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Article: Enhancing obSTORM imaging performance with cubic spline PSF modeling.

Koo, Donghoon / Lee, Minchol / Lee, Youngseop / Kim, Jeongmin

2023 Volume 14, Issue 10, Page(s) 5075–5084

Abstract: Oblique plane microscopy-based single molecule localization microscopy (obSTORM) has shown great potential for super-resolution imaging of thick biological specimens. Despite its compatibility with tissues and small animals, prior uses of the Gaussian ... ...

Abstract	Oblique plane microscopy-based single molecule localization microscopy (obSTORM) has shown great potential for super-resolution imaging of thick biological specimens. Despite its compatibility with tissues and small animals, prior uses of the Gaussian point spread function (PSF) model have resulted in limited imaging resolution and a narrow axial localization range. This is due to the poor fit of the Gaussian PSF model with the actual PSF shapes in obSTORM. To overcome these limitations, we have employed cubic splines for a more accurate modeling of the experimental PSF shapes. This refined PSF model enhances three-dimensional localization precision, leading to significant improvements in obSTORM imaging of mouse retina tissues, such as an approximately 1.2 times increase in imaging resolution, seamless stitching of single molecules between adjacent optical sections, and a doubling of the sectional interval in volumetric obSTORM imaging due to the extended axial range of usable section thickness. The cubic spline PSF model thus offers a path towards more accurate and faster volumetric obSTORM imaging of biological specimens.
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2572216-5
ISSN	2156-7085
ISSN	2156-7085
DOI	10.1364/BOE.500323
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Highly sensitive ultrasound detection using nanofabricated polymer micro-ring resonators

Youngseop Lee / Hao F. Zhang / Cheng Sun

Nano Convergence, Vol 10, Iss 1, Pp 1-

2023 Volume 19

Abstract: Abstract Photoacoustic (PA) imaging enables noninvasive volumetric imaging of biological tissues by capturing the endogenous optical absorption contrast. Conventional ultrasound detectors using piezoelectric materials have been widely used for ... ...

Abstract	Abstract Photoacoustic (PA) imaging enables noninvasive volumetric imaging of biological tissues by capturing the endogenous optical absorption contrast. Conventional ultrasound detectors using piezoelectric materials have been widely used for transducing ultrasound signals into the electrical signals for PA imaging reconstruction. However, their inherent limitations in detection bandwidth and sensitivity per unit area have unfortunately constrained the performance of PA imaging. Optical based ultrasound detection methods emerge to offer very promising solutions. In particular, polymer micro-ring resonators (MRRs) in the form of integrated photonic circuits (IPC) enable significant reduction for the sensing area to 80 μm in diameter, while maintaining highly sensitive ultrasound detection with noise equivalent pressure (NEP) of 0.49 Pa and a broad detection frequency range up to 250 MHz. The continued engineering innovation has further transformed MRRs to be transparent to the light and thus, opens up a wide range of applications, including multi-modality optical microscope with isometric resolution, PA endoscope, photoacoustic computed tomography (PACT), and more. This review article summarizes and discusses the evolution of polymer MRR design and the associated nanofabrication process for improving the performance of ultrasound detection. The resulting novel imaging applications will also be reviewed and discussed.
Keywords	Photoacoustic imaging ; Micro-ring resonator ; Ultrasound detector ; Nano-fabrication ; Maskless lithography ; Nanoimprint lithography ; Technology ; T ; Chemical technology ; TP1-1185 ; Biotechnology ; TP248.13-248.65 ; Science ; Q ; Physics ; QC1-999
Subject code	620
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Highly sensitive ultrasound detection using nanofabricated polymer micro-ring resonators.

Lee, Youngseop / Zhang, Hao F / Sun, Cheng

Nano convergence

2023 Volume 10, Issue 1, Page(s) 30

Abstract: Photoacoustic (PA) imaging enables noninvasive volumetric imaging of biological tissues by capturing the endogenous optical absorption contrast. Conventional ultrasound detectors using piezoelectric materials have been widely used for transducing ... ...

