1
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Wait SJ, Expòsit M, Lin S, Rappleye M, Lee JD, Colby SA, Torp L, Asencio A, Smith A, Regnier M, Moussavi-Harami F, Baker D, Kim CK, Berndt A. Machine learning-guided engineering of genetically encoded fluorescent calcium indicators. Nat Comput Sci 2024; 4:224-236. [PMID: 38532137 DOI: 10.1038/s43588-024-00611-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.
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Affiliation(s)
- Sarah J Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Michael Rappleye
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Samuel A Colby
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lily Torp
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Anthony Asencio
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Annette Smith
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Michael Regnier
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Farid Moussavi-Harami
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Cardiology, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Christina K Kim
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA, USA.
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2
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Lee JD, Nguyen A, Jin ZR, Moghadasi A, Gibbs CE, Wait SJ, Evitts KM, Asencio A, Bremner SB, Zuniga S, Chavan V, Williams A, Smith N, Regnier M, Young JE, Mack D, Nance E, Boyle PM, Berndt A. Far-red and sensitive sensor for monitoring real time H 2O 2 dynamics with subcellular resolution and in multi-parametric imaging applications. bioRxiv 2024:2024.02.06.579232. [PMID: 38370715 PMCID: PMC10871219 DOI: 10.1101/2024.02.06.579232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
H2O2 is a key oxidant in mammalian biology and a pleiotropic signaling molecule at the physiological level, and its excessive accumulation in conjunction with decreased cellular reduction capacity is often found to be a common pathological marker. Here, we present a red fluorescent Genetically Encoded H2O2 Indicator (GEHI) allowing versatile optogenetic dissection of redox biology. Our new GEHI, oROS-HT, is a chemigenetic sensor utilizing a HaloTag and Janelia Fluor (JF) rhodamine dye as fluorescent reporters. We developed oROS-HT through a structure-guided approach aided by classic protein structures and recent protein structure prediction tools. Optimized with JF635, oROS-HT is a sensor with 635 nm excitation and 650 nm emission peaks, allowing it to retain its brightness while monitoring intracellular H2O2 dynamics. Furthermore, it enables multi-color imaging in combination with blue-green fluorescent sensors for orthogonal analytes and low auto-fluorescence interference in biological tissues. Other advantages of oROS-HT over alternative GEHIs are its fast kinetics, oxygen-independent maturation, low pH sensitivity, lack of photo-artifact, and lack of intracellular aggregation. Here, we demonstrated efficient subcellular targeting and how oROS-HT can map inter and intracellular H2O2 diffusion at subcellular resolution. Lastly, we used oROS-HT with the green fluorescent calcium indicator Fluo-4 to investigate the transient effect of the anti-inflammatory agent auranofin on cellular redox physiology and calcium levels via multi-parametric, dual-color imaging.
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Affiliation(s)
- Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Amanda Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Zheyu Ruby Jin
- Department of Chemical Engineering, University of Washington, Seattle WA, USA
| | - Aida Moghadasi
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Chelsea E. Gibbs
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Sarah J. Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Kira M. Evitts
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Anthony Asencio
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle WA, USA
| | - Samantha B Bremner
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Shani Zuniga
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Vedant Chavan
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Andy Williams
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Netta Smith
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle WA, USA
| | - Jessica E. Young
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David Mack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth Nance
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle WA, USA
| | - Patrick M. Boyle
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle WA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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3
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Lee JD, Won W, Kimball K, Wang Y, Yeboah F, Evitts KM, Neiswanger C, Schattauer S, Rappleye M, Bremner SB, Chun C, Smith N, Mack DL, Young JE, Lee CJ, Chavkin C, Berndt A. Structure-guided engineering of a fast genetically encoded sensor for real-time H 2O 2 monitoring. bioRxiv 2024:2024.01.31.578117. [PMID: 38352381 PMCID: PMC10862829 DOI: 10.1101/2024.01.31.578117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Hydrogen Peroxide (H2O2) is a central oxidant in redox biology due to its pleiotropic role in physiology and pathology. However, real-time monitoring of H2O2 in living cells and tissues remains a challenge. We address this gap with the development of an optogenetic hydRogen perOxide Sensor (oROS), leveraging the bacterial peroxide binding domain OxyR. Previously engineered OxyR-based fluorescent peroxide sensors lack the necessary sensitivity or response speed for effective real-time monitoring. By structurally redesigning the fusion of Escherichia coli (E. coli) ecOxyR with a circularly permutated green fluorescent protein (cpGFP), we created a novel, green-fluorescent peroxide sensor oROS-G. oROS-G exhibits high sensitivity and fast on-and-off kinetics, ideal for monitoring intracellular H2O2 dynamics. We successfully tracked real-time transient and steady-state H2O2 levels in diverse biological systems, including human stem cell-derived neurons and cardiomyocytes, primary neurons and astrocytes, and mouse neurons and astrocytes in ex vivo brain slices. These applications demonstrate oROS's capabilities to monitor H2O2 as a secondary response to pharmacologically induced oxidative stress, G-protein coupled receptor (GPCR)-induced cell signaling, and when adapting to varying metabolic stress. We showcased the increased oxidative stress in astrocytes via Aβ-putriscine-MAOB axis, highlighting the sensor's relevance in validating neurodegenerative disease models. oROS is a versatile tool, offering a window into the dynamic landscape of H2O2 signaling. This advancement paves the way for a deeper understanding of redox physiology, with significant implications for diseases associated with oxidative stress, such as cancer, neurodegenerative disorders, and cardiovascular diseases.
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Affiliation(s)
- Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Woojin Won
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea
| | - Kandace Kimball
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Yihan Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Fred Yeboah
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Kira M Evitts
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Carlie Neiswanger
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Selena Schattauer
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Michael Rappleye
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Samantha B Bremner
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Changho Chun
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Netta Smith
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - David L Mack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, USA
| | - Jessica E Young
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - C Justin Lee
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea
| | - Charles Chavkin
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
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Lee JH, Lee JD, Paulson K, Voillet V, Berndt A, Church C, Lachance K, Park SY, Yamamoto NK, Cromwell EA, Gottardo R, Chapuis AG, Nghiem P. Enhancing immunogenic responses through CDK4/6 and HIF2α inhibition in Merkel cell carcinoma. Heliyon 2024; 10:e23521. [PMID: 38173534 PMCID: PMC10761584 DOI: 10.1016/j.heliyon.2023.e23521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Approximately 50% of Merkel cell carcinoma (MCC) patients facing this highly aggressive skin cancer initially respond positively to PD-1-based immunotherapy. Nevertheless, the recurrence of MCC post-immunotherapy emphasizes the pressing need for more effective treatments. Recent research has highlighted Cyclin-dependent kinases 4 and 6 (CDK4/6) as pivotal cell cycle regulators gaining prominence in cancer studies. This study reveals that the CDK4/6 inhibitor, palbociclib can enhance PD-L1 gene transcription and surface expression in MCC cells by activating HIF2α. Inhibiting HIF2α with TC-S7009 effectively counteracts palbociclib-induced PD-L1 transcription and significantly intensifies cell death in MCC. Simultaneously, co-targeting CDK4/6 and HIF2α boosts ROS levels while suppressing SLC7A11, a key regulator of cellular redox balance, promoting ferroptosis- a form of immunogenic cell death linked to iron. Considering the rising importance of immunogenic cell death in immunotherapy, this strategy holds promise for improving future MCC treatments, markedly increasing immunogenic cell death various across various MCC cell lines, thus advancing cancer immunotherapy.
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Affiliation(s)
- Jung Hyun Lee
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Justin Daho Lee
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Kelly Paulson
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andre Berndt
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Candice Church
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Kristina Lachance
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Song Y. Park
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Naomi K. Yamamoto
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | | | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aude G. Chapuis
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
- Seattle Cancer Care Alliance, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul Nghiem
- Department of Dermatology, School of Medicine, University of Washington, Seattle, WA, USA
- Seattle Cancer Care Alliance, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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5
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Rappleye M, Wait SJ, Lee JD, Siebart JC, Torp L, Smith N, Muster J, Matreyek KA, Fowler DM, Berndt A. Optogenetic Microwell Array Screening System: A High-Throughput Engineering Platform for Genetically Encoded Fluorescent Indicators. ACS Sens 2023; 8:4233-4244. [PMID: 37956352 PMCID: PMC10683761 DOI: 10.1021/acssensors.3c01573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Genetically encoded fluorescent indicators (GEFIs) are protein-based optogenetic tools that change their fluorescence intensity when binding specific ligands in cells and tissues. GEFI encoding DNA can be expressed in cell subtypes while monitoring cellular physiological responses. However, engineering GEFIs with physiological sensitivity and pharmacological specificity often requires iterative optimization through trial-and-error mutagenesis while assessing their biophysical function in vitro one by one. Here, the vast mutational landscape of proteins constitutes a significant obstacle that slows GEFI development, particularly for sensors that rely on mammalian host systems for testing. To overcome these obstacles, we developed a multiplexed high-throughput engineering platform called the optogenetic microwell array screening system (Opto-MASS) that functionally tests thousands of GEFI variants in parallel in mammalian cells. Opto-MASS represents the next step for engineering optogenetic tools as it can screen large variant libraries orders of magnitude faster than current methods. We showcase this system by testing over 13,000 dopamine and 21,000 opioid sensor variants. We generated a new dopamine sensor, dMASS1, with a >6-fold signal increase to 100 nM dopamine exposure compared to its parent construct. Our new opioid sensor, μMASS1, has a ∼4.6-fold signal increase over its parent scaffold's response to 500 nM DAMGO. Thus, Opto-MASS can rapidly engineer new sensors while significantly shortening the optimization time for new sensors with distinct biophysical properties.
