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Article ; Online: FTO elicits tumor neovascularization in cancer-associated fibroblasts through eliminating m

Liao, Qili / Shi, Hanhan / Yang, Jie / Ge, Shengfang / Jia, Ruobing / Song, Xin / Jia, Renbing / Chai, Peiwei

2024 , Page(s) 216911

Abstract: Cancer-associated fibroblasts (CAFs) exhibit notable versatility, plasticity, and robustness, actively participating in cancer progression through intricate interactions within the tumor microenvironment (TME). N6-methyladenosine ( ... ...

Abstract	Cancer-associated fibroblasts (CAFs) exhibit notable versatility, plasticity, and robustness, actively participating in cancer progression through intricate interactions within the tumor microenvironment (TME). N6-methyladenosine (m
Language	English
Publishing date	2024-04-27
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	195674-7
ISSN	1872-7980 ; 0304-3835
ISSN (online)	1872-7980
ISSN	0304-3835
DOI	10.1016/j.canlet.2024.216911
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Zs.A 1177: Show issues

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Article ; Online: Multiomics profiling of the therapeutic effect of Dan-deng-tong-nao capsule on cerebral ischemia-reperfusion injury.

Shi, Yingying / Du, Qiuzheng / Li, Zhuolun / Xue, Lianping / Jia, Qingquan / Zheng, Tianyuan / Liu, Jiyun / Ren, Ruobing / Sun, Zhi

Phytomedicine : international journal of phytotherapy and phytopharmacology

2024 Volume 128, Page(s) 155335

Abstract: Background: Stroke is a complex physiological process associated with intestinal flora dysbiosis and metabolic disorders. Dan-deng-tong-nao capsule (DDTN) is a traditional Chinese medicine used clinically to treat cerebral ischemia-reperfusion injury ( ... ...

Abstract	Background: Stroke is a complex physiological process associated with intestinal flora dysbiosis and metabolic disorders. Dan-deng-tong-nao capsule (DDTN) is a traditional Chinese medicine used clinically to treat cerebral ischemia-reperfusion injury (CIRI) for many years. However, little is known about the effects of DDTN in the treatment of CIRI from the perspective of gut microbiota and metabolites. Purpose: This study aimed to investigate the regulatory roles of DDTN in endogenous metabolism and gut microbiota in CIRI rats, thus providing a basis for clinical rational drug use and discovering natural products with potential physiological activities in DDTN for the treatment of CIRI. Methods: The chemical composition of DDTN in vitro and in vivo was investigated using ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLCHRMS), followed by target prediction using reverse molecular docking. Secondly, a biological evaluation of DDTN ameliorating neural damage in CIRI was performed at the whole animal level. Then, an integrated omics approach based on UHPLCHRMS and 16S rRNA sequencing was proposed to reveal the anti-CIRI effect and possible mechanism of DDTN. Finally, exploring the intrinsic link between changes in metabolite profiles, changes in the intestinal flora, and targets of components to reveal DDTN for the treatment of CIRI. Results: A total of 112 chemical components of DDTN were identified in vitro and 10 absorbed constituents in vivo. The efficacy of DDTN in the treatment of CIRI was confirmed by alleviating cerebral infarction and neurological deficits. After the DDTN intervention, 21 and 26 metabolites were significantly altered in plasma and fecal, respectively. Based on the fecal microbiome, a total of 36 genera were enriched among the different groups. Finally, the results of the network integration analysis showed that the 10 potential active ingredients of DDTN could mediate the differential expression of 24 metabolites and 6 gut microbes by targeting 25 target proteins. Conclusion: This study was the first to outline the landscapes of metabolites as well as gut microbiota regulated by DDTN in CIRI rats using multi-omics data, and comprehensively revealed the systematic relationships among ingredients, targets, metabolites, and gut microbiota, thus providing new perspectives on the mechanism of DDTN in the treatment of CIRI.
MeSH term(s)	Animals ; Drugs, Chinese Herbal/pharmacology ; Drugs, Chinese Herbal/chemistry ; Reperfusion Injury/drug therapy ; Gastrointestinal Microbiome/drug effects ; Male ; Rats, Sprague-Dawley ; Rats ; Brain Ischemia/drug therapy ; Molecular Docking Simulation ; Chromatography, High Pressure Liquid ; RNA, Ribosomal, 16S ; Capsules ; Multiomics
Chemical Substances	Drugs, Chinese Herbal ; RNA, Ribosomal, 16S ; Capsules
Language	English
Publishing date	2024-01-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1205240-1
ISSN	1618-095X ; 0944-7113
ISSN (online)	1618-095X
ISSN	0944-7113
DOI	10.1016/j.phymed.2023.155335
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Zs.A 4115: Show issues

