bluuebunny/crossref_metadata_2025 huggingface dataset:
Economic Feasibility Study of a Carbon Capture and Storage (CCS) Integration Project in an Oil-Driven Economy: The Case of the State of Kuwait
Authors: Naseeb Adel , Ramadan Ashraf , Al-Salem Sultan Majed
Published: May 2022

The rapid growth and urbanization rate, coupled with hot climate and scarce rainfall, makes it essential for a country like Kuwait to have several power and desalination plants with high-generating capacity. These plants are entirely reliant on burning fossil fuels as a source of thermal energy. These plants are also universally accepted to be the largest CO2 emitters; hence, they present a potential for carbon capture and storage (CCS). Having established the suitability of the existing conditions for post-combustion CCS, a techno-economic-based feasibility study, which took into consideration local power generation technologies and economic conditions, was performed. Relying on fifteen case study models and utilizing the concept of levelized cost of electricity (LCOE), the statistical average method (SAM) was used to assess CCS based on realistic and reliable economic indicators. Zour power station, offering the highest potential CO2 stream, was selected as a good candidate for the analysis at hand. Heavy fuel oil (HFO) was assumed to be the only fuel type used at this station with affixed price of USD 20/barrel. The analysis shows that the internal rate of return (IRR) was about 7%, which could be attributed to fuel prices in Kuwait and governmental support, i.e., waived construction tax and subsidized workforce salaries. Furthermore, the net present value (NPV) was also estimated as USD 47,928 million with a 13-year payback period (PBP). Moreover, 1–3% reductions in the annual operational cost were reflected in increasing the IRR and the NPV to 9–11% and USD 104,085–193,945 million, respectively, and decreasing the PBP to 12–11 years. On the contrary, increasing the annual operational cost by 1% made the project economically unfeasible, while an increase of 3% resulted in negative IRR (−1%), NVP (−USD 185,458 million) and increased PBP to 30 years. Similarly, increasing the HFO barrel price by USD 5 resulted in negative IRR (−10%) and NVP (−USD 590,409); hence, a CCS project was deemed economically unfeasible. While the study considered the conditions in Kuwait, it is expected that similar results could be obtained for other countries with an oil-driven economy. Considering that around 62% of the fossil fuel blend in Kuwait is consumed by electricity and water generation, it is inevitable to consider the possibility and practicality of having a carbon network with neighboring countries where other oil-driven economies, such as Kingdom of Saudi Arabia and Iraq, can utilize a CCS-based mega infrastructure in Kuwait. The choice of Kuwait is also logical due to being a mid-point between both countries and can initiate a trading scheme in oil derivatives with both countries.
Efficient Calculation of Distance Transform on Discrete Global Grid Systems
Authors: Kazemi Meysam , Wecker Lakin , Samavati Faramarz
Published: May 2022

Geospatial data analysis often requires the computing of a distance transform for a given vector feature. For instance, in wildfire management, it is helpful to find the distance of all points in an area from the wildfire’s boundary. Computing a distance transform on traditional Geographic Information Systems (GIS) is usually adopted from image processing methods, albeit prone to distortion resulting from flat maps. Discrete Global Grid Systems (DGGS) are relatively new low-distortion globe-based GIS that discretize the Earth into highly regular cells using multiresolution grids. In this paper, we introduce an efficient distance transform algorithm for DGGS. Our novel algorithm heavily exploits the hierarchy of a DGGS and its mathematical properties and applies to many different DGGSs. We evaluate our method by comparing its speed and distortion with the distance transform methods used in traditional GIS and general 3D meshes. We demonstrate that our method is efficient and has minimal distortion.
Long- and Short-Term Preference Modeling Based on Multi-Level Attention for Next POI Recommendation
Authors: Wang Xueying , Liu Yanheng , Zhou Xu , Leng Zhaoqi , Wang Xican
Published: May 2022

The next point-of-interest (POI) recommendation is one of the most essential applications in location-based social networks (LBSNs). Its main goal is to research the sequential patterns of user check-in activities and then predict a user’s next destination. However, most previous studies have failed to make full use of spatio-temporal information to analyze user check-in periodic regularity, and some studies omit the user’s transition preference for the category at the POI semantic level. These are important for analyzing the user’s preference for check-in behavior. Long- and short-term preference modeling based on multi-level attention (LSMA) is put forward to solve the above problem and enhance the accuracy of the next POI recommendation. This can capture the user’s long-term and short-term preferences separately, and consider the multi-faceted utilization of spatio-temporal information. In particular, it can analyze the periodic hobbies contained in the user’s check-in. Moreover, a multi-level attention mechanism is designed to study the multi-factor dynamic representation of user check-in behavior and non-linear dependence between user check-ins, which can multi-angle and comprehensively explore a user’s check-in interest. We also study the user’s category transition preference at a coarse-grained semantic level to help construct the user’s long-term and short-term preferences. Finally, experiments were carried out on two real-world datasets; the findings showed that LSMA modeling outperformed state-of-the-art recommendation systems.
Expression Profiles and Characteristics of Apple lncRNAs in Roots, Phloem, Leaves, Flowers, and Fruit
Authors: Wang Dajiang , Gao Yuan , Sun Simiao , Li Lianwen , Wang Kun
Published: May 2022

