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Gene expression profiling:Canonical molecular changes and clinicopathological features in sporadic colorectal cancers

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World Journal of Gastroenterology 2008年第43期14卷 6662-6672页

作者： Jin Cheon kim seon young kim seon Ae Roh Dong-Hyung Cho Dae Dong kim Jeong Hyun kim Yong Sung kim Department of Surgery University of Ulsan College of Medicine and Asan Medical Centerand Laboratory of Cancer Biology & GeneticsAsan Institute for Life SciencesSeoul 138-736South Korea Medical Genomics Research Center Korea Research Institute of Bioscience & BiotechnologyDaejeon 305-806South Korea

AIM： To investigate alternative or subordinate pathways involved in colorectal tumorigenesis and tumor growth, possibly determining at-risk populations and predicting responses to treatment. METHODS： Using microarray gene-expression analysis, we analyzed patterns of gene expression relative to canonical molecular changes and clinicopathological features in 84 sporadic colorectal cancer patients, standardized by tumor location. Subsets of differentially expressed genes were confirmed by real-time reverse-transcript polymerase chain reaction （RT-PCR）. RESULTS： The largest number of genes identified as being differentially expressed was by tumor location, and the next largest number by lymphovascular or neural invasion of tumor cells and by mismatch repair （NMR） defects. Amongst biological processes, the immune response was significantly implicated in entire molecular changes observed during colorectal tumorigenesis （P 〈 0.001）. Amongst 47 differentially expressed genes, seven （PISD, NIBP, BAI2, STOML1, MRPL21, MRPL16, and MKKS） were newly found to correlate with tumorigenesis and tumor growth. Most location-associated molecular changes had distinct effects on gene expression, but the effects of the latter were sometimes contradictory. CONCLUSION： We show that several differentially expressed genes were associated with canonical molecular changes in sporadic colorectal cancers, possibly constituting alternative or subordinate pathways of tumorigenesis. As tumor location was the dominant factor influencing differential gene expression, location-specific analysis may identify location-associated pathways and enhance the accuracy of class prediction.

关键词： Colorectal adenocarcinomas Sporadic Gene expression Profiling Tumorigenesis

Clinical assessment and identification of immuno-oncology markers concerning the 19-gene based risk classifier in stage Ⅳ colorectal cancer

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World Journal of Gastroenterology 2019年第11期25卷 1341-1354页

作者： Jong Lyul Lee seon Ae Roh Chan Wook kim Yi Hong Kwon Ye Jin Ha seon-Kyu kim seon-young kim Dong-Hyung Cho Yong Sung kim Jin Cheon kim Department of Surgery University of Ulsan College of Medicine Institute of Innovative Cancer Research Asan Medical Center Medical Genomics Research Center Korea Research Institute of Bioscience and Biotechnology School of Life Sciences Kyungpook National University

BACKGROUND Genomic profiling of tumors has contributed to the understanding of colorectal cancer(CRC), facilitating diagnosis, prognosis and selection of treatments,including targeted regimens. A report suggested that a 19-gene-based risk classifier(TCA19) was a prognostic tool for patients with stage III CRC. The survival outcomes in patients with stage IV CRC are still poor and appropriate selection of targeted therapies and immunotherapies is *** To assess clinical implication of TCA19 in patients with stage IV CRC, and to identify TCA19 with involvement in *** A retrospective review of the medical records of 60 patients with stage IV CRC was conducted, assessing clinicopathological variables and progression-free survival(PFS). TCA19 gene expression was determined by quantitative polymerase chain reaction(qPCR) in matched normal and tumor tissues taken from the study cohort. Expression of potential immune-oncology regulatory proteins and targets was examined by immunohistochemistry(IHC), western blot, immunofluorescence staining in tissues from a validation cohort of 10 patients, and in CRC cell lines co-cultured with monocyte in *** In the patients with TCA19 score higher than the median, the PFS rates of eight patients who received the targeted regimens were significantly higher than the PFS rates of four patients who received 5-fluorouracil-based regimen(P = 0.041).In multivariate analysis, expression of signaling lymphocytic activation molecule family, member 7(SLAMF7) and triggering receptor expressed on myeloid cells 1(TREM1) was associated with PFS in the 60-patient cohort. After checking another 10 validate set, the expression of the IHC, the level of real-time qPCR,and the level of western blot were lower for SLAMF7 and higher for TREM7 in primary and metastatic tumors than in normal tissues. In CRC cells expressing SLAMF7 that were co-cultured with a monocytic cell line, levels of CD 68 and CD73 were significant

关键词： Colorectal cancer Prognosis Immunotherapy Signaling lymphocytic activation molecule family,member 7 Triggering receptor expressed on myeloid cells 1

KoNA:Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 161-167页

作者： Gunhwan Ko Jae Ho Lee young Mi Sim Wangho Song Byung-Ha Yoon Iksu Byeon Bang Hyuck Lee Sang-Ok kim Jinhyuk Choi Insoo Jang Hyerin kim Jin Ok Yang Kiwon Jang Sora kim Jong-Hwan kim Jongbum Jeon Jaeeun Jung Seungwoo Hwang Ji-Hwan Park Pan-Gyu kim seon-young kim Byungwook Lee Korea Bioinformation Center Korea Research Institute of Bioscience&BiotechnologyDaejeon 34141Republic of Korea

During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of *** promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data ***,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence *** of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome *** ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database *** standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual *** ensure fast and stable data transfer,a high-speed transmission system called GBox is used in ***,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called *** seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide *** not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in *** KoNA is available at https://***/kona/.

关键词： Korea BioData Station Nucleotide sequence Next-generation sequencing repository Genomics Deposition and access of big data

A New Encryption Mechanism Supporting the Update of Encrypted Data for Secure and Efficient Collaboration in the Cloud Environment

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 813-834页

作者： Chanhyeong Cho Byeori kim Haehyun Cho Taek-young Youn Department of Cyber Security Dankook UniversityYongin16890Republic of Korea Department of Software Soongsil UniversitySeoul07027Republic of Korea

With the rise of remote collaboration,the demand for advanced storage and collaboration tools has rapidly ***,traditional collaboration tools primarily rely on access control,leaving data stored on cloud servers vulnerable due to insufficient *** paper introduces a novel mechanism that encrypts data in‘bundle’units,designed to meet the dual requirements of efficiency and security for frequently updated collaborative *** bundle includes updated information,allowing only the updated portions to be reencrypted when changes *** encryption method proposed in this paper addresses the inefficiencies of traditional encryption modes,such as Cipher Block Chaining(CBC)and Counter(CTR),which require decrypting and re-encrypting the entire dataset whenever updates *** proposed method leverages update-specific information embedded within data bundles and metadata that maps the relationship between these bundles and the plaintext *** utilizing this information,the method accurately identifies the modified portions and applies algorithms to selectively re-encrypt only those *** approach significantly enhances the efficiency of data updates while maintaining high performance,particularly in large-scale data *** validate this approach,we conducted experiments measuring execution time as both the size of the modified data and the total dataset size *** show that the proposed method significantly outperforms CBC and CTR modes in execution speed,with greater performance gains as data size ***,our security evaluation confirms that this method provides robust protection against both passive and active attacks.

关键词： Cloud collaboration mode of operation data update efficiency

Maximizing biomass utilization: An integrated strategy for coproducing multiple chemicals

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Journal of Energy Chemistry 2025年第1期100卷 180-191页

作者： Byeongchan Ahn Sua Jo Jonggeol Na J.Jay Liu young-Ju kim Wangyun Won Department of Chemical and Biological Engineering Korea University Department of Chemical Engineering (Integrated process) Kyung Hee University Department of Chemical Engineering and Materials Science Ewha Womans University Department of Chemical Engineering Pukyong National University Resources Engineering Plant Research Department Korea Institute of Geoscience and Mineral Resources

Lignocellulosic biomass is one of the viable solutions to alleviate the global warming. However, the limited utilization of biomass majorly focused on cellulose and hemicellulose restricts the economic and environmental feasibilities. To cope with this issue, we proposed an integrated process of co-producing 1,6-hexanediol（1,6-HDO） with tetrahydrofuran and adipic acid from biomass, referred to as Strategy A. To compare the impacts of lignin upgrading and feedstock, Strategy B, which co-produces tetrahydrofuran alone, and Strategy C, which is the traditional route to produce 1,6-HDO from fossil fuels, were used. Heat networks are also designed to reduce operating costs and indirect carbon emissions due to energy consumption, saving 87% and 83% of the heat and cooling requirements, respectively, in Strategy A. The market competitiveness of Strategy A was evaluated by determining the minimum selling price through techno-economic analysis, and sustainability was thoroughly investigated by quantifying the environmental impacts through both midpoint and endpoint life-cycle assessments（LCAs）.Strategy A was found to be the most favorable both economically（USRDSCHARDOLLAR3,402/ton） and environmentally（-26.9 kg CO2eq.）. This indicates that lignin valorization is not only economically but also environmentally preferred. Finally, changes in economic and environmental feasibilities depending on economic, process, and environmental parameters were investigated using sensitivity and uncertainty analyses. The results of these analyses provide valuable insight into bio-based chemical production.

关键词： Biorefinery Carbon mitigation Climate change Global warming Lignin utilization Bioeconomy

High mobility group box 1 in the central nervous system:regeneration hidden beneath inflammation

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Neural Regeneration Research 2025年第1期20卷 107-115页

作者： Hanki kim Bum Jun kim Seungyon Koh Hyo Jin Cho Xuelian Jin Byung Gon kim Jun young Choi Department of Brain Science Ajou University School of MedicineSuwonSouth Korea Department of Biomedical Sciences Ajou University Graduate School of MedicineSuwonSouth Korea Department of Neurology Ajou University School of MedicineSuwonSouth Korea Department of Geriatrics The Affiliated Suqian First People’s Hospital of Nanjing Medical UniversitySuqianJiangsu ProvinceChina

High-mobility group box 1 was first discovered in the calf thymus as a DNA-binding nuclear protein and has been widely studied in diverse fields,including neurology and ***-mobility group box 1 in the extracellular space functions as a pro-inflammatory damage-associated molecular pattern,which has been proven to play an important role in a wide variety of central nervous system disorders such as ischemic stroke,Alzheimer’s disease,frontotemporal dementia,Parkinson’s disease,multiple sclerosis,epilepsy,and traumatic brain *** drugs that inhibit high-mobility group box 1 as a damage-associated molecular pattern,such as glycyrrhizin,ethyl pyruvate,and neutralizing anti-high-mobility group box 1 antibodies,are commonly used to target high-mobility group box 1 activity in central nervous system *** it is commonly known for its detrimental inflammatory effect,high-mobility group box 1 has also been shown to have beneficial pro-regenerative roles in central nervous system *** this narrative review,we provide a brief summary of the history of high-mobility group box 1 research and its characterization as a damage-associated molecular pattern,its downstream receptors,and intracellular signaling pathways,how high-mobility group box 1 exerts the repair-favoring roles in general and in the central nervous system,and clues on how to differentiate the pro-regenerative from the pro-inflammatory *** targeting high-mobility group box 1 in the central nervous system may benefit from differentiating between the two functions rather than overall suppression of high-mobility group box 1.

关键词： central nervous system damage-associated molecular pattern ethyl pyruvate glycyrhizzin high mobility group box 1 inflammation neural stem cells neurodevelopment oligodendrocyte progenitor cells redox status regeneration

A Rapid Adaptation Approach for Dynamic Air‑Writing Recognition Using Wearable Wristbands with Self‑Supervised Contrastive Learning

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Nano-Micro Letters 2025年第2期17卷 417-431页

作者： Yunjian Guo Kunpeng Li Wei Yue Nam‑young kim Yang Li Guozhen Shen Jong‑Chul Lee Department of Electronic Convergence Engineering Kwangwoon UniversitySeoul 01897South Korea Radio Frequency Integrated Circuit(RFIC)Bio Centre Kwangwoon UniversitySeoul 01897South Korea Department of Electronic Engineering Kwangwoon UniversitySeoul 01897South Korea School of Microelectronics Shandong UniversityJinan 250101People’s Republic of China State Key Laboratory of Integrated Chips and Systems Fudan UniversityShanghai 200433People’s Republic of China School of Integrated Circuits and Electronics Beijing Institute of TechnologyBeijing 100081People’s Republic of China

Wearable wristband systems leverage deep learning to revolutionize hand gesture recognition in daily *** existing approaches that often focus on static gestures and require extensive labeled data,the proposed wearable wristband with selfsupervised contrastive learning excels at dynamic motion tracking and adapts rapidly across multiple *** features a four-channel sensing array composed of an ionic hydrogel with hierarchical microcone structures and ultrathin flexible electrodes,resulting in high-sensitivity capacitance *** wireless transmission from a Wi-Fi module,the proposed algorithm learns latent features from the unlabeled signals of random wrist ***,only few-shot labeled data are sufficient for fine-tuning the model,enabling rapid adaptation to various *** system achieves a high accuracy of 94.9%in different scenarios,including the prediction of eight-direction commands,and air-writing of all numbers and *** proposed method facilitates smooth transitions between multiple tasks without the need for modifying the structure or undergoing extensive task-specific *** utility has been further extended to enhance human–machine interaction over digital platforms,such as game controls,calculators,and three-language login systems,offering users a natural and intuitive way of communication.

关键词： Wearable wristband Self-supervised contrastive learning Dynamic gesture Air-writing Human-machine interaction

Apolipoprotein A-I binding protein-mediated neuroprotection in glaucomatous neuroinflammation and neurodegeneration

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Neural Regeneration Research 2025年第5期20卷 1414-1415页

作者： Sinwoo Hwang Seunghwan Choi Soo-Ho Choi Keun-young kim Yury I.Miller Won-Kyu Ju Hamilton Glaucoma Center and Shiley Eye Institute The Viterbi Family Department of OphthalmologyUniversity of California San DiegoLa JollaCAUSA Department of Medicine University of California San DiegoLa JollaCAUSA National Center for Microscopy and Imaging Research Department of NeurosciencesUniversity of California San DiegoLa JollaCAUSA

Glaucoma is a multifactorial eye disorder that can cause vision loss and irreversible blindness,affecting individ uals aged 40 to 80 yea rs *** to the aging population,it is expected that the number of people affected by glaucoma will surpass 111 million by 2040 as the disease becomes more *** primarily contributes to optic nerve axon loss and the progressive degeneration of retinal ganglion cells (RGCs),subsequently leading to vision impairment.

关键词： irreversible pass primarily

Fast ethylamine gas sensing based on intermolecular charge-transfer complexation

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Chinese Chemical Letters 2012年第4期23卷 484-487页

作者： Eun Mi Lee seon young Gwon young A Son Sung Hoon kim BK21 FTIT Department of Advanced Organic Materials and Textile System EngineeringChungnam National UniversityDaejeon 305-764Republic of Korea Department of Textile System Engineering Kyungpook National UniversityDaegu 702-701 Republic of Korea School of Chemistry Science & Technology Zhanjiang Normal UniversityZhanjiang 524048China

We have investigated the fast ethylamine gas sensing of 2-chloro-3,5-dinitrobenzotrifluoride（CDBF） loaded poly（acrylonitrile） nanofiber based on an intermolecular charge-transfer *** response and recovery were ach... 详细信息

关键词： Ethylamine gas Fast gas sensing 2-Chloro-3 5-dinitrobenzotrifluoride(CDBF) Electrospinning PAN nanofiber Intermolecular charge-transfer(CT) complexation