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Nikitin PV, Ryzhova MV, Galstyan SA, Kim DS, Zubova IV, Khokhlova EA, Shugay SV. Identification of different cell clusters in the endothelium of atherosclerotic vessels and determination of inter-cluster gradient of proliferative and inflammatory activity as new diagnostic markers. Biotech Histochem 2020; 96:487-497. [PMID: 32938242 DOI: 10.1080/10520295.2020.1823016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
To characterize atherogenesis functionally, we studied the functional heterogeneity of endotheliocytes in carotid vessels with atherosclerotic plaques and identified several distinct cell clusters. We measured the Ki-67 labeling index (Ki-67 LI), percentage of Bcl-2 cells (CP) and expression of CCL5, IL 6 and VCAM1 in each cell cluster. We also investigated how these indicators change when the plaque becomes unstable and how they affect the risk of adverse cerebrovascular events in patients. We evaluated the inter-cluster gradient of marker activity and its relation to patient prognosis. We identified five endothelial clusters: the under plaque cluster (UPC), peripheral cluster (PC), marginal cluster (MC), transient cluster (TC) and outside plaque cluster (OC). The UPC exhibited the greatest proliferative, proinflammatory and adhesive activity, but low anti-apoptotic activity. The PC exhibited the second greatest proliferative, adhesive and proinflammatory activity. Progression of atherosclerosis and transition of a stable atherosclerotic plaque to an unstable one was accompanied by increased expression of nearly all markers. The proliferative activity in the UPC, PC and OC, and the pro-inflammatory activity in UPC and anti-apoptotic activity in the PC, were correlated with prognosis. Also, two gradients of proliferative activity and a gradient of pro-inflammatory activity were associated with risk of adverse events.
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Kim D, Lim K, Kim DE, Kim JS. Genome-wide specificity of dCpf1 cytidine base editors. Nat Commun 2020; 11:4072. [PMID: 32792663 PMCID: PMC7426837 DOI: 10.1038/s41467-020-17889-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
Cpf1-linked base editors broaden the targeting scope of programmable cytidine deaminases by recognizing thymidine-rich protospacer-adjacent motifs (PAM) without inducing DNA double-strand breaks (DSBs). Here we present an unbiased in vitro method for identifying genome-wide off-target sites of Cpf1 base editors via whole genome sequencing. First, we treat human genomic DNA with dLbCpf1-BE ribonucleoprotein (RNP) complexes, which convert C-to-U at on-target and off-target sites and, then, with a mixture of E. coli uracil DNA glycosylase (UDG) and DNA glycosylase-lyase Endonuclease VIII, which removes uracil and produces single-strand breaks (SSBs) in vitro. Whole-genome sequencing of the resulting digested genome (Digenome-seq) reveals that, on average, dLbCpf1-BE induces 12 SSBs in vitro per crRNA in the human genome. Off-target sites with an editing frequency as low as 0.1% are successfully identified by this modified Digenome-seq method, demonstrating its high sensitivity. dLbCpf1-BEs and LbCpf1 nucleases often recognize different off-target sites, calling for independent analysis of each tool.
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Nazarov VV, Linde NN, Kim DS, Danilov GV, Cherekaev VA, Kozlov AV. [Glioblastoma in the region of previously resected meningioma. Case report and literature review]. ZHURNAL VOPROSY NEĬROKHIRURGII IMENI N. N. BURDENKO 2020; 84:61-68. [PMID: 32759928 DOI: 10.17116/neiro20208404161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Combination of meningioma and glioblastoma within the same anatomical region is casuistry. We found only 13 case reports in the available literature. Some of the authors reported induced nature of the second tumor, i.e. development under the influence of the primary neoplasm. We report a patient with glioblastoma of the right frontoparietotemporal region in 3 years after previous resection of benign right-sided meningioma of sphenoid wings. Mathematical analysis of the discovered pattern resulted conclusion about its random nature, i.e. no causal relationship between both neoplasms.