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Affiliation(s)
- Michael Rappleye
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Sarah J. Wait
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, 3946 W Stevens Way NE, Seattle, Washington 98195, United States
| | - Justin Daho Lee
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, 3946 W Stevens Way NE, Seattle, Washington 98195, United States
| | - Jamison C. Siebart
- The Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr NW, Atlanta, Georgia 30332, United States
| | - Lily Torp
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Netta Smith
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Jeanot Muster
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Kenneth A. Matreyek
- Department
of Pathology, Case Western Reserve University
School of Medicine, 2103 Cornell Road, Wolstein Research Building, Cleveland, Ohio 44106, United States
| | - Douglas M. Fowler
- Department
of Genome Sciences, Foege
Building S-250, 3720 15th Ave NE, Seattle, Washington 98195-5065, United States
| | - Andre Berndt
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
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6
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Wait SJ, Rappleye M, Lee JD, Goy ME, Smith N, Berndt A. Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators. Res Sq 2023:rs.3.rs-3146778. [PMID: 37609342 PMCID: PMC10441480 DOI: 10.21203/rs.3.rs-3146778/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
In this study, we focused on the transformative potential of machine learning in the engineering of genetically encoded fluorescent indicators (GEFIs), protein-based sensing tools that are critical for real-time monitoring of biological activity. GEFIs are complex proteins with multiple dynamic states, rendering optimization by trial-and-error mutagenesis a challenging problem. We applied an alternative approach using machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. We used the trained ensemble to perform an in silico functional screen on 1423 novel, uncharacterized GCaMP variants. As a result, we identified the novel ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, that achieve both faster kinetics and larger fluorescent responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, that outperforms the tested 6th, 7th, and 8th generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient pre-screening of mutants for functional characteristics. By leveraging the learning capabilities of our ensemble, we were able to accelerate the identification of promising mutations and reduce the experimental burden associated with trial-and-error mutagenesis. Overall, these findings have significant implications for optimizing GEFIs and other protein-based tools, demonstrating the utility of machine learning as a powerful asset in protein engineering.
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Affiliation(s)
- Sarah J. Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Michael Rappleye
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Marc Exposit Goy
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
| | - Netta Smith
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA
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7
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Lee SY, Yun WS, Lee JD. Strain-induced dark exciton generation in rippled monolayer MoS 2. Phys Chem Chem Phys 2023; 25:9894-9900. [PMID: 36946280 DOI: 10.1039/d2cp05879k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Recently, it has been revealed that dark excitons play a significant role in optically controlled information processing due to their much longer radiative lifetimes than those of bright ones. For the realizable implementation of the features, it is important to understand and manipulate conditions in which dark excitons could exist. We adopt strain-engineered rippling as a new parameter for the modification of the electronic structure of monolayer MoS2 and demonstrate the efficient conversion of bright to dark excitons via a first-principles study. For rippled monolayer MoS2 above a strain of ∼6.8%, we show that the spin order of the conduction band is reversed and the spin forbidden dark exciton then goes below the bright one.
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Affiliation(s)
- Su Yeong Lee
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea.
| | - Won Seok Yun
- Convergence Research Institute, DGIST, Daegu 42988, Republic of Korea
| | - J D Lee
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea.
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8
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Wei X, Roudier MP, Kwon OJ, Lee JD, Kong K, Dumpit R, True L, Morrissey C, Lin DW, Nelson PS, Xin L. Paracrine Wnt signaling is necessary for prostate epithelial proliferation. Prostate 2022; 82:517-530. [PMID: 35014711 PMCID: PMC8866211 DOI: 10.1002/pros.24298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022]
Abstract
INTRODUCTION The Wnt proteins play key roles in the development, homeostasis, and disease progression of many organs including the prostate. However, the spatiotemporal expression patterns of Wnt proteins in prostate cell lineages at different developmental stages and in prostate cancer remain inadequately characterized. METHODS We isolated the epithelial and stromal cells in the developing and mature mouse prostate by flow cytometry and determined the expression levels of Wnt ligands. We used Visium spatial gene expression analysis to determine the spatial distribution of Wnt ligands in the mouse prostatic glands. Using laser-capture microscopy in combination with gene expression analysis, we also determined the expression patterns of Wnt signaling components in stromal and cancer cells in advanced human prostate cancer specimens. To investigate how the stroma-derived Wnt ligands affect prostate development and homeostasis, we used a Col1a2-CreERT2 mouse model to disrupt the Wnt transporter Wntless specifically in prostate stromal cells. RESULTS We showed that the prostate stromal cells are a major source of several Wnt ligands. Visium spatial gene expression analysis revealed a distinct spatial distribution of Wnt ligands in the prostatic glands. We also showed that Wnt signaling components are highly expressed in the stromal compartment of primary and advanced human prostate cancer. Blocking stromal Wnt secretion attenuated prostate epithelial proliferation and regeneration but did not affect cell survival and lineage maintenance. DISCUSSION Our study demonstrates a critical role of stroma-derived Wnt ligands in prostate development and homeostasis.
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Affiliation(s)
- Xing Wei
- Department of Urology, University of Washington, Seattle, WA, USA 98109
| | | | - Oh-Joon Kwon
- Department of Urology, University of Washington, Seattle, WA, USA 98109
| | - Justin Daho Lee
- Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA, USA 98109
- Department of Bioengineering, University of Washington, Seattle, WA, USA 98109
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA 98109
| | - Kevin Kong
- Department of Biology, University of Washington, Seattle, WA, USA 98109
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA 98109
| | - Lawrence True
- Department of Urology, University of Washington, Seattle, WA, USA 98109
- Department of Pathology, University of Washington, Seattle, WA, USA 98109
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA 98109
| | - Daniel W. Lin
- Department of Urology, University of Washington, Seattle, WA, USA 98109
| | - Peter S. Nelson
- Department of Urology, University of Washington, Seattle, WA, USA 98109
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA 98109
- Department of Pathology, University of Washington, Seattle, WA, USA 98109
| | - Li Xin
- Department of Urology, University of Washington, Seattle, WA, USA 98109
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA 98109
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9
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Kim Y, Kim H, Jang H, Ahn JH, Lee JD. Dual Resonant Sum Frequency Generations from Two-Dimensional Materials. Nano Lett 2020; 20:4530-4536. [PMID: 32422047 DOI: 10.1021/acs.nanolett.0c01363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We propose dual resonant optical sum frequency generation (SFG), where the two most singular resonances could be selected, and report for the monolayer (1L-) WSe2 when one (ω1) of two excitation pulses is resonant to A exciton and their sum frequency (ω1 + ω2) to D exciton. The dual resonant SFG confirms that, under an irradiation of ω1 and ω2 pulses with the same fluence of ∼1.4 × 1010 W/m2, its signal intensity could be enhanced about 20 times higher than the resonant SHG (i.e., 2ω1 to the D excitonic absorption). Further, the dual resonant SFG intensity of 1L-WSe2 is found to be 1 order of magnitude higher than the single resonant SFG intensity of 1L-WS2 under the same condition of two-pulse irradiation. Finally, observations of the dual resonant SFG are thoroughly examined using real-time time-dependent density functional theory (rt-TDDFT), and the relevant nonlinear optical characteristics are scrutinized using the Greenwood-Kubo formalism.
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Affiliation(s)
- Youngjae Kim
- Department of Emerging Materials Science, DGIST, Daegu 42988, Republic of Korea
| | - Hyunmin Kim
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Houk Jang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jong-Hyun Ahn
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - J D Lee
- Department of Emerging Materials Science, DGIST, Daegu 42988, Republic of Korea
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10
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Lee JD, Eftekari H, Paul G, Zhupaj A, Panikker S, Dhanjal T, Yusuf S, Hayat S, Osman F. P6561Diagnostic yield of implantable loop recorders: a comparison of arrhythmia nurse specialists versus clinicians. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz746.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Implantable loop recorders (ILR) are recommended in guidelines to determine symptom-rhythm correlation. Arrhythmia Nurse Specialists (ANS) play a critical role in the assessment of such patients. Their effectiveness at risk stratification for ILR implantation is unknown. The ESC 2018 Syncope guidelines recommend more research in this field.
Aim
To evaluate the diagnostic yield of consecutive ILR implants at a tertiary centre over a 2year period and compare ANS versus Clinicians.
Methods
A retrospective study of all patients undergoing ILR implant between April 2016 and April 2018. Data collected included baseline patient demographics, referral source and management changes made by ILR findings.
Results
305 patients had an ILR; median age was 71yrs (interquartile range 52–81), 55% male. Median follow-up time was 15months. Referrals were from general cardiology (GC) = 98 (32%), electrophysiology (EP) = 105 (34%), and ANS-led syncope clinic = 102 (34%). Indications for ILR implant were syncope = 203 (65.9%), palpitation = 21 (6.9%), pre-syncope = 16 (5.2%), cryptogenic stroke = 35 (11.5%) and others 7 (8.9%) (falls, channelopathies). Of the entire cohort, 102 (34.0%) experienced arrhythmias recorded on the ILR that resulted in a change of management. This included: pacemaker implant = 49 (16.1%), complex-device implant = 7 (2.3%), AF=28 (9.2%), SVT=14 (4.6%), VT=1 (0.3%). Of those with a syncope indication (n=203), findings on ILR altered management in 73patients (36.0%) over a median follow-up of 18months; a pacing indication in this syncope group was present in 44 (21.9%) patients (median time to diagnosis: 2.7 months) with 24 receiving a pacemaker indication within 3 months of ILR insertion. ANS had a higher pacemaker implant rate. Overall, an ILR resulted in a diagnostic yield of 34.1% (n=104). Specialist nurse referral resulted in an overall greater trend towards change of management in 38.2% of patients compared with GC (32.7%) and EP (31.0%) (p=0.593 nurse vs. consultant).
Conclusion
The overall diagnostic yield of ILR insertion was 34% in our study. ANS had a trend towards a greater diagnostic yield compared with clinicians, and significantly more pacemaker indications. Our data suggests that ANS patient selection for ILR insertion are at least comparable to clinicians.
