Correction: Fundamental and practical approaches for single-cell ATAC-seq analysis.

[This corrects the article DOI: 10.1007/s42994-022-00082-5.].

The role and therapeutic potential of macrophages in the pathogenesis of diabetic cardiomyopathy.

This review provides a comprehensive analysis of the critical role played by macrophages and their underlying mechanisms in the progression of diabetic cardiomyopathy (DCM). It begins by discussing the origins and diverse subtypes of macrophages, elucidating their spatial distribution and modes of intercellular communication, thereby emphasizing their significance in the pathogenesis of DCM. The review then delves into the intricate relationship between macrophages and the onset of DCM, particularly focusing on the epigenetic regulatory mechanisms employed by macrophages in the context of DCM condition. Additionally, the review discusses various therapeutic strategies aimed at targeting macrophages to manage DCM. It specifically highlights the potential of natural food components in alleviating diabetic microvascular complications and examines the modulatory effects of existing hypoglycemic drugs on macrophage activity. These findings, summarized in this review, not only provide fresh insights into the role of macrophages in diabetic microvascular complications but also offer valuable guidance for future therapeutic research and interventions in this field.

Deciphering cell types by integrating scATAC-seq data with genome sequences.

The single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) technology provides insight into gene regulation and epigenetic heterogeneity at single-cell resolution, but cell annotation from scATAC-seq remains challenging due to high dimensionality and extreme sparsity within the data. Existing cell annotation methods mostly focus on the cell peak matrix without fully utilizing the underlying genomic sequence. Here we propose a method, SANGO, for accurate single-cell annotation by integrating genome sequences around the accessibility peaks within scATAC data. The genome sequences of peaks are encoded into low-dimensional embeddings, and then iteratively used to reconstruct the peak statistics of cells through a fully connected network. The learned weights are considered as regulatory modes to represent cells, and utilized to align the query cells and the annotated cells in the reference data through a graph transformer network for cell annotations. SANGO was demonstrated to consistently outperform competing methods on 55 paired scATAC-seq datasets across samples, platforms and tissues. SANGO was also shown to be able to detect unknown tumor cells through attention edge weights learned by the graph transformer. Moreover, from the annotated cells, we found cell-type-specific peaks that provide functional insights/biological signals through expression enrichment analysis, cis-regulatory chromatin interaction analysis and motif enrichment analysis.

Removal of multiple lipids from human plasma using a hydroxyl-functionalized covalent organic framework aerogel as a new sorbent.

A hydroxyl-functionalized covalent organic framework aerogel COFTHB-TAPB-aerogel was designed and prepared as an adsorbent for the removal of multiple lipids from human plasma. The applications of 1,3,5-tris(4'-hydroxy-5'-formylphenyl)benzene (THB) and 1,3,5-tris(4-aminophenyl)benzene (TAPB) as monomers, DMSO/mesitylene (v/v, 4/1) as reaction solvent, and n-propylamine as reaction regulator endow COFTHB-TAPB-aerogel with good adsorption performance for multiple lipids. The morphology, phase purity, specific surface area, pore size, surface charge, and stability of COFTHB-TAPB-aerogel were characterized. Adsorption thermodynamics and adsorption kinetics studies showed that COFTHB-TAPB-aerogel had high equilibrium adsorption capacities (> 15913 mg g-1) and fast adsorption equilibrium (≤ 10 s) for the four model lipids tested. COFTHB-TAPB-aerogel had good reusability with the removal of the model lipids being still more than 91% after 10 use cycles. The sample pretreatment conditions and adsorbent amounts used in lipids removal experiments were optimized. Under the optimized conditions, the method of ultra-high performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) using COFTHB-TAPB-aerogel as solid-phase extraction sorbent was validated with negligible matrix effects (0.4-3.0%) and good accuracy (86.7-110%) and was applied to determine  20 amino acids in human plasma samples from healthy individuals and gastric adenocarcinoma (GA) patients. The established method has been proved to have good application potential for the removal of multiple lipids in human plasma to reduce the matrix effects and improve the accuracy of clinical LC-MS analysis.

Effect of Alcaligenes sp. on corrosion behavior of X65 steel in simulated offshore oilfield-produced water.

In this paper, the effect of Alcaligenes sp. on the corrosion process of X65 steel was investigated by using non-targeted metabolomics techniques for comprehensive characterization of metabolites, combined with surface analysis techniques and electrochemical testing. The results showed that the organic acids produced by Alcaligenes sp. accelerated the corrosion process of X65 steel in the early stage, and the presence of Alcaligenes sp. promoted the deposition of stable corrosion products and minerals in the middle and late stages. In addition, proteoglycans and corrosion inhibiting substances were enriched on the metal surface, which enhanced the stability of the film. The combined effect of multiple factors makes the mixed film of biofilm and corrosion products more dense and complete, which effectively inhibits the corrosion of X65 steel.

Fundamental and practical approaches for single-cell ATAC-seq analysis.

Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

Overexpression of C9orf72 exacerbates Aß25­35­induced oxidative stress and apoptosis in PC12 cells.

Alzheimer's disease (AD) is the most common neurodegenerative disease and is manifested by memory loss and spatial disorientation. There is currently no effective treatment for AD. Abnormalities of the chromosome 9 open reading frame 72 (C9ORF72) gene have been associated with various neurodegenerative diseases. However, its intrinsic roles in AD remain to be elucidated. Here we found that Aß25­35 increased the expression of C9orf72 in PC12 cells at both mRNA and protein levels. In Aß25­35­treated PC12 cells, C9orf72 overexpression induced an abnormally condensed and fragmented nucleus and apoptosis, as well as significantly enhanced reactive oxygen species (ROS) levels. Mechanistically, an Aß25­35­induced decrease of superoxide dismutase activity was augmented by C9orf72 overexpression, which in contrast increased malondialdehyde content. Consistently, further apoptotic analysis revealed significant downregulation of Bcl­2 and Bcl­xL expression and enhanced cleavage of caspase­3 with Aß25­35 treatment, all of which were exacerbated by C9orf72 overexpression. In addition, tau phosphorylation, another hallmark of AD pathology, was induced by Aß25­35 and was remarkably enhanced by C9orf72 overexpression. Our data indicate that C9orf72 plays important roles in intracellular ROS signaling and Aß25­35­induced neuronal apoptosis in AD. These findings provide insights into C9orf72 function in the pathogenesis of many related neurodegenerative diseases and provide a basis for potential therapeutic interventions.

A novel functionalized covalent organic framework/carbon nanotube composite as an effective online solid-phase extraction sorbent for simultaneous detection of 33 steroid hormones in pork.

A novel functionalized covalent organic framework/carbon nanotube composite (CNT@COFTHB-TAPB) was synthesized by covalent bonding and exhibited large surface area, good crystallinity and chemical stability, and high adsorption capacity for steroid hormones. Therefore, online solid-phase extraction using CNT@COFTHB-TAPB as the adsorbent coupled with Q/Orbitrap mass spectrometer was applied to simultaneously detect 33 steroid hormones in pork samples. The characterization, chemical stability and adsorption capacity of the CNT@COFTHB-TAPB sorbent were investigated, and the effects of sorbent amount and extraction velocity on the online SPE efficiency were optimized. The low limits of quantitation were in the range of 0.02-0.30 µg kg-1, and the reliable recoveries were between 82.12% and 116.49%. Using the validated method, hydrocortisone and estriol in two samples were positively screened at trace levels. The established method was sensitive and efficient for simultaneous detection of multiclass steroid hormones in animal-derived food.

Ultrasonic Sputter Desorption Mass Spectrometry Technique for Minimally Invasive Tissue Analysis.

Minimally invasive techniques for in vivo tissue analysis are desired by life science and medical research. Herein, a new ionization interface coupled with ultrasonic sputter desorption (USD) was developed for in vitro and in vivo tissue analysis. Sample molecules were effectively sputtered out when the high-frequency ultrasonic probe touched the tissue. Then, the sputtered molecules were collected and ionized by a custom-made heated quartz tube and finally analyzed by mass spectrometry (MS) online. The sample pretreatment of the USD-MS technique was quite simple and required no other steps except for wetting the tissue surface with ethanol to assist molecular extraction. Experimental results demonstrated that the proposed method was suitable for the analysis of different morphologies of tissues (such as liver, brain, kidney, and lung) and performed well in the analysis of liver tumors and paracancerous tissues. Moreover, as the proposed method caused little damage to the tissues during analysis, rats and mice with orthotopic tumors still survived after the experiments. Overall, the newly developed USD-MS technique was an effective tool for minimally invasive tissue analysis and could be used as a new candidate method for in situ and real-time analysis of biological tissues in vitro and in vivo.

Study on the separation mechanism of solid-substrate electrospray ionization mass spectrometry.

Solid-substrate electrospray ionization mass spectrometry is an important ambient ionization technology to simplify mass spectrometry analysis. Nowadays, its separation application has been reported increasingly, however, the detailed separation mechanism is still indistinct although the chromatographic effect was reported as a possible factor. In this study, substrate-filled capillary electrospray ionization mass spectrometry was developed as an ideal model to investigate the separation mechanism using over thirty small molecules (neutral, basic, and weakly acidic) as model compounds with C18-bonded silica gel and silica gel as the substrates. The chromatographic effect was validated by the negative t-value of oil-water distribution coefficient, and the electric field effect was verified by the paired t-test (p < 0.01) between the retention times at 5.5 and 4.0 kV. A differential equation was proposed to quantify the compound retention under electric field. The quantitative method was validated to rapidly quantify proline (31.88 µg/mL) and hydroxyproline (20.71 µg/mL) in plasma with acceptable selectivity and accuracy. In conclusion, the separation mechanism of solid-substrate electrospray ionization mass spectrometry was the combination of the chromatographic and electric field effects, which could provide theoretical guidance for the separation optimization, and also promote its applications in biological, pharmaceutical, forensic, food and environmental analyses, etc.

Extensive screening of cyclopeptide toxins in mushrooms by ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap mass spectrometry.

A non-target screening method of cyclopeptide toxins and their analogues in mushroom was developed, using ultra-high-performance liquid chromatography coupled with quadrupole Orbitrap mass spectrometry (UHPLC-Q-Orbitrap MS) followed by mass spectrometry databases retrieval and software tools analysis for the candidate analogues. Three cyclopeptide toxins in the toxic mushroom Amanita rimosa were firstly screened without standard, and two of them were unknown analogues which were tentatively identified by the accurate masses, isotopic patterns and characteristic fragments. A validated quantitative method was performed to rapidly quantify three major cyclopeptide toxins in the Amanita rimosa sample including α-manitin, ß-amanitin and phalloidin, and their contents were detected to be 4.52 mg/kg, 2.37 mg/kg and 2.53 mg/kg, respectively. The developed method has good selectivity and sensitivity for rapid and comprehensive screening the cyclopeptide toxins and their analogues in mushrooms at trace levels. Successful non-target screening of trace cyclopeptide toxin analogues will guarantee the food safety in mushrooms consumption.

Topiramate for hypoxic ischemic encephalopathy: A systematic review protocol.

BACKGROUND: Hypoxic ischemic encephalopathy (HIE) is brain injury caused by different reasons and the most common diagnosed is neonatal HIE. Most of the existing treatments have their own shortcomings or there are still some unexplained mechanisms in it. Topiramate (TPM) is a new drug for the treatment for seizures in neonates with HIE, but is currently used off-label. Our protocol aims to access the efficiency and safety of TPM for HIE. METHODS AND ANALYSIS: Eight databases will be searched by 2 independent researchers for the article on the topic of using TPM as treatment for HIE, including PubMed, the Cochrane Central Register of Controlled Trials (Cochrane Library), Embase, and Web of Science, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), Wang Fang Database and Chinese Science and Technology Periodical database (VIP). The included papers are those published from the established date of the databases to 2019. The therapeutic effects based on the grade of neonatal behavioral neurological assessment will be regarded as the primary outcomes. RevMan V5.3 will be used to compute the data synthesis and carry out meta-analysis. The risk of bias will be appraised by the Cochrane risk of bias tool. Rare ratio for dichotomous outcomes and mean different for continuous data will be expressed with 95% confidence intervals (CI) for analysis. A random effects model or a fixed effects model will be employed, when heterogeneity is found or not. Subgroup analysis and sensitivity analysis will be applied if the heterogeneity is obvious. RESULTS: This study will provide the recent evidence of TPM for HIE from reducing seizure acticity. CONCLUSION: The conclusion of this study will provide proof to evaluate if TPM is effective and safe in the treatment of HIE.PROSPERO registration number: PROSPERO CRD42018117981.

