Chi-Chun Hsieh

Kaohsiung Medical University

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King‐Fu Lin

Taiwan Food and Drug Administration

An‐Ting Chien

Georgia Institute of Technology

Yung‐Shun Juan

Kaohsiung Medical University

Yuh‐Show Tsai

Chung Yuan Christian University

Chia‐Hsin Lee

Stem Cell Technology (Taiwan)

Chia‐Yen Lee

National Pingtung University of Science and Technology

Ching‐Chia Li

Kaohsiung Medical University

Yhu‐Chering Huang

Chang Gung University

Wei-Ming Li

Kaohsiung Medical University

C.-Y Lin

National Taiwan University

Cooperative Institutions

National Taiwan University

Kaohsiung Medical University

Kaohsiung Medical University Chung-Ho Memorial Hospital

Taiwan Semiconductor Manufacturing Company (Taiwan)

Chung Yuan Christian University

Chang Gung University

Kaohsiung Municipal Ta-Tung Hospital

Taipei Veterans General Hospital

Linkou Chang Gung Memorial Hospital

Taiwan Semiconductor Manufacturing Company (United States)

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IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico

BMC Bioinformatics (2009)

Tzong‐Yuan Wu Chi-Chun Hsieh Jun-Jie Hong Chung‐Yung Chen Yuh‐Show Tsai

Abstract Background Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements. Results We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters. Conclusion IRSS is freely available at this website http://140.135.61.9/ires/ . In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.

Eukaryotic translation

10.1186/1471-2105-10-160

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Citations (33)

Molecular aggregations and supramolecular architectures of amphiphilic PEO17–OPV3 and its hybrid with silica

Journal of Materials Chemistry (2005)

Chi-Chun Hsieh King‐Fu Lin

The synthesis, luminescence properties and self-assembly of a specifically-designed amphiphilic PEO17–OPV3 molecule (and its hybrid with silicates) to form ring-like disks are described. The synthesis was begun with the Wittig–Horner reaction to form a co-planar π-conjugated PPV oligomer segment, followed by linking with PEO17 through a sulfonate group that causes a twist in the molecule between the hydrophobic and hydrophilic segments. Due to its amphiphilic nature, its photoluminescence behavior is greatly affected by the solvent type and concentration. The deposition of PEO17–OPV3 molecules on mica with a proper co-solvent was able to form a ring-like supramolecular architecture of ca. 30 nm in diameter as observed by atomic force microscopy (AFM). The width of the enclosed peripheral area on both sides of the ring is on the same order of magnitude as the length of the PEO17–OPV3 molecule. The self-assembly of a PEO17–OPV3 hybrid with silica to form a ring-like disk of ca. 150 nm diameter and ca. 0.65 nm thickness was also observed. The latter is roughly equal to the width of rod segment, implying that π–π stacking governs the self-assembly process in the co-organization between PEO17–OPV3 molecules and silicates, whereas the twist in molecules orients the ring formation. As a result, a multi-lamellar phase transformation mechanism is proposed for the formation of such a supramolecular architecture.

Lamellar phase

Oligomer

10.1039/b503393d

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Citations (4)

Methicillin-resistant Staphylococcus aureus nasal carriage and infection among patients with diabetic foot ulcer

Journal of Microbiology Immunology and Infection (2018)