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Affiliation(s)
- J D Lee
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - H Eftekari
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - G Paul
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - A Zhupaj
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - S Panikker
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - T Dhanjal
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - S Yusuf
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - S Hayat
- University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - F Osman
- University Hospital Coventry and Warwickshire NHS Trust, and Warwick Medical School, Coventry, United Kingdom
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11
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Kim Y, Lee JD. Anomalous Electron Dynamics Induced through the Valley Magnetic Domain: A Pathway to Valleytronic Current Processing. Nano Lett 2019; 19:4166-4173. [PMID: 31148458 DOI: 10.1021/acs.nanolett.9b01676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An interplay between an applied strain and the Berry curvature reconstruction in the uniaxially strained monolayer MoS2 is explored that leads to the unbalanced Berry curvatures centered at K and -K points and, eventually, the valley magnetization under an external electric field. This is shown to explain a recent experimental observation of the valley magnetoelectric effect and develop a novel concept of the valley magnetic domain (VMD), i.e., a real-space homogeneous distribution of the valley magnetization. A realization of VMD guarantees a sufficient number of stable valley-polarized carriers, one of the most essential prerequisites of the valleytronics. Furthermore, we discover the anomalous electron dynamics through the VMD activation and achieve a manipulation of the anomalous transverse current perpendicular to the electric field, directly accessible to the signal processing [for instance, the current modulation under the VMD (i.e., the VMD wall) moving and the terahertz current rectification under the VMD switching]. This suggests a concept of VMD for use in providing new physical insight into the valleytronic functionality and its manipulation as a key ingredient of potential device applications.
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Affiliation(s)
- Youngjae Kim
- Department of Emerging Materials Science , DGIST , Daegu 42988 , Korea
| | - J D Lee
- Department of Emerging Materials Science , DGIST , Daegu 42988 , Korea
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12
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Sherwen T, Evans MJ, Sommariva R, Hollis LDJ, Ball SM, Monks PS, Reed C, Carpenter LJ, Lee JD, Forster G, Bandy B, Reeves CE, Bloss WJ. Effects of halogens on European air-quality. Faraday Discuss 2018; 200:75-100. [PMID: 28581558 DOI: 10.1039/c7fd00026j] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halogens (Cl, Br) have a profound influence on stratospheric ozone (O3). They (Cl, Br and I) have recently also been shown to impact the troposphere, notably by reducing the mixing ratios of O3 and OH. Their potential for impacting regional air-quality is less well understood. We explore the impact of halogens on regional pollutants (focussing on O3) with the European grid of the GEOS-Chem model (0.25° × 0.3125°). It has recently been updated to include a representation of halogen chemistry. We focus on the summer of 2015 during the ICOZA campaign at the Weybourne Atmospheric Observatory on the North Sea coast of the UK. Comparisons between these observations together with those from the UK air-quality network show that the model has some skill in representing the mixing ratios/concentration of pollutants during this period. Although the model has some success in simulating the Weybourne ClNO2 observations, it significantly underestimates ClNO2 observations reported at inland locations. It also underestimates mixing ratios of IO, OIO, I2 and BrO, but this may reflect the coastal nature of these observations. Model simulations, with and without halogens, highlight the processes by which halogens can impact O3. Throughout the domain O3 mixing ratios are reduced by halogens. In northern Europe this is due to a change in the background O3 advected into the region, whereas in southern Europe this is due to local chemistry driven by Mediterranean emissions. The proportion of hourly O3 above 50 nmol mol-1 in Europe is reduced from 46% to 18% by halogens. ClNO2 from N2O5 uptake onto sea-salt leads to increases in O3 mixing ratio, but these are smaller than the decreases caused by the bromine and iodine. 12% of ethane and 16% of acetone within the boundary layer is oxidised by Cl. Aerosol response to halogens is complex with small (∼10%) reductions in PM2.5 in most locations. A lack of observational constraints coupled to large uncertainties in emissions and chemical processing of halogens make these conclusions tentative at best. However, the results here point to the potential for halogen chemistry to influence air quality policy in Europe and other parts of the world.
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Affiliation(s)
- T Sherwen
- Wolfson Atmospheric Chemistry Laboratory, University of York, York, UK.
| | - M J Evans
- Wolfson Atmospheric Chemistry Laboratory, University of York, York, UK. and National Centre for Atmospheric Science (NCAS), University of York, York, UK
| | - R Sommariva
- Department of Chemistry, University of Leicester, Leicester, UK
| | - L D J Hollis
- Department of Chemistry, University of Leicester, Leicester, UK
| | - S M Ball
- Department of Chemistry, University of Leicester, Leicester, UK
| | - P S Monks
- Department of Chemistry, University of Leicester, Leicester, UK
| | - C Reed
- Wolfson Atmospheric Chemistry Laboratory, University of York, York, UK.
| | - L J Carpenter
- Wolfson Atmospheric Chemistry Laboratory, University of York, York, UK.
| | - J D Lee
- Wolfson Atmospheric Chemistry Laboratory, University of York, York, UK. and National Centre for Atmospheric Science (NCAS), University of York, York, UK
| | - G Forster
- NCAS, School of Environmental Sciences, University of East Anglia, Norwich, UK and School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - B Bandy
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - C E Reeves
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - W J Bloss
- School of Geography, Earth and Environmental Science, University of Birmingham, Birmingham, UK
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13
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Yun WS, Lee JD. Schottky barrier tuning of the single-layer MoS 2 on magnetic metal substrates through vacancy defects and hydrogenation. Phys Chem Chem Phys 2018; 18:31027-31032. [PMID: 27808310 DOI: 10.1039/c6cp05384j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the practical device application of the two-dimensional semiconducting MoS2, it is a critical issue to manipulate the electronic and magnetic properties locally at its contact to the metal electrode. For the tuning of those properties, we have proposed the vacancy-defective 1L-MoS2 or the hydrogenated 1L-MoS2 at the metal [Co(0001) or Ni(111)] contacts and performed first-principles electronic structure calculations. By controlling the atomic vacancy defects and the hydrogen coverages, we investigate the Schottky barrier heights and charge and spin transfers at the interface. Our findings provide a physical insight into the practical device design using the two-dimensional MoS2.
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Affiliation(s)
- Won Seok Yun
- Department of Emerging Materials Science, DGIST, Daegu 42988, Republic of Korea.
| | - J D Lee
- Department of Emerging Materials Science, DGIST, Daegu 42988, Republic of Korea.
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14
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Yun WS, Lee JD. Two-dimensional semiconductors ZrNCl and HfNCl: Stability, electric transport, and thermoelectric properties. Sci Rep 2017; 7:17330. [PMID: 29229935 PMCID: PMC5725492 DOI: 10.1038/s41598-017-17590-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/27/2017] [Indexed: 11/13/2022] Open
Abstract
Searching for novel two-dimensional (2D) semiconducting materials is a challenging issue. We investigate novel 2D semiconductors ZrNCl and HfNCl which would be isolated to single layers from van der Waals layered bulk materials, i.e., ternary transition-metal nitride halides. Their isolations are unquestionably supported through an investigation of their cleavage energies as well as their thermodynamic stability based on the ab initio molecular dynamics and phonon dispersion calculations. Strain engineering is found to be available for both single-layer (1L) ZrNCl and 1L-HfNCl, where a transition from an indirect to direct band gap is attained under a tensile strain. It is also found that 1L-ZrNCl has an excellent electron mobility of about 1.2 × 103 cm2 V−1 s−1, which is significantly higher than that of 1L-MoS2. Lastly, it is indicated that these systems have good thermoelectric properties, i.e., high Seebeck coefficient and high power factor. With these findings, 1L-ZrNCl and 1L-HfNCl would be novel promising 2D materials for a wide range of optoelectronic and thermoelectric applications.
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Affiliation(s)
- Won Seok Yun
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - J D Lee
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea.
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15
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Abstract
This paper reviews the fundamentals of micropolar fluid dynamics (MFD), and proposes a numerical scheme integrating Chorin’s projection method and time-centred split method (TCSM) for solving unsteady forms of MFD equations. It has been known that Navier–Stokes equations are incapable of explaining the phenomena at micro and nano scales. On the contrary, MFD can naturally pick up the physical phenomena at micro and nano scales owingto its additional degrees of freedom for gyration. In this study, the analytical and exact solutions of Couette and Hagen–Poiseuille flow are provided. Though this study is limited to the steady flow cases, the unsteady term in the MFD has been taken into account. This present work initiates the development of a general-purpose code of computational micropolar fluid dynamics (CMFD). The discretization scheme in space is demonstrated with nearly second-order accuracy on multiple meshes.
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Affiliation(s)
- J Chen
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, USA
| | - C Liang
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, USA
| | - J D Lee
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, USA
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16
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McDonald JL, Lopez AA, Lee JD, Capaldi VF, LoPresti ML. 0269 INSOMNIA, SHORT SLEEP DURATION, AND FAILED TEST PERFORMANCE IN A MILITARY ACADEMIC SETTING. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Lee SY, Yun WS, Lee JD. New Method to Determine the Schottky Barrier in Few-Layer Black Phosphorus Metal Contacts. ACS Appl Mater Interfaces 2017; 9:7873-7877. [PMID: 28182398 DOI: 10.1021/acsami.7b00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Schottky barrier height and carrier polarity are seminal concepts for a practical device application of the interface between semiconductor and metal electrode. Investigation of those concepts is usually made by a conventional method such as the Schottky-Mott rule, incorporating the metal work function and semiconductor electron affinity, or the Fermi level pinning effect, resulting from the metal-induced gap states. Both manners are, however, basically applied to the bulk semiconductor metal contacts. To explore few-layer black phosphorus metal contacts far from the realm of bulk, we propose a new method to determine the Schottky barrier by scrutinizing the layer-by-layer phosphorus electronic structure from the first-principles calculation combined with the state-of-the-art band unfolding technique. In this study, using the new method, we calculate the Schottky barrier height and determine the contact polarity of Ti, Sc, and Al metal contacts to few-layer (mono-, bi-, tri-, and quadlayer) black phosphorus. This gives a significant physical insight toward the utmost layer-by-layer manipulation of electronic properties of few-layer semiconductor metal contacts.