LncRNAs impart crucial effects on various biological processes, including biotic stress responses, abiotic stress responses, fertility and development. The apple tree is one of the four major fruit trees in the world. However, lncRNAs’s roles in different tissues of apple are unknown. We identified the lncRNAs in five tissues of apples including the roots, phloem, leaves, flowers, and fruit, and predicted the intricate regulatory networks. A total of 9440 lncRNAs were obtained. LncRNA target prediction revealed 10,628 potential lncRNA–messenger RNA (mRNA) pairs, 9410 pairs functioning in a cis-acting fashion, and 1218 acting in a trans-acting fashion. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to photosynthesis-antenna proteins, single-organism metabolic process and glutathione metabolism. Additionally, a total of 88 lncRNAs have various functions related to microRNAs (miRNAs) as miRNA precursors. Interactions between lncRNAs and miRNAs were predicted, 1341 possible interrelations between 187 mdm-miRNAs and 174 lncRNAs (1.84%) were identified. MSTRG.121644.5, MSTRG.121644.8, MSTRG.2929.2, MSTRG.3953.2, MSTRG.63448.2, MSTRG.9870.2, and MSTRG.9870.3 could participate in the functions in roots as competing endogenous RNAs (ceRNAs). MSTRG.11457.2, MSTRG.138614.2, and MSTRG.60895.2 could adopt special functions in the fruit by working with miRNAs. A further analysis showed that different tissues formed special lncRNA–miRNA–mRNA networks. MSTRG.60895.2–mdm-miR393–MD17G1009000 may participate in the anthocyanin metabolism in the fruit. These findings provide a comprehensive view of potential functions for lncRNAs, corresponding target genes, and related lncRNA–miRNA–mRNA networks, which will increase our knowledge of the underlying development mechanism in apple.
Insight into the Impact of Oxidative Stress on the Barrier Properties of Lipid Bilayer Models
Authors: Nasri Zahra , Ahmadi Mohsen , Striesow Johanna , Ravandeh Mehdi , von Woedtke Thomas , Wende Kristian
Published: May 2022

As a new field of oxidative stress-based therapy, cold physical plasma is a promising tool for several biomedical applications due to its potential to create a broad diversity of reactive oxygen and nitrogen species (RONS). Although proposed, the impact of plasma-derived RONS on the cell membrane lipids and properties is not fully understood. For this purpose, the changes in the lipid bilayer functionality under oxidative stress generated by an argon plasma jet (kINPen) were investigated by electrochemical techniques. In addition, liquid chromatography-tandem mass spectrometry was employed to analyze the plasma-induced modifications on the model lipids. Various asymmetric bilayers mimicking the structure and properties of the erythrocyte cell membrane were transferred onto a gold electrode surface by Langmuir-Blodgett/Langmuir-Schaefer deposition techniques. A strong impact of cholesterol on membrane permeabilization by plasma-derived species was revealed. Moreover, the maintenance of the barrier properties is influenced by the chemical composition of the head group. Mainly the head group size and its hydrogen bonding capacities are relevant, and phosphatidylcholines are significantly more susceptible than phosphatidylserines and other lipid classes, underlining the high relevance of this lipid class in membrane dynamics and cell physiology.
Mechanism of Ir(ppy)3 Guest Exciton Formation with the Exciplex-Forming TCTA:TPBI Cohost within a Phosphorescent Organic Light-Emitting Diode Environment
Authors: Park Jae Whee , Cho Kwang Hyun , Rhee Young Min
Published: May 2022

Cohosts based on hole transporting and electron transporting materials often act as exciplexes in the form of intermolecular charge transfer complexes. Indeed, exciplex-forming cohosts have been widely developed as the host materials for efficient phosphorescent organic light-emitting diodes (OLEDs). In host–guest systems of OLEDs, the guest can be excited by two competing mechanisms, namely, excitation energy transfer (EET) and charge transfer (CT). Experimentally, it has been reported that the EET mechanism is dominant and the excitons are primarily formed in the host first and then transferred to the guest in phosphorescent OLEDs based on exciplex-forming cohosts. With this, exciplex-forming cohosts are widely employed for avoiding the formation of trapped charge carriers in the phosphorescent guest. However, theoretical studies are still lacking toward elucidating the relative importance between EET and CT processes in exciting the guest molecules in such systems. Here, we obtain the kinetics of guest excitation processes in a few trimer model systems consisting of an exciplex-forming cohost pair and a phosphorescent guest. We adopt the Förster resonance energy transfer (FRET) rate constants for the electronic transitions between excited states toward solving kinetic master equations. The input parameters for calculating the FRET rate constants are obtained from density functional theory (DFT) and time-dependent DFT. The results show that while the EET mechanism is important, the CT mechanism may still play a significant role in guest excitations. In fact, the relative importance of CT over EET depends strongly on the location of the guest molecule relative to the cohost pair. This is understandable as both the coupling for EET and the interaction energy for CT are strongly influenced by the geometric constraints. Understanding the energy transfer pathways from the exciplex state of cohost to the emissive state of guest may provide insights for improving exciplex-forming materials adopted in OLEDs.
Allelic Diversification of the Wx and ALK Loci in Indica Restorer Lines and Their Utilisation in Hybrid Rice Breeding in China over the Last 50 Years
Authors: Pan Li-Xu , Sun Zhi-Zhong , Zhang Chang-Quan , Li Bu , Yang Qing-Qing , Chen Fei , Fan Xiao-Lei , Zhao Dong-Sheng , Lv Qi-Ming , Yuan Ding-Yang , Liu Qiao-Quan
Published: May 2022