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Kim DS, Foster BE, Collen JF, Eliasson AH. 1034 Should We Recommend More Sleep To Prevent Obesity? Sleep 2020. [DOI: 10.1093/sleep/zsaa056.1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
According to the 2015-2016 National Health and Nutrition Examination Survey (NHANES), the national adult obesity rate was 40% with the incidence of adult obesity having increased by 70% over the last 30 years. Paralleling the obesity epidemic have been worsening sleep deprivation and eroding sleep quality. We analyzed data from a Cardiovascular Health Registry to explore a link between total sleep time and obesity.
Methods
Registry participants underwent anthropometrics and completed validated questionnaires assessing health behaviors and symptoms including total sleep time (TST), Epworth Sleepiness Scale (ESS), Fatigue Severity Scale (FSS), Pittsburgh Sleep Quality Index (PSQI), Perceived Stress Scale (PSS), and exercise time. Differences between subjects with sufficient (≥7 hours) and insufficient (<7 hours) sleep were analyzed using T-tests.
Results
Registry participants (n=630) had mean age 55.3±9.9 years (45% men, 391W, 182B, 26H, 12A, 19O). The subgroup with sufficient sleep (n=261, 48% men), had mean BMI 29.3±5.6 while the subgroup with insufficient sleep (n=369, 44% men) had mean BMI of 30.5±5.3, p=0.008. The insufficient sleep group was noted to be sleepier (ESS 9.7±4.9 vs 7.4±4.6, p<0.001), more fatigued (FSS 4.9±2.3 vs 3.5±2.4, p<0.001) and have worse sleep quality (PSQI 8.6±3.7 vs 4.7±2.8, p<0.001). Insufficient sleepers also perceived greater stress levels (PSS 22.2±8.4 vs 18.9±6.2, p<0.001), and showed a trend toward less exercise per week (143±134 vs 163±106 minutes, p=0.13).
Conclusion
Participants with insufficient sleep were significantly more overweight on average and were more symptomatic for insufficient sleep. While current approaches to weight management focus largely on diet and physical activity, the data from this study suggest that insufficient sleep should also be considered as a risk factor for obesity and should be incorporated into management plans for obesity.
Support
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Andreev DN, Kim DS, Shishkina LV, Kalinin PL, Astafieva LI, Tropinskaya OF, Voronina IA, Turkin AM, Nazarov VV, Kadashev BA. [Breast cancer metastasis into a giant hormone-inactive pituitary adenoma adenoma. (Clinical case and literature review)]. ZHURNAL VOPROSY NEĬROKHIRURGII IMENI N. N. BURDENKO 2020; 84:55-61. [PMID: 32207743 DOI: 10.17116/neiro20208401155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Brain metastases of various types of cancer are diagnosed in 8-10% of all cancer patients. In the world literature, only 30 cases of cancer metastasis to the pituitary adenoma are described. This article presents yet another observation of a patient with breast cancer metastasis into the hormone-inactive pituitary adenoma at the Burdenko neurosurgical center, Russia The patient underwent endoscopic endonasal transsphenoid removal of the neoplasm. During microscopy and immunohistochemical studies of the biopsy, two types of tissue (pituitary adenoma and cancer metastasis) with different Ki-67 treated surgically (1% and over 40%) were found.
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Lee SH, Park JS, Kim SY, Kim DS, Kim YW, Chung MP, Uh ST, Park CS, Park SW, Jeong SH, Park YB, Lee HL, Shin JW, Lee JH, Jegal Y, Lee HK, Kim YH, Song JW, Park MS. Clinical features and prognosis of patients with idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease. Int J Tuberc Lung Dis 2020; 23:678-684. [PMID: 31315699 DOI: 10.5588/ijtld.18.0194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
<sec> <title>BACKGROUND</title> Idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) share common risk factors. They could therefore be expressed in a single patient. However, the prevalence, clinical characteristics and prognosis of individuals with comorbid IPF and COPD are not known. </sec> <sec> <title>METHOD</title> From 2003 to 2007, the Korean Interstitial Lung Disease Study Group created a register for idiopathic interstitial pneumonia using 2002 ATS/ERS (American Thoracic Society/European Respiratory Society) criteria. Of the 1546 IPF patients assessed, 143 had decreased lung function consistent with COPD (IPF-COPD). COPD was diagnosed based on age (≥40 years) and pulmonary function (forced expiratory volume in 1 sec [FEV1]/forced vital capacity [FVC] ratio < 0.7). </sec> <sec> <title>RESULTS</title> The median age of the IPF-COPD group was 71.0 years (interquartile range 66.0-76.0); most patients were male (88.1%). FVC (%) was significantly higher in the IPF-COPD group; however, FEV1 (%) was significantly lower in the IPF-COPD group (P < 0.001). Diffusing capacity of the lung for carbon monoxide (DLCO) was not significantly different between the two groups. In survival analysis, age and FVC (%), but not COPD, were significantly associated with prognosis (respectively P = 0.003, 0.001 and 0.401). COPD severity was also not related to prognosis (P = 0.935). </sec> <sec> <title>CONCLUSION</title> The prevalence of IPF-COPD was estimated to be ∼9.2% among all IPF patients; prognosis of patients with IPF-COPD was not worse than those with IPF alone. </sec>.