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Affiliation(s)
- Su Yeong Lee
- Department of Emerging Materials Science, DGIST , Daegu 42988, Republic of Korea
| | - Won Seok Yun
- Department of Emerging Materials Science, DGIST , Daegu 42988, Republic of Korea
| | - J D Lee
- Department of Emerging Materials Science, DGIST , Daegu 42988, Republic of Korea
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18
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Tofighi B, Campbell ANC, Pavlicova M, Hu MC, Lee JD, Nunes EV. Recent Internet Use and Associations with Clinical Outcomes among Patients Entering Addiction Treatment Involved in a Web-Delivered Psychosocial Intervention Study. J Urban Health 2016; 93:871-883. [PMID: 27653383 PMCID: PMC5052150 DOI: 10.1007/s11524-016-0077-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The acceptability and clinical impact of a web-based intervention among patients entering addiction treatment who lack recent internet access are unclear. This secondary analysis of a national multisite treatment study (NIDA Clinical Trials Network-0044) assessed for acceptability and clinical impact of a web-based psychosocial intervention among participants enrolling in community-based, outpatient addiction treatment programs. Participants were randomly assigned to 12 weeks of a web-based therapeutic education system (TES) based on the community reinforcement approach plus contingency management versus treatment as usual (TAU). Demographic and clinical characteristics, and treatment outcomes were compared among participants with recent internet access in the 90 days preceding enrollment (N = 374) and without internet access (N = 133). Primary outcome variables included (1) acceptability of TES (i.e., module completion; acceptability of web-based intervention) and (2) clinical impact (i.e., self-reported abstinence confirmed by urine drug/breath alcohol tests; retention measured as time to dropout). Internet use was common (74 %) and was more likely among younger (18-49 years old) participants and those who completed high school (p < .001). Participants randomized to TES (n = 255) without baseline internet access rated the acceptability of TES modules significantly higher than those with internet access (t = 2.49, df = 218, p = .01). There was a near significant interaction between treatment, baseline abstinence, and internet access on time to dropout (χ 2(1) = 3.8089, p = .051). TES was associated with better retention among participants not abstinent at baseline who had internet access (X 2(1) = 6.69, p = .01). These findings demonstrate high acceptability of this web-based intervention among participants that lacked recent internet access.
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Affiliation(s)
- B Tofighi
- Department of Population Health Medicine, New York University School of Medicine, 227 E.30th St. 718, 10016, New York, NY, USA.
| | - A N C Campbell
- New York State Psychiatric Institute, Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | - M Pavlicova
- Mailman School of Public Health, Department of Biostatistics, Columbia University, New York, NY, USA
| | - M C Hu
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - J D Lee
- Department of Population Health Medicine, New York University School of Medicine, 227 E.30th St. 718, 10016, New York, NY, USA
| | - E V Nunes
- New York State Psychiatric Institute, Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
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19
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Abstract
Investigating a theoretical model of the optical-field-induced current in dielectrics driven by strong few-cycle laser pulses, we propose an asymmetric conducting of the current by forming a heterojunction made of two distinct dielectrics with a low hole mass (m_{h}^{*}≪m_{e}^{*}) and low electron mass (m_{e}^{*}≪m_{h}^{*}), respectively. This proposition introduces the novel concept of a petahertz (10^{15} Hz) diode to rectify the current in the petahertz domain, which should be a key ingredient for the electric signal manipulation of future light-wave electronics. Further, we suggest the candidate dielectrics for the heterojunction.
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Affiliation(s)
- J D Lee
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Won Seok Yun
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Noejung Park
- School of Natural Science and Low-Dimensional Carbon Materials Center, UNIST, Ulsan 689-798, Korea
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20
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Sadovnick AD, Traboulsee AL, Lee JD, Ross JP, Bernales CQ, Vilariño-Güell C. Colony stimulation factor 1 receptor (CSF1R) is not a common cause of multiple sclerosis. Eur J Neurol 2014; 20:e115-6. [PMID: 23889897 DOI: 10.1111/ene.12213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 04/28/2013] [Indexed: 11/30/2022]
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21
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Song J, Suh CH, Park YB, Lee SH, Yoo NC, Lee JD, Kim KH, Lee SK. A phase I/IIa study on intra-articular injection of holmium-166-chitosan complex for the treatment of knee synovitis of rheumatoid arthritis. ACTA ACUST UNITED AC 2014; 28:489-97. [PMID: 11357500 DOI: 10.1007/s002590000470] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Previous animal studies have established that the intra-articular injection of holmium-166-chitosan complex (DW-166HC) causes effective necrosis of the inflamed synovium with litle leakage of radioactivity from the injected joint. Based on these findings, we conducted a phase I/IIa study to examine the biodistribution of DW-166HC and to assess the safety of DW-166HC for the treatment of knee synovitis in patients with rheumatoid arthritis (RA). A total of 16 patients [1 man, 15 women; median age 49 (range 36-65) years] who had RA knee synovitis refractory to disease-modifying anti-rheumatic drug treatments of > 3 months' duration were randomly assigned to three treatment groups with different radiation doses of DW-166HC: 370 MBq (n = 6), 555 MBq (n = 5) and 740 MBq (n = 5). In each treatment group, blood and urine radioactivity were analysed by beta counter and biodistribution of the injected DW-166HC was evaluated using a gamma scan camera. Clinical assessment was done according to three variables (evaluation method): knee joint pain (visual analogue scale), range of motion (goniometry) and joint swelling (circumference of knee joint). The duration of follow-up observation was 3 months. Following the intra-articular injection of DW-166HC, the blood radioactivity was little changed from the baseline measurement and the accumulated radioactivity excreted in urine was minimal. Gamma scan study indicated that most of the injected radiochemical was localized within the injected joint cavity, and the extra-articular leakage was negligible at 24 h after the injection: brain, 0.3%; lung, 0.6%; abdomen, 0.7%; and pelvis, 0.8%. Major adverse events were transient post-injection knee joint pain and swelling. These results suggest that DW-166HC might be a safe agent for radiation synovectomy, particularly for the treatment of knee synovitis of RA, and further trials in a larger patient population are warranted to evaluate the therapeutic efficacy of DW-166HC.
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Affiliation(s)
- J Song
- Department of Internal Medicine, Yonsei University College of Medicine, 134 Shinchon-dong, Seodaemun-ku, 120-752, Seoul, Korea
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22
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Chi JF, Uzui H, Guo HY, Ueda T, Lee JD. Effects of eplerenone on the activation of matrix metalloproteinase-2 stimulated by high glucose and interleukin-1β in human cardiac fibroblasts. Genet Mol Res 2014; 13:4845-55. [PMID: 24615074 DOI: 10.4238/2014.january.24.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this study was to determine the influence of high glucose (HG) and interleukin (IL)-1β on human cardiac fibroblast (HCF) functions, and to evaluate the effects of eplerenone in these responses. HCFs were cultured in normal or HG media in the absence or presence of IL-1β and/or eplerenone. We assessed matrix metalloproteinase-2 (MMP-2) activity in the supernatant by in-gel zymography, and determined mRNA expression levels of MMP-2 and tissue inhibitor of metalloproteinase-2 (TIMP-2) by reverse transcription-polymerase chain reaction. Equimolar D-mannitol was used as an osmotic control. HG stimulated MMP-2 activity and promoted MMP-2 mRNA synthesis. Increased effects were also observed in equimolar D-mannitol treatments, but these effects were weaker compared to those of glucose. The combination of HG and IL-1β resulted in a 2-fold increase in MMP-2 activity and mRNA expression compared with HG or IL-1β alone. Increases in HG- or IL-1β-induced MMP-2 activity and mRNA expression were blocked by eplerenone. Neither HG nor IL-1β affected TIMP-2 mRNA expression. HG increased MMP-2 activity by regulation of MMP- 2 mRNA expression in HCFs through osmotic and non-osmotic pathways. Synergistic effects of IL-1β added to HG media on MMP-2 activity and mRNA expression were observed in HCFs. Eplerenone normalized the effect of MMP-2 activity and HG- or IL-1β-induced expression in HCFs.
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Affiliation(s)
- J F Chi
- Division of Cardiovascular Medicine, Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Shimoaizuki, Matsuoka, Eiheiji-Cho, Fukui, Japan
| | - H Uzui
- Division of Cardiovascular Medicine, Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Shimoaizuki, Matsuoka, Eiheiji-Cho, Fukui, Japan
| | - H Y Guo
- Department of Cardiology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang, China
| | - T Ueda
- Division of Cardiovascular Medicine, Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Shimoaizuki, Matsuoka, Eiheiji-Cho, Fukui, Japan
| | - J D Lee
- Division of Cardiovascular Medicine, Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Shimoaizuki, Matsuoka, Eiheiji-Cho, Fukui, Japan
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Lee JD. Model for the attosecond resonant photoemission of copper dichloride: evidence for high-order Fano resonances and a time-domain core-hole clock. Phys Rev Lett 2013; 111:027401. [PMID: 23889440 DOI: 10.1103/physrevlett.111.027401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 06/02/2023]
Abstract
We present a model of the attosecond resonant dynamics of valence electron photoemission and MMM Auger electron emission in copper dichloride. At τ(h)≫1/ω(IR) (where τ(h) is the core-hole relaxation time and ω(IR) is the energy of the infrared probe field), high-order Fano sideband resonances on both sides of the original (zeroth-order) resonance are found in the energy domain on the time scale of τ(h). This is confirmed by a coherent π rotation of the relative phase between the photoelectron and Auger electron at each resonance, due to the subfemtosecond quantum correlation. We also find a core-hole clock, the asymmetry factor q of the first-order Fano sideband resonance, which can directly trace the core-hole relaxation in the time domain.
