bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel PTP1B Inhibitor-Phosphate of Polymannuronic Acid Ameliorates Insulin Resistance by Regulating IRS-1/Akt Signaling
Authors: Li Dan , Zhang Shuai , Yang Cheng , Li Quancai , Wang Shixin , Xu Ximing , Hao Jiejie , Li Chunxia
Published: November 2021

Protein tyrosine phosphatase 1B (PTP1B) is a critical negative modulator of insulin signaling and has attracted considerable attention in treating type 2 diabetes mellitus (T2DM). Low-molecular-weight polymannuronic acid phosphate (LPMP) was found to be a selective PTP1B inhibitor with an IC50 of 1.02 ± 0.17 μM. Cellular glucose consumption was significantly elevated in insulin-resistant HepG2 cells after LPMP treatment. LPMP could alleviate oxidative stress and endoplasmic reticulum stress, which are associated with the development of insulin resistance. Western blot and polymerase chain reaction (PCR) analysis demonstrated that LPMP could enhance insulin sensitivity through the PTP1B/IRS/Akt transduction pathway. Furthermore, animal study confirmed that LPMP could decrease blood glucose, alleviate insulin resistance, and exert hepatoprotective effects in diabetic mice. Taken together, LPMP can effectively inhibit insulin resistance and has high potential as an anti-diabetic drug candidate to be further developed.
Developmental Toxicity and Biotransformation of Two Anti-Epileptics in Zebrafish Embryos and Early Larvae
Authors: Bars Chloé , Hoyberghs Jente , Valenzuela Allan , Buyssens Laura , Ayuso Miriam , Van Ginneken Chris , Labro Alain J. , Foubert Kenn , Van Cruchten Steven J.
Published: November 2021

The zebrafish (Danio rerio) embryo is gaining interest as a bridging tool between in-vitro and in-vivo developmental toxicity studies. However, cytochrome P450 (CYP)-mediated drug metabolism in this model is still under debate. Therefore, we investigated the potential of zebrafish embryos and larvae to bioactivate two known anti-epileptics, carbamazepine (CBZ) and phenytoin (PHE), to carbamazepine-10,11-epoxide (E-CBZ) and 5-(4-hydroxyphenyl)-5-phenylhydantoin (HPPH), respectively. First, zebrafish were exposed to CBZ, PHE, E-CBZ and HPPH from 5¼- to 120-h post fertilization (hpf) and morphologically evaluated. Second, the formations of E-CBZ and HPPH were assessed in culture medium and in whole-embryo extracts at different time points by targeted LC-MS. Finally, E-CBZ and HPPH formation was also assessed in adult zebrafish liver microsomes and compared with those of human, rat, and rabbit. The present study showed teratogenic effects for CBZ and PHE, but not for E-CBZ and HPPH. No HPPH was detected during organogenesis and E-CBZ was only formed at the end of organogenesis. E-CBZ and HPPH formation was also very low-to-negligible in adult zebrafish compared with the mammalian species. As such, other metabolic pathways than those of mammals are involved in the bioactivation of CBZ and PHE, or, these anti-epileptics are teratogens and do not require bioactivation in the zebrafish.
Inhibition of Virulence Factors and Biofilm Formation by Wogonin Attenuates Pathogenicity of Pseudomonas aeruginosa PAO1 via Targeting pqs Quorum-Sensing System
Authors: Wang Shiwei , Feng Yuqi , Han Xiaofeng , Cai Xinyu , Yang Liu , Liu Chaolan , Shen Lixin
Published: November 2021

Pseudomonas aeruginosa, an important opportunistic pathogen, is capable of producing various virulence factors and forming biofilm that are regulated by quorum sensing (QS). It is known that targeting virulence factor production and biofilm formation instead of exerting selective pressure on growth such as conventional antibiotics can reduce multidrug resistance in bacteria. Therefore, many quorum-sensing inhibitors (QSIs) have been developed to prevent or treat this bacterial infection. In this study, wogonin, as an active ingredient from Agrimonia pilosa, was found to be able to inhibit QS system of P. aeruginosa PAO1. Wogonin downregulated the expression of QS-related genes and reduced the production of many virulence factors, such as elastase, pyocyanin, and proteolytic enzyme. In addition, wogonin decreased the extracellular polysaccharide synthesis and inhibited twitching, swimming, and swarming motilities and biofilm formation. The attenuation of pathogenicity in P. aeruginosa PAO1 by wogonin application was further validated in vivo by cabbage infection and fruit fly and nematode survival experiments. Further molecular docking analysis, pathogenicity examination of various QS-related mutants, and PQS signal molecule detection revealed that wogonin could interfere with PQS signal molecular synthesis by affecting pqsA and pqsR. Taken together, the results indicated that wogonin might be used as an anti-QS candidate drug to attenuate the infection caused by P. aeruginosa.
Variability in Behavioral Phenotypes after Forced Swimming-Induced Stress in Rats Is Associated with Expression of the Glucocorticoid Receptor, Nurr1, and IL-1β in the Hippocampus
Authors: Ruiz-Sánchez Elizabeth , López-Ramírez Arely M. , Ruiz-Chow Ángel , Calvillo Minerva , Reséndiz-Albor Aldo A. , Anguiano Brenda , Rojas Patricia
Published: November 2021

