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Article ; Online: Systematically amino acid analysis: Advancements in extinction coefficient determination for therapeutic proteins.

Xu, Ya / Shao, Zhenzhen / Zhang, Lei / Cao, Yanjing / Liu, Zhuoyu / Zhang, Zhongli

2024 Volume 690, Page(s) 115508

Abstract: Biologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, ... ...

Abstract	Biologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the eight given proteins examined.
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2024.115508
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Article ; Online: Light energy utilization and microbial catalysis for enhanced biohydrogen: Ternary coupling system of triethanolamine-mediated Fe@C-Rhodobacter sphaeroides.

Jiang, Qiushi / Li, Yanjing / Wang, Minmin / Cao, Wen / Yang, Xueying / Zhang, Sihu / Guo, Liejin

Bioresource technology

2024 Volume 401, Page(s) 130733

Abstract: This study investigated the mediating effect of Triethanolamine on Fe@C-Rhodobacter sphaeroides hybrid photosynthetic system to achieve efficient biohydrogen production. The biocompatible Fe@C generates excited electrons upon exposure to light, releasing ...

Abstract	This study investigated the mediating effect of Triethanolamine on Fe@C-Rhodobacter sphaeroides hybrid photosynthetic system to achieve efficient biohydrogen production. The biocompatible Fe@C generates excited electrons upon exposure to light, releasing ferrum for nitrogenase synthesis, and regulating the pH of the fermentation environment. Triethanolamine was introduced to optimize the electron transfer chain, thereby improving system stability, prolonging electron lifespan, and facilitating ferrum corrosion. This, in turn, stimulated the lactic acid synthetic metabolic pathway of Rhodobacter sphaeroides, resulting in increased reducing power in the biohybrid system. The ternary coupling system was analyzed through the regulation of concentration, initial pH, and light intensity. The system achieved the highest total H
Language	English
Publishing date	2024-04-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2024.130733
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Article ; Online: In-Depth Characterization of mAb Charge Variants by On-Line Multidimensional Liquid Chromatography-Mass Spectrometry.

Liu, Zhuoyu / Cao, Yanjing / Zhang, Lei / Xu, Ya / Zhang, Zhongli

Analytical chemistry

2023 Volume 95, Issue 20, Page(s) 7977–7984

Abstract: In-depth characterization of charge heterogeneity is a pivotal step desired in the therapeutics antibody development. To this end, a novel on-line multidimensional liquid chromatography-mass spectrometry (MDLC-MS) method for charge variant ... ...

Abstract	In-depth characterization of charge heterogeneity is a pivotal step desired in the therapeutics antibody development. To this end, a novel on-line multidimensional liquid chromatography-mass spectrometry (MDLC-MS) method for charge variant characterization was developed to dig out potential risks on safety and efficacy. This method implemented 96-well plate fractionation and on-column preconcentration by multi-injection, thereby facilitating detection of charged species at low abundance. Eleven charge variants of mAb-A were preliminarily characterized by 2DLC(CEX × RP-C
MeSH term(s)	Antibodies, Monoclonal/chemistry ; Mass Spectrometry ; Chromatography, Liquid ; Chemical Fractionation ; Protein Sorting Signals
Chemical Substances	Antibodies, Monoclonal ; Protein Sorting Signals
Language	English
Publishing date	2023-05-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c00791
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Article ; Online: Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods.

Fan, Jianing / Shi, Shaohua / Xiang, Hong / Fu, Li / Duan, Yanjing / Cao, Dongsheng / Lu, Hongwei

Journal of chemical information and modeling

2024 Volume 64, Issue 8, Page(s) 3080–3092

Abstract: Half-life is a significant pharmacokinetic parameter included in the excretion phase of absorption, distribution, metabolism, and excretion. It is one of the key factors for the successful marketing of drug candidates. Therefore, predicting half-life is ... ...

Abstract	Half-life is a significant pharmacokinetic parameter included in the excretion phase of absorption, distribution, metabolism, and excretion. It is one of the key factors for the successful marketing of drug candidates. Therefore, predicting half-life is of great significance in drug design. In this study, we emplo
MeSH term(s)	Quantitative Structure-Activity Relationship ; Machine Learning ; Half-Life ; Pharmaceutical Preparations/chemistry ; Pharmaceutical Preparations/metabolism ; Small Molecule Libraries/chemistry ; Pharmacokinetics ; Support Vector Machine
Chemical Substances	Pharmaceutical Preparations ; Small Molecule Libraries
Language	English
Publishing date	2024-04-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c02030
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Association between the severity of metabolic dysfunction-associated fatty liver disease and the risk of colorectal neoplasm: a systematic review and meta-analysis.

Zeng, Yunqing / Cao, Ruyue / Tao, Ziwen / Gao, Yanjing

Lipids in health and disease

2022 Volume 21, Issue 1, Page(s) 52

Abstract: Background: The severity of metabolic dysfunction-associated fatty liver disease (MAFLD) reportedly plays a part in the etiology of colorectal tumors. However, there is no consensus.: Methods: Studies relevant with the impact of MAFLD severity on the ...