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Affiliation(s)
- J D Lee
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
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24
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Abstract
Workforce planning is an inexact science. Specialty and Associate Specialist (SAS) doctors are rarely included in workforce analyses. Past studies have shown that SAS doctors are significant contributors to the work in genitourinary (GU) medicine clinics. This survey confirms the large amount of clinical work undertaken by SAS doctors. It appears that 51% of SAS doctors in GU plan to retire in the next 15 years and it is uncertain what effect the 2008 SAS contract will have on SAS recruitment. This information should be taken into consideration in future GUM workforce planning.
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Affiliation(s)
- J D Lee
- Josephine Butler Centre for Sexual Health, Clayton Hospital, Wakefield
| | - E M Carlin
- Department of Genitourinary Medicine, King's Mill Hospital, Sutton in Ashfield
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Han SW, Hwang YH, Kim SH, Yun WS, Lee JD, Park MG, Ryu S, Park JS, Yoo DH, Yoon SP, Hong SC, Kim KS, Park YS. Controlling ferromagnetic easy axis in a layered MoS2 single crystal. Phys Rev Lett 2013; 110:247201. [PMID: 25165955 DOI: 10.1103/physrevlett.110.247201] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/31/2013] [Indexed: 06/03/2023]
Abstract
We report the effective methods to induce weak ferromagnetism in pristine MoS2 persisting up to room temperature with the improved transport property, which would lead to new spintronics devices. The hydrogenation of MoS2 by heating at 300 °C for 1 h leads to the easy axis out of plane, while the irradiation of proton with a dose of 1 × 10(13) P/cm(2) leads to the easy axis in plane. The theoretical modeling supports such magnetic easy axes.
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Affiliation(s)
- Sang Wook Han
- Department of Physics and Energy Harvest-Storage Research Center, University of Ulsan, Ulsan 680-749, Korea
| | - Young Hun Hwang
- Department of Physics and Energy Harvest-Storage Research Center, University of Ulsan, Ulsan 680-749, Korea
| | - Seon-Ho Kim
- Department of Chemistry and Department of Physics, Center for Superfunctional Materials, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Won Seok Yun
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - J D Lee
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Min Gyu Park
- Department of Applied Chemistry, Kyung Hee University, Yongin 446-701, Korea
| | - Sunmin Ryu
- Department of Applied Chemistry, Kyung Hee University, Yongin 446-701, Korea
| | - Ju Sang Park
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 120-749, Korea
| | - Dae-Hwang Yoo
- Department of Physics and Energy Harvest-Storage Research Center, University of Ulsan, Ulsan 680-749, Korea
| | - Sang-Pil Yoon
- Proton Engineering Frontier Project, Korea Atomic Energy Research Institute, Daejeon 989-111, Korea
| | - Soon Cheol Hong
- Department of Physics and Energy Harvest-Storage Research Center, University of Ulsan, Ulsan 680-749, Korea
| | - Kwang S Kim
- Department of Chemistry and Department of Physics, Center for Superfunctional Materials, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Young S Park
- Department of Chemistry and Department of Physics, Center for Superfunctional Materials, Pohang University of Science and Technology, Pohang 790-784, Korea
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26
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Read KA, Carpenter LJ, Arnold SR, Beale R, Nightingale PD, Hopkins JR, Lewis AC, Lee JD, Mendes L, Pickering SJ. Multiannual observations of acetone, methanol, and acetaldehyde in remote tropical atlantic air: implications for atmospheric OVOC budgets and oxidative capacity. Environ Sci Technol 2012; 46:11028-39. [PMID: 22963451 DOI: 10.1021/es302082p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Oxygenated volatile organic compounds (OVOCs) in the atmosphere are precursors to peroxy acetyl nitrate (PAN), affect the tropospheric ozone budget, and in the remote marine environment represent a significant sink of the hydroxyl radical (OH). The sparse observational database for these compounds, particularly in the tropics, contributes to a high uncertainty in their emissions and atmospheric significance. Here, we show measurements of acetone, methanol, and acetaldehyde in the tropical remote marine boundary layer made between October 2006 and September 2011 at the Cape Verde Atmospheric Observatory (CVAO) (16.85° N, 24.87° W). Mean mixing ratios of acetone, methanol, and acetaldehyde were 546 ± 295 pptv, 742 ± 419 pptv, and 428 ± 190 pptv, respectively, averaged from approximately hourly values over this five-year period. The CAM-Chem global chemical transport model reproduced annual average acetone concentrations well (21% overestimation) but underestimated levels by a factor of 2 in autumn and overestimated concentrations in winter. Annual average concentrations of acetaldehyde were underestimated by a factor of 10, rising to a factor of 40 in summer, and methanol was underestimated on average by a factor of 2, peaking to over a factor of 4 in spring. The model predicted summer minima in acetaldehyde and acetone, which were not apparent in the observations. CAM-Chem was adapted to include a two-way sea-air flux parametrization based on seawater measurements made in the Atlantic Ocean, and the resultant fluxes suggest that the tropical Atlantic region is a net sink for acetone but a net source for methanol and acetaldehyde. Inclusion of the ocean fluxes resulted in good model simulations of monthly averaged methanol levels although still with a 3-fold underestimation in acetaldehyde. Wintertime acetone levels were better simulated, but the observed autumn levels were more severely underestimated than in the standard model. We suggest that the latter may be caused by underestimated terrestrial biogenic African primary and/or secondary OVOC sources by the model. The model underestimation of acetaldehyde concentrations all year round implies a consistent significant missing source, potentially from secondary chemistry of higher alkanes produced biogenically from plants or from the ocean. We estimate that low model bias in OVOC abundances in the remote tropical marine atmosphere may result in up to 8% underestimation of the global methane lifetime due to missing model OH reactivity. Underestimation of acetaldehyde concentrations is responsible for the bulk (∼70%) of this missing reactivity.
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Affiliation(s)
- K A Read
- National Centre for Atmospheric Science, University of York, York, YO10 5DD, U.K
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Siddiqui FM, Pride GL, Lee JD. Use of the Penumbra system 054 plus low dose thrombolytic infusion for multifocal venous sinus thrombosis. A report of two cases. Interv Neuroradiol 2012; 18:314-9. [PMID: 22958771 DOI: 10.1177/159101991201800311] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/10/2012] [Indexed: 11/15/2022] Open
Abstract
Multifocal cerebral venous sinus thrombosis (CVST) has a high mortality rate especially when patients present with stupor or coma. Medical treatment including anticoagulation raises concerns about the associated high risk of intracerebral hemorrhage. Treatment of multifocal CVST with mechanical thrombectomy devices and local tPA infusion have previously been reported. However, these devices may have technical limitations. Success of the new-generation aspiration thrombectomy device like the Penumbra system has been reported in few cases of isolated CVST without the use of chemical thrombolysis. We describe two cases in which mechanical thrombectomy were used in conjunction with intra-sinus tPA infusion. Both cases were complicated and failed initial anticoagulation. Penumbra 054 was used in both cases. The Penumbra 054 is a novel device that has a bigger lumen which provides compatibility with other microcatheters, if additional therapies are required. The larger internal diameter of this catheter also allows for stronger thrombo-aspiration, potentially effecting more rapid sinus recanalization. Both cases showed remarkable clinical recovery without any major complications. This is the first reported simultaneous use of the Penumbra system 054 along with tPA infusion. New devices such as the Penumbra system may offer additional therapeutic options in the treatment of multifocal CVST.
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Affiliation(s)
- F M Siddiqui
- Department of Neurology, UT Southwestern Medical center; Dallas, TX, USA.
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Steyn FJ, Ngo ST, Lee JD, Leong JW, Buckley AJ, Veldhuis JD, McCombe PA, Chen C, Bellingham MC. Impairments to the GH-IGF-I axis in hSOD1G93A mice give insight into possible mechanisms of GH dysregulation in patients with amyotrophic lateral sclerosis. Endocrinology 2012; 153:3735-46. [PMID: 22621959 DOI: 10.1210/en.2011-2171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GH deficiency has been found in subjects with amyotrophic lateral sclerosis (ALS). Disrupted endocrine function could contribute to the progressive muscle loss and hypermetabolism seen in ALS. It is not possible to study all the elements of the GH-IGF-I axis in ALS patients. Consequently, it remains unclear whether dysfunctional GH secretion contributes to disease pathogenesis and why GH and IGF-I directed treatment strategies are ineffective in human ALS. The hSOD1(G93A) transgenic mouse model is useful for the detailed investigation of the pathogenesis of ALS. We report that symptomatic male hSOD1(G93A) transgenic mice exhibit a deficiency in GH secretion similar to that seen in human ALS. Further characterization of the GH-IGF-I axis in hSOD1(G93A) mice reveals central and peripheral abnormalities that are not found in wild-type age-matched controls. Specifically, we observe aberrant endogenous pulsatile GH secretion, reduced pituitary GH content, and decreased circulating levels of IGF-I, indicating global GH deficiency in hSOD1(G93A) mice. Furthermore, a reduction in the expression of the IGF-I receptor α-subunit in skeletal muscle and lumbar spinal cords of hSOD1(G93A) mice suggests impaired IGF-I signaling within these tissues. This is the first account of disrupted GH secretion in a transgenic mouse model of ALS. These observations are essential for the development of effective GH and IGF-I targeted therapies in ALS.
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Affiliation(s)
- F J Steyn
- School of Biomedical Sciences, University of Queensland, St. Lucia 4072, Australia.
