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Liu K, Fan P, Jia Z, Wang Z, Qi S. Analysis of four heavy metal concentrations in sediments fromthe Jiaozhou Bay, China by visible and near infrared spectroscopy (225-975 nm). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124367. [PMID: 38692111 DOI: 10.1016/j.saa.2024.124367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 04/20/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
As an important component ofbiogeochemical cyclein coastal ecosystems, sediments are the sink of heavy metals. Therefore, distribution and dynamics of heavy metals in sediments could assess ecological quality and predict ecological risks. In the new era, rapid and green technology are highly needed, especially that could determine multi-parameters simultaneously. Here, we explored a new method to rapidly determine concentrations of heavy metals in sediments by visible and near infrared reflectance spectroscopy (VIRS).We sampled sediments in the Jiaozhou Bay, China, collected their reflectance spectra, and measured concentrations of four heavy metals (As, Cr, Cu, and Zn). Heavy metal models were established and evaluated using substances highly correlated with heavy metals. This study provides an effective reference for rapid analysis of As, Cr, Cu, and Zn simultaneously in sediments, at least in the Jiaozhou Bay, and for ecological environment protection and resource development of the Jiaozhou Bay.
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You W, Zhang C, Yu R, Zhang X, Li J, Li M, Xu Z, Fan P, Pan G, Mao Y. Excitation power-dependent multicolor upconversion in NaLnF 4:Er 3+ under 1532 nm irradiation for anti-counterfeiting application. OPTICS LETTERS 2024; 49:2978-2981. [PMID: 38824307 DOI: 10.1364/ol.525417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Upconversion (UC) materials are renowned for their ability to convert low-energy photons into high-energy ones. The manipulation of parameters allows for the observation of multicolored UC luminescence (UCL) within a single material system. While modulation of multicolored UCL commonly relies on excitation at approximately 980 nm, investigation into multicolored UC materials activated by a 1532 nm excitation source remains comparatively scarce. In this work, we introduce NaLnF4:Er3+ as a novel class of smart luminescent materials. When the power density of a 1532 nm laser increases from 0.5 to 20.0 W/cm2, the emission peak positions remain unchanged, but the red-to-green (R/G) ratio decreases significantly from 18.82 to 1.48, inducing a color shift from red to yellow and ultimately to green. In contrast, no color variation is observed when NaLnF4:Er3+ is excited with a 980 nm laser at different power densities. This power-dependent multicolored UCL of NaLnF4:Er3+ excited at 1532 nm can be attributed to the competitive processes of upward pumping and downward relaxation of electrons on the 4I9/2 level of Er3+. By utilizing the unique UC characteristics of NaLnF4:Er3+, its potential utility in anti-counterfeiting applications is demonstrated. Our research highlights the distinctive optical properties of NaLnF4:Er3+ and provides novel insights into the use of luminescent materials in optical anti-counterfeiting technologies.
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Fan P, Cao Z, Zhang S, Wang Y, Xiao Y, Jia W, Zhang P, Huang S. Nanopore analysis of cis-diols in fruits. Nat Commun 2024; 15:1969. [PMID: 38443434 PMCID: PMC10915164 DOI: 10.1038/s41467-024-46303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.
