LIVIVO - Search results -

Search results

Result 1 - 10 of total 103

Search options

Article: Adult pancreatoblastoma with atypical histological morphology combined with familial adenomatous polyposis: a rare case report.

Wang, Ying-Xia / Fan, Su-Su / Peng, Xue-Rong / Zhu, Yu-Shan / Zhang, Xuan

2024 Volume 14, Page(s) 1346964

Abstract: Pancreatoblastoma (PB) is a rare malignant pancreatic epithelial tumor that mostly occurs in children and occasionally occurs in adults. The tumor has acinar cell differentiation and squamous corpuscles/squamous epithelial islands, which are frequently ... ...

Abstract	Pancreatoblastoma (PB) is a rare malignant pancreatic epithelial tumor that mostly occurs in children and occasionally occurs in adults. The tumor has acinar cell differentiation and squamous corpuscles/squamous epithelial islands, which are frequently separated by fibrous bundles. Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease characterized by the presence of numerous adenomatous polyps in the colon and rectum. Cases of pancreatoblastoma combined with familial adenomatous polyposis (FAP) are rarely reported. A review of a rare case of adult pancreatoblastoma with atypical histological morphology combined with familial adenomatous polyposis is presented herein. In this case, the patient was first diagnosed with familial adenomatous polyposis and subsequently found to have pancreatoblastoma 1 year and 3 months later. This suggests pancreatoblastoma may occur in patients with familial adenomatous polyposis or a family history of the condition, indicating a possible association between the two tumors. Therefore, pancreatoblastoma should be included in a differential diagnosis for FAP patients with a pancreatic mass. The final diagnosis of pancreatoblastoma depends on the pathological diagnosis. Acinar-like cells and squamous corpuscles/squamous epithelial cell islands under light microscopy are the key diagnostic points. This case report also can improve the awareness of clinicians, radiologists, and pathologists on the presence of rare tumor-adult pancreatoblastoma in patients with familial adenomatous polyposis.
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2024.1346964
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes.

Wang, Pengyu / Zhang, Jun / Zhang, Shengyu / Lu, Diannan / Zhu, Yushan

Journal of chemical information and modeling

2023 Volume 63, Issue 4, Page(s) 1323–1337

Abstract: Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling ... ...

Abstract	Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling accuracy of current computational enzyme design methods should be improved. Here, high-throughput molecular dynamics simulations were used to enhance computational enzyme design, thus allowing the identification of variants with higher activities in silico. Different time schemes of high-throughput molecular dynamics simulations were tested to identify the catalytic features of evolved Kemp eliminases. The 20 × 1 ns molecular dynamics simulation scheme was sufficiently accurate and computationally viable to screen the computationally designed massive variants of Kemp elimination enzymes. The developed hybrid computational strategy was used to redesign the most active Kemp eliminase, HG3.17, and five variants were generated and experimentally confirmed to afford higher catalytic efficiencies than that of HG3.17, with one double variant (D52Q/A53S) exhibiting a 55% increase. The hybrid computational enzyme design strategy is general and computationally economical, with which we anticipate the efficient creation of practical enzymes for industrial biocatalysis.
MeSH term(s)	Molecular Dynamics Simulation ; Biocatalysis ; Catalysis ; Enzymes/metabolism ; Protein Engineering
Chemical Substances	Enzymes
Language	English
Publishing date	2023-02-13
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.3c00002
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1230: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences.

Li, Mengyu / Wang, Hongzhao / Yang, Zhenwu / Zhang, Longgui / Zhu, Yushan

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 5544–5560

Abstract: Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting ... ...

Abstract	Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting temperature (
Language	English
Publishing date	2023-11-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.11.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A noncanonical autophagy function of ATG9A for Golgi integrity and dynamics.

Meng, Yuanyuan / Luo, Qian / Chen, Quan / Zhu, Yushan

Autophagy

2022 Volume 19, Issue 5, Page(s) 1607–1608

Abstract: In mammalian cells, the Golgi apparatus serves as the central hub for membrane trafficking. Notably, the membrane trafficking and Golgi integrity are tightly regulated by reversible post-translational modifications, such as glycosylation, phosphorylation ...

