LIVIVO - Search results -

Search results

Result 1 - 10 of total 154

Search options

Article ; Online: Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees

Xiang Ge Luo / Jack Kuipers / Niko Beerenwinkel

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the ... ...

Abstract	Abstract Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the extensive diversity across tumors and patients. Resolving the interactions among mutations and recovering recurrent evolutionary processes may offer greater opportunities for successful therapeutic strategies. To this end, we present a novel probabilistic framework, called TreeMHN, for the joint inference of exclusivity patterns and recurrent trajectories from a cohort of intra-tumor phylogenetic trees. Through simulations, we show that TreeMHN outperforms existing alternatives that can only focus on one aspect of the task. By analyzing datasets of blood, lung, and breast cancers, we find the most likely evolutionary trajectories and mutational patterns, consistent with and enriching our current understanding of tumorigenesis. Moreover, TreeMHN facilitates the prediction of tumor evolution and provides probabilistic measures on the next mutational events given a tumor tree, a prerequisite for evolution-guided treatment strategies.
Keywords	Science ; Q
Subject code	006
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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 ; Online: Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees.

Luo, Xiang Ge / Kuipers, Jack / Beerenwinkel, Niko

Nature communications

2023 Volume 14, Issue 1, Page(s) 3676

Abstract: Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the extensive ... ...

Abstract	Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the extensive diversity across tumors and patients. Resolving the interactions among mutations and recovering recurrent evolutionary processes may offer greater opportunities for successful therapeutic strategies. To this end, we present a novel probabilistic framework, called TreeMHN, for the joint inference of exclusivity patterns and recurrent trajectories from a cohort of intra-tumor phylogenetic trees. Through simulations, we show that TreeMHN outperforms existing alternatives that can only focus on one aspect of the task. By analyzing datasets of blood, lung, and breast cancers, we find the most likely evolutionary trajectories and mutational patterns, consistent with and enriching our current understanding of tumorigenesis. Moreover, TreeMHN facilitates the prediction of tumor evolution and provides probabilistic measures on the next mutational events given a tumor tree, a prerequisite for evolution-guided treatment strategies.
MeSH term(s)	Humans ; Phylogeny ; Neoplasms/genetics ; Neoplasms/pathology ; Mutation ; Sequence Analysis
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39400-w
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: Vertebral bone quality different in magnetic resonance imaging parameters.

Liu, Xiang-Ge / Chen, Xin / Chen, Biao / Liang, Pei-Jie / Liu, Han-Hui / Fu, Meiqi

Journal of orthopaedic surgery and research

2023 Volume 18, Issue 1, Page(s) 772

Abstract: Objective: This was a single-center retrospective study that aimed to measure the vertebral bone quality (VBQ) in people of all ages and compare changes in VBQ across ages. Differences in VBQ under various MRI parameters were compared.: Methods: We ... ...

Abstract	Objective: This was a single-center retrospective study that aimed to measure the vertebral bone quality (VBQ) in people of all ages and compare changes in VBQ across ages. Differences in VBQ under various MRI parameters were compared. Methods: We first screened patients without underlying disease and no history of fractures who underwent lumbar MRI in our center in the past four years. Over the span of 10 years, 200 patients (100 males and 100 females) were randomly recruited into each cohort to undergo 1.5 T and 3.0 T MRI scans. Subsequently, we tabulated the number of patients admitted to our hospital with OVCF over the past four years. There were 30 healthy adults under 4 times of MRI scans in different parameters to determine the differentiation of VBQ. The 30 healthy adults were recruited to validate the differentiation of VBQ under various parameters. Results: A total of 2400 patients without OVCF and 405 patients with OVCF were enrolled. The VBQ value of 1.5 T was significantly higher compared with that of 3.0 T (2.769 ± 0.494 > 2.199 ± 0.432, P < 0.0001). VBQ of 43.31 kHz in 1.5 T was significantly lower than that of 35.36 kHz (2.447 ± 0.350 < 2.632 ± 0.280, P < 0.05). The differentiation of VBQ in 1.5 T and 3.0 T was validated using results of healthy adults. Conclusions: VBQ is an effective tool for differentiating patients with OVCF and can be used as a primary screening tool for osteoporosis. However, VBQ is significantly affected by magnetic field intensity and bandwidth and cannot achieve its universality as it originally proposed.
MeSH term(s)	Male ; Female ; Humans ; Osteoporotic Fractures/diagnosis ; Retrospective Studies ; Spinal Fractures/diagnostic imaging ; Fractures, Compression/diagnosis ; Magnetic Resonance Imaging ; Lumbar Vertebrae/diagnostic imaging ; Lumbar Vertebrae/injuries
Language	English
Publishing date	2023-10-12
Publishing country	England
Document type	Letter
ZDB-ID	2252548-8
ISSN	1749-799X ; 1749-799X
ISSN (online)	1749-799X
ISSN	1749-799X
DOI	10.1186/s13018-023-04268-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Epigenome-Metabolome-Epigenome signaling cascade in cell biological processes.

Li, Linpeng / Chen, Keshi / Wu, Yi / Xiang, Ge / Liu, Xingguo

Journal of genetics and genomics = Yi chuan xue bao

2021 Volume 49, Issue 4, Page(s) 279–286

Abstract: Cell fate determination as a fundamental question in cell biology has been extensively studied at different regulatory levels for many years. However, the mechanisms of multilevel regulation of cell fate determination remain unclear. Recently, we have ... ...

Abstract	Cell fate determination as a fundamental question in cell biology has been extensively studied at different regulatory levels for many years. However, the mechanisms of multilevel regulation of cell fate determination remain unclear. Recently, we have proposed an Epigenome-Metabolome-Epigenome (E-M-E) signaling cascade model to describe the cross-over cooperation during mouse somatic cell reprogramming. In this review, we summarize the broad roles of E-M-E signaling cascade in different cell biological processes, including cell differentiation and dedifferentiation, cell specialization, cell proliferation, and cell pathologic processes. Precise E-M-E signaling cascades are critical in these cell biological processes, and it is of worth to explore each step of E-M-E signaling cascade. E-M-E signaling cascade model sheds light on and may open a window to explore the mechanisms of multilevel regulation of cell biological processes.
MeSH term(s)	Animals ; Biological Phenomena ; Cell Differentiation ; Epigenome/genetics ; Metabolome ; Mice ; Signal Transduction/genetics
Language	English
Publishing date	2021-10-12
Publishing country	China
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2374568-X
ISSN	1873-5533 ; 1673-8527
ISSN (online)	1873-5533
ISSN	1673-8527
DOI	10.1016/j.jgg.2021.09.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

Article ; Online: A superior articular process morphology of 5th lumbar vertebra prone to screws placement failure: an anatomical study of 299 patients.

Liu, Xiang-Ge / Liang, Pei-Jie / Liu, Han-Hui / Chen, Guang-Fu / Zhao, Xiao-Dong

Journal of orthopaedic surgery and research

2022 Volume 17, Issue 1, Page(s) 505

Abstract: Purposes: This study aimed to investigate whether the morphology of the superior articular processes of L5 vertebra affected the accuracy of pedicle screw placement by reviewing 299 patients who had undergone L5 pedicle screw fixation over the past 12 ... ...

Abstract	Purposes: This study aimed to investigate whether the morphology of the superior articular processes of L5 vertebra affected the accuracy of pedicle screw placement by reviewing 299 patients who had undergone L5 pedicle screw fixation over the past 12 months and measuring relevant parameters. Methods: We retrospectively analyzed patients who underwent L5 vertebra fixation at our spine surgery department from October 20, 2020 to October 20, 2021. Patients with spondylolisthesis, spondylolysis, and scoliosis were excluded. Parameters associated with the superior articular process were analyzed, including Mammillary process-Spinal canal Distance (MCD), Inter-Facet Distance (IFD), Inter-Pedicle Distance (IPD), Zygapophysial Joints Angle (ZJA), Superior Articular Width, and Lateral Recess Transverse Diameter. The L5 vertebral body was reconstructed by Mimics 21.0, and the simulated L5 screws were inserted at multiple entry points to measure the Maximum Safe Transverse Angle (STA Results: A total of 299 patients who underwent L5 vertebra fixation with 556 pedicle screws were analyzed. An MCD < 6 mm was associated with a significant increase in screw placement failure rate and decrease in ZJA. The MCD was positively correlated with IFD. No significant change in IPD was observed. Mimics software analysis showed that the STA Conclusions: The superior articular process tended to narrow the spinal canal and exhibit a steep and a "cloverleaf" morphology when the MCD was < 6 mm. This morphology increased the risk of operator mis-judgement resulting in screw placement failure. Assessment of the relationship between the trans-mammillary vertical line and the pedicle represents a simple method to predict abnormal morphology of the superior articular process before surgery.
MeSH term(s)	Humans ; Retrospective Studies ; Lumbar Vertebrae/diagnostic imaging ; Lumbar Vertebrae/surgery ; Spondylolisthesis/diagnostic imaging ; Spondylolisthesis/surgery ; Pedicle Screws ; Spinal Fusion/methods
Language	English
Publishing date	2022-11-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2252548-8
ISSN	1749-799X ; 1749-799X
ISSN (online)	1749-799X
ISSN	1749-799X
DOI	10.1186/s13018-022-03403-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: [Interferon-α mediating the functional damage of CD56

Zhao, Xiang Ge / Liu, Jia Qing / Huang, Hui Na / Lu, Zhi Min / Bai, Zi Ran / Li, Xia / Qi, Jing Jing

Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences

2023 Volume 55, Issue 6, Page(s) 975–981

Abstract: Objective: To investigate the regulatory effect of interferon-α (IFN-α) on the apoptosis and killing function of CD56: Methods: A total of sixty-four newly treated SLE patients and sixteen healthy controls (HC) enrolled in the Second Hospital of ... ...

Abstract	Objective: To investigate the regulatory effect of interferon-α (IFN-α) on the apoptosis and killing function of CD56 Methods: A total of sixty-four newly treated SLE patients and sixteen healthy controls (HC) enrolled in the Second Hospital of Dalian Medical University were selected as the research subjects. And the gene expression levels of molecules related to NK cell-killing function were detected by real-time quantitative polymerase chain reaction. CD56 Results: Compared with HC( Conclusion: High serum IFN-α level in SLE patients may induce apoptosis by promoting mtROS production and inhibit perforin expression, which can down-regulate CD56
MeSH term(s)	Humans ; Interferon-alpha/pharmacology ; Interferon-alpha/metabolism ; Perforin/metabolism ; Leukocytes, Mononuclear/metabolism ; Hydrogen Peroxide/metabolism ; Interferon-gamma/metabolism ; CD56 Antigen/metabolism ; Killer Cells, Natural/metabolism ; Lupus Erythematosus, Systemic
Chemical Substances	Interferon-alpha ; Perforin (126465-35-8) ; Hydrogen Peroxide (BBX060AN9V) ; Interferon-gamma (82115-62-6) ; CD56 Antigen
Language	Chinese
Publishing date	2023-12-19
Publishing country	China
Document type	English Abstract ; Journal Article
ZDB-ID	2452593-5
ISSN	1671-167X
ISSN	1671-167X
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A high-affinity fluorescent probe for human uridine-disphosphate glucuronosyltransferase 1A9 function monitoring under environmental pollutant exposure.

Miao, Yi-Sheng / Wang, Jia-Yue / Zhuang, Rui-Rui / Huo, Xiao-Kui / Yi, Zi-Chang / Sun, Xiao-Nan / Yu, Zhen-Long / Tian, Xiang-Ge / Ning, Jing / Feng, Lei / Ma, Xiao-Chi / Lv, Xia

Journal of hazardous materials

2024 Volume 465, Page(s) 133439

Abstract: Uridine-disphosphate glucuronosyltransferase 1A9 (UGT1A9), an important detoxification and inactivation enzyme for toxicants, regulates the exposure level of environmental pollutants in the human body and induces various toxicological consequences. ... ...