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Ahn D, Song JD, Kang SS, Lim JY, Yang SH, Ko S, Park SH, Park SJ, Kim DS, Chang HJ, Chang J. Intrinsically p-type cuprous iodide semiconductor for hybrid light-emitting diodes. Sci Rep 2020; 10:3995. [PMID: 32132624 PMCID: PMC7055318 DOI: 10.1038/s41598-020-61021-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/17/2020] [Indexed: 11/25/2022] Open
Abstract
Cuprous halides, characterized by a direct wide band-gap and a good lattice matching with Si, is an intrinsic p-type I-VII compound semiconductor. It shows remarkable optoelectronic properties, including a large exciton binding energy at room temperature and a very small piezoelectric coefficient. The major obstacle to its application is the difficulty in growing a single-crystal epitaxial film of cuprous halides. We first demonstrate the single crystal epitaxy of high quality cuprous iodide (CuI) film grown on Si and sapphire substrates by molecular beam epitaxy. Enhanced photoluminescence on the order of magnitude larger than that of GaN and continuous-wave optically pumped lasing were found in MBE grown CuI film. The intrinsic p-type characteristics of CuI were confirmed using an n-AlGaN/p-CuI junction that emits blue light. The discovery will provide an alternative way towards highly efficient optoelectronic devices compatible with both Si and III-nitride technologies.
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Lee JS, Lee JY, Song DW, Bae HS, Doo HM, Yu HS, Lee KJ, Kim HK, Hwang H, Kwak G, Kim D, Kim S, Hong YB, Lee JM, Choi BO. Targeted PMP22 TATA-box editing by CRISPR/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice. Nucleic Acids Res 2020; 48:130-140. [PMID: 31713617 PMCID: PMC7145652 DOI: 10.1093/nar/gkz1070] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/26/2022] Open
Abstract
Charcot-Marie-Tooth 1A (CMT1A) is the most common inherited neuropathy without a known therapy, which is caused by a 1.4 Mb duplication on human chromosome 17, which includes the gene encoding the peripheral myelin protein of 22 kDa (PMP22). Overexpressed PMP22 protein from its gene duplication is thought to cause demyelination and subsequently axonal degeneration in the peripheral nervous system (PNS). Here, we targeted TATA-box of human PMP22 promoter to normalize overexpressed PMP22 level in C22 mice, a mouse model of CMT1A harboring multiple copies of human PMP22. Direct local intraneural delivery of CRISPR/Cas9 designed to target TATA-box of PMP22 before the onset of disease, downregulates gene expression of PMP22 and preserves both myelin and axons. Notably, the same approach was effective in partial rescue of demyelination even after the onset of disease. Collectively, our data present a proof-of-concept that CRISPR/Cas9-mediated targeting of TATA-box can be utilized to treat CMT1A.
