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Lee JY, Bentzon R, Di Nucci E. What Is A Family? A Constitutive-Affirmative Account. J Bioeth Inq 2024:10.1007/s11673-024-10339-x. [PMID: 38528309 DOI: 10.1007/s11673-024-10339-x] [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] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/25/2024] [Indexed: 03/27/2024]
Abstract
Bio-heteronormative conceptions of the family have long reinforced a nuclear ideal of the family as a heterosexual marriage, with children who are the genetic progeny of that union. This ideal, however, has also long been resisted in light of recent social developments, exhibited through the increased incidence and acceptance of step-families, donor-conceived families, and so forth. Although to this end some might claim that the bio-heteronormative ideal is not necessary for a social unit to count as a family, a more systematic conceptualization of the family-the kind of family that matters morally-is relatively underexplored in the philosophical literature. This paper makes a start at developing and defending an account of the family that is normatively attractive and in line with the growing prevalence of non-conventional families and methods of family-formation. Our account, which we call a constitutive-affirmative model of the family, takes the family to be constituted by an ongoing process of relevant affective and affirmative relations between the putative family members.
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Affiliation(s)
- J Y Lee
- University of Copenhagen, Øster Farimagsgade 5, København K, Denmark.
| | - R Bentzon
- University of Copenhagen, Øster Farimagsgade 5, København K, Denmark
| | - E Di Nucci
- University of Copenhagen, Øster Farimagsgade 5, København K, Denmark
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2
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Kim SJ, Jo Y, Park SJ, Ji E, Lee JY, Choi E, Baek JY, Jang IY, Jung HW, Kim K, Ryu D, Yoo HJ, Kim BJ. Metabolomic profiles of ovariectomized mice and their associations with body composition and frailty-related parameters in postmenopausal women. J Endocrinol Invest 2024:10.1007/s40618-024-02338-x. [PMID: 38493245 DOI: 10.1007/s40618-024-02338-x] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/12/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Menopause, a dramatical estrogen-deficient condition, is considered the most significant milestone in women's health. PURPOSE To investigate the metabolite changes attributed to estrogen deficiency using random forest (RF)-based machine learning (ML) modeling strategy in ovariectomized (OVX) mice as well as determine the clinical relevance of selected metabolites in older women. METHODS AND RESULTS Untargeted and targeted metabolomic analyses revealed that metabolites related to TCA cycle, sphingolipids, phospholipids, fatty acids, and amino acids, were significantly changed in the plasma and/or muscle of OVX mice. Subsequent ML classifiers based on RF algorithm selected alpha-ketoglutarate (AKG), arginine, carnosine, ceramide C24, phosphatidylcholine (PC) aa C36:6, and PC ae C42:3 in plasma as well as PC aa 34:1, PC aa C34:3, PC aa C36:5, PC aa C32:1, PC aa C36:2, and sphingosine in muscle as top featured metabolites that differentiate the OVX mice from the sham-operated group. When circulating levels of AKG, arginine, and carnosine, which showed the most significant changes in OVX mice blood, were measured in postmenopausal women, higher plasma AKG levels were associated with lower bone mass, weak grip strength, poor physical performance, and increased frailty risk. CONCLUSIONS Metabolomics- and ML-based methods identified the key metabolites of blood and muscle that were significantly changed after ovariectomy in mice, and the clinical implication of several metabolites was investigated by looking at their correlation with body composition and frailty-related parameters in postmenopausal women. These findings provide crucial context for understanding the diverse physiological alterations caused by estrogen deficiency in women.
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Affiliation(s)
- S J Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center,, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea
| | - Y Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - S J Park
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - E Ji
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - J Y Lee
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - E Choi
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - J-Y Baek
- Division of Geriatrics, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - I Y Jang
- Division of Geriatrics, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - H-W Jung
- Division of Geriatrics, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - K Kim
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - D Ryu
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
| | - H J Yoo
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center,, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea.
| | - B-J Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea.
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Vitko D, Chou WF, Nouri Golmaei S, Lee JY, Belthangady C, Blume J, Chan JK, Flores-Campuzano G, Hu Y, Liu M, Marispini MA, Mora MG, Ramaswamy S, Ranjan P, Williams PB, Zawada RJX, Ma P, Wilcox BE. timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery. J Proteome Res 2024; 23:929-938. [PMID: 38225219 PMCID: PMC10913052 DOI: 10.1021/acs.jproteome.3c00646] [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: 10/03/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Mass spectrometry (MS) is a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide-ranging plasma protein concentrations, along with technical and biological variabilities, present significant challenges for deep and reproducible protein quantitation. Here, we evaluated the qualitative and quantitative performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for analysis of neat plasma samples (unfractionated) and plasma samples processed using the Proteograph Product Suite (Proteograph) that enables robust deep proteomics sampling prior to mass spectrometry. Samples were evaluated across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV < 20%) with timsTOF HT compared to Pro 2. Additionally, approximately 4.5 fold more plasma peptide precursors were detected by both timsTOF HT and timsTOF Pro 2 in the Proteograph analyzed plasma vs neat plasma. In an exploratory analysis of 20 late-stage lung cancer and 20 control plasma samples with the Proteograph, which were expected to exhibit distinct proteomes, an approximate 50% increase in total and statistically significant plasma peptide precursors (q < 0.05) was observed with timsTOF HT compared to Pro 2. Our data demonstrate the superior performance of timsTOF HT for identifying and quantifying differences between biologically diverse samples, allowing for improved disease biomarker discovery in large cohort studies. Moreover, researchers can leverage data sets from this study to optimize their liquid chromatography-mass spectrometry (LC-MS) workflows for plasma protein profiling and biomarker discovery. (ProteomeXchange identifier: PXD047854 and PXD047839).
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Affiliation(s)
- Dijana Vitko
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Wan-Fang Chou
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Sara Nouri Golmaei
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Joon-Yong Lee
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Chinmay Belthangady
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - John Blume
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Jessica K. Chan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | | | - Yuntao Hu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Manway Liu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Mark A. Marispini
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Megan G. Mora
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Saividya Ramaswamy
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Purva Ranjan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Preston B. Williams
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Robert J. X. Zawada
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Philip Ma
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Bruce E. Wilcox
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
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Chiang KS, Chang YM, Liu HI, Lee JY, Jarroudi ME, Bock CH. Survival Analysis as a Basis for Testing Hypotheses when Using Quantitative Ordinal Scale Disease Severity Data. Phytopathology 2024; 114:378-392. [PMID: 37606348 DOI: 10.1094/phyto-02-23-0055-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Disease severity in plant pathology is often measured by the amount of a plant or plant part that exhibits disease symptoms. This is typically assessed using a numerical scale, which allows a standardized, convenient, and quick method of rating. These scales, known as quantitative ordinal scales (QOS), divide the percentage scale into a predetermined number of intervals. There are various ways to analyze these ordinal data, with traditional methods involving the use of midpoint conversion to represent the interval. However, this may not be precise enough, as it is only an estimate of the true value. In this case, the data may be considered interval-censored, meaning that we have some knowledge of the value but not an exact measurement. This type of uncertainty is known as censoring, and techniques that address censoring, such as survival analysis (SA), use all available information and account for this uncertainty. To investigate the pros and cons of using SA with QOS measurements, we conducted a simulation based on three pathosystems. The results showed that SA almost always outperformed midpoint conversion with data analyzed using a t test, particularly when data were not normally distributed. Midpoint conversion is currently a standard procedure. In certain cases, the midpoint approach required a 400% increase in sample size to achieve the same power as the SA method. However, as the mean severity increases, fewer additional samples are needed (approximately an additional 100%), regardless of the assessment method used. Based on these findings, we conclude that SA is a valuable method for enhancing the power of hypothesis testing when analyzing QOS severity data. Future research should investigate the wider use of survival analysis techniques in plant pathology and their potential applications in the discipline.
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Affiliation(s)
- K S Chiang
- Division of Biometrics, Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Y M Chang
- Department of Statistics, Tunghai University, Taichung 407, Taiwan
| | - H I Liu
- Bachelor Program in Industrial Artificial Intelligence, Ming Chi University of Technology, New Taipei City 243, Taiwan
| | - J Y Lee
- Department of Statistics, Feng Chia University, Taichung 407, Taiwan
| | - M El Jarroudi
- University of Liège, Department of Environmental Sciences and Management, SPHERES Research Unit, Arlon, Belgium
| | - C H Bock
- U.S. Department of Agriculture-Agricultural Research Service-SEFTNRL, Byron, GA 31008, U.S.A
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Adhikari G, Carlin N, Choi JJ, Choi S, Ezeribe AC, França LE, Ha C, Hahn IS, Hollick SJ, Jeon EJ, Jo JH, Joo HW, Kang WG, Kauer M, Kim BH, Kim HJ, Kim J, Kim KW, Kim SH, Kim SK, Kim WK, Kim YD, Kim YH, Ko YJ, Lee DH, Lee EK, Lee H, Lee HS, Lee HY, Lee IS, Lee J, Lee JY, Lee MH, Lee SH, Lee SM, Lee YJ, Leonard DS, Luan NT, Manzato BB, Maruyama RH, Neal RJ, Nikkel JA, Olsen SL, Park BJ, Park HK, Park HS, Park KS, Park SD, Pitta RLC, Prihtiadi H, Ra SJ, Rott C, Shin KA, Cavalcante DFFS, Scarff A, Spooner NJC, Thompson WG, Yang L, Yu GH. Search for Boosted Dark Matter in COSINE-100. Phys Rev Lett 2023; 131:201802. [PMID: 38039466 DOI: 10.1103/physrevlett.131.201802] [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: 06/01/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023]
Abstract
We search for energetic electron recoil signals induced by boosted dark matter (BDM) from the galactic center using the COSINE-100 array of NaI(Tl) crystal detectors at the Yangyang Underground Laboratory. The signal would be an excess of events with energies above 4 MeV over the well-understood background. Because no excess of events are observed in a 97.7 kg·yr exposure, we set limits on BDM interactions under a variety of hypotheses. Notably, we explored the dark photon parameter space, leading to competitive limits compared to direct dark photon search experiments, particularly for dark photon masses below 4 MeV and considering the invisible decay mode. Furthermore, by comparing our results with a previous BDM search conducted by the Super-Kamionkande experiment, we found that the COSINE-100 detector has advantages in searching for low-mass dark matter. This analysis demonstrates the potential of the COSINE-100 detector to search for MeV electron recoil signals produced by the dark sector particle interactions.