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Bai X, Fan P, Li Z, Mossa-Basha M, Ju Y, Zhao X, Kong Q, Pei X, Zhang X, Sui B, Zhu C. Evaluating Middle Cerebral Artery Plaque Characteristics and Lenticulostriate Artery Morphology Associated With Subcortical Infarctions at 7T MRI. J Magn Reson Imaging 2024; 59:1045-1055. [PMID: 37259904 DOI: 10.1002/jmri.28839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Lenticulostriate artery (LSA) obstruction is a potential cause of subcortical infarcts. However, MRI LSA evaluation at 3T is challenging. PURPOSE To investigate middle cerebral artery (MCA) plaque characteristics and LSA morphology associated with subcortical infarctions in LSA territories using 7-T vessel wall MRI (VW-MRI) and time-of-flight MR angiography (TOF-MRA). STUDY TYPE Prospective. POPULATION Sixty patients with 80 MCA atherosclerotic plaques (37 culprit and 43 non-culprit). FIELD STRENGTH/SEQUENCE 7-T with 3D TOF-MRA and T1-weighted 3D sampling perfection with application-optimized contrast using different flip angle evolutions (SPACE) sequences. ASSESSMENT Plaque distribution (superior, inferior, ventral, or dorsal walls), LSA origin involvement, LSA morphology (numbers of stems, branches, and length), and plaque characteristics (normalized wall index, maximal wall thickness, plaque length, remodeling index, intraplaque hemorrhage, and plaque surface morphology (regular or irregular)) were assessed. STATISTICAL TESTS Least absolute shrinkage and selection operator regression, generalized estimating equations regression, receiver operating characteristic curve, independent t-test, Mann-Whitney U test, Chi-square test, Fisher's exact test, and intra-class coefficient. A P value <0.05 was considered statistically significant. RESULTS Plaque irregular surface, superior wall plaque, longer plaque length, LSA origin involvement, fewer LSA stems, and shorter total and average lengths of LSAs were significantly associated with culprit plaques. Multivariable logistic analysis confirmed that LSA origin involvement (OR, 28.51; 95% CI, 6.34-181.02) and plaque irregular surface (OR, 8.32; 95% CI, 1.41-64.73) were independent predictors in differentiating culprit from non-culprit plaques. A combination of LSA origin involvement and plaque irregular surface (area under curve = 0.92; [95% CI, 0.86-0.98]) showed good performance in identifying culprit plaques, with sensitivity and specificity of 86.5% and 86.0%, respectively. DATA CONCLUSION 7-T VW-MRI and TOF-MRA can demonstrate plaque involvement with LSA origins. MCA plaque characteristics derived from 7-T VW-MRI showed good diagnostic accuracy in determining the occurrence of subcortical infarctions. EVIDENCE LEVEL 2 TECHNICAL EFFICACY: Stage 3.
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Zhang S, Cao Z, Fan P, Sun W, Xiao Y, Zhang P, Wang Y, Huang S. Discrimination of Disaccharide Isomers of Different Glycosidic Linkages Using a Modified MspA Nanopore. Angew Chem Int Ed Engl 2024; 63:e202316766. [PMID: 38116834 DOI: 10.1002/anie.202316766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Disaccharides are composed of two monosaccharide subunits joined by a glycosidic linkage in an α or β configuration. Different combinations of isomeric monosaccharide subunits and different glycosidic linkages result in different isomeric disaccharide products. Thus, direct discrimination of these disaccharide isomers from a mixture is extremely difficult. In this paper, a hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore conjugated with a phenylboronic acid (PBA) adapter was applied for disaccharide sensing, with which three most widely known disaccharides in nature, including sucrose, lactose and maltose, were clearly discriminated. Besides, all six isomeric α-D-glucopyranosyl-D-fructoses, differing only in their glycosidic linkages, were also well resolved. Assisted by a custom machine learning algorithm, a 0.99 discrimination accuracy is achieved. Nanopore discrimination of disaccharide isomers with different glycosidic linkages, which has never been previously demonstrated, is inspiring for nanopore saccharide sequencing. This sensing capacity was also applied in direct identification of isomaltulose additives in a commercial sucrose-free yogurt, from which isomaltulose, lactose and L-lactic acid were simultaneously detected.
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Wang K, Zhang S, Zhou X, Yang X, Li X, Wang Y, Fan P, Xiao Y, Sun W, Zhang P, Li W, Huang S. Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore. Nat Methods 2024; 21:92-101. [PMID: 37749214 DOI: 10.1038/s41592-023-02021-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/21/2023] [Indexed: 09/27/2023]
Abstract
Natural proteins are composed of 20 proteinogenic amino acids and their post-translational modifications (PTMs). However, due to the lack of a suitable nanopore sensor that can simultaneously discriminate between all 20 amino acids and their PTMs, direct sequencing of protein with nanopores has not yet been realized. Here, we present an engineered hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore containing a sole Ni2+ modification. It enables full discrimination of all 20 proteinogenic amino acids and 4 representative modified amino acids, Nω,N'ω-dimethyl-arginine (Me-R), O-acetyl-threonine (Ac-T), N4-(β-N-acetyl-D-glucosaminyl)-asparagine (GlcNAc-N) and O-phosphoserine (P-S). Assisted by machine learning, an accuracy of 98.6% was achieved. Amino acid supplement tablets and peptidase-digested amino acids from peptides were also analyzed using this strategy. This capacity for simultaneous discrimination of all 20 proteinogenic amino acids and their PTMs suggests the potential to achieve protein sequencing using this nanopore-based strategy.
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Fan P, Lu YT, Han B, Zhou XL, Tian T. [Advances in Sengers syndrome]. ZHONGHUA NEI KE ZA ZHI 2023; 62:1245-1248. [PMID: 37766448 DOI: 10.3760/cma.j.cn112138-20221029-00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
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Li X, Li Z, Qiu H, Chen G, Fan P. Soil carbon content prediction using multi-source data feature fusion of deep learning based on spectral and hyperspectral images. CHEMOSPHERE 2023; 336:139161. [PMID: 37302502 DOI: 10.1016/j.chemosphere.2023.139161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Visible near-infrared reflectance spectroscopy (VNIR) and hyperspectral images (HSI) have their respective advantages in soil carbon content prediction, and the effective fusion of VNIR and HSI is of great significance for improving the prediction accuracy. But the contribution difference analysis of multiple features in the multi-source data is inadequate, and there is a lack of in-depth research on the contribution difference analysis of artificial feature and deep learning feature. In order to solve the problem, soil carbon content prediction methods based on VNIR and HSI multi-source data feature fusion are proposed. The multi-source data fusion network under the attention mechanism and the multi-source data fusion network with artificial feature are designed. For the multi-source data fusion network based on the attention mechanism, the information are fused through the attention mechanism according to the contribution difference of each feature. For the other network, artificial feature are introduced to fuse multi-source data. The results show that multi-source data fusion network based on the attention mechanism can improve the prediction accuracy of soil carbon content, and multi-source data fusion network combined with artificial feature has better prediction effect. Compared with two single-source data from the VNIR and HSI, the relative percent deviation of Neilu, Aoshan Bay and Jiaozhou Bay based on multi-source data fusion network combined with artificial feature are increased by 56.81% and 149.18%, 24.28% and 43.96%, 31.16% and 28.73% respectively. This study can effectively solve the problem of the deep fusion of multiple features in the soil carbon content prediction by VNIR and HSI, so as to improve the accuracy and stability of soil carbon content prediction, promote the application and development of soil carbon content prediction in spectral and hyperspectral image, and provide technical support for the study of carbon cycle and the carbon sink.
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Krivinko JM, DeChellis-Marks MR, Zeng L, Fan P, Lopez OL, Ding Y, Wang L, Kofler J, MacDonald ML, Sweet RA. Targeting the post-synaptic proteome has therapeutic potential for psychosis in Alzheimer Disease. Commun Biol 2023; 6:598. [PMID: 37268664 PMCID: PMC10238472 DOI: 10.1038/s42003-023-04961-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023] Open
Abstract
Individuals with Alzheimer Disease who develop psychotic symptoms (AD + P) experience more rapid cognitive decline and have reduced indices of synaptic integrity relative to those without psychosis (AD-P). We sought to determine whether the postsynaptic density (PSD) proteome is altered in AD + P relative to AD-P, analyzing PSDs from dorsolateral prefrontal cortex of AD + P, AD-P, and a reference group of cognitively normal elderly subjects. The PSD proteome of AD + P showed a global shift towards lower levels of all proteins relative to AD-P, enriched for kinases, proteins regulating Rho GTPases, and other regulators of the actin cytoskeleton. We computationally identified potential novel therapies predicted to reverse the PSD protein signature of AD + P. Five days of administration of one of these drugs, the C-C Motif Chemokine Receptor 5 inhibitor, maraviroc, led to a net reversal of the PSD protein signature in adult mice, nominating it as a novel potential treatment for AD + P.
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Husnain A, Arshad U, Poindexter MB, Zimpel R, Marinho MN, Perdomo MC, Fan P, Jeong KC, Nelson CD, Sheldon IM, Bromfield JJ, Santos JEP. Induced endometritis in early lactation compromises production and reproduction in dairy cows. J Dairy Sci 2023; 106:4198-4213. [PMID: 37080784 DOI: 10.3168/jds.2022-22846] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/13/2022] [Indexed: 04/22/2023]
Abstract
Objectives of this experiment were to study the effect of infusing utero-pathogenic bacteria to induce endometrial inflammation on productive performance in early lactation and subsequent reproduction. Although endometritis is associated with perturbed reproduction, numerous factors may contribute to the observed association. It was hypothesized that induced endometrial inflammation, resulting in localized and systemic inflammatory responses, compromises production and reproduction. Holstein cows without clinical disease and with less than 18% polymorphonuclear leukocytes (PMN) in endometrial cytology on d 31 ± 3 postpartum had their estrous cycle synchronized. Cows were blocked by parity and genomic breeding value for cow conception rate and, within block, assigned randomly to remain as untreated controls (CON; n = 37) or to receive an intrauterine infusion of 5.19 × 108 cfu Escherichia coli and 4.34 × 108 cfu Trueperella pyogenes during the luteal phase to induce endometrial inflammation (INF; n = 48). Endometrial cytology was taken on d 2 and 7 after treatment to evaluate the proportion of PMN. Rectal temperature, dry matter intake, and yields of milk and components were measured in the first 7 d after treatment. Blood serum was analyzed for concentration of haptoglobin. Leukocytes were isolated from blood on d 2 and 7 after treatment and on d 19 after artificial insemination (AI) and mRNA was quantified for a select group of genes. Cows received AI and reproduction was followed for 300 d postpartum. Bacterial infusion induced endometrial inflammation with increased proportions of PMN in the endometrial cytology on d 2 (4.4 ± 0.7 vs. 26.3 ± 2.8%) and 7 (10.9 ± 1.7 vs. 17.4 ± 2.1%) after treatment, resulting in increased mean prevalence of subclinical endometritis (>10% PMN; 23.3 ± 6.3 vs. 80.9 ± 5.1%). Rectal temperature did not differ between CON and INF, but the concentration of haptoglobin in serum tended to increase in INF compared with CON (113 ± 14 vs. 150 ± 16 µg/mL). Induced endometrial inflammation reduced yields of milk (44.9 ± 0.8 vs. 41.6 ± 0.8 kg/d), protein (1.19 ± 0.03 vs. 1.12 ± 0.03 kg/d), and lactose (2.17 ± 0.04 vs. 2.03 ± 0.04 kg/d) and tended to reduce dry matter intake (20.7 ± 0.5 vs. 19.4 ± 0.6 kg/d) in the first 7 d after treatment. Indeed, the reduction in milk yield lasted 4 wk. However, treatment did not affect yields of energy-corrected milk or fat because treatment with INF increased the concentration of fat in milk (3.54 ± 0.10 vs. 3.84 ± 0.10%). Induced endometrial inflammation reduced pregnancy per AI at all inseminations (33.4 ± 5.1 vs. 21.6 ± 3.7%) and the hazard of pregnancy (0.61; 95% CI = 0.36-1.04), which extended the median days open by 24 d. Blood leukocytes from INF cows had increased mRNA expression of the pro-inflammatory gene IL1B on d 2 and 7 after treatment, but reduced expression of the IFN-stimulated genes ISG15 and MX2 on d 19 after AI. Induced endometrial inflammation depressed production and caused long-term negative effects on reproduction in lactating dairy cows.
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Fan P, Lei R, Wang Y, Zhang M, Guo C, Fan L, Wang J. WCN23-0135 IMG-025, EXHIBITS PROMISING POTENTIAL IN AMELIORATING IMMUNOGLOBULIN A NEPHROPATHY VIA INHIBITION OF LECTIN-MEDIATED COMPLEMENT ACTIVATION. Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
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Du X, Zhang S, Wang L, Wang Y, Fan P, Jia W, Zhang P, Huang S. Single-Molecule Interconversion between Chiral Configurations of Boronate Esters Observed in a Nanoreactor. ACS NANO 2023; 17:2881-2892. [PMID: 36655995 DOI: 10.1021/acsnano.2c11286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Isomers of some chemical compounds may be dynamically interconvertible. Due to a lack of sensing methods with a sufficient resolution, however, direct monitoring of such processes can be difficult. Engineered Mycobacterium smegmatis porin A (MspA) nanopores can be applied as nanoreactors so that chemical reactions can be directly monitored. Here, an MspA modified with a phenylboronic acid (PBA) adapter was prepared and was used to observe dynamic interconversion between chiral configurations of boronate esters, which appears as telegraphic switching on top of nanopore events. The mechanism of this behavior was further confirmed by trials with different halogenated catechols, dopamine, adenosine, 1,2-propanediol, and (2R,3R)-2,3-butanediol, and its generality has been demonstrated. These results suggest that an engineered MspA possesses an exceptional resolution in its monitoring of chemical reaction processes and may inspire the future design of nanopore small-molecule sensors.