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29
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MacKenzie AR, Langford B, Pugh TAM, Robinson N, Misztal PK, Heard DE, Lee JD, Lewis AC, Jones CE, Hopkins JR, Phillips G, Monks PS, Karunaharan A, Hornsby KE, Nicolas-Perea V, Coe H, Gabey AM, Gallagher MW, Whalley LK, Edwards PM, Evans MJ, Stone D, Ingham T, Commane R, Furneaux KL, McQuaid JB, Nemitz E, Seng YK, Fowler D, Pyle JA, Hewitt CN. The atmospheric chemistry of trace gases and particulate matter emitted by different land uses in Borneo. Philos Trans R Soc Lond B Biol Sci 2012; 366:3177-95. [PMID: 22006961 DOI: 10.1098/rstb.2011.0053] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report measurements of atmospheric composition over a tropical rainforest and over a nearby oil palm plantation in Sabah, Borneo. The primary vegetation in each of the two landscapes emits very different amounts and kinds of volatile organic compounds (VOCs), resulting in distinctive VOC fingerprints in the atmospheric boundary layer for both landscapes. VOCs over the Borneo rainforest are dominated by isoprene and its oxidation products, with a significant additional contribution from monoterpenes. Rather than consuming the main atmospheric oxidant, OH, these high concentrations of VOCs appear to maintain OH, as has been observed previously over Amazonia. The boundary-layer characteristics and mixing ratios of VOCs observed over the Borneo rainforest are different to those measured previously over Amazonia. Compared with the Bornean rainforest, air over the oil palm plantation contains much more isoprene, monoterpenes are relatively less important, and the flower scent, estragole, is prominent. Concentrations of nitrogen oxides are greater above the agro-industrial oil palm landscape than over the rainforest, and this leads to changes in some secondary pollutant mixing ratios (but not, currently, differences in ozone). Secondary organic aerosol over both landscapes shows a significant contribution from isoprene. Primary biological aerosol dominates the super-micrometre aerosol over the rainforest and is likely to be sensitive to land-use change, since the fungal source of the bioaerosol is closely linked to above-ground biodiversity.
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Affiliation(s)
- A R MacKenzie
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
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Pyle JA, Warwick NJ, Harris NRP, Abas MR, Archibald AT, Ashfold MJ, Ashworth K, Barkley MP, Carver GD, Chance K, Dorsey JR, Fowler D, Gonzi S, Gostlow B, Hewitt CN, Kurosu TP, Lee JD, Langford SB, Mills G, Moller S, MacKenzie AR, Manning AJ, Misztal P, Nadzir MSM, Nemitz E, Newton HM, O'Brien LM, Ong S, Oram D, Palmer PI, Peng LK, Phang SM, Pike R, Pugh TAM, Rahman NA, Robinson AD, Sentian J, Samah AA, Skiba U, Ung HE, Yong SE, Young PJ. The impact of local surface changes in Borneo on atmospheric composition at wider spatial scales: coastal processes, land-use change and air quality. Philos Trans R Soc Lond B Biol Sci 2012; 366:3210-24. [PMID: 22006963 DOI: 10.1098/rstb.2011.0060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present results from the OP3 campaign in Sabah during 2008 that allow us to study the impact of local emission changes over Borneo on atmospheric composition at the regional and wider scale. OP3 constituent data provide an important constraint on model performance. Treatment of boundary layer processes is highlighted as an important area of model uncertainty. Model studies of land-use change confirm earlier work, indicating that further changes to intensive oil palm agriculture in South East Asia, and the tropics in general, could have important impacts on air quality, with the biggest factor being the concomitant changes in NO(x) emissions. With the model scenarios used here, local increases in ozone of around 50 per cent could occur. We also report measurements of short-lived brominated compounds around Sabah suggesting that oceanic (and, especially, coastal) emission sources dominate locally. The concentration of bromine in short-lived halocarbons measured at the surface during OP3 amounted to about 7 ppt, setting an upper limit on the amount of these species that can reach the lower stratosphere.
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Affiliation(s)
- J A Pyle
- National Centre for Atmospheric Science, NCAS, UK.
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31
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Standley RA, Harber MP, Lee JD, Konopka AR, Trappe SW, Trappe TA. Influence of aerobic cycle exercise training on patellar tendon cross-sectional area in older women. Scand J Med Sci Sports 2011; 23:367-73. [PMID: 22092782 DOI: 10.1111/j.1600-0838.2011.01396.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2011] [Indexed: 11/29/2022]
Abstract
Nine to 12 weeks of resistance exercise training in young individuals induces quadriceps muscle (∼6%) and region-specific patellar tendon (4-6%) hypertrophy. However, 12 weeks of resistance exercise training (∼1 h total exercise time) in older individuals (60-78 years) induces quadriceps muscle hypertrophy (9%) without impacting patellar tendon size. The current study examined if a different loading paradigm using cycle exercise would promote patellar tendon hypertrophy or alter the internal tendon properties, measured with magnetic resonance imaging signal intensity, in older individuals. Nine women (70 ± 2 years) completed 12 weeks of aerobic upright cycle exercise training (∼28 h total exercise time). Aerobic exercise training increased (P < 0.05) quadriceps muscle size (11 ± 2%) and VO2max (30 ± 9%). Mean patellar tendon cross-sectional area (CSA) (2 ± 1%) and signal intensity (-1 ± 2%) were unchanged (P > 0.05) over the 12 weeks of training. Region-specific CSA was unchanged (P > 0.05) at the proximal (-1 ± 3%) and mid regions (2 ± 2%) of the tendon but tended (P = 0.069) to increase at the distal region (5 ± 3%). Region-specific signal intensity differed along the tendon but was unchanged (P > 0.05) with training. Although more studies are needed, exercise-induced patellar tendon hypertrophy, compared with skeletal muscle, appears to be attenuated in older individuals, while the loading pattern associated with aerobic exercise seems to have more impact than resistance exercise in promoting patellar tendon hypertrophy.
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Affiliation(s)
- R A Standley
- Human Performance Laboratory, Ball State University, Muncie, Indiana, USA
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Lee JE, Park HJ, Song SK, Sohn YH, Lee JD, Lee PH. Neuroanatomic basis of amnestic MCI differs in patients with and without Parkinson disease. Neurology 2010; 75:2009-16. [PMID: 21115956 DOI: 10.1212/wnl.0b013e3181ff96bf] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To explore the neuroanatomic basis of amnestic mild cognitive impairment (aMCI) in patients with Parkinson disease (PD; aMCI-PD(+)) and without PD (aMCI-PD(-)). METHODS A total of 119 patients with aMCI (aMCI-PD(-), n = 78, and aMCI-PD(+), n = 41) underwent T1-weighted MRI, and the image data were analyzed using voxel-based morphometry. RESULTS No significant differences in demographic characteristics or general cognition were found between patients with aMCI-PD(-) and aMCI-PD(+). Comparisons of neuropsychological tests between groups revealed that patients with aMCI-PD(-) had lower scores in delayed verbal and visual recognition memory, whereas visuospatial dysfunction was more severe in patients with aMCI-PD(+). Gray matter (GM) density in the right temporal and posterior cingular cortices was significantly lower in the aMCI-PD(-) group compared with controls. In contrast, GM density in the aMCI-PD(+) group was significantly lower in the precuneus and left prefrontal and primary motor areas relative to controls. A direct comparison between groups showed that decreased GM density in aMCI-PD(-) relative to aMCI-PD(+) was localized in the right temporal and anterior prefrontal areas, whereas decreased GM density in aMCI-PD(+) relative to aMCI-PD(-) was involved in the bilateral precuneus, left primary motor, and right parietal areas. Memory decline was correlated with temporal area atrophy in aMCI-PD(-) and with posterior cingulate cortex atrophy in aMCI-PD(+). CONCLUSIONS Our data suggest that different neuroanatomic systems underlie memory dysfunction in patients with aMCI-PD(-) and aMCI-PD(+).
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Affiliation(s)
- J E Lee
- Department of Neurology, Yonsei University Medical College, 250 Seongsanno, Seodaemun-gu, Seoul, 120-752, South Korea
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Abstract
A 32-year-old British Asian man presented with what appeared clinically and on ultrasound to be a testicular tumour. However, syphilis serology, histology and detection of Treponema pallidum DNA by polymerase chain reaction confirmed that the lesion was a gumma. Without routine syphilis serology, the correct diagnosis may have been missed.
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Affiliation(s)
| | - J D Lee
- Chadwick Clinic for Sexual Health
| | - I W C Macdonald
- Department of Pathology, Dewsbury and District Hospital, Dewsbury WF13 4HS
| | - C Shekhar
- Department of Urology, Pinderfields General Hospital, Wakefield, UK
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Abstract
The effects of a live attenuated influenza vaccine and subsequent challenge with virulent influenza virus on the delayed hypersensitivity skin test, and the in vitro response of lymphocytes were evaluated. Volunteers were skin tested before and after administration of vaccine or placebo and challenge with PPD (a purified protein derivative of Mycobacterium tuberculosis), candida, mumps, and trichophytin, and their lymphocytes were tested for [(3)H]thymidine uptake in response to phytohemagglutin. Of eight volunteers who showed evidence of viral replication after administration of the attenuated vaccine, four had a significant diminution in their skin test response, whereas 8 of 13 volunteers infected with virulent influenza virus showed a diminution. Of the 21 volunteers who were infected with either attenuated or virulent influenza virus, 12 showed suppression of their phytohemagglutin response. None of the volunteers who were given placebo vaccine, or who showed no evidence for viral replication after immunization or challenge, had a suppression of their skin test or phytohemagglutin responses. Although most of the infected volunteers demonstrated suppression of their T-cell function, there was no evidence of a similar suppression of B-cell function.
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Affiliation(s)
- G B Kantzler
- Departments of Medicine and Immunology and Medical Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610
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Dickinson JM, Lee JD, Sullivan BE, Harber MP, Trappe SW, Trappe TA. A new method to study in vivo protein synthesis in slow- and fast-twitch muscle fibers and initial measurements in humans. J Appl Physiol (1985) 2010; 108:1410-6. [PMID: 20203068 DOI: 10.1152/japplphysiol.00905.2009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to develop an approach to directly assess protein fractional synthesis rate (FSR) in isolated human muscle fibers in a fiber type-specific fashion. Individual muscle fibers were isolated from biopsies of the vastus lateralis (VL) and soleus (SOL) obtained from eight young men during a primed, continuous infusion of [5,5,5-(2)H3]leucine performed under basal conditions. To determine mixed protein FSR, a portion of each fiber was used to identify fiber type, fibers of the same type were pooled, and the [5,5,5-(2)H3]leucine enrichment was determined via GC-MS. Processing isolated slow-twitch [myosin heavy chain (MHC) I] and fast-twitch (MHC IIa) fibers for mixed protein bound [5,5,5-(2)H3]leucine enrichment yielded mass ion chromatographic peaks that were similar in shape, abundance, and measurement reliability as tissue homogenates. In the VL, MHC I fibers exhibited a 33% faster (P<0.05) mixed protein FSR compared with MHC IIa fibers (0.068+/-0.006 vs. 0.051+/-0.003%/h). MHC I fibers from the SOL (0.060+/-0.005%/h) and MHC I fibers from the VL displayed similar (P>0.05) mixed protein FSR. Feasibility of processing isolated human muscle fibers for analysis of myofibrillar protein [5,5,5-(2)H3]leucine enrichment was also confirmed in non-fiber-typed pooled fibers from the VL. These methods can be applied to the study of fiber type-specific responses in human skeletal muscle. The need for this level of investigation is underscored by the different contributions of each fiber type to whole muscle function and the numerous distinct adaptive functional and metabolic changes in MHC I and MHC II fibers originating from the same muscle.
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Affiliation(s)
- J M Dickinson
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
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36
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Park ES, Rha DW, Lee JD, Yoo JK, Chang WH. The short-term effects of combined modified constraint-induced movement therapy and botulinum toxin injection for children with spastic hemiplegic cerebral palsy. Neuropediatrics 2009; 40:269-74. [PMID: 20446220 DOI: 10.1055/s-0030-1252049] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE The aim of this study was to investigate whether modified constraint-induced movement therapy (mCIMT) following a botulinum type A toxin (BoNT-A) injection enhances the effects of the BoNT-A injection into the spastic upper limb of children with hemiplegic cerebral palsy (CP). METHODS A combined therapy with mCIMT and BoNT-A was given to 17 children in group A. Fifteen children in group B received only the BoNT-A injection. The muscle tone, the movement pattern, and the How Often and the How Well scales in the revised Pediatric Motor Activity Log (revised PMAL) were assessed before and 3 weeks after intervention. RESULTS Three participants in group A dropped out due to poor tolerance of mCIMT. There were significant improvements in the muscle tone and the movement patterns for both groups (p<0.05), and the changes were not significantly different between the two groups. The How Often and the How Well scales in the revised PMAL were significantly improved in group A (p<0.05), but not in group B. CONCLUSION A combined therapy of mCIMT and BoNT-A seems to be helpful to enhance the effects of the BoNT-A injection in the functional use of the affected limb in children with hemiplegic CP.
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Affiliation(s)
- E S Park
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Korea
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37
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Lee JD, Han SW, Miyawaki N, Gomi H. Comment on "temperature-dependent localized excitations of doped carriers in superconducting diamond". Phys Rev Lett 2009; 102:199701-199702. [PMID: 19519005 DOI: 10.1103/physrevlett.102.199701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Indexed: 05/27/2023]
Abstract
A Comment on the Letter by K. Ishizaka et al., Phys. Rev. Lett. 100, 166402 (2008)10.1103/PhysRevLett.100.166402. The authors of the Letter offer a Reply.
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38
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Affiliation(s)
- J W HA
- Cardiology Division, Yonsei University of College of Medicine, Seoul, Korea
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39
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Koo BS, Lee SW, Lee YM, Lee JD, Koh YW. Sialolithiasis in a stump of Wharton's duct of an aplastic unilateral submandibular gland. Int J Oral Maxillofac Surg 2008; 38:93-5. [PMID: 19095409 DOI: 10.1016/j.ijom.2008.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 04/10/2008] [Accepted: 11/10/2008] [Indexed: 11/29/2022]
Abstract
Congenital absence of the salivary glands is an uncommon disorder. Isolated aplasia of a unilateral submandibular gland is rare and only 6 cases have been reported. The formation of a sialolith within the remaining Wharton's duct, associated with isolated aplasia of a unilateral submandibular gland, has not been reported previously. The authors report two cases of sialolithiasis within the ipsilateral remaining Wharton's duct in patients with isolated aplasia of a unilateral submandibular gland.
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Affiliation(s)
- B S Koo
- Department of Otolaryngology, Head and Neck Surgery, Cancer Research Institute, College of Medicine, Chungnam National University, Daejeon, Korea
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Lee JD, Hase M. Coherent optical control of the ultrafast dephasing of phonon-plasmon coupling in a polar semiconductor using a pulse train of below-band-gap excitation. Phys Rev Lett 2008; 101:235501. [PMID: 19113565 DOI: 10.1103/physrevlett.101.235501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Indexed: 05/27/2023]
Abstract
In the investigation of the nonequilibrium ultrafast dynamics of the coherent phonon-plasmon coupled modes in a polar semiconductor, we predict theoretically that their coherent oscillations can be efficiently controlled by using the pulse train of below-band-gap excitation. The dynamics of the coherent modes are driven by the virtual electron-hole pairs, which would avoid dephasing sources such as accumulation of photoexcited charges and spontaneous emission. This implies that carrier mobility can also be efficiently controlled and dramatically enhanced by synchronizing the pulse train with the coherent oscillation of the carrier-relevant coupled mode.
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Affiliation(s)
- J D Lee
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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Lee JD, Han SW, Inoue J. Sharp contrasts in low-energy quasiparticle dynamics of graphite between Brillouin zone K and H points. Phys Rev Lett 2008; 100:216801. [PMID: 18518624 DOI: 10.1103/physrevlett.100.216801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Indexed: 05/26/2023]
Abstract
The low-energy quasiparticle (QP) dynamics of graphite are governed by a coupling with the E(2g) longitudinal optical phonon of omega(LO) approximately 200 meV, which is found to dramatically depend on the electronic band dispersion epsilon(k). A discontinuity of the QP linewidth develops near omega(LO) for a linear band with a quadratic band top [near the Brillouin zone (BZ) K point], while it disappears for a pure linear band (near the BZ H point). It is also found that the effective electron-phonon coupling near the K point is stronger than near the H point by more than 50%. This finding makes possible a consistent understanding of recent angle-resolved photoemission observations near the K point.
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Affiliation(s)
- J D Lee
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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Kim CH, Cheon KA, Koo MS, Ryu YH, Lee JD, Chang JW, Lee HS. Dopamine transporter density in the basal ganglia in obsessive-compulsive disorder, measured with [123I]IPT SPECT before and after treatment with serotonin reuptake inhibitors. Neuropsychobiology 2007; 55:156-62. [PMID: 17657168 DOI: 10.1159/000106474] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Accepted: 05/27/2007] [Indexed: 11/19/2022]
Abstract
It has been suggested that dopamine as well as serotonin are associated with the pathophysiology of obsessive-compulsive disorder (OCD). 5-Hydroxytryptophan inhibits dopamine release in healthy persons as well as in patients with OCD, and serotonin tonic inhibition affects dopamine function in basal ganglia, indicating a close relationship between serotonin and the dopamine system. Using iodine-123-labeled N-(3-iodopropen-2-yl)-2 beta-carbomethoxy-3beta-(4-chlorophenyl) tropane ([(123)I]IPT) single photon emission computed tomography (SPECT), we investigated the dopamine transporter (DAT) density in the basal ganglia of patients with OCD. The test consists of two measurements before and after treatment with serotonin reuptake inhibitors (SRIs). Ten patients with OCD before and after treatment with SRIs were included. We performed brain SPECT 2 h after intravenous administration of [(123)I]IPT using a dual-head SPECT camera (Vertex, ADAC, Calif., USA) and analyzed the SPECT data, reconstructed for the assessment of the specific/nonspecific DAT binding ratio in the basal ganglia. We then examined the correlation between the scores of OCD symptom changes, assessed with the Yale-Brown Obsessive-Compulsive Scale (Y-BOCS), and DAT binding ratio. Patients with OCD after treatment with SRIs showed a significantly decreased DAT binding ratio in the right basal ganglia compared with baseline. A significant correlation was found between the total scores and compulsion score changes of the Y-BOCS and the changes of the DAT binding ratio of the right basal ganglia. These findings suggest that the dopaminergic neurotransmitter system of the basal ganglia could play an important role in the symptom improvement of OCD patients.
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Affiliation(s)
- C H Kim
- Department of Psychiatry,Yonsei University, Seoul, Korea
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Abstract
Automotive collision warning systems (CWS) can enhance hazard identification and management. However, false alarms (FAs), which occur as a random activation of the system not corresponding to a threat and not interpretable by the driver, and unnecessary alarms (UAs), which occur in situations judged hazardous by the algorithm but not by the driver, may limit CWS effectiveness. A driving simulator was used to investigate the influence of CWS (accurate, UA, FA, none) and distraction on driver performance during non-critical and critical events. FAs and UAs differentially influenced trust and compliance. FAs diminished trust and compliance, whereas the context associated with UAs fostered trust and compliance during subsequent events. This study suggests current warning descriptions based on signal detection theory need to be expanded to represent how different types of alarms affect drivers.
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Affiliation(s)
- M N Lees
- Department of Mechanical and Industrial Engineering, University of Iowa, Iowa City, IA, USA.