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Affiliation(s)
- G Adhikari
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - N Carlin
- Physics Institute, University of São Paulo, 05508-090, São Paulo, Brazil
| | - J J Choi
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - S Choi
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - A C Ezeribe
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - L E França
- Physics Institute, University of São Paulo, 05508-090, São Paulo, Brazil
| | - C Ha
- Department of Physics, Chung-Ang University, Seoul 06973, Republic of Korea
| | - I S Hahn
- Department of Science Education, Ewha Womans University, Seoul 03760, Republic of Korea
- Center for Exotic Nuclear Studies, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - S J Hollick
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - E J Jeon
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - J H Jo
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - H W Joo
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - W G Kang
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - M Kauer
- Department of Physics and Wisconsin IceCube Particle Astrophysics Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - B H Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - H J Kim
- Department of Physics, Kyungpook National University, Daegu 41566, Republic of Korea
| | - J Kim
- Department of Physics, Chung-Ang University, Seoul 06973, Republic of Korea
| | - K W Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - S H Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - S K Kim
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - W K Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Y D Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Physics, Sejong University, Seoul 05006, Republic of Korea
| | - Y H Kim
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Y J Ko
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - D H Lee
- Department of Physics, Kyungpook National University, Daegu 41566, Republic of Korea
| | - E K Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - H Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - H S Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - H Y Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - I S Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - J Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - J Y Lee
- Department of Physics, Kyungpook National University, Daegu 41566, Republic of Korea
| | - M H Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - S H Lee
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - S M Lee
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Y J Lee
- Department of Physics, Chung-Ang University, Seoul 06973, Republic of Korea
| | - D S Leonard
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - N T Luan
- Department of Physics, Kyungpook National University, Daegu 41566, Republic of Korea
| | - B B Manzato
- Physics Institute, University of São Paulo, 05508-090, São Paulo, Brazil
| | - R H Maruyama
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - R J Neal
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - J A Nikkel
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - S L Olsen
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - B J Park
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - H K Park
- Department of Accelerator Science, Korea University, Sejong 30019, Republic of Korea
| | - H S Park
- Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - K S Park
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - S D Park
- Department of Physics, Kyungpook National University, Daegu 41566, Republic of Korea
| | - R L C Pitta
- Physics Institute, University of São Paulo, 05508-090, São Paulo, Brazil
| | - H Prihtiadi
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - S J Ra
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - C Rott
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Physics and Astronomy, University of Utah, Salt Lake City, Utah 84112, USA
| | - K A Shin
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - D F F S Cavalcante
- Physics Institute, University of São Paulo, 05508-090, São Paulo, Brazil
| | - A Scarff
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - N J C Spooner
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - W G Thompson
- Department of Physics and Wright Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - L Yang
- Department of Physics, University of California San Diego, La Jolla, California 92093, USA
| | - G H Yu
- Center for Underground Physics, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
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6
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Lee JY, Dess RT, Zelefsky MJ, Davis BJ, Horwitz EM, Cooperberg MR, Zaorsky NG, Jia AY, Sandler HM, Efstathiou JA, Pisansky TM, Hall E, Tree A, Roy S, Bolla M, Nabid A, Zapatero A, Kishan AU, Spratt DE, Sun Y. Individual Patient Data Analysis of 17 Randomized Trials vs. Real-World Data for Men with Localized Prostate Cancer Receiving Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e404-e405. [PMID: 37785347 DOI: 10.1016/j.ijrobp.2023.06.1543] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Prior work has demonstrated poor correlation between the results of randomized controlled trials (RCTs) and real-world evidence (RWD). However, patients enrolled in RCTs are often considered to poorly represent the real-world population. Herein, we utilize multiple large data repositories to determine differences in baseline characteristics and long-term outcomes between patients enrolled in RCTs and RWD that received radiotherapy for localized prostate cancer. MATERIALS/METHODS Meta-Analysis of Randomized trials in Cancer of the Prostate (MARCAP) Consortium was leveraged, and 17 phase III randomized trials were included. RWD were accessed through the Staging Collaboration for Cancer of the Prostate (STAR-CAP) cohort, a cohort that is comprised of >60 centers across the United States and Europe. Additionally, RWD was assessed via the Surveillance, Epidemiology, and End Results (SEER) database. MARCAP and STAR-CAP both contain outcomes for distant metastasis (DM), metastasis-free survival (MFS), prostate cancer-specific mortality (PCSM), and overall survival (OS). SEER only contains PCSM and OS. Wilcoxon signed-rank test and chi-square test were used to compare continuous and categorical variables, respectively. Inverse probability of treatment weighting (IPTW) analysis was conducted, balancing for age, PSA, Gleason score, T stage, and treatment year in the three cohorts. Cox and Fine-Gray regression models were used to compare disease outcomes between RCTs vs. RWD. RESULTS Data from 10,666 patients from RCTs, 6,530 patients in STAR-CAP, and 117,586 patients in SEER were included. SEER patients were slightly younger (p<0.001, median age 68 (IQR 62-73) than those in RCTs (70, IQR 65-74) and in STAR-CAP (70, IQR 64-74). 10-year OS in RCTs was 65.4%, STAR-CAP 70.2%, SEER 64.1%. OS was superior in STAR-CAP (RCTs as reference; HR 0.91, 95% CI 0.85-0.96, p<0.0001), but there was no significant difference between SEER and RCTs (HR 0.96, 95% CI 0.91-1.02, p = 0.22). 10-year PCSM cumulative incidence was 7.4% in RCTs, 8.1% in STAR-CAP, and 11.0% in SEER. There was no significant difference in PCSM between STAR-CAP RWD and RCTs (HR 0.88, 95% CI 0.78-1.01, p = 0.08), whereas PCSM was worse in SEER than RCTs (HR 1.37, 95% CI 1.21-1.55, p<0.0001). There was no significant difference in DM between STAR-CAP RWD and RCTs (HR 0.93, 95% CI 0.83-1.04, p = 0.2). CONCLUSION While baseline differences exist in patients enrolled on localized prostate cancer RCTs and real-world datasets, there were small if any significant relative differences in oncologic outcomes. This provides reassurance that RCT results are generally applicable to patients in routine practice.
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Affiliation(s)
- J Y Lee
- Case Western Reserve University School of Medicine, Cleveland, OH; University Hospitals Cleveland Medical Center, Cleveland, OH
| | - R T Dess
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - M J Zelefsky
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - B J Davis
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - E M Horwitz
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | - M R Cooperberg
- University of California, San Francisco, San Francisco, CA
| | - N G Zaorsky
- University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH
| | - A Y Jia
- Weill Cornell Medical College/New York Presbyterian Hospital, New York, NY
| | - H M Sandler
- Cedars-Sinai Medical Center, Los Angeles, CA
| | - J A Efstathiou
- Department of Radiation Oncology, Harvard School of Medicine, Boston, MA
| | - T M Pisansky
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - E Hall
- The Institute of Cancer Research, Clinical Trials and Statistics Unit, London, United Kingdom
| | - A Tree
- Radiotherapy and Imaging Division, Institute of Cancer Research, London, United Kingdom
| | - S Roy
- Rush University Medical Centre, Chicago, IL
| | - M Bolla
- Department of Radiation Oncology. CHU Grenoble, Grenoble, France
| | - A Nabid
- Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - A Zapatero
- Hospital Universitario de La Princesa, Madrid, Spain
| | - A U Kishan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA
| | - D E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center and Case Western Reserve University, Cleveland, OH
| | - Y Sun
- University Hospitals Seidman Cancer Center, Case Western Reserve School of Medicine, Cleveland, OH
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Scior K, Patel M, Goldsmith-Sumner A, Hayden N, Lee JY, Lunsky Y, Osborne M, Richardson L, Stewart-Brown S, Hastings RP. Development and initial psychometric properties of the Warwick-Edinburgh Mental Wellbeing Scale-Intellectual Disability version. J Intellect Disabil Res 2023; 67:893-900. [PMID: 37129069 DOI: 10.1111/jir.13039] [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] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS; Tennant et al., 2007) is yet to be validated in the intellectual disability (ID) population. The aim of this study was to report the development process and assess the psychometric properties of a newly adapted version of the WEMWBS and the Short WEMWBS for individuals with mild to moderate IDs (WEMWBS-ID/SWEMWBS-ID). METHOD The WEMWBS item wordings and response options were revised by clinicians and researchers expert in the field of ID, and a visual aid was added to the scale. The adapted version was reviewed by 10 individuals with IDs. The measure was administered by researchers online using screenshare, to individuals aged 16+ years with mild to moderate IDs. Data from three UK samples were collated to evaluate the WEMWBS-ID (n = 96). A subsample (n = 22) completed the measure again 1 to 2 weeks later to assess test-retest reliability, and 95 participants additionally completed an adapted version of the adapted Rosenberg Self-Esteem Scale to examine convergent validity. Additional data from a Canadian sample (n = 27) were used to evaluate the SWEMWBS-ID (n = 123). RESULTS The WEMWBS-ID demonstrated good internal consistency (ω = 0.77-0.87), excellent test-retest reliability [intraclass correlation coefficient (ICC) = .88] and good convergent validity with the self-esteem scale (r = .48-.60) across samples. A confirmatory factor analysis for a single factor model demonstrated an adequate fit. The SWEMWBS-ID showed poor to good internal consistency (ω = 0.36-0.74), moderate test-retest reliability (ICC = .67) and good convergent validity (r = .48-.60) across samples, and a confirmatory factor analysis indicated good model fit for a single factor structure. CONCLUSIONS The WEMWBS-ID and short version demonstrated promising psychometric properties, when administered virtually by a researcher. Further exploration of the scales with larger, representative samples is warranted.
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Affiliation(s)
- K Scior
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - M Patel
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - A Goldsmith-Sumner
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - N Hayden
- CEDAR, University of Warwick, Coventry, UK
| | - J Y Lee
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Y Lunsky
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - M Osborne
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - L Richardson
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
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Lee JY. Consent and the problem of epistemic injustice in obstetric care. J Med Ethics 2023; 49:618-619. [PMID: 37344201 DOI: 10.1136/jme-2023-109156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Affiliation(s)
- J Y Lee
- University of Copenhagen, Kobenhavn 1017, Denmark
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Heo E, Jeong Y, Heo KN, Kim H, Kang HR, Park SK, Lee JY. Impact of β-lactam allergies on antibiotic use, clinical outcomes, and economic costs in patients receiving surgical prophylactic antibiotics. J Hosp Infect 2023; 139:249-250. [PMID: 37286106 DOI: 10.1016/j.jhin.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Affiliation(s)
- E Heo
- Department of Pharmacy, Seoul National University Bundang Hospital, Seongnam, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Y Jeong
- Department of Pharmacy, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - K N Heo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - H Kim
- Regional Pharmacovigilance Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - H R Kang
- Regional Pharmacovigilance Center, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - S K Park
- College of Pharmacy, The Catholic University of Korea, Bucheon, Republic of Korea
| | - J Y Lee
- Department of Pharmacy, Seoul National University Bundang Hospital, Seongnam, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
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Lee JY. Who should provide the uterus? The ethics of live donor recruitment for uterus transplantation. J Med Ethics 2023:jme-2023-109227. [PMID: 37640534 DOI: 10.1136/jme-2023-109227] [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] [Received: 04/29/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Uterus transplantation (UTx) is an experimental surgery likely to face the issue of organ shortage. In my article, I explore how this issue might be addressed by changing the prevailing practices around live uterus donor recruitment. Currently, women with children - often the mothers of recipients - tend to be overrepresented as donors. Yet, other potentially eligible groups who may have an interest in providing their uterus - such as transgender men, or cisgender women who do not wish to gestate or to have children - tend to be excluded as potential donors. Moving forward, I recommend that donor inclusion criteria for UTx be broadened to be more inclusive of these latter groups.
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Affiliation(s)
- J Y Lee
- Department of Public Health, University of Copenhagen, Kobenhavn 1172, Denmark
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Hyung J, Lee JY, Kim JE, Yoon S, Yoo C, Hong YS, Jeong JH, Kim TW, Jeon S, Jun HR, Jung CK, Jang JP, Kim J, Chun SM, Ahn JH. Safety and efficacy of trastuzumab biosimilar plus irinotecan or gemcitabine in patients with previously treated HER2 (ERBB2)-positive non-breast/non-gastric solid tumors: a phase II basket trial with circulating tumor DNA analysis. ESMO Open 2023; 8:101583. [PMID: 37327700 DOI: 10.1016/j.esmoop.2023.101583] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Human epidermal growth factor receptor 2 (HER2) (ERBB2)-directed agents are standard treatments for patients with HER2-positive breast and gastric cancer. Herein, we report the results of an open-label, single-center, phase II basket trial to investigate the efficacy and safety of trastuzumab biosimilar (Samfenet®) plus treatment of physician's choice for patients with previously treated HER2-positive advanced solid tumors, along with biomarker analysis employing circulating tumor DNA (ctDNA) sequencing. METHODS Patients with HER2-positive unresectable or metastatic non-breast, non-gastric solid tumors who failed at least one prior treatment were included in this study conducted at Asan Medical Center, Seoul, Korea. Patients received trastuzumab combined with irinotecan or gemcitabine at the treating physicians' discretion. The primary endpoint was the objective response rate as per RECIST version 1.1. Plasma samples were collected at baseline and at the time of disease progression for ctDNA analysis. RESULTS Twenty-three patients were screened from 31 December 2019 to 17 September 2021, and 20 were enrolled in this study. Their median age was 64 years (30-84 years), and 13 patients (65.0%) were male. The most common primary tumor was hepatobiliary cancer (seven patients, 35.0%), followed by colorectal cancer (six patients, 30.0%). Among 18 patients with an available response evaluation, the objective response rate was 11.1% (95% confidence interval 3.1% to 32.8%). ERBB2 amplification was detected from ctDNA analysis of baseline plasma samples in 85% of patients (n = 17), and the ERBB2 copy number from ctDNA analysis showed a significant correlation with the results from tissue sequencing. Among 16 patients with post-progression ctDNA analysis, 7 (43.8%) developed new alterations. None of the patients discontinued the study due to adverse events. CONCLUSIONS Trastuzumab plus irinotecan or gemcitabine was safe and feasible for patients with previously treated HER2-positive advanced solid tumors with modest efficacy outcomes, and ctDNA analysis was useful for detecting HER2 amplification.