Hybrid rice technology has been used for more than 50 years, and eating and cooking quality (ECQ) has been a major focus throughout this period. Waxy (Wx) and alkaline denaturation (ALK) genes have received attention owing to their pivotal roles in determining rice characteristics. However, despite significant effort, the ECQ of restorer lines (RLs) has changed very little. By contrast, obvious changes have been seen in inbred rice varieties (IRVs), and the ECQ of IRVs is influenced by Wx, which reduces the proportion of Wxa and increases the proportion of Wxb, leading to a decrease in amylose content (AC) and an increase in ECQ. Meanwhile, ALK is not selected in the same way. We investigated Wx alleles and AC values of sterile lines of female parents with the main mating combinations in widely used areas. The results show that almost all sterile lines were Wxa-type with a high AC, which may explain the low ECQ of hybrid rice. Analysis of hybrid rice varieties and RLs in the last 5 years revealed serious homogenisation among hybrid rice varieties.
Oxidative Stress in Malaria: Potential Benefits of Antioxidant Therapy
Authors: Gomes Antonio Rafael Quadros , Cunha Natasha , Varela Everton Luiz Pompeu , Brígido Heliton Patrick Cordovil , Vale Valdicley Vieira , Dolabela Maria Fâni , De Carvalho Eliete Pereira , Percário Sandro
Published: May 2022

Malaria is an infectious disease and a serious public health problem in the world, with 3.3 billion people in endemic areas in 100 countries and about 200 million new cases each year, resulting in almost 1 million deaths in 2018. Although studies look for strategies to eradicate malaria, it is necessary to know more about its pathophysiology to understand the underlying mechanisms involved, particularly the redox balance, to guarantee success in combating this disease. In this review, we addressed the involvement of oxidative stress in malaria and the potential benefits of antioxidant supplementation as an adjuvant antimalarial therapy.
Surface Chemical and Morphological Analysis of Chitosan/1,3-β-d-Glucan Polysaccharide Films Cross-Linked at 90 °C
Authors: Gieroba Barbara , Sroka-Bartnicka Anna , Kazimierczak Paulina , Kalisz Grzegorz , Lewalska-Graczyk Agnieszka , Vivcharenko Vladyslav , Nowakowski Robert , Pieta Izabela S. , Przekora Agata
Published: May 2022

The cross-linking temperature of polymers may affect the surface characteristics and molecular arrangement, which are responsible for their mechanical and physico-chemical properties. The aim of this research was to determine and explain in detail the mechanism of unit interlinkage of two-component chitosan/1,3-β-d-glucan matrices gelled at 90 °C. This required identifying functional groups interacting with each other and assessing surface topography providing material chemical composition. For this purpose, various spectroscopic and microscopic approaches, such as attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), were applied. The results indicate the involvement mainly of the C-C and C-H groups and C=O⋯HN moieties in the process of biomaterial polymerization. Strong chemical interactions and ionocovalent bonds between the N-glucosamine moieties of chitosan and 1,3-β-d-glucan units were demonstrated, which was also reflected in the uniform surface of the sample without segregation. These unique properties, hybrid character and proper cell response may imply the potential application of studied biomaterial as biocompatible scaffolds used in regenerative medicine, especially in bone restoration and/or wound healing.
Beneficial Effect of H2S-Releasing Molecules in an In Vitro Model of Sarcopenia: Relevance of Glucoraphanin
Authors: Micheli Laura , Mitidieri Emma , Turnaturi Carlotta , Vanacore Domenico , Ciampi Clara , Lucarini Elena , Cirino Giuseppe , Ghelardini Carla , Sorrentino Raffaella , Di Cesare Mannelli Lorenzo , d’Emmanuele di Villa Bianca Roberta
Published: May 2022