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Abstract
Adaptive cruise control (ACC) requires that the driver intervene in situations that exceed the capability of ACC. A brake pulse might provide a particularly compatible means of alerting the driver to situations in which the acceleration authority of the ACC has been exceeded. This study examined the sensitivity of the driver to brake pulses of five different amplitudes (0.01-0.025 g) and five different durations (50-800 ms). Drivers were sensitive to accelerations as low as 0.015 g. Pulse duration interacted with pulse amplitude, such that moderate duration pulses were more detectable than long and short duration pulses at intermediate levels of pulse amplitude. A power function with an exponent of 1.0 accounted for 99% of the variance in drivers' sensitivity to pulse amplitude; however, a power function with an exponent of 0.23 accounted for only 70% of the variance in drivers' sensitivity to pulse duration. These results can help designers create ACC algorithms and develop brake pulse warnings.
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Affiliation(s)
- J D Lee
- Department of Mechanical and Industrial Engineering, University of Iowa, Iowa City, IA 52242, USA.
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Lee JD, Chang TC, Huang CH, Wu SJ, Chen CJ. Computer-aided diagnosis system for acute stroke using diffusion weighted images with volume calculation. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:1529-32. [PMID: 17271988 DOI: 10.1109/iembs.2004.1403468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The diffusion weighted image (DWI) technique is routinely used for diagnosis and treatment of early stroke due to its superior performance, especially when it is compared with conventional magnetic resonance image (MRI) for detection of acute ischemic stroke. Using DWI examination, This work has proposed a computer-aided diagnosis system, which can effectively calculate the volume size of a lesion and provide clinical doctor the 3D reconstruction data of the lesion. The potential benefits of using our system include the higher accuracy of acute stroke lesion definition, the reduced time and procedure of calculating the volume of a lesion, and providing 3D reconstruction image of stroke patients, which can effectively assist doctors in making more accurate diagnoses and treating patients in a more convenient way. Compared with the traditional method, the experimental results have shown the superior performance of this proposed system.
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Affiliation(s)
- J D Lee
- Dept. of Electr. Eng, Chang Gung Univ., Tao-Yuan, Taiwan
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Lee JD, Inoue J, Hase M. Ultrafast Fano resonance between optical phonons and electron-hole pairs at the onset of quasiparticle generation in a semiconductor. Phys Rev Lett 2006; 97:157405. [PMID: 17155359 DOI: 10.1103/physrevlett.97.157405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Indexed: 05/12/2023]
Abstract
Based on the many-body time-dependent approach applied to the ultrafast time region, we investigate the dynamics of creation of an optical phonon incorporating with the electron-hole continuum in a semiconductor. In the transient Fano resonance, due to an interference between those sharp (optical phonon) and continuum (electron-hole pair) quasiparticles, we find the robust destructive interference at birth of them, i.e., tau approximately 0 if the created phonon is coherent under the irradiation of ultrashort optical pulses. The origin is found to be the potential scattering of the electron-hole pair by the q=0 coherent phonon. This finding agrees well with the recent experiment.
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Affiliation(s)
- J D Lee
- International Center for Young Scientists, National Institute for Materials Science, Tsukuba 305-0044, Japan
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Abstract
We study the optical absorption, especially the (far-) infrared absorption by phonons, of semiconducting and metallic nanospheres. In the nanoscopic sphere, phonons as well as states of electronic excitations are quantized by confinement. It is also known that in the nanoscopic geometry, the confined electron-phonon interaction has a different form from the usual one in the bulk. First, we analyze the phonon and electron contributions to the dielectric response of nanospheres like epsilon(q,omega)=epsilon(ph)(q,omega)+epsilon(el)(q,omega) or 1epsilon(q,omega)=1epsilon(sc-ph)(q,omega)+1epsilon(el)(q,omega) from the confined electron-phonon interaction for three cases: the intrinsic semiconductor, the doped semiconductor, and the metal. From the dielectric response, the optical absorption spectra are calculated within the semiclassical framework concentrating on the (far-) infrared region and compared to the spectra without imposing confinement. Nontrivial differences of the spectra with confined phonons stem from two features: the electron-phonon coupling matrix has a different form and the phase space q of the confined phonon is reduced because of its quantization to q(n). Finally, size distribution effects in an ensemble of isolated nanospheres are briefly discussed. Those effects are found to be important in metallic spheres with rapid sweepings of resonances by a small change of the sphere size.
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Affiliation(s)
- J D Lee
- International Center for Young Scientists, National Institute for Materials Science, Tsukuba 305-0044, Japan.
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Harrison RM, Yin J, Tilling RM, Cai X, Seakins PW, Hopkins JR, Lansley DL, Lewis AC, Hunter MC, Heard DE, Carpenter LJ, Creasey DJ, Lee JD, Pilling MJ, Carslaw N, Emmerson KM, Redington A, Derwent RG, Ryall D, Mills G, Penkett SA. Measurement and modelling of air pollution and atmospheric chemistry in the U.K. West Midlands conurbation: overview of the PUMA Consortium project. Sci Total Environ 2006; 360:5-25. [PMID: 16289266 DOI: 10.1016/j.scitotenv.2005.08.053] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The PUMA (Pollution of the Urban Midlands Atmosphere) Consortium project involved intensive measurement campaigns in the Summer of 1999 and Winter of 1999/2000, respectively, in which a wide variety of air pollutants were measured in the UK West Midlands conurbation including detailed speciation of VOCs and major component analysis of aerosol. Measurements of the OH and HO2 free radicals by the FAGE technique demonstrated that winter concentrations of OH were approximately half of those measured during the summer despite a factor of 15 reduction in production through the photolysis of ozone. Detailed box modelling of the fast reaction chemistry revealed the decomposition of Criegee intermediates formed from ozone-alkene reactions to be responsible for the majority of the formation of hydroxyl in both the summer and winter campaigns, in contrast to earlier rural measurements in which ozone photolysis was predominant. The main sinks for hydroxyl are reactions with NO2, alkenes and oxygenates. Concentrations of the more stable hydrocarbons were found to be relatively invariant across the conurbation, but the impacts of photochemistry were evident through analyses of formaldehyde which showed the majority to be photochemical in origin as opposed to emitted from road traffic. Measurements on the upwind and downwind boundaries of the conurbation revealed substantial enhancements in NOx as a result of emissions within the conurbation, especially during westerly winds which carried relatively clean air. Using calcium as a tracer for crustal particles, it proved possible to reconstruct aerosol mass from the major chemical components with a fairly high degree of success. The organic to elemental carbon ratios showed a far greater influence of photochemistry in summer than winter, presumably resulting mainly from the greater availability of biogenic precursors during the summer campaign. Two urban airshed models were developed and applied to the conurbation, one Eulerian, the other Lagrangian. Both were able to give a good simulation of concentrations of both primary and secondary pollutants at urban background locations.
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Affiliation(s)
- R M Harrison
- School of Geography, Earth & Environmental Sciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Hopkins JR, Boddy RK, Hamilton JF, Lee JD, Lewis AC, Purvis RM, Watson NJ. An observational case study of ozone and precursors inflow to South East England during an anticyclone. ACTA ACUST UNITED AC 2006; 8:1195-202. [PMID: 17133276 DOI: 10.1039/b608062f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Summertime photochemical air pollution episodes within the United Kingdom have been proposed via modelling studies to be strongly influenced by regional scale inflow of air from the continental European boundary layer. We present a vertically resolved case study using measurements made from the NERC/Met Office BAe 146 research aircraft on 18th August 2005 over the South East of England and the North Sea during a weak anticyclone centred over Northern Europe. The vertical distribution of ozone, CO, NO(x), peroxyacetyl nitrate (PAN) and a wide range of both nonmethane hydrocarbons (NMHC) and oxygenated volatile organic compounds (OVOCs) were determined between 500 ft (approximately 152 m) and 7000 ft (approximately 2134 m) over the East Anglia coastline and 50 km inland. In excess of 80 ppbV ozone was observed within inflowing boundary layer air over the North Sea coast in a broad N-S sloping feature around 60 km wide. The inflowing feature of European origin was also observed further inland within the boundary layer albeit with lower, more variable, ozone mixing ratios. The increased variability in ozone over land was a product of titration by fresh surface emissions of NO via rapid upward transport in thermals, a hypothesis supported by the observed vertical wind speed component. Fast boundary layer mixing over land was further illustrated by a uniform distribution in reactive alkenes. A comparison between aircraft and surface O(3) UK AUN (Automatic Urban Network) measurements showed good agreement with the inland site, Sibton, but marked differences with the coastal monitoring site at Weybourne, potentially due to gradients established by ocean deposition in stably stratified marine air.
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Affiliation(s)
- J R Hopkins
- Department of Chemistry, University of York, York, UK.
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Abstract
A 64-year-old woman presented with a 2-week history of an asymptomatic mass involving the lower lip. Histopathological examination showed a well-circumscribed tumour composed of many lobules separated by thin, fibrous connective tissue. Individual lobules were composed of round or polyhedral tumour cells, which had a characteristic finely granular and vacuolated cytoplasm and eccentric hyperchromatic nuclei. Positive staining was observed with Periodic acid-Shiff, and immunohistochemistry for cytokeratin, alpha-1 antitrypsin, and S-100 protein resulting in a final diagnosis of acinic cell carcinoma. Acinic cell carcinoma represents a well-established, although uncommon, entity in the classification of neoplasms of salivary gland origin. The parotid salivary gland is the most frequent site of acinic cell carcinoma, whereas the lip is a particularly unusual site. The unusual presentation of this tumour may lead to confusion with a mucocele. Given these findings, we suggest that acinic cell carcinoma should be considered in the differential diagnosis of any mucocele-like mass on the lower lip.
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Affiliation(s)
- J H Cho
- Department of Dermatology, Our Lady of Mercy Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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