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Corynebacterium glutamicum, a well-studied industrial model microorganism, has garnered widespread attention due to its ability for producing amino acids with a long history. In recent years, research efforts have been increasingly focused on exploring its potential for producing various organic acids beyond amino acids. Organic acids, which are characterized by their acidic functional groups, have diverse applications across industries such as food, agriculture, pharmaceuticals, and biobased materials. Leveraging advancements in metabolic engineering and synthetic biology, the metabolic pathways of C. glutamicum have been broadened to facilitate the production of numerous high-value organic acids. This review summarizes the recent progress in metabolic engineering for the production of both amino acids and other organic acids by C. glutamicum. Notably, these acids include, amino acids (lysine, isoleucine, and phenylalanine), TCA cycle-derived organic acids (succinic acid, α-ketoglutaric acid), aromatic organic acids (protocatechuate, 4-amino-3-hydroxybenzoic acid, anthranilate, and para-coumaric acid), and other organic acids (itaconic acid and cis, cis-muconic acid)., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024. Published by Elsevier Inc.)

Coronaviruses (CoVs) are significant animal and human pathogens, characterized by being enveloped RNA viruses with positive-sense single-stranded RNA. The Coronaviridae family encompasses four genera, among which gammacoronaviruses pose a major threat to the poultry industry, which infectious bronchitis virus (IBV) being the most prominent of these threats. Particularly, IBV adversely affects broiler growth and egg production, causing substantial losses. The IBV strains currently circulating in Taiwan include the IBV Taiwan-I (TW-I) serotype, IBV Taiwan-II (TW-II) serotype, and vaccine strains. Therefore, ongoing efforts have focused on developing novel vaccines and discovering antiviral agents. The envelope (E) proteins of CoVs accumulate in the endoplasmic reticulum-Golgi intermediate compartment prior to virus budding. These E proteins assemble into viroporins, exhibiting ion channel activity that leads to cell membrane disruption, making them attractive targets for antiviral therapy. In this study, we investigated the E proteins of IBV H-120, as well as IBV serotypes TW-I and TW-II. E protein expression resulted in inhibited bacteria growth, increased permeability of bacteria to β-galactosidase substrates, and blocked protein synthesis of bacteria by hygromycin B (HygB). Furthermore, in the presence of E proteins, HygB also impeded protein translation in DF-1 cells and damaged their membrane integrity. Collectively, these findings confirm the viroporin activity of the E proteins from IBV H-120, IBV serotype TW-I, and IBV serotype TW-II. Next, the viroporin inhibitors, 5-(N,N-hexamethylene) amiloride (HMA) and 4,4'-diisothiocyano stilbene-2,2'-disulphonic acid (DIDS) were used to inhibit the viroporin activities of the E proteins of IBV H-120, IBV serotype TW-I, and IBV serotype TW-II. In chicken embryos and chickens infected with IBV serotypes TW-I and IBV TW-II, no survivors were observed at 6 and 11 days post-infection (dpi), respectively. However, treatments with both DIDS and HMA increased the survival rates in infected chicken embryos and chickens and mitigated histopathological lesions in the trachea and kidney. Additionally, a 3D pentameric structure of the IBV E protein was constructed via homology modeling. As expected, both inhibitors were found to bind to the lipid-facing surface within the transmembrane domain of the E protein, inhibiting ion conduction. Taken together, our findings provide comprehensive evidence supporting the use of viroporin inhibitors as promising antiviral agents against IBV Taiwan isolates., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

The quasispecies of the influenza virus poses a significant challenge for developing effective therapies. Current antiviral drugs such as oseltamivir, zanamivir, peramivir and baloxavir marboxil along with seasonal vaccines have limitations due to viral variability caused by antigenic drift and shift as well as the development of drug resistance. Therefore, there is a clear need for novel antiviral agents targeting alternative mechanisms, either independently or in combination with existing modalities, to reduce the impact of influenza virus-related infections. The influenza nucleoprotein (NP) is a key component of the viral ribonucleoprotein complex. The multifaceted nature of the NP makes it an attractive target for antiviral intervention. Recent reports have identified inhibitors that specifically target this protein. Recognizing the importance of developing influenza treatments for potential pandemics, this review explores the structural and functional aspects of NP and highlights its potential as an emerging target for anti-influenza drugs. We discuss various strategies for targeting NP, including RNA binding, oligomerization, and nuclear export, and also consider the potential of NP-based vaccines. Overall, this review provides insights into recent developments and future perspectives on targeting influenza NP for antiviral therapies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Background: A combination treatment of surgery, chemotherapy, and radiotherapy can improve the survivals of pediatric patients with Ewing sarcoma (ES). However, prognosis remains poor for patients with metastatic disease at diagnosis or recurrence. Other high-risk (HR) features include large tumor burden, tumors of the axial skeleton and poor histologic response. Several studies have documented high dose chemotherapy with autologous stem cell rescue (HDC-ASCR) to be effective in such patients. In this retrospective study, we present the results of HDC-ASCR for high-risk Ewing sarcoma in children and young adults in a single institute., Methods: From March 2004 to March 2021, patients with ES, Ewing-like sarcoma, or round cell sarcoma received HDC-ASCR as part of treatment were included. The patients' characteristics, disease status, stem cell dose, engraftment status, post-transplant complications, and outcomes were analyzed., Results: Twenty patients receiving HDC-ASCR at complete response (n = 6), partial response (n = 13), and stable disease (n = 1) were enrolled. The male to female ratio was 11:9. Median age at diagnosis and transplant was 15.6 years old (range: 3.3-28.9) and 16.2 (range: 4.2-29.9), respectively. The conditioning regimens included ifosfamide-based in two and melphalan-based in 19. All patients achieved successful engraftment without tansplant-related mortality. The 5-year progression-free and overall survival (OS) rate were 35% and 54.5%, respectively. The causes of death (n = 8) were all contributed to disease progression. Patients in the complete response group or with localized HRES exhibited a higher 5-year OS (p = 0.047 and 0.05, respectively). Compared to the historical cohort without HDC-ASCR as part of primary treatment, the current cohort had a significantly better 5-year OS (p = 0.018)., Conclusion: HDC-ASCR seems promising as an alternative treatment for HRES in improving OS in this retrospective study with limited case number., Competing Interests: Conflicts of interest: Dr. Po-Kuei Wu and Dr. Wei-Ming Chen, editorial board member at the Journal of the Chinese Medical Association, had no role in the peer review process or decision to publish this article. The other authors declare that they have no conflicts of interest related to the subject matter or materials discussed in this article., (Copyright © 2024, the Chinese Medical Association.)

