Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.

GANSamples-ac4C: Enhancing ac4C site prediction via generative adversarial networks and transfer learning

RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model. This study introduces GANSamples-ac4C, a novel framework that synergizes transfer learning and generative adversarial network (GAN) to generate synthetic RNA sequences to train a better ac4C modification site prediction model. Comparative analysis reveals that GANSamples-ac4C outperforms existing state-of-the-art methods in identifying ac4C sites. Moreover, our result underscores the potential of synthetic data in mitigating the issue of data scarcity for biological sequence prediction tasks. Another major advantage of GANSamples-ac4C is its interpretable decision logic. Multi-faceted interpretability analyses detect key regions in the ac4C sequences influencing the discriminating decision between positive and negative samples, a pronounced enrichment of G in this region, and ac4C-associated motifs. These findings may offer novel insights for ac4C research. The GANSamples-ac4C framework and its source code are publicly accessible at http://www.healthinformaticslab.org/supp/.

MMGAT: a graph attention network framework for ATAC-seq motifs finding

BACKGROUND

Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene regulation. Deep learning technologies including convolutional neural networks (CNNs) and graph neural networks (GNNs), have achieved success in finding ATAC-seq motifs. However, CNN-based methods are limited by the fixed width of the convolutional kernel, which makes it difficult to find multiple transcription factor binding sites with different lengths. GNN-based methods has the limitation of using the edge weight information directly, makes it difficult to aggregate the neighboring nodes' information more efficiently when representing node embedding.

RESULTS

To address this challenge, we developed a novel graph attention network framework named MMGAT, which employs an attention mechanism to adjust the attention coefficients among different nodes. And then MMGAT finds multiple ATAC-seq motifs based on the attention coefficients of sequence nodes and k-mer nodes as well as the coexisting probability of k-mers. Our approach achieved better performance on the human ATAC-seq datasets compared to existing tools, as evidenced the highest scores on the precision, recall, F1_score, ACC, AUC, and PRC metrics, as well as finding 389 higher quality motifs. To validate the performance of MMGAT in predicting TFBSs and finding motifs on more datasets, we enlarged the number of the human ATAC-seq datasets to 180 and newly integrated 80 mouse ATAC-seq datasets for multi-species experimental validation. Specifically on the mouse ATAC-seq dataset, MMGAT also achieved the highest scores on six metrics and found 356 higher-quality motifs. To facilitate researchers in utilizing MMGAT, we have also developed a user-friendly web server named MMGAT-S that hosts the MMGAT method and ATAC-seq motif finding results.

CONCLUSIONS

The advanced methodology MMGAT provides a robust tool for finding ATAC-seq motifs, and the comprehensive server MMGAT-S makes a significant contribution to genomics research. The open-source code of MMGAT can be found at https://github.com/xiaotianr/MMGAT , and MMGAT-S is freely available at https://www.mmgraphws.com/MMGAT-S/ .

Effect of ubiquinol on electrophysiology during high-altitude acclimatization and de-acclimatization: A substudy of the Shigatse CARdiorespiratory fitness (SCARF) randomized clinical trial

BACKGROUND

High-altitude exposure changes the electrical conduction of the heart. However, reports on electrocardiogram (ECG) characteristics and potent prophylactic agents during high-altitude acclimatization and de-acclimatization are inadequate. This study aimed to investigate the effects of ubiquinol on electrophysiology after high-altitude hypoxia and reoxygenation.

METHODS

The study was a prospective, randomized, double-blind, placebo-controlled trial. Forty-one participants were randomly divided into two groups receiving ubiquinol 200 mg daily or placebo orally 14 days before flying to high altitude (3900 m) until the end of the study. Cardiopulmonary exercise testing was performed at baseline (300 m), on the third day after reaching high altitude, and on the seventh day after returning to baseline.

RESULTS

Acute high-altitude exposure prolonged resting ventricular repolarization, represented by increased corrected QT interval (455.9 ± 23.4 vs. 427.1 ± 19.1 ms, P < 0.001) and corrected Tpeak-Tend interval (155.5 ± 27.4 vs. 125.3 ± 21.1 ms, P < 0.001), which recovered after returning to low altitude. Ubiquinol supplementation shortened the hypoxia-induced extended Tpeak-Tend interval (-7.7 ms, [95% confidence interval (CI), -13.8 to -1.6], P = 0.014), Tpeak-Tend /QT interval (-0.014 [95% CI, -0.027 to -0.002], P = 0.028), and reserved maximal heart rate (11.9 bpm [95% CI, 3.2 to 20.6], P = 0.013) during exercise at high altitude. Furthermore, the decreased resting amplitude of the ST-segment in the V3 lead was correlated with decreased peak oxygen pulse (R = 0.713, P < 0.001) and maximum oxygen consumption (R = 0.595, P < 0.001).

CONCLUSIONS

Our results illustrated the electrophysiology changes during high-altitude acclimatization and de-acclimatization. Similarly, ubiquinol supplementation shortened the prolonged Tpeak-Tend interval and reserved maximal heart rate during exercise at high altitude.

REGISTRATION

URL: www.chictr.org.cn; Unique identifier: ChiCTR2200059900.

Impact of guideline-directed medical therapy on systolic blood pressure and cardiovascular outcomes in patients with heart failure and low blood pressure: A systematic review and meta-analysis

AIMS

Existing research indicates that patients with heart failure (HF) may have restricted access to guideline-directed medical therapy (GDMT) when their blood pressure (BP) is comparatively low. However, recent clinical trials suggest that HF patients with low BP could still benefit from certain HF medications, which have a minimal impact on BP. This systematic review and meta-analysis was conducted to determine whether this applies to all GDMT.

METHODS AND RESULTS

A systematic search of MEDLINE and EMBASE was conducted for studies published from inception to 10 January 2024. Randomized controlled trials were selected if they reported on the longitudinal change of systolic BP (SBP) due to GDMT, or the risks of cardiovascular events in HF patients based on SBP categories. Weighted mean difference (WMD), hazard ratio or relative risk, and corresponding 95% confidence intervals (CI) were pooled for meta-analysis where possible. Data from 20 studies, encompassing information on 84 782 individuals, were analysed. Overall, GDMT is associated with lower SBP (WMD, -2.16; 95% CI -2.86 to -1.46), with no significant difference between baseline low and non-low BP subgroups (interaction p = 0.810). However, SBP of the treatment group increased by 5.8 mmHg from baseline in the low SBP subgroup during follow-up, while it decreased by 4.0 mmHg in the baseline non-low SBP subgroup. GDMT demonstrated similar cardiovascular benefits and risk of hypotension between low and non-low SBP subgroups (interaction p = 0.318 and 0.903, respectively).

CONCLUSIONS

Guideline-directed medical therapy is associated with a negligible decrease in SBP, but can provide similar cardiovascular benefits in both low and non-low SBP HF patients, with no significant interaction with SBP as to hypotension. Therefore, GDMT should be initiated and maintained in HF patients with low BP.

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of different variants of concerns with immune evasion that have been prevalent over the past three years. Nanobodies, the functional variable regions of camelid heavy-chain-only antibodies, have garnered interest in developing neutralizing antibodies due to their smaller size, structural stability, ease of production, high affinity, and low immunogenicity, among other characteristics. In this work, we describe an integrated proteomics platform for the high-throughput screening of nanobodies against different SARS-CoV-2 spike variants. To demonstrate this platform, we immunized a camel with subunit 1 (S1) of the wild-type spike protein and constructed a nanobody phage library. The binding and neutralizing activities of the nanobodies against 72 spike variants were then measured, resulting in the identification of two nanobodies (C-282 and C-39) with broad neutralizing activity against six non-Omicron variants (D614G, Alpha, Beta, Gamma, Delta, Kappa) and five Omicron variants (BA.1-5). Their neutralizing capability was validated using in vitro pseudovirus-based neutralization assays. All these results demonstrate the utility of our proteomics platform to identify new nanobodies with broad neutralizing capability and to develop a treatment for patients with SARS-CoV-2 variant infection in the future.

Mechanism of autocatalytic activation during proteasome assembly

Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the proteasome, where protein degradation occurs, its six active sites are simultaneously activated via cleavage of N-terminal propeptides. Such activation is autocatalytic and coupled to fusion of two half-CP intermediates, which protects cells by preventing activation until enclosure of the active sites within the CP interior. Here we uncover key mechanistic aspects of autocatalytic activation, which proceeds through alignment of the β5 and β2 catalytic triad residues, respectively, with these triads being misaligned before fusion. This mechanism contrasts with most other zymogens, in which catalytic centers are preformed. Our data also clarify the mechanism by which individual subunits can be added in a precise, temporally ordered manner. This work informs two decades-old mysteries in the proteasome field, with broader implications for protease biology and multisubunit complex assembly.