Sarcopenia is a gradual and generalized skeletal muscle (SKM) syndrome, characterized by the impairment of muscle components and functionality. Hydrogen sulfide (H2S), endogenously formed within the body from the activity of cystathionine-γ-lyase (CSE), cystathionine- β-synthase (CBS), and mercaptopyruvate sulfurtransferase, is involved in SKM function. Here, in an in vitro model of sarcopenia based on damage induced by dexamethasone (DEX, 1 μM, 48 h treatment) in C2C12-derived myotubes, we investigated the protective potential of exogenous and endogenous sources of H2S, i.e., glucoraphanin (30 μM), L-cysteine (150 μM), and 3-mercaptopyruvate (150 μM). DEX impaired the H2S signalling in terms of a reduction in CBS and CSE expression and H2S biosynthesis. Glucoraphanin and 3-mercaptopyruvate but not L-cysteine prevented the apoptotic process induced by DEX. In parallel, the H2S-releasing molecules reduced the oxidative unbalance evoked by DEX, reducing catalase activity, O2− levels, and protein carbonylation. Glucoraphanin, 3-mercaptopyruvate, and L-cysteine avoided the changes in myotubes morphology and morphometrics after DEX treatment. In conclusion, in an in vitro model of sarcopenia, an impairment in CBS/CSE/H2S signalling occurs, whereas glucoraphanin, a natural H2S-releasing molecule, appears more effective for preventing the SKM damage. Therefore, glucoraphanin supplementation could be an innovative therapeutic approach in the management of sarcopenia.
Global DNA Methylation Profiling Reveals Differentially Methylated CpGs between Salivary Gland Pleomorphic Adenomas with Distinct Clinical Course
Authors: Kiwerska Katarzyna , Kowal-Wisniewska Ewelina , Ustaszewski Adam , Bartkowiak Ewelina , Jarmuz-Szymczak Malgorzata , Wierzbicka Malgorzata , Giefing Maciej
Published: May 2022

Pleomorphic adenomas (PAs) are the most frequently diagnosed benign salivary gland tumors. Although the majority of PAs are characterized by slow growth, some develop very fast and are more prone to recur. The reason for such differences remains unidentified. In this study, we performed global DNA methylation profiling using the Infinium Human Methylation EPIC 850k BeadChip Array (Illumina) to search for epigenetic biomarkers that could distinguish both groups of tumors. The analysis was performed in four fast-growing tumors (FGTs) and four slow-growing tumors (SGTs). In all, 85 CpG dinucleotides differentiating both groups were identified. Six CpG tags (cg06748470, cg18413218, cg10121788, cg08249296, cg18455472, and cg19930657) were selected for bisulfite pyrosequencing in the extended group of samples. We confirmed differences in DNA methylation between both groups of samples. To evaluate the potential diagnostic accuracy of the selected markers, ROC curves were constructed. We indicated that CpGs included in two assays showed an area under the curve with an acceptable prognostic value (AUC > 0.7). However, logistic regression analysis allowed us to indicate a more optimal model consisting of five CpGs ((1) cg06748470, (2) cg00600454, (3) CpG located in chr14: 77,371,501–77,371,502 (not annotated in GRCh37/hg19), (4) CpG2 located in chr16: 77,469,589–77,469,590 (not annotated GRCh37/hg19), and (5) cg19930657) with AUC > 0.8. This set of epigenetic biomarkers may be considered as differentiating factors between FGT and SGT during salivary gland tumor diagnosis. However, this data should be confirmed in a larger cohort of samples.
A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research
Authors: Gim Jeong-An
Published: May 2022

Improvements in next-generation sequencing (NGS) technology and computer systems have enabled personalized therapies based on genomic information. Recently, health management strategies using genomics and big data have been developed for application in medicine and public health science. In this review, I first discuss the development of a genomic information management system (GIMS) to maintain a highly detailed health record and detect diseases by collecting the genomic information of one individual over time. Maintaining a health record and detecting abnormal genomic states are important; thus, the development of a GIMS is necessary. Based on the current research status, open public data, and databases, I discuss the possibility of a GIMS for clinical use. I also discuss how the analysis of genomic information as big data can be applied for clinical and research purposes. Tremendous volumes of genomic information are being generated, and the development of methods for the collection, cleansing, storing, indexing, and serving must progress under legal regulation. Genetic information is a type of personal information and is covered under privacy protection; here, I examine the regulations on the use of genetic information in different countries. This review provides useful insights for scientists and clinicians who wish to use genomic information for healthy aging and personalized medicine.
Could a Lower Toll-like Receptor (TLR) and NF-κB Activation Due to a Changed Charge Distribution in the Spike Protein Be the Reason for the Lower Pathogenicity of Omicron?
Authors: Kircheis Ralf , Planz Oliver
Published: May 2022

The novel SARS-CoV-2 Omicron variant B.1.1.529, which emerged in late 2021, is currently active worldwide, replacing other variants, including the Delta variant, due to an enormously increased infectivity. Multiple substitutions and deletions in the N-terminal domain (NTD) and the receptor binding domain (RBD) in the spike protein collaborate with the observed increased infectivity and evasion from therapeutic monoclonal antibodies and vaccine-induced neutralizing antibodies after primary/secondary immunization. In contrast, although three mutations near the S1/S2 furin cleavage site were predicted to favor cleavage, observed cleavage efficacy is substantially lower than in the Delta variant and also lower compared to the wild-type virus correlating with significantly lower TMPRSS2-dependent replication in the lungs, and lower cellular syncytium formation. In contrast, the Omicron variant shows high TMPRSS2-independent replication in the upper airway organs, but lower pathogenicity in animal studies and clinics. Based on recent data, we present here a hypothesis proposing that the changed charge distribution in the Omicron’s spike protein could lead to lower activation of Toll-like receptors (TLRs) in innate immune cells, resulting in lower NF-κB activation, furin expression, and viral replication in the lungs, and lower immune hyper-activation.
Prophylactic Evidence of MSCs-Derived Exosomes in Doxorubicin/Trastuzumab-Induced Cardiotoxicity: Beyond Mechanistic Target of NRG-1/Erb Signaling Pathway
Authors: Ebrahim Nesrine , Al Saihati Hajir A. , Mostafa Ola , Hassouna Amira , Abdulsamea Sameh , Abd El Aziz M. El Gebaly Eman , Abo-Rayah Nashwa Hassan , Sabry Dina , El-Sherbiny Mohamed , Madboly Abdelmonem G. , Hussien Noha Ibrahim , Saadani Raja El Hasnaoui , Ebrahim Hasnaa Ali , Badr Omnia A. M. , Elsherbiny Nehal M. , Salim Rabab F.
Published: May 2022