Abstract	Photoacoustic (PA) imaging enables noninvasive volumetric imaging of biological tissues by capturing the endogenous optical absorption contrast. Conventional ultrasound detectors using piezoelectric materials have been widely used for transducing ultrasound signals into the electrical signals for PA imaging reconstruction. However, their inherent limitations in detection bandwidth and sensitivity per unit area have unfortunately constrained the performance of PA imaging. Optical based ultrasound detection methods emerge to offer very promising solutions. In particular, polymer micro-ring resonators (MRRs) in the form of integrated photonic circuits (IPC) enable significant reduction for the sensing area to 80 μm in diameter, while maintaining highly sensitive ultrasound detection with noise equivalent pressure (NEP) of 0.49 Pa and a broad detection frequency range up to 250 MHz. The continued engineering innovation has further transformed MRRs to be transparent to the light and thus, opens up a wide range of applications, including multi-modality optical microscope with isometric resolution, PA endoscope, photoacoustic computed tomography (PACT), and more. This review article summarizes and discusses the evolution of polymer MRR design and the associated nanofabrication process for improving the performance of ultrasound detection. The resulting novel imaging applications will also be reviewed and discussed.
Language	English
Publishing date	2023-06-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2760386-6
ISSN	2196-5404 ; 2196-5404
ISSN (online)	2196-5404
ISSN	2196-5404
DOI	10.1186/s40580-023-00378-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Machine Learning Approach for Recommending Herbal Formulae with Enhanced Interpretability and Applicability

Won-Yung Lee / Youngseop Lee / Siwoo Lee / Young Woo Kim / Ji-Hwan Kim

Biomolecules, Vol 12, Iss 1604, p

2022 Volume 1604

Abstract: Herbal formulae (HFs) are representative interventions in Korean medicine (KM) for the prevention and treatment of various diseases. Here, we proposed a machine learning-based approach for HF recommendation with enhanced interpretability and ... ...

Abstract	Herbal formulae (HFs) are representative interventions in Korean medicine (KM) for the prevention and treatment of various diseases. Here, we proposed a machine learning-based approach for HF recommendation with enhanced interpretability and applicability. A dataset consisting of clinical symptoms, Sasang constitution (SC) types, and prescribed HFs was derived from a multicenter study. Case studies published over 10 years were collected and curated by experts. Various classifiers, oversampling methods, and data imputation techniques were comprehensively considered. The local interpretable model-agnostic explanation (LIME) technique was applied to identify the clinical symptoms that led to the recommendation of specific HFs. We found that the cascaded deep forest (CDF) model with data imputation and oversampling yielded the best performance on the training set and holdout test set. Our model also achieved top-1 and top-3 accuracies of 0.35 and 0.89, respectively, on case study datasets in which clinical symptoms were only partially recorded. We performed an expert evaluation on the reliability of interpretation results using case studies and achieved a score close to normal. Taken together, our model will contribute to the modernization of KM and the identification of an HF selection process through the development of a practically useful HF recommendation model.
Keywords	herbal formula ; Korean medicine ; recommendation model ; LIME ; Microbiology ; QR1-502
Subject code	006
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Machine Learning Approach for Recommending Herbal Formulae with Enhanced Interpretability and Applicability.

Lee, Won-Yung / Lee, Youngseop / Lee, Siwoo / Kim, Young Woo / Kim, Ji-Hwan

Biomolecules

2022 Volume 12, Issue 11

Abstract	Herbal formulae (HFs) are representative interventions in Korean medicine (KM) for the prevention and treatment of various diseases. Here, we proposed a machine learning-based approach for HF recommendation with enhanced interpretability and applicability. A dataset consisting of clinical symptoms, Sasang constitution (SC) types, and prescribed HFs was derived from a multicenter study. Case studies published over 10 years were collected and curated by experts. Various classifiers, oversampling methods, and data imputation techniques were comprehensively considered. The local interpretable model-agnostic explanation (LIME) technique was applied to identify the clinical symptoms that led to the recommendation of specific HFs. We found that the cascaded deep forest (CDF) model with data imputation and oversampling yielded the best performance on the training set and holdout test set. Our model also achieved top-1 and top-3 accuracies of 0.35 and 0.89, respectively, on case study datasets in which clinical symptoms were only partially recorded. We performed an expert evaluation on the reliability of interpretation results using case studies and achieved a score close to normal. Taken together, our model will contribute to the modernization of KM and the identification of an HF selection process through the development of a practically useful HF recommendation model.
MeSH term(s)	Reproducibility of Results ; Machine Learning
Language	English
Publishing date	2022-10-31
Publishing country	Switzerland
Document type	Multicenter Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12111604
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A micro-fragmented collagen gel as a cell-assembling platform for critical limb ischemia repair

Haeun Chung / Jung-Kyun Choi / Changgi Hong / Youngseop Lee / Ki Hyun Hong / Seung Ja Oh / Jeongmin Kim / Soo-Chang Song / Jong-Wan Kim / Sang-Heon Kim

Bioactive Materials, Vol 34, Iss , Pp 80-

2024 Volume 97

Abstract: Critical limb ischemia (CLI) is a devastating disease characterized by the progressive blockage of blood vessels. Although the paracrine effect of growth factors in stem cell therapy made it a promising angiogenic therapy for CLI, poor cell survival in ... ...