Triterpenoids from the Leaves of Diospyros digyna and Their PTP1B Inhibitory Activity

Six new 2α-hydroxy ursane triterpenoids, 3α-cis-p-coumaroyloxy-2α,19α-dihydroxy-12-ursen-28-oic acid (1), 3α-trans-p-coumaroyloxy-2α,19α-dihydroxy-12-ursen-28-oic acid (2), 3α-trans-p-coumaroyloxy-2α-hydroxy-12-ursen-28-oic acid (3), 3β-trans-p-coumaroyloxy-2α-hydroxy-12,20(30)-ursadien-28-oic acid (4), 3β-trans-feruloyloxy-2α-hydroxy-12,20(30)-ursadien-28-oic acid (5), and 3α-trans-feruloyloxy-2α-hydroxy-12,20(30)-ursadien-28-oic acid (6), along with eleven known triterpenoids (7-17), were isolated from the leaves of Diospyros digyna. Their chemical structures were elucidated by comprehensive analysis of UV, IR, HRESIMS, and NMR spectra. All the isolated compounds were evaluated for their PTP1B inhibitory activity. 3β-O-trans-feruloyl-2α-hydroxy-urs-12-en-28-oic acid (13) showed the best inhibition activity with an IC50 value of 10.32 ± 1.21 μM. The molecular docking study found that the binding affinity of compound 13 for PTP1B was comparable to that of oleanolic acid (positive control).

SUMOylation of annexin A6 retards cell migration and tumor growth by suppressing RHOU/AKT1-involved EMT in hepatocellular carcinoma

BACKGROUND

The protein annexin A6 (AnxA6) is involved in numerous membrane-related biological processes including cell migration and invasion by interacting with other proteins. The dysfunction of AnxA6, including protein expression abundance change and imbalance of post-translational modification, is tightly related to multiple cancers. Herein we focus on the biological function of AnxA6 SUMOylation in hepatocellular carcinoma (HCC) progression.

METHODS

The modification sites of AnxA6 SUMOylation were identified by LC-MS/MS and amino acid site mutation. AnxA6 expression was assessed by immunohistochemistry and immunofluorescence. HCC cells were induced into the epithelial-mesenchymal transition (EMT)-featured cells by 100 ng/mL 12-O-tetradecanoylphorbol-13-acetate exposure. The ability of cell migration was evaluated under AnxA6 overexpression by transwell assay. The SUMO1 modified AnxA6 proteins were enriched from total cellular proteins by immunoprecipitation with anti-SUMO1 antibody, then the SUMOylated AnxA6 was detected by Western blot using anti-AnxA6 antibody. The nude mouse xenograft and orthotopic hepatoma models were established to determine HCC growth and tumorigenicity in vivo. The HCC patient's overall survival versus AnxA6 expression level was evaluated by the Kaplan-Meier method.

RESULTS

Lys579 is a major SUMO1 modification site of AnxA6 in HCC cells, and SUMOylation protects AnxA6 from degradation via the ubiquitin-proteasome pathway. Compared to the wild-type AnxA6, its SUMO site mutant AnxA6K579R leads to disassociation of the binding of AnxA6 with RHOU, subsequently RHOU-mediated p-AKT1ser473 is upregulated to facilitate cell migration and EMT progression in HCC. Moreover, the SENP1 deSUMOylates AnxA6, and AnxA6 expression is negatively correlated with SENP1 protein expression level in HCC tissues, and a high gene expression ratio of ANXA6/SENP1 indicates a poor overall survival of patients.

CONCLUSIONS

AnxA6 deSUMOylation contributes to HCC progression and EMT phenotype, and the combination of AnxA6 and SENP1 is a better tumor biomarker for diagnosis of HCC grade malignancy and prognosis.

Research progress on the regulatory mechanism of integrin-mediated mechanical stress in cells involved in bone metabolism

Mechanical stress is an internal force between various parts of an object that resists external factors and effects that cause an object to deform, and mechanical stress is essential for various tissues that are constantly subjected to mechanical loads to function normally. Integrins are a class of transmembrane heterodimeric glycoprotein receptors that are important target proteins for the action of mechanical stress stimuli on cells and can convert extracellular physical and mechanical signals into intracellular bioelectrical signals, thereby regulating osteogenesis and osteolysis. Integrins play a bidirectional regulatory role in bone metabolism. In this paper, relevant literature published in recent years is reviewed and summarized. The characteristics of integrins and mechanical stress are introduced, as well as the mechanisms underlying responses of integrin to mechanical stress stimulation. The paper focuses on integrin-mediated mechanical stress in different cells involved in bone metabolism and its associated signalling mechanisms. The purpose of this review is to provide a theoretical basis for the application of integrin-mediated mechanical stress to the field of bone tissue repair and regeneration.

Animal models of hepatitis E infection: Advances and challenges

Hepatitis E virus (HEV) is one of the leading causes of acute viral hepatitis worldwide. Although most of HEV infections are asymptomatic, some patients will develop the symptoms, especially pregnant women, the elderly, and patients with preexisting liver diseases, who often experience anorexia, nausea, vomiting, malaise, abdominal pain, and jaundice. HEV infection may become chronic in immunosuppressed individuals. In addition, HEV infection can also cause several extrahepatic manifestations. HEV exists in a wide range of hosts in nature and can be transmitted across species. Hence, animals susceptible to HEV can be used as models. The establishment of animal models is of great significance for studying HEV transmission, clinical symptoms, extrahepatic manifestations, and therapeutic strategies, which will help us understand the pathogenesis, prevention, and treatment of hepatitis E. This review summarized the animal models of HEV, including pigs, monkeys, rabbits, mice, rats, and other animals. For each animal species, we provided a concise summary of the HEV genotypes that they can be infected with, the cross-species transmission pathways, as well as their role in studying extrahepatic manifestations, prevention, and treatment of HEV infection. The advantages and disadvantages of these animal models were also emphasized. This review offers new perspectives to enhance the current understanding of the research landscape surrounding HEV animal models.

[Retrospective analysis of perioperative anaphylactic shock induced by cefuroxime]

This study investigated the characteristics and frequency of perioperative anaphylactic shock induced by cefuroxime, so as to provide a reference for the safe and rational use of cefuroxime in the perioperative period. Cases of perioperative anaphylactic shock caused by cefuroxime in our hospital from 2011 to 2021 were extracted from the Adverse Drug Reaction Monitoring System. Literature reporting adverse drug reactions (ADR) including cefuroxime-induced anaphylactic shock in perioperative settings was collected from the CNKI, VIP, Wanfang, PubMed, and Web of Science databases from their respective inception to May 2022. Statistical analysis was performed for all cases of cefuroxime-induced perioperative anaphylactic shock. A total of 31 patients were included [13 men (48.1%) and 14 women (51.9%)], most of whom were over 60 years old (n=16, 59.3%); 9 (29.0%) patients had a history of drug allergy; 5 (16.1%) patients had received skin tests, but with negative results; 28 (90.3%) patients received treatment intravenously; 22 (71.0%) patients were treated after anesthesia. For 20 (64.5%) patients the ADR occurred within 10 minutes after anesthesia. The main manifestations were hypotension, dyspnea, rash, and tachycardia. For all patients, symptoms resolved after withdrawal of the drug and active rescue, and there were no deaths. A history of allergy and skin test findings may have limitations in predicting perioperative anaphylactic shock caused by cefuroxime; greater vigilance should be exercised when using cefuroxime in the perioperative period. Close monitoring is recommended for patients undergoing treatment with cefuroxime. Rescue therapy should be administered for allergic shock, and suitable response measures must be taken in a timely manner to ensure the safety of patients.

MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning

MOTIVATION

Predicting molecular properties is a pivotal task in various scientific domains, including drug discovery, material science, and computational chemistry. This problem is often hindered by the lack of annotated data and imbalanced class distributions, which pose significant challenges in developing accurate and robust predictive models.

RESULTS

This study tackles these issues by employing pretrained molecular models within a few-shot learning framework. A novel dynamic contrastive loss function is utilized to further improve model performance in the situation of class imbalance. The proposed MolFeSCue framework not only facilitates rapid generalization from minimal samples, but also employs a contrastive loss function to extract meaningful molecular representations from imbalanced datasets. Extensive evaluations and comparisons of MolFeSCue and state-of-the-art algorithms have been conducted on multiple benchmark datasets, and the experimental data demonstrate our algorithm's effectiveness in molecular representations and its broad applicability across various pretrained models. Our findings underscore MolFeSCues potential to accelerate advancements in drug discovery.