Abstract	Background: The severity of metabolic dysfunction-associated fatty liver disease (MAFLD) reportedly plays a part in the etiology of colorectal tumors. However, there is no consensus. Methods: Studies relevant with the impact of MAFLD severity on the risk of colorectal neoplasms published before 24th April 2022 were screened. The pooled odds ratio (OR) with corresponding 95% confidence intervals (95% CI) was obtained using standard and cumulative meta-analyses. Subgroup, meta-regression, and sensitivity analyses were carried out to identify heterogeneity. Results: Fourteen studies with data from 37,824 MAFLD patients were included. The prevalence of colorectal neoplasms escalated with the progression of MAFLD compared to simple steatosis (OR = 1.93; 95% CI = 1.42-2.62). The magnitude and direction of the effect on these outcomes remained largely constant over time. Even after limiting the meta-analysis to 8 studies with available adjusted OR (aOR), the findings still suggested that MAFLD severity was positively related to colorectal neoplasms (aOR = 3.03; 95% CI = 2.02-4.53). Severe MAFLD was more likely to cause left colon tumors (OR = 3.86, 95% CI = 2.16-6.91) than right colon neoplasms (OR = 1.94, 95% CI = 1.15-3.28). Conclusion: The severity of MAFLD was independently related to colorectal neoplasms and severe MAFLD was more likely to cause left colon tumors.
MeSH term(s)	Colonic Neoplasms ; Colorectal Neoplasms/epidemiology ; Colorectal Neoplasms/etiology ; Humans ; Non-alcoholic Fatty Liver Disease/pathology ; Prevalence
Language	English
Publishing date	2022-06-06
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Review ; Systematic Review
ZDB-ID	2091381-3
ISSN	1476-511X ; 1476-511X
ISSN (online)	1476-511X
ISSN	1476-511X
DOI	10.1186/s12944-022-01659-1
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Book ; Online: Confidence-driven Bounding Box Localization for Small Object Detection

Sun, Huixin / Zhang, Baochang / Li, Yanjing / Cao, Xianbin

2023

Abstract: Despite advancements in generic object detection, there remains a performance gap in detecting small objects compared to normal-scale objects. We for the first time observe that existing bounding box regression methods tend to produce distorted gradients ...

Abstract	Despite advancements in generic object detection, there remains a performance gap in detecting small objects compared to normal-scale objects. We for the first time observe that existing bounding box regression methods tend to produce distorted gradients for small objects and result in less accurate localization. To address this issue, we present a novel Confidence-driven Bounding Box Localization (C-BBL) method to rectify the gradients. C-BBL quantizes continuous labels into grids and formulates two-hot ground truth labels. In prediction, the bounding box head generates a confidence distribution over the grids. Unlike the bounding box regression paradigms in conventional detectors, we introduce a classification-based localization objective through cross entropy between ground truth and predicted confidence distribution, generating confidence-driven gradients. Additionally, C-BBL describes a uncertainty loss based on distribution entropy in labels and predictions to further reduce the uncertainty in small object localization. The method is evaluated on multiple detectors using three object detection benchmarks and consistently improves baseline detectors, achieving state-of-the-art performance. We also demonstrate the generalizability of C-BBL to different label systems and effectiveness for high resolution detection, which validates its prospect as a general solution.
Keywords	Computer Science - Computer Vision and Pattern Recognition
Publishing date	2023-03-03
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In-Depth Characterization of mAb Charge Variants by On-Line Multidimensional Liquid Chromatography-Mass Spectrometry

Liu, Zhuoyu / Cao, Yanjing / Zhang, Lei / Xu, Ya / Zhang, Zhongli

Analytical Chemistry. 2023 May 12, v. 95, no. 20 p.7977-7984

2023

Abstract	In-depth characterization of charge heterogeneity is a pivotal step desired in the therapeutics antibody development. To this end, a novel on-line multidimensional liquid chromatography-mass spectrometry (MDLC-MS) method for charge variant characterization was developed to dig out potential risks on safety and efficacy. This method implemented 96-well plate fractionation and on-column preconcentration by multi-injection, thereby facilitating detection of charged species at low abundance. Eleven charge variants of mAb-A were preliminarily characterized by 2DLC(CEX × RP-C₄)-MS. TRVHS and RVHS signal peptide variants of mAb-A were found in basic peaks of the CEX profile. The results supported process development in a timely manner, and the signal peptide-containing variants with potential immunogenicity were successfully removed by an optimized purification process. The retained seven charge variants of mAb-A were further characterized by 4DLC(CEX × RP-C₄ × Trypsin×RP-C₁₈)-MS. Post-translational modifications including deamidation, cyclization of N-terminal glutamine, C-terminal lysine truncation as well as proline amidation, and methionine oxidation were identified, and their potential risks were evaluated. Biological activity of the seven charge variants was evaluated by 2DLC (CEX × FcγRIIIa). Increased FcγRIIIa receptor binding affinity was observed in the acidic variants. The MDLC-MS detection can be completed in 72 h with 1.25 mg of mAb, demonstrating to be sample-economic, time-effective, and labor-saving. It provided a powerful and timely tool for charge variant characterization and met the aggressive timeline desired for antibody development.
Keywords	analytical chemistry ; antibodies ; bioactive properties ; deamidation ; fractionation ; glutamine ; immunogenicity ; liquid chromatography ; lysine ; mass spectrometry ; methionine ; oxidation ; proline ; purification methods ; signal peptide ; therapeutics
Language	English
Dates of publication	2023-0512
Size	p. 7977-7984.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c00791
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Selective Anchoring by Surface Sulfur Species Coupled with Rapid Interface Electron Transfer for Ultrahigh Capacity Extraction of Uranium from Seawater.