Abstract	Uridine-disphosphate glucuronosyltransferase 1A9 (UGT1A9), an important detoxification and inactivation enzyme for toxicants, regulates the exposure level of environmental pollutants in the human body and induces various toxicological consequences. However, an effective tool for high-throughput monitoring of UGT1A9 function under exposure to environmental pollutants is still lacking. In this study, 1,3-dichloro-7-hydroxy-9,9-dimethylacridin-2(9H)-one (DDAO) was found to exhibit excellent specificity and high affinity towards human UGT1A9. Remarkable changes in absorption and fluorescence signals after reacting with UGT1A9 were observed, due to the intramolecular charge transfer (ICT) mechanism. Importantly, DDAO was successfully applied to monitor the biological functions of UGT1A9 in response to environmental pollutant exposure not only in microsome samples, but also in living cells by using a high-throughput screening method. Meanwhile, the identified pollutants that disturb UGT1A9 functions were found to significantly influence the exposure level and retention time of bisphenol S/bisphenol A in living cells. Furthermore, the molecular mechanism underlying the inhibition of UGT1A9 by these pollutant-derived disruptors was elucidated by molecular docking and molecular dynamics simulations. Collectively, a fluorescent probe to characterize the responses of UGT1A9 towards environmental pollutants was developed, which was beneficial for elucidating the health hazards of environmental pollutants from a new perspective.
MeSH term(s)	Humans ; Glucuronosyltransferase ; Fluorescent Dyes ; Environmental Pollutants ; Uridine ; Molecular Docking Simulation ; Dimethylamines
Chemical Substances	Glucuronosyltransferase (EC 2.4.1.17) ; Fluorescent Dyes ; Environmental Pollutants ; Uridine (WHI7HQ7H85) ; dodecyldimethylamine oxide (4F6FC4MI8W) ; Dimethylamines
Language	English
Publishing date	2024-01-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2024.133439
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A Three-Dimensional Cement Quantification Method for Decision Prediction of Vertebral Recompression after Vertebroplasty

Yanming Zhang / Tao Zhang / Xiang Ge / Yong Ma / Zhenduo Cui / Shuilin Wu / Yanqin Liang / Shengli Zhu / Zhaoyang Li

Computational and Mathematical Methods in Medicine, Vol

2022 Volume 2022

Abstract: Objective. Proposing parameters to quantify cement distribution and increasing accuracy for decision prediction of vertebroplasty postoperative complication. Methods. Finite element analysis was used to biomechanically assess vertebral mechanics (n=51) ... ...

Abstract	Objective. Proposing parameters to quantify cement distribution and increasing accuracy for decision prediction of vertebroplasty postoperative complication. Methods. Finite element analysis was used to biomechanically assess vertebral mechanics (n=51) after percutaneous vertebroplasty (PVP) or kyphoplasty (PKP). The vertebral space was divided into 27 portions. The numbers of cement occupied portions and numbers of cement-endplate contact portions were defined as overall distribution number (oDN) and overall endplate contact number (oEP), respectively. And cement distribution was parametrized by oDN and oEP. The determination coefficients of vertebral mechanics and parameters (R2) can validate the correlation of proposed parameters with vertebral mechanics. Results. oDN and oEP were mainly correlated with failure load (R2=0.729) and stiffness (R2=0.684), respectively. oDN, oEP, failure load, and stiffness had obvious difference between the PVP group and the PKP group (P<0.05). The regional endplate contact number in the front column is most correlated with vertebral stiffness (R2=0.59) among all regional parameters. Cement volume and volume fraction are not dominant factors of vertebral augmentation, and they are not suitable for postoperative fracture risk prediction. Conclusions. Proposed parameters with high correlation on vertebral mechanics are promising for clinical utility. The oDN and oEP can strongly affect augmented vertebral mechanics thus is suitable for postoperative fracture risk prediction. The parameters are beneficial for decision-making process of revision surgery necessity. Parametrized methods are also favorable for surgeon’s preoperative planning. The methods can be inspirational for clinical image recognition development and auxiliary diagnosis.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	600
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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 ; Online: Evaluation of Soil Quality in a Composite Pecan Orchard Agroforestry System Based on the Smallest Data Set

Cheng Huang / Zhaocheng Wang / Xiaoliang Ren / Xiaomin Ma / Mengyu Zhou / Xiang Ge / Hua Liu / Songling Fu

Sustainability, Vol 14, Iss 10665, p

2022 Volume 10665

Abstract: Agroforestry not only takes into account the use of land for forestry and agriculture but can also improve the efficacy of utilized above- and belowground resources, which have always garnered widespread attention. The objective of this study is to ... ...

Abstract	Agroforestry not only takes into account the use of land for forestry and agriculture but can also improve the efficacy of utilized above- and belowground resources, which have always garnered widespread attention. The objective of this study is to evaluate the quality of pecan orchard soil following the implementation of agroforestry. Consequently, 15 indices were selected for a principal component analysis (PCA), which was then combined with the norm value of each index and the correlation coefficients between indices to establish a minimum data set (MDS). A comprehensive index model was used to calculate the soil quality index (SQI) of the total data set (TDS) and MDS (SQI-TDS and SQI-MDS, respectively), and a linear regression of the two was performed. The results revealed that the MDS indices for the evaluation of soil fertility included the pH, electrical conductivity value (EC), bulk density (BD), available potassium (AK), total nitrogen (TN), magnesium (Mg), and the index screening and filtering rates attained 60%. The Soil Quality Index (SQI-MDS) of the four planting patterns, sorted from largest to smallest, were: PPS (0.573) > PPH (0.519) > PPL (0.355) > CK (0.315). BD and AK were the main factors that affected the quality of hickory orchard soils. The agroforestry composite system improved the availability of nutrients and soil quality. Thus, the promotion of understory intercropping and appropriate increases in potassium fertilizers for plantations are recommended.
Keywords	pecan ; soil quality evaluation ; minimum data set ; principal component analysis ; environmental factors ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	630
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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 ; Online: Pecan agroforestry systems improve soil quality by stimulating enzyme activity

Zhaocheng Wang / Mengyu Zhou / Hua Liu / Cheng Huang / Yuhua Ma / Hao xin Ge / Xiang Ge / Songling Fu

PeerJ, Vol 10, p e

2022 Volume 12663

Abstract: Background Forest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and ... ...

Abstract	Background Forest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and chemical properties of the soil. Methods The treatments for this study included a single cultivation (CK) pecan control and three agroforestry systems (pecan + Paeonia suffruticosa + Hemerocallis citrina, pecan + Paeonia suffruticosa, and pecan + Paeonia lactiflora). Soil samples were categorized according to the sampling depth (0–20 cm, 20–40 cm, 40–60 cm). Results The results demonstrated that the bulk density (BD) of soil under the pecan agroforestry system (PPH and PPL) was reduced by 16.13% and 7.10%, respectively, and the soil moisture content (MC) and total soil porosity (TPO) increased. Improvements in the physical properties of the soil under the PPS agroforestry system were not obvious when compared with the pecan monoculture. The soil total phosphorus (TP), total nitrogen (TN), available potassium (AK), and total carbon (TC) increased significantly, while the soil urease (S-UE), alkaline phosphatase (S-AKP), and 1,4-β-N-acetylglucosamines (S-NAG) enzyme activity also increased significantly, following agroforestry. Overall, the pecan agroforestry system significantly improved the physical properties of the pecan plantation soil, enriched the soil nutrients, and increased the activity of soil enzymes related to TC, TN, and TP cycles.
Keywords	Pecan ; Agroforestry ; Soil nutrients ; Enzyme activity ; Medicine ; R
Subject code	571 ; 630
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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.

To top

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED