Microwave-Assisted Hydrothermal Method
Authors: Kumar Shalendra , Ahmed Faheem , Shaalan Nagih M. , Kumar Rajesh , Alshoaibi Adil , Arshi Nishat , Dalela Saurabh , Sayeed Fatima , Dwivedi Sourabh , Kumari Kavita
Published: November 2022

Magnetic nanostructures of CoFe2O4 were synthesized via a microwave-assisted hydrothermal route. The prepared nanostructures were investigated using X-ray diffraction (XRD), field emission electron microscopy (FE-SEM), energy dispersive X-ray (EDX) spectroscopy, high-resolution transmission electron microscopy (HR-TEM), selective area electron diffraction (SAED) pattern, DC magnetization, and dielectric spectroscopy measurements. The crystal structure studied using HR-TEM, SAED, and XRD patterns revealed that the synthesized nanostructures had a single-phase nature and ruled out the possibility of any secondary phase. The lattice parameters and unit cell volume determined from the XRD data were found to be 8.4821 Å and 583.88 Å3. The average crystallite size (~7.0 nm) was determined using Scherrer’s equation. The FE-SEM and TEM micrographs revealed that the prepared nanostructures had a spherical shape morphology. The EDX results showed that the major elements present in the samples were Co, Fe, and O. The magnetization (M) versus temperature (T) measurements specified that the CoFe2O4 nanostructures showed ferromagnetic ordering at room temperature. The blocking temperature (TB) determined using the M-T curve was found to be 315 K. The magnetic hysteresis (M-H) loop of the CoFe2O4 nanostructures recorded at different temperatures showed the ferromagnetic behavior of the CoFe2O4 nanostructures at temperatures of 200 K and 300 K, and a superparamagnetic behavior at 350 K. The dielectric spectroscopy studies revealed a dielectric constant (ε′) and loss tangent (tanδ) decrease with the increase in the frequency, as well as demonstrating a normal dispersion behavior, which is due to the Maxwell–Wagner type of interfacial polarization. The values of ε′ and tanδ were observed to increase with the increase in the temperature.