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Kudryashev VA, Kim DS. DETERMINATION OF THE TOTAL EFFECTIVE DOSE OF EXTERNAL AND INTERNAL EXPOSURE BY DIFFERENT IONIZING RADIATION SOURCES. RADIATION PROTECTION DOSIMETRY 2019; 187:129-137. [PMID: 31506690 DOI: 10.1093/rpd/ncz170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/28/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
The purpose of the research is to develop an integrated technique for determining the effective dose (E) of external and internal exposure by different sources of ionizing radiation. The proposing technique for determining the total effective dose is based on three methods of calculation. The first one is multiplying the value of the individual dose equivalent $H_{p}(10)$ by the factor of 0.642 to account for radiation shielding by various organs and tissues and its backscattering. The second method is multiplying $H_{p}(10)$ by the conversion factor of air kerma in free air in a plate phantom, depending on the photon energy. The third method is multiplying $H_{p}(10)$ by the sum of the radiosensitivity coefficients of various organs and tissues. As a result of research, a complex method was developed for determining the total effective dose, composed of doses of cosmic radiation, external gamma-, beta- and neutron radiation, internal exposure from radionuclides, including CDP of radon and thoron, entering the body through the organs of digestion and respiration. The proposed technique for determining the total effective dose allows one to take into account the comprehensive effect of ionizing radiation sources on a person and to obtain a more accurate measure of radiation risk than the existing methods provide.
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Park JW, Kim T, Kim D, Hong Y, Gong HS. Measurement of finger joint angle using stretchable carbon nanotube strain sensor. PLoS One 2019; 14:e0225164. [PMID: 31725818 PMCID: PMC6855427 DOI: 10.1371/journal.pone.0225164] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 10/14/2019] [Indexed: 11/18/2022] Open
Abstract
Strain sensors capable of monitoring complex human motions are highly desirable for the development of wearable electronic devices and healthcare monitoring systems. Excellent sensitivity and a wide working range of the sensor material are important requirements for distinguishing dynamic human motion. In this study, a highly stretchable strain sensor was fabricated via inkjet printing of single-walled carbon nanotube (SWCNT) thin films on a stretchable polydimethylsiloxane substrate. The sensor was attached to the metacarpophalangeal (MCP) joint of the hand in 12 healthy male subjects. The subjects placed their hands next to a conventional goniometer and flexed the MCP joint to predetermined angles. A linear relationship was found between the change in the length of the strain sensor and the intended angle of the MCP joint. The fabricated thin films showed high durability during repeated cycling (1,000 cycles) and good sensitivity with a gauge factor of 2.75. This study demonstrates that the newly developed stretchable CNT strain sensor can be used for effectively measuring MCP joint angles. This sensor may also be useful for the analysis of complex and dynamic hand motions that are difficult to measure using a conventional goniometer.
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Jo DH, Song DW, Cho CS, Kim UG, Lee KJ, Lee K, Park SW, Kim D, Kim JH, Kim JS, Kim S, Kim JH, Lee JM. CRISPR-Cas9-mediated therapeutic editing of Rpe65 ameliorates the disease phenotypes in a mouse model of Leber congenital amaurosis. SCIENCE ADVANCES 2019; 5:eaax1210. [PMID: 31692906 PMCID: PMC6821465 DOI: 10.1126/sciadv.aax1210] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/13/2019] [Indexed: 05/12/2023]
Abstract
Leber congenital amaurosis (LCA), one of the leading causes of childhood-onset blindness, is caused by autosomal recessive mutations in several genes including RPE65. In this study, we performed CRISPR-Cas9-mediated therapeutic correction of a disease-associated nonsense mutation in Rpe65 in rd12 mice, a model of human LCA. Subretinal injection of adeno-associated virus carrying CRISPR-Cas9 and donor DNA resulted in >1% homology-directed repair and ~1.6% deletion of the pathogenic stop codon in Rpe65 in retinal pigment epithelial tissues of rd12 mice. The a- and b-waves of electroretinograms were recovered to levels up to 21.2 ± 4.1% and 39.8 ± 3.2% of their wild-type mice counterparts upon bright stimuli after dark adaptation 7 months after injection. There was no definite evidence of histologic perturbation or tumorigenesis during 7 months of observation. Collectively, we present the first therapeutic correction of an Rpe65 nonsense mutation using CRISPR-Cas9, providing new insight for developing therapeutics for LCA.