Trastuzumab (Trz) is a humanized monoclonal antibody targeting epidermal growth factor receptor 2 (HER2; ErbB2). The combined administration of Trz and doxorubicin (DOX) has shown potent anti-cancer efficacy; however, this regimen may be accompanied by severe cardiac toxicity. Mesenchymal stem cells (MSCs)-derived exosomes are nanosized vesicles that play a crucial role in cell–cell communication and have shown efficacy in the treatment of various diseases. In this study, we aim to investigate the cardioprotective effects of MSCs-derived exosomes in a DOX/Trz- mediated cardiotoxicity model, and the possible mechanisms underlying these effects are elucidated. Forty-nine male rats were randomly assigned into four groups: Group I (control); Group II (Dox/Trz); Group III (protective group); and Group IV (curative group). Cardiac hemodynamic parameters, serum markers of cardiac injury, oxidative stress indices, and cardiac histopathology were investigated. Further, transcript profile of specific cardiac tissue injury markers, apoptotic markers, and fibrotic markers were analyzed using qRT-PCR, while the protein expressions of pAkt/Akt, pERK/ERK, pJNK/JNK, pJNK/JNK, and pSTAT3/STAT3 were evaluated by ELISA. Additionally, cardiac mirR-21 and miR-26a were assessed. A combined administration of DOX/Trz disrupted redox and Ca2+ homeostasis in cardiac tissue induced myocardial fibrosis and myofibril loss and triggered cardiac DNA damage and apoptosis. This cardiotoxicity was accompanied by decreased NRG-1 mRNA expression, HER2 protein expression, and suppressed AKT and ERK phosphorylation, while triggering JNK phosphorylation. Histological and ultra-structural examination of cardiac specimens revealed features typical of cardiac tissue injury. Moreover, a significant decline in cardiac function was observed through biochemical testing of serum cardiac markers and echocardiography. In contrast, the intraperitoneal administration of MSCs-derived exosomes alleviated cardiac injury in both protective and curative protocols; however, superior effects were observed in the protective protocol. The results of the current study indicate the ability of MSCs-derived exosomes to protect from and attenuate DOX/Trz-induced cardiotoxicity. The NRG-1/HER2, MAPK, PI3K/AKT, PJNK/JNK, and PSTAT/STAT signaling pathways play roles in mediating these effects.
Advantages and Limitations of Animal Schizophrenia Models
Authors: Białoń Magdalena , Wąsik Agnieszka
Published: May 2022

Mental illness modeling is still a major challenge for scientists. Animal models of schizophrenia are essential to gain a better understanding of the disease etiopathology and mechanism of action of currently used antipsychotic drugs and help in the search for new and more effective therapies. We can distinguish among pharmacological, genetic, and neurodevelopmental models offering various neuroanatomical disorders and a different spectrum of symptoms of schizophrenia. Modeling schizophrenia is based on inducing damage or changes in the activity of relevant regions in the rodent brain (mainly the prefrontal cortex and hippocampus). Such artificially induced dysfunctions approximately correspond to the lesions found in patients with schizophrenia. However, notably, animal models of mental illness have numerous limitations and never fully reflect the disease state observed in humans.
Structure and Function of the Polycomb Repressive Complexes PRC1 and PRC2
Authors: Angrand Pierre-Olivier
Published: May 2022

Epigenetic regulation contributes to the control of gene expression programs through local chromatin rearrangements [...]
Epigenomic Analysis Reveals the KCNK9 Potassium Channel as a Potential Therapeutic Target for Adenomyosis
Authors: Chu Ling-Hui , Liao Chi-Chun , Liew Phui-Ly , Chen Chien-Wen , Su Po-Hsuan , Wen Kuo-Chang , Lai Hung-Cheng , Huang Rui-Lan , Chen Lin-Yu
Published: May 2022

Adenomyosis is linked to dysmenorrhea and infertility. The pathogenesis of adenomyosis remains unclear, and little is known of the genetic and epigenetic changes in the eutopic endometrium in adenomyosis, which may predispose patients to the invasion and migration of endometrial tissues into the myometrium. Transcriptome studies have identified genes related to various cell behaviors but no targets for therapeutic intervention. The epigenetics of the eutopic endometrium in adenomyosis have rarely been investigated. Endometrial tissue was obtained from premenopausal women with (n = 32) or without adenomyosis (n = 17) who underwent hysterectomy aged 34–57 years at a tertiary hospital. The methylome and transcriptome were assessed by using a Methylation 450 K BeadChip array and Affymetrix expression microarray. Protein expression was examined by immunohistochemistry. Differential methylation analysis revealed 53 lowly methylated genes and 176 highly methylated genes with consistent gene expression in adenomyosis, including three genes encoding potassium ion channels. High expression of KCNK9 in the eutopic and ectopic endometria in patients with adenomyosis but not in normal controls was observed. Hormone-free, antibody-based KCNK9 targeting is a potential therapeutic strategy for adenomyosis-related dysmenorrhea, menorrhagia, and infertility.
Does Trophectoderm Mitochondrial DNA Content Affect Embryo Developmental and Implantation Potential?
Authors: Lukaszuk Krzysztof , Podolak Amira
Published: May 2022