Shin‐Yi Lin Nai-Yu Lin Yu‐Yao Huang Chi-Chun Hsieh Yhu‐Chering Huang

To evaluate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage in patients with diabetic foot ulcer (DFU) in Taiwan, and to assess the concordance between colonizing and clinical MRSA isolates from the patients.A total of 354 nasal specimens were collected from 112 to 242 diabetic patients with and without foot ulcer, respectively. MRSA clinical isolates from DFU wound cultures were collected for comparison.Nasal carriage rate of S. aureus and MRSA was similar between diabetic patients with and without foot ulcer (15.2% vs. 16.9% for S. aureus and 5.4% vs. 1.7% for MRSA). Nasal S. aureus colonization was an independent predictor for wound S. aureus infection (Odds ratio [OR]: 5.33, 95% confidence interval [CI]: 1.61-17.59), so did nasal MRSA colonization (OR: 19.09, 95% CI: 2.12-171.91). The levels of glycated hemoglobin, and the usage with immunosuppressant agent were associated with S. aureus nasal colonization while oral hypoglycemic agent usage a protective factor. Sequence type 59/staphylococcal chromosome cassette mec IV or V, the local endemic community-associated clone, accounted for 42% and 70% of the clinical and colonizing isolates, respectively. Six of 10 patients with paired colonizing and clinical isolates, either MRSA or methicillin-sensitive S. aureus, had a genetically identical strain from a single patient.Less than one-fifth of patients with DFU have nasal S. aureus, including MRSA, colonization; however, the colonization is significantly associated with S. aureus diabetic foot infection. Screening for S. aureus colonizing status in DFU patients might have a potential clinical implication.

Carriage

Diabetic foot ulcer

10.1016/j.jmii.2018.03.005

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Citations (44)

TSV RF de-embedding method and modeling for 3DIC

Hsiao-Tsung Yen Yu‐Ling Lin C. Hu S. B. Jan Chi-Chun Hsieh

TSV (Thru-Silicon-Via) for 3D packaging technique is a further passive component, for connecting two dies by stacking. RF characteristics of TSV with modeling up to 50GHz are presented in this paper, where a L-2L de-embedding method (double delay) is in use, which is the first applied for TSV on-wafer measurement. Furthermore, a new T-model is proposed for modeling a single TSV of 28nm CMOS process.

Component (thermodynamics)

Through-Silicon Via

Semiconductor device modeling

Wafer-level packaging

10.1109/asmc.2012.6212934

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Citations (19)

Fabrication of PEO₁₇−OPV₃ Templated Titania Nano-Hollow Rods and Their Aggregating Microspheres

Macromolecules (2006)

Chi-Chun Hsieh King‐Fu Lin An‐Ting Chien

In this work, PEO17−OPV3, a light-emitting amphiphilic molecule, was served as a structure-directing agent to fabricate the nano-hollow rods and microspheres through self-assembling with titania precursors. FT-IR and EDX were employed to examine the composition of these hybrid materials. In the beginning, the microspheres of ∼1 μm composed of bundles of nanorods were observed by SEM. By grinding the microspheres, isolated hollow rods of ∼100 nm in diameter were observed and investigated by TEM and AFM. Two sets of crystalline planes, rutile (110) and (101), in the skin of hollow rods were resolved. As we stained the OPV3 packing domains of hollow rods with RuO4, the rutile layer of the skin was ripped off, and the stained inner layer of ∼20 nm diameter was clearly identified. On the basis of the experimental evidence, we proposed a cylinder with a core−shell skin model to explain the formation of nano-hollow rods.

Rod

Nanorod

Rutile

10.1021/ma052518z

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Citations (7)

Arsenic exposure and trend of incidence in urinary cancer from 1979 to 2019: A nationwide population-based study

Journal of the Formosan Medical Association (2025)

Chi-Chun Hsieh Liang-Ju Tsai Hsiang‐Ying Lee Yung‐Shun Juan Hao-Han Chang

Cancer Incidence

10.1016/j.jfma.2025.02.011

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Citations (0)

Impact of dialysis on intravesical recurrence and survival outcomes in upper tract urothelial cancer patients undergoing radical nephroureterectomy

Renal Failure (2025)

Chi-Chun Hsieh Ching‐Chia Li Yung‐Shun Juan Wei-Ming Li Wen‐Jeng Wu

Upper tract urothelial carcinoma (UTUC) presents a significant recurrence risk following radical nephroureterectomy (RNU). Patients on dialysis may experience unique clinical trajectories due to uremic states and altered immune responses. To evaluate the impact of dialysis on intravesical recurrence and survival outcomes in patients with UTUC undergoing RNU, and to identify predictive factors influencing prognosis. A retrospective cohort study analyzed 402 patients with non-metastatic UTUC treated with RNU between 2001 and 2014. Patients were stratified into dialysis (n = 66) and non-dialysis (n = 336) groups. Survival and recurrence outcomes were assessed using Kaplan-Meier and Cox regression analyses. Dialysis patients were predominantly female, younger, and exhibited less advanced pathological tumor stages. Dialysis was associated with higher intravesical recurrence rates (p = 0.009), which were largely attributable to a history of bladder cancer (42.4% vs. 26.5%; p = 0.009). After adjustment for bladder cancer history, dialysis was not an independent predictor of bladder recurrence-free survival (BRFS). Advanced pT stages (HR: 3.9, p = 0.012) and prior bladder cancer were the primary factors influencing BRFS. Dialysis does not independently worsen surgical outcomes or BRFS in UTUC patients post-RNU when accounting for prior bladder cancer. Prognostic models should integrate these findings to enhance individualized surveillance and treatment strategies.

Urothelial cancer

Upper urinary tract

10.1080/0886022x.2025.2458762

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Exfoliation of montmorillonite by the insertion of disklike micelles via the soap‐free emulsion polymerization of methyl methacrylate

Journal of Polymer Science Part A Polymer Chemistry (2006)

King‐Fu Lin Shanq-Chyang Lin An‐Ting Chien Chi-Chun Hsieh Ming‐Huei Yen

Abstract Montmorillonites (MMTs) intercalating a potassium persulfate initiator were readily exfoliated in the presence of polymerizing methyl methacrylate during soap‐free emulsion polymerization. Because of the confined space, the polymerizing chains were aggregated into a disk form inside the clay interlayer regions for micellation. It was surprising to find from X‐ray diffraction analysis that the exfoliation of MMT was almost completed in the micellation stage. Further polymerization afforded latex particles of exfoliated poly(methyl methacrylate) (PMMA)–MMT nanocomposites. In addition, two kinds of MMT nanosheets were collected by the removal of PMMA with toluene: One was a single‐layer nanosheet with a thickness of 1.25 nm, and the other was a stacked sheet with an average thickness of 7.5 nm that may have consisted of six individual layers. Electron diffraction analysis revealed that if the individual layer of an MMT nanosheet were not a single crystal, it should contain an ultrathin layer of ice with a commonly occurring hexagonal phase. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5572–5579, 2006

Exfoliation joint

Emulsion polymerization

Potassium persulfate

10.1002/pola.21657

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Citations (29)

Segmentation of sonographic breast lesions: fuzzy cell-competition algorithm and bias field reduction

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE (2008)

Chia‐Yen Lee Chi-Chun Hsieh Chung‐Ming Chen

Bias field is a common phenomenon in a breast sonogram. Although artifacts caused by bias filed may carry important information, e.g., shadowing behind a lesion, they are generally disturbing in the process of automatic boundary delineation for sonographic breast lesions. This paper presents a new segmentation algorithm aiming to decompose the region of interest (ROI) into prominent components while estimating the bias field in the ROI. A prominent component is a contiguous region with a visually perceivable boundary, which might be a noise, an artifact, a substructure of a tissue or a part of breast lesion. The prominent components may be used as the basic constructs for a higher level segmentation algorithm to identify the lesion boundary. The bias field in an ROI is modeled as a spatially-variant Gaussian distribution with a constant variance and spatially-variant means, which is a polynomial surface of order n. The true gray levels of the pixels in a prominent component are assumed to be Gaussian-distributed. The proposed algorithm is formulated as an EM-algorithm composed of two major steps. In the E-step, the ROI is decomposed into prominent components using a new fuzzy cell-competition algorithm based on the bias field and model parameters estimated in the previous M-step. In the M-step, the bias field and model parameters are estimated based on the prominent components derived in the E-step using a least squared approach. The results show that the effect of bias field on segmentation has been reduced and better segmentation results have been attained.

Region of interest

Artifact (error)

10.1117/12.770884

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