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Pu Y, Liu Q, Liu H, Bai H, Huang W, Xi M, Fan P. Association between CYP2E1 C-1054T and 96-bp I/D genetic variations and the risk of polycystic ovary syndrome in Chinese women. J Endocrinol Invest 2023; 46:67-78. [PMID: 35943720 DOI: 10.1007/s40618-022-01885-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
PURPOSE To investigate the association of cytochrome P450 2E1 (CYP2E1) C-1054T (rs2031920) and 96-bp I/D genetic variations with the risk of polycystic ovary syndrome (PCOS), and to estimate the effects of genotypes on the clinical, metabolic, hormonal, and oxidative stress indicators. METHODS This case-control study included 762 control women and 1034 patients with PCOS. Genotypes were determined using polymerase chain reaction and/or restriction fragment length polymorphism analysis. Clinical and biochemical parameters were also analyzed. RESULTS Frequencies of the TT + CT genotype (35.4 vs. 28.9%) and T allele (19.6 vs. 16.0%) of the CYP2E1 C-1054T polymorphism were significantly higher in the PCOS group than in the control group (OR = 1.350, 95% CI 1.103-1.652, P = 0.004 for the dominant model). Genotype TT + CT remained a significant predictor of PCOS in a logistic regression model including age, body mass index (BMI), and recruitment year of participants (OR = 1.345, 95% CI 1.071-1.688, P = 0.011). No statistical differences were found in the genotype and allele frequencies of CYP2E1 96-bp I/D polymorphism. However, the combined genotype DD/TT + CT was related to an increased risk of PCOS when the DD/CC wild-type combined genotype was used as a reference. Patients with the I allele of 96-bp I/D polymorphism had a lower BMI but higher plasma apolipoprotein B and oxidized low-density lipoprotein cholesterol levels than those with the DD genotype. CONCLUSION CYP2E1 C-1054T, but not 96-bp I/D, genetic polymorphism is associated with an increased risk of PCOS in Chinese women.
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Wang Y, Fan P, Zhang S, Wang L, Li X, Jia W, Liu Y, Wang K, Du X, Zhang P, Huang S. Discrimination of Ribonucleoside Mono-, Di-, and Triphosphates Using an Engineered Nanopore. ACS NANO 2022; 16:21356-21365. [PMID: 36475606 DOI: 10.1021/acsnano.2c09662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ribonucleotides, which widely exist in all living organisms and are essential to both physiological and pathological processes, can naturally appear as ribonucleoside mono-, di-, and triphosphates. Natural ribonucleotides can also dynamically switch between different phosphorylated forms, posing a great challenge for sensing. A specially engineered nanopore sensor is promising for full discrimination of all canonical ribonucleoside mono-, di-, and triphosphates. However, such a demonstration has never been reported, due to the lack of a suitable nanopore sensor that has a sufficient resolution. In this work, we utilized a phenylboronic acid (PBA) modified Mycobacterium smegmatis porin A (MspA) hetero-octamer for ribonucleotide sensing. Twelve types of ribonucleotides, including mono-, di-, and triphosphates of cytidine (CMP, CDP, CTP), uridine (UMP, UDP, UTP), adenosine (AMP, ADP, ATP), and guanosine (GMP, GDP, GTP) were simultaneously discriminated. A machine-learning algorithm was also developed, which achieved a general accuracy of 99.9% for ribonucleotide sensing. This strategy was also further applied to identify ribonucleotide components in ATP tablets and injections. This sensing strategy provides a direct, accurate, easy, and rapid solution to characterize ribonucleotide components in different phosphorylated forms.
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Fan P, Ye YZ, Ma X. [Comparison on the prognosis of severe aortic stenosis patients treated with transcatheter aortic valve replacement versus surgical aortic valve replacement: a systematic review and meta-analysis]. ZHONGHUA XIN XUE GUAN BING ZA ZHI 2022; 50:913-919. [PMID: 36096710 DOI: 10.3760/cma.j.cn112148-20220211-00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To systematically review the prognosis of transcatheter aortic valve replacement (TAVR) versus surgical aortic valve replacement (SAVR) in patients with severe aortic stenosis. Methods: A systematic search of PubMed, EMBASE, Scopus, Cochrane Library, China biomedical literature database, China journal full text database (CNKI), Wanfang database and VIP database from January 2012 to February 2022 was conducted for randomized controlled trial (RCT) that comparing TAVR and SAVR in the treatment of severe aortic stenosis. The primary outcomes were the incidence of all-cause mortality, stroke incidence, reoperation rate and complications (pacemaker implantation, atrial fibrillation) at 1 month and 1, 2, 5 years after operation. Jadad scale was used to evaluate the literature quality of RCTs. All statistical analyses were performed using the standard statistical procedures provided in RevMan 5.4.1. Results: A total of 17 studies including 11 712 patients were identified, including 6 007 patients treated with TAVR and 5 705 patients treated with SAVR. There were 4 high-quality studies and 13 medium-quality studies. The results of meta-analysis showed that the rate of new onset atrial fibrillation was lower in TAVR group than that in SAVR group (RR=0.28, 95%CI 0.21-0.38, P<0.001), and there was no significant difference in all-cause death, stroke, pacemaker implantation and reoperation rate (all P>0.05) at 30 days follow-up. At one year after TAVR and SAVR treatment, all-cause mortality (RR=0.85, 95%CI 0.74-0.97, P=0.01) and new onset atrial fibrillation (RR=0.28, 95%CI 0.20-0.39, P<0.001) were lower in TAVR group than SAVR group. However, the pacemaker implantation rate was higher in TAVR group than that of SAVR group (RR=1.79, 95%CI 1.11-2.89, P=0.02), while there was no significant difference in the incidence of stroke and reoperation between the two groups (P>0.05). At two years after TAVR and SAVR treatment, the pacemaker implantation rate was higher in TAVR group than that in SAVR group (RR=2.23, 95%CI 1.28-3.86, P=0.004), and the rate of new atrial fibrillation was lower in TAVR group than that in SAVR group (RR=0.46, 95%CI 0.38-0.56, P<0.001). There was no significant difference in all-cause death, stroke and reoperation rates between the two groups (P>0.05). At five years after TAVR and SAVR treatment, the pacemaker implantation rate (RR=1.89, 95%CI 1.13-3.17, P=0.02) and reoperation rate (RR=3.64, 95%CI 1.75-7.58, P=0.000 5) were higher in TAVR group than those in SAVR group, while the rate of new onset atrial fibrillation was lower in TAVR group than that in SAVR group (RR=0.45, 95%CI 0.37-0.55, P<0.001). There was no significant difference in all-cause death and stroke incidence between the two groups (all P>0.05). Conclusions: The all-cause mortality and the incidence of new onset atrial fibrillation after TAVR are lower than SAVR, and TAVR is a preferred therapy for patients with aortic stenosis.
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Wang Y, Zhang S, Jia W, Fan P, Wang L, Li X, Chen J, Cao Z, Du X, Liu Y, Wang K, Hu C, Zhang J, Hu J, Zhang P, Chen HY, Huang S. Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore. NATURE NANOTECHNOLOGY 2022; 17:976-983. [PMID: 35851382 DOI: 10.1038/s41565-022-01169-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/01/2022] [Indexed: 05/25/2023]
Abstract
RNA modifications play critical roles in the regulation of various biological processes and are associated with many human diseases. Direct identification of RNA modifications by sequencing remains challenging, however. Nanopore sequencing is promising, but the current strategy is complicated by sequence decoding. Sequential nanopore identification of enzymatically cleaved nucleoside monophosphates may simultaneously provide accurate sequence and modification information. Here we show a phenylboronic acid-modified hetero-octameric Mycobacterium smegmatis porin A nanopore, with which direct distinguishing between monophosphates of canonical nucleosides, 5-methylcytidine, N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, inosine, pseudouridine and dihydrouridine was achieved. A custom machine learning algorithm, which reports an accuracy of 0.996, was also applied to the quantitative analysis of modifications in microRNA and natural transfer RNA. It is generally suitable for sensing of a variety of other nucleoside or nucleotide derivatives and may bring new insights to epigenetic RNA sequencing.
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Feng ST, Fan P, Hao S, Bai Q, Wang LX, Jia L. [Factors analysis of worsening renal function in patients with acute right ventricular myocardial infarction during hospitalization]. ZHONGHUA YI XUE ZA ZHI 2022; 102:2368-2373. [PMID: 35970796 DOI: 10.3760/cma.j.cn112137-20220219-00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To analyze the related factors of worsening renal function (WRF) in patients with acute right ventricular myocardial infarction (RVMI) during hospitalization. Methods: A total of 98 patients with acute RVMI admitted to the emergency comprehensive ward of Beijing Anzhen Hospital from August 2011 to January 2020 were enrolled in this cross-sectional study. According to the situation of WRF, the patients were divided into non-WRF group (76 cases) and WRF group (22 cases). WRF was defined as ≥0.3 mg/dL increase in serum creatinine level from baseline on day 6 of hospitalization (if hospital stay<6 days, it was at discharge). Baseline data, intravenous fluid infusion, diuretic and significant positive balance of patients' intake and output volume [any 24 h intakes and outputs ≥1 000 ml or any consecutive 72 h intakes and outputs ≥2 000 ml within 6 d of hospitalization (if hospitalization<6 d, it was from admission to discharge)] were obtained, and the differences of above indicators between the two groups were analyzed. Multiple logistic regression model was used to analyze the related factors of WRF. Results: The ages of patients in WRF group and non-WRF group were 60 (50, 68) and 63 (52, 72) years, and the male proportions were 63.6% (14 cases) and 76.3% (58 cases), respectively, and there was no significant difference (all P>0.05). The proportion of positive balance was 31.8% (7 cases) in WRF group, which was higher than 14.5% (11 cases) in non-WRF group (P=0.034). The rate of loop diuretic use in WRF group was 4.5% (1 case), lower than that in non-WRF group 10.5% (8 cases) (P=0.027). After adjusting for age, sex, baseline estimated glomerular filtration rate (eGFR), preoperative isoproterenol/temporary pacemaker/atropine use, significant positive balance of intake and output volume, and loop diuretic use, it was found that eGFR≥60 ml·min-1·1.73 m-2 and significant positive balance were associated with WRF, the OR (95%CI) were 0.71 (0.62-0.86) and 1.21 (1.02-1.43) (both P<0.05); After eliminating the variable of significant positive balance in the above model, loop diuretic use was found to be a correlation factor for WRF, with an OR (95%CI) of 0.89 (0.72-0.97) (P<0.05). Conclusions: Significant positive balance of intake and output volume during hospitalization in patients with acute RVMI is a risk factor for WRF on day 6 or at discharge. In the presence of a significant positive balance, loop diuretic use is a protective factor for WRF.