A retrospective case control study was undertaken at the molecular biology department of a private center for reproductive medicine in order to determine whether any correlation exists between the mitochondrial DNA (mtDNA) content of trophectoderm and embryo developmental potential. A total of 275 couples underwent IVF treatment, producing a total of 716 embryos. The trophectoderm was biopsied from each embryo at the blastocyst stage (day 5 or day 6 post-fertilization) subjected to low-pass next-generation sequencing (NGS), for the purpose of detecting aneuploidy. For each sample, the number of mtDNA reads obtained after analysis using NGS was divided by the number of reads attributable to the nuclear genome. The mtDNA copy number was found to be higher in aneuploid embryos than in those that were euploid (mean mtDNA ratio ± SD: 1.13 ± 1.37 versus 1.45 ± 1.78, p = 0.02) and in day 5 biopsies compared to day 6 biopsies (1.41 ± 1.66 vs. 1.19 ± 1.27, p = 0.001), whereas no statistically significant differences in mtDNA content were seen in relation to embryo morphology (1.58 ± 2.44 vs. 2.19 ± 2.89, p = 0.12), genetic sex (1.27 ± 1.29 vs. 1.27 ± 1.18, p = 0.99), maternal age (1.31 ± 1.41 vs. 1.33 ± 1.29, p = 0.43), or its ability to implant (1.14 ± 0.88 vs. 1.21 ± 1.16, p = 0.39). mtDNA has small potential to serve as an additional, independent biomarker for embryo selection.
Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches
Authors: Aviña-Padilla Katia , Zambada-Moreno Octavio , Herrera-Oropeza Gabriel Emilio , Jimenez-Limas Marco A. , Abrahamian Peter , Hammond Rosemarie W. , Hernández-Rosales Maribel
Published: May 2022

Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
Understanding the Formation and Mechanism of Anticipatory Responses in Escherichia coli
Authors: Rai Navneet , Kim Minseung , Tagkopoulos Ilias
Published: May 2022

Microorganisms often live in complex habitats, where changes in the environment are predictable, providing an opportunity for microorganisms to learn, anticipate the upcoming environmental changes and prepare in advance for better survival and growth. One such environment is the mammalian intestine, where the abundance of different carbon sources is spatially distributed. In this study, we identified seven spatially distributed carbon sources in the mammalian intestine and tested whether Escherichia coli exhibits phenotypes that are consistent with an anticipatory response given their spatial order and abundance within the mammalian intestine. Through RNA-Seq and RT-PCR validation measurements, we found that there was a 67% match in the expression patterns between the measured phenotypes and what would otherwise be expected in the case of anticipatory behavior, while 83% and 0% were in agreement with the homeostatic and random response, respectively. To understand the genetic and phenotypic basis of the discrepancies between the expected and measured anticipatory responses, we thoroughly investigated the discrepancy in D-galactose treatment and the expression of maltose operon in E. coli. Here, the expected anticipatory response, based on the spatial distribution of D-galactose and D-maltose, was that D-galactose should upregulate the maltose operon, but it was the opposite in experimental validation. We performed whole genome random mutagenesis and screening and identified E. coli strains with positive expression of maltose operon in D-galactose. Targeted Sanger sequencing and mutation repair identified that the mutations in the promoter region of malT and in the coding region of the crp gene were the factors responsible for the reversion in the association. Further, to identify why positive association in the D-galactose treatment and the expression of the maltose operon did not evolve naturally, fitness measurements were performed. Fitness experiments demonstrated that the fitness of E. coli strains with a positive association in the D-galactose treatment and the expression of the maltose operon was 12% to 20% lower than that of the wild type strain.
Inhibition of Respiratory Syncytial Virus Infection by Small Non-Coding RNA Fragments
Authors: Pålsson Sandra Axberg , Sekar Vaishnovi , Kutter Claudia , Friedländer Marc R. , Spetz Anna-Lena
Published: May 2022

Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants, immunocompromised individuals and the elderly. As the only current specific treatment options for RSV are monoclonal antibodies, there is a need for efficacious antiviral treatments against RSV to be developed. We have previously shown that a group of synthetic non-coding single-stranded DNA oligonucleotides with lengths of 25–40 nucleotides can inhibit RSV infection in vitro and in vivo. Based on this, herein, we investigate whether naturally occurring single-stranded small non-coding RNA (sncRNA) fragments present in the airways have antiviral effects against RSV infection. From publicly available sequencing data, we selected sncRNA fragments such as YRNAs, tRNAs and rRNAs present in human bronchoalveolar lavage fluid (BALF) from healthy individuals. We utilized a GFP-expressing RSV to show that pre-treatment with the selected sncRNA fragments inhibited RSV infection in A549 cells in vitro. Furthermore, by using a flow cytometry-based binding assay, we demonstrate that these naturally occurring sncRNAs fragments inhibit viral infection most likely by binding to the RSV entry receptor nucleolin and thereby preventing the virus from binding to host cells, either directly or via steric hindrance. This finding highlights a new function of sncRNAs and displays the possibility of using naturally occurring sncRNAs as treatments against RSV.
Synergistic Effects of A Combined Treatment of Glioblastoma U251 Cells with An Anti-miR-10b-5p Molecule and An AntiCancer Agent Based on 1-(3′,4′,5′-Trimethoxyphenyl)-2-Aryl-1H-Imidazole Scaffold
Authors: Zurlo Matteo , Romagnoli Romeo , Oliva Paola , Gasparello Jessica , Finotti Alessia , Gambari Roberto
Published: May 2022

(1) Background: In the development of new and more effective anticancer approaches, combined treatments appear of great interest. Combination therapy could be of importance in the management of glioblastoma (GBM), a lethal malignancy that accounts for 42% of cancer of the central nervous system, with a median survival of 15 months. This study aimed to verify the activity on a glioblastoma cancer cell line of one of the most active compounds of a novel series of tubulin polymerization inhibitors based on the 1-(3′,4′,5′-trimethoxyphenyl)-2-aryl-1H-imidazole scaffold, used in combination with a miRNA inhibitor molecule targeting the oncomiRNA miR-10b-5p. This microRNA was selected in consideration of the role of miR-10b-5p on the onset and progression of glioblastoma. (2) Methods: Apoptosis was analyzed by Annexin-V and Caspase 3/7 assays, efficacy of the anti-miR-10b-5p was assessed by determining the miR-10b-5p content by RT-qPCR. (3) Results: The results obtained show that a “combination therapy” performed by combining the use of an anti-miR-10b-5p and a 1-(3′,4′,5′-trimethoxyphenyl)-2-aryl-1H-imidazole derivative is an encouraging strategy to boost the efficacy of anticancer therapies and at the same time to reduce side effects.
Improving Homology-Directed Repair in Genome Editing Experiments by Influencing the Cell Cycle
Authors: Smirnikhina Svetlana A. , Zaynitdinova Milyausha I. , Sergeeva Vasilina A. , Lavrov Alexander V.
Published: May 2022

Genome editing is currently widely used in biomedical research; however, the use of this method in the clinic is still limited because of its low efficiency and possible side effects. Moreover, the correction of mutations that cause diseases in humans seems to be extremely important and promising. Numerous attempts to improve the efficiency of homology-directed repair-mediated correction of mutations in mammalian cells have focused on influencing the cell cycle. Homology-directed repair is known to occur only in the late S and G2 phases of the cell cycle, so researchers are looking for safe ways to enrich the cell culture with cells in these phases of the cell cycle. This review surveys the main approaches to influencing the cell cycle in genome editing experiments (predominantly using Cas9), for example, the use of cell cycle synchronizers, mitogens, substances that affect cyclin-dependent kinases, hypothermia, inhibition of p53, etc. Despite the fact that all these approaches have a reversible effect on the cell cycle, it is necessary to use them with caution, since cells during the arrest of the cell cycle can accumulate mutations, which can potentially lead to their malignant transformation.
Arginine-Containing Tripeptides as Analgesic Substances: The Possible Mechanism of Ligand-Receptor Binding to the Slow Sodium Channel
Authors: Rogachevskii Ilya V. , Plakhova Vera B. , Penniyaynen Valentina A. , Kalinina Arina D. , Podzorova Svetlana A. , Samosvat Dmitriy M. , Zegrya Georgy G. , Krylov Boris V.
Published: May 2022

Two short arginine-containing tripeptides, H-Arg-Arg-Arg-OH (TP1) and Ac-Arg-Arg-Arg-NH2 (TP2), have been shown by the patch-clamp method to modulate the NaV1.8 channels of DRG primary sensory neurons, which are responsible for the generation of nociceptive signals. Conformational analysis of the tripeptides indicates that the key role in the ligand-receptor binding of TP1 and TP2 to the NaV1.8 channel is played by two positively charged guanidinium groups of the arginine side chains located at the characteristic distance of ~9 Å from each other. The tripeptide effect on the NaV1.8 channel activation gating device has been retained when the N- and C-terminal groups of TP1 were structurally modified to TP2 to protect the attacking peptide from proteolytic cleavage by exopeptidases during its delivery to the molecular target, the NaV1.8 channel. As demonstrated by the organotypic tissue culture method, the agents do not affect the DRG neurite growth, which makes it possible to expect the absence of adverse side effects at the tissue level upon administration of TP1 and TP2. The data obtained indicate that both tripeptides can have great therapeutic potential as novel analgesic medicinal substances.
The BCC7 Protein Contributes to the Toxoplasma Basal Pole by Interfacing between the MyoC Motor and the IMC Membrane Network
Authors: Vigetti Luis , Labouré Tatiana , Roumégous Chloé , Cannella Dominique , Touquet Bastien , Mayer Claudine , Couté Yohann , Frénal Karine , Tardieux Isabelle , Renesto Patricia
Published: May 2022