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Kim D, Luk K, Wolfe SA, Kim JS. Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases. Annu Rev Biochem 2019; 88:191-220. [PMID: 30883196 DOI: 10.1146/annurev-biochem-013118-111730] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Programmable nucleases and deaminases, which include zinc-finger nucleases, transcription activator-like effector nucleases, CRISPR RNA-guided nucleases, and RNA-guided base editors, are now widely employed for the targeted modification of genomes in cells and organisms. These gene-editing tools hold tremendous promise for therapeutic applications. Importantly, these nucleases and deaminases may display off-target activity through the recognition of near-cognate DNA sequences to their target sites, resulting in collateral damage to the genome in the form of local mutagenesis or genomic rearrangements. For therapeutic genome-editing applications with these classes of programmable enzymes, it is essential to measure and limit genome-wide off-target activity. Herein, we discuss the key determinants of off-target activity for these systems. We describe various cell-based and cell-free methods for identifying genome-wide off-target sites and diverse strategies that have been developed for reducing the off-target activity of programmable gene-editing enzymes.
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Kim D, Kim DE, Lee G, Cho SI, Kim JS. Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat Biotechnol 2019; 37:430-435. [PMID: 30833658 DOI: 10.1038/s41587-019-0050-1] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
Adenine base editors1 enable efficient targeted adenine-to-guanine single nucleotide conversions to induce or correct point mutations in human cells, animals, and plants1-4. Here we present a modified version of Digenome-seq, an in vitro method for identifying CRISPR (clustered regularly interspaced short palindromic repeats)-induced double-strand breaks using whole-genome sequencing5-8, to assess genome-wide target specificity of adenine base editors. To produce double-strand breaks at sites containing inosines, the products of adenine deamination, we treat human genomic DNA with an adenine base editor 7.10 protein-guide RNA complex and either endonuclease V or a combination of human alkyladenine DNA glycosylase and endonuclease VIII in vitro. Digenome-seq detects adenine base editor off-target sites with a substitution frequency of 0.1% or more. We show that adenine base editor 7.10, the cytosine base editor BE3, and unmodified CRISPR-associated protein 9 (Cas9) often recognize different off-target sites, highlighting the need for independent assessments of their genome-wide specificities6. Using targeted sequencing, we also show that use of preassembled adenine base editor ribonucleoproteins, modified guide RNAs5,8-11, and Sniper/Cas9 (ref. 12) reduces adenine base editor off-target activity in human cells.
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Yoon J, Joo Y, Oh E, Lee B, Kim D, Lee S, Kim T, Byun J, Hong Y. Soft Modular Electronic Blocks (SMEBs): A Strategy for Tailored Wearable Health-Monitoring Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801682. [PMID: 30886798 PMCID: PMC6402283 DOI: 10.1002/advs.201801682] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/15/2018] [Indexed: 05/09/2023]
Abstract
Precise monitoring of human body signals can be achieved by soft, conformal contact and precise arrangement of wearable devices to the desired body positions. So far, no design and fabrication methodology in soft wearable devices is able to address the variations in the form factor of the human body such as the various sizes and shapes of individual body parts, which can significantly cause misalignments and the corresponding inaccurate monitoring. Here, a concept of soft modular electronic blocks (SMEBs) enabling the assembly of soft wearable systems onto human skin with functions and layouts tailored to the form factors of individuals' bodies is presented. Three types of SMEBs are developed as fundamental building blocks for functional modularization. The physical design of SMEBs is optimized for a mechanically stable island-bridge configuration. The prepared SMEBs can be integrated onto a target body part through rapid, room-temperature (RT) assembly (<5 s) using an oxygen plasma-induced siloxane bonding method. A soft metacarpophalangeal (MP) joints flexion monitoring system that is tailored to allow for accurate monitoring for multiple individuals with unique joint and hand sizes is demonstrated.
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Oh S, Jang JH, Kim HJ, Seo NS, Byun SH, Kim SW, Kim DS. Long-term Follow-up of Complicated Crown Fracture With Fragment Reattachment: Two Case Reports. Oper Dent 2019; 44:574-580. [PMID: 30702408 DOI: 10.2341/18-201-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two cases of complicated crown fracture of the maxillary incisors were restored using the fragment reattachment technique. Root canal treatment was performed, and the fractured fragment was bonded to the tooth structure using a dentin adhesive system and a flowable composite resin, followed by the insertion of a fiber post using dual-cured resin cement. Reattached fragments have shown reliable prognosis without inflammatory signs around bonded junctions after long-term follow-up.
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Kim D, Kim JS. DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA. Genome Res 2018; 28:1894-1900. [PMID: 30413470 PMCID: PMC6280750 DOI: 10.1101/gr.236620.118] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
Abstract
To investigate whether and how CRISPR-Cas9 on-target and off-target activities are affected by chromatin in eukaryotic cells, we first identified a series of identical endogenous DNA sequences present in both open and closed chromatin regions and then measured mutation frequencies at these sites in human cells using Cas9 complexed with matched or mismatched sgRNAs. Unlike matched sgRNAs, mismatched sgRNAs were highly sensitive to chromatin states, suggesting that off-target but not on-target DNA cleavage is hindered by chromatin. We next performed Digenome-seq using cell-free chromatin DNA (now termed DIG-seq) and histone-free genomic DNA in parallel and found that only a subset of sites, cleaved in histone-free DNA, were cut in chromatin DNA, suggesting that chromatin can inhibit Cas9 off-target effects in favor of its genome-wide specificity in cells.
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Shrestha R, Atluri R, Simmons DP, Kim DS, Choi TY. A micro-pipette thermal sensing technique for measuring the thermal conductivity of non-volatile fluids. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:114902. [PMID: 30501312 DOI: 10.1063/1.5044214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
This research work demonstrates an innovative technique to measure the thermal conductivity of a small volume of non-volatile liquids. The method utilizes a micro-pipette thermal sensor (MPTS) (tip diameter < 2 μm) and is based on laser point heating thermometry and transient heat transfer. A laser beam is irradiated at the sensor tip immersed in a few microliters of the test fluid and the transient temperature change is recorded with the sensor. This temperature change is dependent on the surrounding fluid's thermal properties, such as thermal conductivity and diffusivity. The numerical solution for transient temperature profile for a point source is obtained using the finite element method in the COMSOL software. To determine the optimizing parameters such as thermal conductivity and power absorbed at the sensor tip, the multi-parameter fitting technique is used in MATLAB, which will fit the COMSOL simulation result with the experimental data. Three liquids with known thermal conductivity were tested to verify that the technique can be used to determine the thermal conductivity with high accuracy, and in addition, the thermal conductivity of growth media and serum used for culturing cancer cells is estimated. With the sensor size of 1-2 μm, we demonstrate the possibility of using this described method as the MPTS technique for measuring the thermal properties of microfluidic samples and biological fluids.
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Heo JS, Kim KT, Ban SG, Kim YJ, Kim D, Kim T, Hong Y, Kim IS, Park SK. Stable Logic Operation of Fiber-Based Single-Walled Carbon Nanotube Transistor Circuits Toward Thread-Like CMOS Circuitry. MATERIALS 2018; 11:ma11101878. [PMID: 30275425 PMCID: PMC6213233 DOI: 10.3390/ma11101878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/23/2018] [Accepted: 09/25/2018] [Indexed: 11/25/2022]
Abstract
A fiber-based single-walled carbon nanotube (SWCNT) thin-film-transistor (TFT) has been proposed. We designed complementary SWCNT TFT circuit based on SPICE simulations, with device parameters extracted from the fabricated fiber-based SWCNT TFTs, such as threshold voltage, contact resistance, and off-/gate-leakage current. We fabricated the SWCNTs CMOS inverter circuits using the selective passivation and n-doping processes on a fiber substrate. By comparing the simulation and experimental results, we could enhance the circuit’s performance by tuning the threshold voltage between p-type and n-type TFTs, reducing the source/drain contact resistance and off current level, and maintaining a low output capacitance of the TFTs. Importantly, it was found that the voltage gain, output swing range, and frequency response of the fiber-based inverter circuits can be dramatically improved.