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Jia W, Suo LM, Fan P, Dong T, Li YJ, Ji JM, Xue YF, An CQ, Zhao YX, Zhang JX, Duan J. [Clinical and genetic studies of a family with hereditary angioedema]. ZHONGHUA ER BI YAN HOU TOU JING WAI KE ZA ZHI = CHINESE JOURNAL OF OTORHINOLARYNGOLOGY HEAD AND NECK SURGERY 2022; 57:980-985. [PMID: 36058666 DOI: 10.3760/cma.j.cn115330-20211209-00789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To diagnose a large family of patients with hereditary angioedema, and to study its inheritance pattern and gene locus. Methods: A retrospective analysis was carried out from August 2021 to February 2022 in a proband (female, 48 years old) and 12 family members who underwent medical history collection and laboratory examinations in the Department of Otorhinolaryngology and Head and Neck Surgery, the Second Hospital of Shanxi Medical University. The clinical data of members and non-affected members [including 7 males and 5 females, aged 12-78 (median 24) years old], were drawn a family map while confirming the diagnosis. Whole exome sequencing technology was used to detect the genetic sequence of the proband and to verify its family members to map the genetic pedigree of the mutation. Results: The inheritance pattern of the family was autosomal dominant, and 8 members of the family were diagnosed with hereditary angioedema by laboratory examination, including 7 cases of type I and 1 case of type Ⅱ. Whole exome sequencing analysis was performed on 2 patients with 2 phenotypes, and it was found that they both carried the same pathogenic mutation locus, which was c.890-2A>G. The family members were verified by next-generation sequencing, and it was found that all members of the family who had a history of edema contained this mutation site, while the younger brother of the proband who had no history of edema did not have this mutation. Conclusion: Both type Ⅰ and type Ⅱ phenotypes are present in this hereditary angioedema family, and the mutation of SERPING1 gene c.890-2A>G causes the onset of each patient in this family.
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Liu Y, Zhang S, Wang Y, Wang L, Cao Z, Sun W, Fan P, Zhang P, Chen HY, Huang S. Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products. J Am Chem Soc 2022; 144:13717-13728. [PMID: 35867993 DOI: 10.1021/jacs.2c04595] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore‐Based Saccharide Sensor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore-Based Saccharide Sensor. Angew Chem Int Ed Engl 2022; 61:e202203769. [PMID: 35718742 DOI: 10.1002/anie.202203769] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 12/19/2022]
Abstract
Saccharides play critical roles in many forms of cellular activities. Saccharide structures are however complicated and similar, setting a technical hurdle for direct identification. Nanopores, which are emerging single molecule tools sensitive to minor structural differences between analytes, can be engineered to identity saccharides. A hetero-octameric Mycobacterium smegmatis porin A nanopore containing a phenylboronic acid was prepared, and was able to clearly identify nine monosaccharide types, including D-fructose, D-galactose, D-mannose, D-glucose, L-sorbose, D-ribose, D-xylose, L-rhamnose and N-acetyl-D-galactosamine. Minor structural differences between saccharide epimers can also be distinguished. To assist automatic event classification, a machine learning algorithm was developed, with which a general accuracy score of 0.96 was achieved. This sensing strategy is generally suitable for other saccharide types and may bring new insights to nanopore saccharide sequencing.