AVAILABILITY AND IMPLEMENTATION

We have made all the source code utilized in this study publicly accessible via GitHub at http://www.healthinformaticslab.org/supp/ or https://github.com/zhangruochi/MolFeSCue. The code (MolFeSCue-v1-00) is also available as the supplementary file of this paper.

What Factors Can Affect the Occurrence of Vertigo in Patients After Craniofacial Surgery in China?

Vertigo is a complication of craniomaxillofacial contour plastic surgery characterized by dizziness from hypovolemia in the cerebral hemispheres and brainstem. The authors analyzed the current status and influencing factors of postoperative vertigo in patients who undergo craniomaxillofacial contouring and discussed improvements in nursing strategies. The authors investigated 418 patients admitted to the authors' hospital who underwent craniomaxillofacial contouring between November 2020 and October 2023 and divided them into asymptomatic and symptomatic groups based on syncopal precursors or vertigo. The authors screened the current status of vertigo in patients after craniomaxillofacial contouring and the factors affecting vertigo and determined nursing improvement strategies. After craniomaxillofacial contouring, 125 patients had vertigo symptoms. Postcraniomaxillofacial contouring syncope or vertigo was associated with age, patient vertigo history, family history, depression, weight loss, blood pressure at admission, feeding before getting out of bed, and the level of intraoperative hemorrhage Multifactorial logistic regression analysis revealed the association between postcraniomaxillofacial contouring syncope or vertigo and vertigo history, depression, weight loss, feeding before getting out of bed, and intraoperative bleeding volume. Vertigo precursor incidence after craniomaxillofacial contouring surgery is 29.90%. Its influencing factors are complex, suggesting that nurses need to improve the perioperative health education of craniomaxillofacial contouring surgery and optimize the nursing care, encourage patients to have a reasonable diet or provide parenteral nutritional support preoperatively, help patients get out of bed early postoperatively, encourage them to have multiple meals in little quantity before getting out of bed, and control the intraoperative bleeding, to ensure patient safety postoperatively.

Mono-UFMylation promotes misfolding-associated secretion of α-synuclein

Stressed cells secret misfolded proteins lacking signaling sequence via an unconventional protein secretion (UcPS) pathway, but how misfolded proteins are targeted selectively in UcPS is unclear. Here, we report that misfolded UcPS clients are subject to modification by a ubiquitin-like protein named ubiquitin-fold modifier 1 (UFM1). Using α-synuclein (α-Syn) as a UcPS model, we show that mutating the UFMylation sites in α-Syn or genetic inhibition of the UFMylation system mitigates α-Syn secretion, whereas overexpression of UFBP1, a component of the endoplasmic reticulum-associated UFMylation ligase complex, augments α-Syn secretion in mammalian cells and in model organisms. UFM1 itself is cosecreted with α-Syn, and the serum UFM1 level correlates with that of α-Syn. Because UFM1 can be directly recognized by ubiquitin specific peptidase 19 (USP19), a previously established UcPS stimulator known to associate with several chaperoning activities, UFMylation might facilitate substrate engagement by USP19, allowing stringent and regulated selection of misfolded proteins for secretion and proteotoxic stress alleviation.

Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

BACKGROUND

The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.

RESULTS

The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.

CONCLUSIONS

Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Pyruvate kinase deficiency and PKLR gene mutations: Insights from molecular dynamics simulation analysis

Pyruvate kinase deficiency is a rare hereditary erythrocyte enzyme disease caused by mutations in the pyruvate kinase liver and red blood cell gene. The clinical presentations of pyruvate kinase deficiency are significantly heterogeneous, ranging from just mild anemia to hemolytic crisis or even death. The proband in our study was a 2-year-old girl for severe skin and scleral icterus with progressive aggravation. We collected the family's data for further analysis. Whole exome genome sequencing of the pedigree revealed a novel compound heterozygous mutation, c.1097del (p.P366Lfs*12) and c.1493G > A (p.R498H), in the pyruvate kinase liver and red blood cell gene. Furthermore, molecular dynamics simulations were employed to uncover differences between the wild type and mutant pyruvate kinase liver and red blood cell proteins, focusing on structural stability, protein flexibility, secondary structure, and overall conformation. The combined bioinformatic tools were also utilised to assess the effects of the missense mutation on protein function. Thereafter, wild type and mutant plasmids were constructed and transfected into 293T cells, and Western blot assay was conducted to validate the impact of the mutations on the expression of pyruvate kinase liver and red blood cell protein. The data presented in our study enriches the genotype database and provides evidence for genetic counseling and molecular diagnosis of pyruvate kinase deficiency.

Heterocyclic-Modified Imidazoquinoline Derivatives: Selective TLR7 Agonist Regulates Tumor Microenvironment against Melanoma

Immunotherapy targeting the toll-like receptor 7 (TLR7) is a promising strategy for cancer treatment. Herein, we describe the design and synthesis of a series of imidazoquinoline-based TLR7 agonists and assess NF-κB pathway activation using HEK-Blue hTLR7 cells to identify the most potent small-molecule TLR7 agonist, SMU-L11 (EC50 = 0.024 ± 0.002 μM). In vitro experiments demonstrated that SMU-L11 specifically activated TLR7, resulting in recruitment of the MyD88 adaptor protein and activation of the NF-κB and MAPK signaling pathways. Moreover, SMU-L11 was found to exert immune-enhancing effects by significantly inducing the secretion of proinflammatory cytokines in murine dendritic cells, macrophages, and human peripheral blood mononuclear cells while promoting M1 macrophage polarization. In vivo studies using a B16-F10 mouse tumor model showed that SMU-L11 significantly enhanced immune cell activation and augmented CD4+ T and CD8+ T-cell proliferation, directly killing tumor cells and inhibiting tumor growth.

Surfactant-like Additives Assisted the Lateral Growth of Pentacene Films

Lateral growth of thin films is crucial for organic electronic devices, such as field-effect transistors. Here, we report a strategy to improve the lateral growth of pentacene films using rubrene as a surfactant-like additive. Atomic force microscopy (AFM) images confirm the enhanced lateral growth with the presence of rubrene, resulting in smooth and enlarged molecule domains in the films in comparison to those without rubrene. Molecular dynamics simulations are conducted to explore the interlayer diffusion of pentacene molecules during the growth. With the rubrene molecules as surfactant-like additives, mean square displacement (MSD) analysis shows that the pentacene molecules have a descending diffusion coefficient of 2.0 × 10-5 cm2 s-1, which is greater than the ascending diffusion coefficient of 1.6 × 10-5 cm2 s-1. The more descending molecules lead to an enhanced lateral growth of pentacene films, which is in good agreement with the experiments. As a result, the pentacene films grown with rubrene exhibit a rapid increase in carrier mobility over thickness due to the well-connected domains resulting from enhanced lateral growth. This finding will provide a new strategy to modulate the morphology of organic films for high-performance devices.

Novel inhibitors targeting the PGK1 metabolic enzyme in glycolysis exhibit effective antitumor activity against kidney renal clear cell carcinoma in vitro and in vivo

Our previous research has revealed phosphoglycerate kinase 1 (PGK1) enhances tumorigenesis and sorafenib resistance of kidney renal clear cell carcinoma (KIRC) by regulating glycolysis, so that PGK1 is a promising drug target. Herein we performed structure-based virtual screening and series of anticancer pharmaceutical experiments in vitro and in vivo to identify novel small-molecule PGK1-targeted compounds. As results, the compounds CHR-6494 and Z57346765 were screened and confirmed to specifically bind to PGK1 and significantly reduced the metabolic enzyme activity of PGK1 in glycolysis, which inhibited KIRC cell proliferation in a dose-dependent manner. While CHR-6494 showed greater anti-KIRC efficacy and fewer side effects than Z57346765 on nude mouse xenograft model. Mechanistically, CHR-9464 impeded glycolysis by decreasing the metabolic enzyme activity of PGK1 and suppressed histone H3T3 phosphorylation to inhibit KIRC cell proliferation. Z57346765 induced expression changes of genes related to cell metabolism, DNA replication and cell cycle. Overall, we screened two novel PGK1 inhibitors, CHR-6494 and Z57346765, for the first time and discovered their potent anti-KIRC effects by suppressing PGK1 metabolic enzyme activity in glycolysis.

Teacher support in language learning: a picture of the effects on language progress, academic immunity, and academic enjoyment

Teacher support encompasses the provision of educational, instrumental, sentimental, or evaluative assistance by a teacher to a student, regardless of the setting. Learning a new language brings with it different ups and downs that may hinder the actual progress of the learners. The journey of learning may be made easier by supportive instructors. During the course of this inquiry, two groups (85 participants in total) including the experimental and control groups were chosen to gauge the influence of Teacher support in virtual instruction on English as a foreign language (EFL) learners' progress, academic immunity, and academic enjoyment. In contrast to the experimental group (EG, n = 42), which had the chance to connect with a teacher in order to ask questions and get feedback plus the off-line education, the control group (CG, n = 44) was subjected to off-line instruction of language input (Top Notch 3). The status of the participants' language growth, immunity, and enjoyment was investigated both before and after the treatment. The findings of independent samples t-tests as well as the multivariate analysis of variance (MANOVA) indicated that learners in EG did much better than their counterparts in CG. In addition, the ramifications and recommendations for potential future directions are analyzed.

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets

Transcriptome represents the expression levels of many genes in a sample and has been widely used in biological research and clinical practice. Researchers usually focused on transcriptomic biomarkers with differential representations between a phenotype group and a control group of samples. This study presented a multitask graph-attention network (GAT) learning framework to learn the complex inter-genic interactions of the reference samples. A demonstrative reference model was pre-trained on the healthy samples (HealthModel), which could be directly used to generate the model-based quantitative transcriptional regulation (mqTrans) view of the independent test transcriptomes. The generated mqTrans view of transcriptomes was demonstrated by prediction tasks and dark biomarker detection. The coined term "dark biomarker" stemmed from its definition that a dark biomarker showed differential representation in the mqTrans view but no differential expression in its original expression level. A dark biomarker was always overlooked in traditional biomarker detection studies due to the absence of differential expression. The source code and the manual of the pipeline HealthModelPipe can be downloaded from http://www.healthinformaticslab.org/supp/resources.php.

SLCO4A1, as a novel prognostic biomarker of non‑small cell lung cancer, promotes cell proliferation and migration

Solute carrier organic anion transporter family member 4A1 (SLCO4A1) is a membrane transporter protein. The role of this molecule in non‑small cell lung cancer (NSCLC) remains unclear. Bulk sequencing was carried out using early‑stage NSCLC tissues with lymph node metastasis to identify SLCO4A1 that influences NSCLC cell proliferation, metastasis and prognosis. The in vitro functional assays carried out included the following: Cell Counting Kit‑8, plate colony formation, Transwell and wound healing assays. The molecular techniques used included reverse transcription‑quantitative PCR, western blotting and immunohistochemistry. The present study revealed the role of SLCO4A in NSCLC. SLCO4A1 was found to be expressed at high levels in NSCLC tissues and cells, and promotes cell proliferation, migration and invasion. Kaplan‑Meier survival analysis indicated that patients with NSCLC and high expression of SLCO4A1 had a poor prognosis. SLCO4A was revealed to regulate the expression of the proliferation‑related proteins Ki‑67 and PCNA, and that of the extracellular matrix proteins vimentin and E‑cadherin. Mechanistically, SLCO4A1 may affect the MAPK signaling pathway to promote NSCLC cell proliferation, migration and invasion. In addition, bioinformatics analysis demonstrated a strong association between SLCO4A1 and tumor infiltrating immune cells, highlighting its critical role in immune therapies such as immune checkpoint inhibitor treatment of patients with NSCLC.

Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference-Advancing Biological and Pharmaceutical Mass Spectrometry

Following the highly successful Chinese American Society for Mass Spectrometry (CASMS) conferences in the previous 2 years, the 3rd CASMS Conference was held virtually on August 28-31, 2023, using the Gather.Town platform to bring together scientists in the MS field. The conference offered a 4-day agenda with a scientific program consisting of two plenary lectures, and 14 parallel symposia in which a total of 70 speakers presented technological innovations and their applications in proteomics and biological MS and metabo-lipidomics and pharmaceutical MS. In addition, 16 invited speakers/panelists presented at two research-focused and three career development workshops. Moreover, 86 posters, 12 lightning talks, 3 sponsored workshops, and 11 exhibitions were presented, from which 9 poster awards and 2 lightning talk awards were selected. Furthermore, the conference featured four young investigator awardees to highlight early-career achievements in MS from our society. The conference provided a unique scientific platform for young scientists (i.e. graduate students, postdocs, and junior faculty/investigators) to present their research, meet with prominent scientists, learn about career development, and job opportunities (http://casms.org).

Multi-Omics Analysis Reveals That Anthocyanin Degradation and Phytohormone Changes Regulate Red Color Fading in Rapeseed (Brassica napus L.) Petals

Flower color is an important trait for the ornamental value of colored rapeseed (Brassica napus L.), as the plant is becoming more popular. However, the color fading of red petals of rapeseed is a problem for its utilization. Unfortunately, the mechanism for the process of color fading in rapeseed is unknown. In the current study, a red flower line, Zhehuhong, was used as plant material to analyze the alterations in its morphological and physiological characteristics, including pigment and phytohormone content, 2 d before flowering (T1), at flowering (T2), and 2 d after flowering (T3). Further, metabolomics and transcriptomics analyses were also performed to reveal the molecular regulation of petal fading. The results show that epidermal cells changed from spherical and tightly arranged to totally collapsed from T1 to T3, according to both paraffin section and scanning electron microscope observation. The pH value and all pigment content except flavonoids decreased significantly during petal fading. The anthocyanin content was reduced by 60.3% at T3 compared to T1. The content of three phytohormones, 1-aminocyclopropanecarboxylic acid, melatonin, and salicylic acid, increased significantly by 2.2, 1.1, and 30.3 times, respectively, from T1 to T3. However, auxin, abscisic acid, and jasmonic acid content decreased from T1 to T3. The result of metabolomics analysis shows that the content of six detected anthocyanin components (cyanidin, peonidin, pelargonidin, delphinidin, petunidin, and malvidin) and their derivatives mainly exhibited a decreasing trend, which was in accordance with the trend of decreasing anthocyanin. Transcriptomics analysis showed downregulation of genes involved in flavonol, flavonoid, and anthocyanin biosynthesis. Furthermore, genes regulating anthocyanin biosynthesis were preferentially expressed at early stages, indicating that the degradation of anthocyanin is the main issue during color fading. The corresponding gene-encoding phytohormone biosynthesis and signaling, JASMONATE-ZIM-DOMAIN PROTEIN, was deactivated to repress anthocyanin biosynthesis, resulting in fading petal color. The results clearly suggest that anthocyanin degradation and phytohormone regulation play essential roles in petal color fading in rapeseed, which is a useful insight for the breeding of colored rapeseed.

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.

Comparing the Analgesic Effects Between the Pre- and Post-costal Cartilage Harvest Cohorts Using Ultrasound-Guided Deep Serratus Anterior Plane Block in Children with Microtia Undergoing Auricular Reconstruction: A Randomized Clinical Trial

PURPOSE

Pain following costal cartilage harvest surgery is the most common complaint of auricular reconstruction (AR). Anesthesiologists are continuously searching for an effective postoperative pain control method.

METHODS

This study was conducted from 10 April 2022 to 10 June 2022. Sixty children undergoing AR using costal cartilage were randomly assigned to either a serratus anterior plane block performed before costal cartilage harvest (SAPB-pre-cohort; n = 30) or the SAPB-post-cohort (Post-costal cartilage Harvest Cohort: n = 30). The primary endpoint measures were the Numerical Rating Scale (NRS) scores of the chest and ear pain degrees recorded at 1-, 6-, 12-, 24-, and 48-h after surgery. Intraoperative anesthetic and analgesic dosages, sufentanil consumption and rescue analgesia consumption during the first 24 h post-operation, cough score during extubation, extubation agitation score, length of stay, the extubation time, first ambulatory time, analgesia duration, and opioid-related adverse effects and SAPB-related adverse effects were the secondary endpoints.

RESULTS

The rest and coughing NRS scores were significantly reduced in the SAPB-pre-cohort 6 and 12 h post-operation in comparison with the SAPB-post-cohort (rest 6 h p = 0.002, others p < 0.001). No significant difference in the NRS ear scores existed between the two cohorts (p > 0.05). The use of propofol and remifentanil for general anesthesia during the SAPB-pre-procedure was significantly reduced compared to the SAPB-post-group, with statistical significance (p < 0.001). Sufentanil consumption and rescue analgesia consumption were significantly reduced in the SAPB-pre-cohort (p = 0.001, p = 0.033). The extubation time and first ambulatory time were markedly shorter in the SAPB-pre-cohort (all p < 0.001). Analgesia duration was markedly longer in the SAPB-pre-cohort (p < 0.001). No significant differences were noted in the cough score during extubation, extubation agitation score, length of stay between the two cohorts (all p > 0.05). Opioid-related adverse effects occurred more in the SAPB-post-cohort, while there was no statistical significance (16.7 vs. 36.7%; p = 0.082). There were no blockade-related complications observed in either cohort.

CONCLUSION

The analgesic effect of the SAPB-pre-cohort was better than the SAPB-post-cohort suggesting both efficacy and feasibility of preemptive analgesia.

LEVEL OF EVIDENCE II

This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Discovery of Unusual Ajmaline-Macroline Type Bisindole Alkaloids from Alstonia macrophylla by Building Blocks-Based Molecular Networking

Three unusual ajmaline-macroline type bisindole alkaloids, alsmaphylines A-C, together with their postulated biogenetic precursors, were isolated from the stem barks and leaves of Alstonia macrophylla via the building blocks-based molecular network (BBMN) strategy. Alsmaphyline A represents a rare ajmaline-macroline type bisindole alkaloid with an S-shape polycyclic ring system. Alsmaphylines B and C are two novel ajmaline-macroline type bisindole alkaloids with N-1-C-21' linkages, and the former possesses an unconventional stacked conformation due to the presence of intramolecular noncovalent interactions. The chemical structures including absolute configurations of alsmaphylines A-C were established by comprehensive spectroscopic analyses, electronic circular dichroism (ECD) calculations, and single-crystal X-ray crystallography. In addition, a plausible biosynthetic pathway of these bisindole alkaloids as well as their ability to promote the protein synthesis on HT22 cells were discussed.

[Construction of an evaluation index system for the capability of comprehensive control of mountain - type zoonotic visceral leishmaniasis based on the One Health concept]

OBJECTIVE

To construct an evaluation index system for the capability of comprehensive control of mountain-type zoonotic visceral leishmaniasis based on the One Health concept, so as to provide insights into the control and elimination of mountain-type zoonotic visceral leishmaniasis using the One Health approach.

METHODS

A preliminary evaluation index system was constructed based on literature review, panel discussions and field surveys. Thirty-three experts were selected from 7 provincial disease control and prevention centers in Beijing Municipality, Hebei Province, Shanxi Province, Henan Province, Sichuan Province, Shaanxi Province and Gansu Province where mountain-type zoonotic visceral leishmaniasis was endemic, and two rounds of expert consultations were conducted to screen the indicators. The positive coefficient, degree of concentration, degree of coordination, and authority of the experts were calculated, and the normalized weights of each index were calculated with the analytic hierarchy process.

RESULTS

The response rates of questionnaires during two rounds of expert consultation were both 100.00% (33/33), and the authority coefficients of the experts were 0.86 and 0.88, respectively. The coefficients of coordination among experts on the rationality, importance, and operability of the indicators were 0.392, 0.437, 0.258, and 0.364, 0.335, 0.263, respectively (all P values < 0.05). Following screening, the final evaluation index system included 3 primary indicators, 17 secondary indicators, and 50 tertiary indicators. The normalized weights of primary indicators "external environment", "internal support" and "comprehensive control" were 16.98%, 38.73% and 44.29%, respectively. Among the secondary indicators of the primary indicator "external environment", the highest weight was seen for natural environment (66.67%), and among the secondary indicators of the primary indicator "internal support", the lowest weight was seen for the scientific research for visceral leishmaniasis control (8.26%), while other indicators had weights of 12.42% to 13.38%. Among the secondary indicators of the primary indicator "comprehensive control", the weight was 16.67% for each indicator.

CONCLUSIONS

An evaluation index system has been constructed for the capability of comprehensive control of mountain-type zoonotic visceral leishmaniasis based on the One Health concept. In addition to assessment of the effect of conventional mountain-type zoonotic visceral leishmaniasis control measures, this index system integrates the importance of top-level design, organizational management, and implementation of control measures, and includes indicators related to multi-sectoral cooperation.

Prokaryotic Expression and Affinity Purification of DDX3 Protein

BACKGROUND

DDX3 is a protein with RNA helicase activity that is involved in a variety of biological processes, and it is an important protein target for the development of broad-spectrum antiviral drugs, multiple cancers and chronic inflammation.

OBJECTIVE

The objective of this study is to establish a simple and efficient method to express and purify DDX3 protein in E. coli, and the recombinant DDX3 should maintain helicase activity for further tailor-made screening and biochemical function validation.

METHODS

DDX3 cDNA was simultaneously cloned into pET28a-TEV and pNIC28-Bsa4 vectors and transfected into E. coli BL21 (DE3) to compare one suitable prokaryotic expression system. The 6×His-tag was fused to the C-terminus of DDX3 to form a His-tagging DDX3 fusion protein for subsequent purification. Protein dissolution buffer and purification washing conditions were optimized. The His-tagged DDX3 protein would bind with the Ni-NTA agarose by chelation and collected by affinity purification. The 6×His-tag fused with N-terminal DDX3 was eliminated from DDX3 by TEV digestion. A fine purification of DDX3 was performed by gel filtration chromatography.

RESULTS

The recombinant plasmid pNIC28-DDX3, which contained a 6×His-tag and one TEV cleavage site at the N terminal of DDX3 sequence, was constructed for DDX3 prokaryotic expression and affinity purification based on considering the good solubility of the recombinant His-tagging DDX3, especially under 0.5 mM IPTG incubation at 18 °C for 18 h to obtain more soluble DDX3 protein. Finally, the exogenous recombinant DDX3 protein was obtained with more than 95% purity by affinity purification on the Ni-NTA column and removal of miscellaneous through gel filtration chromatography. The finely-purified DDX3 still retained its ATPase activity.

CONCLUSION

A prokaryotic expression pNIC28-DDX3 system is constructed for efficient expression and affinity purification of bioactive DDX3 protein in E. coli BL21(DE3), which provides an important high-throughput screening and validation of drugs targeting DDX3.

The adsorption effects of biochar on carbofuran in water and the mixture toxicity of biochar-carbofuran in rats

Carbofuran, a widely used carbamate insecticide, is frequently detected in water. In this study, a high-performance adsorbent (WAB4) for carbofuran was obtained from laboratory-synthesized biochars. The maximum adsorption of carbofuran by WAB4 reaches 113.7 mg/g approximately. The adsorption of carbofuran by biochar was a multi-molecular layer and the adsorption process conforms to the pseudo-second-order kinetic model (R2 = 0.9984) and Freundlich isotherm model (R2 = 0.99). Importantly, an in vivo rat model was used to assess the combined toxicological effects of biochar-carbofuran complexes. The toxicity of the complexes (LD50 > 12 mg/kg) is lower than that of carbofuran (LD50 = 7.9 mg/kg) alone. The damage of biochar-carbofuran complex on rat liver and lung is significantly less than that of carbofuran. The Cmax and bioavailability of carbofuran were found to be reduced by 64% and 68%, respectively, when biochar was present, by UPLC-MS/MS analysis of carbofuran in rat plasma. Furthermore, it was confirmed that the biochar-carbofuran complex is relatively stable in the gastrointestinal tract, by performing a carbofuran release assay in artificial gastrointestinal fluids in vitro. Collectively, biochar is a bio-friendly material for the removal of carbofuran from water.

[Prevalence of taeniasis and sero - prevalence of anti - cysticercus antibody among residents in Tibetan agricultural areas of Sichuan Province]

OBJECTIVE

To investigate the prevalence and epidemiological characteristics of taeniasis and cysticercosis among residents in Tibetan agricultural areas of Sichuan Province, so as to provide insights for the prevention and control of taeniasis and cysticercosis.

METHODS

From 2016 to 2022, Kangding City, Daocheng County, Derong County, Ruoergai County and Muli Tibetan Autonomous County were sampled from Tibetan agricultural areas of Ganzi Tibetan Autonomous Prefecture, Aba Tibetan and Qiang Autonomous Prefecture and Liangshan Yi Autonomous Prefecture in Sichuan Province, and 1 to 6 townships were sampled from each county (district), followed by 4 to 7 villages sampled from each township. Primary school children were sampled using a cluster sampling method, and permanent residents at ages of over 16 years were randomly sampled from each village. Participants' demographics, history of tapeworm excretion during the past year and clinical symptoms and signs of cysticercosis were collected through questionnaire surveys, and participants' stool and venous blood samples were collected. Taenia eggs were detected in stool samples using the direct smear method, and deworming was performed among taeniasis patients with areca nut-squash seeds. The tapeworm species were identified using a multiplex PCR assay, and serum specific IgG antibody against cysticercus was detected using enzyme-linked immunosorbent assay (ELISA).