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Article ; Online: An efficient framework for lesion segmentation in ultrasound images using global adversarial learning and region-invariant loss.

Manh, Van / Jia, Xiaohong / Xue, Wufeng / Xu, Wenwen / Mei, Zihan / Dong, Yijie / Zhou, Jianqiao / Huang, Ruobing / Ni, Dong

Computers in biology and medicine

2024 Volume 171, Page(s) 108137

Abstract: Lesion segmentation in ultrasound images is an essential yet challenging step for early evaluation and diagnosis of cancers. In recent years, many automatic CNN-based methods have been proposed to assist this task. However, most modern approaches often ... ...

Abstract	Lesion segmentation in ultrasound images is an essential yet challenging step for early evaluation and diagnosis of cancers. In recent years, many automatic CNN-based methods have been proposed to assist this task. However, most modern approaches often lack capturing long-range dependencies and prior information making it difficult to identify the lesions with unfixed shapes, sizes, locations, and textures. To address this, we present a novel lesion segmentation framework that guides the model to learn the global information about lesion characteristics and invariant features (e.g., morphological features) of lesions to improve the segmentation in ultrasound images. Specifically, the segmentation model is guided to learn the characteristics of lesions from the global maps using an adversarial learning scheme with a self-attention-based discriminator. We argue that under such a lesion characteristics-based guidance mechanism, the segmentation model gets more clues about the boundaries, shapes, sizes, and positions of lesions and can produce reliable predictions. In addition, as ultrasound lesions have different textures, we embed this prior knowledge into a novel region-invariant loss to constrain the model to focus on invariant features for robust segmentation. We demonstrate our method on one in-house breast ultrasound (BUS) dataset and two public datasets (i.e., breast lesion (BUS B) and thyroid nodule from TNSCUI2020). Experimental results show that our method is specifically suitable for lesion segmentation in ultrasound images and can outperform the state-of-the-art approaches with Dice of 0.931, 0.906, and 0.876, respectively. The proposed method demonstrates that it can provide more important information about the characteristics of lesions for lesion segmentation in ultrasound images, especially for lesions with irregular shapes and small sizes. It can assist the current lesion segmentation models to better suit clinical needs.
MeSH term(s)	Humans ; Image Processing, Computer-Assisted/methods ; Ultrasonography ; Breast ; Thyroid Nodule
Language	English
Publishing date	2024-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108137
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Zs.A 653: Show issues

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Article ; Online: Preparation of novel gallic acid-based dummy-template molecularly imprinted polymer adsorbents for rapid adsorption of dibutyl phthalate from water.

Li, Shunying / Zhou, Yuanhao / Xu, Qiangqiang / Chen, Haoxiang / Shi, Shengpeng / Jia, Ruobing / Zhang, Yingying / Ye, Hong

Environmental pollution (Barking, Essex : 1987)

2024 Volume 349, Page(s) 123917

Abstract: Phthalate esters (PAEs) are plasticizers widely used in the industry and easily released into the environment, posing a serious threat to human health. Molecularly imprinted polymers (MIPs) are important as selective adsorbents for the removal of PAEs. ... ...

Abstract	Phthalate esters (PAEs) are plasticizers widely used in the industry and easily released into the environment, posing a serious threat to human health. Molecularly imprinted polymers (MIPs) are important as selective adsorbents for the removal of PAEs. In this study, three kinds of mussel-inspired MIPs for the removal of PAEs were first prepared with gallic acid (GA), hexanediamine (HD), tannic acid (TA), and dopamine (DA) under mild conditions. The adsorption results showed that the MIP with low cost derived from GA and HD (GAHD-MIP) obtained the highest adsorption capacity among these materials. Furthermore, 97.43% of equilibrium capacity could be reached within the first 5 min of adsorption. Especially, the dummy template of diallyl phthalate (DAP) with low toxicity was observed to be more suitable to prepare MIPs than dibutyl phthalate (DBP), although DBP was the target of adsorption. The adsorption process was in accordance with the pseudo-second-order kinetics model. In the isotherm analysis, the adsorption behavior agreed with the Freundlich model. Additionally, the material maintained high adsorption performance after 7 cycles of regeneration tests. The GAHD-MIP adsorbents in this study, with low cost, rapid adsorption equilibrium, green raw materials, and low toxicity dummy template, provide a valuable reference for the design and development of new MIPs.
MeSH term(s)	Adsorption ; Dibutyl Phthalate/chemistry ; Water Pollutants, Chemical/chemistry ; Gallic Acid/chemistry ; Molecularly Imprinted Polymers/chemistry ; Phthalic Acids/chemistry ; Kinetics ; Water Purification/methods
Chemical Substances	Dibutyl Phthalate (2286E5R2KE) ; Water Pollutants, Chemical ; Gallic Acid (632XD903SP) ; Molecularly Imprinted Polymers ; Phthalic Acids
Language	English
Publishing date	2024-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2024.123917
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Zs.A 2599: Show issues

Location:
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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: MYC-targeted genes predict distant recurrence in patients with ocular adnexal extranodal marginal zone lymphoma.

Zhu, Tianyu / Shi, Jiahao / Zhou, Xiaowen / Qiu, Cen / Jia, Ruobing / Huang, Shiyun / Jia, Renbing / Wang, Yefei / Song, Xin / Zhou, Yixiong

Annals of hematology

2023 Volume 102, Issue 9, Page(s) 2413–2423

Abstract: Ocular adnexal extranodal marginal zone lymphoma (OA-EMZL) is the most frequent subtype of ocular adnexal lymphoma, with a high propensity for recurrence. Distant recurrence (DR) as an essential prognostic event has unique clinical risk factors, but ... ...

Abstract	Ocular adnexal extranodal marginal zone lymphoma (OA-EMZL) is the most frequent subtype of ocular adnexal lymphoma, with a high propensity for recurrence. Distant recurrence (DR) as an essential prognostic event has unique clinical risk factors, but whether distinct molecular features exist remains poorly understood. Here, we identified potential biomarkers using proteomic analysis of 27 OA-EMZL samples. The MYC-targeted genes PCNA, MCM6, and MCM4 were identified as candidates. MYC-targeted genes were further identified as the most significantly activated gene set in patients with DR. The candidate genes were verified in samples from 11 patients with DR and 33 matched controls using immunohistochemistry. The 3-year and 5-year AUC values of MCM6 (0.699 and 0.757) were higher than those of Ki-67 (0.532 and 0.592). High expressions of MCM6 and MCM4 were significantly associated with shorter distant recurrence-free survival (Log-rank p = 0.017, Log-rank p = 0.0053). Multivariate Cox regression identified MCM6 expression as an independent risk factor for DR (HR, 6.86; 95% CI, 1.32-35.79; P = 0.02). Knockdown of c-Myc in B cells resulted in decreased MCM6 and MCM4 expression and reduced proliferative capacity. Our results suggest that activation of the MYC-targeted gene is a distinct molecular feature of DR in OA-EMZL. MYC-targeted gene, MCM6, is a promising pathological biomarker for DR.
MeSH term(s)	Humans ; Proteomics ; Eye Neoplasms/genetics ; Eye Neoplasms/metabolism ; Lymphoma, B-Cell, Marginal Zone/pathology ; Prognosis ; Immunohistochemistry
Language	English
Publishing date	2023-04-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1064950-5
ISSN	1432-0584 ; 0939-5555 ; 0945-8077
ISSN (online)	1432-0584
ISSN	0939-5555 ; 0945-8077
DOI	10.1007/s00277-023-05203-8
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Uh III Zs.181: Show issues

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Article ; Online: Evolution of the morphological, structural, and molecular properties of gluten protein in dough with different hydration levels during mixing.

Jia, Ruobing / Zhang, Mengli / Yang, Tianbao / Ma, Meng / Sun, Qingjie / Li, Man

Food chemistry: X

2022 Volume 15, Page(s) 100448

Abstract: To understand the formation process of dough with different hydration levels upon mixing and the response of dough rheology, the dynamic evolution of gluten protein was tracked and quantified at morphological, structural, and molecular levels. Both ... ...

Abstract	To understand the formation process of dough with different hydration levels upon mixing and the response of dough rheology, the dynamic evolution of gluten protein was tracked and quantified at morphological, structural, and molecular levels. Both macroscopical and microscopic distribution images showed that partial and full hydration induced quick formation of a more compact gluten network compared with limited hydration. Gluten network in highly hydrated samples was more susceptible to the formation and collapse induced by mechanical force. SE-HPLC results indicated significant depolymerization of glutenin macropolymer (GMP) in fully and partially hydrated samples. Sufficient mixing was accompanied by the increase of ionic and hydrogen bonds, while excessive mixing increased exposure of free -SH. Higher hydration level induced more ordered secondary structure. Correlation and principal component analysis revealed the patterns and dynamics of gluten evolution during dough formation with different hydration levels, and their contribution to the changes in dough modulus.
Language	English
Publishing date	2022-09-14
Publishing country	Netherlands
Document type	Journal Article
ISSN	2590-1575
ISSN (online)	2590-1575
DOI	10.1016/j.fochx.2022.100448
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Article: Evolution of the morphological, structural, and molecular properties of gluten protein in dough with different hydration levels during mixing

Jia, Ruobing / Zhang, Mengli / Yang, Tianbao / Ma, Meng / Sun, Qingjie / Li, Man

Food chemistry: X. 2022 Oct. 30, v. 15

2022

Abstract	To understand the formation process of dough with different hydration levels upon mixing and the response of dough rheology, the dynamic evolution of gluten protein was tracked and quantified at morphological, structural, and molecular levels. Both macroscopical and microscopic distribution images showed that partial and full hydration induced quick formation of a more compact gluten network compared with limited hydration. Gluten network in highly hydrated samples was more susceptible to the formation and collapse induced by mechanical force. SE-HPLC results indicated significant depolymerization of glutenin macropolymer (GMP) in fully and partially hydrated samples. Sufficient mixing was accompanied by the increase of ionic and hydrogen bonds, while excessive mixing increased exposure of free -SH. Higher hydration level induced more ordered secondary structure. Correlation and principal component analysis revealed the patterns and dynamics of gluten evolution during dough formation with different hydration levels, and their contribution to the changes in dough modulus.
Keywords	depolymerization ; dough ; evolution ; food chemistry ; forces ; gluten ; glutenins ; hydrogen ; principal component analysis ; rheology
Language	English
Dates of publication	2022-1030
Publishing place	Elsevier Ltd
Document type	Article
ISSN	2590-1575
DOI	10.1016/j.fochx.2022.100448
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Nanoscale Phase Change Material Array by Sub-Resolution Assist Feature for Storage Class Memory Application

Jiarui Zhang / Wencheng Fang / Ruobing Wang / Chengxing Li / Jia Zheng / Xixi Zou / Sannian Song / Zhitang Song / Xilin Zhou

Nanomaterials, Vol 13, Iss 1050, p

2023 Volume 1050

Abstract: High density phase change memory array requires both minimized critical dimension (CD) and maximized process window for the phase change material layer. High in-wafer uniformity of the nanoscale patterning of chalcogenides material is challenging given ... ...