Abstract	In mammalian cells, the Golgi apparatus serves as the central hub for membrane trafficking. Notably, the membrane trafficking and Golgi integrity are tightly regulated by reversible post-translational modifications, such as glycosylation, phosphorylation and ubiquitination. Nonetheless, how the Golgi apparatus responses to stress to ensure appropriate membrane assembly and distribution of cargo is poorly understood. The Golgi resident protein ATG9A is the only multi-spanning membrane protein in the ATG family and has been demonstrated to traffic through the plasma membrane, endosomes and Golgi to deliver materials for the initiation of macroautophagy/autophagy. Our recent work reveals a noncanonical function of ATG9A for Golgi dynamics and identifies a pathway for sensing Golgi stress via the MARCHF9-ATG9A axis.
MeSH term(s)	Animals ; Autophagy ; Vesicular Transport Proteins/metabolism ; Protein Transport ; Membrane Proteins/metabolism ; Golgi Apparatus/metabolism ; Autophagy-Related Proteins/metabolism ; Mammals/metabolism
Chemical Substances	Vesicular Transport Proteins ; Membrane Proteins ; Autophagy-Related Proteins
Language	English
Publishing date	2022-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2022.2131244
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6741: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: A preorganization oriented computational method for de novo design of Kemp elimination enzymes.

Zhang, Shengyu / Zhang, Jun / Luo, Wenjia / Wang, Pengyu / Zhu, Yushan

Enzyme and microbial technology

2022 Volume 160, Page(s) 110093

Abstract: A preorganization oriented computational strategy for de novo enzyme design based on computational enzyme design tool PRODA was developed and demonstrated by the creation of Kemp elimination enzymes. A pre-organized active site model of proton transfer ... ...

Abstract	A preorganization oriented computational strategy for de novo enzyme design based on computational enzyme design tool PRODA was developed and demonstrated by the creation of Kemp elimination enzymes. A pre-organized active site model of proton transfer from carbon with a low energy barrier was proposed and then anchored into the scaffold 3AOF, the endoglucanase from Thermotoga maritima, which was selected from the protein structural database. The low-energy amino acid sequences at the binding pocket to stabilize the catalytic productive geometry were computationally generated via the iterative protein redesign and molecular dynamics simulation. The designed variant (3AOF-KE03) bearing 17 mutations was experimentally confirmed to afford catalytic activity (k
MeSH term(s)	Catalysis ; Catalytic Domain ; Enzymes/metabolism ; Molecular Dynamics Simulation ; Protons
Chemical Substances	Enzymes ; Protons
Language	English
Publishing date	2022-07-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	423729-8
ISSN	1879-0909 ; 0141-0229
ISSN (online)	1879-0909
ISSN	0141-0229
DOI	10.1016/j.enzmictec.2022.110093
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.B 2182: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Solitary Fibrous Tumors of the Lung: A Clinicopathological Analysis of 52 Cases.

Wang, Ying-Xia / Zhong, Yan / Fan, Su-Su / Zhu, Yu-Shan / Peng, Xue-Rong / Zhang, Xuan

Current oncology (Toronto, Ont.)

2023 Volume 30, Issue 2, Page(s) 1784–1793

Abstract: Objective: To explore the clinicopathological features of solitary fibrous tumors (SFTs) of the lung.: Methods: We collected the clinical data of 52 patients with SFTs of the lung confirmed by pathology, and summarized the clinical, radiological, and ...

Abstract	Objective: To explore the clinicopathological features of solitary fibrous tumors (SFTs) of the lung. Methods: We collected the clinical data of 52 patients with SFTs of the lung confirmed by pathology, and summarized the clinical, radiological, and morphological features, the immunophenotypes, and the prognosis of SFTs. Results: Fifty-two cases of SFTs of the lung were enrolled in this study, including 51 cases of borderline and 1 case of malignancy, 22 males and 30 females. The average onset age was 52.7 years. The lower lobe of the left lung was the preferred site of SFTs, accounting for 30.77% (16/52). Chest CT showed regular and well-demarcated soft tissue density mass, and the tumor size of most cases (46/52, 88.46%) was 1-10 cm. Morphological features: The distribution of tumor cells showed sparse and dense areas. Tumor cells were spindle-shaped, in whorls or hemangiopericytoma-like conformation. Atypia, mitotic figures, and necrosis were found. Immunohistochemistry showed positive expression of CD34, STAT6, Vimentin, BCL2, and CD99. Ki-67 was ≤ 5% in borderline SFTs and >20% in a malignant SFT. Conclusions: Solitary fibrous tumors of the lung occur more frequently in middle-aged and elderly people, and there is no significant difference in gender. The lower lobe of the left lung is the preferred site of SFTs. The size of most SFTs is 1-10 cm. Chest CT shows morphologically regular and well-demarcated soft tissue density mass. Pathologically, SFTs of the lung are mostly borderline and occasionally malignant. Immunohistochemistry shows the positive expression of CD34, STAT6, Vimentin, BCL2, and CD99.
MeSH term(s)	Aged ; Middle Aged ; Male ; Female ; Humans ; Vimentin ; Severe Fever with Thrombocytopenia Syndrome ; Biomarkers, Tumor/analysis ; Solitary Fibrous Tumors/genetics ; Solitary Fibrous Tumors/metabolism ; Solitary Fibrous Tumors/pathology ; Lung/pathology ; Proto-Oncogene Proteins c-bcl-2
Chemical Substances	Vimentin ; Biomarkers, Tumor ; Proto-Oncogene Proteins c-bcl-2
Language	English
Publishing date	2023-02-01
Publishing country	Switzerland
Document type	Case Reports ; Research Support, Non-U.S. Gov't
ZDB-ID	1236972-x
ISSN	1718-7729 ; 1198-0052
ISSN (online)	1718-7729
ISSN	1198-0052
DOI	10.3390/curroncol30020138
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 4305: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Computational design of penicillin acylase variants with improved kinetic selectivity for the enzymatic synthesis of cefazolin

