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A Transfer Function Design for Medical Volume Data Using a Knowledge Database Based on Deep Image and Primitive Intensity Profile Features Retrieval

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Journal of Computer Science & Technology 2024年第2期39卷 320-335页

作者： Younhyun Jung Jim Kong 盛斌 Jinman kim School of Computing Gachon UniversitySeongnam 13120Korea School of Computer Science The University of SydneySydney 2006Australia Department of Computer Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Direct volume rendering(DVR)is a technique that emphasizes structures of interest(SOIs)within a volume visually,while simultaneously depicting adjacent regional information,e.g.,the spatial location of a structure concerning its *** DVR,transfer function(TF)plays a key role by enabling accurate identification of SOIs interactively as well as ensuring appropriate visibility of *** generation typically involves non-intuitive trial-and-error optimization of rendering parameters,which is time-consuming and *** at mitigating this manual process have led to approaches that make use of a knowledge database consisting of pre-designed TFs by domain *** these approaches,a user navigates the knowledge database to find the most suitable pre-designed TF for their input volume to visualize the *** these approaches potentially reduce the workload to generate the TFs,they,however,require manual TF navigation of the knowledge database,as well as the likely fine tuning of the selected TF to suit the *** this work,we propose a TF design approach,CBR-TF,where we introduce a new content-based retrieval(CBR)method to automatically navigate the knowledge *** of pre-designed TFs,our knowledge database contains volumes with SOI *** an input volume,our CBR-TF approach retrieves relevant volumes(with SOI labels)from the knowledge database;the retrieved labels are then used to generate and optimize TFs of the *** approach largely reduces manual TF navigation and fine *** our CBR-TF approach,we introduce a novel volumetric image feature which includes both a local primitive intensity profile along the SOIs and regional spatial semantics available from the co-planar images to the *** the regional spatial semantics,we adopt a convolutional neural network to obtain high-level image feature *** the intensity profile,we extend the dynamic time warping technique to address subtle alignment

关键词： data retrieval direct volume rendering ray analysis transfer function

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Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

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Synthetic and Systems Biotechnology 2024年第3期9卷 391-405页

作者： Truc Ly Nguyen Heebal kim Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National UniversitySeoul08826Republic of Korea eGnome Inc.Seoul05836Republic of Korea

Mycobacterium tuberculosis(MTB)is the causative agent of tuberculosis(TB),a prevalent airborne infectious *** the availability of the Bacille Calmette-Guerin vaccine,its global efficacy remains modest,and tuberculosis persists as a significant global public health *** this challenge and advancing towards the End MTB Strategy,we developed a multiepitope vaccine(MEV)based on immunoinformatics and compu-tational *** screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex(MHC)allele binding,immunogenicity,antigenicity,allergenicity,toxicity,and cytokine *** epitopes were integrated into an MEV construct with adjuvant and linkers,forming a fully immunogenic vaccine *** analyses encompassed the evaluation of immunological and physicochemical properties,determination of tertiary structure,molecular docking with Toll-Like Receptors(TLR),molecular dynamics(MD)simulations for all atoms,and immune *** MEV comprises 534 amino acids,featuring 6 cytotoxic T lymphocyte,8 helper T lymphocyte,and 7 linear B lymphocyte epitopes,demonstrating high antigenicity and ***,molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to *** addition,the immune simulation indicated the capacity to effectively induce elevated levels of an-tibodies and cytokines,emphasizing the vaccine’s robust immunogenic *** study presents a promising MEV against TB,exhibiting favorable immunological and physicochemical *** findings provide theoretical support for TB vaccine *** study aligns with the global initiative of the End MTB Strategy,emphasizing its potential impact on addressing persistent challenges in TB control.

关键词： Mycobacterium tuberculosis Tuberculosis Multiepitope vaccine Docking molecular Molecular dynamics simulation Immune simulation

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Metabolic relationships between marine red algae and algae‑associated bacteria

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Marine Life Science & Technology 2024年第2期6卷 298-314页

作者： Kyung Hyun kim Jeong Min kim Ju Hye Baek Sang Eun Jeong Hocheol kim Hwan Su Yoon Che Ok Jeon Department of Biological Sciences and Biotechnology Hannam UniversityDaejon 34054Republic of Korea Department of Life Science Chung-Ang UniversitySeoul 06974Republic of Korea Department of Biological Sciences Sungkyunkwan UniversitySuwon 16419Republic of Korea

Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their success-ful survival in the ocean,but little is known about their metabolic ***,bacterial communities in the algal sphere(AS)and bulk solution(BS)of nine marine red algal cultures were analyzed,and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in *** metabolic features of Roseibium RMAR6-6(isolated and genome-sequenced),Phycisphaera MAG 12(obtained by metagenomic sequencing),and a marine red alga,Porphyridium purpureum CCMP1328(from GenBank),were analyzed ***6-6 has the genetic capability to fix nitrogen and produce B vitamins(B1,B2,B5,B6,B9,and B12),bacterioferritin,dimethylsulfoniopropionate(DMSP),and phenylacetate that may enhance algal growth,whereas MAG 12 may have a limited metabolic capability,not producing vitamins B9 and B12,DMSP,phenylacetate,and siderophores,but with the ability to produce bacitracin,possibly modulating algal *** CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12,DMSP,phenylacetate,and *** was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of ***-pureum,and DMSP reduced the oxidative stress of *** metabolic interactions between strain RMAR6-6 and *** CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and *** together,potential metabolic relationships between Roseibium and *** were *** study provides a bet-ter understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth.

关键词： Metabolic relationship Marine red algae Symbiotic bacteria Roseibium Phycisphaera Porphyridium

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Electric-field-controlled highly regioselective thiocyanation of N-containing heterocycles

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Science China Chemistry 2024年第4期67卷 1263-1269页

作者： Ming Gong Qian wu Jung Keun kim Mengmeng Huang Yabo Li Yangjie wu Jong Seung kim Henan Key Laboratory of Chemical Biology and Organic Chemistry Key Laboratory of Applied Chemistry of Henan UniversitiesCollege of ChemistryZhengzhou UniversityZhengzhou 450052China Department of Chemistry Korea UniversitySeoul 02841Korea

Achieving highly regioselective synthesis in organic chemistry is challenging due to the uncontrollable orientation between reacting *** electric fields(EEFs)can influence the reactivity and selectivity of the substrate by causing directional ***,scalable and efficient techniques for using EEFs as“smart catalysts”have been lacking,hindering their *** this study,we present a novel method for modifying the regioselectivity of quinoxaline-2(1H)-ones by functionalizing their C7-position using the electric double layer(EDL)*** approach led to moderate to good yields of the corresponding C7-thiocyanation *** calculations and control experiments demonstrated that EEFs could reverse the regioselectivity of quinoxaline-2(1H)-ones,allowing the C7-thiocyanation to proceed via a radical reaction ***,the resulting 7-thiocyano-1-methylquinoxaline-2(1H)-ones exhibited promising AIE *** work showcases a promising strategy for achieving highly regioselective functionalization by aligning the electric field with the desired reaction/bond axis.

关键词： electric fields reaction-axis rule electric double layer C7-thiocyanation C-S bond formation

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Cathode nanoarchitectonics with Na_(3)VFe_(0.5)Ti_(0.5)(PO_(4))_(3): Overcoming the energy barriers of multielectron reactions for sodium-ion batteries

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Carbon Energy 2024年第9期6卷 1-14页

作者： Vaiyapuri Soundharrajan Sungjin kim Subramanian Nithiananth Muhammad H.Alfaruqi JunJi Piao Duong Tung Pham Vinod Mathew Sang A.Han Jung Ho kim Jaekook kim Department of Materials Science and Engineering Chonnam National UniversityBukguGwangjuRepublic of Korea Graduate School of Science and Technology Shizuoka UniversityHamamatsuShizuokaJapan Departemen Teknik Metalurgi Universitas Teknologi SumbawaSumbawaIndonesia School of Engineering Physics Hanoi University of Science and TechnologyHanoiVietnam Institute for Superconducting and Electronic Materials(ISEM) Australian Institute of Innovative Materials(AIIM)University of WollongongNorth WollongongNew South WalesAustralia Research Center for Artificial Intelligence Assisted Ionics Based Materials Development Platform Chonnam National UniversityGwangjuRepublic of Korea

High electrochemical stability and safety make Na+superionic conductor(NASICON)-class cathodes highly desirable for Na-ion batteries(SIBs).However,their practical capacity is limited,leading to low specific ***,the low electrical conductivity combined with a decline in capacity upon prolonged cycling(>1000 cycles)related to the loss of active material-carbon conducting contact regions contributes to moderate rate performance and cycling *** need for high specific energy cathodes that meet practical electrochemical requirements has prompted a search for new ***,we introduce a new carbon-coated Na_(3)VFe_(0.5)Ti_(0.5)(PO_(4))_(3)(NVFTP/C)material as a promising candidate in the NASICON family of cathodes for *** a high specific energy of∼457 wh kg^(-1) and a high Na+insertion voltage of 3.0 V versus Na^(+)/Na,this cathode can undergo a reversible single-phase solid-solution and two-phase(de)sodiation evolution at 28 C(1 C=174.7 mAh g^(-1))for up to 10,000 *** study highlights the potential of utilizing low-cost and highly efficient cathodes made from Earth-abundant and harmless materials(Fe and Ti)with enriched Na^(+)-storage properties in practical SIBs.

