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Article: SpecReFlow: an algorithm for specular reflection restoration using flow-guided video completion.

Yin, Haoli / Eimen, Rachel / Moyer, Daniel / Bowden, Audrey K

Journal of medical imaging (Bellingham, Wash.)

2024 Volume 11, Issue 2, Page(s) 24012

Abstract: Purpose: Specular reflections (SRs) are highlight artifacts commonly found in endoscopy videos that can severely disrupt a surgeon's observation and judgment. Despite numerous attempts to restore SR, existing methods are inefficient and time consuming ... ...

Abstract	Purpose: Specular reflections (SRs) are highlight artifacts commonly found in endoscopy videos that can severely disrupt a surgeon's observation and judgment. Despite numerous attempts to restore SR, existing methods are inefficient and time consuming and can lead to false clinical interpretations. Therefore, we propose the first complete deep-learning solution, SpecReFlow, to detect and restore SR regions from endoscopy video with spatial and temporal coherence. Approach: SpecReFlow consists of three stages: (1) an image preprocessing stage to enhance contrast, (2) a detection stage to indicate where the SR region is present, and (3) a restoration stage in which we replace SR pixels with an accurate underlying tissue structure. Our restoration approach uses optical flow to seamlessly propagate color and structure from other frames of the endoscopy video. Results: Comprehensive quantitative and qualitative tests for each stage reveal that our SpecReFlow solution performs better than previous detection and restoration methods. Our detection stage achieves a Dice score of 82.8% and a sensitivity of 94.6%, and our restoration stage successfully incorporates temporal information with spatial information for more accurate restorations than existing techniques. Conclusions: SpecReFlow is a first-of-its-kind solution that combines temporal and spatial information for effective detection and restoration of SR regions, surpassing previous methods relying on single-frame spatial information. Future work will look to optimizing SpecReFlow for real-time applications. SpecReFlow is a software-only solution for restoring image content lost due to SR, making it readily deployable in existing clinical settings to improve endoscopy video quality for accurate diagnosis and treatment.
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article
ISSN	2329-4302
ISSN	2329-4302
DOI	10.1117/1.JMI.11.2.024012
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Book ; Online: Prostate Lesion Detection and Salient Feature Assessment Using Zone-Based Classifiers

Yin, Haoli / Buduma, Nithin

2022

Abstract: Multi-parametric magnetic resonance imaging (mpMRI) has a growing role in detecting prostate cancer lesions. Thus, it is pertinent that medical professionals who interpret these scans reduce the risk of human error by using computer-aided detection ... ...

Abstract	Multi-parametric magnetic resonance imaging (mpMRI) has a growing role in detecting prostate cancer lesions. Thus, it is pertinent that medical professionals who interpret these scans reduce the risk of human error by using computer-aided detection systems. The variety of algorithms used in system implementation, however, has yielded mixed results. Here we investigate the best machine learning classifier for each prostate zone. We also discover salient features to clarify the models' classification rationale. Of the data provided, we gathered and augmented T2 weighted images and apparent diffusion coefficient map images to extract first through third order statistical features as input to machine learning classifiers. For our deep learning classifier, we used a convolutional neural net (CNN) architecture for automatic feature extraction and classification. The interpretability of the CNN results was improved by saliency mapping to understand the classification mechanisms within. Ultimately, we concluded that effective detection of peripheral and anterior fibromuscular stroma (AS) lesions depended more on statistical distribution features, whereas those in the transition zone (TZ) depended more on textural features. Ensemble algorithms worked best for PZ and TZ zones, while CNNs were best in the AS zone. These classifiers can be used to validate a radiologist's predictions and reduce inter-reader variability in patients suspected to have prostate cancer. The salient features reported in this study can also be investigated further to better understand hidden features and biomarkers of prostate lesions with mpMRIs.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
Subject code	006
Publishing date	2022-08-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prediction of false-positive PI-RADS 5 lesions on prostate multiparametric MRI: development and internal validation of a clinical-radiological characteristics based nomogram.

Cheng, Yongbing / Fan, Bo / Fu, Yao / Yin, Haoli / Lu, Jiaming / Li, Danyan / Li, Xiaogong / Qiu, Xuefeng / Guo, Hongqian

BMC urology

2024 Volume 24, Issue 1, Page(s) 76

Abstract: Background: To develop a risk model including clinical and radiological characteristics to predict false-positive The Prostate Imaging Reporting and Data System (PI-RADS) 5 lesions.: Methods: Data of 612 biopsy-naïve patients who had undergone ... ...

