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Article: Using Machine Learning and Finite Element Analysis to Extract Traction-Separation Relations at Bonding Wire Interfaces of Insulated Gate Bipolar Transistor Modules.

Zhao, Shengjun / An, Tong / Wang, Qi / Qin, Fei

2024 Volume 17, Issue 5

Abstract: For insulated gate bipolar transistor (IGBT) modules using wire bonding as the interconnection method, the main failure mechanism is cracking of the bonded interface. Studying the mechanical properties of the bonded interface is crucial for assessing the ...

Abstract	For insulated gate bipolar transistor (IGBT) modules using wire bonding as the interconnection method, the main failure mechanism is cracking of the bonded interface. Studying the mechanical properties of the bonded interface is crucial for assessing the reliability of IGBT modules. In this paper, first, shear tests are conducted on the bonded interface to test the bonded interface's strength. Then, finite element-cohesive zone modeling (FE-CZM) is established to describe the mechanical behavior of the bonded interface. A novel machine learning (ML) architecture integrating a convolutional neural network (CNN) and a long short-term memory (LSTM) network is used to identify the shape and parameters of the traction separation law (TSL) of the FE-CZM model accurately and efficiently. The CNN-LSTM architecture not only has excellent feature extraction and sequence-data-processing abilities but can also effectively address the long-term dependency problem. A total of 1800 sets of datasets are obtained based on numerical computations, and the CNN-LSTM architecture is trained with load-displacement (
Language	English
Publishing date	2024-02-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma17051002
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Book ; Online: Gaussianization of peculiar velocities and bulk flow measurement

Qin, Fei

2021

Abstract: The line-of-sight peculiar velocities are good indicators of the gravitational fluctuation of the density field. Techniques have been developed to extract cosmological information from the peculiar velocities in order to test the cosmological models. ... ...

Abstract	The line-of-sight peculiar velocities are good indicators of the gravitational fluctuation of the density field. Techniques have been developed to extract cosmological information from the peculiar velocities in order to test the cosmological models. These techniques include measuring cosmic flow, measuring two-point correlation and power spectrum of the peculiar velocity fields, reconstructing the density field using peculiar velocities. However, some measurements from these techniques are biased due to the non-Gaussianity of the estimated peculiar velocities. Therefore, we use the 2MTF survey to explore a power transform that can Gaussianize the estimated peculiar velocities. We find a tight linear relation between the transformation parameters and the measurement errors of log-distance ratio. To show an example for the implement of the Gaussianized peculiar velocities in cosmology, we develop a bulk flow estimator and estimate bulk flow from the Gaussianized peculiar velocities. We use 2MTF mocks to test the algorithm, we find the algorithm yields unbiased measurements. We also find this technique gives smaller measurement errors compared to other techniques. Under the Galactic coordinates, at the depth of $30$ $h^{-1}$ Mpc, we measure a bulk flow of $332\pm27$ km s$^{-1}$ in the direction $(l,b)=(293\pm 5^{\circ}, 13\pm 4^{\circ})$. The measurement is consistent with the $\Lambda$CDM prediction. Comment: 19 pages, 14 figures, 4 tables. Research in Astronomy and Astrophysics, April/2021
Keywords	Astrophysics - Cosmology and Nongalactic Astrophysics
Subject code	621
Publishing date	2021-05-11
Publishing country	us
Document type	Book ; Online
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Article ; Online: Physically based simulation of focusing schlieren imaging for a hypersonic boundary layer flow.

Chen, Mingjia / Liu, Bing / Qin, Fei / Liu, Xiao / Zhou, Bo

Applied optics

2024 Volume 63, Issue 6, Page(s) A44–A51

Abstract: Focusing schlieren systems are more advantageous than conventional schlieren systems in providing a schlieren image with certain spatial discrimination along the light path. The present work employed a hybrid of the optical-transfer matrix and ray- ... ...

Abstract	Focusing schlieren systems are more advantageous than conventional schlieren systems in providing a schlieren image with certain spatial discrimination along the light path. The present work employed a hybrid of the optical-transfer matrix and ray-tracing method to faithfully replicate complete physical imaging processes throughout a focusing schlieren optic system. A direct numerical simulation of a hypersonic boundary layer flow was employed to synthesize focusing schlieren images. The influence of various configuration parameters on the properties of focusing schlieren image such as local schlieren structure, brightness, sensitivity, and depth of field were systematically explored. In addition, an approximation method was proposed as a simplified means to facilitate the simulation of a focusing schlieren image.
Language	English
Publishing date	2024-03-04
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.509665
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Article ; Online: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.

Qin, Fei / Cai, Guoshuai / Amos, Christopher I / Xiao, Feifei

Genome research

2024 Volume 34, Issue 1, Page(s) 85–93

Abstract: The availability of single-cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in ...

Abstract	The availability of single-cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, as cells comprising a subpopulation are found to share a genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified variants) in the procedure of CNA detection, thereby diminishing the accuracy of subclone identification within a large, complex cell population. In this study, we developed a subclone clustering method based on a fused lasso model, referred to as FLCNA, which can simultaneously detect CNAs in single-cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant chemotherapy-treated samples and pretreated samples. We show that FLCNA is a practical and powerful method for subclone identification and CNA detection with scDNA-seq data.
MeSH term(s)	DNA Copy Number Variations ; Sequence Analysis, DNA/methods ; Base Sequence ; Cluster Analysis
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.278098.123
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Article ; Online: Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.

Qin, Fei / Cai, Guoshuai / Amos, Christopher I / Xiao, Feifei

Genome research

2024 Volume 34, Issue 3, Page(s) 514

Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.279293.124
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Article: A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data.

Qin, Fei / Cai, Guoshuai / Xiao, Feifei

bioRxiv : the preprint server for biology

2023

Abstract: The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in ...

Abstract	The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, since cells comprising a subpopulation are found to share genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified CNAs) in the procedure of CNA detection, hence diminishing the accuracy of subclone identification from a large complex cell population. In this study, we developed a CNA detection method based on a fused lasso model, referred to as FLCNA, which can simultaneously identify subclones in single cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA benchmarking to existing copy number estimation methods (SCOPE, HMMcopy) in combination with the existing and commonly used clustering methods. Interestingly, application of FLCNA to a real scDNA-seq dataset of breast cancer revealed remarkably different genomic variation patterns in neoadjuvant chemotherapy treated samples and pre-treated samples. We show that FLCNA is a practical and powerful method in subclone identification and CNA detection with scDNA-seq data.
Language	English
Publishing date	2023-04-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.18.537346
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Article ; Online: Evaluation and clinical significance of contrast-enhanced ultrasound on changes in liver blood flow perfusion after TIPS surgery.

Yang, Meirong / Qin, Fei / Zhou, Yan / Yao, Yueping / Lu, Zhonghua / Chen, Wei

Medicine

2024 Volume 103, Issue 17, Page(s) e37899

Abstract: To investigate the clinical value of contrast-enhanced ultrasound in the prediction of hepatic encephalopathy (HE) in patients with hepatitis B cirrhosis after intrahepatic portal-systemic shunt via jugular vein. In this retrospective study, we collected ...

Abstract	To investigate the clinical value of contrast-enhanced ultrasound in the prediction of hepatic encephalopathy (HE) in patients with hepatitis B cirrhosis after intrahepatic portal-systemic shunt via jugular vein. In this retrospective study, we collected data from 75 patients with hepatitis B, cirrhosis, and portal hypertension who underwent jugular intrahepatic portosystemic shunt from February 2019 to February 2022. The diagnostic instrument used was the TOSHIBA Aplio500 color Doppler ultrasound with contrast-enhanced ultrasound capabilities. The trial group comprised 20 patients with HE within 3 months postsurgery, while the control group (CG) included 55 patients without HE within the same postoperative period. All patients underwent various examinations before and within 48 hours after surgery, including observation of liver and spleen size and stent position, as well as assessment of blood flow direction in portal and hepatic veins. Subsequently, contrast-enhanced ultrasound was employed to examine and observe perfusion changes of contrast agents in hepatic veins, hepatic arteries, and portal veins (PV). Changes in PV pressure gradient, intrahepatic, and stent blood flow perfusion (BFP) were explored in both postoperative trials and CGs. The trial group exhibited higher BFP volume, PV pressure gradient difference, and percentage decrease compared to the CG. A weak positive correlation was observed between blood flow within the liver stent and PV pressure gradient difference, as well as the percentage decrease in PV pressure gradient. The correlation coefficient between blood flowing perfusion volume within the stent and the difference in PV pressure gradient was R = 0.415 (P = .000). The correlating coefficient between BFP amount within the stent and the percentage decrease in PV pressure gradient was R = 0.261 (P = .027). The area under the receiver operating characteristic curve for stent perfusion volume, difference in PV pressure gradient, and percentage decrease in PV pressure gradient was 0.691, 0.759, and 0.742, respectively. An increase in PV pressure gradient accelerates blood flow within the stent, predisposing to HE. Changes in hepatic BFP following transjugular intrahepatic portosystemic shunt can effectively predict the occurrence of HE, demonstrating significant clinical relevance.
MeSH term(s)	Humans ; Male ; Portasystemic Shunt, Transjugular Intrahepatic/methods ; Female ; Middle Aged ; Retrospective Studies ; Contrast Media ; Hypertension, Portal/surgery ; Hypertension, Portal/physiopathology ; Hypertension, Portal/diagnostic imaging ; Liver/blood supply ; Liver/diagnostic imaging ; Liver/surgery ; Ultrasonography, Doppler, Color/methods ; Adult ; Liver Cirrhosis/surgery ; Liver Cirrhosis/physiopathology ; Liver Cirrhosis/diagnostic imaging ; Liver Circulation/physiology ; Aged ; Portal Vein/diagnostic imaging ; Portal Vein/physiopathology ; Clinical Relevance
Chemical Substances	Contrast Media
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article ; Observational Study
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000037899
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Article ; Online: Analysis of cancer-associated fibroblasts related genes identifies COL11A1 associated with lung adenocarcinoma prognosis.

Zheng, Haosheng / Tan, Jian / Qin, Fei / Zheng, Yuzhen / Yang, Xingping / Qin, Xianyu / Liao, Hongying

BMC medical genomics

2024 Volume 17, Issue 1, Page(s) 97

Abstract: Background: The treatment of lung adenocarcinoma is difficult due to the limited therapeutic options. Cancer-associated fibroblasts play an important role in the development of cancers. This study aimed to identify a promising molecular target ... ...

Abstract	Background: The treatment of lung adenocarcinoma is difficult due to the limited therapeutic options. Cancer-associated fibroblasts play an important role in the development of cancers. This study aimed to identify a promising molecular target associated with cancer-associated fibroblasts for the treatment of lung adenocarcinoma. Methods: The Cancer Genome Atlas lung adenocarcinoma dataset was used to screen hub genes associated with cancer-associated fibroblasts via the EPIC algorithm and Weighted Gene Co-expression Network Analysis. Multiple databases were used together with our data to verify the differential expression and survival of COL11A1. Functional enrichment analysis and the single-cell TISCH database were used to elucidate the mechanisms underlying COL11A1 expression. The correlation between COL11A1 and immune checkpoint genes in human cancers was also evaluated. Results: Using the EPIC algorithm and Weighted Gene Co-expression Network Analysis, 13 hub genes associated with cancer-associated fibroblasts in lung adenocarcinoma were screened. Using the GEPIA database, Kaplan-Meier Plotter database, GSE72094, GSE75037, GSE32863, and our immunohistochemistry experiment data, we confirmed that COL11A1 overexpresses in lung adenocarcinoma and that high expression of COL11A1 is associated with a poor prognosis. COL11A1 has a genetic alteration frequency of 22% in patients with lung adenocarcinoma. COL11A1 is involved in the extracellular matrix activities of lung adenocarcinoma. Using the TISCH database, we found that COL11A1 is mainly expressed by cancer-associated fibroblasts in the tumor microenvironment rather than by lung adenocarcinoma cells. Finally, we found that COL11A1 is positively correlated with HAVCR2(TIM3), CD274 (PD-L1), CTLA4, and LAG3 in lung adenocarcinoma. Conclusion: COL11A1 may be expressed and secreted by cancer-associated fibroblasts, and a high expression of COL11A1 may result in T cell exhaustion in the tumor microenvironment of lung adenocarcinoma. COL11A1 may serve as an attractive biomarker to provide new insights into cancer therapeutics.
MeSH term(s)	Humans ; Collagen Type XI/genetics ; Adenocarcinoma of Lung/genetics ; Adenocarcinoma of Lung/pathology ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Cancer-Associated Fibroblasts/metabolism ; Cancer-Associated Fibroblasts/pathology ; Prognosis ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; Databases, Genetic ; Gene Regulatory Networks ; Tumor Microenvironment/genetics ; Gene Expression Profiling
Chemical Substances	COL11A1 protein, human ; Collagen Type XI ; Biomarkers, Tumor
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-024-01863-1
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Article ; Online: Spatial differentiation of carbon emissions reduction potential for construction and demolition waste recycling.

Wang, Zhenshuang / Qin, Fei / Liu, Jingkuang / Xia, Bo / Chileshe, Nicholas

Environmental science and pollution research international

2023 Volume 30, Issue 58, Page(s) 122304–122321

Abstract: Identifying the regional differences and drivers for carbon reduction of construction and demolition waste (C&DW) recycling is essential to combat climate change. This study aims to calculate the carbon reduction potential for C&DW recycling from 2006 to ...

Abstract	Identifying the regional differences and drivers for carbon reduction of construction and demolition waste (C&DW) recycling is essential to combat climate change. This study aims to calculate the carbon reduction potential for C&DW recycling from 2006 to 2021 in China and investigates the spatial differences and driving factors of carbon reduction potential for C&DW waste by combining the Theil index, Gini coefficient, and geographic detector methods. The carbon reduction potential for C&DW recycling in China was "high in the east and low in the west" overall level, with an average annual growth rate of 6.27%. The overall differences in carbon reduction potential for C&DW recycling are decreasing, mainly due to intraregional differences and inter-provincial differences in Northeast China. The population size, urbanization rate, and technological effect are the key factors influencing carbon reduction potential for C&DW recycling. There are two types of interactions between influencing factor pairs: nonlinear enhancement and two-factor enhancement. This study's results can guide policymakers to devise relevant, regionally specific policies.
MeSH term(s)	Waste Management/methods ; Construction Materials ; Recycling ; China ; Urbanization ; Carbon ; Construction Industry ; Industrial Waste
Chemical Substances	Carbon (7440-44-0) ; Industrial Waste
Language	English
Publishing date	2023-11-15
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-30953-3
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Article: Spiritual Care in PICUs: A U.S. Survey of 245 Training Fellows 2020-2021.

Stevens, Paige E / Rassbach, Caroline E / Qin, FeiFei / Kuo, Kevin W

Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies

2023

Abstract: Objectives: To understand the perspectives of pediatric fellows training in critical care subspecialties about providing spiritual care.: Design: Cross-sectional survey of United States National Residency Matching Program pediatric fellows training ... ...

Abstract	Objectives: To understand the perspectives of pediatric fellows training in critical care subspecialties about providing spiritual care. Design: Cross-sectional survey of United States National Residency Matching Program pediatric fellows training in critical care specialties. Setting: Online survey open from April to May 2021. Subjects: A total of 720 fellows (165 cardiology, 259 critical care, and 296 neonatology) were contacted, with a response rate of 245 of 720 (34%). Interventions: None. Measurements and main results: We assessed fellows' survey responses about spiritual care in neonatal and pediatric critical care units. Categorical data were compared using chi-square test or Fisher exact tests. The Wilcoxon rank-sum test was used to compare the percentage correct on ten multiple-choice questions about world religions. Free-text responses were independently coded by two research investigators. A total of 203 of 245 (83%) responding fellows had never received training about spiritual care and 176 of 245 (72%) indicated that they would be likely to incorporate spiritual care into their practice if they received training. Prior training was associated with increased familiarity with a framework for taking a spiritual history (p < 0.001) and increased knowledge of spiritual practices that could influence medical care (p = 0.03). Prior training was also associated with increased self-reported frequency of taking a spiritual history (p < 0.001) and comfort in referring families to spiritual care resources (p = 0.02). Lack of time and training were the most reported barriers to providing spiritual care. Conclusions: Providing spiritual care for families is important in critical care settings. In 2020-2021, in the United States, 245 pediatric critical care fellows responded to a survey about spiritual care in their practice and reported that they lacked training in this subject. An opportunity exists to implement spiritual care curricula into pediatric fellowship training.
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2052349-X
ISSN	1947-3893 ; 1529-7535
ISSN (online)	1947-3893
ISSN	1529-7535
DOI	10.1097/PCC.0000000000003429
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