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Article ; Online: Development of a certified reference material for accurate determination of the leaching of Pb and Zn in solid waste.

Zhang, Menghuan / Pan, Dajian / Jin, Bi / Zheng, Ruru / Xuan, Yuzhi

2023 Volume 415, Issue 25, Page(s) 6355–6362

Abstract: Certified reference materials (CRMs) with high accuracy and traceability play a significant role in the calibration of equipment and validation of analytical methods. However, there is still a lack of suitable solid waste CRMs for quality assurance and ... ...

Abstract	Certified reference materials (CRMs) with high accuracy and traceability play a significant role in the calibration of equipment and validation of analytical methods. However, there is still a lack of suitable solid waste CRMs for quality assurance and quality control. Thus, a CRM (GBW(E)085538) was developed for accurate determination and reliable measurement of the leaching of Pb and Zn in solid waste according to the requirements of ISO 17034 and the recommendations of ISO Guide 35. This study describes the steps performed for the development of the CRM. These steps include material preparation, homogeneity, and stability during transport and storage, assignment of certified values, and their uncertainties. The material was dried, ground, sieved and well-mixed, and the final bulk material was bottled in 1 kg portions. Analytical techniques like inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-optical emission spectrometry (ICP-OES), and flame atomic absorption spectrometry (AAS) have been used for the characterization of property values. Concurrently, an inter-laboratory comparison study involving 9 qualified laboratories was implemented to support the certification study. The certified values of Pb and Zn were (4.66 ± 0.21) mg/L and (2.95 ± 0.14) mg/L with 7-month stability.
Language	English
Publishing date	2023-08-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-023-04912-3
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Article ; Online: Recurrence Prediction by Circulating Tumor DNA in the Patient with Colorectal Liver Metastases After Hepatectomy: A Prospective Biomarker Study.

Liu, Wei / Jin, Ke-Min / Zhang, Meng-Huan / Bao, Quan / Liu, Ming / Xu, Da / Wang, Kun / Xing, Bao-Cai

Annals of surgical oncology

2023 Volume 30, Issue 8, Page(s) 4916–4926

Abstract: Background: The recurrence rate after hepatic resection of colorectal liver metastases (CRLM) remains high. This study aimed to investigate postoperative circulating tumor DNA (ctDNA) based on ultra-deep next-generation sequencing (NGS) to predict ... ...

Abstract	Background: The recurrence rate after hepatic resection of colorectal liver metastases (CRLM) remains high. This study aimed to investigate postoperative circulating tumor DNA (ctDNA) based on ultra-deep next-generation sequencing (NGS) to predict patient recurrence and survival. Methods: Using the high-throughput NGS method tagged with a dual-indexed unique molecular identifier, named the CRLM-specific 25-gene panel (J25), this study sequenced ctDNA in peripheral blood samples collected from 134 CRLM patients who underwent hepatectomy after postoperative day 6. Results: Of 134 samples, 42 (31.3%) were shown to be ctDNA-positive, and 37 resulted in recurrence. Kaplan-Meier survival analysis showed that disease-free survival (DFS) in the ctDNA-positive subgroup was significantly shorter than in the ctDNA-negative subgroup (hazard ratio [HR], 2.96; 95% confidence interval [CI], 1.91-4.6; p < 0.05). When the 42 ctDNA-positive samples were further divided by the median of the mean allele frequency (AF, 0.1034%), the subgroup with higher AFs showed a significantly shorter DFS than the subgroup with lower AFs (HR, 1.98; 95% CI, 1.02-3.85; p < 0.05). The ctDNA-positive patients who received adjuvant chemotherapy longer than 2 months showed a significantly longer DFS than those who received treatment for 2 months or less (HR, 0.377; 95% CI, 0.189-0.751; p < 0.05). Uni- and multivariable Cox regression indicated two factors independently correlated with prognosis: ctDNA positivity and no preoperative chemotherapy. Conclusion: The study demonstrated that ctDNA status 6 days postoperatively could sensitively and accurately predict recurrence for patients with CRLM using the J25 panel.
MeSH term(s)	Humans ; Circulating Tumor DNA/genetics ; Hepatectomy ; Biomarkers, Tumor/genetics ; Liver Neoplasms/genetics ; Liver Neoplasms/surgery ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/surgery ; Colorectal Neoplasms/pathology ; Neoplasm Recurrence, Local/genetics ; Neoplasm Recurrence, Local/surgery ; Neoplasm Recurrence, Local/drug therapy
Chemical Substances	Circulating Tumor DNA ; Biomarkers, Tumor
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1200469-8
ISSN	1534-4681 ; 1068-9265
ISSN (online)	1534-4681
ISSN	1068-9265
DOI	10.1245/s10434-023-13362-1
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Article: Nitrogen Biogeochemistry of Anaerobic Biodegradation of Naphthalene

