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Article ; Online: On the uncertainty quantification of the active uterine contraction during the second stage of labor simulation.

Nguyen, Trieu-Nhat-Thanh / Ballit, Abbass / Lecomte-Grosbras, Pauline / Colliat, Jean-Baptiste / Dao, Tien-Tuan

Medical & biological engineering & computing

2024

Abstract: Uterine contractions in the myometrium occur at multiple scales, spanning both organ and cellular levels. This complex biological process plays an essential role in the fetus delivery during the second stage of labor. Several finite element models of ... ...

Abstract	Uterine contractions in the myometrium occur at multiple scales, spanning both organ and cellular levels. This complex biological process plays an essential role in the fetus delivery during the second stage of labor. Several finite element models of active uterine contractions have already been developed to simulate the descent of the fetus through the birth canal. However, the developed models suffer severe reliability issues due to the uncertain parameters. In this context, the present study aimed to perform the uncertainty quantification (UQ) of the active uterine contraction simulation to advance our understanding of pregnancy mechanisms with more reliable indicators. A uterus model with and without fetus was developed integrating a transversely isotropic Mooney-Rivlin material with two distinct fiber orientation architectures. Different contraction patterns with complex boundary conditions were designed and applied. A global sensitivity study was performed to select the most valuable parameters for the uncertainty quantification (UQ) process using a copula-based Monte Carlo method. As results, four critical material parameters (
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	282327-5
ISSN	1741-0444 ; 0025-696X ; 0140-0118
ISSN (online)	1741-0444
ISSN	0025-696X ; 0140-0118
DOI	10.1007/s11517-024-03059-2
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Article: Optimization of Multiplex-PCR Technique To Determine Azf Deletions in infertility Male Patients.

Thanh, Tung Nguyen / Tien, Sang Trieu / Van, Phong Nguyen / Thai, Son Dang / Cong, Thuc Luong / Le, Tuan Dinh / Nguyen, Son Tien / Van, Tuan Tran / Duong, Hoang Huy / Bui, Tien Minh / Nguyen, Kien Trung

International journal of general medicine

2024 Volume 17, Page(s) 1579–1589

Abstract: Background: To optimize the multiplex polymerase chain reaction (M-PCR) technique to diagnose microdeletions of azoospermia factors (AZF) on the Y chromosome and initially apply the technique to diagnose male patients with sperm density less than 5×10!## ...

Abstract	Background: To optimize the multiplex polymerase chain reaction (M-PCR) technique to diagnose microdeletions of azoospermia factors (AZF) on the Y chromosome and initially apply the technique to diagnose male patients with sperm density less than 5×10 Methods: Based on the positive control samples which belong to male subjects who have had 2 healthy children without any assisted reproductive technologies, the M-PCR method was developed to detect simultaneously and accurately AZF microdeletions on 32 male patients with sperm densities below 5×10 Results: Successful optimization of the M-PCR technique including 7 reactions arranged according to each AZFabc region using 24 STS/gene on the Y chromosome. Initial application to diagnose AZF deletion on 32 azoospermic and oligospermic men reveals that AZFa deletion accounts for 6.25% (2/32); deletion of all 3 regions AZFa,b,c with 18.75% (6/32 cases); The combined deletion rate of AZFb,c is highest, accounting for 56.24% (18/32 patients). Conclusion: Successfully optimized the M-PCR technique in identifying AZF microdeletions using 24 sequence tagged sites (STS)/gene for azoospermic and oligozoospermic men. The M-PCR technique has great potential in the application of AZF deletion diagnosis.
Language	English
Publishing date	2024-04-24
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2452220-X
ISSN	1178-7074
ISSN	1178-7074
DOI	10.2147/IJGM.S455513
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Article ; Online: DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Trieu, Tuan / Martinez-Fundichely, Alexander / Khurana, Ekta

Genome biology

2020 Volume 21, Issue 1, Page(s) 79

Abstract: Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on ... ...

Abstract	Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on variants from whole-genome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least 10% of patients. Our results show mutations at loop anchors are associated with upregulation of the cancer driver genes BCL2 and MYC in malignant lymphoma thus pointing to a possible new mechanism for their dysregulation via alteration of insulator loops.
MeSH term(s)	CCCTC-Binding Factor/metabolism ; Cell Cycle Proteins/metabolism ; Cell Line, Tumor ; Chromatin/chemistry ; Chromosomal Proteins, Non-Histone/metabolism ; Deep Learning ; Humans ; Insulator Elements ; Mutation ; Neoplasms/genetics ; Whole Genome Sequencing ; Cohesins
Chemical Substances	CCCTC-Binding Factor ; Cell Cycle Proteins ; Chromatin ; Chromosomal Proteins, Non-Histone
Language	English
Publishing date	2020-03-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-01987-4
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Article: Minimally Invasive Treatment of Chyle Leak After Thyroidectomy and Cervical Lymph Node Dissection in Patients with Thyroid Carcinoma: Results of a Study Involving 36 Patients.

Cuong, Nguyen Ngoc / Hoan, Le / Tra My, Thieu Thi / Luu, Doan Tien / Tuan Linh, Le / Canh, Pham Hong / Tinh, Trieu Quoc / Khanh Chi, Tran Nguyen / Trung, Nguyen Quang / Hoa, Tran Quoc

Therapeutics and clinical risk management

2024 Volume 20, Page(s) 75–82

Abstract: Objective: Chyle leak (CL) after head and neck surgery is a rare but well-known complication. In patients with high-output leakage, the treatment can be complicated. This study aims to report on a recent innovation in lymphatic intervention for treating ...

Abstract	Objective: Chyle leak (CL) after head and neck surgery is a rare but well-known complication. In patients with high-output leakage, the treatment can be complicated. This study aims to report on a recent innovation in lymphatic intervention for treating such patients. Materials and methods: A retrospective review of 36 patients with chyle leak after neck surgery for thyroid cancer was conducted to assess the efficacy of percutaneous lymphatic embolization and thoracic duct (TD) disruption. Results: Antegrade catheterization of the thoracic duct was achieved in 31 of 36 patients (86.1%). Therefore, embolization of the thoracic duct and thoracic duct branches was performed in 26 and 5 patients, respectively. In 5 cases of unsuccessful antegrade catheterization into the thoracic duct, transcervical access embolization was performed in 2 patients, and TD disruption (TDD) was performed in 3 patients. The pooled overall technical success rate of lymphatic embolization was 33/36 patients (91.7%). One patient who underwent thoracic duct embolization (TDE) with technical success (1/33 patients) but clinical failure had additional treatment directly sclerosing the TD under computed tomography scan. Cervical fluid collection sclerotherapy was done in 7 patients as an additional treatment. Resolution of the chyle leak after procedures was observed in all patients (100%). The mean time to resolution was 3 days (1-7 days). There was no complication intra and after procedures. Conclusion: TDE, selective TD branches embolization and TDD are safe and effective minimally invasive treatments for CL post-surgery for thyroid carcinoma. Sclerosing cervical fluid collection contributes to clinical success.
Language	English
Publishing date	2024-02-09
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2186560-7
ISSN	1178-203X ; 1176-6336
ISSN (online)	1178-203X
ISSN	1176-6336
DOI	10.2147/TCRM.S446113
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Article ; Online: Risk factors for cannula-associated arterial thrombosis following extracorporeal membrane oxygenation support: a retrospective study.

Trieu, Ngan Hoang Kim / Phan, Xuan Thi / Tran, Linh Thanh / Pham, Huy Minh / Huynh, Dai Quang / Nguyen, Tuan Manh / Mai, Anh Tuan / Du, Quan Quoc Minh / Nguyen, Bach Xuan / Pham, Thao Thi Ngoc

Acute and critical care

2023 Volume 38, Issue 3, Page(s) 315–324

Abstract: Background: Hemostatic dysfunction during extracorporeal membrane oxygenation (ECMO) due to blood-circuit interaction and the consequences of shear stress imposed by flow rates lead to rapid coagulation cascade and thrombus formation in the ECMO system ... ...

Abstract	Background: Hemostatic dysfunction during extracorporeal membrane oxygenation (ECMO) due to blood-circuit interaction and the consequences of shear stress imposed by flow rates lead to rapid coagulation cascade and thrombus formation in the ECMO system and blood vessels. We aimed to identify the incidence and risk factors for cannula-associated arterial thrombosis (CaAT) post-decannulation. Methods: A retrospective study of patients undergoing arterial cannula removal following ECMO was performed. We evaluated the incidence of CaAT and compared the characteristics, ECMO machine parameters, cannula sizes, number of blood products transfused during ECMO, and daily hemostasis parameters in patients with and without CaAT. Multivariate analysis identified the risk factors for CaAT. Results: Forty-seven patients requiring venoarterial ECMO (VA-ECMO) or hybrid methods were recruited for thrombosis screening. The median Sequential Organ Failure Assessment score was 11 (interquartile range, 8-13). CaAT occurred in 29 patients (61.7%), with thrombosis in the superficial femoral artery accounting for 51.7% of cases. The rate of limb ischemia complications in the CaAT group was 17.2%. Multivariate analysis determined that the ECMO flow rate-body surface area (BSA) ratio (100 ml/min/m2) was an independent factor for CaAT, with an odds ratio of 0.79 (95% confidence interval, 0.66-0.95; P=0.014). Conclusions: We found that the incidence of CaAT was 61.7% following successful decannulation from VA-ECMO or hybrid modes, and the ECMO flow rate-BSA ratio was an independent risk factor for CaAT. We suggest screening for arterial thrombosis following VA-ECMO, and further research is needed to determine the risks and benefits of such screening.
Language	English
Publishing date	2023-08-23
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	3003021-3
ISSN	2586-6060 ; 2586-6052
ISSN (online)	2586-6060
ISSN	2586-6052
DOI	10.4266/acc.2023.00500
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Article ; Online: DeepMILO

Tuan Trieu / Alexander Martinez-Fundichely / Ekta Khurana

Genome Biology, Vol 21, Iss 1, Pp 1-

a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure

2020 Volume 11

Abstract: Abstract Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO ...

Abstract	Abstract Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on variants from whole-genome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least 10% of patients. Our results show mutations at loop anchors are associated with upregulation of the cancer driver genes BCL2 and MYC in malignant lymphoma thus pointing to a possible new mechanism for their dysregulation via alteration of insulator loops.
Keywords	3D genome ; Non-coding mutation ; Cancer ; BCL2 ; MYC ; Deep learning ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: 3D genome structure modeling by Lorentzian objective function.

Trieu, Tuan / Cheng, Jianlin

Nucleic acids research

2017 Volume 45, Issue 3, Page(s) 1049–1058

Abstract: The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation ... ...

Abstract	The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.
MeSH term(s)	Chromosomes, Human/genetics ; Chromosomes, Human/ultrastructure ; Computational Biology ; Databases, Genetic ; Genome, Human ; Genomics/methods ; Genomics/statistics & numerical data ; Humans ; Imaging, Three-Dimensional ; In Situ Hybridization, Fluorescence ; Models, Molecular ; Nucleic Acid Conformation
Language	English
Publishing date	2017--17
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkw1155
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Article ; Online: Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.

Trieu, Tuan / Oluwadare, Oluwatosin / Cheng, Jianlin

Scientific reports

2019 Volume 9, Issue 1, Page(s) 4971

Abstract: Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed ...