RESULTS

A total of 5 249 respondents participated in the questionnaire survey, including 603 respondents (11.5%) with a self-reported history of proglottids secretion during the past year. A total of 3 976 residents were subjected to stool examinations, and the detection of Taenia eggs was 6.5%. Of 258 participants undergoing deworming, there were 403 cases (94.2%) with excretions of Taenia worms or proglottids. The mean prevalence of taeniasis was 10.9% (439/4 043), and there were gender-, age- and region-specific prevalence rates of taeniasis (χ2 = 36.73, 126.31 and 163.41, all P values < 0.05). Multiplex PCR assays detected 41 cases with T. solium infections (12.5%), 197 cases with T. saginata infections (59.9%) and 91 cases with T. asiatica infections (27.6%) among 329 patients undergoing deworming, and there were region-specific prevalence rates of T. solium, T. saginata and T. asiatica infections (χ2 = 45.39, P < 0.05). In addition, the sero-prevalence of anti-cysticercus IgG antibody was 7.0% (345/4 933), and there were age- and region-specific sero-prevalence rates of anti-cysticercus IgG antibody (χ2 = 13.49 and 51.76, both P values < 0.05).

CONCLUSIONS

Multiple Taenia species are prevalent in Tibetan agricultural areas of Sichuan Province and the sero-prevalence of anti-cysticercus antibody is high among residents. Monitoring and control of taeniasis and cysticercosis should be strengthened.

Effect of norepinephrine, vasopressin, and dopamine for survivals of the elderly with sepsis and pre-existing heart failure

Our study focused on evaluating the effect of three common vasoactive drugs on the prognosis of elderly patients with sepsis and pre-existing heart failure. The Medical Information Mart for Intensive Care III database, Version 1.4, was used. Our study included critically ill older patients (aged ≥ 65 years) with sepsis and heart failure treated with vasoactive drugs. Patients were divided into norepinephrine group, norepinephrine combined with vasopressin group, and dopamine group. The baseline characteristics, primary outcome, and secondary outcome measures were compared among the three groups. In total, 1357 elderly patients were included (766 in norepinephrine group, 250 in norepinephrine combined with vasopressin group, and 341 in dopamine group). After propensity score matching, statistically significant differences in 28-d and 90-d mortality (P = 0.046, P = 0.031) were observed; meanwhile, there was a significant difference in the incidence of mechanical ventilation, AKI, and malignant arrhythmias. Cox regression analysis revealed that norepinephrine combined with vasopressin decreased 5-year survival statistically(P = 0.001). Multiple linear regression analysis indicated dopamine as an independent risk factor in reducing ICU and hospital length of stay (P = 0.001, P = 0.017). Logistic regression analysis showed dopamine was an independent risk factor for new-onset arrhythmias (P < 0.001), while norepinephrine combined with vasopressin was an independent risk factor for new-onset malignant arrhythmias (P < 0.001). Norepinephrine in combination with vasopressin decreased survival and increased the incidence of malignant arrhythmias in elderly sepsis patients with pre-existing heart failure. Dopamine alone reduces ICU and hospital length of stay but increases the new-onset arrhythmias.

Mitochondrial genome provides species-specific targets for the rapid detection of early invasive populations of Hylurgus ligniperda in China

BACKGROUND

Hylurgus ligniperda, a major international forestry quarantine pest, was recently found to have invaded and posed a serious threat to the Pinus forests of the Jiaodong Peninsula in China. Continuous monitoring and vigilance of the early population is imperative, and rapid molecular detection technology is urgently needed. We focused on developing a single-gene-based species-specific PCR (SS-PCR) method.

RESULTS

We sequenced and assembled the mitochondrial genome of H. ligniperda to identify suitable target genes. We identified three closely related species for detecting the specificity of SS-PCR through phylogenetic analysis based on 13 protein-coding genes (PCGs). Subsequently, we analyzed the evolution of 13 PCGs and selected four mitochondrial genes to represent slow-evolving gene (COI) and faster-evolving genes (e.g. ND2, ND4, and ND5), respectively. We developed four species-specific primers targeting COI, ND2, ND4, and ND5 to rapidly identify H. ligniperda. The results showed that the four species-specific primers exhibited excellent specificity and sensitivity in the PCR assays, with consistent performance across a broader range of species. This method demonstrates the ability to identify beetles promptly, even during their larval stage. The entire detection process can be completed within 2-3 h.

CONCLUSIONS

This method is suitable for large-scale species detection in laboratory settings. Moreover, the selection of target genes in the SS-PCR method is not affected by the evolutionary rate. SS-PCR can be widely implemented at port and forestry workstations, significantly enhancing early management strategies and quarantine measures against H. ligniperda. This approach will help prevent the spread of the pest and effectively preserve the resources of Chinese pine forests.

A Survey of Deep Learning for Detecting miRNA-Disease Associations: Databases, Computational Methods, Challenges, and Future Directions

MicroRNAs (miRNAs) are an important class of non-coding RNAs that play an essential role in the occurrence and development of various diseases. Identifying the potential miRNA-disease associations (MDAs) can be beneficial in understanding disease pathogenesis. Traditional laboratory experiments are expensive and time-consuming. Computational models have enabled systematic large-scale prediction of potential MDAs, greatly improving the research efficiency. With recent advances in deep learning, it has become an attractive and powerful technique for uncovering novel MDAs. Consequently, numerous MDA prediction methods based on deep learning have emerged. In this review, we first summarize publicly available databases related to miRNAs and diseases for MDA prediction. Next, we outline commonly used miRNA and disease similarity calculation and integration methods. Then, we comprehensively review the 48 existing deep learning-based MDA computation methods, categorizing them into classical deep learning and graph neural network-based techniques. Subsequently, we investigate the evaluation methods and metrics that are frequently used to assess MDA prediction performance. Finally, we discuss the performance trends of different computational methods, point out some problems in current research, and propose 9 potential future research directions. Data resources and recent advances in MDA prediction methods are summarized in the GitHub repository https://github.com/sheng-n/DL-miRNA-disease-association-methods.

[Exploring the factors affecting music-related quality of life in post-lingual deaf adults with cochlear implants]

Objective: To observe the feelings of listening to music and the importance of music in the daily life of post-lingual deaf adults with cochlear implants, and to explore the relevant influencing factors. Methods: This was a cross-sectional survey study. From January 2021 to August 2021,the Music-Related Quality of Life Scale was used to evaluate the music needs and music experiences of 63 post-lingual deaf adults who met the inclusion criteria, including 27 males and 36 females, aged (40.7±12.3) years, at the time of surgery (36.8±13.1) years, and with a preoperative hearing aid ineffective time of (3.9±5.8) years. Indicators analyzed included age, duration of ineffective preoperative hearing aid wear, preoperative music preference, duration of postoperative cochlear implant use, current hearing aid modality, and auditory rehabilitation outcomes. Whether the six factors mentioned above constituted an influence on the subjects' music listening was investigated using SPSS 25.0 statistical software. Results: All of the observations in the scale were correlated with a single factor. The two sub-dimensions of music experience section were related to the effect of auditory rehabilitation. In the importance section, the effect of auditory rehabilitation was the influential factor of the dimension of "participation importance", and the preoperative enjoyment of music was the relevant influential factor of the dimension of "perceived importance". There was a significant difference between the groups when they were grouped by the above factors (P value<0.05), while there was no statistically significance between the groups when they were grouped by other factors (P value>0.05). Conclusions: Post-lingual deaf adults show the need and attempt to listen to music after cochlear implantation. The effectiveness of auditory rehabilitation and the degree of music preference preoperatively are two important factors that influence music listening in implant recipients. Once the level of auditory communication has been restored to a certain degree, it is important to pay more attention to the needs of music for implant recipients and train them in time, especially for those with music preferences preoperatively.

2.5D transfer deep learning model for segmentation of contrast-enhancing lesions on brain magnetic resonance imaging of multiple sclerosis and neuromyelitis optica spectrum disorder

Background

Multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) are the two mimic autoimmune diseases of the central nervous system, which are rare in East Asia. Quantitative detection of contrast-enhancing lesions (CELs) on contrast-enhancing T1-weighted magnetic resonance (MR) images is of great significance for assessing the disease activity of MS and NMOSD. However, it is challenging to develop automatic segmentation algorithms due to the lack of data. In this work, we present an automatic segmentation model of CELs based on Fully Convolutional with Attention DenseNet (FCA-DenseNet) and transfer learning strategy to address the challenge of CEL quantification in small-scale datasets.

Methods

A transfer learning approach was employed in this study, whereby pretraining was conducted using 77 MS subjects from the open access datasets (MICCAI 2016, MICCAI 2017, ISBI 2015) for white matter hyperintensity segmentation, followed by fine-tuning using 24 MS and NMOSD subjects from the local dataset for CEL segmentation. The proposed FCA-DenseNet combined the Fully Convolutional DenseNet and Convolutional Block Attention Module in order to improve the learning capability. A 2.5D data slicing strategy was used to process complex 3D MR images. U-Net, ResUNet, TransUNet, and Attention-UNet are used as comparison models to FCA-DenseNet. Dice similarity coefficient (DSC), positive predictive value (PPV), true positive rate (TPR), and volume difference (VD) are used as evaluation metrics to evaluate the performances of different models.

Results

FCA-DenseNet outperforms all other models in terms of all evaluation metrics, with a DSC of 0.661±0.187, PPV of 0.719±0.201, TPR of 0.680±0.254, and VD of 0.388±0.334. Transfer learning strategy has achieved success in building segmentation models on a small-scale local dataset where traditional deep learning approaches fail to train effectively.

Conclusions

The improved FCA-DenseNet, combined with transfer learning strategy and 2.5D data slicing strategy, has successfully addressed the challenges in constructing deep learning models on small-scale datasets, making it conducive to clinical quantification of brain CELs and diagnosis of MS and NMOSD.

THE EFFECT OF CHILDHOOD SUBJECTIVE SOCIOECONOMIC STATUS ON MENTAL HEALTH: THE MEDIATING ROLES OF PERCEIVED DISCRIMINATION AND STATUS ANXIETY

This study explored the effect of childhood subjective socioeconomic status on mental health and the chain-mediating mechanism of perceived discrimination and status anxiety. A random survey was conducted via an online survey platform with 999 college students in east China. Participants completed the Childhood Subjective Socioeconomic Status Scale, General Health Questionnaire, Status Anxiety Scale, and the Perceived Personal Discrimination Scale. The sample comprised 323 men and 676 women. The mean age was 20.49±2.70 years. Mediation analysis using Model 6 and 5,000 bootstrap samples was employed to explore the mediating role of perceived discrimination and status anxiety in the relationship between childhood subjective socioeconomic status and mental health. Mental health was significantly positively correlated with childhood socioeconomic status, and significantly negatively correlated with perceived discrimination and status anxiety. Perceived discrimination and status anxiety played a partial chain mediating role between childhood socioeconomic status and mental health. The mediation model accounted for 31% of the variance in mental health. Moreover, the results indicated that the significant mediating effect of perceived discrimination between childhood subjective SES and mental health had a value of 0.029 and a 95% confidence interval of [0.019, 0.041]. Furthermore, the significant mediating effect of status anxiety between childhood subjective SES and mental health had a value of 0.010 and a 95% confidence interval of [0.006, 0.014]. The results provide an explanation of how childhood subjective socioeconomic status influences their mental health. Interventions to address perceived discrimination and status anxiety can improve the mental health status of children who experience childhood adversity. The study's findings contribute to understanding mental health in childhood and inform potential interventions to improve the well-being of individuals who have experienced childhood adversity. The limitations of the study were self-report scales and potential biases in the sample population. Addressing these limitations will enhance the credibility of the research and pave the way for future studies.

Knowledge domain and emerging trends in sacubitril/valsartan study from 2008 to 2023 - a visualized conclusive analysis based on novel scientometric tools

OBJECTIVE

This study aimed to determine the evolution of sacubitril-valsartan research and analyze the publications quantitatively and qualitatively.

MATERIALS AND METHODS

We used the bibliometric method and a combination of CiteSpace_6.1.6 and VOSviewer_1.6.18 to identify top authors, countries, institutions, co-cited articles, co-cited journals, keywords, and trends. This study prioritized key aspects in the existing global research on Entresto (Sacubitril/Valsartan) to assess our depth of knowledge in this field and identify potential insights. The objective was to generate a reference for the utilization of the "angiotensin receptor-neprilysin inhibitor" (ARNI).

RESULTS

From 2008 to 2022, citations of sacubitril-valsartan showed an upward trend. VOSviewer keyword analysis of 3,408 publications identified 624 keywords and divided them into seven different clusters. The clustered network was constructed based on 1,191 references cited by 3,408 publications that met the terms, where the clustered network of sacubitril-valsartan was presented. These publications can be regarded as fundamental to Entresto's research. Analysis of co-cited reference clusters showed that other than Entresto's novel application in other diseases, the new combination with other medication or mechanical assistance therapies against heart failure was Entresto's latest focus. Analysis of citation bursts showed that the rank of the top 25 keywords, according to the chronological sequence, marked Entresto's research entering a new era of exploring the extended application in other diseases and novel combinations with other diverse therapies.

CONCLUSIONS

We found that emerging new mechanisms in sacubitril-valsartan therapy intended for more targets in the pathogenesis of specific diseases will be the focus of further studies.

Metabolomics reveals that chronic restraint stress alleviates carbon tetrachloride-induced hepatic fibrosis through the INSR/PI3K/AKT/AMPK pathway

Hepatic fibrosis (HF) could be developed into liver cirrhosis or even hepatocellular carcinoma. Stress has an important role in the occurrence and development of various considerable diseases. However, the effect of a certain degree stress on HF is still controversial. In our study, stress was simulated with regular chronic restraint stress (CRS) and HF model was induced with CCl4 in mice. We found that CRS was able to attenuate CCl4-induced liver injury and fibrosis in mice. Surprisingly, behavioral analysis showed that the mice in the HF group exhibited depression-like behavior. Further, the metabolomic analysis revealed that 119 metabolites and 20 metabolic pathways were altered in mice liver, especially the betaine metabolism pathway. Combined with the results of Ingenuity Pathway Analysis (IPA), the key proteins INSR, PI3K, AKT, and p-AMPK were identified and verified, and the results showed that CRS could upregulate the protein levels and mRNA expression of INSR, PI3K, AKT, and p-AMPK in liver tissues of HF mice. It suggested that CRS alleviated CCl4-induced liver fibrosis in mice through upregulation of the INSR/PI3K/AKT/AMPK pathway. Proper stress might be a potential therapeutic strategy for the treatment of chronic liver disease, which provided new insights into the treatment of HF. KEY MESSAGES: Chronic restraint stress mitigated CCl4-induced liver injury and hepatic fibrosis. CCl4-induced liver fibrosis could cause depression-like behavior. Chronic restraint stress altered metabolomic profiles in hepatic fibrosis mice, especially the betaine metabolism pathway. Chronic restraint stress increased betaine levels in liver tissue. Chronic restraint stress regulated the INSR/PI3K/AKT/AMPK signaling pathway in hepatic fibrosis mice.

Netrin-1 inducing antiapoptotic effect of acute myeloid leukemia cells in a concentration-dependent manner through the Unc-5 netrin receptor B-focal adhesion kinase axis

Acute myeloid leukemia (AML) is a hematological malignancy that commonly occurs in children. The prognosis of pediatric AML is relatively poor, thus threatening the patient's survival. The aberrant expression of the axon guidance factor, netrin-1, is observed in various types of malignancies, and it participates in the proliferation and apoptosis of tumor cells. Herein, we aimed to explore the role of netrin-1 in AML cells. Netrin-1 is highly expressed in AML patients. Proliferation and anti-apoptosis were observed in AML cells treated with netrin-1. The interaction between netrin-1 and Unc-5 netrin receptor B (UNC5B) was detected through coimmunoprecipitation, and UNC5B ribonucleic acid interference restrained the influence of netrin-1 on the AML cells. The phosphorylation of focal adhesion kinase-protein kinase B (FAK-Akt) was upregulated in AML cells treated with netrin-1. Both FAK and Akt inhibitors abrogated the effects of netrin-1 on the proliferation and apoptosis of AML cells. In conclusion, netrin-1 could promote the growth and reduce the apoptosis of AML cells in a concentration-dependent manner, and that these effects were mediated by activating the FAK-Akt signaling pathway via the UNC5B.

ELM-KL-LSTM: a robust and general incremental learning method for efficient classification of time series data

Efficiently analyzing and classifying dynamically changing time series data remains a challenge. The main issue lies in the significant differences in feature distribution that occur between old and new datasets generated constantly due to varying degrees of concept drift, anomalous data, erroneous data, high noise, and other factors. Taking into account the need to balance accuracy and efficiency when the distribution of the dataset changes, we proposed a new robust, generalized incremental learning (IL) model ELM-KL-LSTM. Extreme learning machine (ELM) is used as a lightweight pre-processing model which is updated using the new designed evaluation metrics based on Kullback-Leibler (KL) divergence values to measure the difference in feature distribution within sliding windows. Finally, we implemented efficient processing and classification analysis of dynamically changing time series data based on ELM lightweight pre-processing model, model update strategy and long short-term memory networks (LSTM) classification model. We conducted extensive experiments and comparation analysis based on the proposed method and benchmark methods in several different real application scenarios. Experimental results show that, compared with the benchmark methods, the proposed method exhibits good robustness and generalization in a number of different real-world application scenarios, and can successfully perform model updates and efficient classification analysis of incremental data with varying degrees improvement of classification accuracy. This provides and extends a new means for efficient analysis of dynamically changing time-series data.

[Investigating ocular parameters for predicting anomalous vault among phakic intraocular lens patients]

Objective: To analyze the relationships between preoperative ocular parameters and postoperative anomalous vaults, and research their predictive diagnostic value. Methods: In this retrospective case series study, 664 eyes from 332 patients underwent posterior chamber phakic intraocular lens (pIOL) implantation at Shanghai Bright Eye Hospital and Wuxi Huaxia Eye Hospital from November 2020 to November 2021. Preoperative ocular parameters, including spherical equivalent, intraocular pressure, horizontal/vertical ciliary sulcus diameters (HCS/VCS), white-to-white diameters (WTW), corneal steep/flat curvature, central corneal thickness, anterior chamber depth (ACD), lens thickness (LT), and axial length were collected. The pIOL vaults were measured 3 months after surgery. Patients were categorized into low vault group, optimal vault group, and high vault group based on whether the vault fell within the ideal range (250 to 750 μm). Using the optimal vault group as a benchmark, receiver operating characteristic (ROC) curves were drawn for each ocular parameter of the low and high vault groups to analyze diagnostic efficiency and cut-off values for abnormal vaults after pIOL operation. Each ocular parameter was used as an independent variable to establish a multivariate logistic regression model for two different vault anomalies. ROC curves were drawn and analyzed again based on the regression results. Results: Statistically significant differences were observed in WTW, HCS-WTW, ACD, and LT among the three groups. Comparisons between each pair of groups indicated that WTW in the high vault group significantly differed from the other two groups (P<0.05), HCS-WTW in the low vault group significantly differed from the other groups (P<0.05), and ACD and LT explained statistical differences among the three groups (P<0.05), while other parameters showed no differences. ROC curves illustrated that independent ocular parameters such as LT, HCS-WTW, and ACD had clinical predictive diagnostic significance for low vault abnormalities. The area under the curve (AUC), sensitivity, and specificity for these parameters were 0.829(0.952, 0.561), 0.745(0.857, 0.644), and 0.730(0.619, 0.853), respectively. The diagnostic cut-off values were 3.745, 0.020, and 2.975 mm, respectively. The clinical predictive significance of independent ocular parameters in diagnosing the high vault group was poor (AUC<0.7). The predictive Logistic model equation for low vault was Logistic(V1)=-10.067+5.328·HCS-3.620·WTW+6.263·LT, and the predictive model for high vault was Logistic(V2)=6.232+1.323·WTW-3.358·LT. The new parameters in the predictive equation significantly improved the diagnostic efficiency of low and high vault abnormalities, reaching 0.884(0.810, 0.824) and 0.736(0.810, 0.554), respectively. Conclusions: Preoperative predictive diagnostic parameters for postoperative low vault group included LT, HCS-WTW, and ACD, while the high vault group had no independent predictive diagnostic parameters. Logistic regression improved the predictive diagnostic efficiency of abnormal vaults.

[From treatment to whole course management: envisioning comprehensive management of Talaromycosis marneffei]

Talaromycosis marneffei has been increasing in recent years. Our understanding of this disease has gradually deepened through extensive basic and clinical research, but there are still many limitations. In this article, by incorporating the latest research advancements, we discuss important issues in managing Talaromycosis marneffei trends, aiming to guide effective prevention and control of the disease, improving public health, and reducing the healthcare burden.

The Specific Copper(II) Chelator TDMQ20 Is Efficient for the Treatment of Wilson's Disease in Mice

(1) Background: In patients with Wilson's disease, the deficiency of the copper carrier ATP7B causes the accumulation of copper in the liver, brain and various other organs. Lifelong treatment is therefore mandatory, using copper chelators to increase the excretion of copper and to avoid life-threatening damage. The clinically used reference drug, D-penicillamine, exhibit numerous adverse effects, especially a frequent severe and irreversible neurological worsening, mainly due to its lack of metal selectivity; (2) Methods: A new tetradentate ligand based on an 8-aminoquinoline entity, named TDMQ20, which is highly selective for copper compared with other metal ions, is evaluated in "toxic milk" TX mice as an oral treatment of this Wilson's disease murine model; (3) Results: The concentration of copper in the liver of "toxic milk" TX mice decreased and the fecal excretion of copper increased upon oral treatment with TDMQ20. Both effects are dose-dependent, and more pronounced than those of D-penicillamine; (4) Conclusions: The TDMQ20 copper chelator is more efficient than the reference drug D-penicillamine for the treatment of a Wilson's disease murine model. Pharmacological data obtained with TDMQ20 on the TX mouse model strongly support the selection of this ligand as a drug candidate for this genetic disease.

One hundred single-copy nuclear sequence markers for olive variety identification: a case of fingerprinting database construction in China

Olive is an ancient oil-producing tree, widely cultivated in Mediterranean countries, and now spread to other areas of the world, including China. Recently, several molecular databases were constructed in different countries and platforms for olive identification using simple sequence repeats (SSRs) or single-nucleotide polymorphisms (SNPs). However, comparing their results across laboratories was difficult. Herein, hundreds of polymorphic single-copy nuclear sequence markers were developed from the olive genome. Using the advantage of multiplex PCR amplification and high-throughput sequencing, a fingerprint database was constructed for the majority of olives cultivated in China. We used 100 high-quality sequence loci and estimated the genetic diversity and structure among all these varieties. We found that compared with that based on SSRs, the constructed fingerprint database based on these 100 sequences or a few of them, could provide a reliable olive variety identification platform in China, with high discrimination among different varieties using the principle of BLAST algorithm. An example of such identification platform based on this study was displayed on the web for the olive database in China (http://olivedb.cn/jianding). After resolving redundant genotypes, we identified 126 olive varieties with distinct genotypes in China. These varieties could be divided into two clusters, and it was revealed that the grouping of the varieties has a certain relationship with their origin. Herein, it is concluded that these single-copy orthologous nuclear sequences could be used to construct a universal fingerprint database of olives across different laboratories and platforms inexpensively. Based on such a database, variety identification can be performed easily by any laboratory, which would further facilitate olive breeding and variety exchange globally.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01434-9.

Computational Characterization of Undifferentially Expressed Genes with Altered Transcription Regulation in Lung Cancer

A transcriptome profiles the expression levels of genes in cells and has accumulated a huge amount of public data. Most of the existing biomarker-related studies investigated the differential expression of individual transcriptomic features under the assumption of inter-feature independence. Many transcriptomic features without differential expression were ignored from the biomarker lists. This study proposed a computational analysis protocol (mqTrans) to analyze transcriptomes from the view of high-dimensional inter-feature correlations. The mqTrans protocol trained a regression model to predict the expression of an mRNA feature from those of the transcription factors (TFs). The difference between the predicted and real expression of an mRNA feature in a query sample was defined as the mqTrans feature. The new mqTrans view facilitated the detection of thirteen transcriptomic features with differentially expressed mqTrans features, but without differential expression in the original transcriptomic values in three independent datasets of lung cancer. These features were called dark biomarkers because they would have been ignored in a conventional differential analysis. The detailed discussion of one dark biomarker, GBP5, and additional validation experiments suggested that the overlapping long non-coding RNAs might have contributed to this interesting phenomenon. In summary, this study aimed to find undifferentially expressed genes with significantly changed mqTrans values in lung cancer. These genes were usually ignored in most biomarker detection studies of undifferential expression. However, their differentially expressed mqTrans values in three independent datasets suggested their strong associations with lung cancer.