High-sensitivity detection of therapeutic drugs in complex biofluids using a packed ballpoint-electrospray ionization technique.

A simple and sensitive C18 packed ballpoint-electrospray ionization (PBP-ESI) technique was developed for biofluid analysis. In this technique, the configuration of a commercial ballpoint consisting of a hollow chamber, an intermediate socket, and a metal ball was fully exploited. The rear-end hollow chamber was used for loading C18 adsorbent and sample, and the front metal ball served as a spray emitter for online ionization. The good electrical conductivity of the metal body allowed high voltage to be conveniently applied to the ballpoint without inserting the electrode into the solution for electrical connection. Urine sample was directly analyzed with the C18 packed ballpoint; plasma and whole blood samples were premixed with C18 adsorbent before being packed into the ballpoint for detection. As a result of the sample cleanup by C18 adsorbent, the salt matrix in the urine sample as well as the phospholipid and protein matrices in plasma and whole blood samples was significantly reduced. The lower limits of quantitation (LLOQs) for urine, plasma, and whole blood samples reached the subnanogram-per-milliliter level. Graphical abstract.

Guizhi Gancao Longgu Muli decoction for insomnia: A protocol for a systematic review.

BACKGROUND: Insomnia is a prevalent and bothersome disorder of sleep initiation and maintenance. Although efficacious treatments for insomnia have been available for decades, they all have their own limitations. Guizhi Gancao Longgu Muli Decoction (GGLMD), a popular complementary and alternative therapy, has been widely applied to treat insomnia in some Asian countries for centuries. Yet no systematic reviews have comprehensively assessed the efficacy and safety of GGLMD as a treatment for insomnia. METHODS: A comprehensive search up to November, 2019 will be conducted in the following electronic databases: the Cochrane Library, Embase, PubMed, Web of Science, the Chinese National Knowledge Infrastructure (CNKI), the Chinese Biomedical Literature Database (CBM), the Chinese Scientific Journal Database (VIP), and the Wanfang Database. The primary outcomes will be sleep quality including Pittsburgh Sleep Quality Index (PSQI) and polysomnography (PSG). Stata 15 will be used for data analysis as well. RESULTS: This study will provide the current evidence of insomnia treated with GGLMD from the several points including PSQI and PSG. CONCLUSION: The consequence of this summary will furnish proof to evaluate if GGLMD is effective in the treatment of insomnia. ETHICS AND DISSEMINATION: Without personal information involved, ethical approval and informed consent form is no need. The review will be submitted to a peer-reviewed journal prospectively to spread our findings. PROSPERO REGISTRATION NUMBER: PROSPERO CRD42018118336.

Taohong Siwu decoction for femoral head necrosis: A protocol for systematic review.

BACKGROUNDS: Femoral head necrosis is one of the most common orthopedic diseases which can be diagnosed in all ages with different reasons. Taohong Siwu decoction (TSD) has been widely used in the treatment of femoral head necrosis. However, as far as we know, there is still a lack of supporting evidence regarding the efficacy of TSD for femoral head necrosis. Therefore, this protocol aims to evaluate the effectiveness and safety of TSD for femoral head necrosis. METHODS: Eight electronic databases, including PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, Web of Science, Chinese Biomedical Literature Database, China National Knowledge Infrastructure, Technology Periodical database, (Chinese Scientific Journal Database) and Wanfang Database will be searched from the time when the respective databases were established to January 2020. Randomized controlled trials of TSD in the treatment of femoral head necrosis will be collected. After evaluating the quality of methodology and extracting valid data, the final meta-analysis will be carried out with software Revman 5.3. ETHICS AND DISSEMINATION: The results of this systematic review will offer implications of the use of TSD treatment for Femoral Head Necrosis. It uses aggregated published data instead of individual patient data and does not require an ethical board review and approval. The findings will be published in a peer-reviewed journal and disseminated in conference presentations. RESULTS: The results of this study will offer implications of the use of TSD treatment for FHN with this meta-analysis. CONCLUSION: The conclusion of this study will provide recent evidence to assess whether TSD is effective and safe in the treatment of FHN.

Efficacy and safety of grain moxibustion in hemiplegia: A systematic review and meta-analysis protocol.