Abstract	Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality high-resolution 3D models is still challenging with existing methods. Hence, we designed a hierarchical algorithm, called Hierarchical3DGenome, to reconstruct 3D chromosome models at high resolution (<=5 Kilobase (KB)). The algorithm first reconstructs high-resolution 3D models at TAD level. The TAD models are then assembled to form complete high-resolution chromosomal models. The assembly of TAD models is guided by a complete low-resolution chromosome model. The algorithm is successfully used to reconstruct 3D chromosome models at 5 KB resolution for the human B-cell (GM12878). These high-resolution models satisfy Hi-C chromosomal contacts well and are consistent with models built at lower (i.e. 1 MB) resolution, and with the data of fluorescent in situ hybridization experiments. The Java source code of Hierarchical3DGenome and its user manual are available here https://github.com/BDM-Lab/Hierarchical3DGenome .
MeSH term(s)	Algorithms ; Base Pairing/genetics ; Cell Line ; Chromosomes, Human/chemistry ; Genome ; Humans ; Imaging, Three-Dimensional ; Models, Molecular ; Reproducibility of Results ; Statistics, Nonparametric
Language	English
Publishing date	2019-03-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-41369-w
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Article: Multilayer Soft Photolithography Fabrication of Microfluidic Devices Using a Custom-Built Wafer-Scale PDMS Slab Aligner and Cost-Efficient Equipment.

Nguyen, Trieu / Sarkar, Tanoy / Tran, Tuan / Moinuddin, Sakib M / Saha, Dipongkor / Ahsan, Fakhrul

Micromachines

2022 Volume 13, Issue 8

Abstract: We present a robust, low-cost fabrication method for implementation in multilayer soft photolithography to create a PDMS microfluidic chip with features possessing multiple height levels. This fabrication method requires neither a cleanroom facility nor ... ...

Abstract	We present a robust, low-cost fabrication method for implementation in multilayer soft photolithography to create a PDMS microfluidic chip with features possessing multiple height levels. This fabrication method requires neither a cleanroom facility nor an expensive UV exposure machine. The central part of the method stays on the alignment of numerous PDMS slabs on a wafer-scale instead of applying an alignment for a photomask positioned right above a prior exposure layer using a sophisticated mask aligner. We used a manual XYZR stage attached to a vacuum tweezer to manipulate the top PDMS slab. The bottom PDMS slab sat on a rotational stage to conveniently align with the top part. The movement of the two slabs was observed by a monocular scope with a coaxial light source. As an illustration of the potential of this system for fast and low-cost multilayer microfluidic device production, we demonstrate the microfabrication of a 3D microfluidic chaotic mixer. A discussion on another alternative method for the fabrication of multiple height levels is also presented, namely the micromilling approach.
Language	English
Publishing date	2022-08-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2620864-7
ISSN	2072-666X
ISSN	2072-666X
DOI	10.3390/mi13081357
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Article ; Online: GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure

Trieu, Tuan / Oluwadare, Oluwatosin / Wopata, Julia / Cheng, Jianlin

Bioinformatics. 2019 Apr. 15, v. 35, no. 8, p. 1416-1418

2019 , Page(s) 1416–1418

Abstract: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome ... ...

Abstract	Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization. We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models and the integration of these models with functional genomics data. This graphical tool is the first of its kind in reconstructing, storing, analyzing and annotating 3D genome models. It can reconstruct 3D genome models from Hi-C data and visualize them in real-time. This tool also allows users to overlay gene annotation, gene expression data and genome methylation data on top of 3D genome models. The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow. Supplementary data are available at Bioinformatics online.
Keywords	bioinformatics ; chromosomes ; gene expression ; genes ; genomics ; methylation
Language	English
Dates of publication	2019-0415
Size	p. 1416-1418
Publishing place	Oxford University Press
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	1468345-3
ISSN	1367-4811 ; 1460-2059
ISSN	1367-4811 ; 1460-2059
DOI	10.1093/bioinformatics/bty802
Database	NAL-Catalogue (AGRICOLA)

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