Individual differences in coping with stress may determine either a vulnerable or resilient phenotype. Therefore, it is important to better understand the biology underlying the behavioral phenotype. We assessed whether individual behavioral phenotype to acute stress is related with the hippocampal expression of glucocorticoid receptor (GR), Nurr1, interleukin-1 beta (IL-1β) or brain-derived neurotrophic factor (BDNF). Wistar male rats were exposed to forced swimming for 15 min and sacrificed at different times. Behavioral response was analyzed, and it was compared with the gene and protein expression of GR, Nurr1, IL-1β and BDNF in the hippocampus for each time point. Behavioral phenotyping showed a group with high immobility (vulnerable) while another had low immobility (resilient). No significant differences were found in the Nurr1, IL-1β and BDNF mRNA levels between resilient and vulnerable rats at different recovery times except for Nr3c1 (gene for GR). However, exposure to stress caused significantly higher levels of GR, Nurr1 and IL-1β proteins of vulnerable compared to resilient rats. This variability of behavioral phenotypes is associated with a differential molecular response to stress that involves GR, Nurr1, and IL-1β as mediators in coping with stress. This contributes to identifying biomarkers of susceptibility to stress.
Effects of the Combined Treatment with a G-Quadruplex-Stabilizing Ligand and Photon Beams on Glioblastoma Stem-like Cells: A Magnetic Resonance Study
Authors: Palma Alessandra , Grande Sveva , Luciani Anna Maria , Ricci-Vitiani Lucia , Buccarelli Mariachiara , Pallini Roberto , Triveri Alice , Pirota Valentina , Doria Filippo , D’Alessandris Quintino Giorgio , Berardinelli Francesco , Antoccia Antonio , Rosi Antonella
Published: November 2021

Glioblastoma multiforme is a malignant primary brain tumor with a poor prognosis and high rates of chemo-radiotherapy failure, mainly due to a small cell fraction with stem-like properties (GSCs). The mechanisms underlying GSC response to radiation need to be elucidated to enhance sensitivity to treatments and to develop new therapeutic strategies. In a previous study, two GSC lines, named line #1 and line #83, responded differently to carbon ions and photon beams, with the differences likely attributable to their own different metabolic fingerprint rather than to radiation type. Data from the literature showed the capability of RHPS4, a G-quadruplex stabilizing ligand, to sensitize the glioblastoma radioresistant U251MG cells to X-rays. The combined metabolic effect of ligand #190, a new RHPS4-derivative showing reduced cardiotoxicity, and a photon beam has been monitored by magnetic resonance (MR) spectroscopy for the two GSC lines, #1 and #83, to reveal whether a synergistic response occurs. MR spectra from both lines were affected by single and combined treatments, but the variations of the analysed metabolites were statistically significant mainly in line #1, without synergistic effects due to combination. The multivariate analysis of ten metabolites shows a separation between control and treated samples in line #1 regardless of treatment type, while separation was not detected in line #83.
C-X-C Motif Chemokine Ligand 9 and Its CXCR3 Receptor Are the Salt and Pepper for T Cells Trafficking in a Mouse Model of Gaucher Disease
Authors: Magnusen Albert Frank , Rani Reena , McKay Mary Ashley , Hatton Shelby Loraine , Nyamajenjere Tsitsi Carol , Magnusen Daniel Nii Aryee , Köhl Jörg , Grabowski Gregory Alex , Pandey Manoj Kumar
Published: November 2021

Gaucher disease is a lysosomal storage disease, which happens due to mutations in GBA1/Gba1 that encodes the enzyme termed as lysosomal acid β-glucosidase. The major function of this enzyme is to catalyze glucosylceramide (GC) into glucose and ceramide. The deficiency of this enzyme and resultant abnormal accumulation of GC cause altered function of several of the innate and adaptive immune cells. For example, augmented infiltration of T cells contributes to the increased production of pro-inflammatory cytokines, (e.g., IFNγ, TNFα, IL6, IL12p40, IL12p70, IL23, and IL17A/F). This leads to tissue damage in a genetic mouse model (Gba19V/−) of Gaucher disease. The cellular mechanism(s) by which increased tissue infiltration of T cells occurs in this disease is not fully understood. Here, we delineate role of the CXCR3 receptor and its exogenous C-X-C motif chemokine ligand 9 (CXCL9) in induction of increased tissue recruitment of CD4+ T and CD8+ T cells in Gaucher disease. Intracellular FACS staining of macrophages (Mϕs) and dendritic cells (DCs) from Gba19V/− mice showed elevated production of CXCL9. Purified CD4+ T cells and the CD8+ T cells from Gba19V/− mice showed increased expression of CXCR3. Ex vivo and in vivo chemotaxis experiments showed CXCL9 involvement in the recruitment of Gba19V/− T cells. Furthermore, antibody blockade of the CXCL9 receptor (CXCR3) on T cells caused marked reduction in CXCL9- mediated chemotaxis of T cells in Gba19V/− mice. These data implicate abnormalities of the CXCL9-CXCR3 axis leading to enhanced tissue recruitment of T cells in Gaucher disease. Such results provide a rationale for blockade of the CXCL9/CXCR3 axis as potential new therapeutic targets for the treatment of inflammation in Gaucher disease.
Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts
Authors: Damián Alejandra , Ionescu Raluca Oancea , Rodríguez de Alba Marta , Tamayo Alejandra , Trujillo-Tiebas María José , Cotarelo-Pérez María Carmen , Pérez Rodríguez Olga , Villaverde Cristina , de la Fuente Lorena , Romero Raquel , Núñez-Moreno Gonzalo , Mínguez Pablo , Ayuso Carmen , Cortón Marta
Published: November 2021

Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.
Telmisartan Attenuates Kanamycin-Induced Ototoxicity in Rats
Authors: Lee Chang Ho , Lee So Min , Kim So Young
Published: November 2021

Telmisartan (TM) has been proposed to relieve inflammatory responses by modulating peroxisome proliferator activator receptor-γ (PPARγ) signaling. This study aimed to investigate the protective effects of TM on kanamycin(KM)-induced ototoxicity in rats. Forty-eight, 8-week-old female Sprague Dawley rats were divided into four groups: (1) control group, (2) TM group, (3) KM group, and (4) TM + KM group. Auditory brainstem response was measured. The histology of the cochlea was examined. The protein expression levels of angiotensin-converting enzyme 2 (ACE2), HO1, and PPARγ were measured by Western blotting. The auditory threshold shifts at 4, 8, 16, and 32 kHz were lower in the TM + KM group than in the KM group (all p < 0.05). The loss of cochlear outer hair cells and spiral ganglial cells was lower in the TM + KM group than in the KM group. The protein expression levels of ACE2, PPARγ, and HO1 were higher in the KM group than in the control group (all p < 0.05). The TM + KM group showed lower expression levels of PPARγ and HO1 than the KM group.TM protected the cochlea from KM-induced injuries in rats. TM preserved hearing levels and attenuated the increase in PPARγ and HO1 expression levels in KM-exposed rat cochleae.
Non-Woven Infection Prevention Fabrics Coated with Biobased Cranberry Extracts Inactivate Enveloped Viruses Such as SARS-CoV-2 and Multidrug-Resistant Bacteria
Authors: Takayama Kazuo , Tuñón-Molina Alberto , Cano-Vicent Alba , Muramoto Yukiko , Noda Takeshi , Aparicio-Collado José Luis , Sabater i Serra Roser , Martí Miguel , Serrano-Aroca Ángel
Published: November 2021

The Coronavirus Disease (COVID-19) pandemic is demanding the rapid action of the authorities and scientific community in order to find new antimicrobial solutions that could inactivate the pathogen SARS-CoV-2 that causes this disease. Gram-positive bacteria contribute to severe pneumonia associated with COVID-19, and their resistance to antibiotics is exponentially increasing. In this regard, non-woven fabrics are currently used for the fabrication of infection prevention clothing such as face masks, caps, scrubs, shirts, trousers, disposable gowns, overalls, hoods, aprons and shoe covers as protective tools against viral and bacterial infections. However, these non-woven fabrics are made of materials that do not exhibit intrinsic antimicrobial activity. Thus, we have here developed non-woven fabrics with antimicrobial coatings of cranberry extracts capable of inactivating enveloped viruses such as SARS-CoV-2 and the bacteriophage phi 6 (about 99% of viral inactivation in 1 min of viral contact), and two multidrug-resistant bacteria: the methicillin-resistant Staphylococcus aureus and the methicillin-resistant Staphylococcus epidermidis. The morphology, thermal and mechanical properties of the produced filters were characterized by optical and electron microscopy, differential scanning calorimetry, thermogravimetry and dynamic mechanical thermal analysis. The non-toxicity of these advanced technologies was ensured using a Caenorhabditis elegans in vivo model. These results open up a new prevention path using natural and biodegradable compounds for the fabrication of infection prevention clothing in the current COVID-19 pandemic and microbial resistant era.
Placental Endocrine Activity: Adaptation and Disruption of Maternal Glucose Metabolism in Pregnancy and the Influence of Fetal Sex
Authors: Stern Christina , Schwarz Sarah , Moser Gerit , Cvitic Silvija , Jantscher-Krenn Evelyn , Gauster Martin , Hiden Ursula
Published: November 2021

The placenta is an endocrine fetal organ, which secretes a plethora of steroid- and proteo-hormones, metabolic proteins, growth factors, and cytokines in order to adapt maternal physiology to pregnancy. Central to the growth of the fetus is the supply with nutrients, foremost with glucose. Therefore, during pregnancy, maternal insulin resistance arises, which elevates maternal blood glucose levels, and consequently ensures an adequate glucose supply for the developing fetus. At the same time, maternal β-cell mass and function increase to compensate for the higher insulin demand. These adaptations are also regulated by the endocrine function of the placenta. Excessive insulin resistance or the inability to increase insulin production accordingly disrupts physiological modulation of pregnancy mediated glucose metabolism and may cause maternal gestational diabetes (GDM). A growing body of evidence suggests that this adaptation of maternal glucose metabolism differs between pregnancies carrying a girl vs. pregnancies carrying a boy. Moreover, the risk of developing GDM differs depending on the sex of the fetus. Sex differences in placenta derived hormones and bioactive proteins, which adapt and modulate maternal glucose metabolism, are likely to contribute to this sexual dimorphism. This review provides an overview on the adaptation and maladaptation of maternal glucose metabolism by placenta-derived factors, and highlights sex differences in this regulatory network.
Tuning Physicochemical Properties of a Macroporous Polysaccharide-Based Scaffold for 3D Neuronal Culture
Authors: Gerschenfeld Gaspard , Aid Rachida , Simon-Yarza Teresa , Lanouar Soraya , Charnay Patrick , Letourneur Didier , Topilko Piotr
Published: November 2021

Central nervous system (CNS) lesions are a leading cause of death and disability worldwide. Three-dimensional neural cultures in biomaterials offer more physiologically relevant models for disease studies, toxicity screenings or in vivo transplantations. Herein, we describe the development and use of pullulan/dextran polysaccharide-based scaffolds for 3D neuronal culture. We first assessed scaffolding properties upon variation of the concentration (1%, 1.5%, 3% w/w) of the cross-linking agent, sodium trimetaphosphate (STMP). The lower STMP concentration (1%) allowed us to generate scaffolds with higher porosity (59.9 ± 4.6%), faster degradation rate (5.11 ± 0.14 mg/min) and lower elastic modulus (384 ± 26 Pa) compared with 3% STMP scaffolds (47 ± 2.1%, 1.39 ± 0.03 mg/min, 916 ± 44 Pa, respectively). Using primary cultures of embryonic neurons from PGKCre, Rosa26tdTomato embryos, we observed that in 3D culture, embryonic neurons remained in aggregates within the scaffolds and did not attach, spread or differentiate. To enhance neuronal adhesion and neurite outgrowth, we then functionalized the 1% STMP scaffolds with laminin. We found that treatment of the scaffold with a 100 μg/mL solution of laminin, combined with a subsequent freeze-drying step, created a laminin mesh network that significantly enhanced embryonic neuron adhesion, neurite outgrowth and survival. Such scaffold therefore constitutes a promising neuron-compatible and biodegradable biomaterial.
Synthesis, In Vitro and In Silico Anticancer Activity of New 4-Methylbenzamide Derivatives Containing 2,6-Substituted Purines as Potential Protein Kinases Inhibitors
Authors: Kalinichenko Elena , Faryna Aliaksandr , Bozhok Tatyana , Panibrat Alesya
Published: November 2021

A novel class of potential protein kinase inhibitors 7–16 was synthesized in high yields using various substituted purines. The most promising compounds, 7 and 10, exhibited inhibitory activity against seven cancer cell lines. The IC50 values for compounds 7 and 10 were 2.27 and 2.53 μM for K562 cells, 1.42 and 1.52 μM for HL-60 cells, and 4.56 and 24.77 μM for OKP-GS cells, respectively. In addition, compounds 7 and 10 dose-dependently induced the apoptosis and cell cycle arrest at G2/M phase, preventing the cell division of OKP-GS cells. Compounds 7, 9, and 10 showed 36–45% inhibitory activity against PDGFRα and PDGFRβ at the concentration of 1 μM. Molecular modeling experiments showed that obtained compounds could bind to PDGFRα as either type 1 (compound 7, ATP-competitive) or type 2 (compound 10, allosteric) inhibitors, depending on the substituent in the amide part of the molecule.
Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the ‘Regulatory Loop’
Authors: Padariya Monikaben , Fahraeus Robin , Hupp Ted , Kalathiya Umesh
Published: November 2021

The nonsense-mediated mRNA decay (NMD) pathway rapidly detects and degrades mRNA containing premature termination codons (PTCs). UP-frameshift 1 (UPF1), the master regulator of the NMD process, has two alternatively-spliced isoforms; one carries 353-GNEDLVIIWLR-363 insertion in the ‘regulatory loop (involved in mRNA binding)’. Such insertion can induce catalytic and/or ATPase activity, as determined experimentally; however, the kinetics and molecular level information are not fully understood. Herein, applying all-atom molecular dynamics, we probe the binding specificity of UPF1 with different GC- and AU-rich mRNA motifs and the influence of insertion to the viable control over UPF1 catalytic activity. Our results indicate two distinct conformations between 1B and RecA2 domains of UPF1: ‘open (isoform_2; without insertion)’ and ‘closed (isoform_1; with insertion)’. These structural movements correspond to an important stacking pattern in mRNA motifs, i.e., absence of stack formation in mRNA, with UPF1 isoform_2 results in the ‘open conformation’. Particularly, for UPF1 isoform_1, the increased distance between 1B and RecA2 domains has resulted in reducing the mRNA–UPF1 interactions. Lower fluctuating GC-rich mRNA motifs have better binding with UPF1, compared with AU-rich sequences. Except CCUGGGG, all other GC-rich motifs formed a 4-stack pattern with UPF1. High occupancy R363, D364, T627, and G862 residues were common binding GC-rich motifs, as were R363, N535, and T627 for the AU-rich motifs. The GC-rich motifs behave distinctly when bound to either of the isoforms; lower stability was observed with UPF1 isoform_2. The cancer-associated UPF1 variants (P533L/T and A839T) resulted in decreased protein–mRNA binding efficiency. Lack of mRNA stacking poses in the UPF1P533T system significantly decreased UPF1-mRNA binding efficiency and increased distance between 1B-RecA2. These novel findings can serve to further inform NMD-associated mechanistic and kinetic studies.
Dexmedetomidine Promotes Lipopolysaccharide-Induced Differentiation of Cardiac Fibroblasts and Collagen I/III Synthesis through α2A Adrenoreceptor-Mediated Activation of the PKC-p38-Smad2/3 Signaling Pathway in Mice
Authors: Liao Jia , Li Kaiying , Su Xingyu , Chen Yihua , Wang Yingwei , Tang Xiangxu , Xing Yun , Xu Yaqian , Dai Xiaomeng , Teng Jiashuo , Li Hongmei , Wang Huadong , Lv Xiuxiu , Wang Yiyang
Published: November 2021