Abstract	Background: To develop a risk model including clinical and radiological characteristics to predict false-positive The Prostate Imaging Reporting and Data System (PI-RADS) 5 lesions. Methods: Data of 612 biopsy-naïve patients who had undergone multiparametric magnetic resonance imaging (mpMRI) before prostate biopsy were collected. Clinical variables and radiological variables on mpMRI were adopted. Lesions were divided into the training and validation cohort randomly. Stepwise multivariate logistic regression analysis with backward elimination was performed to screen out variables with significant difference. A diagnostic nomogram was developed in the training cohort and further validated in the validation cohort. Calibration curve and receiver operating characteristic (ROC) analysis were also performed. Results: 296 PI-RADS 5 lesions in 294 patients were randomly divided into the training and validation cohort (208 : 88). 132 and 56 lesions were confirmed to be clinically significant prostate cancer in the training and validation cohort respectively. The diagnostic nomogram was developed based on prostate specific antigen density, the maximum diameter of lesion, zonality of lesion, apparent diffusion coefficient minimum value and apparent diffusion coefficient minimum value ratio. The C-index of the model was 0.821 in the training cohort and 0.871 in the validation cohort. The calibration curve showed good agreement between the estimation and observation in the two cohorts. When the optimal cutoff values of ROC were 0.288 in the validation cohort, the sensitivity, specificity, PPV, and NPV were 90.6%, 67.9%, 61.7%, and 92.7% in the validation cohort, potentially avoiding 9.7% unnecessary prostate biopsies. Conclusions: We developed and validated a diagnostic nomogram by including 5 factors. False positive PI-RADS 5 lesions could be distinguished from clinically significant ones, thus avoiding unnecessary prostate biopsy.
MeSH term(s)	Male ; Humans ; Prostate/diagnostic imaging ; Prostate/pathology ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/pathology ; Nomograms ; Multiparametric Magnetic Resonance Imaging ; Magnetic Resonance Imaging/methods ; Prostate-Specific Antigen ; Retrospective Studies ; Image-Guided Biopsy/methods
Chemical Substances	Prostate-Specific Antigen (EC 3.4.21.77)
Language	English
Publishing date	2024-04-02
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2059857-9
ISSN	1471-2490 ; 1471-2490
ISSN (online)	1471-2490
ISSN	1471-2490
DOI	10.1186/s12894-024-01465-0
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Book ; Online: UniCat

Crawford, Jennifer / Yin, Haoli / McDermott, Luke / Cummings, Daniel

Crafting a Stronger Fusion Baseline for Multimodal Re-Identification

2023

Abstract: Multimodal Re-Identification (ReID) is a popular retrieval task that aims to re-identify objects across diverse data streams, prompting many researchers to integrate multiple modalities into a unified representation. While such fusion promises a holistic ...

Abstract	Multimodal Re-Identification (ReID) is a popular retrieval task that aims to re-identify objects across diverse data streams, prompting many researchers to integrate multiple modalities into a unified representation. While such fusion promises a holistic view, our investigations shed light on potential pitfalls. We uncover that prevailing late-fusion techniques often produce suboptimal latent representations when compared to methods that train modalities in isolation. We argue that this effect is largely due to the inadvertent relaxation of the training objectives on individual modalities when using fusion, what others have termed modality laziness. We present a nuanced point-of-view that this relaxation can lead to certain modalities failing to fully harness available task-relevant information, and yet, offers a protective veil to noisy modalities, preventing them from overfitting to task-irrelevant data. Our findings also show that unimodal concatenation (UniCat) and other late-fusion ensembling of unimodal backbones, when paired with best-known training techniques, exceed the current state-of-the-art performance across several multimodal ReID benchmarks. By unveiling the double-edged sword of "modality laziness", we motivate future research in balancing local modality strengths with global representations. Comment: Accepted NeurIPS 2023 UniReps, 9 pages, 4 tables
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2023-10-28
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Small ankyrin 1 (sANK1) promotes docetaxel resistance in castration‐resistant prostate cancer cells by enhancing oxidative phosphorylation

Yang, Yang / Qin, Haixiang / Ding, Meng / Ji, Changwei / Chen, Wei / Diao, Wenli / Yin, Haoli / Chen, Mengxia / Gan, Weidong / Guo, Hongqian

FEBS Open Bio. 2023 Feb., v. 13, no. 2, p. 257-269

2023 , Page(s) 257–269

Abstract: Docetaxel (DTX) plays an important role in treating advanced prostate cancer (PCa). However, nearly all patients receiving DTX therapy ultimately progress to DTX resistance. How to address DTX resistance in PCa remains a key challenge for all urologists. ...

Abstract	Docetaxel (DTX) plays an important role in treating advanced prostate cancer (PCa). However, nearly all patients receiving DTX therapy ultimately progress to DTX resistance. How to address DTX resistance in PCa remains a key challenge for all urologists. Small ankyrin 1 (sAnk1) is an integral membrane protein in the endoplasmic reticulum. In the present study, we identified that sAnk1 is upregulated in PCa tissues and is positively associated with DTX therapy resistance in PCa. Further investigation demonstrated that overexpression of sAnk1 can significantly increase the DTX‐resistant ability of PCa cells in vitro and in vivo. In addition, overexpression of sAnk1 could enhance oxidative phosphorylation (OXPHOS) levels in PCa cells, which was consistent with the higher OXPHOS levels observed in DTX‐resistant PCa cells as compared to DTX‐sensitive PCa cells. sAnk1 was also found to interact with polypyrimidine‐tract‐binding protein (PTBP1), an alternative splicing factor, and suppressed PTBP1‐mediated alternative splicing of the pyruvate kinase gene (PKM). Thus, overexpression of sAnk1 decreased the ratio of PKM2/PKM1, enhanced the OXPHOS level, and ultimately promoted the resistance of PCa cells to DTX. In summary, our data suggest that sAnk1 enhances DTX resistance in PCa cells.
Keywords	endoplasmic reticulum ; genes ; membrane proteins ; oxidative phosphorylation ; prostatic neoplasms ; pyruvate kinase ; therapeutics
Language	English
Dates of publication	2023-02
Size	p. 257-269
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2651702-4
ISSN	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13535
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: GALNT12 suppresses the bone-specific prostate cancer metastasis by activating BMP pathway via the O-glycosylation of BMPR1A.

Yang, Yang / Ding, Meng / Yin, Haoli / Chen, Wei / Shen, Hongwei / Diao, Wenli / Yang, Lin / Qin, Haixiang / Gan, Weidong / Qiu, Xuefeng / Guo, Hongqian

International journal of biological sciences

2024 Volume 20, Issue 4, Page(s) 1297–1313

Abstract: Bone metastasis caused the majority death of prostate cancer (PCa) but the mechanism remains poorly understood. In this present study, we show that polypeptide N-acetylgalactosaminyltransferase 12 (GALNT12) suppresses bone-specific metastasis of PCa. ... ...

Abstract	Bone metastasis caused the majority death of prostate cancer (PCa) but the mechanism remains poorly understood. In this present study, we show that polypeptide N-acetylgalactosaminyltransferase 12 (GALNT12) suppresses bone-specific metastasis of PCa. GALNT12 suppresses proliferation, migration, invasion and cell division ability of PCa cells by activating the BMP pathway. Mechanistic investigations showed that GALNT12 augments the O-glycosylation of BMPR1A then actives the BMP pathway. Activated BMP signaling inhibits the expression of integrin αVβ3 to reduce the bone-specific seeding of PCa cells. Furthermore, activated BMP signaling remolds the immune microenvironment by suppressing the STAT3 pathway. Our results of this study illustrate the role and mechanism of GALNT12 in the process of bone metastasis of PCa and identify GALNT12 as a potential therapeutic target for metastatic PCa.
MeSH term(s)	Male ; Humans ; Glycosylation ; Cell Line, Tumor ; Signal Transduction/genetics ; Prostatic Neoplasms/metabolism ; Bone Neoplasms/metabolism ; Tumor Microenvironment ; Bone Morphogenetic Protein Receptors, Type I/genetics ; Bone Morphogenetic Protein Receptors, Type I/metabolism ; N-Acetylgalactosaminyltransferases/genetics ; N-Acetylgalactosaminyltransferases/metabolism
Chemical Substances	BMPR1A protein, human (EC 2.7.11.30) ; Bone Morphogenetic Protein Receptors, Type I (EC 2.7.11.30) ; GALNT12 protein, human (EC 2.4.1.-) ; N-Acetylgalactosaminyltransferases (EC 2.4.1.-)
Language	English
Publishing date	2024-01-27
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2179208-2
ISSN	1449-2288 ; 1449-2288
ISSN (online)	1449-2288
ISSN	1449-2288
DOI	10.7150/ijbs.91925
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Article ; Online: MicroRNA-582-5p regulates cell invasion in bladder cancer through targeting Forkhead Box G1.

Zhuang, Junlong / Hao, Jiange / Bu, Fan / Yin, Haoli / Chen, Wei / Guo, Hongqian

Pathology, research and practice

2021 Volume 230, Page(s) 153752

Abstract: Burgeoning evidence shows that microRNAs (miRNAs) are associated with tumorigenesis and progression. However, the alteration and function of many miRNAs in bladder cancer (BCa) are not clear. Here, we explored the regulatory effect of microRNA-582 (miR- ... ...

Abstract	Burgeoning evidence shows that microRNAs (miRNAs) are associated with tumorigenesis and progression. However, the alteration and function of many miRNAs in bladder cancer (BCa) are not clear. Here, we explored the regulatory effect of microRNA-582 (miR-582) on cell invasion in BCa and underlying mechanisms. The expression of miR-582 in BCa tissues and cell lines was examined by quantitative real-time PCR (qRT-PCR). The target gene of miR-582 and their binding site were predicted by bioinformatics analysis. Luciferase reporter assay and western blot analysis were performed to confirm miR-582 directly targeting Forkhead Box G1 (FOXG1). The role of miR-582-FOXG1 axis in regulating BCa invasion was evaluated in cell models. The association of miR-582 with clinicopathologic features and prognosis was analyzed. Experimental results indicated that miR-582 was downregulated in BCa tissues and cell lines. Forced miR-582 decreased cell invasion, regulating expression levels of invasion-related proteins, such as MMP2, MMP9 and ZO-1. MiR-582 directly targeted FOXG1 by binding to its 3'UTR. Overexpression of FOXG1 rescued the regulating function in BCa cells induced by miR-582. Moreover, miR-582-FOXG1 axis has obvious clinical relevance with prognosis in BCa patients. Our results indicate that miR-582-FOXG1 axis may act as a key role on cell invasion and serve as a potential prognostic predicted biomarker.
MeSH term(s)	3' Untranslated Regions ; Aged ; Binding Sites ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Cell Movement ; Female ; Forkhead Transcription Factors/genetics ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Middle Aged ; Neoplasm Invasiveness ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Signal Transduction ; Urinary Bladder Neoplasms/genetics ; Urinary Bladder Neoplasms/metabolism ; Urinary Bladder Neoplasms/pathology
Chemical Substances	3' Untranslated Regions ; Biomarkers, Tumor ; FOXG1 protein, human ; Forkhead Transcription Factors ; MIRN582 microRNA, human ; MicroRNAs ; Nerve Tissue Proteins
Language	English
Publishing date	2021-12-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2021.153752
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Article ; Online: Small ankyrin 1 (sANK1) promotes docetaxel resistance in castration-resistant prostate cancer cells by enhancing oxidative phosphorylation.

Yang, Yang / Qin, Haixiang / Ding, Meng / Ji, Changwei / Chen, Wei / Diao, Wenli / Yin, Haoli / Chen, Mengxia / Gan, Weidong / Guo, Hongqian

FEBS open bio

2022 Volume 13, Issue 2, Page(s) 257–269

Abstract	Docetaxel (DTX) plays an important role in treating advanced prostate cancer (PCa). However, nearly all patients receiving DTX therapy ultimately progress to DTX resistance. How to address DTX resistance in PCa remains a key challenge for all urologists. Small ankyrin 1 (sAnk1) is an integral membrane protein in the endoplasmic reticulum. In the present study, we identified that sAnk1 is upregulated in PCa tissues and is positively associated with DTX therapy resistance in PCa. Further investigation demonstrated that overexpression of sAnk1 can significantly increase the DTX-resistant ability of PCa cells in vitro and in vivo. In addition, overexpression of sAnk1 could enhance oxidative phosphorylation (OXPHOS) levels in PCa cells, which was consistent with the higher OXPHOS levels observed in DTX-resistant PCa cells as compared to DTX-sensitive PCa cells. sAnk1 was also found to interact with polypyrimidine-tract-binding protein (PTBP1), an alternative splicing factor, and suppressed PTBP1-mediated alternative splicing of the pyruvate kinase gene (PKM). Thus, overexpression of sAnk1 decreased the ratio of PKM2/PKM1, enhanced the OXPHOS level, and ultimately promoted the resistance of PCa cells to DTX. In summary, our data suggest that sAnk1 enhances DTX resistance in PCa cells.
MeSH term(s)	Male ; Humans ; Docetaxel/pharmacology ; Ankyrins/genetics ; Ankyrins/metabolism ; Prostatic Neoplasms, Castration-Resistant/drug therapy ; Prostatic Neoplasms, Castration-Resistant/genetics ; Prostatic Neoplasms, Castration-Resistant/metabolism ; Oxidative Phosphorylation ; Drug Resistance, Neoplasm/genetics ; Cell Line, Tumor ; Cytoskeletal Proteins/metabolism ; Heterogeneous-Nuclear Ribonucleoproteins/metabolism ; Polypyrimidine Tract-Binding Protein/metabolism
Chemical Substances	Docetaxel (15H5577CQD) ; Ankyrins ; Cytoskeletal Proteins ; PTBP1 protein, human ; Heterogeneous-Nuclear Ribonucleoproteins ; Polypyrimidine Tract-Binding Protein (139076-35-0)
Language	English
Publishing date	2022-12-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13535
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Article: Second generation androgen receptor antagonist, TQB3720 abrogates prostate cancer growth

Zhang, Zhongqing / Xie, Tianlei / Zhang, Shun / Yin, Haoli / Zhang, Xuyu / Zhang, Siyuan / Chen, Wei / Yu, Ding / Qiu, Xuefeng / Zhao, Wei / Guo, Hongqian / Zhuang, Junlong

Frontiers in pharmacology

2023 Volume 14, Page(s) 1110146

Abstract: Purpose: ...

Abstract	Purpose:
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1110146
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Article: circCYP24A1 promotes Docetaxel resistance in prostate Cancer by Upregulating ALDH1A3.

Yin, Haoli / Qin, Haixiang / Yang, Lei / Chen, Mengxia / Yang, Yang / Zhang, Wenlong / Hao, Jiange / Lu, Qun / Shi, Jingyan / Zhuang, Junlong / Qiu, Xuefeng / Guo, Hongqian

Biomarker research

2022 Volume 10, Issue 1, Page(s) 48

Abstract: Background: Docetaxel (DTX) is the most widely prescribed first-line chemotherapy for advanced prostate cancer (PCa). Unfortunately, DTX resistance invariably emerges, leading to worse prognosis of PCa. Growing evidence has shown that circRNAs had ... ...

Abstract	Background: Docetaxel (DTX) is the most widely prescribed first-line chemotherapy for advanced prostate cancer (PCa). Unfortunately, DTX resistance invariably emerges, leading to worse prognosis of PCa. Growing evidence has shown that circRNAs had complex spatiotemporal specificity during the tumor development and oncogenesis. This study was designed to investigate the biological functions and possible molecular mechanisms of circRNAs in DTX resistance of PCa. Methods: circRNAs in established DTX-resistant DU145 cell line were identified by RNA sequencing. Biological function of circCYP24A1 was verified in vitro and in vivo. The potential role of circCYP24A1 in the development of DTX-resistant PCa was investigated via dual-luciferase reporter assays, RIP assays and RNA pull-down assays. Univariate and multivariate logistic regression analyses was used to predict DTX-chemotherapy response based on patients' clinical and biological information. Results: CircCYP24A1 was identified to be upregulated in DTX-resistant DU145 cells. Upregulated circCYP24A1 was found to suppress the DTX chemosensitivity in vitro and in vivo. Furthermore, we found that circCYP24A1 promoted DTX resistance in PCa via regulating ALDH1A3 expression by sponging miR-1301-3p and activating PI3K/AKT/mTOR signaling pathway. Statistical analyses elucidated that circCYP24A1 was an independent risk factor to predict DTX response (OR = 0.165; 95% CI: 0.038-0.723; P = 0.017). Conclusions: This study demonstrated that circCYP24A played an essential role in DTX resistance in PCa, suggesting that circCYP24A1 could be a promising biomarker to predict DTX response and a potential therapeutic target in PCa patients resistant to DTX chemotherapy.
Language	English
Publishing date	2022-07-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2699926-2
ISSN	2050-7771
ISSN	2050-7771
DOI	10.1186/s40364-022-00393-1
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