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  1. Article ; Online: Exploring Chemical Information in PubChem.

    Kim, Sunghwan

    Current protocols

    2021  Volume 1, Issue 8, Page(s) e217

    Abstract: PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database that serves scientific communities as well as the general public. This database collects chemical information from hundreds of data sources and organizes them into multiple data ... ...

    Abstract PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database that serves scientific communities as well as the general public. This database collects chemical information from hundreds of data sources and organizes them into multiple data collections, including Substance, Compound, BioAssay, Protein, Gene, Pathway, and Patent. These collections are interlinked with each other, allowing users to discover related records in the various collections (e.g., drugs targeting a protein or genes modulated by a chemical). PubChem can be searched by keyword (e.g., a chemical, protein, or gene name) as well as by chemical structure. The input structure can be provided using popular line notations or drawn with the PubChem Sketcher. PubChem supports various types of structure searches, including identity search, 2-D and 3-D similarity searches, and substructure and superstructure searches. Results from multiple searches can be combined using Boolean operators (i.e., AND, OR, and NOT) to formulate complex queries. PubChem allows the user to quickly retrieve a list of records annotated with a particular classification or ontological term. This paper provides step-by-step instructions on how to explore PubChem data with examples of commonly requested tasks. © 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Finding genes and proteins that interact with a given compound Basic Protocol 2: Finding drug-like compounds similar to a query compound through a two-dimensional (2-D) similarity search Basic Protocol 3: Finding compounds similar to a query compound through a three-dimensional (3-D) similarity search Support Protocol: Computing similarity scores between compounds Basic Protocol 4: Getting the bioactivity data for the hit compounds from substructure search Basic Protocol 5: Finding drugs that target a particular gene Basic Protocol 6: Getting bioactivity data of all chemicals tested against a protein. Basic Protocol 7: Finding compounds annotated with classifications or ontological terms Basic Protocol 8: Finding stereoisomers and isotopomers of a compound through identity search.
    MeSH term(s) Biological Assay ; Databases, Chemical ; Databases, Factual ; Information Storage and Retrieval ; Proteins ; United States
    Chemical Substances Proteins
    Language English
    Publishing date 2021-08-16
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.217
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: DNA-Nanocrystal Assemblies for Environmentally Responsive and Highly Efficient Energy Harvesting and Storage.

    Kesama, Mallikarjuna Reddy / Kim, Sunghwan

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2023  Volume 10, Issue 14, Page(s) e2206848

    Abstract: Natural polymer-based and self-powered bioelectronic devices are attracting attention owing to an increased interest in human health monitoring and human-machine interfaces. However, obtaining both high efficiency and multifunctionality from a single ... ...

    Abstract Natural polymer-based and self-powered bioelectronic devices are attracting attention owing to an increased interest in human health monitoring and human-machine interfaces. However, obtaining both high efficiency and multifunctionality from a single natural polymer-based bioelectronics platform is still challenging. Here, molybdenum disulfide (MoS
    MeSH term(s) Humans ; Molybdenum ; Nanotechnology ; Nanocomposites ; Nanoparticles ; Polymers ; DNA
    Chemical Substances Molybdenum (81AH48963U) ; Polymers ; DNA (9007-49-2)
    Language English
    Publishing date 2023-03-22
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202206848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Microscopic Projection Lithography for Integrating Metallic Microstructures on Silk Protein for Biodevice Applications.

    Choi, Juwan / Kim, Sunghwan

    ACS biomaterials science & engineering

    2023  Volume 9, Issue 11, Page(s) 6390–6397

    Abstract: Precise patterning of metallic micro/nanostructures enables application of silk protein in biomedical devices with a seamless human-machine interface. However, high-quality, expensive equipment and facilities involved in micro/nanofabrication hinder ... ...

    Abstract Precise patterning of metallic micro/nanostructures enables application of silk protein in biomedical devices with a seamless human-machine interface. However, high-quality, expensive equipment and facilities involved in micro/nanofabrication hinder rapid prototyping for explorative laboratory-based research. Here, we report cost-effective and high-resolution light-emitting diode-based projection lithography methods for fabricating a Cr photomask and metallic microstructures on a silk protein layer. After two-step photolithography performed using a commercial camera and microscopic objective lens, inkjet-printed patterns are successfully projected on the silk layers with 100× and 500× demagnification ratios. A lift-off process is conducted to integrate Au patterns on the lithographic-patterned resist/silk layer, and various Au microstructures with sizes <2 μm are generated. In all the processes, the silk protein exhibits a high resistance to chemicals for resist solvent, development, resist strip, and lift-off, as well as a strong adhesion to gold, along with low cytotoxicity. Dopamine sensing and transistor operating capabilities are proved by measuring the changes in the electrical signals through the Au patterns. The proposed method is a cost-effective and simple approach for rapid prototyping of silk-based biomedical devices.
    MeSH term(s) Humans ; Silk/chemistry ; Nanostructures/chemistry ; Gold/chemistry
    Chemical Substances Silk ; Gold (7440-57-5)
    Language English
    Publishing date 2023-10-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2373-9878
    ISSN (online) 2373-9878
    DOI 10.1021/acsbiomaterials.3c01116
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Weakly mutually uncorrelated codes with maximum run length constraint for DNA storage.

    Lu, Xiaozhou / Kim, Sunghwan

    Computers in biology and medicine

    2023  Volume 165, Page(s) 107439

    Abstract: DNA storage systems have begun to attract considerable attention as next-generation storage technologies due to their high densities and longevity. However, efficient primer design for random-access in synthesized DNA strands is still an issue that needs ...

    Abstract DNA storage systems have begun to attract considerable attention as next-generation storage technologies due to their high densities and longevity. However, efficient primer design for random-access in synthesized DNA strands is still an issue that needs to be solved. Although previous studies have explored various constraints for primer design in DNA storage systems, there is no attention paid to the combination of weakly mutually uncorrelated codes with the maximum run length constraint. In this paper, we first propose a code design by combining weakly mutually uncorrelated codes with the maximum run length constraint. Moreover, we also explore the weakly mutually uncorrelated codes to satisfy combinations of maximum run length constraint with more constraints such as being almost-balanced and having large Hamming distance, which are also efficient constraints for random-access in DNA storage systems. To guarantee that the proposed codes can be adapted to primer design with variable length, we present modified code construction methods to achieve different lengths of the code. Then, we provide an analysis of the size of the proposed codes, which indicates the capacity to support primer design. Finally, we compare the codes with those of previous works to show that the proposed codes can always guarantee the maximum run length constraint, which is helpful for random-access for DNA storage.
    MeSH term(s) DNA ; Salaries and Fringe Benefits
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-09-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107439
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    Zs.A 653: Show issues Location:
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  5. Article ; Online: Prevalence and Associations Between Metabolic Syndrome Components and Hyperuricemia by Race: Findings from US population, 2011 - 2020.

    Kim, Yun Jin / Kim, Sunghwan / Seo, Ji Hwan / Cho, Sung Kweon

    Arthritis care & research

    2024  

    Abstract: Objective: We explored the trend in prevalence of hyperuricemia and metabolic syndrome in the US populations and investigated associations between components of metabolic syndrome and hyperuricemia by race.: Methods: We analyzed data from the four ... ...

    Abstract Objective: We explored the trend in prevalence of hyperuricemia and metabolic syndrome in the US populations and investigated associations between components of metabolic syndrome and hyperuricemia by race.
    Methods: We analyzed data from the four most recent NHANES cycles (2011 to March 2020), comprising 10,175 participants. Hyperuricemia is defined as serum urate > 7.0 mg/dL (men) or > 5.7 mg/dL (women), following the NHANES III guideline. Definition of metabolic syndrome follows National Cholesterol Education Program's Adult Treatment Panel III (NCEP ATP III) guideline. We estimated the prevalence of metabolic syndrome and hyperuricemia in each cycle and performed subgroup analyses with logistic regression to investigate the patterns of associated components of metabolic syndrome with hyperuricemia.
    Results: In the most recent cycle (2017-March 2020), the prevalence of metabolic syndrome was 45.9% and that of hyperuricemia was 20.7%. Over the 2011-2020 period, a significant rise in metabolic syndrome prevalence was observed among Hispanic and Asian populations, and the prevalence of hyperuricemia has increased significantly only in Hispanic. After adjustment for confounding factors, subjects with metabolic syndrome exhibited a higher hyperuricemia in women than in men. Elevated BP was the strongest factor with hyperuricemia. The association was the weakest in Asian population. Waist circumference was the only significant factor associated with hyperuricemia in Asian.
    Conclusion: The prevalence of metabolic syndrome has increasing pattern, but there was no specific decadal trend in prevalence of hyperuricemia. There is an ethnic-specific association of metabolic syndrome and hyperuricemia, especially in Asian.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 645059-3
    ISSN 2151-4658 ; 0893-7524 ; 2151-464X
    ISSN (online) 2151-4658
    ISSN 0893-7524 ; 2151-464X
    DOI 10.1002/acr.25338
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    Zs.A 2446: Show issues Location:
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  6. Article ; Online: A biomaterial-silicon junction for photodetection.

    Gogurla, Narendar / Wahab, Abdul / Kim, Sunghwan

    Materials today. Bio

    2023  Volume 20, Page(s) 100642

    Abstract: Bio-integrated optoelectronics can be interfaced with biological tissues, thereby offering opportunities for clinical diagnosis and therapy. However, finding a suitable biomaterial-based semiconductor to interface with electronics is still challenging. ... ...

    Abstract Bio-integrated optoelectronics can be interfaced with biological tissues, thereby offering opportunities for clinical diagnosis and therapy. However, finding a suitable biomaterial-based semiconductor to interface with electronics is still challenging. In this study, a semiconducting layer is assembled comprising a silk protein hydrogel and melanin nanoparticles (NPs). The silk protein hydrogel provides a water-rich environment for the melanin NPs that maximizes their ionic conductivity and bio-friendliness. An efficient photodetector is produced by forming a junction between melanin NP-silk and a
    Language English
    Publishing date 2023-04-24
    Publishing country England
    Document type Journal Article
    ISSN 2590-0064
    ISSN (online) 2590-0064
    DOI 10.1016/j.mtbio.2023.100642
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  7. Article: Clinical Application of an Augmented Reality Navigation System for Transforaminal Epidural Injection: A Randomized Controlled Trial.

    Jang, Yookyung / Lim, Sunghwan / Lee, Sunhee / Je, Lee Gyeong / Kim, Taesan / Joo, Subin / Seo, Joonho / Lee, Deukhee / Koh, Jae Chul

    Journal of clinical medicine

    2024  Volume 13, Issue 7

    Abstract: Objectives: ...

    Abstract Objectives:
    Language English
    Publishing date 2024-03-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm13071992
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  8. Article: Neighborhood and Depressive Symptoms in Older Adults Living in Rural and Urban Regions in South Korea.

    Kim, Seon / Cho, Sunghwan / Morgan, Matthew R

    Healthcare (Basel, Switzerland)

    2023  Volume 11, Issue 4

    Abstract: Neighborhoods have a significant impact on depressive symptoms in older adults. In response to the increasing depression of older adults in Korea, this study aims to identify the relationship between perceived and objective neighborhood characteristics ... ...

    Abstract Neighborhoods have a significant impact on depressive symptoms in older adults. In response to the increasing depression of older adults in Korea, this study aims to identify the relationship between perceived and objective neighborhood characteristics in depressive symptoms and find differences between rural and urban areas. We used a National survey collected in 2020 of 10,097 Korean older adults aged 65 and older. We also utilized Korean administration data for identifying the objective neighborhood characteristics. Multilevel modeling results indicated that depressive symptoms decreased when older adults perceived their housing condition (b = -0.04,
    Language English
    Publishing date 2023-02-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2721009-1
    ISSN 2227-9032
    ISSN 2227-9032
    DOI 10.3390/healthcare11040476
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  9. Article: Profiling of Secondary Metabolites of Optimized Ripe Ajwa Date Pulp (

    Alshammari, Fanar / Alam, Md Badrul / Naznin, Marufa / Javed, Ahsan / Kim, Sunghwan / Lee, Sang-Han

    Pharmaceuticals (Basel, Switzerland)

    2023  Volume 16, Issue 2

    Abstract: The date palm ( ...

    Abstract The date palm (
    Language English
    Publishing date 2023-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph16020319
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  10. Article ; Online: Development of a rapid screening method utilizing 2D LC for effect-directed analysis in the identification of environmental toxicants.

    Ahmad, Raees / Alam, Md Badrul / Cho, Eunji / Park, Chang-Beom / Shafique, Imran / Lee, Sang-Han / Sunghwan, Kim

    The Science of the total environment

    2024  Volume 927, Page(s) 172199

    Abstract: Effect-directed analysis (EDA) is a crucial tool in environmental toxicology, effectively integrating toxicity testing with chemical analysis. The conventional EDA approach, however, presents challenges such as significant solvent consumption, extended ... ...

    Abstract Effect-directed analysis (EDA) is a crucial tool in environmental toxicology, effectively integrating toxicity testing with chemical analysis. The conventional EDA approach, however, presents challenges such as significant solvent consumption, extended analysis time, labor intensity, and potential contamination risks. In response, we introduce an innovative alternative to the conventional EDA. This method utilizes the MTT bioassay and online two-dimensional liquid chromatography (2D LC) coupled with high-resolution mass spectrometry (HR-MS), significantly reducing the fractionation steps and leveraging the enhanced sensitivity of the bioassay and automated chemical analysis. In the chemical analysis phase, a switching valve interface is employed for comprehensive analysis. We tested the performance of both the conventional and our online 2D LC-based methods using a household product. Both methods identified the same number of toxicants in the sample. Our alternative EDA is 22.5 times faster than the conventional method, fully automated, and substantially reduces solvent consumption. This novel approach offers ease, cost-effectiveness, and represents a paradigm shift in EDA methodologies. By integrating a sensitive bioassay with online 2D LC, it not only enhances efficiency but also addresses the challenges associated with traditional methods, marking a significant advancement in environmental toxicology research.
    MeSH term(s) Chromatography, Liquid/methods ; Environmental Pollutants/toxicity ; Environmental Pollutants/analysis ; Toxicity Tests/methods ; Environmental Monitoring/methods ; Mass Spectrometry/methods ; Biological Assay/methods ; Ecotoxicology/methods
    Chemical Substances Environmental Pollutants
    Language English
    Publishing date 2024-04-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2024.172199
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    Zs.A 949: Show issues Location:
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