Abstract	Critical limb ischemia (CLI) is a devastating disease characterized by the progressive blockage of blood vessels. Although the paracrine effect of growth factors in stem cell therapy made it a promising angiogenic therapy for CLI, poor cell survival in the harsh ischemic microenvironment limited its efficacy. Thus, an imperative need exists for a stem-cell delivery method that enhances cell survival. Here, a collagen microgel (CMG) cell-delivery scaffold (40 × 20 μm) was fabricated via micro-fragmentation from collagen–hyaluronic acid polyionic complex to improve transplantation efficiency. Culturing human adipose-derived stem cells (hASCs) with CMG enabled integrin receptors to interact with CMG to form injectable 3-dimensional constructs (CMG-hASCs) with a microporous microarchitecture and enhanced mass transfer. CMG-hASCs exhibited higher cell survival (p < 0.0001) and angiogenic potential in tube formation and aortic ring angiogenesis assays than cell aggregates. Injection of CMG-hASCs intramuscularly into CLI mice increased blood perfusion and limb salvage ratios by 40 % and 60 %, respectively, compared to cell aggregate-treated mice. Further immunofluorescent analysis revealed that transplanted CMG-hASCs have greater muscle regenerative and angiogenic potential, with enhanced cell survival than cell aggregates (p < 0.05). Collectively, we propose CMG as a cell-assembling platform and CMG-hASCs as promising therapeutics to treat CLI.
Keywords	Regenerative medicine ; Stem cell therapy ; Collagen microgel ; 3D cell culture ; Critical limb ischemia ; Materials of engineering and construction. Mechanics of materials ; TA401-492 ; Biology (General) ; QH301-705.5
Subject code	571 ; 610
Language	English
Publishing date	2024-04-01T00:00:00Z
Publisher	KeAi Communications Co., Ltd.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Theoretical and experimental study on the detection limit of the micro-ring resonator based ultrasound point detectors.

Lee, Youngseop / Rong, Qiangzhou / Song, Ki-Hee / Czaplewski, David A / Zhang, Hao F / Yao, Junjie / Sun, Cheng

Photoacoustics

2023 Volume 34, Page(s) 100574

Abstract: Combining the diffusive laser excitation and the photoacoustic signals detection, photoacoustic computed tomography (PACT) is uniquely suited for deep tissue imaging. A diffraction-limited ultrasound point detector is highly desirable for maximizing the ... ...

Abstract	Combining the diffusive laser excitation and the photoacoustic signals detection, photoacoustic computed tomography (PACT) is uniquely suited for deep tissue imaging. A diffraction-limited ultrasound point detector is highly desirable for maximizing the spatial resolution and the field-of-view of the reconstructed volumetric images. Among all the available ultrasound detectors, micro-ring resonator (MRR) based ultrasound detectors offer the lowest area-normalized limit of detection (nLOD) in a miniature form-factor, making it an ideal candidate as an ultrasound point detector. However, despite their wide adoption for photoacoustic imaging, the underlying signal transduction process has not been systematically studied yet. Here we report a comprehensive theoretical model capturing the transduction of incident acoustic signals into digital data, and the associated noise propagation process, using experimentally calibrated key process parameters. The theoretical model quantifies the signal-to-noise ratio (SNR) and the nLOD under the influence of the key process variables, including the quality factor (Q-factor) of the MRR and the driving wavelength. While asserting the need for higher Q-factors, the theoretical model further quantifies the optimal driving wavelength for optimizing the nLOD. Given the MRR with a Q-factor of 1 × 10
Language	English
Publishing date	2023-11-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2716706-9
ISSN	2213-5979
ISSN	2213-5979
DOI	10.1016/j.pacs.2023.100574
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: What Is Fecal Incontinence That Urologists Need to Know?

Kim, HongWook / Shim, Jisung / Seo, Yumi / Lee, Changho / Chang, Youngseop

International neurourology journal

2021 Volume 25, Issue 1, Page(s) 23–33

Abstract: Fecal incontinence (FI) undoubtedly reduces quality of life and adversely affects the social life of the affected individual. FI has a higher prevalence with age and has an equivalent prevalence to urinary incontinence in patients with genitourinary ... ...