BACKGROUND: The increasing morbidity of stroke brings enormous social and economic pressure to the countries. Hemiplegia is the common sequela of stroke patients, which affects their physical activities and daily life, and its optimal treatment is still an urgent problem. In Asian countries, moxibustion therapy is widely combined with rehabilitation in poststroke hemiplegia. Among them, grain moxibustion, due to its concentration on stimulating the acupoints and deep heat penetration, can promote neurorehabilitation after stroke. Therefore, based on the current literatures, the effectiveness and safety of grain moxibustion were systematically evaluated to provide possible alternative therapy for the rehabilitation of hemiplegia. METHODS: Studies search for eligible randomized controlled trials (RCTs) that use grain moxibustion as the sole treatment for hemiplegia and their data extraction will be done by two researchers. Mean difference (MD) or relative risk (RR) with fixed or random effect model in terms of 95% confidence interval (CI) will be adopted for the data synthesis. To evaluate the risk of bias, the Cochrane's risk of bias assessment tool will be utilized. The sensitivity or subgroup analysis will also be conducted when meeting high heterogeneity (I > 50%). RESULTS: This meta-analysis will provide an authentic synthesis of the grain moxibustion's effect for hemiplegia. CONCLUSION: The findings of the review offer updated evidence and identify whether grain moxibustion can be an effective treatment for hemiplegia. PROSPERO REGISTRATION NUMBER: PROSPERO CRD 42018117765.

Early application of citicoline in the treatment of acute stroke: A meta-analysis of randomized controlled trials.

This study was to evaluate the efficacy and safety of early application of citicoline in the treatment of patients with acute stroke by meta-analysis. Randomized controlled trials published until May 2015 were electronically searched in MEDLINE, Embase, the Cochrane Central Register of Controlled Trials, WHO International Clinical Trial Registration Platform, Clinical Trial.gov, and China Biology Medicine disc. Two reviewers independently screened the articles and extracted the data based on the inclusion and exclusion criteria. The quality of included articles was evaluated by using Revman5.0, and meta-analysis was performed. The results showed that 1027 articles were obtained in initial retrieval, and finally 7 articles, involving a total of 4039 cases, were included for analysis. The meta-analysis showed that no significant differences were found in the long-term mortality (OR=0.91, 95% CI 0.07 to 1.09, P=0.30), the rate of dependency (OR=1.02, 95% CI 0.87 to 1.24, P=0.85), and the effective rate (OR=0.98, 95% CI 0.84 to 1.14, P=0.82) between citicoline group and control group. The overall rate of adverse events in citicoline group was not significantly different from that in control group (P=0.30). The quality of included articles reached moderate-low level. In conclusion, citicolne cannot reduce long-term mortality and dependence rate in the treatment of acute stroke, and the effective rate of citivoline may be not better than that of controls but with reliable safety.

Tofacitinib for acute rheumatoid arthritis patients who have had an inadequate response to disease-modifying antirheumatic drug (DMARD): a systematic review and meta-analysis.

The aim of this systematic review and meta-analysis is to assess the efficacy and safety of tofacitinib for the treatment of patients with acute rheumatoid arthritis (RA) who have had an inadequate response to disease-modifying antirheumatic drug (DMARD). Randomized controlled trials were searched in MEDLINE (1966-2013), Embase (1947-2013), the Cochrane Central Register of Controlled Trials (1948-2013), WHO International Clinical Trial Registration Platform (2004-2013), Clinical Trial.gov (1999-2013), and China Biology Medicine disc (1978-2013). The review included 10 studies involving 4,929 patients. A pooled analysis of six studies showed that tofacitinib had a superior effect over placebo (both with background therapy) at weeks 12 and 24. Also, the pooled results of three studies showed that tofacitinib monotherapy had a significantly greater effect over placebo. Compared to adalimumab, tofacitinib was found to be more efficacious as well. For safety, tofacitinib monotherapy had less serious adverse events (sAE) than placebo but not other adverse effects (oAE). In the comparison of tofacitinib and placebo both with background therapy, no difference in sAE and oAE were found. However, the quality of the evidence was quite low when evaluated using GRADE. Tofacitinib alone, or together with non-biologic DMARDs, was associated with more favorable remission in the signs and symptoms of RA than adalimumab or placebo. Also, tofacitinib monotherapy was safer than placebo with regards to reported sAE, but not oAE. However, the quality of evidence is exceedingly low; long-term, large-scale, and high-quality post-marketing research is suggested to further verify the conclusion.