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Jang JH, Kim HY, Shin SM, Lee CO, Kim DS, Choi KK, Kim SY. Clinical Effectiveness of Different Polishing Systems and Self-Etch Adhesives in Class V Composite Resin Restorations: Two-Year Randomized Controlled Clinical Trial. Oper Dent 2018; 42:19-29. [PMID: 28002695 DOI: 10.2341/16-104-c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this randomized controlled clinical trial was to compare the clinical effectiveness of different polishing systems and self-etch adhesives in class V composite resin restorations. A total of 164 noncarious cervical lesions (NCCLs) from 35 patients were randomly allocated to one of four experimental groups, each of which used a combination of polishing systems and adhesives. The two polishing systems used were Sof-Lex XT (Sof), a multistep abrasive disc, and Enhance/Pogo (EP), a simplified abrasive-impregnated rubber instrument. The adhesive systems were Clearfil SE bond (CS), a two-step self-etch adhesive, and Xeno V (XE), a one-step self-etch adhesive. All NCCLs were restored with light-cured microhybrid resin composites (Z250). Restorations were evaluated at baseline and at 6, 12, 18, and 24 months by two blinded independent examiners using modified FDI criteria. The Fisher exact test and generalized estimating equation analysis considering repeated measurements were performed to compare the outcomes between the polishing systems and adhesives. Three restorations were dislodged: two in CS/Sof and one in CS/EP. None of the restorations required any repair or retreatment except those showing retention loss. Sof was superior to EP with regard to surface luster, staining, and marginal adaptation (p<0.05). CS and XE did not show differences in any criteria (p>0.05). Sof is clinically superior to EP for polishing performance in class V composite resin restoration. XE demonstrates clinically equivalent bonding performance to CS.
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Ma H, Marti-Gutierrez N, Park SW, Wu J, Hayama T, Darby H, Van Dyken C, Li Y, Koski A, Liang D, Suzuki K, Gu Y, Gong J, Xu X, Ahmed R, Lee Y, Kang E, Ji D, Park AR, Kim D, Kim ST, Heitner SB, Battaglia D, Krieg SA, Lee DM, Wu DH, Wolf DP, Amato P, Kaul S, Belmonte JCI, Kim JS, Mitalipov S. Ma et al. reply. Nature 2018; 560:E10-E23. [DOI: 10.1038/s41586-018-0381-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Lee JK, Jeong E, Lee J, Jung M, Shin E, Kim YH, Lee K, Jung I, Kim D, Kim S, Kim JS. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun 2018; 9:3048. [PMID: 30082838 PMCID: PMC6078992 DOI: 10.1038/s41467-018-05477-x] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/09/2018] [Indexed: 12/26/2022] Open
Abstract
The use of CRISPR-Cas9 as a therapeutic reagent is hampered by its off-target effects. Although rationally designed S. pyogenes Cas9 (SpCas9) variants that display higher specificities than the wild-type SpCas9 protein are available, these attenuated Cas9 variants are often poorly efficient in human cells. Here, we develop a directed evolution approach in E. coli to obtain Sniper-Cas9, which shows high specificities without killing on-target activities in human cells. Unlike other engineered Cas9 variants, Sniper-Cas9 shows WT-level on-target activities with extended or truncated sgRNAs with further reduced off-target activities and works well in a preassembled ribonucleoprotein (RNP) format to allow DNA-free genome editing.
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Ishii H, Mihai R, Watkinson JC, Kim DS. Systematic review of cure and recurrence rates following minimally invasive parathyroidectomy. BJS Open 2018; 2:364-370. [PMID: 30511037 PMCID: PMC6254009 DOI: 10.1002/bjs5.77] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/03/2018] [Indexed: 11/28/2022] Open
Abstract
Background The majority of patients with primary hyperparathyroidism (PHPT) have a single overactive adenoma. Advances in preoperative imaging and surgical adjuncts have given rise to minimally invasive parathyroidectomy (MIP), with lower complication rates in comparison with bilateral neck exploration. Misdiagnosis and undertreatment of multiglandular disease, leading to potentially higher recurrence rates, remains a concern. This study evaluated risks of long‐term (1 year or more) recurrence following ‘targeted’ MIP in PHPT. Methods Multiple databases were searched for studies published between January 2004 and March 2017, looking at long‐term outcomes (1 year or more) following targeted MIP for PHPT. English‐language studies, with at least 50 patients and a mean follow‐up of 1 year, were included. Results A total of 5282 patients from 14 studies were included. Overall mean recurrence and cure rates were 1·6 (range 0–3·5) and 96·9 (95·5–100) per cent respectively. Mean follow‐up was 33·5 (1–145) months. When intraoperative parathyroid hormone (PTH) measurements were not done, cure rates were higher (99·3 per cent versus 98·1 per cent with use of intraoperative PTH measurement; P < 0·001) and recurrence rates lower (0·2 versus 1·5 per cent respectively; P < 0·001). Conclusion Targeted MIP for a presumed single overactive adenoma was associated with very low recurrence rates, without the need for intraoperative PTH measurement when preoperative imaging studies were concordant. Targeted MIP should be encouraged.