Wang, Pengyu / Zhang, Shengyu / Zhang, Jun / Zhu, Yushan

Biochemical engineering journal. 2021 Nov., v. 175

2021

Abstract: Enzymatic synthesis plays a pivotal role in the sustainable production of semi-synthetic β-lactam antibiotics. However, these types of green syntheses are being developed slowly because of a lack of appropriate enzymes. In the present work, a ... ...

Abstract	Enzymatic synthesis plays a pivotal role in the sustainable production of semi-synthetic β-lactam antibiotics. However, these types of green syntheses are being developed slowly because of a lack of appropriate enzymes. In the present work, a computational strategy was developed to identify variants of penicillin G acylase that can catalyze the condensation between methyl 1H-tetrazol-1-yl acetate (TZAM) and 7-amino-3-[(5-methyl-1,3,4-thiadiazol-2-yl) thiomethyl] cephalosphoranic acid (7-ZACA) to produce cefazolin in a fully aqueous medium. An initial library containing 770 sequences was generated by our computational enzyme design program PRODA, which applied a deterministic global minimization algorithm to optimize the binding between the acyl donor and the attacking nucleophile for high kinetic selectivity. The 13 top-ranked variants were subjected to experimental testing based on evaluation by multiple short-time molecular dynamics simulations. A single variant (R145αG) was experimentally confirmed to afford higher kinetic selectivity with a synthesis/hydrolysis ratio (S/H) that was increased by approximately 40% compared with the wild type, and the immobilized enzyme catalyst gave a yield of cefazolin of up to 92% with a 1.8:1 molar ratio of TZAM/7-ZACA, which to our knowledge is the lowest molar ratio of TZAM/7-ZACA to produce a yield over 90%. This study represents considerable progress toward cefazolin synthesis under practical conditions and indicates that this computational strategy could improve enzyme properties for the bio-manufacturing of non-natural molecules.
Keywords	Lewis bases ; acetates ; algorithms ; catalysts ; cefazolin ; hydrolysis ; immobilized enzymes ; molecular dynamics ; penicillin amidase
Language	English
Dates of publication	2021-11
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2012139-8
ISSN	1369-703X
ISSN	1369-703X
DOI	10.1016/j.bej.2021.108149
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article: Classification of JAK1 Inhibitors and SAR Research by Machine Learning Methods

Yang, Zhenwu / Tian, Yujia / Kong, Yue / Zhu, Yushan / Yan, Aixia

Artificial intelligence in the life sciences. 2022 Dec., v. 2

2022

Abstract: Janus kinase 1 (JAK1) is a key regulator of gene transcription, inhibition of JAK1 is an intervention for many diseases including rheumatoid arthritis and Crohn's disease. In this study, we collected a dataset containing 2982 JAK1 inhibitors, ... ...

Abstract	Janus kinase 1 (JAK1) is a key regulator of gene transcription, inhibition of JAK1 is an intervention for many diseases including rheumatoid arthritis and Crohn's disease. In this study, we collected a dataset containing 2982 JAK1 inhibitors, characterized molecules by MACCS fingerprints and Morgan fingerprints. We used support vector machine (SVM), decision tree (DT), random forest (RF) and extreme gradient boosting tree (XGBoost) algorithms to build 16 traditional machine learning classification models. Additionally, we utilized deep neural networks (DNN) to develop four deep learning models. The best model (Model 3B) built by RF and Morgan fingerprints achieved the accuracy (ACC) of 93.6% and Mathews correlation coefficient (MCC) of 0.87 on the test set. Furthermore, we made structure–activity relationship (SAR) analyses for JAK1 inhibitors, based on the output from the random forest models. After analyzing the important keys of two types of fingerprints, it was observed that some substructures such as pyrazole, pyrrolotriazolopyrimidine and pyrazolopyrimidine appeared frequently in highly active JAK1 inhibitors.
Keywords	Crohn disease ; data collection ; decision support systems ; non-specific protein-tyrosine kinase ; rheumatoid arthritis ; structure-activity relationships ; support vector machines ; transcription (genetics) ; trees
Language	English
Dates of publication	2022-12
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2667-3185
DOI	10.1016/j.ailsci.2022.100039
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: A preorganization oriented computational method for de novo design of Kemp elimination enzymes

Zhang, Shengyu / Zhang, Jun / Luo, Wenjia / Wang, Pengyu / Zhu, Yushan

Enzyme and microbial technology. 2022 Oct., v. 160

2022

Abstract	A preorganization oriented computational strategy for de novo enzyme design based on computational enzyme design tool PRODA was developed and demonstrated by the creation of Kemp elimination enzymes. A pre-organized active site model of proton transfer from carbon with a low energy barrier was proposed and then anchored into the scaffold 3AOF, the endoglucanase from Thermotoga maritima, which was selected from the protein structural database. The low-energy amino acid sequences at the binding pocket to stabilize the catalytic productive geometry were computationally generated via the iterative protein redesign and molecular dynamics simulation. The designed variant (3AOF-KE03) bearing 17 mutations was experimentally confirmed to afford catalytic activity (kcat/KM=14.04M−1s−1) towards Kemp elimination, with measured rate (kcat=0.033s−1) enhancement of up to 10⁴-fold. This computational strategy is general, and we anticipate the creation of a wide range of artificial enzymes to catalyze reactions with industrial significance in the future.
Keywords	Thermotoga maritima ; active sites ; amino acids ; carbon ; catalytic activity ; databases ; endo-1,4-beta-glucanase ; energy ; geometry ; models ; molecular dynamics
Language	English
Dates of publication	2022-10
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	423729-8
ISSN	1879-0909 ; 0141-0229
ISSN (online)	1879-0909
ISSN	0141-0229
DOI	10.1016/j.enzmictec.2022.110093
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.B 2182: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Computational design of new enzymes for hydrolysis and synthesis of third-generation cephalosporin antibiotics.

Xue, Jing / Wang, Pengyu / Kuang, Jianyong / Zhu, Yushan

Enzyme and microbial technology

2020 Volume 140, Page(s) 109649

Abstract: Engineering active sites in inert scaffolds to catalyze chemical transformations with unnatural substrates is still a great challenge for enzyme catalysis. In this research, a p-nitrobenzyl esterase from Bacillus subtilis was identified from the ... ...

Abstract	Engineering active sites in inert scaffolds to catalyze chemical transformations with unnatural substrates is still a great challenge for enzyme catalysis. In this research, a p-nitrobenzyl esterase from Bacillus subtilis was identified from the structural database, and a double mutant E115A/E188A was designed to afford catalytic activities toward the hydrolysis of ceftizoxime. A quadruple mutant E115A/E188A/L362S/I270A with enhanced catalytic efficiency was created to catalyze the condensation reaction of ethyl-2-methoxy-amino-2-(2-aminothiazole-4-yl) acetate with 7-amino-3-nor-cephalosporanic acid to produce ceftizoxime in a fully aqueous medium. The catalytic efficiencies of the computationally designed mutants E115A/E188A/L362S/I270A and E115A/Y118 K/E188 V/I270A/L362S can be taken as starting points to further improve their properties towards the practical application in designing more ecology-friendly production of third-generation cephalosporins.
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Bacillus subtilis/enzymology ; Bacillus subtilis/genetics ; Carboxylic Ester Hydrolases/chemistry ; Carboxylic Ester Hydrolases/genetics ; Carboxylic Ester Hydrolases/metabolism ; Catalysis ; Catalytic Domain ; Ceftizoxime/chemistry ; Ceftizoxime/metabolism ; Cephalosporins/chemistry ; Cephalosporins/metabolism ; Hydrolysis ; Kinetics ; Models, Molecular ; Mutation ; Protein Engineering/methods
Chemical Substances	Anti-Bacterial Agents ; Cephalosporins ; Ceftizoxime (C43C467DPE) ; 4-nitrobenzyl esterase (EC 3.1.1.-) ; Carboxylic Ester Hydrolases (EC 3.1.1.-)
Language	English
Publishing date	2020-08-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	423729-8
ISSN	1879-0909 ; 0141-0229
ISSN (online)	1879-0909
ISSN	0141-0229
DOI	10.1016/j.enzmictec.2020.109649
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.B 2182: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito