AntDAS-GCMS: A New Comprehensive Data Analysis Platform for GC-MS-Based Untargeted Metabolomics with the Advantage of Addressing the Time Shift Problem.

Over the years, a number of state-of-the-art data analysis tools have been developed to provide a comprehensive analysis of data collected from gas chromatography-mass spectrometry (GC-MS). Unfortunately, the time shift problem remains unsolved in these tools. Here, we developed a novel comprehensive data analysis strategy for GC-MS-based untargeted metabolomics (AntDAS-GCMS) to perform total ion chromatogram peak detection, peak resolution, time shift correction, component registration, statistical analysis, and compound identification. Time shift correction was specifically optimized in this work. The information on mass spectra and elution profiles of compounds was used to search for inherent landmarks within analyzed samples to resolve the time shift problem across samples efficiently and accurately. The performance of our AntDAS-GCMS was comprehensively investigated by using four complex GC-MS data sets with various types of time shift problems. Meanwhile, AntDAS-GCMS was compared with advanced GC-MS data analysis tools and classic time shift correction methods. Results indicated that AntDAS-GCMS could achieve the best performance compared to the other methods.

AntDAS-DDA: A New Platform for Data-Dependent Acquisition Mode-Based Untargeted Metabolomic Profiling Analysis with Advantage of Recognizing Insource Fragment Ions to Improve Compound Identification.

Data-dependent acquisition (DDA) mode in ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) can provide massive amounts of MS1 and MS/MS information of compounds in untargeted metabolomics and can thus facilitate compound identification greatly. In this work, we developed a new platform called AntDAS-DDA for the automatic processing of UHPLC-HRMS data sets acquired under the DDA mode. Several algorithms, including extracted ion chromatogram extraction, feature extraction, MS/MS spectrum construction, fragment ion identification, and MS1 spectrum construction, were developed within the platform. The performance of AntDAS-DDA was investigated comprehensively with a mixture of standard and complex plant data sets. Results suggested that features in complex sample matrices can be extracted effectively, and the constructed MS1 and MS/MS spectra can benefit in compound identification greatly. The efficiency of compound identification can be improved by about 20%. AntDAS-DDA can take full advantage of MS/MS information in multiple sample analyses and provide more MS/MS spectra than single sample analysis. A comparison with advanced data analysis tools indicated that AntDAS-DDA may be used as an alternative for routine UHPLC-HRMS-based untargeted metabolomics. AntDAS-DDA is freely available at http://www.pmdb.org.cn/antdasdda.

Health-related quality of life questionnaires used in primary biliary cholangitis: a systematic review.

OBJECTIVE: The purpose of this systematic review was to assess the suitability of health-related quality of life (HRQOL) questionnaires in patients with primary biliary cholangitis. METHODS: Relevant studies were compiled from a search of five electronic databases. The properties under investigation included the validity of the translated questionnaires, floor and ceiling effects, internal consistency and test-retest reliability. RESULTS: Forty-four studies were included, from which fifteen HRQOL questionnaires were identified. The most frequently used instruments were the PBC-40 (n = 22), the SF-36 (n = 19), the PBC-27 (n = 4), the CLDQ (n = 3) and the NIDDK-QA (n = 2). The remaining instruments were used only once. Twenty-six studies used a translated HRQOL questionnaire, but only six reported or referenced validating the translated questionnaire. CONCLUSIONS: PBC-specific HRQOL questionnaires generally have good psychometric properties. However, many studies have directly applied HRQOL tools without verifying their validity and reliability in PBC patients. There was no clear indication that one HRQOL tool was superior to another, although the PBC-40 is the most well-studied. Thus, more robust psychometric studies are needed to investigate the measurement properties of HRQOL questionnaires.

[Research progress on common pesticide residues in Chinese medicinal materials].