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Koo T, Park SW, Jo DH, Kim D, Kim JH, Cho HY, Kim J, Kim JH, Kim JS. CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration. Nat Commun 2018; 9:1855. [PMID: 29748595 PMCID: PMC5945874 DOI: 10.1038/s41467-018-04175-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/06/2018] [Indexed: 12/26/2022] Open
Abstract
LbCpf1, derived from Lachnospiraceae bacterium ND2006, is a CRISPR RNA-guided endonuclease and holds promise for therapeutic applications. Here we show that LbCpf1 can be used for therapeutic gene editing in a mouse model of age-related macular degeneration (AMD). The intravitreal delivery of LbCpf1, targeted to two angiogenesis-associated genes encoding vascular endothelial growth factor A (Vegfa) and hypoxia inducing factor 1a (Hif1a), using adeno-associated virus, led to efficient gene disruption with no apparent off-target effects in the retina and retinal pigment epithelium (RPE) cells. Importantly, LbCpf1 targeted to Vegfa or Hif1a in RPE cells reduced the area of laser-induced choroidal neovascularization as efficiently as aflibercept, an anti-VEGF drug currently used in the clinic, without inducing cone dysfunction. Unlike aflibercept, LbCpf1 targeted to Vegfa or Hif1a achieved a long-term therapeutic effect on CNV, potentially avoiding repetitive injections. Taken together, these results indicate that LbCpf1-mediated in vivo genome editing to ablate pathologic angiogenesis provides an effective strategy for the treatment of AMD and other neovascularization-associated diseases.
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Georgiadis C, Preece R, Nickolay L, Etuk A, Petrova A, Ladon D, Danyi A, Humphryes-Kirilov N, Ajetunmobi A, Kim D, Kim JS, Qasim W. Long Terminal Repeat CRISPR-CAR-Coupled "Universal" T Cells Mediate Potent Anti-leukemic Effects. Mol Ther 2018; 26:1215-1227. [PMID: 29605708 PMCID: PMC5993944 DOI: 10.1016/j.ymthe.2018.02.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/25/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
Gene editing can be used to overcome allo-recognition, which otherwise limits allogeneic T cell therapies. Initial proof-of-concept applications have included generation of such "universal" T cells expressing chimeric antigen receptors (CARs) against CD19 target antigens combined with transient expression of DNA-targeting nucleases to disrupt the T cell receptor alpha constant chain (TRAC). Although relatively efficient, transgene expression and editing effects were unlinked, yields variable, and resulting T cell populations heterogeneous, complicating dosing strategies. We describe a self-inactivating lentiviral "terminal" vector platform coupling CAR expression with CRISPR/Cas9 effects through incorporation of an sgRNA element into the ΔU3 3' long terminal repeat (LTR). Following reverse transcription and duplication of the hybrid ΔU3-sgRNA, delivery of Cas9 mRNA resulted in targeted TRAC locus cleavage and allowed the enrichment of highly homogeneous (>96%) CAR+ (>99%) TCR- populations by automated magnetic separation. Molecular analyses, including NGS, WGS, and Digenome-seq, verified on-target specificity with no evidence of predicted off-target events. Robust anti-leukemic effects were demonstrated in humanized immunodeficient mice and were sustained longer than by conventional CAR+TCR+ T cells. Terminal-TRAC (TT) CAR T cells offer the possibility of a pre-manufactured, non-HLA-matched CAR cell therapy and will be evaluated in phase 1 trials against B cell malignancies shortly.
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Kim DS, Son E, Lee YS, Lee YM, Park YH, Kim DH, Lee KW. Herbal Complex DKB114 for Hyperuricemia and Gout. Am J Transl Res 2018. [DOI: 10.1055/s-0038-1644979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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