关键词： Fe and Ti swapping Na_(3)VFe_(0.5)Ti_(0.5)(PO_(4))_(3) prolonged cycle life structural stabilit

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Photo-induced crosslinked and anti-PD-L1 peptide incorporated liposomes to promote PD-L1 multivalent binding for effective immune checkpoint blockade therapy

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1428-1440页

作者： Youngjoo Lee Sukyung Song Suah Yang Jinseong kim Yujeong Moon Nayeon Shim Hong Yeol Yoon Sehoon kim Man Kyu Shim Kwangmeyung kim KU-KIST Graduate School of Converging Science and Technology Korea UniversitySeoul 02841Republic of Korea Medicinal Materials Research Center Biomedical Research DivisionKorea Institute of Science and Technology(KIST)Seoul 02792Republic of Korea College of Pharmacy Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoul 03760Republic of Korea Department of Bioengineering Korea UniversitySeoul 02841Republic of Korea

Immune checkpoint blockade(ICB)therapy targeting PD-L1 via monoclonal antibody(m Ab)has shown extensive clinical benefits in the diverse types of advanced ***,most patients are completely refractory to ICB therapy owing to the PD-L1 recycling ***,we propose photo-induced crosslinked and anti-PD-L1 peptide incorporated liposomes(immune checkpoint blockade liposomes;ICB-LPs)to promote PD-L1 multivalent binding for inducing lysosomal degradation of PD-L1 in tumor *** ICB-LPs are prepared by formulation of DC_(8,9)PC with photo-polymerized diacetylenic moiety,1,2-dipalmitoylphosphatidylcholine(DPPC)and anti-PD-L1peptide(D-form NYSKPTDRQYHF)-conjugated DSPE-PEG_(2k)(anti-PD-L1-DSPE-PEG_(2k))in a molar ratio of 45:45:10,followed by cross-linking of liposomal bilayer upon UV *** 10 mol% antiPD-L1-DSPE-PEG_(2k)incorporated ICB-LPs have a nano-sized lipid bilayer structure with an average diameter of 137.7±1.04 nm,showing a high stability in serum ***,the ICB-LPs efficiently promote the multivalent binding with PD-L1 on the tumor cell membrane,which are endocytosed with aim to deliver PD-L1 to the lysosomes,wherein the durable PD-L1 degradation is observed for72 h,in contrast to anti PD-L1 m Abs showing the rapid PD-L1 recycling within 9 *** in vitro coculture experiments with CD8^(+)T cells show that ICB-LPs effectively enhance the T cell-mediated antitumor immune responses against tumor cells by blocking the PD-L1/PD-1 *** ICB-LPs are intravenously injected into colon tumor-bearing mice,they efficiently accumulate within the targeted tumor tissues via both passive and active tumor targeting,inducing a potent T cell-mediated antitumor immune response by effective and durable PD-L1 ***,this study demonstrates the superior antitumor efficacy of crosslinked and anti-PD-L1 peptide incorporated liposome formulation that promotes PD-L1 multivalent binding for trafficking of PD-L1 toward

关键词： Cancer immunotherapy Immune checkpoint blockade PEGylated liposome Crosslinked lipid nanoparticles Anti-PD-L1 peptide Tumor-targeting PD-L1 multivalent binding Lysosomal PD-L1 degradation

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The neurovascular unit-on-a-chip:modeling ischemic stroke to stem cell therapy

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Neural Regeneration Research 2024年第7期19卷 1431-1432页

作者： Seonghun kim Minjun kim Gerald A.Grant wonjae Lee Department of Neurosurgery Duke University School of MedicineDurhamNCUSA Department of Neurobiology Duke University School of MedicineDurhamNCUSA Duke Institute for Brain Sciences Duke University School of MedicineDurhamNCUSA Duke Cancer Institute Duke University School of MedicineDurhamNCUSA

The neurovascular unit and stem cell therapy in ischemic stroke:Ischemic stroke,accounts for approximately 85% of all stroke incidents and is a major global health *** is the leading cause of disability and death worldwide,posing immense societal and economic challenges due to the long-term care required for stro ke survivors and the significant healthcare costs associated with its treatment and management(Amarenco et al.,2009).

关键词： death unit

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Microsphere-assisted hyperspectral imaging:super-resolution,non-destructive metrology for semiconductor devices

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Light(Science & Applications) 2024年第6期13卷 1098-1111页

作者： Jangryul Park Youngsun Choi Soonyang Kwon Youngjun Lee Jiwoong kim Jae-joon kim Jihye Lee Jeongho Ahn Hidong Kwak Yusin Yang Taeyong Jo Myungjun Lee Kwangrak kim Metrology and Inspection Equipment R&D Team Mechatronics ResearchSamsung Electronics Co.Ltd.1-1 Samsungjeonja-rohwaseong-siGyeonggi-do18848Republic of Korea Process Development Department DRAM Process Development TeamSemiconductor R&D CenterSamsung Electronics Co.Ltd.1-1 Samsungjeonja-rohwaseong-siGyeonggi-do18848Republic of Korea Process Development Department Semiconductor R&D CenterSamsung Electronics Co.Ltd.1-1 Samsungjeonja-rohwaseong-siGyeonggi-do18848Republic of Korea

As semiconductor devices shrink and their manufacturing processes advance,accurately measuring in-cell critical dimensions(CD)becomes increasingly *** test element group(TEG)measurements are becoming inadequate for representing the fine,repetitive patterns in cell *** non-destructive metrology technologies like optical critical dimension(OCD)are limited due to their large spot diameter of approximately 25μm,which impedes their efficacy for detailed in-cell structural ***,there is a pressing need for small-spot and non-destructive metrology *** address this limitation,we demonstrate a microsphere-assisted hyperspectral imaging(MAHSI)system,specifically designed for small spot optical metrology with *** microsphere-assisted super-resolution imaging,this system achieves an optical resolution of 66 nm within a field of view of 5.6μm×5.6μ*** approach effectively breaks the diffraction limit,significantly enhancing the magnification of the *** MAHSI system incorporating hyperspectral imaging with a wavelength range of 400–790 nm,enables the capture of the reflection spectrum at each camera *** achieved pixel resolution,which is equivalent to the measuring spot size,is 14.4 nm/pixel and the magnification is *** MAHSI system enables measurement of local uniformity in critical areas like corners and edges of DRAM cell blocks,areas previously challenging to inspect with conventional OCD *** our knowledge,this approach represents the first global implementation of microsphere-assisted hyperspectral imaging to address the metrology challenges in complex 3D structures of semiconductor devices.

关键词： metrology resolution enable

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On breakthroughs and limits: Resolving structural fine-tuning of photosynthetic supercomplexes

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Molecular Plant 2024年第2期17卷 224-226页

作者： Eunchul kim Marcel Dann Division of Environmental Photobiology National Institute for Basic BiologySOKENDAlOkazaki 444-8585Japan Department of Basic Biology The Graduate University for Advanced StudiesSOKENDAlOkazaki 444-8585Japan Bio-Inspired Energy Conversion Technical University of DarmstadtSchnittspahnstraBe 1064287 DarmstadtGermany

Dynamic regulation of photosynthetic supercomplexes is a key strategy allowing plants to adjust their light-harvesting system in response to varying environmental light conditions(Bassi and Dall'Osto,2021).State transition(i.e.,acclimative re-distribution of peripheral antennae between photosystems[PSs]I and II)is one such regulation mechanism that maintains excitation balance between PSl and PSll.

关键词： complexes breakthrough maintain

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Rapid monitoring of indoor airborne influenza and coronavirus with high air flowrate electrostatic sampling and PCR analysis

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Frontiers of Environmental Science & Engineering 2024年第7期18卷 73-85页

作者： Sanggwon An Sangsoo Choi Hyeong Rae kim Jungho Hwang School of Mechanical Engineering Yonsei UniversitySeoul 02876Republic of Korea Gas Metrology Group Korea Research Institute of Standards and Science(KRISS)Daejeon 34113Republic of Korea

The world Health Organization has raised concerns about the possibility of airborne transmission in enclosed and poorly ventilated ***,rapid monitoring of airborne viruses is necessary in multi-use facilities with dense ***,an electrostatic air sampler(250 L/min)was developed in this work to obtain indoor viral aerosol samples for analysis via the Polymerase Chain Reaction(PCR).Aerosol tests with H1N1 and HCoV-229E were performed to evaluate the sample collection *** analysis,along with another aerosol test,was conducted to evaluate the recovery of the virus particles collected by the *** laboratory tests,our electrostatic sampler obtained viral samples that were detectable by PCR under the simulated viral pandemic scenario(3000 RNA copies per cubic meter of air)within 40 *** resulting cycle threshold(C)values were 35.07 and 37.1 for H1N1 and HCoV-229E,*** the performance evaluation in the laboratory,field tests were conducted in a university classroom from October 28 to December 2,*** A and HCoV-229E were detected in two air samples,and the corresponding C,values were 35.3 and *** PCR results are similar to those obtained from laboratory tests,considering the simulatedviralpandemic scenario.

关键词： Airborne virus Electrostatic sampler Rapid monitoring Indoor environment Field test

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