Wei, Jianrong / Chen, Siping / Jiang, Yimin / Liu, Zhijuan / Wang, Yanjing / You, Jie / Zhang, Fei / Cao, Yu / Wang, Shuangyin / Wang, Yanyong

Environmental science & technology

2023 Volume 57, Issue 51, Page(s) 21908–21916

Abstract: Improving the adsorption selectivity, enhancing the extraction capacity, and ensuring the structural stability of the adsorbent are the key to realize the high efficiency recovery of uranium. In this work, we utilized the strong Lewis acid-base ... ...

Abstract	Improving the adsorption selectivity, enhancing the extraction capacity, and ensuring the structural stability of the adsorbent are the key to realize the high efficiency recovery of uranium. In this work, we utilized the strong Lewis acid-base interaction between S
MeSH term(s)	Uranium/chemistry ; Electrons ; Electron Transport ; Sulfur ; Adsorption ; Seawater
Chemical Substances	Uranium (4OC371KSTK) ; Sulfur (70FD1KFU70)
Language	English
Publishing date	2023-12-12
Publishing country	United States
Document type	Journal Article
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c07719
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Article ; Online: An Anisotropic Hydrogel by Programmable Ionic Crosslinking for Sequential Two-Stage Actuation under Single Stimulus.

Zhang, Yanjing / Cao, Xingyu / Zhao, Yuyu / Li, Huahuo / Xiao, Shengwei / Chen, Zhangxin / Huang, Guobo / Sun, Ye / Liu, Zhenzhong / He, Zhicai

Gels (Basel, Switzerland)

2023 Volume 9, Issue 4

Abstract: As one of the most important anisotropic intelligent materials, bi-layer stimuli-responsive actuating hydrogels have proven their wide potential in soft robots, artificial muscles, biosensors, and drug delivery. However, they can commonly provide a ... ...

Abstract	As one of the most important anisotropic intelligent materials, bi-layer stimuli-responsive actuating hydrogels have proven their wide potential in soft robots, artificial muscles, biosensors, and drug delivery. However, they can commonly provide a simple one-actuating process under one external stimulus, which severely limits their further application. Herein, we have developed a new anisotropic hydrogel actuator by local ionic crosslinking on the poly(acrylic acid) (PAA) hydrogel layer of the bi-layer hydrogel for sequential two-stage bending under a single stimulus. Under pH = 13, ionic-crosslinked PAA networks undergo shrinking (-COO
Language	English
Publishing date	2023-03-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813982-3
ISSN	2310-2861 ; 2310-2861
ISSN (online)	2310-2861
ISSN	2310-2861
DOI	10.3390/gels9040279
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Book ; Online: Bi-ViT

Li, Yanjing / Xu, Sheng / Lin, Mingbao / Cao, Xianbin / Liu, Chuanjian / Sun, Xiao / Zhang, Baochang

Pushing the Limit of Vision Transformer Quantization

2023

Abstract: Vision transformers (ViTs) quantization offers a promising prospect to facilitate deploying large pre-trained networks on resource-limited devices. Fully-binarized ViTs (Bi-ViT) that pushes the quantization of ViTs to its limit remain largely unexplored ... ...

Abstract	Vision transformers (ViTs) quantization offers a promising prospect to facilitate deploying large pre-trained networks on resource-limited devices. Fully-binarized ViTs (Bi-ViT) that pushes the quantization of ViTs to its limit remain largely unexplored and a very challenging task yet, due to their unacceptable performance. Through extensive empirical analyses, we identify the severe drop in ViT binarization is caused by attention distortion in self-attention, which technically stems from the gradient vanishing and ranking disorder. To address these issues, we first introduce a learnable scaling factor to reactivate the vanished gradients and illustrate its effectiveness through theoretical and experimental analyses. We then propose a ranking-aware distillation method to rectify the disordered ranking in a teacher-student framework. Bi-ViT achieves significant improvements over popular DeiT and Swin backbones in terms of Top-1 accuracy and FLOPs. For example, with DeiT-Tiny and Swin-Tiny, our method significantly outperforms baselines by 22.1% and 21.4% respectively, while 61.5x and 56.1x theoretical acceleration in terms of FLOPs compared with real-valued counterparts on ImageNet.
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	306
Publishing date	2023-05-21
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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