Dexmedetomidine (DEX), a selective α2 adrenergic receptor (AR) agonist, is commonly used as a sedative drug during critical illness. In the present study, we explored a novel accelerative effect of DEX on cardiac fibroblast (CF) differentiation mediated by LPS and clarified its potential mechanism. LPS apparently increased the expression of α-SMA and collagen I/III and the phosphorylation of p38 and Smad-3 in the CFs of mice. These effects were significantly enhanced by DEX through increasing α2A-AR expression in CFs after LPS stimulation. The CFs from α2A-AR knockout mice were markedly less sensitive to DEX treatment than those of wild-type mice. Inhibition of protein kinase C (PKC) abolished the enhanced effects of DEX on LPS-induced differentiation of CFs. We also found that the α-SMA level in the second-passage CFs was much higher than that in the nonpassage and first-passage CFs. However, after LPS stimulation, the TNF-α released from the nonpassage CFs was much higher than that in the first- and second-passage CFs. DEX had no effect on LPS-induced release of TNF-α and IL-6 from CFs. Further investigation indicated that DEX promoted cardiac fibrosis and collagen I/III synthesis in mice exposed to LPS for four weeks. Our results demonstrated that DEX effectively accelerated LPS-induced differentiation of CFs to myofibroblasts through the PKC-p38-Smad2/3 signaling pathway by activating α2A-AR.
Ligand-Based Virtual Screening Based on the Graph Edit Distance
Authors: Rica Elena , Álvarez Susana , Serratosa Francesc
Published: November 2021

Chemical compounds can be represented as attributed graphs. An attributed graph is a mathematical model of an object composed of two types of representations: nodes and edges. Nodes are individual components, and edges are relations between these components. In this case, pharmacophore-type node descriptions are represented by nodes and chemical bounds by edges. If we want to obtain the bioactivity dissimilarity between two chemical compounds, a distance between attributed graphs can be used. The Graph Edit Distance allows computing this distance, and it is defined as the cost of transforming one graph into another. Nevertheless, to define this dissimilarity, the transformation cost must be properly tuned. The aim of this paper is to analyse the structural-based screening methods to verify the quality of the Harper transformation costs proposal and to present an algorithm to learn these transformation costs such that the bioactivity dissimilarity is properly defined in a ligand-based virtual screening application. The goodness of the dissimilarity is represented by the classification accuracy. Six publicly available datasets—CAPST, DUD-E, GLL&GDD, NRLiSt-BDB, MUV and ULS-UDS—have been used to validate our methodology and show that with our learned costs, we obtain the highest ratios in identifying the bioactivity similarity in a structurally diverse group of molecules.
Synthesis, Properties, and Selected Technical Applications of Magnesium Oxide Nanoparticles: A Review
Authors: Hornak Jaroslav
Published: November 2021

In the last few decades, there has been a trend involving the use of nanoscale fillers in a variety of applications. Significant improvements have been achieved in the areas of their preparation and further applications (e.g., in industry, agriculture, and medicine). One of these promising materials is magnesium oxide (MgO), the unique properties of which make it a suitable candidate for use in a wide range of applications. Generally, MgO is a white, hygroscopic solid mineral, and its lattice consists of Mg2+ ions and O2− ions. Nanostructured MgO can be prepared through different chemical (bottom-up approach) or physical (top-down approach) routes. The required resultant properties (e.g., bandgap, crystallite size, and shape) can be achieved depending on the reaction conditions, basic starting materials, or their concentrations. In addition to its unique material properties, MgO is also potentially of interest due to its nontoxicity and environmental friendliness, which allow it to be widely used in medicine and biotechnological applications.
Transdermal Drug Delivery Systems and Their Use in Obesity Treatment
Authors: Li Zhiguo , Fang Xuexun , Yu Dahai
Published: November 2021

Transdermal drug delivery (TDD) has recently emerged as an effective alternative to oral and injection administration because of its less invasiveness, low rejection rate, and excellent ease of administration. TDD has made an important contribution to medical practice such as diabetes, hemorrhoids, arthritis, migraine, and schizophrenia treatment, but has yet to fully achieve its potential in the treatment of obesity. Obesity has reached epidemic proportions globally and posed a significant threat to human health. Various approaches, including oral and injection administration have widely been used in clinical setting for obesity treatment. However, these traditional options remain ineffective and inconvenient, and carry risks of adverse effects. Therefore, alternative and advanced drug delivery strategies with higher efficacy and less toxicity such as TDD are urgently required for obesity treatment. This review summarizes current TDD technology, and the main anti-obesity drug delivery system. This review also provides insights into various anti-obesity drugs under study with a focus on the recent developments of TDD system for enhanced anti-obesity drug delivery. Although most of presented studies stay in animal stage, the application of TDD in anti-obesity drugs would have a significant impact on bringing safe and effective therapies to obese patients in the future.
Sparsely Connected Autoencoders: A Multi-Purpose Tool for Single Cell omics Analysis
Authors: Alessandri Luca , Ratto Maria Luisa , Contaldo Sandro Gepiro , Beccuti Marco , Cordero Francesca , Arigoni Maddalena , Calogero Raffaele A.
Published: November 2021

Background: Biological processes are based on complex networks of cells and molecules. Single cell multi-omics is a new tool aiming to provide new incites in the complex network of events controlling the functionality of the cell. Methods: Since single cell technologies provide many sample measurements, they are the ideal environment for the application of Deep Learning and Machine Learning approaches. An autoencoder is composed of an encoder and a decoder sub-model. An autoencoder is a very powerful tool in data compression and noise removal. However, the decoder model remains a black box from which is impossible to depict the contribution of the single input elements. We have recently developed a new class of autoencoders, called Sparsely Connected Autoencoders (SCA), which have the advantage of providing a controlled association among the input layer and the decoder module. This new architecture has the benefit that the decoder model is not a black box anymore and can be used to depict new biologically interesting features from single cell data. Results: Here, we show that SCA hidden layer can grab new information usually hidden in single cell data, like providing clustering on meta-features difficult, i.e. transcription factors expression, or not technically not possible, i.e. miRNA expression, to depict in single cell RNAseq data. Furthermore, SCA representation of cell clusters has the advantage of simulating a conventional bulk RNAseq, which is a data transformation allowing the identification of similarity among independent experiments. Conclusions: In our opinion, SCA represents the bioinformatics version of a universal “Swiss-knife” for the extraction of hidden knowledgeable features from single cell omics data.
Emerging View on the Molecular Functions of Sec62 and Sec63 in Protein Translocation
Authors: Jung Sung-jun , Kim Hyun
Published: November 2021

Most secreted and membrane proteins are targeted to and translocated across the endoplasmic reticulum (ER) membrane through the Sec61 protein-conducting channel. Evolutionarily conserved Sec62 and Sec63 associate with the Sec61 channel, forming the Sec complex and mediating translocation of a subset of proteins. For the last three decades, it has been thought that ER protein targeting and translocation occur via two distinct pathways: signal recognition particle (SRP)-dependent co-translational or SRP-independent, Sec62/Sec63 dependent post-translational translocation pathway. However, recent studies have suggested that ER protein targeting and translocation through the Sec translocon are more intricate than previously thought. This review summarizes the current understanding of the molecular functions of Sec62/Sec63 in ER protein translocation.
Modified Low-Temperature Extraction Method for Isolation of Bletilla striata Polysaccharide as Antioxidant for the Prevention of Alzheimer’s Disease
Authors: Lin Yi-Wen , Fang Chih-Hsiang , Liang Ya-Jyun , Liao Hong-Hsiang , Lin Feng-Huei
Published: November 2021

Amyloid-β (Aβ) peptides play a key role in Alzheimer’s disease (AD), the most common type of dementia. In this study, a polysaccharide from Bletilla striata (BSP), with strong antioxidant and anti-inflammatory properties, was extracted using a low-temperature method and tested for its efficacy against AD, in vitro using N2a and BV-2 cells, and in vivo using an AD rat model. The characterization of the extracted BSP for its molecular structure and functional groups demonstrated the effectiveness of the modified method for retaining its bioactivity. In vitro, BSP reduced by 20% reactive oxygen species (ROS) levels in N2a cells (p = 0.0082) and the expression levels of inflammation-related genes by 3-fold TNF-α (p = 0.0048), 4-fold IL-6 (p = 0.0019), and 2.5-fold IL-10 (p = 0.0212) in BV-2 cells treated with Aβ fibrils. In vivo, BSP recovered learning memory, ameliorated morphological damage in the hippocampus and cortex, and reduced the expression of the β-secretase protein in AlCl3-induced AD rats. Collectively, these findings demonstrated the efficacy of BSP for preventing and alleviating the effects of AD.
Regulation of the Cell-Intrinsic DNA Damage Response by the Innate Immune Machinery
Authors: Hayman Thomas J. , Glazer Peter M.
Published: November 2021

Maintenance of genomic integrity is crucial for cell survival. As such, elegant DNA damage response (DDR) systems have evolved to ensure proper repair of DNA double-strand breaks (DSBs) and other lesions that threaten genomic integrity. Towards this end, most therapeutic studies have focused on understanding of the canonical DNA DSB repair pathways to enhance the efficacy of DNA-damaging therapies. While these approaches have been fruitful, there has been relatively limited success to date and potential for significant normal tissue toxicity. With the advent of novel immunotherapies, there has been interest in understanding the interactions of radiation therapy with the innate and adaptive immune responses, with the ultimate goal of enhancing treatment efficacy. While a substantial body of work has demonstrated control of the immune-mediated (extrinsic) responses to DNA-damaging therapies by several innate immune pathways (e.g., cGAS–STING and RIG-I), emerging work demonstrates an underappreciated role of the innate immune machinery in directly regulating tumor cell-intrinsic/cell-autonomous responses to DNA damage.
Toll-like Receptor Signaling Inhibitory Peptide Improves Inflammation in Animal Model and Human Systemic Lupus Erythematosus
Authors: Baek Wook-Young , Choi Yang-Seon , Lee Sang-Won , Son In-Ok , Jeon Ki-Woong , Choi Sang-Dun , Suh Chang-Hee
Published: November 2021

Toll-like receptors (TLRs) play a major role in the innate immune system. Several studies have shown the regulatory effects of TLR-mediated pathways on immune and inflammatory diseases. Dysregulated functions of TLRs within the endosomal compartment, including TLR7/9 trafficking, may cause systemic lupus erythematosus (SLE). TLR signaling pathways are fine-tuned by Toll/interleukin-1 receptor (TIR) domain-containing adapters, leading to interferon (IFN)-α production. This study describes a TLR inhibitor peptide 1 (TIP1) that primarily suppresses the downstream signaling mediated by TIR domain-containing adapters in an animal model of lupus and patients with SLE. The expression of most downstream proteins of the TLR7/9/myeloid differentiation factor 88 (MyD88)/IFN regulatory factor 7 signaling was downregulated in major tissues such as the kidney, spleen, and lymph nodes of treated mice. Furthermore, the pathological analysis of the kidney tissue confirmed that TIP1 could improve inflammation in MRL/lpr mice. TIP1 treatment downregulated many downstream proteins associated with TLR signaling, such as MyD88, interleukin-1 receptor-associated kinase, tumor necrosis factor receptor-associated factor 6, and IFN-α, in the peripheral blood mononuclear cells of patients with SLE. In conclusion, our data suggest that TIP1 can serve as a potential candidate for the treatment of SLE.
The Complex Interplay between Autophagy and NLRP3 Inflammasome in Renal Diseases
Authors: Ding Yong , Fu Xiaodi , Wang Qimeng , Liu Huiyang , Wang Honggang , Wu Dongdong
Published: November 2021