Zhang, Menghuan / Zhang, Fengjun / Ma, Zhe / Wan, Yuyu

Water, air, and soil pollution. 2019 Sept., v. 230, no. 9

2019

Abstract: A mixed community of bacteria was enriched from groundwater contaminated with naphthalene as the sole carbon source. Based on the results of 16S rRNA sequences, Acinetobacter and Pseudomonas were the predominant species in the naphthalene-enriched ... ...

Abstract	A mixed community of bacteria was enriched from groundwater contaminated with naphthalene as the sole carbon source. Based on the results of 16S rRNA sequences, Acinetobacter and Pseudomonas were the predominant species in the naphthalene-enriched culture. Different initial forms of nitrogen, including nitrate, nitrite, and ammonium, were beneficial to naphthalene degradation, which was considered second-order kinetics and naphthalene could be decreased by 94.68% during the incubation period of 30 days with an initial naphthalene concentration of 0.5 mg/L. These clear biogeochemical denitrification signals, the consumption and accumulation of nitrate, nitrite, and ammonium during the incubation period, suggested that naphthalene degradation may be coupled with denitrification and DNRA metabolism. Nitrate and nitrite were reduced mainly as electron acceptors, and ammonium was utilized by microorganisms as an important inorganic nutrient for their growth and reproduction, which promoted the degradation of naphthalene. The results of this study contributed to the removal pathway and transformational mechanism of nitrogen and reveal their involvement in the anaerobic biodegradation of naphthalene.
Keywords	Acinetobacter ; Pseudomonas ; ammonium ; bacteria ; biodegradation ; carbon ; denitrification ; groundwater ; metabolism ; naphthalene ; nitrates ; nitrites ; nitrogen ; nucleotide sequences ; reproduction ; ribosomal RNA
Language	English
Dates of publication	2019-09
Size	p. 222.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	120499-3
ISSN	1573-2932 ; 0049-6979 ; 0043-1168
ISSN (online)	1573-2932
ISSN	0049-6979 ; 0043-1168
DOI	10.1007/s11270-019-4276-9
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Article: A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers.

Ren, Jin / Yang, Yun / Li, Chuanyin / Xie, Lu / Hu, Ronggui / Qin, Xiong / Zhang, Menghuan

Frontiers in genetics

2021 Volume 11, Page(s) 634634

Abstract: Lung adenocarcinoma (LUAD) is caused by multiple biological factors. Therefore, it will be more meaningful to study the prognosis from the perspective of omics integration. Given the significance of epigenetic modification and immunity in tumorigenesis ... ...