T. gondii is a eukaryotic parasite that has evolved a stage called tachyzoite which multiplies in host cells by producing two daughter cells internally. These nascent tachyzoites bud off their mother and repeat the division process until the expanding progenies escape to settle and multiply in other host cells. Over these intra- and extra-cellular phases, the tachyzoite maintains an essential apicobasal polarity that emerges through a unique bidirectional budding process of the elongating cells. This process requires the assembly of several molecular complexes that, at the nascent pole, encompass structural and myosin motor elements. To characterize a recently identified basal pole marker named BCC7 with respect to the posterior myosin J and myosin C motors, we used conventional biochemistry as well as advanced proteomic and in silico analysis in conjunction with live and super resolution microscopy of transgenic fluorescent tachyzoites. We document that BCC7 forms a ribbed ring below which myosin C motor entities distribute regularly. In addition, we identified—among 13 BCC7 putative partners—two novel and five known members of the inner membrane complex (IMC) family which ends at the apical side of the ring. Therefore, BCC7 could assist the stabilization of the IMC plaques and contribute to the parasite biomechanical properties.
MEC Computation Offloading-Based Learning Strategy in Ultra-Dense Networks
Authors: Duo Chunhong , Dong Peng , Gao Qize , Li Baogang , Li Yongqian
Published: May 2022

Mobile edge computing (MEC) has the potential to realize intensive applications in 5G networks. Through migrating intensive tasks to edge servers, MEC can expand the computing power of wireless networks. Fifth generation networks need to meet service requirements, such as wide coverage, high capacity, low latency and low power consumption. Therefore, the network architecture of MEC combined with ultra-dense networks (UDNs) will become a typical model in the future. This paper designs a MEC architecture in a UDN, which is our research background. First, the system model is established in the UDN, and the optimization problems is proposed. Second, the action classification (AC) algorithm is utilized to filter the effective action in Q-learning. Then, the optimal computation offloading strategy and resource allocation scheme are obtained using a deep reinforcement learning-based AC algorithm, which is known as the DQN-AC algorithm. Finally, the simulation experiments show that the proposed DQN-AC algorithm can effectively reduce the system weighted cost compared with the full local computation algorithm, full offloading computation algorithm and Q-learning algorithm.
A Comparison of Machine Learning Techniques for the Quality Classification of Molded Products
Authors: Polenta Andrea , Tomassini Selene , Falcionelli Nicola , Contardo Paolo , Dragoni Aldo Franco , Sernani Paolo
Published: May 2022

The developments in the internet of things (IoT), artificial intelligence (AI), and cyber-physical systems (CPS) are paving the way to the implementation of smart factories in what is commonly recognized as the fourth industrial revolution. In the manufacturing sector, these technological advancements are making Industry 4.0 a reality, with data-driven methodologies based on machine learning (ML) that are capable of extracting knowledge from the data collected by sensors placed on production machines. This is particularly relevant in plastic injection molding, with the objective of monitoring the quality of molded products from the parameters of the production process. In this regard, the main contribution of this paper is the systematic comparison of ML techniques to predict the quality classes of plastic molded products, using real data collected during the production process. Specifically, we compare six different classifiers on the data coming from the production of plastic road lenses. To run the comparison, we collected a dataset composed of the process parameters of 1451 road lenses. On such samples, we tested a multi-class classification, providing a statistical analysis of the results as well as of the importance of the input features. Among the tested classifiers, the ensembles of decision trees, i.e., random forest and gradient-boosted trees (GBT), achieved 95% accuracy in predicting the quality classes of molded products, showing the viability of the use of ML-based techniques for this purpose. The collected dataset and the source code of the experiments are available in a public, open-access repository, making the presented research fully reproducible.
Sweep Sampling Comparison of Terrestrial Insect Communities Associated with Herbaceous Stratum in the Riparian Zone of the Miho River, Korea
Authors: Hwang Jeong Ho , Yim Mean-Young , Kim Sung-Yeol , Ji Seong Jin , Lee Wang-Hee
Published: May 2022

To investigate insect and plant community relationships in riparian zones, terrestrial insect communities were compared in plant communities in the riparian zone of the Miho River, Korea. The sweep netting method was used to sample insects in 50 m transects in three herbaceous plant communities. In 2020, each plant community—Chenopodium album, Beckmannia syzigachne, and Artemisia indica—was swept 100 times (50 sweeps × 2). In 2021, two communities had an additional 100 sweeps collected using 10 subsamples of 10 sweeps (excluding C. album communities). The surveyed dominant species or subdominant species of the insect community in each site preyed on the dominant plant species at the site. The Bray–Curtis similarity was significantly higher than the Sørensen similarity when comparing datasets across different years for the same plant species community. The predicted optimum sampling size to obtain approximately 80% of the total species estimated to be at each survey site, for effective quantitative collection of terrestrial insect herbivores in each plant community, was examined. Fifty sweeps were required for the A. indica community and 100 sweeps were required for the B. syzigachne community. The results of this study provide important data for riparian biodiversity conservation and future pest monitoring.