Autophagy is a highly conserved process of the eukaryotic cell cycle. It plays an important role in the survival and maintenance of cells by degrading organelles, proteins, and macromolecules in the cytoplasm and the circulation of degraded products. The dysfunction of autophagy can lead to the pathology of many human diseases. The nucleotide-binding oligomerization domain-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome belongs to the family of nucleotide-binding and oligomerization domain-like receptors (NLRs) and can induce caspase-1 activation, thus leading to the maturation and secretion of interleukin-1beta (IL-1β) and IL-18. It has been reported that the interplay between autophagy and NLRP3 inflammasome is involved in many diseases, including renal diseases. In this review, the interplay between autophagy and the NLRP3 inflammasome and the mechanisms in renal diseases are explored to provide ideas for relevant basic research in the future.
State-Targeting Stabilization of Adenosine A2A Receptor by Fusing a Custom-Made De Novo Designed α-Helical Protein
Authors: Mitsumoto Masaya , Sugaya Kanna , Kazama Kazuki , Nakano Ryosuke , Kosugi Takahiro , Murata Takeshi , Koga Nobuyasu
Published: November 2021

G-protein coupled receptors (GPCRs) are known for their low stability and large conformational changes upon transitions between multiple states. A widely used method for stabilizing these receptors is to make chimeric receptors by fusing soluble proteins (i.e., fusion partner proteins) into the intracellular loop 3 (ICL3) connecting the transmembrane helices 5 and 6 (TM5 and TM6). However, this fusion approach requires experimental trial and error to identify appropriate soluble proteins, residue positions, and linker lengths for making the fusion. Moreover, this approach has not provided state-targeting stabilization of GPCRs. Here, to rationally stabilize a class A GPCR, adenosine A2A receptor (A2AR) in a target state, we carried out the custom-made de novo design of α-helical fusion partner proteins, which can fix the conformation of TM5 and TM6 to that in an inactive state of A2AR through straight helical connections without any kinks or intervening loops. The chimeric A2AR fused with one of the designs (FiX1) exhibited increased thermal stability. Moreover, compared with the wild type, the binding affinity of the chimera against the agonist NECA was significantly decreased, whereas that against the inverse agonist ZM241385 was similar, indicating that the inactive state was selectively stabilized. Our strategy contributes to the rational state-targeting stabilization of GPCRs.
Recent Advances in Dialogue Machine Translation
Authors: Liu Siyou , Sun Yuqi , Wang Longyue
Published: December 2021

Recent years have seen a surge of interest in dialogue translation, which is a significant application task for machine translation (MT) technology. However, this has so far not been extensively explored due to its inherent characteristics including data limitation, discourse properties and personality traits. In this article, we give the first comprehensive review of dialogue MT, including well-defined problems (e.g., 4 perspectives), collected resources (e.g., 5 language pairs and 4 sub-domains), representative approaches (e.g., architecture, discourse phenomena and personality) and useful applications (e.g., hotel-booking chat system). After systematical investigation, we also build a state-of-the-art dialogue NMT system by leveraging a breadth of established approaches such as novel architectures, popular pre-training and advanced techniques. Encouragingly, we push the state-of-the-art performance up to 62.7 BLEU points on a commonly-used benchmark by using mBART pre-training. We hope that this survey paper could significantly promote the research in dialogue MT.
Early Stage Identification of COVID-19 Patients in Mexico Using Machine Learning: A Case Study for the Tijuana General Hospital
Authors: Castillo-Olea Cristián , Conte-Galván Roberto , Zuñiga Clemente , Siono Alexandra , Huerta Angelica , Bardhi Ornela , Ortiz Eric
Published: December 2021

Background: The current pandemic caused by SARS-CoV-2 is an acute illness of global concern. SARS-CoV-2 is an infectious disease caused by a recently discovered coronavirus. Most people who get sick from COVID-19 experience either mild, moderate, or severe symptoms. In order to help make quick decisions regarding treatment and isolation needs, it is useful to determine which significant variables indicate infection cases in the population served by the Tijuana General Hospital (Hospital General de Tijuana). An Artificial Intelligence (Machine Learning) mathematical model was developed in order to identify early-stage significant variables in COVID-19 patients. Methods: The individual characteristics of the study subjects included age, gender, age group, symptoms, comorbidities, diagnosis, and outcomes. A mathematical model that uses supervised learning algorithms, allowing the identification of the significant variables that predict the diagnosis of COVID-19 with high precision, was developed. Results: Automatic algorithms were used to analyze the data: for Systolic Arterial Hypertension (SAH), the Logistic Regression algorithm showed results of 91.0% in area under ROC (AUC), 80% accuracy (CA), 80% F1 and 80% Recall, and 80.1% precision for the selected variables, while for Diabetes Mellitus (DM) with the Logistic Regression algorithm it obtained 91.2% AUC, 89.2% accuracy, 88.8% F1, 89.7% precision, and 89.2% recall for the selected variables. The neural network algorithm showed better results for patients with Obesity, obtaining 83.4% AUC, 91.4% accuracy, 89.9% F1, 90.6% precision, and 91.4% recall. Conclusions: Statistical analyses revealed that the significant predictive symptoms in patients with SAH, DM, and Obesity were more substantial in fatigue and myalgias/arthralgias. In contrast, the third dominant symptom in people with SAH and DM was odynophagia.
Hardware-Based Emulator with Deep Learning Model for Building Energy Control and Prediction Based on Occupancy Sensors’ Data
Authors: Ye Zhijing , O’Neill Zheng , Hu Fei
Published: December 2021

Heating, ventilation, and air conditioning (HVAC) is the largest source of residential energy consumption. Occupancy sensors’ data can be used for HVAC control since it indicates the number of people in the building. HVAC and sensors form a typical cyber-physical system (CPS). In this paper, we aim to build a hardware-based emulation platform to study the occupancy data’s features, which can be further extracted by using machine learning models. In particular, we propose two hardware-based emulators to investigate the use of wired/wireless communication interfaces for occupancy sensor-based building CPS control, and the use of deep learning to predict the building energy consumption with the sensor data. We hypothesize is that the building energy consumption may be predicted by using the occupancy data collected by the sensors, and question what type of prediction model should be used to accurately predict the energy load. Another hypothesis is that an in-lab hardware/software platform could be built to emulate the occupancy sensing process. The machine learning algorithms can then be used to analyze the energy load based on the sensing data. To test the emulator, the occupancy data from the sensors is used to predict energy consumption. The synchronization scheme between sensors and the HVAC server will be discussed. We have built two hardware/software emulation platforms to investigate the sensor/HVAC integration strategies, and used an enhanced deep learning model—which has sequence-to-sequence long short-term memory (Seq2Seq LSTM)—with an attention model to predict the building energy consumption with the preservation of the intrinsic patterns. Because the long-range temporal dependencies are captured, the Seq2Seq models may provide a higher accuracy by using LSTM architectures with encoder and decoder. Meanwhile, LSTMs can capture the temporal and spatial patterns of time series data. The attention model can highlight the most relevant input information in the energy prediction by allocating the attention weights. The communication overhead between the sensors and the HVAC control server can also be alleviated via the attention mechanism, which can automatically ignore the irrelevant information and amplify the relevant information during CNN training. Our experiments and performance analysis show that, compared with the traditional LSTM neural network, the performance of the proposed method has a 30% higher prediction accuracy.
Optimizing Photoperiod, Exposure Time, and Host-to-Parasitoid Ratio for Mass-Rearing of Telenomus remus, an Egg Parasitoid of Spodoptera frugiperda, on Spodoptera litura Eggs
Authors: Chen Wanbin , Weng Qingfen , Nie Rui , Zhang Hongzhi , Jing Xiaoyu , Wang Mengqing , Li Yuyan , Mao Jianjun , Zhang Lisheng
Published: December 2021

Telenomus remus (Nixon) is a dominant egg parasitoid of the destructive agricultural pest Spodoptera frugiperda (J. E. Smith), and so is used in augmentative biocontrol programs in several countries. An optimized mass-rearing system is essential to produce biological control products in a timely and cost-effective manner. In this study, the photoperiod, host egg:parasitoid ratio, and exposure time were evaluated to identify the optimal rearing conditions for T. remus on the alternative host Spodoptera litura (Fabricius) eggs. Results showed that increasing photoperiod above 12L:12D remarkably improved parasitoid progeny yield and life table parameters. Overlong photoperiods shortened female longevity, but within acceptable limits. There was a significant negative correlation between parasitism rate and host egg:parasitoid ratio under exposure times of 12 and 36 h, but not 24 h. Percentage of female progeny increased significantly along with increasing the host egg:parasitoid ratio. A significant negative relationship between the number of emerged adults per egg and the host egg:parasitoid ratio was observed at an exposure time of 36 h. It was concluded that T. remus may be mass-reared most efficiently on S. litura eggs using a photoperiod of more than 12L:12D, a 14–20:1 host egg:parasitoid ratio, and an exposure time of 24 h. These findings can be used to produce T. remus more efficiently and at lower costs.
The Key Glutathione S-Transferase Family Genes Involved in the Detoxification of Rice Gramine in Brown Planthopper Nilaparvata lugens
Authors: Yang Jun , Kong Xiang-Dong , Zhu-Salzman Keyan , Qin Qing-Ming , Cai Qing-Nian
Published: December 2021

Phytochemical toxins are considered a defense measure for herbivore invasion. To adapt this defensive strategy, herbivores use glutathione S-transferases (GSTs) as an important detoxification enzyme to cope with toxic compounds, but the underlying molecular basis for GST genes in this process remains unclear. Here, we investigated the basis of how GST genes in brown planthopper (BPH, Nilaparvata lugens (Stål)) participated in the detoxification of gramine by RNA interference. For BPH, the LC25 and LC50 concentrations of gramine were 7.11 and 14.99 μg/mL at 72 h after feeding, respectively. The transcriptions of seven of eight GST genes in BPH were induced by a low concentration of gramine, and GST activity was activated. Although interferences of seven genes reduced BPH tolerance to gramine, only the expression of NlGST1-1, NlGSTD2, and NlGSTE1 was positively correlated with GST activities, and silencing of these three genes inhibited GST activities in BPH. Our findings reveal that two new key genes, NlGSTD2 and NlGSTE1, play an essential role in the detoxification of gramine such as NlGST1-1 does in BPH, which not only provides the molecular evidence for the coevolution theory, but also provides new insight into the development of an environmentally friendly strategy for herbivore population management.