Abstract	Lung adenocarcinoma (LUAD) is caused by multiple biological factors. Therefore, it will be more meaningful to study the prognosis from the perspective of omics integration. Given the significance of epigenetic modification and immunity in tumorigenesis and development, we tried to combine aberrant methylation and tumor infiltration CD8 T cell-related genes to build a prognostic model, to explore the key biomarkers of early-stage LUAD. On the basis of RNA-seq and methylation microarray data downloaded from The Cancer Genome Atlas (TCGA), differentially expressed genes and aberrant methylated genes were calculated with "DEseq2" and "ChAMP" packages, respectively. A Chi-square test was performed to obtain methylation driver genes. Weighted correlation network analysis (WGCNA) was utilized to mine cancer biomarkers related to CD8 T cells. With the consequences of univariate Cox proportional hazards analysis and least absolute shrinkage and selection operator (LASSO) COX regression analysis, the prognostic index based on 17 methylation driver genes (ZNF677, FAM83A, TRIM58, CLDN6, NKD1, NFE2L3, FKBP5, ITGA5, ASCL2, SLC24A4, WNT3A, TMEM171, PTPRH, ITPKB, ITGA2, SLC6A17, and CCDC81) and four CD8 T cell-related genes (SPDL1, E2F7, TK1, and TYMS) was successfully established, which could make valuable predictions for the survival risk of patients with early-stage LUAD.
Language	English
Publishing date	2021-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2020.634634
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Article: Evaluation of infarct core and ischemic penumbra by absolute quantitative cerebral dynamic susceptibility contrast perfusion magnetic resonance imaging using self-calibrated echo planar imaging sequencing in patients with acute ischemic stroke.

Ma, Xiaoyue / Wang, Yan / Wang, Mengke / Zhang, Menghuan / Meng, Nan / Zhang, Long / Zhang, Jinlong / Dou, Shewei / Wang, Meiyun

Quantitative imaging in medicine and surgery

2022 Volume 12, Issue 8, Page(s) 4286–4295

Abstract: Background: It has been hypothesized that an absolute quantitative dynamic susceptibility contrast (DSC) cerebral perfusion-weighted imaging (PWI) technique based on self-calibrated echo-planar imaging (EPI) could be a reliable measurement of ... ...

Abstract	Background: It has been hypothesized that an absolute quantitative dynamic susceptibility contrast (DSC) cerebral perfusion-weighted imaging (PWI) technique based on self-calibrated echo-planar imaging (EPI) could be a reliable measurement of quantitative cerebral blood flow (qCBF) and quantitative cerebral blood volume (qCBV). This study aimed to investigate the clinical value of this technique in offering a unique insight into ischemic stroke (IS) pathophysiology and improving the sensitivity of IS diagnosis. Methods: A total of 14 patients with IS who underwent routine magnetic resonance imaging (MRI) and Self-CALibrated EPI Perfusion-Weighted Imaging (SCALE-PWI) scanning were prospectively recruited as a consecutive convenience sample. qCBF and qCBV maps were processed immediately online after the scan. Then, 2 radiologists independently drew the region of interest (ROI) of the infarct core, ischemic penumbra, and the contralateral normal tissues on each map for the statistical analyses. The paired-samples Results: All the values of qCBF and qCBV in the lesions were lower than those in the contralateral normal tissues (all P<0.05). The values of qCBF and qCBV in the infarct core were lower than those in the ischemic penumbra (mean values: 16.42 Conclusions: Different from the previous semi-quantitative measurement, the SCALE-PWI technique has the potential to provide absolute quantitative hemodynamic information which may be used to detect the infarct core and ischemic penumbra in a relatively short scan time.
Language	English
Publishing date	2022-07-16
Publishing country	China
Document type	Journal Article
ZDB-ID	2653586-5
ISSN	2223-4306 ; 2223-4292
ISSN (online)	2223-4306
ISSN	2223-4292
DOI	10.21037/qims-21-975
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Article: Retinoic Acid Supplementation Rescues the Social Deficits in

Yang, Liqin / Xia, Zhixiong / Feng, Jianhua / Zhang, Menghuan / Miao, Pu / Nie, Yingjie / Zhang, Xiangyan / Hao, Zijian / Hu, Ronggui

Frontiers in genetics

2022 Volume 13, Page(s) 928393

Abstract: Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder with the underlying etiology yet incompletely understood and no cure treatment. Patients of fragile X syndrome (FXS) also manifest symptoms, e.g. deficits in social behaviors, that ...

Abstract	Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder with the underlying etiology yet incompletely understood and no cure treatment. Patients of fragile X syndrome (FXS) also manifest symptoms, e.g. deficits in social behaviors, that are core traits with ASD. Several studies demonstrated that a mutual defect in retinoic acid (RA) signaling was observed in FXS and ASD. However, it is still unknown whether RA replenishment could pose a positive effect on autistic-like behaviors in FXS. Herein, we found that RA signaling was indeed down-regulated when the expression of
Language	English
Publishing date	2022-06-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.928393
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Article: Investigation of relative permeability, saturation and capillary pressure relations of NAPL-contaminated sands

Mao, Baiyang / Liu, Songyu / Liu, Zhibin / Lu, Taishan / Zhang, Menghuan

Journal of soils and sediments. 2020 Mar., v. 20, no. 3

2020

Abstract: PURPOSE: The relations among relative permeability, saturation degree and capillary pressure (kr–S–P) in a three-phase system are important theoretical bases for the modelling of organic contaminant transport and physical remediation. The main purpose of ...

Abstract	PURPOSE: The relations among relative permeability, saturation degree and capillary pressure (kr–S–P) in a three-phase system are important theoretical bases for the modelling of organic contaminant transport and physical remediation. The main purpose of this study was to investigate the kr–S–P relations of organic contaminated sands. MATERIALS AND METHODS: Fine sand and medium sand were selected as the test media. Diesel, heptane and toluene were selected as the representative non-aqueous-phase liquids (NAPLs), and distilled water was taken as the aqueous phase. By using modified Parker’s scaling method, the S–P relations in two-phase systems (water–air, NAPL–air and water–NAPL) obtained by Buchner funnel tests were extended to a three-phase system. Then, applying the Mualem kr–S model to the S–P relations, the kr values of air, water and NAPL in a three-phase system were obtained and discussed. RESULTS AND DISCUSSION: The results showed that the entry pressure of the non-wetting phase in the two-phase system was jointly influenced by the interface tension between the non-wetting phase and the wetting phase. In the three-phase system, the kr of water and NAPL were smaller than 0.05 when the effective air saturation was greater than 0.7. The results also suggested that the kr of air has an approximate linear relation with [Formula: see text] from 0 to 0.6. CONCLUSIONS: When the air phase is dominant in the three-phase system, the aqueous phase and NAPL can be considered as the immobile phase, and the kr of the air phase can be approximately expressed as a linear decreasing relationship with [Formula: see text], which can be applied to simplify the modelling of soil vapour extraction (SVE). Furthermore, the study provides a useful theoretical reference for contaminant transport and physical remediation in organic contaminated sandy soils.
Keywords	air ; heptane ; nonaqueous phase liquids ; permeability ; remediation ; sand ; sandy soils ; soil vapor extraction ; toluene
Language	English
Dates of publication	2020-03
Size	p. 1609-1620.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	2050898-0
ISSN	1614-7480 ; 1439-0108
ISSN (online)	1614-7480
ISSN	1439-0108
DOI	10.1007/s11368-019-02506-0
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Article: Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Yang, Kankan / Zhang, Menghuan / Liu, Qi / Cao, Yingli / Zhang, Wuyin / Liang, Yueqiao / Song, Xiangjun / Ji, Kaiyuan / Shao, Ying / Qi, Kezong / Tu, Jian

Viruses. 2021 Nov. 15, v. 13, no. 11

2021

Abstract: Porcine circovirus-like virus (PCLV) is a type of circular Rep-encoding single-stranded DNA virus and may be associated with the development of diarrheal symptoms in pigs. In this study, we retrospectively analyzed three years of past cases in Anhui, ... ...

Abstract	Porcine circovirus-like virus (PCLV) is a type of circular Rep-encoding single-stranded DNA virus and may be associated with the development of diarrheal symptoms in pigs. In this study, we retrospectively analyzed three years of past cases in Anhui, China, and reported a case of hemorrhagic enteritis and death in a pregnant sow possibly caused by PCLV. In addition, we analyzed the evolutionary characteristics of PCLV and found that mutation, recombination and selective pressure all played an important role in the evolution of PCLV. We identified N15D and T17S as well as L56T, T58R, K59Q, M62R, L75I and R190K mutations in two different branches, and we noted recombination events in the Rep of a group of Chinese strains. Analysis of selection pressure revealed that PCLV gained more positive selection, indicating that the virus is in a continuous evolutionary state. The PR2 plot, ENC-plot and neutrality analysis showed a greater role of natural selection than that of mutational pressure in the formation of codon usage patterns. This study is the first to identify PCLV in sows with hemorrhagic dysentery and death, and it provides new epidemiological information on PCLV infection in pigs in China.
Keywords	DNA viruses ; codon usage ; death ; dysentery ; epidemiology ; hemorrhagic enteritis ; mutation ; natural selection ; selection pressure ; single-stranded DNA ; viruses ; China
Language	English
Dates of publication	2021-1115
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112282
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Article: PhoPepMass: A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data

Zhang, Menghuan / Hui Cui / Lanming Chen / Ying Yu / Michael O. Glocker / Lu Xie

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China Journal of genetics and genomics. 2018 July 20, v. 45, no. 7

2018

Abstract: Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides (phosphopeptides) and their corresponding phosphorylation sites ( ... ...

Abstract	Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides (phosphopeptides) and their corresponding phosphorylation sites (phosphosites) will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry (MS) provides a high-throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm. It contains 244,915 phosphosites from several public sources. Moreover, the accurate masses of peptides and fragments with phosphosites were calculated. It is the first database that provides a systematic resource for the query of phosphosites on peptides and their corresponding masses. This allows researchers to search certain proteins of which phosphosites have been reported, to browse detailed phosphopeptide and fragment information, to match masses from MS analyses with defined threshold to the corresponding phosphopeptide, and to compare proprietary phosphopeptide discovery results with results from previous studies. Additionally, a database search software is created and a “two-stage search strategy” is suggested to identify phosphopeptides from tandem mass spectra of proteomics data. We expect PhoPepMass to be a useful tool and a source of reference for proteomics researchers. PhoPepMass is available at https://www.scbit.org/phopepmass/index.html.
Keywords	algorithms ; browsing ; computer software ; databases ; humans ; mass spectrometry ; phosphopeptides ; protein phosphorylation ; proteins ; proteomics
Language	English
Dates of publication	2018-0720
Size	p. 381-388.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2374568-X
ISSN	1873-5533 ; 1673-8527
ISSN (online)	1873-5533
ISSN	1673-8527
DOI	10.1016/j.jgg.2018.07.005
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Article ; Online: ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.

Li, Yuyu / Wang, Guangzhi / Tan, Xiaoxiu / Ouyang, Jian / Zhang, Menghuan / Song, Xiaofeng / Liu, Qi / Leng, Qibin / Chen, Lanming / Xie, Lu

BMC medical genomics

2020 Volume 13, Issue Suppl 5, Page(s) 52

Abstract: Background: Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based ... ...

Abstract	Background: Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. Results: Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. Conclusions: The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
MeSH term(s)	Antigens, Neoplasm/analysis ; Antigens, Neoplasm/genetics ; Antigens, Neoplasm/immunology ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Histocompatibility Antigens Class I/immunology ; Humans ; Mutation ; Neoplasms/genetics ; Neoplasms/immunology ; Neoplasms/metabolism ; Neoplasms/pathology ; Proteogenomics ; Software ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism ; Workflow
Chemical Substances	Antigens, Neoplasm ; Histocompatibility Antigens Class I
Language	English
Publishing date	2020-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-020-0683-4
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