Chinese medicinal materials are the precious resources of China and favored by patients at home and abroad because of their natural sources and curative effects. Pesticides are often used to prevent and control diseases and insect pests and regulate the growth of Chinese medicinal plants, so as to improve the yield and quality of Chinese medicinal materials. Most of the pesticides can play a role in pest control through systemic action, stomach toxicity, contact, fumigation and other ways, especially the systemic pesticides can kill hidden pests by entering the Chinese medicinal plants. Despite the good pest control effect, it is difficult to remove the systemic pesticides by simple cleaning, which poses a great risk to the safety of Chinese medicinal materials. At the same time, excessive or non-standard use of pesticides leads to serious pesticide residues in Chinese medicinal materials, which affects not only the quality and efficacy of the materials and harm human health but also the international development of Chinese medicinal materials industry. Pesticide residues have become a bottleneck affecting the industry development and hindering the export of Chinese medicinal materials. Therefore, it is of great significance to study how to quickly, sensitively, and accurately detect and remove pesticide residues in Chinese medicinal materials. We reviewed the common pesticide residues in Chinese medicinal materials in recent years in terms of characteristics, harm, and detection and removal techniques, and discussed the future development of the detection and removal deve-lopment. With this review, we aimed to provide a reference for the quality control of Chinese medicinal materials and promote the healthy development of Chinese medicine industry.

Iodination/Amidation of the N-Alkyl (Iso)quinolinium Salts.

The NaIO4-mediated sequential iodination/amidation reaction of N-alkyl quinolinium iodide salts has been first developed. This cascade process provides an efficient way to rapidly synthesize 3-iodo-N-alkyl quinolinones with high regioselectivity and good functional group tolerance. This protocol was also amenable to the isoquinolinium salts, thus providing a complementary method for preparing the 4-iodo-N-alkyl isoquinolinones.

Palladium-Catalyzed Direct Arylation of Alkylpyridine via Activated N-Methylpyridinium Salts.

An efficient Pd-catalyzed arylation of alkylpyridine based on the pyridinium activation strategy has been developed for synthesis of mixed aryl alkylpyridines. It was found that (1) the N-methyl group in the pyridinium salts acted as a transient activator and could be automatically departed after the reaction, (2) CuBr was an indispensable additive for achieving the C6-selective arylation, (3) the α-branched alkyl chain on the alkylpyridine greatly increased the yield of the product. Deuterium labelling experiment revealed that in the case of the α-branched alkylpyridine, the presence of CuBr completely inhibited the H/D exchange at the benzylic position and thus enabled the selective arylation at the C6 position. This protocol demonstrates a broad substrate scope, and with respect to both the aryl iodides and the α-branched alkylpyridine, the desired mixed aryl alkylpyridines were obtained in generally good to excellent yields.

Differentiating Westlake Longjing tea from the first- and second-grade producing regions using ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry-based untargeted metabolomics in combination with chemometrics.

There are numerous articles published for geographical discrimination of tea. However, few research works focused on the authentication and traceability of Westlake Longjing green tea from the first- and second-grade producing regions because the tea trees are planted in a limited growing zone with identical cultivate condition. In this work, a comprehensive analytical strategy was proposed by ultrahigh performance liquid chromatography-quadrupole time-of-flight mass spectrometry-based untargeted metabolomics coupled with chemometrics. The automatic untargeted data analysis strategy was introduced to screen metabolites that expressed significantly among different regions. Chromatographic features of metabolites can be automatically and efficiently extracted and registered. Meanwhile, those that were valuable for geographical origin discrimination were screened based on statistical analysis and contents in samples. Metabolite identification was performed based on high-resolution mass values and tandem mass spectra of screened peaks. Twenty metabolites were identified, based on which the two-way encoding partial least squares discrimination analysis was built for geographical origin prediction. Monte Caro simulation results indicated that prediction accuracy was up to 99%. Our strategy can be applicable for practical applications in the quality control of Westlake Longjing green tea.

Kupffer Cells Regulate Natural Killer Cells Via the NK group 2, Member D (NKG2D)/Retinoic Acid Early Inducible-1 (RAE-1) Interaction and Cytokines in a Primary Biliary Cholangitis Mouse Model.

BACKGROUND Kupffer cells and natural killer (NK) cells has been identified as contributing factors in the pathogenesis of hepatitis, but the detailed mechanism of these cell types in the pathogenesis of primary biliary cholangitis (PBC) is poorly understood. MATERIAL AND METHODS In this study, polyinosinic: polycytidylic acid (poly I: C), 2-octynoic acid-bovine serum albumin (2OA-BSA) and Freund's adjuvant (FA) were injected to establish a murine PBC model, from which NK cells and Kupffer cells were extracted and isolated. The cells were then co-cultivated in a designed culture system, and then NK group 2, member D (NKG2D), retinoic acid early inducible-1 (RAE-1), F4/80, and cytokine expression levels were detected. RESULTS The results showed close crosstalk between Kupffer cells and NK cells. PBC mice showed increased surface RAE-1 protein expression and Kupffer cell cytokine secretion, which subsequently activated NK cell-mediated target cell killing via NKG2D/RAE-1 recognition, and increased inflammation. NK cell-derived interferon-γ (IFN-γ) and Kupffer cell-derived tumor necrosis factor alpha (TNF-alpha) were found to synergistically regulate inflammation. Moreover, interleukin (IL)-12 and IL-10 improved the crosstalk between NK cells and Kupffer cells. CONCLUSIONS Our findings in mice are the first to suggest the involvement of the NKG2D/RAE-1 interaction and cytokines in the synergistic effects of NK and Kupffer cells in PBC.

Automatic scratch detector for optical surface.

Scratches on the surface of optical components have serious impacts on optical system such as imaging quality of lens and/or mirrors in optical imaging systems, light-collecting abilities of laser fusion and solar concentrator systems. The size of the scratches is a key issue for analyzing and assessing the impacts quantitatively. Most of the available testing methods for scratches depend on human visual inspection (HVI) with naked eyes by workers, which leads to low efficiency and accuracy. This paper presents an automatic detecting method for the scratches on optical surface with machine vision inspection (MVI) method. The microscopic dark-field scattering imaging system is used as the front end of the detection system. A dedicated algorithm is designed for non-closing scratch detection. The core merits of this algorithm lies in three folds: 1) automatic processing capabilities, which includes positioning, clustering, and precise estimation of the length of the scratches; 2) high efficiency, which is characterized by a short time interval, i.e., about 0.138 second per binary image with 2724 × 2724 pixels in our experiments; 3) high accuracy, where the error rate of the total length of the scratches detected is less than 5% when compared with the nominal visual measurement result obtained via HVI method. The proposed scratch detecting algorithm can be used for non-destructive testing (NDT) of the glass-like surfaces.

Dehydrogenation of Alcohols to Carboxylic Acid Catalyzed by in Situ-Generated Facial Ruthenium-CPP Complex.

A selective catalytic system for the dehydrogenation of primary alcohols to carboxylic acids using a facial ruthenium complex generated in situ from the [Ru(COD)Cl2]n and a hybrid N-heterocyclic carbene (NHC)-phosphine-phosphine ligand (CPP) has been first reported. The facial coordination model was unveiled by NMR analysis of the reaction mixture. Such a fac-ruthenium catalyst system exhibited high catalytic activity and stability, and a high turnover number of 20 000 could be achieved with catalyst loading as low as 0.002 mol %. The exceedingly high catalyst stability was tentatively attributed to both the anchoring role of NHC and the hemi-lability of phosphines. The catalytic system also features a wide substrate scope. In particular, the facial coordination of CPP ligands was found to be beneficial for sterically hindered alcohols, and ortho-substituted benzylic alcohols and bulky adamantanyl methanol as well as cholesterol were all found to be viable dehydrogenation substrates.

Iridium-Catalyzed Alkylation of Amine and Nitrobenzene with Alcohol to Tertiary Amine under Base- and Solvent-Free Conditions.

Herein, an efficient and green method for the selective synthesis of tertiary amines has been developed that involves iridium-catalyzed alkylation of various primary amines with aromatic or aliphatic alcohols. Notably, the catalytic protocol enables this transformation in the absence of additional base and solvent. Furthermore, the alkylation of nitrobenzene with primary alcohol to tertiary amine has also been achieved by the same catalytic system. Deuterium-labeling experiments and a series of control experiments were conducted, and the results suggested that an intermolecular borrowing hydrogen pathway might exist in the alkylation process.

Prenylated Indole Diterpene Alkaloids from a Mine-Soil-Derived Tolypocladium sp.

Ten new prenylated indole diterpene alkaloids, tolypocladin A-J (1-10), including four chlorinated metabolites, have been isolated from a culture of a mine-soil-derived fungus, Tolypocladium sp. XL115. The structures and absolute configurations of 1-10 were determined by spectroscopic analysis, ECD calculations, and comparison with known compounds. Compounds 1 and 8 displayed significant antimicrobial activities. In addition, compound 1 also showed weak cytotoxic activity against all tested human cancer cell lines and suppressed the growth and viability of the patient-derived HCC cells T1224.

[Value of serum gamma-glutamyl transpeptidase combined with direct bilirubin in the diagnosis of biliary atresia in infants].

OBJECTIVE: To study the value of serum gamma-glutamyl transpeptidase (GGT) combined with direct bilirubin (DB) in the diagnosis of biliary atresia. METHODS: A total of 667 infants with cholestasis who were hospitalized and treated from July 2010 to December 2018 were enrolled as subjects. According to the results of intraoperative cholangiography and follow-up, they were divided into biliary atresia group with 234 infants and cholestasis group with 433 infants. The two groups were compared in terms of age of onset, sex, and serum levels of total bilirubin (TB), DB, alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bile acid (TBA), and GGT. A receiver operating characteristic (ROC) curve analysis was performed for indices with statistical significance, and the area under the ROC curve (AUC) and the optimal cut-off value for diagnosis were calculated. RESULTS: The biliary atresia group had a significantly younger age of onset than the cholestasis group (P<0.001). There were no significant differences in sex, ALT, and AST between the two groups (P>0.05), while the biliary atresia group had significantly higher serum levels of TB, DB, TBA, and GGT than the cholestasis group (P<0.05). GGT combined with DB had the highest AUC of 0.892 (95% confidence interval: 0.868-0.916) in the diagnosis of biliary atresia. At the optimal cut-off values of 324.0 U/L for GGT and 115.1 µmmol/L for DB, GGT combined with DB had a sensitivity of 79.8% and a specificity of 83.2% in the diagnosis of biliary atresia. CONCLUSIONS: GGT combined with DB has high sensitivity and specificity in the diagnosis of biliary atresia and can be used as an effective indicator for diagnosis of biliary atresia in infants.

Palladium-Catalyzed Domino Reaction for Stereoselective Synthesis of Multisubstituted Olefins: Construction of Blue Luminogens.

The first Pd-catalyzed multicomponent reaction of aryl iodides, alkenyl bromides, and strained alkenes has been developed, which allowed us to synthesize a variety of multisubsituted olefins in yields of 45-96% with excellent stereoselectivity. The configuration of the product was controlled by the configuration of the alkenyl bromides. Moreover, this practical methodology employing readily available substrates was found to be tolerant to a wide range of functional groups. Fifty six examples of highly stereoselective tri- or tetrasubstituted olefins have been successfully synthesized via this methodology. Most of the synthesized tetrasubstituted olefins are good aggregation-induced emission (AIE) luminogens.

Nrf2 inhibition affects cell cycle progression during early mouse embryo development.

Brusatol, a quassinoid isolated from the fruit of Bruceajavanica, has recently been shown to inhibit nuclear factor erythroid 2-related factor 2 (Nrf2) via Keap1-dependent ubiquitination and proteasomal degradation or protein synthesis. Nrf2 is a transcription factor that regulates the cellular defense response. Most studies have focused on the effects of Nrf2 in tumor development. Here, the critical roles of Nrf2 in mouse early embryonic development were investigated. We found that brusatol treatment at the zygotic stage prevented the early embryo development. Most embryos stayed at the two-cell stage after 5 days of culture (P < 0.05). This effect was associated with the cell cycle arrest, as the mRNA level of CDK1 and cyclin B decreased at the two-cell stage after brusatol treatment. The embryo development potency was partially rescued by the injection of Nrf2 CRISPR activation plasmid. Thus, brusatol inhibited early embryo development by affecting Nrf2-related cell cycle transition from G2 to M phase that is dependent on cyclin B-CDK1 complex.

AntDAS: Automatic Data Analysis Strategy for UPLC-QTOF-Based Nontargeted Metabolic Profiling Analysis.

High-quality data analysis methodology remains a bottleneck for metabolic profiling analysis based on ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry. The present work aims to address this problem by proposing a novel data analysis strategy wherein (1) chromatographic peaks in the UPLC-QTOF data set are automatically extracted by using an advanced multiscale Gaussian smoothing-based peak extraction strategy; (2) a peak annotation stage is used to cluster fragment ions that belong to the same compound. With the aid of high-resolution mass spectrometer, (3) a time-shift correction across the samples is efficiently performed by a new peak alignment method; (4) components are registered by using a newly developed adaptive network searching algorithm; (5) statistical methods, such as analysis of variance and hierarchical cluster analysis, are then used to identify the underlying marker compounds; finally, (6) compound identification is performed by matching the extracted peak information, involving high-precision m/z and retention time, against our compound library containing more than 500 plant metabolites. A manually designed mixture of 18 compounds is used to evaluate the performance of the method, and all compounds are detected under various concentration levels. The developed method is comprehensively evaluated by an extremely complex plant data set containing more than 2000 components. Results indicate that the performance of the developed method is comparable with the XCMS. The MATLAB GUI code is available from http://software.tobaccodb.org/software/antdas .