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Qiu H, Fan P, Hou G, Li X, Wang Y. Analysis and Model Comparison of Carbon and Nitrogen Concentrations in Sediments of the Yellow Sea and Bohai Sea by Visible-Near Infrared Spectroscopy. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 108:1124-1131. [PMID: 35064279 DOI: 10.1007/s00128-021-03456-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Visible-near infrared spectroscopy is considered an effective method for rapidly determining total carbon (TC) and total nitrogen (TN) in terrestrial soils. However, reports on measuring them by VNIR in marine sediments are limited. This article provides an analysis and spectral model comparison of TC and TN in marine sediments using VNIR. The best TC and TN spectral models were established when using the least square support vector machine algorithm with a wavelength, which extended from 226 nm to 975 nm. The prediction results of TN have a high coefficient of determination and residual predictive deviation, providing accurate quantitative predictions. The TC spectral model comes with a disadvantage might due to its usual high concentrations of organic carbon. Characteristic wavelength extraction may lead to the loss of identification information for the characteristics of TC and TN, and full wavelength spectrum contains more information helps more to the quantification.
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Yan S, Wang L, Wang Y, Cao Z, Zhang S, Du X, Fan P, Zhang P, Chen HY, Huang S. Non-binary Encoded Nucleic Acid Barcodes Directly Readable by a Nanopore. Angew Chem Int Ed Engl 2022; 61:e202116482. [PMID: 35261129 DOI: 10.1002/anie.202116482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Indexed: 01/13/2023]
Abstract
A large collection of unique molecular barcodes is useful in the simultaneous sensing or screening of molecular analytes. Though the sequence of DNA has been widely applied to encode for molecular barcodes, decoding of these barcodes is normally assisted by sequencing. We here demonstrate a barcode system based solely on self-assembly of synthetic nucleic acids and direct nanopore decoding. Each molecular barcode is composed of "n" distinct information nodes in a non-binary manner and can be sequentially scanned and decoded by a Mycobacterium smegmatis porin A (MspA) nanopore. Nanopore events containing step-shaped features were consistently reported. 14 unique information nodes were developed which in principle could encode for 14n unique molecular barcodes in a barcode containing "n" information nodes. These barcode probes were adapted to detect different antibody proteins or cancer-related microRNAs, suggesting their immediate application in a wide variety of sensing applications.
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Fan P, Shan W, Yang H, Zheng Y, Wu Z, Chan SW, Wang Q, Gao P, Liu Y, He K, Sui B. Cerebral Microbleed Automatic Detection System Based on the “Deep Learning”. Front Med (Lausanne) 2022; 9:807443. [PMID: 35402427 PMCID: PMC8988858 DOI: 10.3389/fmed.2022.807443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Objective To validate the reliability and efficiency of clinical diagnosis in practice based on a well-established system for the automatic segmentation of cerebral microbleeds (CMBs). Method This is a retrospective study based on Magnetic Resonance Imaging-Susceptibility Weighted Imaging (MRI-SWI) datasets from 1,615 patients (median age, 56 years; 1,115 males, 500 females) obtained between September 2018 and September 2019. All patients had been diagnosed with cerebral small vessel disease (CSVD) with clear cerebral microbleeds (CMBs) on MRI-SWI. The patients were divided into training and validation cohorts of 1,285 and 330 patients, respectively, and another 30 patients were used for internal testing. The model training and validation data were labeled layer by layer and rechecked by two neuroradiologists with 15 years of work experience. Afterward, a three-dimensional convolutional neural network (CNN) was applied to the MRI data from the training and validation cohorts to construct a deep learning system (DLS) that was tested with the 72 patients, independent of the aforementioned MRI cohort. The DLS tool was used as a segmentation program for these 72 patients. These results were evaluated and revised by five neuroradiologists and subjected to an output analysis divided into the missed label, incorrect label, and correct label. The interneuroradiologists DLS agreement rate, which was assessed using the interrater agreement kappas test, was used for the quality analysis. Results In the detection and segmentation of the CMBs, the DLS achieved a Dice coefficient of 0.72. In the evaluation of the independent clinical data, the neuroradiologists reported that more than 90% of the lesions were directly detected and less than 10% of lesions were incorrectly labeled or the label was missed by our DLS. The kappa value for interneuroradiologist DLS agreement reached 0.79 on average. Conclusion Based on the results, the automatic detection and segmentation of CMBs are feasible. The proposed well-trained DLS system might represent a trusted tool for the segmentation and detection of CMB lesions.
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