Abstract	Fecal incontinence (FI) undoubtedly reduces quality of life and adversely affects the social life of the affected individual. FI has a higher prevalence with age and has an equivalent prevalence to urinary incontinence in patients with genitourinary disease, but is often not confirmed in these cases. A thorough investigation is needed to diagnose FI, with the common etiology of this condition in mind, and several questionnaires can be used to identify symptoms. The physical examination contains digital rectal examination carries out to identify the patient's condition. Ultrasound, colonoscopy, and rectum pressure test can be performed. Patients educated in diet-related issues, bowel movements, and defecation mechanism. Nonoperative options such as diet control and Kegel exercise should be performed at first. Surgical treatment of FI is considered when conservative management and oral medications produce no improvement. Surgical options include less invasive procedures like bulking agent injections, and more involved approaches from sacral nerve stimulation to invasive direct sphincter repair and artificial bowel sphincter insertion. Good outcomes in FI cases have also recently been reported for barrier devices.
Language	English
Publishing date	2021-01-19
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2584447-7
ISSN	2093-6931 ; 2093-4777
ISSN (online)	2093-6931
ISSN	2093-4777
DOI	10.5213/inj.2040240.120
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A micro-fragmented collagen gel as a cell-assembling platform for critical limb ischemia repair.

Chung, Haeun / Choi, Jung-Kyun / Hong, Changgi / Lee, Youngseop / Hong, Ki Hyun / Oh, Seung Ja / Kim, Jeongmin / Song, Soo-Chang / Kim, Jong-Wan / Kim, Sang-Heon

Bioactive materials

2023 Volume 34, Page(s) 80–97

Abstract	Critical limb ischemia (CLI) is a devastating disease characterized by the progressive blockage of blood vessels. Although the paracrine effect of growth factors in stem cell therapy made it a promising angiogenic therapy for CLI, poor cell survival in the harsh ischemic microenvironment limited its efficacy. Thus, an imperative need exists for a stem-cell delivery method that enhances cell survival. Here, a collagen microgel (CMG) cell-delivery scaffold (40 × 20 μm) was fabricated via micro-fragmentation from collagen-hyaluronic acid polyionic complex to improve transplantation efficiency. Culturing human adipose-derived stem cells (hASCs) with CMG enabled integrin receptors to interact with CMG to form injectable 3-dimensional constructs (CMG-hASCs) with a microporous microarchitecture and enhanced mass transfer. CMG-hASCs exhibited higher cell survival (p < 0.0001) and angiogenic potential in tube formation and aortic ring angiogenesis assays than cell aggregates. Injection of CMG-hASCs intramuscularly into CLI mice increased blood perfusion and limb salvage ratios by 40 % and 60 %, respectively, compared to cell aggregate-treated mice. Further immunofluorescent analysis revealed that transplanted CMG-hASCs have greater muscle regenerative and angiogenic potential, with enhanced cell survival than cell aggregates (p < 0.05). Collectively, we propose CMG as a cell-assembling platform and CMG-hASCs as promising therapeutics to treat CLI.
Language	English
Publishing date	2023-12-16
Publishing country	China
Document type	Journal Article
ISSN	2452-199X
ISSN (online)	2452-199X
DOI	10.1016/j.bioactmat.2023.12.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antireflective structures on highly flexible and large area elastomer membrane for tunable liquid-filled endoscopic lens.

Bae, Sang-In / Lee, Youngseop / Seo, Yeong-Hyeon / Jeong, Ki-Hun

Nanoscale

2019 Volume 11, Issue 3, Page(s) 856–861

Abstract: The antireflection coating on an optical lens plays a key role not only in minimizing specular reflection but also in maximizing light transmission. Antireflective structures (ARS) found in the eyes of moths have the same role as conventional ... ...

Abstract	The antireflection coating on an optical lens plays a key role not only in minimizing specular reflection but also in maximizing light transmission. Antireflective structures (ARS) found in the eyes of moths have the same role as conventional antireflection coating, and they also provide many intriguing features such as broadband coverage, self-antireflection, and strong water repellence. In particular, ARS on a highly flexible membrane can effectively deliver antireflective properties, which are rarely achieved by conventional hard coating. Herein, we report antireflective structures on a highly flexible elastomeric lens membrane for tunable endoscopic imaging applications. A thin antireflective membrane was fabricated using a large-area nanohole template and replica molding. The thin membrane increases light transmittance up to 96.8% in the visible region while enhancing the image contrast up to 56%, higher than that of a smooth membrane during lens deformation. This antireflective, tunable, liquid-filled lens offers new opportunities for compact endoscopic laparoscopy enabling maximum transmittance and variable zoom imaging in narrow and low-illumination environments.
Language	English
Publishing date	2019-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/c8nr06553e
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