An Approach to the Synthesis of 1-Propenylnaphthols and 3-Arylnaphtho[2,1-b]furans.

A simple and efficient strategy for the synthesis of 1-propenylnaphthols from readily accessible 3-arylallylnaphthyl ethers has been developed. By using K2CO3 as base and 2-methoxyethanol as solvent, direct access to a wide range of 1-propenylnaphthols can be achieved in generally good yield (up to 99%) with high stereoselectivity toward the Z isomer. The control experiments indicate that the reaction proceeds through a sequential Claisen rearrangement/isomerization process. Furthermore, starting from the same material, the highly valuable 3-arylnaphtho[2,1-b]furans can be obtained in N,N-dimethylformamide and in the presence of Ag2O as the oxidant via a one-pot sequential Claisen rearrangement/isomerization/cyclization reaction. Mechanistic studies confirm that 1-propenylnaphthols are the key intermediates to form the 3-arylnaphtho[2,1-b]furans. In addition, these two operationally simple and practical protocols could be scaled up to a gram level.

Emodin alleviates lung injury in rats with sepsis.

BACKGROUND: Sepsis has high morbidity and mortality. The aim of this study was to investigate whether emodin, an anthraquinone derived from Chinese herb, exerts protective effects on lung injury in rat model of sepsis. MATERIALS AND METHODS: Forty-eight male Wistar rats were randomly divided into four groups (n = 12): normal group, sham-operated group, cecal ligation and puncture (CLP) model group, and emodin-treated group. Saline or emodin (25 mg/kg) was injected intraperitoneally 0.5 h before CLP. The rats were sacrificed 48 h after CLP. Lung wet-to-dry weight ratio and pathologic changes in the lung were examined, the contents of malondialdehyde and myeloperoxidase in lung tissue were detected, serum tumor necrosis factor alpha and interleukin 6 levels were measured by enzyme-linked immunosorbent assay, and the phosphorylation of p38 mitogen-activated protein kinase (p38 MAPK) was detected by Western blot analysis. RESULTS: Compared with control group, CLP group exhibited higher wet-to-dry weight ratio and water content in the lung (P < 0.01), but these indexes were reduced and pathologic changes in the lung were relieved in the emodin-treated group. In addition, lung malondialdehyde and myeloperoxidase contents, serum levels of tumor necrosis factor alpha and interleukin 6, and phosphorylation of p38 MAPK increased in the CLP group but decreased in the emodin-treated group (P < 0.05). CONCLUSIONS: Emodin exerts protective effects on lung injury in septic rats, which is related to the inhibition of p38 MAPK pathway and the reduction of oxidative stress and inflammation response during sepsis.

Palladium(II)-catalyzed highly enantioselective C-H arylation of cyclopropylmethylamines.

C-H arylation via a Pd(II)/Pd(IV) catalytic cycle has been one of the most extensively studied C-H activation reactions since the 1990s. Despite the rapid development of this reaction in the past two decades, an enantioselective version has not been reported to date. Herein, we report a Pd(II)-catalyzed highly enantioselective (up to 99.5% ee) arylation of cyclopropyl C-H bonds with aryl iodides using mono-N-protected amino acid (MPAA) ligands, providing a new route for the preparation of chiral cis-aryl-cyclopropylmethylamines. The enantiocontrol is also shown to override the diastereoselectivity of chiral substrates.

Ligand-Enabled Stereoselective ß-C(sp(3))-H Fluorination: Synthesis of Unnatural Enantiopure anti-ß-Fluoro-α-amino Acids.

A quinoline-based ligand was shown to promote palladium-catalyzed ß-C(sp(3))-H fluorination for the first time. A range of unnatural enantiopure fluorinated α-amino acids were obtained through sequential ß-C(sp(3))-H arylation and subsequent stereoselective fluorination from readily available L-alanine.