Native oxides form on the surface of many metals. Here, using gallium-based liquid metal alloys, Johnson-Kendall-Roberts (JKR) measurements are employed to show that native oxide dramatically lower the tension of the metal interface from 724 to 10 mN m -1 . Like conventional surfactants, the oxide has asymmetry between the composition of its internal and external interfaces. Yet, in comparison to conventional surfactants, oxides are an order of magnitude more effective at lowering tension and do not need to be added externally to the liquid (i.e., oxides form naturally on metals). This surfactant-like asymmetry explains the adhesion of oxide-coated metals to surfaces. The resulting low interfacial energy between the metal and the interior of the oxide helps stabilize non-spherical liquid metal structures. In addition, at small enough macroscopic contact angles, the finite tension of the liquid within the oxide can drive fluid instabilities that are useful for separating the oxide from the metal to form oxide-encased bubbles or deposit thin oxide films (1-5 nm) on surfaces. Since oxides form on many metals, this work can have implications for a wide range of metals and metal oxides in addition to explaining the physical behavior of liquid metal., (© 2024 The Author(s). Advanced Materials published by Wiley‐VCH GmbH.)

Autologous peripheral blood stem cell (PBSC) transplantation is crucial in pediatric cancer treatment, and tandem transplantation is beneficial in certain malignancies. Collecting PBSCs in small children with low body weight is challenging. We retrospectively analyzed data of pediatric cancer patients weighing <15 kg who underwent autologous PBSC harvesting in our hospital. Collections were performed in the pediatric intensive care unit over 2 or 3 consecutive days, to harvest sufficient stem cells (goal ≥2 × 10 6 CD34 + cells/kg per apheresate). From April 2006 to August 2021, we performed 129 collections after 50 mobilizations in 40 patients, with a median age of 1.9 (range, 0.6-5.6) years and a body weight of 11.0 (range, 6.6-14.7) kg. The median CD34 + cells in each apheresate were 4.2 (range, 0.01-40.13) × 10 6 /kg. 78% and 56% of mobilizations achieved sufficient cell dose for single or tandem transplantation, respectively, without additional aliquoting. The preapheresis hematopoietic progenitor cell (HPC) count was highly correlated with the CD34 + cell yield in the apheresate (r = 0.555, P < 0.001). Granulocyte colony-stimulating factor alone was not effective for mobilization in children ≥2 years of age, even without radiation exposure. By combining the preapheresis HPC count ≥20/μL and the 3 significant host factors, including age <2 years, no radiation exposure and use of chemotherapy, the prediction rate of goal achievement was increased (area under the curve 0.787)., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2024 International Society for Cell & Gene Therapy. Published by Elsevier Inc. All rights reserved.)

Purpose: Atopic march is defined as the development of atopic dermatitis in early childhood. We recently developed an atopic march mouse model through skin sensitization with aeroallergens from house dust mites and cockroaches. Using this model, this study aimed to evaluate the oral immunotherapy efficacy of Lactococcus lactis harboring specific antigens on the progression of atopic march., Methods: Dust mite major allergen Der p 2 and cockroach Per a 2-372 were expressed in L. lactis as a fusion recombinant clone (D2P2). L. lactis -D2P2 was administered intragastrically to Aeroallergen patch-sensitized mice once a day for a total of 35 times. The immunological variables in sera, scratching behavior, airway hyperresponsiveness (AHR), and pathology of lungs and skin were evaluated., Results: Our data showed that L. lacti s-D2P2 significantly lowered total immunoglobulin E levels, decreased scratch bouts, and relieved AHR compared with the control mice. Histological analysis of the skin and lung tissue demonstrated the therapeutic effects of L. lactis -D2P2 to modulate immune responses via decreased eosinophil infiltration and reduced expression of key cytokines, interleukin (IL)-31 and IL-13, respectively., Conclusions: The results imply that mucosal allergen-specific immunotherapy of L. lactis -D2P2 is a more cost-effective alternative to conventional subcutaneous allergen-specific immunotherapy. This study provides a promising platform for the development of novel oral protein-based vaccines in the early prevention of allergies., Competing Interests: There are no financial or other issues that might lead to conflict of interest., (Copyright © 2024 The Korean Academy of Asthma, Allergy and Clinical Immunology • The Korean Academy of Pediatric Allergy and Respiratory Disease.)

Targeting inter-duplex junctions in catenated DNA with bidirectional bis-intercalators is a potential strategy for enhancing anticancer effects. In this study, we used d(CGTATACG)2, which forms a tetraplex base-pair junction that resembles the DNA-DNA contact structure, as a model target for two alkyl-linked diaminoacridine bis-intercalators, DA4 and DA5. Cross-linking of the junction site by the bis-intercalators induced substantial structural changes in the DNA, transforming it from a B-form helical end-to-end junction to an over-wounded side-by-side inter-duplex conformation with A-DNA characteristics and curvature. These structural perturbations facilitated the angled intercalation of DA4 and DA5 with propeller geometry into two adjacent duplexes. The addition of a single carbon to the DA5 linker caused a bend that aligned its chromophores with CpG sites, enabling continuous stacking and specific water-mediated interactions at the inter-duplex contacts. Furthermore, we have shown that the different topological changes induced by DA4 and DA5 lead to the inhibition of topoisomerase 2 activities, which may account for their antitumor effects. Thus, this study lays the foundations for bis-intercalators targeting biologically relevant DNA-DNA contact structures for anticancer drug development., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Metal oxide films are essential in most electronic devices, yet they are typically deposited at elevated temperatures by using slow, vacuum-based processes. We printed native oxide films over large areas at ambient conditions by moving a molten metal meniscus across a target substrate. The oxide gently separates from the metal through fluid instabilities that occur in the meniscus, leading to uniform films free of liquid residue. The printed oxide has a metallic interlayer that renders the films highly conductive. The metallic character of the printed films promotes wetting of trace amounts of evaporated gold that would otherwise form disconnected islands on conventional oxide surfaces. The resulting ultrathin (<10 nanometers) conductors can be patterned into flexible circuits that are transparent, mechanically robust, and electrically stable, even at elevated temperatures.

Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Pastes and "foams" containing liquid metal (LM) as the continuous phase (liquid metal foams, LMFs) exhibit metallic properties while displaying paste or putty-like rheological behavior. These properties enable LMFs to be patterned into soft and stretchable electrical and thermal conductors through processes conducted at room temperature, such as printing. The simplest LMFs, featured in this work, are made by stirring LM in air, thereby entraining oxide-lined air "pockets" into the LM. Here, it is reported that mixing small amounts of water (as low as 1 wt%) into such LMFs gives rise to significant foaming by harnessing known reactions that evolve hydrogen and produce oxides. The resulting structures can be ≈4-5× their original volume and possess a fascinating combination of attributes: porosity, electrical conductivity, and responsiveness to environmental conditions. This expansion can be utilized for a type of 4D printing in which patterned conductors "grow," fill cavities, and change shape and density with respect to time. Excessive exposure to water in the long term ultimately consumes the metal in the LMF. However, when exposure to water is controlled, the metallic properties of porous LMFs can be preserved., (© 2024 The Authors. Advanced Materials published by Wiley‐VCH GmbH.)

3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense., (© 2024. The Author(s).)

The K + uptake system KtrAB is essential for bacterial survival in low K + environments. The activity of KtrAB is regulated by nucleotides and Na + . Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na + activates KtrAB and the Na + binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na + , as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na + binding stabilizes the ATP-bound BsKtrAB complex and enhances its K + flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na + in activating BsKtrAB is likely applicable to Na + -activated K + channels in central nervous system., (© 2024. The Author(s).)

The fluid nature of liquid metals combined with their ability to form a solid native oxide skin enables them to be patterned in ways that would be challenging for solid metals. The present work shows a unique way of patterning liquid metals by injecting liquid metals into a mold. The mold contains a nonstick coating that enables the removal of the mold, thereby leaving just the liquid metal on the target substrate. This approach offers the simplicity and structural control of molding but without having the mold become part of the device. Thus, the metal can be encapsulated with very soft polymers that collapse if used as microchannels. The same mold can be used multiple times for high-volume patterning of liquid metal. The injection molding method is rapid and reliably produces structures with complex geometries on both flat and curved surfaces. We demonstrate the method by fabricating an elastomeric Joule heater and an electroadhesive soft gripper to show the potential of the method for soft and stretchable devices.

Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Biophysical Society. All rights reserved.)

Artificial intelligence has made significant advances in the field of protein structure prediction in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated the capability to predict three-dimensional structures of numerous unknown proteins with accuracy levels comparable to those of experimental methods. This breakthrough has opened up new possibilities for understanding protein structure and function as well as accelerating drug discovery and other applications in the field of biology and medicine. Despite the remarkable achievements of artificial intelligence in the field, there are still some challenges and limitations. In this Review, we discuss the recent progress and some of the challenges in protein structure prediction. These challenges include predicting multidomain protein structures, protein complex structures, multiple conformational states of proteins, and protein folding pathways. Furthermore, we highlight directions in which further improvements can be conducted.

The cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) signaling pathway plays a critical protective role against viral infections. Metazoan STING undergoes multilayers of regulation to ensure specific signal transduction. However, the mechanisms underlying the regulation of bacterial STING remain unclear. In this study, we determined the crystal structure of anti-parallel dimeric form of bacterial STING, which keeps itself in an inactive state by preventing cyclic dinucleotides access. Conformational transition between inactive and active states of bacterial STINGs provides an on-off switch for downstream signaling. Some bacterial STINGs living in extreme environment contain an insertion sequence, which we show codes for an additional long lid that covers the ligand-binding pocket. This lid helps regulate anti-phage activities. Furthermore, bacterial STING can bind cyclic di-AMP in a triangle-shaped conformation via a more compact ligand-binding pocket, forming spiral-shaped protofibrils and higher-order fibril filaments. Based on the differences between cyclic-dinucleotide recognition, oligomerization, and downstream activation of different bacterial STINGs, we proposed a model to explain structure-function evolution of bacterial STINGs., (© 2023. The Author(s).)

Importance: Pseudomonas aeruginosa is an opportunistic bacterial pathogen. Many of its virulence genes are regulated by quorum sensing (QS), a form of cell-to-cell communication. P. aeruginosa QS consists of three interlinked circuits, LasI-R, Rhl-R, and Pseudomonas quinolone signal (PQS). Additionally, its QS system is interconnected with other regulatory networks, which help optimize gene expression under variable conditions. The numbers of genes regulated by QS differ substantially among P. aeruginosa strains. We show that a regulatory factor MexT, which is activated in response to certain antibiotics, downregulates the RhlI-R circuit and in turn measurably lowers virulence in a nematode worm infection model. Our findings help understand how existing and future therapeutic interventions for P. aeruginosa infections may impact this bacterium's gene regulation and physiology., Competing Interests: The authors declare no conflict of interest.

Background: Donor lymphocyte infusion (DLI) is effective for managing patients with hematologic malignancies after allogeneic hematopoietic stem cell transplant (HSCT). However, few studies have explored its optimal use in pediatric populations. Herein, we report our single-center experiences of DLI and factors for predicting its outcomes., Methods: This retrospective study included pediatric patients who had received DLI (between June 1998 and December 2022) after allogeneic HSCT. Data regarding patient characteristics, preemptive DLI disease status, and DLI characteristics were collected. The primary outcomes were overall survival (OS), event-free survival (EFS), and graft-vs-host-disease (GVHD) development., Results: The study cohort comprised 17 patients with acute leukemia, 3 with chronic leukemia, and 3 with lymphoma. Prophylactic, preemptive, and therapeutic DLI were used in seven, seven, and nine patients, respectively. Patients' median age and DLI dose were 9 years and 4.6 × 10 7 CD3 + cells/kg, respectively. The 5-year OS, EFS, and nonrelapse mortality were 43.5%, 38.3%, and 13.3%, respectively. Approximately 39% of the patients developed grade III or IV acute GVHD, whereas moderate/severe chronic GVHD (cGVHD) occurred in 30% of the evaluable patients. Patients' disease status before HSCT ( p = 0.009) and DLI ( p = 0.018) were the key factors influencing EFS. The implementation of a dose escalation schedule was associated with a marginal reduction in the risk of moderate/severe cGVHD ( p = 0.051). A DLI dose of ≥5 × 10 7 CD3 + cells/kg was significantly associated with a high moderate to severe cGVHD risk ( p = 0.002) and reduced OS ( p = 0.089)., Conclusion: Patients' disease status before HSCT and DLI may help predict EFS. The use of DLI as a prophylactic and preemptive modality leads to a favorable 5-year EFS. To safely deliver DLI in children, clinicians must maintain vigilant monitoring and prepare patients in advance when escalating the dose to ≥5 × 10 7 CD3 + cells/kg., Competing Interests: Conflicts of interest: The authors declare that they have no conflicts of interest related to the subject matter or materials discussed in this article., (Copyright © 2023, the Chinese Medical Association.)

Purine-containing nucleotide second messengers regulate diverse cellular activities. Cyclic di-pyrimidines mediate anti-phage functions in bacteria; however, the synthesis mechanism remains elusive. Here, we determine the high-resolution structures of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases (CD-NTases) in clade E (CdnE) in its apo, substrate-, and intermediate-bound states. A conserved (R/Q)xW motif controlling the pyrimidine specificity of donor nucleotide is identified. Mutation of Trp or Arg from the (R/Q)xW motif to Ala rewires its specificity to purine nucleotides, producing mixed purine-pyrimidine cyclic dinucleotides (CDNs). Preferential binding of uracil over cytosine bases explains the product specificity of cyclic di-pyrimidine-synthesizing CdnE to cyclic di-UMP (cUU). Based on the intermediate-bound structures, a synthetic pathway for cUU containing a unique 2'3'-phosphodiester linkage through intermediate pppU[3'-5']pU is deduced. Our results provide a framework for pyrimidine selection and establish the importance of conserved residues at the C-terminal loop for the specificity determination of CD-NTases., (© 2023. Springer Nature Limited.)

Secondary structures formed by expanded CUG RNA are involved in the pathobiology of myotonic dystrophy type 1. Understanding the molecular basis of toxic RNA structures can provide insights into the mechanism of disease pathogenesis and accelerate the drug discovery process. Here, we report the crystal structure of CUG repeat RNA containing three U-U mismatches between C-G and G-C base pairs. The CUG RNA crystallizes as an A-form duplex, with the first and third U-U mismatches adopting a water-mediated asymmetric mirror isoform geometry. We found for the first time that a symmetric, water-bridged U-H 2 O-U mismatch is well tolerated within the CUG RNA duplex, which was previously suspected but not observed. The new water-bridged U-U mismatch resulted in high base-pair opening and single-sided cross-strand stacking interactions, which in turn dominate the CUG RNA structure. Furthermore, we performed molecular dynamics simulations that complemented the structural findings and proposed that the first and third U-U mismatches are interchangeable conformations, while the central water-bridged U-U mismatch represents an intermediate state that modulates the RNA duplex conformation. Collectively, the new structural features provided in this work are important for understanding the recognition of U-U mismatches in CUG repeats by external ligands such as proteins or small molecules., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduction: Malignant germ cell tumors (MGCTs) can develop either extracranially or intracranially. Growing teratoma syndrome (GTS) may develop in these patients following chemotherapy. Reports on the clinical characteristics and outcomes of GTS in children with MGCTs are limited., Methods: We retrospectively collected the data, including the clinical characteristics and outcomes of five patients in our series and 93 pediatric patients selected through a literature review of MGCTs. This study aimed to analyze survival outcomes and risk factors for subsequent events in pediatric patients with MGCTs developing GTS., Results: The sex ratio was 1.09 (male/female). In total, 52 patients (53.1%) had intracranial MGCTs. Compared with patients with extracranial GCTs, those with intracranial GCTs were younger, predominantly boys, had shorter intervals between MGCT and GTS, and had GTS mostly occurring over the initial site (all p < 0.001). Ninety-five patients (96.9%) were alive. However, GTS recurrence (n = 14), GTS progression (n = 9), and MGCT recurrence (n = 19) caused a substantial decrease in event-free survival (EFS). Multivariate analyses showed that the only significant risk factors for these events were incomplete GTS resection and different locations of GCT and GTS. Patients without any risk had a 5-year EFS of 78.8% ± 7.8%, whereas those with either risk had 41.7% ± 10.2% (p < 0.001)., Conclusion: For patients with high-risk features, every effort should be made to closely monitor, completely remove, and pathologically prove any newly developed mass to guide relevant treatment. Further studies incorporating the risk factors into treatment strategies may be required to optimize adjuvant therapy., (© 2023 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.)

Under selective pressure, bacteria have evolved diverse defense systems against phage infections. The SMODS-associated and fused to various effector domains (SAVED)-domain containing proteins were identified as major downstream effectors in cyclic oligonucleotide-based antiphage signaling system (CBASS) for bacterial defense. Recent study structurally characterizes a cGAS/DncV-like nucleotidyltransferase (CD-NTase)-associated protein 4 from Acinetobacter baumannii (AbCap4) in complex with 2'3'3'-cyclic AMP-AMP-AMP (cAAA). However, the homologue Cap4 from Enterobacter cloacae (EcCap4) is activated by 3'3'3'-cyclic AMP-AMP-GMP (cAAG). To elucidate the ligand specificity of Cap4 proteins, we determined the crystal structures of full-length wild-type and K74A mutant of EcCap4 to 2.18 and 2.42 Å resolution, respectively. The DNA endonuclease domain of EcCap4 shares similar catalytic mechanism with type II restriction endonuclease. Mutating the key residue K74 in the conserved DX n (D/E)XK motif completely abolishes its DNA degradation activity. The potential ligand-binding cavity of EcCap4 SAVED domain is located adjacent to its N-terminal domain, significantly differing from the centrally located cavity of AbCap4 SAVED domain which recognizes cAAA. Based on structural and bioinformatic analysis, we found that Cap4 proteins can be classified into two types: the type I Cap4, like AbCap4, recognize cAAA and the type II Cap4, like EcCap4, bind cAAG. Several conserved residues identified at the surface of potential ligand-binding pocket of EcCap4 SAVED domain are confirmed by ITC experiment for their direct binding roles for cAAG. Changing Q351, T391 and R392 to alanine abolished the binding of cAAG by EcCap4 and significantly reduced the anti-phage ability of the E. cloacae CBASS system constituting EcCdnD (CD-NTase in clade D) and EcCap4. In summary, we revealed the molecular basis for specific cAAG recognition by the C-terminal SAVED domain of EcCap4 and demonstrates the structural differences for ligand discrimination among different SAVED-domain containing proteins., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Background: Successful weaning from mechanical ventilation is important for patients admitted to intensive care units. However, models for predicting real-time weaning outcomes remain inadequate. Therefore, this study aimed to develop a machine-learning model for predicting successful extubation only using time-series ventilator-derived parameters with good accuracy., Methods: Patients with mechanical ventilation admitted to the Yuanlin Christian Hospital in Taiwan between August 2015 and November 2020 were retrospectively included. A dataset with ventilator-derived parameters was obtained before extubation. Recursive feature elimination was applied to select the most important features. Machine-learning models of logistic regression, random forest (RF), and support vector machine were adopted to predict extubation outcomes. In addition, the synthetic minority oversampling technique (SMOTE) was employed to address the data imbalance problem. The area under the receiver operating characteristic (AUC), F1 score, and accuracy, along with the 10-fold cross-validation, were used to evaluate prediction performance., Results: In this study, 233 patients were included, of whom 28 (12.0%) failed extubation. The six ventilatory variables per 180 s dataset had optimal feature importance. RF exhibited better performance than the others, with an AUC value of 0.976 (95% confidence interval [CI], 0.975-0.976), accuracy of 94.0% (95% CI, 93.8-94.3%), and an F1 score of 95.8% (95% CI, 95.7-96.0%). The difference in performance between the RF and the original and SMOTE datasets was small., Conclusion: The RF model demonstrated a good performance in predicting successful extubation in mechanically ventilated patients. This algorithm made a precise real-time extubation outcome prediction for patients at different time points., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Huang, Hsu, Chen, Horng, Chung, Lin, Xu and Hou.)

Combination cancer chemotherapy is one of the most useful treatment methods to achieve a synergistic effect and reduce the toxicity of dosing with a single drug. Here, we use a combination of two well-established anticancer DNA intercalators, actinomycin D (ActD) and echinomycin (Echi), to screen their binding capabilities with DNA duplexes containing different mismatches embedded within Watson-Crick base-pairs. We have found that combining ActD and Echi preferentially stabilised thymine-related T:T mismatches. The enhanced stability of the DNA duplex-drug complexes is mainly due to the cooperative binding of the two drugs to the mismatch duplex, with many stacking interactions between the two different drug molecules. Since the repair of thymine-related mismatches is less efficient in mismatch repair (MMR)-deficient cancer cells, we have also demonstrated that the combination of ActD and Echi exhibits enhanced synergistic effects against MMR-deficient HCT116 cells and synergy is maintained in a MMR-related MLH1 gene knockdown in SW620 cells. We further accessed the clinical potential of the two-drug combination approach with a xenograft mouse model of a colorectal MMR-deficient cancer, which has resulted in a significant synergistic anti-tumour effect. The current study provides a novel approach for the development of combination chemotherapy for the treatment of cancers related to DNA-mismatches., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

This review highlights the unique techniques for patterning liquid metals containing gallium (e.g., eutectic gallium indium, EGaIn). These techniques are enabled by two unique attributes of these liquids relative to solid metals: 1) The fluidity of the metal allows it to be injected, sprayed, and generally dispensed. 2) The solid native oxide shell allows the metal to adhere to surfaces and be shaped in ways that would normally be prohibited due to surface tension. The ability to shape liquid metals into non-spherical structures such as wires, antennas, and electrodes can enable fluidic metallic conductors for stretchable electronics, soft robotics, e-skins, and wearables. The key properties of these metals with a focus on methods to pattern liquid metals into soft or stretchable devices are summari., (© 2023 The Authors. Advanced Materials published by Wiley-VCH GmbH.)

Background: Extensive knowledge of allergic multimorbidities is required to improve the management of allergic diseases with the industrialization of China. However, the demography and allergen distribution patterns of allergic multimorbidities in China remain unclear, despite the increasing prevalence of allergies., Methods: This was a real-world, cross-sectional study of 1273 outpatients diagnosed with one or more allergic diseases in Guangzhou, the most populated city of southern China, with leading industrial and commercial centers, between April 2021 and March 2022. Seven allergic diseases (allergic rhinitis (AR), asthma (AS)/cough variant asthma (CVA), atopic dermatitis (AD)/eczema, food allergy (FA), allergic conjunctivitis (AC), drug allergy (DA), and anaphylaxis) were assessed. Positive rates of sensitization to different allergens were measured using an allergen detection system of the UniCAP (Pharmacia Diagnostics, Sweden) instrument platform to compare the groups of allergic multimorbidities against a single entity., Results: There were 659 (51.8%) males and 614 (48.2%) females aged from 4 months to 74 years included in the analysis. The study participants who were diagnosed with allergic diseases had an average of 1.6 diagnoses. Overall, 46.5% (592 of 1273) of the patients had more than one allergic condition, and allergic rhinitis was the most common type of multimorbidity. Women were more likely to suffer from an allergic disease alone, whereas allergic multimorbidities were more likely to be diagnosed in men ( p = 0.005). In addition, allergic multimorbidities were common in all age groups, with an incidence ranging from 37.1% to 57.4%, in which children and adolescents were more frequently diagnosed with allergic multimorbidities than adults (18-60 years old) (all p < 0.05). Allergic multimorbidity was observed throughout the year. A difference in the positive rate of allergens sensitization and total immunoglobulin E (tIgE) levels between different allergic multimorbidities was observed., Conclusions: Allergic multimorbidities were very commonly found in nearly half of all patients with allergies. The proportion of allergic multimorbidities varied with the type of disease, sex, age, and allergen distribution pattern. These findings may help clinicians to develop "One health" strategies for the clinical management of allergic diseases.

Soft materials tend to be highly permeable to gases, making it difficult to create stretchable hermetic seals. With the integration of spacers, we demonstrate the use of liquid metals, which show both metallic and fluidic properties, as stretchable hermetic seals. Such soft seals are used in both a stretchable battery and a stretchable heat transfer system that involve volatile fluids, including water and organic fluids. The capacity retention of the battery was ~72.5% after 500 cycles, and the sealed heat transfer system showed an increased thermal conductivity of approximately 309 watts per meter-kelvin while strained and heated. Furthermore, with the incorporation of a signal transmission window, we demonstrated wireless communication through such seals. This work provides a route to create stretchable yet hermetic packaging design solutions for soft devices.

DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Coronavirus disease 2019 (COVID-19) is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several vaccines against SARS-CoV-2 have been approved; however, variants of concern (VOCs) can evade vaccine protection. Therefore, developing small compound drugs that directly block the interaction between the viral spike glycoprotein and ACE2 is urgently needed to provide a complementary or alternative treatment for COVID-19 patients. We developed a viral infection assay to screen a library of approximately 126 small molecules and showed that peimine inhibits VOCs viral infections. In addition, a fluorescence resonance energy transfer (FRET) assay showed that peimine suppresses the interaction of spike and ACE2. Molecular docking analysis revealed that peimine exhibits a higher binding affinity for variant spike proteins and is able to form hydrogen bonds with N501Y in the spike protein. These results suggest that peimine, a compound isolated from Fritillaria, may be a potent inhibitor of SARS-CoV-2 variant infection. PRACTICAL APPLICATIONS: In this study, we identified a naturally derived compound of peimine, a major bioactive alkaloid extracted from Fritillaria, that could inhibit SARS-CoV-2 variants of concern (VOCs) viral infection in 293T/ACE2 and Calu-3 lung cells. In addition, peimine blocks viral entry through interruption of spike and ACE2 interaction. Moreover, molecular docking analysis demonstrates that peimine has a higher binding affinity on N501Y in the spike protein. Furthermore, we found that Fritillaria significantly inhibits SARS-CoV-2 viral infection. These results suggested that peimine and Fritillaria could be a potential functional drug and food for COVID-19 patients., (© 2022 Wiley Periodicals LLC.)

Motivation: With the breakthrough of AlphaFold2, the protein structure prediction problem has made remarkable progress through deep learning end-to-end techniques, in which correct folds could be built for nearly all single-domain proteins. However, the full-chain modelling appears to be lower on average accuracy than that for the constituent domains and requires higher demand on computing hardware, indicating the performance of full-chain modelling still needs to be improved. In this study, we investigate whether the predicted accuracy of the full-chain model can be further improved by domain assembly assisted by deep learning., Results: In this article, we developed a structural analogue-based protein structure domain assembly method assisted by deep learning, named SADA. In SADA, a multi-domain protein structure database was constructed for the full-chain analogue detection using individual domain models. Starting from the initial model constructed from the analogue, the domain assembly simulation was performed to generate the full-chain model through a two-stage differential evolution algorithm guided by the energy function with an inter-residue distance potential predicted by deep learning. SADA was compared with the state-of-the-art domain assembly methods on 356 benchmark proteins, and the average TM-score of SADA models is 8.1% and 27.0% higher than that of DEMO and AIDA, respectively. We also assembled 293 human multi-domain proteins, where the average TM-score of the full-chain model after the assembly by SADA is 1.1% higher than that of the model by AlphaFold2. To conclude, we find that the domains often interact in the similar way in the quaternary orientations if the domains have similar tertiary structures. Furthermore, homologous templates and structural analogues are complementary for multi-domain protein full-chain modelling., Availability and Implementation: http://zhanglab-bioinf.com/SADA., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Various high-order orange beams (HOBs) at 588 nm are produced via off-center pumped Nd:YVO 4 /KGW Raman lasers. We experimentally confirm that the HOBs can be fairly sustained at the incident pump power of 2.88 W, where the average output powers are overall from 300 mW to 160 mW with increasing the off-center displacements from 0.14 mm to 0.21 mm. The HOBs are further transformed by using an astigmatic mode converter to generate a variety of structured lights with optical vortices. Moreover, theoretical wave functions are analytically derived to characterize the propagation evolution of the converted HOBs. The experimental patterns for all propagating positions are excellently reconstructed by the derived wave functions, and the evolution of phase structures is numerically calculated to manifest the robust optical vortices.

The use of multiple drugs simultaneously targeting DNA is a promising strategy in cancer therapy for potentially overcoming single drug resistance. In support of this concept, we report that a combination of actinomycin D (ActD) and echinomycin (Echi), can interact in novel ways with native and mismatched DNA sequences, distinct from the structural effects produced by either drug alone. Changes in the former with GpC and CpG steps separated by a A:G or G:A mismatch or in a native DNA with canonical G:C and C:G base pairs, result in significant asymmetric backbone twists through staggered intercalation and base pair modulations. A wobble or Watson-Crick base pair at the two drug-binding interfaces can result in a single-stranded 'chair-shaped' DNA duplex with a straight helical axis. However, a novel sugar-edged hydrogen bonding geometry in the G:A mismatch leads to a 'curved-shaped' duplex. Two non-canonical G:C Hoogsteen base pairings produce a sharply kinked duplex in different forms and a four-way junction-like superstructure, respectively. Therefore, single base pair modulations on the two drug-binding interfaces could significantly affect global DNA structure. These structures thus provide a rationale for atypical DNA recognition via multiple DNA intercalators and a structural basis for the drugs' potential synergetic use., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Hsu, Chen, Lin, Hong, Chen, Jeng, Luo and Hou.)

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely affected human lives around the world as well as the global economy. Therefore, effective treatments against COVID-19 are urgently needed. Here, we screened a library containing Food and Drug Administration (FDA)-approved compounds to identify drugs that could target the SARS-CoV-2 main protease (M pro ), which is indispensable for viral protein maturation and regard as an important therapeutic target. We identified antimalarial drug tafenoquine (TFQ), which is approved for radical cure of Plasmodium vivax and malaria prophylaxis, as a top candidate to inhibit M pro protease activity. The crystal structure of SARS-CoV-2 M pro in complex with TFQ revealed that TFQ noncovalently bound to and reshaped the substrate-binding pocket of M pro by altering the loop region (residues 139-144) near the catalytic Cys145, which could block the catalysis of its peptide substrates. We also found that TFQ inhibited human transmembrane protease serine 2 (TMPRSS2). Furthermore, one TFQ derivative, compound 7, showed a better therapeutic index than TFQ on TMPRSS2 and may therefore inhibit the infectibility of SARS-CoV-2, including that of several mutant variants. These results suggest new potential strategies to block infection of SARS-CoV-2 and rising variants., Competing Interests: Conflict of interest The authors declare that there is no conflict of interests with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Thoracic empyema is a disease with high mortality and morbidity. Video-assisted thoracoscopic surgery (VATS) is recommended to treat advanced stage empyema. The purpose of this study was to explore risk factors associated with post-surgery mortality for community-acquired empyema. Patients and Methods: We retrospectively reviewed 440 patients who received VATS for community-acquired empyema, higher than stage 2, in a tertiary medical center in Taiwan. Patients' age, comorbidities, pleural effusion analysis, and post-surgery outcome were compiled. Cox regression model for survival was applied to identify risk factors of 90-day death after surgery. Results: Fifty-three patients (12.05%) had died within 90 days post-surgery. The risk factors of mortality were advanced age (hazard ratio [HR], 1.027; 95% confidence interval [CI], 1.001-1.052), chronic kidney disease (HR, 5.322; 95% CI, 2.635-10.746), cancer (HR, 6.038; 95% CI, 2.737-13.321), pleural effusion pH ≤7 (HR, 2.61; 95% CI, 1.344-5.069), pleural effusion protein ≤4 (HR, 2.021; 95% CI, 1.035-3.947), and late surgery (HR, 3.014; 95% CI, 1.595-5.696). The 90-day mortality in the early surgery group versus the late group was 6.85% versus 26.05%. The increased mortality risk from late surgery was observed in most subgroups, except for patients who were female, had chronic renal disease, and had coronary artery disease. Conclusions: Patients who are elderly, have chronic kidney disease, cancer history, low pleural effusion pH, low pleural effusion protein, and late surgery are associated with post-surgery mortality for community-acquired advanced empyema. Early VATS surgery for advanced empyema or treatment failure of chest tube drainage appears to beneficial and is recommended.

Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes., (© 2022. The Author(s).)

Objective: To determine the clinical efficacy of linagliptin combined with irbesartan in patients with diabetic nephropathy (DN)., Methods: Seventy-two patients who were admitted to our department of endocrinology in our hospital during January 2018 and June 2019 were randomly divided into a control group (administered with irbesartan only, n=36) and a treatment group (treated with irbesartan and linagliptin, n=36). The course of treatment lasted for three months. FBG (fasting blood glucose), 2hPBG (2h postprandial blood sugar), HbA1C (hemoglobin A1c), Cys-C (cystatin C), SCr (serum creatinine), BUN (blood urea nitrogen), UACR (urine albumin-to-creatinine ratio), CRP (C-reactive protein), IL-6 (interleukin-6), and SOD (superoxide dismutase) were tested pre- and post-treatment to evaluate the clinical efficacy and adverse effects of the two treatment plans after three months of treatment., Results: Compared with the pre-treatment levels, FBG, 2hPBG, HbA1c, Cys-C, SCr, BUN, UACR, CRP, IL-6, and SOD in both groups were significantly improved following the three-month treatment (P<0.05, respectively). Post-treatment levels of FBG, 2hPBG, HbA1c, Cys-C, SCr, BUN, UACR, CRP, and IL-6 in the treatment group were significantly lower than in the control group (P<0.05, respectively), while the treatment group exhibited a higher level of SOD compared with the control group (P<0.05). No serious adverse reaction occurred in either group (P>0.05)., Conclusion: Combined-modality treatment with linagliptin and irbesartan shows favorable clinical efficacy in treating diabetic nephropathy as it effectively protects the kidneys and improves kidney function by inhibiting inflammatory and oxidative stress responses., Competing Interests: Conflicts of interest: None., (Copyright: © Pakistan Journal of Medical Sciences.)

In real-life applications, electroencephalogram (EEG) signals for mental stress recognition require a conventional wearable device. This, in turn, requires an efficient number of EEG channels and an optimal feature set. This study aims to identify an optimal feature subset that can discriminate mental stress states while enhancing the overall classification performance. We extracted multi-domain features within the time domain, frequency domain, time-frequency domain, and network connectivity features to form a prominent feature vector space for stress. We then proposed a hybrid feature selection (FS) method using minimum redundancy maximum relevance with particle swarm optimization and support vector machines (mRMR-PSO-SVM) to select the optimal feature subset. The performance of the proposed method is evaluated and verified using four datasets, namely EDMSS, DEAP, SEED, and EDPMSC. To further consolidate, the effectiveness of the proposed method is compared with that of the state-of-the-art metaheuristic methods. The proposed model significantly reduced the features vector space by an average of 70% compared with the state-of-the-art methods while significantly increasing overall detection performance.

The electroencephalogram (EEG) signal data were obtained from Yayasan Kita dan Buah Hati (YKBH), Jakarta, Indonesia and collected using a Brain Maker EEG machine with 19 channels. The sampling rate of the machine was 250 Hz. Fourteen participants (five females and nine males) participated in the data collection. A psychologist verified that seven of them were addicted to porn, and seven were healthy teenagers. The EEG data were recorded using one protocol with nine tasks for 10 min. The three stages were the baseline (tasks with eyes closed and open), emotional state (happy, calm, sad and fearful tasks) and main (15-words memorisation task, executive task and 15-words recall task) stages. The data obtained was used to analyse the signal pattern of pornography addiction amongst teenagers, as well as the emotional signal pattern and working memory capacity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships which could influence the work reported in this article.., (© 2021 The Authors. Published by Elsevier Inc.)

This work establishes that static contact angles for gallium-based liquid metals have no utility despite the continued and common use of such angles in the literature. In the presence of oxygen, these metals rapidly form a thin (∼1-3 nm) surface oxide "skin" that adheres to many surfaces and mechanically impedes its flow. This property is problematic for contact angle measurements, which presume the ability of liquids to flow freely to adopt shapes that minimize the interfacial energy. We show here that advancing angles for a metal are always high (>140°)-even on substrates to which it adheres-because the solid native oxide must rupture in tension to advance the contact line. The advancing angle for the metal depends subtly on the substrate surface chemistry but does not vary strongly with hydrophobicity of the substrate. During receding measurements, the metal droplet initially sags as the liquid withdraws from the "sac" formed by the skin and thus the contact area with the substrate initially increases despite its volumetric recession. The oxide pins at the perimeter of the deflated "sac" on all the surfaces are tested, except for certain rough surfaces. With additional withdrawal of the liquid metal, the pinned angle gets smaller until eventually the oxide "sac" collapses. Thus, static contact angles can be manipulated mechanically from 0° to >140° due to hysteresis and are therefore uninformative. We also provide recommendations and best practices for wetting experiments, which may find use in applications that use these alloys such as soft electronics, composites, and microfluidics.

Exposure to mental stress for long period leads to serious accidents and health problems. To avoid negative consequences on health and safety, it is very important to detect mental stress at its early stages, i.e., when it is still limited to acute or episodic stress. In this study, we developed an experimental protocol to induce two different levels of stress by utilizing a mental arithmetic task with time pressure and negative feedback as the stressors. We assessed the levels of stress on 22 healthy subjects using frontal electroencephalogram (EEG) signals, salivary alpha-amylase level (AAL), and multiple machine learning (ML) classifiers. The EEG signals were analyzed using a fusion of functional connectivity networks estimated by the Phase Locking Value (PLV) and temporal and spectral domain features. A total of 210 different features were extracted from all domains. Only the optimum multi-domain features were used for classification. We then quantified stress levels using statistical analysis and seven ML classifiers. Our result showed that the AAL level was significantly increased ( p < 0.01) under stress condition in all subjects. Likewise, the functional connectivity network demonstrated a significant decrease under stress, p < 0.05. Moreover, we achieved the highest stress classification accuracy of 93.2% using the Support Vector Machine (SVM) classifier. Other classifiers produced relatively similar results.

The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA-DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA-DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a 'hot-spot' for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Designing hybrid molecules with dual functions is one approach to improve the therapeutic efficacy of combination treatment. We have previously conjugated phthalazine and bis(hydroxymethyl)pyrrole pharmacophores to form hybrids bearing antiangiogenesis and DNA interstrand cross-linking activities. To improve the bioavailability, we adopted a benzology approach to design and synthesize a new series of 1,2-bis(hydroxymethyl)benzo[ g ]pyrrolo[2,1- a ]phthalazines. These new hybrids retained the dual functions and could be formulated into vehicles for intravenous and oral administration. Among them, we demonstrated that compound 19a with dimethylamine at the C6 position markedly suppressed the tumor growth of human small cell lung cancer cell line H526, squamous lung cancer cell line H520, and renal cancer cell line 786-O in nude mice, implying that compound 19a is a broad-spectrum anticancer agent. Our results implicated that the conjugation of antiangiogenic and DNA cross-linking is likely to be a helpful approach to improving the efficacy of combination therapy.

Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

To date, the COVID-19 pandemic has claimed over 1 million human lives, infected another 50 million individuals and wreaked havoc on the global economy. The crisis has spurred the ongoing development of drugs targeting its etiological agent, the SARS-CoV-2. Targeting relevant protein-protein interaction interfaces (PPIIs) is a viable paradigm for the design of antiviral drugs and enriches the targetable chemical space by providing alternative targets for drug discovery. In this review, we will provide a comprehensive overview of the theory, methods and applications of PPII-targeted drug development towards COVID-19 based on recent literature. We will also highlight novel developments, such as the successful use of non-native protein-protein interactions as targets for antiviral drug screening. We hope that this review may serve as an entry point for those interested in applying PPIIs towards COVID-19 drug discovery and speed up drug development against the pandemic., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

The cell surface protein TMPRSS2 (transmembrane protease serine 2) is an androgen-responsive serine protease important for prostate cancer progression and therefore an attractive therapeutic target. Besides its role in tumor biology, TMPRSS2 is also a key player in cellular entry by the SARS-CoV viruses. The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has resulted in huge losses in socio-economy, culture, and human lives for which safe and effective cures are highly demanded. The main protease (M pro /3CL pro ) of SARS-CoV-2 is a critical enzyme for viral propagation in host cells and, like TMPRSS2, has been exploited for treatment of the infectious disease. Numerous natural compounds abundant in common fruits have been suggested with anti-coronavirus infection in the previous outbreaks of SARS-CoV. Here we show that screening of these compounds identified tannic acid a potent inhibitor of both SARS-CoV-2 M pro and TMPRSS2. Molecular analysis demonstrated that tannic acid formed a thermodynamically stable complex with the two proteins at a K D of 1.1 mM for M pro and 1.77 mM for TMPRSS2. Tannic acid inhibited the activities of the two proteases with an IC 50 of 13.4 mM for M pro and 2.31 mM for TMPRSS2. M pro protein. Consistently, functional assays using the virus particles pseudotyped (Vpp) of SARS-CoV2-S demonstrated that tannic acid suppressed viral entry into cells. Thus, our results demonstrate that tannic acid has high potential of developing anti-COVID-19 therapeutics as a potent dual inhibitor of two independent enzymes essential for SARS-CoV-2 infection., Competing Interests: A provisional patent application has been submitted to the United States Patent and Trademark Office (63/106,938). Mien-Chie Hung, Yeh Chen, and Shao-Chun Wang are co-inventors., (AJCR Copyright © 2020.)

Hepatic fibrosis (HF) is a common complication of numerous chronic liver diseases, but predominantly results from persistent liver inflammation or injury. If left untreated, HF can progress and develop into liver cirrhosis and even hepatocellular carcinoma. However, the underlying molecular mechanisms of HF remain unknown. The present study aimed to investigate the role of 11β‑hydroxysteroid dehydrogenase‑1 (11β‑HSD1) during the development of hepatic fibrosis. An experimental rat model of liver fibrosis was induced using porcine serum. 11β‑HSD1 gene expression levels and enzyme activity during hepatic fibrogenesis were assessed. 11β‑HSD1 gene knockdown using small interfering RNA and overexpression were performed in LX2‑human hepatic stellate cells (HSCs). HSCs were stimulated with transforming growth factor‑β1 (TGF‑β1). Cell cycle distribution, proliferation, collagen secretion and 11β‑HSD1 gene activity in HSCs were compared before and after stimulation. As hepatic fibrosis progressed, 11β‑HSD1 gene expression and activity increased, indicating a positive correlation with typical markers of liver fibrosis. 11β‑HSD1 inhibition markedly reduced the degree of fibrosis. The cell proliferation was increased, the number of cells in the G0/G1 phase decreased and the number of cells in the S and G2/M phases increased in the pSuper transfected group compared with the N group. In addition, the overexpression of 11β‑HSD1 enhanced the TGF‑β1‑induced activation of LX2‑HSCs and enzyme activity of connective tissue growth factor. 11β‑HSD1 knockdown suppressed cell proliferation by blocking the G0/G1 phase of the cell cycle, which was associated with HSC stimulation and inhibition of 11β‑HSD1 enzyme activity. In conclusion, increased 11β‑HSD1 expression in the liver may be partially responsible for hepatic fibrogenesis, which is potentially associated with HSC activation and proliferation.