Abstract	High density phase change memory array requires both minimized critical dimension (CD) and maximized process window for the phase change material layer. High in-wafer uniformity of the nanoscale patterning of chalcogenides material is challenging given the optical proximity effect (OPE) in the lithography process and the micro-loading effect in the etching process. In this study, we demonstrate an approach to fabricate high density phase change material arrays with half-pitch down to around 70 nm by the co-optimization of lithography and plasma etching process. The focused-energy matrix was performed to improve the pattern process window of phase change material on a 12-inch wafer. A variety of patternings from an isolated line to a dense pitch line were investigated using immersion lithography system. The collapse of the edge line is observed due to the OPE induced shrinkage in linewidth, which is deteriorative as the patterning density increases. The sub-resolution assist feature (SRAF) was placed to increase the width of the lines at both edges of each patterning by taking advantage of the optical interference between the main features and the assistant features. The survival of the line at the edges is confirmed with around a 70 nm half-pitch feature in various arrays. A uniform etching profile across the pitch line pattern of phase change material was demonstrated in which the micro-loading effect and the plasma etching damage were significantly suppressed by co-optimizing the etching parameters. The results pave the way to achieve high density device arrays with improved uniformity and reliability for mass storage applications.
Keywords	phase change memory ; storage class memory ; SRAF ; optical proximity effect ; micro-loading effect ; Chemistry ; QD1-999
Subject code	620
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Extrachromosomal circular DNA: biogenesis, structure, functions and diseases.

Yang, Ludi / Jia, Ruobing / Ge, Tongxin / Ge, Shengfang / Zhuang, Ai / Chai, Peiwei / Fan, Xianqun

Signal transduction and targeted therapy

2022 Volume 7, Issue 1, Page(s) 342

Abstract: Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to ... ...

Abstract	Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.
MeSH term(s)	Chromatin ; DNA, Circular/genetics ; Humans ; Neoplasms/genetics
Chemical Substances	Chromatin ; DNA, Circular
Language	English
Publishing date	2022-10-02
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2886872-9
ISSN	2059-3635 ; 2095-9907
ISSN (online)	2059-3635
ISSN	2095-9907
DOI	10.1038/s41392-022-01176-8
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Article: Pancreatic fistula and biliary fistula after laparoscopic pancreatoduodenectomy: 500 patients at a single institution.

Wang, Ruobing / Jiang, Peiqiang / Chen, Qingmin / Liu, Songyang / Jia, Feng / Liu, Yahui

Journal of minimal access surgery

2022 Volume 19, Issue 1, Page(s) 28–34

Abstract: Background: Pancreatic fistula (PF) and biliary fistula (BF) are two major leakage complications after pancreatoduodenectomy (PD). The aim of this study is to investigate the risk factors of PF and BF after laparoscopic PD (LPD).: Materials and ... ...

Abstract	Background: Pancreatic fistula (PF) and biliary fistula (BF) are two major leakage complications after pancreatoduodenectomy (PD). The aim of this study is to investigate the risk factors of PF and BF after laparoscopic PD (LPD). Materials and methods: We conducted a retrospective analysis of 500 patients who underwent LPD from 1 April 2015 to 31 March 2020. Clinical data from patients were analysed using multivariate logistic regression analysis. Results: PF occurred in 86 (17.2%) patients. Univariate and multivariate analysis indicated that the soft texture of the pancreas (P = 0.001) was the independent risk factor for PF. BF occurred in 32 (6.4%) patients. Univariate and multivariate analysis indicated that history of cardiovascular disease (P < 0.001), surgical time (P = 0.005), pre-operative CA125 (P = 0.036) and pre-operative total bilirubin (P = 0.044) were independent risk factors for BF. Conclusion: The texture of the pancreas was an independent risk factor for PF after LPD, which was consistent with the literatures. In addition, history of cardiovascular disease, surgical time, pre-operative CA125 and pre-operative total bilirubin were new independent risk factors for BF after LPD. Therefore, patients with high-risk factors of BF should be informed that they are at a high risk for this complication.
Language	English
Publishing date	2022-07-29
Publishing country	India
Document type	Journal Article
ZDB-ID	2186884-0
ISSN	1998-3921 ; 0972-9941
ISSN (online)	1998-3921
ISSN	0972-9941
DOI	10.4103/jmas.jmas_336_21
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