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Affiliation(s)
- J Hyung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - J Y Lee
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul; Asan Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul
| | - J E Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - S Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - C Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Y S Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - J H Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - T W Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - S Jeon
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul; Asan Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul
| | - H R Jun
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul; Asan Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul
| | | | | | - J Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - S M Chun
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul; Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - J H Ahn
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul.
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Ross D, Bilbao A, Lee JY, Zheng X. mzapy: An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format. Anal Chem 2023. [PMID: 37307589 DOI: 10.1021/acs.analchem.3c01653] [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: 06/14/2023]
Abstract
Analysis of ion mobility spectrometry (IMS) data has been challenging and limited the full utility of these measurements. Unlike liquid chromatography-mass spectrometry, where a plethora of tools with well-established algorithms exist, the incorporation of the additional IMS dimension requires upgrading existing computational pipelines and developing new algorithms to fully exploit the advantages of the technology. We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of core libraries in popular programming languages with standard mass spectrometry utilities will facilitate fast software development and broader adoption of the format. To this end, we present a Python package, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format, especially for complex data containing ion mobility spectrometry dimension. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python and having minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multiomics domain. The mzapy package is free and open-source, includes comprehensive documentation, and is structured to support future extension to meet the evolving needs of the MS community. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.
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Affiliation(s)
- Dylan Ross
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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13
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Lee JY, Patel M, Scior K. Self-esteem and its relationship with depression and anxiety in adults with intellectual disabilities: a systematic literature review. J Intellect Disabil Res 2023; 67:499-518. [PMID: 36855028 DOI: 10.1111/jir.13025] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In the general population, low self-esteem has been linked with poorer mental and physical health. This systematic literature review aimed to summarise and evaluate the findings of studies that examined self-esteem in adults with intellectual disabilities and links with mental health outcomes. METHOD A systematic search of PsycINFO, Web of Science and CINAHL was conducted to identify studies published between 1990 and 2021. The studies were appraised using the QualSyst tool. RESULTS Twenty-six articles were identified of which two studies were removed from the review due to low quality. Studies reported mixed evidence regarding levels of self-esteem compared with the general population. Engagement in activities appeared to be linked with positive self-esteem, and perception of negative interpersonal life events as having a negative impact was associated with lower self-esteem. There was evidence of co-occurrence of low self-esteem and depression, but no studies examined the relationship between self-esteem and anxiety. CONCLUSION Reviewed studies provided mixed evidence on levels of self-esteem in this population, suggesting that factors such as engagement in life were related to higher self-esteem and demonstrating the co-occurrence of low self-esteem and depression. However, clear causal links have yet to be identified, and more research is needed using longitudinal designs to answer questions about trajectory.
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Affiliation(s)
- J Y Lee
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - M Patel
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - K Scior
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
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14
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Patel M, Lee JY, Scior K. Psychometric properties of measures designed to assess common mental health problems and wellbeing in adults with intellectual disabilities: a systematic review. J Intellect Disabil Res 2023; 67:397-414. [PMID: 36808653 DOI: 10.1111/jir.13018] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Multiple measures of mental health problems and mental wellbeing for adults with intellectual disabilities are available, but investigations into their reliability and validity are still in the early stages. The aim of this systematic review was to provide an update to previous evaluations of measures of common mental health problems and wellbeing in adults with mild to moderate intellectual disabilities (ID). METHODS A systematic search was performed across three databases (MEDLINE, PsycINFO and SCOPUS). The literature search was limited to the years from 2009 to 2021 and to the original English versions. Ten papers evaluating nine measures were reviewed, and the psychometric properties of these measures were discussed using the Characteristics of Assessment Instructions for Psychiatric Disorders in Persons with Intellectual Developmental Disorders as a framework. RESULTS Four measures had at least one rating of 'good' across both dimensions of reliability and at least one dimension of validity and were deemed to have promising psychometric properties: the Clinical Outcomes in Routine Evaluation-Learning Disabilities, Impact of Events Scale-Intellectual Disabilities, Lancaster and Northgate Trauma Scales and Self-Assessment and Intervention (self-report section). Additionally, these measures were developed through consultations with mental health professionals and/or people with IDs and thus were deemed to have good content validity. CONCLUSIONS This review informs measurement choice for researchers and clinicians while highlighting a need for continued research efforts into the quality of measures available for people with IDs. The results were limited by incomplete psychometric evaluations of measures available. A paucity of psychometrically robust measures of mental wellbeing was observed.
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Affiliation(s)
- M Patel
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - J Y Lee
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - K Scior
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
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Ross DH, Lee JY, Bilbao A, Orton DJ, Eder JG, Burnet MC, Deatherage Kaiser BL, Kyle JE, Zheng X. LipidOz enables automated elucidation of lipid carbon-carbon double bond positions from ozone-induced dissociation mass spectrometry data. Commun Chem 2023; 6:74. [PMID: 37076550 PMCID: PMC10115790 DOI: 10.1038/s42004-023-00867-9] [Citation(s) in RCA: 2] [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] [Received: 01/06/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.
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Affiliation(s)
- Dylan H Ross
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- PrognomiQ, Inc, San Mateo, CA, 94403, USA
| | - Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Josie G Eder
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Meagan C Burnet
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | - Jennifer E Kyle
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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Choi J, Kokate A, Khaledian E, Liu M, Prasad P, Blume J, Chan J, Cuaresma R, Dai K, Khadka M, Khin T, Kodama Y, Lee JY, Malekpour H, Mora M, Mudaliar N, Golmaei SN, Ramaiah M, Ramaswamy S, Spiro P, Vitko D, Swaminathan K, Yee J, Young B, Belthangady C, Wilcox B, Koh B, Ma P. Abstract 6606: Biomarker discovery in non-small-cell lung cancer enabled by deep multi-omics profiling of proteins, metabolites, transcripts, and genes in blood. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6606] [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: 04/07/2023]
Abstract
Abstract
Lung cancer is the leading cause of cancer-related deaths in the United States, with estimates of 236,740 new cases and 118,830 deaths in 2022 secondary to the disease. Blood-based liquid biopsies hold promise to reduce morbidity and mortality from lung cancer by enabling early detection to downstage disease at diagnosis, theragnostic identification of patients most likely to be helped or harmed by therapy, monitoring of therapeutic efficacy, and detection of residual disease. PrognomiQ’s multi-omics platform comprehensively profiles proteins, metabolites, lipids, mRNA, and cfDNA in blood samples which can be used for the development of liquid biopsy tests with high sensitivity and specificity for lung cancer. We conducted a case-control study comprising 1031 subjects: 361 subjects with untreated non-small-cell lung cancer (NSCLC) and 670 matched controls which included 340 subjects with salient pulmonary and gastrointestinal co-morbidities. Blood samples from each subject were processed to provide 7 different `omics readouts. LCMS was used to detect and quantify proteins, metabolites, and lipids. In addition, cfDNA and mRNA were assayed using next-generation sequencing. cfDNA reads were analyzed to estimate fragment-lengths, copy-number variation, and CpG site methylation. All molecular data were normalized using standard methods specific to each assay. Univariate analyses of cases vs controls were performed to identify differentially abundant features on all available samples per assay. We detected 9,868 proteins, 605 lipids, 329 metabolites, and 109,070 mRNA transcripts. Of these, 3,098 proteins, 210 lipids, 57 metabolites, and 30,236 mRNA transcripts were significantly different (FWER < 0.05) in cases versus controls. Gene set enrichment analysis on statistically significant transcripts and proteins identified multiple gene-ontology terms associated with cancer including the Wnt signaling process and IgA immunoglobulin complex, respectively. From cfDNA data, we identified 234 non-contiguous genomic regions associated with the fragment-length disorder, 4,790 with copy-number variation, and 74 differentially methylated genomic regions spanning 184 CpG sites (FWER < 0.05). With the premise that deviations from copy number neutrality are more likely to indicate a tumor contribution, we then focused our examination on those differentially expressed proteins that overlap with differentially expressed mRNA transcripts as well as CNV genomic regions. We identified 52 protein coding genes including E-cadherin (associated with EMT) and related binding proteins such as RAB11B, CAPZB, EPS15, FLNB, MYH9, STK24 and YWHAE. Ongoing machine-learning-based classifier training to distinguish between cancer and non-cancer can serve as the basis for the development of high-sensitivity liquid-biopsy tests for lung cancer.
Citation Format: Jinlyung Choi, Ajinkya Kokate, Ehdieh Khaledian, Manway Liu, Preethi Prasad, John Blume, Jessica Chan, Rea Cuaresma, Kevin Dai, Manoj Khadka, Thidar Khin, Yuya Kodama, Joon-Yong Lee, Hoda Malekpour, Megan Mora, Nithya Mudaliar, Sara Nouri Golmaei, Madhuvanthi Ramaiah, Saividya Ramaswamy, Peter Spiro, Dijana Vitko, Kavya Swaminathan, James Yee, Brian Young, Chinmay Belthangady, Bruce Wilcox, Brian Koh, Philip Ma. Biomarker discovery in non-small-cell lung cancer enabled by deep multi-omics profiling of proteins, metabolites, transcripts, and genes in blood. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6606.
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Blume J, Bundalian G, Chan J, Chao-Shern C, Choi J, Cuaresma R, Dai K, Golmaei SN, Jang JH, Khadka M, Khaledian E, Khin T, Kodama Y, Kokate A, Lee JY, Liu M, Malekpour H, Mora M, Mudaliar N, Prasad P, Ramaiah M, Ramaswamy S, Spiro P, Swaminathan K, Vitko D, Yee J, Young B, Zhang S, Belthangady C, Wilcox B, Koh B, Ma P. Abstract 6597: A multi-omics classifier achieves high sensitivity and specificity for pancreatic ductal adenocarcinoma in a case-control study of 146 subjects. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6597] [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: 04/07/2023]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is currently the 3rd leading cause of cancer-related deaths in the US. Although the all-stage 5-year survival rate is ~10%, early-stage 5-year survival is markedly superior and in excess of 40%. Hence, early detection of PDAC via blood-based liquid biopsies holds promise to reduce morbidity and mortality. PrognomiQ’s multi-omics platform performs deep and unbiased molecular profiling of blood samples to detect proteins, metabolites, lipids, mRNA, miRNA, cfDNA fragmentation and copy-number, and CpG methylation. Here we report results from training and validation of a classifier on a subset of that multi-omic data with the potential to enable the development of high sensitivity and specificity tests for early detection of PDAC.We conducted a case-control study comprising 146 subjects across 16 clinical sites, including 63 pathology-confirmed, untreated PDAC cases (12 stage I, 8 stage II, 4 stage III, 36 stage IV, and 3 stage unknown) and 83 age- and gender- matched controls without any known cancer. For each subject, venous blood samples including plasma were collected. Unbiased LCMS was used to detect and quantify proteins, and targeted, multiplexed MRM-LCMS assays were used for both metabolites and lipids. After data processing, we detected 54,114 proteomic features, 898 lipids, and 373 metabolites. 445 proteomic features, 170 lipids, and 37 metabolites were found to be significantly different as determined by Bonferroni-corrected Wilcoxon tests with FWER < 0.05. For classification, the dataset was split into training (37 cases and 37 controls) and validation (26 cases and 46 controls) sets, with control for collection site and date, age, and gender. XGBoost models were constructed for each analyte class using ten repeats of 10-fold cross-validation. To improve specificity to PDAC, all proteomic features which mapped to GOBP terms associated with acute-phase response, inflammation, and immune response were excluded prior to training. The best-performing hyperparameters were used for a final model built on the full training set and then used for inference on the validation set. At 99% specificity, the proteomic classifier had sensitivities of 77%, 57%, and 88% for Stages 1-4, Stages 1-2, and Stages 3-4, respectively, estimated by bootstrap re-sampling of the validation results. Metabolomics had sensitivities of 81%, 71%, and 88%. Lipidomics had sensitivities of 65%, 71%, and 65%. A joint, multi-omic model was constructed by averaging the scaled probabilities of all models. This joint model improved performance at 99% specificity with sensitivities of 92%, 86%, and 94%, highlighting the synergy of multi-omics data, particularly phenotypically related omics such as those described here. Multi-omic classifiers such as these can serve as the foundation for blood-based liquid biopsies for the early detection of PDAC.
Citation Format: John Blume, Ghristine Bundalian, Jessica Chan, Connie Chao-Shern, Jinlyung Choi, Rea Cuaresma, Kevin Dai, Sara N. Golmaei, Jun Heok Jang, Manoj Khadka, Ehdieh Khaledian, Thidar Khin, Yuya Kodama, Ajinkya Kokate, Joon-Yong Lee, Manway Liu, Hoda Malekpour, Megan Mora, Nithya Mudaliar, Preethi Prasad, Madhuvanthi Ramaiah, Saividya Ramaswamy, Peter Spiro, Kavya Swaminathan, Dijana Vitko, James Yee, Brian Young, Susan Zhang, Chinmay Belthangady, Bruce Wilcox, Brian Koh, Philip Ma. A multi-omics classifier achieves high sensitivity and specificity for pancreatic ductal adenocarcinoma in a case-control study of 146 subjects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6597.
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Lee JY. Surrogacy: beyond the commercial/altruistic distinction. J Med Ethics 2023; 49:196-199. [PMID: 35314464 DOI: 10.1136/medethics-2021-108093] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
In this article, I critique the commonly accepted distinction between commercial and altruistic surrogacy arrangements. The moral legitimacy of surrogacy, I claim, does not hinge on whether it is paid ('commercial') or unpaid ('altruistic'); rather, it is best determined by appraisal of virtue-abiding conditions constitutive of the surrogacy arrangement. I begin my article by problematising the prevailing commercial/altruistic distinction; next, I demonstrate that an assessment of the virtue-abiding or non-virtue-abiding features of a surrogacy is crucial to navigating questions about the moral legitimacy of surrogacy; in the final part, I reject other moral heuristics that might be proposed as alternatives to the commercial/altruistic dichotomy, and reiterate that a virtue-ethical framework is the most suitable way forward.
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Affiliation(s)
- J Y Lee
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
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19
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Kang H, Lee EB, Lee S, Go TH, Lee JY, Lee SH, Song SA, Lim HK, Hong SP. Dipeptidyl peptidase-4 inhibitors increase the risk of bullous pemphigoid in older patients with diabetes: A retrospective analysis using the Korean National Health Insurance Database. J Eur Acad Dermatol Venereol 2023. [PMID: 36799763 DOI: 10.1111/jdv.18975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Affiliation(s)
- H Kang
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - E B Lee
- Department of Anesthesiology and Pain Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - S Lee
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - T-H Go
- Center of Biomedical Data Science, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - J Y Lee
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - S-H Lee
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - S A Song
- Department of Anesthesiology and Pain Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - H K Lim
- Department of Anesthesiology and Pain Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - S-P Hong
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea.,Research Institute of Metabolism and Inflammation, Yonsei University Wonju College of Medicine, Wonju, Korea
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20
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Bilbao A, Ross DH, Lee JY, Donor MT, Williams SM, Zhu Y, Ibrahim YM, Smith RD, Zheng X. MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry. J Proteome Res 2023; 22:508-513. [PMID: 36414245 PMCID: PMC9898216 DOI: 10.1021/acs.jproteome.2c00313] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich spectra challenges existing data storage and access technologies, therefore precluding informatics advancements. We present MZA (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed of a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and cross-programming language access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable, example MS-data and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.
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Affiliation(s)
- Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA,Corresponding authors Aivett Bilbao – Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, United States; .; Xueyun Zheng – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States;
| | - Dylan H. Ross
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Micah T. Donor
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ying Zhu
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | | | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA,Corresponding authors Aivett Bilbao – Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, United States; .; Xueyun Zheng – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States;
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21
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Khaledian E, Prasad P, Blume J, Bundalian G, Chao-Shern C, Choi J, Cuaresma R, Deyarmin J, Jang JH, Khadka M, Khin T, Kodama Y, Kokate A, Lee JY, Liu M, Mudaliar N, Ramaiah M, Ramaswamy S, Spiro P, Swaminathan K, Williams P, Yang M, Yee J, Young B, Zawada R, Zhang S, Belthangady C, Wilcox B, Ma P. Abstract A038: High-dimensional, multi-omics analyses of proteins, metabolites, transcripts, and genes enable biomarker discovery in early- and late-stage pancreatic cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-a038] [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: 11/17/2022]
Abstract
Abstract
Pancreatic cancer is the third leading cause of cancer-related deaths in the United States. Disease biomarkers quantified from blood-based assays may help reduce mortality by enabling early detection, treatment selection, or response and resistance assessment. PrognomiQ has developed a multi-omics assay and analysis platform that comprehensively profiles blood samples to detect proteins, metabolites, lipids, mRNA, miRNA, cfDNA fragments, and methylation at CpG sites. This platform can provide deep insights into the biology of pancreatic cancer and could enable the development of high sensitivity and specificity tests for the early detection of pancreatic cancer. We conducted a case-control study comprising 196 subjects: 92 with untreated pancreatic cancer and 104 matched controls without pancreatic cancer. For each subject, blood was collected in assay-specific tubes and processed to provide 7 different `omics readouts. cfDNA and mRNA were isolated from samples and assayed following standard NGS protocols. cfDNA fragments were processed to estimate fragment-length disorder and copy-number variation along with CpG site methylation. In addition, targeted and untargeted LCMS were used to detect and quantify proteins, metabolites, and lipids. After normalization, non-parametric univariate analyses of cases versus controls were performed to identify differentially abundant features on all available samples for each assay. Unsupervised learning was used to investigate the separation of subjects into groups based on disease status for the subset of 157 subjects for which complete data on all 7 readouts were available. We detected 2,812 proteins, 811 lipids, 373 metabolites, and 110,864 mRNA transcripts in all samples where data for each assay was available. Of these, 275 proteins, 232 lipids, 49 metabolites, and 3385 mRNA transcripts were significantly different (FWER < 0.05) in cases versus controls. From cfDNA data, we identified 35 non-contiguous genomic regions associated with fragment-length disorder, 557 with copy-number variation, and 5 with multiple, differentially methylated CpGs (FWER < 0.05) that aggregately span 307 protein-coding genes; of these, the overlap with the differentially expressed proteins included E-cadherin (tumor suppressor) and N-cadherin (involved in epithelial-to-mesenchymal transition). Statistically significant genes and proteins were found to be associated with processes including Wnt signaling, regulation of focal adhesion assembly, and actin cytoskeleton organization. Multi-omics, unsupervised learning showed separation of early- and late-stage cases and controls. High-dimensional bioinformatics analyses systematically decomposed each `omics data type into joint and orthogonal components associated with pancreatic cancer. Ongoing multivariate analyses, including supervised machine learning, will further elucidate the biology of pancreatic cancer development, and serve as the foundation for high-sensitivity blood tests for the early detection and monitoring of pancreatic cancer.
Citation Format: Ehdieh Khaledian, Preethi Prasad, John Blume, Ghristine Bundalian, Connie Chao-Shern, Jinlyung Choi, Rea Cuaresma, Jared Deyarmin, Jun Heok Jang, Manoj Khadka, Thidar Khin, Yuya Kodama, Ajinkya Kokate, Joon-Yong Lee, Manway Liu, Nithya Mudaliar, Madhuvanthi Ramaiah, Saividya Ramaswamy, Peter Spiro, Kavya Swaminathan, Preston Williams, Mi Yang, James Yee, Brian Young, Robert Zawada, Susan Zhang, Chinmay Belthangady, Bruce Wilcox, Philip Ma. High-dimensional, multi-omics analyses of proteins, metabolites, transcripts, and genes enable biomarker discovery in early- and late-stage pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A038.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mi Yang
- 1PrognomiQ Inc., San Mateo, CA
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22
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Chung H, Seo H, Choi SH, Park CK, Kim TM, Park SH, Won JK, Lee JH, Lee ST, Lee JY, Hwang I, Kang KM, Yun TJ. Cluster Analysis of DSC MRI, Dynamic Contrast-Enhanced MRI, and DWI Parameters Associated with Prognosis in Patients with Glioblastoma after Removal of the Contrast-Enhancing Component: A Preliminary Study. AJNR Am J Neuroradiol 2022; 43:1559-1566. [PMID: 36175084 PMCID: PMC9731243 DOI: 10.3174/ajnr.a7655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/21/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND PURPOSE No report has been published on the use of DSC MR imaging, DCE MR imaging, and DWI parameters in combination to create a prognostic prediction model in glioblastoma patients. The aim of this study was to develop a machine learning-based model to find preoperative multiparametric MR imaging parameters associated with prognosis in patients with glioblastoma. Normalized CBV, volume transfer constant, and ADC of the nonenhancing T2 high-signal-intensity lesions were evaluated using K-means clustering. MATERIALS AND METHODS A total of 142 patients with glioblastoma who underwent preoperative MR imaging and total resection were included in this retrospective study. From the normalized CBV, volume transfer constant, and ADC maps, the parametric data were sorted using the K-means clustering method. Patients were divided into training and test sets (ratio, 1:1), and the optimal number of clusters was determined using receiver operating characteristic analysis. Kaplan-Meier survival analysis and log-rank tests were performed to identify potential parametric predictors. A multivariate Cox proportional hazard model was conducted to adjust for clinical predictors. RESULTS The nonenhancing T2 high-signal-intensity lesions were divided into 6 clusters. The cluster (class 4) with the relatively low normalized CBV and volume transfer constant value and the lowest ADC values was most associated with predicting glioblastoma prognosis. The optimal cutoff of the class 4 volume fraction of nonenhancing T2 high-signal-intensity lesions predicting 1-year progression-free survival was 9.70%, below which the cutoff was associated with longer progression-free survival. Two Kaplan-Meier curves based on the cutoff value showed a statistically significant difference (P = .037). When we adjusted for all clinical predictors, the cluster with the relatively low normalized CBV and volume transfer constant values and the lowest ADC value was an independent prognostic marker (hazard ratio, 3.04; P = .048). The multivariate Cox proportional hazard model showed a concordance index of 0.699 for progression-free survival. CONCLUSIONS Our model showed that nonenhancing T2 high-signal-intensity lesions with the relatively low normalized CBV, low volume transfer constant values, and the lowest ADC values could serve as useful prognostic imaging markers for predicting survival outcomes in patients with glioblastoma.
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Affiliation(s)
- H Chung
- From the Seoul National University College of Medicine (H.C., H.S.), Seoul, Korea
| | - H Seo
- From the Seoul National University College of Medicine (H.C., H.S.), Seoul, Korea
| | - S H Choi
- Department of Radiology (S.H.C., J.Y.L., I.H., K.M.K., T.J.Y.), Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Center for Nanoparticle Research (S.H.C.), Institute for Basic Science, Seoul, Korea
- School of Chemical and Biological Engineering (S.H.C.), Seoul National University, Seoul, Korea
| | - C-K Park
- Department of Neurosurgery (C.-K.P.), Internal Medicine
| | - T M Kim
- Cancer Research Institute (T.M.K.)
| | - S-H Park
- Departments of Pathology (S.-H.P., J.K.W.), Radiation Oncology
| | - J K Won
- Departments of Pathology (S.-H.P., J.K.W.), Radiation Oncology
| | - J H Lee
- Cancer Research Institute (J.H.L.)
| | - S-T Lee
- Neurology (S.-T.L.), Seoul National University Hospital, Seoul, Korea
| | - J Y Lee
- Department of Radiology (S.H.C., J.Y.L., I.H., K.M.K., T.J.Y.), Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - I Hwang
- Department of Radiology (S.H.C., J.Y.L., I.H., K.M.K., T.J.Y.), Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - K M Kang
- Department of Radiology (S.H.C., J.Y.L., I.H., K.M.K., T.J.Y.), Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - T J Yun
- Department of Radiology (S.H.C., J.Y.L., I.H., K.M.K., T.J.Y.), Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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23
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McClure R, Farris Y, Danczak R, Nelson W, Song HS, Kessell A, Lee JY, Couvillion S, Henry C, Jansson JK, Hofmockel KS. Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. mSystems 2022; 7:e0037222. [PMID: 36154140 PMCID: PMC9599572 DOI: 10.1128/msystems.00372-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 12/24/2022] Open
Abstract
Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. The members of MSC-2 were further evaluated via metatranscriptomics and community metabolomics. Intriguingly, the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products. Using a model soil consortium greatly increased our knowledge of how carbon is decomposed and metabolized in a community setting, showing that niche size, rather than species metabolic capacity, can drive success and that certain species become active carbon degraders only in the context of their surrounding community. These conclusions fill important knowledge gaps that are key to our understanding of community interactions that support carbon and nitrogen cycling in soil. IMPORTANCE The soil microbiome performs many functions that are key to ecology, agriculture, and nutrient cycling. However, because of the complexity of this ecosystem we do not know the molecular details of the interactions between microbial species that lead to these important functions. Here, we use a representative but simplified model community of bacteria to understand the details of these interactions. We show that certain species act as primary degraders of carbon sources and that the most successful species are likely those that can take the most advantage of breakdown products, not necessarily the primary degraders. We also show that a species phenotype, including whether it is a primary degrader or not, is driven in large part by the membership of the community it resides in. These conclusions are critical to a better understanding of the soil microbial interaction network and how these interactions drive central soil microbiome functions.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Danczak
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Aimee Kessell
- Department of Biological Systems Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Henry
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten S. Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
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24
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Lee JY. The limitations of liberal reproductive autonomy. Med Health Care Philos 2022; 25:523-529. [PMID: 35687215 DOI: 10.1007/s11019-022-10097-w] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/01/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The common liberal understanding of reproductive autonomy - characterized by free choice and a principle of non-interference - serves as a useful way to analyse the normative appeal of having certain choices open to people in the reproductive realm, especially for issues like abortion rights. However, this liberal reading of reproductive autonomy only offers us a limited ethical understanding of what is at stake in many kinds of reproductive choices, particularly when it comes to different uses of reproductive technologies and third-party reproduction. This is because the liberal framework does not fully capture who benefits from which reproductive options, the extent of the risks and harms involved in various reproductive interventions, and the reasons for why people are driven to make certain reproductive choices.
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Affiliation(s)
- J Y Lee
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
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25
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Giberson C, Singh RK, Chun J, Huntley AP, Zhong J, Ibrahim YM, Schenter GK, Lee JY, Garimella SV. SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry. J Am Soc Mass Spectrom 2022; 33:1453-1457. [PMID: 35852821 DOI: 10.1021/jasms.1c00301] [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] [Indexed: 06/15/2023]
Abstract
Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations─(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N2) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.
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Affiliation(s)
- Cameron Giberson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rajesh K Singh
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Adam P Huntley
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jason Zhong
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gregory K Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joon-Yong Lee
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sandilya Vb Garimella
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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26
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Lee JY, Mitchell HD, Burnet MC, Wu R, Jenson SC, Merkley ED, Nakayasu ES, Nicora CD, Jansson JK, Burnum-Johnson KE, Payne SH. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. J Proteome Res 2022; 21:2023-2035. [PMID: 35793793 PMCID: PMC9361346 DOI: 10.1021/acs.jproteome.2c00334] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Metaproteomics has
been increasingly utilized for high-throughput
characterization of proteins in complex environments and has been
demonstrated to provide insights into microbial composition and functional
roles. However, significant challenges remain in metaproteomic data
analysis, including creation of a sample-specific protein sequence
database. A well-matched database is a requirement for successful
metaproteomics analysis, and the accuracy and sensitivity of PSM identification
algorithms suffer when the database is incomplete or contains extraneous
sequences. When matched DNA sequencing data of the sample is unavailable
or incomplete, creating the proteome database that accurately represents
the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample
composition directly from metaproteomic data. First, we created a
deep learning model, Kaiko, to predict the peptide sequences from
mass spectrometry data and trained it on 5 million peptide–spectrum
matches from 55 phylogenetically diverse bacteria. After training,
Kaiko successfully identified organisms from soil isolates and synthetic
communities directly from proteomics data. Finally, we created a pipeline
for metaproteome database generation using Kaiko. We tested the pipeline
on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary
method to construct the sample-specific protein database instead of
relying on (un)matched metagenomes. Our pipeline identified all highly
abundant taxa from 16S rRNA sequencing of the soil samples and uncovered
several additional species which were strongly represented only in
proteomic data.
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Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah C Jenson
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric D Merkley
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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27
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Farley SE, Kyle JE, Leier HC, Bramer LM, Weinstein JB, Bates TA, Lee JY, Metz TO, Schultz C, Tafesse FG. A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants. Nat Commun 2022; 13:3487. [PMID: 35715395 PMCID: PMC9203258 DOI: 10.1038/s41467-022-31097-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 06/01/2022] [Indexed: 12/31/2022] Open
Abstract
A comprehensive understanding of host dependency factors for SARS-CoV-2 remains elusive. Here, we map alterations in host lipids following SARS-CoV-2 infection using nontargeted lipidomics. We find that SARS-CoV-2 rewires host lipid metabolism, significantly altering hundreds of lipid species to effectively establish infection. We correlate these changes with viral protein activity by transfecting human cells with each viral protein and performing lipidomics. We find that lipid droplet plasticity is a key feature of infection and that viral propagation can be blocked by small-molecule glycerolipid biosynthesis inhibitors. We find that this inhibition was effective against the main variants of concern (alpha, beta, gamma, and delta), indicating that glycerolipid biosynthesis is a conserved host dependency factor that supports this evolving virus.
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Affiliation(s)
- Scotland E Farley
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Hans C Leier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Lisa M Bramer
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Jules B Weinstein
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bates
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Joon-Yong Lee
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA.
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Baek HJ, Heo YJ, Kim D, Yun SY, Baek JW, Jeong HW, Choo HJ, Lee JY, Oh SI. Usefulness of Wave-CAIPI for Postcontrast 3D T1-SPACE in the Evaluation of Brain Metastases. AJNR Am J Neuroradiol 2022; 43:857-863. [PMID: 35618423 DOI: 10.3174/ajnr.a7520] [Citation(s) in RCA: 1] [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] [Received: 02/03/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND PURPOSE High-resolution postcontrast 3D T1WI is a widely used sequence for evaluating brain metastasis, despite the long scan time. This study aimed to compare highly accelerated postcontrast 3D T1-weighted sampling perfection with application-optimized contrasts by using different flip angle evolution by using wave-controlled aliasing in parallel imaging (wave-T1-SPACE) with the commonly used standard high-resolution postcontrast 3D T1-SPACE for the evaluation of brain metastases. MATERIALS AND METHODS Among the 387 patients who underwent postcontrast wave-T1-SPACE and standard SPACE, 56 patients with suspected brain metastases were retrospectively included. Two neuroradiologists assessed the number of enhancing lesions according to lesion size, contrast-to-noise ratiolesion/parenchyma, contrast-to-noise ratiowhite matter/gray matter, contrast ratiolesion/parenchyma, and overall image quality for the 2 different sequences. RESULTS Although there was no significant difference in the evaluation of larger enhancing lesions (>5 mm) between the 2 different sequences (P = .66 for observer 1, P = .26 for observer 2), wave-T1-SPACE showed a significantly lower number of smaller enhancing lesions (<5 mm) than standard SPACE (1.61 [SD, 0.29] versus 2.84 [SD, 0.47] for observer 1; 1.41 [SD, 0.19] versus 2.68 [SD, 0.43] for observer 2). Furthermore, mean contrast-to-noise ratiolesion/parenchyma and overall image quality of wave-T1-SPACE were significantly lower than those in standard SPACE. CONCLUSIONS Postcontrast wave-T1-SPACE showed comparable diagnostic performance for larger enhancing lesions (>5 mm) and marked scan time reduction compared with standard SPACE. However, postcontrast wave-T1-SPACE showed underestimation of smaller enhancing lesions (<5 mm) and lower image quality than standard SPACE. Therefore, postcontrast wave-T1-SPACE should be interpreted carefully in the evaluation of brain metastasis.
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Affiliation(s)
- H J Baek
- From the Department of Radiology (H.J.B.), Gyeongsang National University School of Medicine and Gyeongsang National University Changwon Hospital, Changwon, Republic of Korea
| | - Y J Heo
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - D Kim
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - S Y Yun
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - J W Baek
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - H W Jeong
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - H J Choo
- Department of Radiology (Y.J.H., D.K., S.Y.Y., J.W.B., H.W.J., H.J.C.), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - J Y Lee
- Department of Internal Medicine (J.Y.L), Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - S-I Oh
- Department of Neurology (S.-I.O.), Inje University Busan Paik Hospital, Busan, Republic of Korea
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Lee JY. Framing gestation: assistance, delegation, and beyond. J Med Ethics 2022; 48:medethics-2022-108405. [PMID: 35636916 DOI: 10.1136/medethics-2022-108405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Affiliation(s)
- J Y Lee
- University of Copenhagen, Kobenhavn, Denmark
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Bates TA, McBride SK, Leier HC, Guzman G, Lyski ZL, Schoen D, Winders B, Lee JY, Lee DX, Messer WB, Curlin ME, Tafesse FG. Vaccination before or after SARS-CoV-2 infection leads to robust humoral response and antibodies that effectively neutralize variants. Sci Immunol 2022; 7:eabn8014. [PMID: 35076258 PMCID: PMC8939472 DOI: 10.1126/sciimmunol.abn8014] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022]
Abstract
Current coronavirus disease 2019 (COVID-19) vaccines effectively reduce overall morbidity and mortality and are vitally important to controlling the pandemic. Individuals who previously recovered from COVID-19 have enhanced immune responses after vaccination (hybrid immunity) compared with their naïve-vaccinated peers; however, the effects of post-vaccination breakthrough infections on humoral immune response remain to be determined. Here, we measure neutralizing antibody responses from 104 vaccinated individuals, including those with breakthrough infections, hybrid immunity, and no infection history. We find that human immune sera after breakthrough infection and vaccination after natural infection broadly neutralize SARS-CoV-2 (severe acute respiratory coronavirus 2) variants to a similar degree. Although age negatively correlates with antibody response after vaccination alone, no correlation with age was found in breakthrough or hybrid immune groups. Together, our data suggest that the additional antigen exposure from natural infection substantially boosts the quantity, quality, and breadth of humoral immune response regardless of whether it occurs before or after vaccination.
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Affiliation(s)
- Timothy A. Bates
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Savannah K. McBride
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Hans C. Leier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Gaelen Guzman
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Zoe L. Lyski
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Devin Schoen
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Bradie Winders
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David Xthona Lee
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - William B. Messer
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
- OHSU-PSU School of Public Health, Oregon Health & Science University; Portland, OR 97239, United States
| | - Marcel E. Curlin
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Fikadu G. Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
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Farley SE, Kyle JE, Leier HC, Bramer LM, Weinstein J, Bates TA, Lee JY, Metz TO, Schultz C, Tafesse FG. A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants. bioRxiv 2022:2022.02.14.480430. [PMID: 35194611 PMCID: PMC8863149 DOI: 10.1101/2022.02.14.480430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A comprehensive understanding of host dependency factors for SARS-CoV-2 remains elusive. We mapped alterations in host lipids following SARS-CoV-2 infection using nontargeted lipidomics. We found that SARS-CoV-2 rewires host lipid metabolism, altering 409 lipid species up to 64-fold relative to controls. We correlated these changes with viral protein activity by transfecting human cells with each viral protein and performing lipidomics. We found that lipid droplet plasticity is a key feature of infection and that viral propagation can be blocked by small-molecule glycerolipid biosynthesis inhibitors. We found that this inhibition was effective against the main variants of concern (alpha, beta, gamma, and delta), indicating that glycerolipid biosynthesis is a conserved host dependency factor that supports this evolving virus.
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Loo G, De Leon J, Seow SC, Boey E, Soh R, Tan E, Gan HH, Lee JY, Teo JTL, Yeo C, Kojodjojo P, Tan VH. Acute procedural outcomes of his bundle pacing with or without electrophysiology mapping system: a multicenter study. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehab849.039] [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: 11/14/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Introduction
His bundle pacing (HBP) is associated with improved clinical outcomes compared to right ventricular apical pacing. However, it can be technically challenging and may result in prolonged fluoroscopy and procedural time.
Purpose
We sought to compare the feasibility of performing HBP with or without electrophysiology mapping (EP) system, focusing on evaluating acute procedural success, complication rates and short-term outcomes.
Methods
HBP patients at 3 hospitals were recruited between August 2018 to December 2020. HBP was performed with EP mapping system in 1 center, and without EP mapping in the other 2 centers. Acute procedural success was defined as either selective or non-selective His bundle capture with a threshold of less than or equal to 1.5V at 1ms at the end of procedure implantation.
Results
A total of 233 patients were recruited, of which HBP was performed with EP mapping in 77 patients (33.0%) and without EP mapping in 156 patients (67.0%). Both groups were similar in age (73.2 ± 11.0 years vs 75.3 ± 9.5 years, p = 0.125) and male sex (58.4% vs 48.1%, p = 0.136). There were more patients with ischemic heart disease (45.5% vs 22.4%, p < 0.01) and reduced left ventricular ejection fraction ≤ 40% (28.6% vs 10.9%, p < 0.01) in the group with EP mapping. The indications for HBP was for high-grade atrioventricular block (55.8%), sick sinus syndrome (35.6%) and cardiac resynchronization therapy (CRT) (8.6%). There were more patients who required CRT in the center with EP mapping (18.2% vs 3.8%, p < 0.01). HBP was successful in 39 patients (50.6%) with EP mapping and 93 patients (59.6%) without EP mapping (p= 0.382). The median R wave at implant was similar in both groups [4.0 (2.9 – 6.2) mV vs 4.3 (4.3 – 7.0) mV, p = 0.808]. Impedance at implant (607 ± 195 ohms vs 547 ± 166 ohms, p < 0.01) and selective His bundle bipolar threshold at implant [1.25 (0.75-1.75) V vs 0.7 (0.5 – 1.25) V, p = 0.01] was higher in patients with EP mapping while non-selective His bundle bipolar threshold at implant [1.75 (1.0 – 3.0) V vs 1.5 (0.9 – 2.2) V, p = 0.133] and paced QRS duration (116.4 ± 25.4 ms vs 114.4 ± 24.2 ms, p =0.655) were similar. There were no differences in procedural or fluoroscopy time between groups (111 ± 36.9 min vs 107 ± 40.7 min, p = 0.479; and 10.3 ± 8.9 min vs 12.1± 14.0 min, p = 0.328 respectively). There was a similar rate of acute procedural complications (5.2% vs 1.3%, p = 0.076) and patients requiring wound or lead revision (6.8% vs 1.9%, p = 0.115) after a median follow up duration of 205 days (67-397). The prevalence of new onset paroxysmal atrial fibrillation (11.7% vs 4.2%, p = 0.037) and all cause mortality (12.3% vs 3.2%, p = 0.029) was increased in patients who underwent HBP with EP mapping.
Conclusion
HBP in centers with or without EP mapping showed similar acute procedure success and complication rates. The use of EP mapping system was not shown to affect procedural or fluoroscopy duration.
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Affiliation(s)
- G Loo
- Changi General Hospital, Cardiology, Singapore, Singapore
| | - J De Leon
- National University Hospital, Cardiology, Singapore, Singapore
| | - S C Seow
- National University Hospital, Cardiology, Singapore, Singapore
| | - E Boey
- Ng Teng Fong Hospital, Cardiology, Singapore, Singapore
| | - R Soh
- National University Hospital, Cardiology, Singapore, Singapore
| | - E Tan
- National University Hospital, Cardiology, Singapore, Singapore
| | - H H Gan
- Ng Teng Fong Hospital, Cardiology, Singapore, Singapore
| | - J Y Lee
- National University Hospital, Cardiology, Singapore, Singapore
| | - J T L Teo
- Changi General Hospital, Cardiology, Singapore, Singapore
| | - C Yeo
- Changi General Hospital, Cardiology, Singapore, Singapore
| | - P Kojodjojo
- Ng Teng Fong Hospital, Cardiology, Singapore, Singapore
| | - V H Tan
- Changi General Hospital, Cardiology, Singapore, Singapore
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Lee JY, Shen S, Nishita C. Development of Older Adult Food Insecurity Index to Assess Food Insecurity of Older Adults. J Nutr Health Aging 2022; 26:739-746. [PMID: 35842765 DOI: 10.1007/s12603-022-1816-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Quantifying the number of older adults that are food insecure in a specific geographic area is critical in developing and scaling public health prevention and response programs at the local level. However, current estimates of older adult food insecurity only consider financial constraints, following the same methodology as the general population, even though the drivers for older adults are different and multidimensional. This study aims to build a general approach to quantify the food-insecurity among older adults at the local level, using publicly available data that can be easily obtained across the country. METHODS 13 risk factors for food insecurity among older adults were identified leveraging existing studies, following the Social Ecological Model (SEM), and the weighted impact of each factor was determined. Publicly available data sources were identified for each factor, ZIP code level data was compared to national averages, and the weighted data for each factor were aggregated to determine the overall food insecurity at the local level. RESULTS Based on the averaged odds ratios across all the studies, of the 13 risk factors, beyond financial constraints, having a disability was the most impactful factor and distance to the nearest grocery store was the least impactful. A ZIP code level model of Honolulu County was developed as an example to demonstrate the approach, showing that food insecurity among older adults in the county was 2.5 times that which was reported from the Current Population Survey (16.5% versus 6.5%). CONCLUSION This evidence-based model considered factors that impact food insecurity among older adults across all the spheres of the SEM. The drivers of food insecurity among older adults are different than the drivers for the general population, resulting in a higher percentage of older adults being food insecure than currently reported.
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Affiliation(s)
- J Y Lee
- Jenny Jin Young Lee, Thompson School of Social Work and Public Health, University of Hawai'i at Mānoa, HI, USA,
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Hollerbach AL, Giberson CM, Lee JY, Huntley AP, Smith RD, Ibrahim YM. Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter. J Am Soc Mass Spectrom 2021; 32:2698-2706. [PMID: 34590845 PMCID: PMC8742676 DOI: 10.1021/jasms.1c00226] [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] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it greatly affects signal-to-noise ratio and MS resolution measurements. Here, we report on the integration of a 2 GS/s, 14-bit ADC with structures for lossless ion manipulations (SLIM-IMS-MS) and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided a reduction in the digitized noise by a factor of ∼6, owing largely to the use of smaller bit sizes. The low baseline allowed threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a mixture of heavy labeled phosphopeptides showed that the 14-bit ADC provided a ∼1.5-2× signal-to-noise (S/N) increase for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernible signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ∼14-fold fewer mass spectra to be averaged to produce a mass spectrum with a similar S/N as the 8-bit ADC, demonstrating ∼10× higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra and provides a much better picture of analyte profiles in complex mixtures.
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Affiliation(s)
- Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Cameron M Giberson
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Adam P Huntley
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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Jeong DY, Lee J, Kim JY, Lee KH, Li H, Lee JY, Jeong GH, Yoon S, Park EL, Hong SH, Kang JW, Song TJ, Leyhe T, Eisenhut M, Kronbichler A, Smith L, Solmi M, Stubbs B, Koyanagi A, Jacob L, Stickley A, Thompson T, Dragioti E, Oh H, Brunoni AR, Carvalho AF, Kim MS, Yon DK, Lee SW, Yang JM, Ghayda RA, Shin JI, Fusar-Poli P. Empirical assessment of biases in cerebrospinal fluid biomarkers of Alzheimer's disease: an umbrella review and re-analysis of data from meta-analyses. Eur Rev Med Pharmacol Sci 2021; 25:1536-1547. [PMID: 33629323 DOI: 10.26355/eurrev_202102_24862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Alzheimer's disease (AD) is a leading cause of years lived with disability in older age, and several cerebrospinal fluid (CSF) markers have been proposed in individual meta-analyses to be associated with AD but field-wide evaluation and scrutiny of the literature is not available. MATERIALS AND METHODS We performed an umbrella review for the reported associations between CSF biomarkers and AD. Data from available meta-analyses were reanalyzed using both random and fixed effects models. We also estimated between-study heterogeneity, small-study effects, excess significance, and prediction interval. RESULTS A total of 38 meta-analyses on CSF markers from 11 eligible articles were identified and reanalyzed. In 14 (36%) of the meta-analyses, the summary estimate and the results of the largest study showed non-concordant results in terms of statistical significance. Large heterogeneity (I2≥75%) was observed in 73% and small-study effects under Egger's test were shown in 28% of CSF biomarkers. CONCLUSIONS Our results suggest that there is an excess of statistically significant results and significant biases in the literature of CSF biomarkers for AD. Therefore, the results of CSF biomarkers should be interpreted with caution.
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Affiliation(s)
- D Y Jeong
- Yonsei University College of Medicine, Seoul, Republic of Korea.
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Park GR, Kim HS, Kim YT, Chung HJ, Ha SJ, Kim DW, Kang DR, Kim JY, Lee MY, Lee JY. Waist circumference and the risk of lumbar and femur fractures: a nationwide population-based cohort study. Eur Rev Med Pharmacol Sci 2021; 25:1198-1205. [PMID: 33629289 DOI: 10.26355/eurrev_202102_24822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Although obesity is known to have an influence on fracture, the relationship between lumbar and femur fractures and weight or waist circumference is controversial. We investigated the incidence of fracture with regards to waist circumference using the customised database of the Korean National Health Insurance Service (NHIS). Among 8,922,940 adults who participated at least twice in the NHIS National Health Check-up Program in South Korea between 2009 and 2011, 1,556,751 subjects (780,074 men and 776,677 women) were extracted. Over a mean follow-up of 6.5 years, multivariate-adjusted logistic regression analysis demonstrated that higher waist circumference was associated with an increased risk of femur fractures in both males and females. Moreover, the incidence of lumbar fractures was also positively associated with an increased waist circumference in males and females. An increased waist circumference showed a positive linear relationship with the risk of lumbar and femur fractures in both males and females.
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Affiliation(s)
- G R Park
- Department of Internal Medicine, Yonsei Wonju College of Medicine, Wonju, Republic of Korea.
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Park EA, Kang KY, Lee JH, Lee JY, Kim HS, Choi HS, Song GY, Moon EH, Shiin MY, Hur YJ, Yu EJ, Kim R, Koong MK, Lee KA, Kim MJ. P–153 Comparison outcome of vitrified human embryos stored in vapor phase liquid nitrogen (LN2) and direct LN2. Hum Reprod 2021. [DOI: 10.1093/humrep/deab130.152] [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: 11/12/2022] Open
Abstract
Abstract
Study question
Is vapor cryopreserved LN2 storage beneficial for clinical outcomes of vitrified human embryos that are frozen compared to vitrified human embryos having direct contact with LN2.
Summary answer
There are no significant differences compared to clinical outcomes of human embryos stored in LN2 vapor and direct store in LN2.
What is known already
There has been concerned about potential cross-contamination and biohazard issues of embryos for long term storage using direct LN2. This study aimed to compare clinical outcomes of human embryos transfer between vapor phase and liquid LN2.
Study design, size, duration
The embryo has undergone vitrification for long term storage with vapor or direct contact in LN2. After the thawing of the embryo, we checked on the survival rates. We transferred only one or two embryos per patient and kept analyzing the implantation and pregnancy rates
Participants/materials, setting, methods
This retrospective study was carried out from January 2018 to December 2019 with 3272cycles 4713embryos; vitrified for long term storage in vapor phase or direct contact with LN2. We compared the clinical outcomes of frozen embryo transfer cycles using vitrified for long term storage in vapor phase and direct contact with LN2. Clinical outcomes monitored were embryo survival, subsequent implantation and pregnancy after single or double embryo transfer
Main results and the role of chance
A total of 4713 fertilized human embryos are vitrified and then stored in LN2 vapor (n = 2520 cycles) or direct contact LN2 (n = 752 cycles). The study showed that the blastocyst stored in vapor able to retain full development. Survival was 97.8% (vapor) and 97.6% (direct contact LN2), and the vapor storage of human embryos had no significant difference in survival rates after a long term storage. For single blastocyst transfer, pregnancy and implantation rates were 51.5%, 52.4% in vapor, 54.6%, 54.9% in direct LN2; respectively (p=NS). In double blastocyst transfer, the pregnancy and implantation rates were 61.8%, 42.0% in vapor and 64.7%, 44.5% in direct LN2; respectively (p=NS). There were also no significant differences between two groups.
Limitations, reasons for caution
The study showed that the blastocyst stored in vapor can retain full development. A vapor storage system thus is safe and effective for long term vapor storage of vitrified human embryos.Within the limits of this study, there was no detection of an adverse effect of vapor storage.
Wider implications of the findings: Vapor storage systems thus represent a useful alternative for safe and effective long-term storage of vitrified human embryos that can avoid cross contamination chances from having direct contact with LN2.
Trial registration number
Not applicable
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Affiliation(s)
- E A Park
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - K Y Kang
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - J H Lee
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - J Y Lee
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - H S Kim
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - H S Choi
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - G Y Song
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - E H Moon
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - M Y Shiin
- CHA Fertility Center Seoul Station, Fertility laboratory, Seoul, Korea- South
| | - Y J Hur
- CHA Fertility Center Seoul Station, Department of Obstetrics and Gynecology, Seoul, Korea- South
| | - E J Yu
- CHA Fertility Center Seoul Station, Department of Obstetrics and Gynecology, Seoul, Korea- South
| | - R Kim
- CHA Fertility Center Seoul Station, Department of Obstetrics and Gynecology, Seoul, Korea- South
| | - M K Koong
- CHA Fertility Center Seoul Station, Department of Obstetrics and Gynecology, Seoul, Korea- South
| | - K A Lee
- CHA University, Department of Biomedical Science- College of Life Science, Seoul, Korea- South
| | - M J Kim
- CHA Fertility Center Seoul Station, Department of Obstetrics and Gynecology, Seoul, Korea- South
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Abou Ghayda R, Duck-Young Park D, Lee JY, Kim JY, Lee KH, Hong SH, Yang JW, Kim JS, Jeong GH, Kronbichler A, Koyanagi A, Jacob L, Oh H, Li H, Yang JM, Kim MS, Lee SW, Yon DK, Shin JI, Smith L. Body mass index and mortality in patients with cardiovascular disease: an umbrella review of meta-analyses. Eur Rev Med Pharmacol Sci 2021; 25:273-286. [PMID: 33506916 DOI: 10.26355/eurrev_202101_24393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Although many previous meta-analyses of epidemiological studies have demonstrated a relationship between body mass index (BMI) and mortality, inconsistent findings among cardiovascular disease patients have been observed. Thus, we performed an umbrella review to understand the strength of evidence and validity of claimed associations between BMI and mortality in patients with cardiovascular diseases. MATERIALS AND METHODS We comprehensively re-analyzed the data of meta-analyses of observational studies and randomized controlled trials on associations between BMI and mortality among patients with cardiovascular diseases. We also assessed the strength of evidence of the re-analyzed outcomes, which were determined from the criteria including statistical significance of the p-value of random-effects, as well as fixed-effects meta-analyses, small-study effects, between-study heterogeneity, and a 95% prediction interval. RESULTS We ran comprehensive re-analysis of the data from the 21 selected studies, which contained a total of 108 meta-analyses; 23 were graded as convincing evidence and 12 were suggestive, 42 were weak, and 23 were non-significant. CONCLUSIONS Underweight increased mortality in acute coronary syndrome (ACS), heart failure, and after therapeutic intervention for patients with cardiovascular diseases. Overweight, on the other hand decreased mortality in patient's ACS, atrial fibrillation, and heart failure with convincing evidence.
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Affiliation(s)
- R Abou Ghayda
- Urology Institute, University Hospital System, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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An HM, Yeo SH, Chung HJ, Cho HS, Bae SJ, Kim JY, Kang DR, Lee MY, Lee JY. Visit-to-visit changes in fasting blood sugar and the risk for cardiovascular disease and mortality in the Korean population: a nationwide population-based cohort study. Eur Rev Med Pharmacol Sci 2021; 25:263-272. [PMID: 33506915 DOI: 10.26355/eurrev_202101_24392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The importance of continuous monitoring of fasting blood sugar (FBS) levels of diabetic patients has been established. MATERIALS AND METHODS An observational prospective study was conducted. Our analysis included 1,700,796 individuals from the nationwide South Korean National Health Insurance System cohort. FBS variability was measured by standard deviation (SD). RESULTS Kaplan-Meier curves demonstrated elevated disease probability in the higher FBS fluctuation group compared with the lower FBS fluctuation group. After adjusting for confounding variables, Cox proportional hazards analysis showed that the hazard ratios of 411 individuals in the highest quartile of SD variation of FBS were 1.77 (95% confidence interval 1.37-2.28, p<0.001) compared with the lowest quartile of SD variation of FBS. The impact of FBS fluctuation on the risk of cardiovascular diseases (CVDs), cerebrovascular diseases, CVD mortality and all-cause mortality in the highest quartiles of diabetic and non-diabetic individuals was statistically significant. CONCLUSIONS Visit-to-visit FBS variability has prognostic value for predicting micro- and macrovascular disease, cardiovascular mortality, and all-cause mortality.
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Affiliation(s)
- H M An
- Yonsei University Wonju College of Medicine, Wonju, South Korea.
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Lee JY, Bilbao A, Conant CR, Bloodsworth KJ, Orton DJ, Zhou M, Wilson JW, Zheng X, Webb IK, Li A, Hixson KK, Fjeldsted JC, Ibrahim YM, Payne SH, Jansson C, Smith RD, Metz TO. AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry. Bioinformatics 2021; 37:4193-4201. [PMID: 34145874 PMCID: PMC9502155 DOI: 10.1093/bioinformatics/btab429] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/23/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion's collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. RESULTS We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: 1) stepped-field methods for drift tube-based IMS (DTIMS), 2) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and 3) non-linear calibration methods for traveling wave based-IMS (TWIMS) in Waters Synapt and Structures for Lossless Ion Manipulations (SLIM). We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes, and collision gases, without requiring manual processing. AVAILABILITY https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joon-Yong Lee
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Christopher R Conant
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Daniel J Orton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jesse W Wilson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ian K Webb
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Ailin Li
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kim K Hixson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Christer Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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Lee JY, Lim HM, Lee CM, Park SH, Nam MJ. Indole-3-carbinol inhibits the proliferation of colorectal carcinoma LoVo cells through activation of the apoptotic signaling pathway. Hum Exp Toxicol 2021; 40:2099-2112. [PMID: 34085558 DOI: 10.1177/09603271211021475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Indole-3-carbinol (I3C) is a phytochemical that exhibits growth-inhibitory activity against various cancer cells. However, there are limited studies on the effects of I3C on colon cancer cells. In this study, the growth-inhibitory activity of I3C against the human colorectal carcinoma cell line (LoVo) was examined. The results of the 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide, colony formation, and cell counting assays revealed that I3C suppressed the proliferation of LoVo cells. Microscopy and wound-healing analyses revealed that I3C affected the morphology and inhibited the migration of LoVo cells, respectively. I3C induced apoptosis and DNA fragmentation as evidenced by the results of fluorescein isothiocyanate-conjugated annexin V staining and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling assay, respectively. Additionally, I3C arrested the cell cycle at the G0/G1 phase and enhanced the reactive oxygen species levels. Western blotting analysis revealed that treatment with I3C resulted in the activation of apoptotic proteins, such as poly(ADP-ribose) polymerase, caspase-3, caspase-7, caspase-9, Bax, Bim, and p53 in LoVo cells. These results indicate that I3C induces apoptosis in LoVo cells by upregulating p53, leading to the activation of Bax and caspases. Taken together, I3C exerts cytotoxic effects on LoVo cells by activating apoptosis.
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Affiliation(s)
- J Y Lee
- Department of Biological Science, 65440Gachon University, Sujeong-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - H M Lim
- Department of Biological Science, 65440Gachon University, Sujeong-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - C M Lee
- Department of Bio&Chemical Engineering, 65686Hongik University, Jochiwon-eup, Sejong-si, Republic of Korea
| | - S-H Park
- Department of Bio&Chemical Engineering, 65686Hongik University, Jochiwon-eup, Sejong-si, Republic of Korea
| | - M J Nam
- Department of Biological Science, 65440Gachon University, Sujeong-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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Abstract
Foam cells are one of the major cellular components of atherosclerotic plaques, within which the trace of periodontal pathogens has also been identified in recent studies. In line with these findings, the correlation between periodontitis and atherosclerotic cardiovascular incidences has been repetitively supported by evidence from a number of experimental studies. However, the direct role of periodontal pathogens in altered cellular signaling underlying such cardiovascular events has not been clearly defined. To determine the role of periodontal pathogens in the pathogenesis of atherosclerosis, especially in the evolution of macrophages into foam cells, we monitored the pattern of lipid accumulation within macrophages in the presence of periodontal pathogens, followed by characterization of these lipids and investigation of major molecules involved in lipid homeostasis. The cells were stained with the lipophilic fluorescent dye BODIPY 493/503 and Oil Red O to characterize the lipid profile. The amounts of Oil Red O-positive droplets, representing neutral lipids, as well as fluorescent lipid aggregates were prominently increased in periodontal pathogen-infected macrophages. Subsequent analysis allowed us to locate the accumulated lipids in the endoplasmic reticulum. In addition, the levels of cholesteryl ester in periodontal pathogen-infected macrophages were increased, implying disrupted lipid homeostasis. Further investigations to delineate the key messengers and regulatory factors involved in the altered lipid homeostasis have revealed alterations in cholesterol efflux-related enzymes, such as ABCG1 and CYP46A1, as contributors to foam cell formation, and increased Ca2+ signaling and reactive oxygen species (ROS) production as key events underlying disrupted lipid homeostasis. Consistently, a treatment of periodontal pathogen-infected macrophages with ROS inhibitors and nifedipine attenuated the accumulation of lipid droplets, further confirming periodontal pathogen-induced alterations in Ca2+ and ROS signaling and the subsequent dysregulation of lipid homeostasis as key regulatory events underlying the evolution of macrophages into foam cells.
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Affiliation(s)
- J H Rho
- Department of Oral Pathology and BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
- Department of Periodontology, School of Dentistry, Pusan National University, Pusan National University Dental Hospital, Yangsan, Republic of Korea
| | - H J Kim
- Department of Oral Pathology and BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
- Department of Periodontology, School of Dentistry, Pusan National University, Pusan National University Dental Hospital, Yangsan, Republic of Korea
| | - J Y Joo
- Department of Periodontology, School of Dentistry, Pusan National University, Pusan National University Dental Hospital, Yangsan, Republic of Korea
- Periodontal Disease Signaling Network Research Center, Dental & Life Science Institute, Pusan National University, Yangsan, Republic of Korea
| | - J Y Lee
- Department of Periodontology, School of Dentistry, Pusan National University, Pusan National University Dental Hospital, Yangsan, Republic of Korea
- Periodontal Disease Signaling Network Research Center, Dental & Life Science Institute, Pusan National University, Yangsan, Republic of Korea
| | - J H Lee
- Department of Oral Pathology and BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
- Periodontal Disease Signaling Network Research Center, Dental & Life Science Institute, Pusan National University, Yangsan, Republic of Korea
| | - H R Park
- Department of Oral Pathology and BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
- Periodontal Disease Signaling Network Research Center, Dental & Life Science Institute, Pusan National University, Yangsan, Republic of Korea
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43
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Wehle S, Adachi I, Adamczyk K, Aihara H, Asner DM, Atmacan H, Aulchenko V, Aushev T, Ayad R, Babu V, Behera P, Berger M, Bhardwaj V, Biswal J, Bozek A, Bračko M, Browder TE, Campajola M, Cao L, Chang MC, Chen A, Cheon BG, Chilikin K, Cho K, Choi Y, Choudhury S, Cinabro D, Cunliffe S, Dash N, De Nardo G, Di Capua F, Dubey S, Eidelman S, Epifanov D, Ferber T, Fulsom BG, Garg R, Gaur V, Gabyshev N, Garmash A, Giri A, Goldenzweig P, Greenwald D, Guan Y, Haba J, Hartbrich O, Hayasaka K, Hayashii H, Hedges MT, Higuchi T, Hou WS, Hsu CL, Iijima T, Inami K, Inguglia G, Ishikawa A, Itoh R, Iwasaki M, Iwasaki Y, Jacobs WW, Jia S, Jin Y, Joffe D, Kahn J, Kaliyar AB, Karyan G, Kichimi H, Kim DY, Kim KT, Kim SH, Kim YK, Kinoshita K, Komarov I, Korpar S, Kotchetkov D, Kroeger R, Krokovny P, Kuhr T, Kulasiri R, Kumar R, Kumara K, Kuzmin A, Kwon YJ, Lange JS, Lee JY, Lee SC, Li YB, Libby J, Liptak Z, Liventsev D, Luo T, MacNaughton J, Masuda M, Matsuda T, McNeil JT, Merola M, Metzner F, Miyata H, Mizuk R, Mohanty GB, Moon TJ, Mussa R, Nakao M, Natochii A, Nayak M, Niebuhr C, Niiyama M, Nisar NK, Nishida S, Ogawa K, Ogawa S, Ono H, Onuki Y, Pakhlov P, Pakhlova G, Park H, Park SH, Pedlar TK, Pestotnik R, Piilonen LE, Podobnik T, Popov V, Prencipe E, Prim MT, Resmi PK, Ritter M, Rostomyan A, Rout N, Russo G, Sahoo D, Sakai Y, Sandilya S, Sangal A, Santelj L, Savinov V, Schneider O, Schnell G, Schueler J, Schwanda C, Schwartz AJ, Seino Y, Senyo K, Sevior ME, Shapkin M, Shiu JG, Shwartz B, Solovieva E, Starič M, Strube JF, Sumiyoshi T, Sutcliffe W, Takizawa M, Tamponi U, Tanida K, Tao Y, Tenchini F, Trabelsi K, Uchida M, Uglov T, Unno Y, Uno S, Ushiroda Y, Vahsen SE, Van Tonder R, Varner G, Varvell KE, Vorobyev V, Wang CH, Wang MZ, Wang P, Wang XL, Won E, Xu X, Yang SB, Ye H, Yin JH, Yuan CZ, Zhang ZP, Zhilich V, Zhukova V, Zhulanov V. Test of Lepton-Flavor Universality in B→K^{*}ℓ^{+}ℓ^{-} Decays at Belle. Phys Rev Lett 2021; 126:161801. [PMID: 33961476 DOI: 10.1103/physrevlett.126.161801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
We present a measurement of R_{K^{*}}, the branching fraction ratio B(B→K^{*}μ^{+}μ^{-})/B(B→K^{*}e^{+}e^{-}), for both charged and neutral B mesons. The ratio for the charged case R_{K^{*+}} is the first measurement ever performed. In addition, we report absolute branching fractions for the individual modes in bins of the squared dilepton invariant mass q^{2}. The analysis is based on a data sample of 711 fb^{-1}, containing 772×10^{6} BB[over ¯] events, recorded at the ϒ(4S) resonance with the Belle detector at the KEKB asymmetric-energy e^{+}e^{-} collider. The obtained results are consistent with standard model expectations.
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Affiliation(s)
- S Wehle
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - I Adachi
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - K Adamczyk
- H. Niewodniczanski Institute of Nuclear Physics, Krakow 31-342
| | - H Aihara
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - D M Asner
- Brookhaven National Laboratory, Upton, New York 11973
| | - H Atmacan
- University of Cincinnati, Cincinnati, Ohio 45221
| | - V Aulchenko
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - T Aushev
- Higher School of Economics (HSE), Moscow 101000
| | - R Ayad
- Department of Physics, Faculty of Science, University of Tabuk, Tabuk 71451
| | - V Babu
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - P Behera
- Indian Institute of Technology Madras, Chennai 600036
| | - M Berger
- Stefan Meyer Institute for Subatomic Physics, Vienna 1090
| | - V Bhardwaj
- Indian Institute of Science Education and Research Mohali, SAS Nagar, 140306
| | - J Biswal
- J. Stefan Institute, 1000 Ljubljana
| | - A Bozek
- H. Niewodniczanski Institute of Nuclear Physics, Krakow 31-342
| | - M Bračko
- J. Stefan Institute, 1000 Ljubljana
- University of Maribor, 2000 Maribor
| | - T E Browder
- University of Hawaii, Honolulu, Hawaii 96822
| | - M Campajola
- INFN-Sezione di Napoli, 80126 Napoli
- Università di Napoli Federico II, 80126 Napoli
| | - L Cao
- University of Bonn, 53115 Bonn
| | - M-C Chang
- Department of Physics, Fu Jen Catholic University, Taipei 24205
| | - A Chen
- National Central University, Chung-li 32054
| | - B G Cheon
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - K Chilikin
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - K Cho
- Korea Institute of Science and Technology Information, Daejeon 34141
| | - Y Choi
- Sungkyunkwan University, Suwon 16419
| | - S Choudhury
- Indian Institute of Technology Hyderabad, Telangana 502285
| | - D Cinabro
- Wayne State University, Detroit, Michigan 48202
| | - S Cunliffe
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - N Dash
- Indian Institute of Technology Madras, Chennai 600036
| | - G De Nardo
- INFN-Sezione di Napoli, 80126 Napoli
- Università di Napoli Federico II, 80126 Napoli
| | - F Di Capua
- INFN-Sezione di Napoli, 80126 Napoli
- Università di Napoli Federico II, 80126 Napoli
| | - S Dubey
- University of Hawaii, Honolulu, Hawaii 96822
| | - S Eidelman
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Novosibirsk State University, Novosibirsk 630090
| | - D Epifanov
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - T Ferber
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - B G Fulsom
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - R Garg
- Panjab University, Chandigarh 160014
| | - V Gaur
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - N Gabyshev
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - A Garmash
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - A Giri
- Indian Institute of Technology Hyderabad, Telangana 502285
| | - P Goldenzweig
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - D Greenwald
- Department of Physics, Technische Universität München, 85748 Garching
| | - Y Guan
- University of Cincinnati, Cincinnati, Ohio 45221
| | - J Haba
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - O Hartbrich
- University of Hawaii, Honolulu, Hawaii 96822
| | | | | | - M T Hedges
- University of Hawaii, Honolulu, Hawaii 96822
| | - T Higuchi
- Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, Kashiwa 277-8583
| | - W-S Hou
- Department of Physics, National Taiwan University, Taipei 10617
| | - C-L Hsu
- School of Physics, University of Sydney, New South Wales 2006
| | - T Iijima
- Graduate School of Science, Nagoya University, Nagoya 464-8602
- Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602
| | - K Inami
- Graduate School of Science, Nagoya University, Nagoya 464-8602
| | - G Inguglia
- Institute of High Energy Physics, Vienna 1050
| | - A Ishikawa
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - R Itoh
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - M Iwasaki
- Osaka City University, Osaka 558-8585
| | - Y Iwasaki
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - W W Jacobs
- Indiana University, Bloomington, Indiana 47408
| | - S Jia
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - Y Jin
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - D Joffe
- Kennesaw State University, Kennesaw, Georgia 30144
| | - J Kahn
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - A B Kaliyar
- Tata Institute of Fundamental Research, Mumbai 400005
| | - G Karyan
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - H Kichimi
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - D Y Kim
- Soongsil University, Seoul 06978
| | - K T Kim
- Korea University, Seoul 02841
| | - S H Kim
- Seoul National University, Seoul 08826
| | - Y-K Kim
- Yonsei University, Seoul 03722
| | - K Kinoshita
- University of Cincinnati, Cincinnati, Ohio 45221
| | - I Komarov
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - S Korpar
- J. Stefan Institute, 1000 Ljubljana
- University of Maribor, 2000 Maribor
| | | | - R Kroeger
- University of Mississippi, University, Mississippi 38677
| | - P Krokovny
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - T Kuhr
- Ludwig Maximilians University, 80539 Munich
| | - R Kulasiri
- Kennesaw State University, Kennesaw, Georgia 30144
| | - R Kumar
- Punjab Agricultural University, Ludhiana 141004
| | - K Kumara
- Wayne State University, Detroit, Michigan 48202
| | - A Kuzmin
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | | | - J S Lange
- Justus-Liebig-Universität Gießen, 35392 Gießen
| | - J Y Lee
- Seoul National University, Seoul 08826
| | - S C Lee
- Kyungpook National University, Daegu 41566
| | - Y B Li
- Peking University, Beijing 100871
| | - J Libby
- Indian Institute of Technology Madras, Chennai 600036
| | - Z Liptak
- Hiroshima Institute of Technology, Hiroshima 731-5193
| | - D Liventsev
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
- Wayne State University, Detroit, Michigan 48202
| | - T Luo
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | | | - M Masuda
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047
- Earthquake Research Institute, University of Tokyo, Tokyo 113-0032
| | - T Matsuda
- University of Miyazaki, Miyazaki 889-2192
| | - J T McNeil
- University of Florida, Gainesville, Florida 32611
| | - M Merola
- INFN-Sezione di Napoli, 80126 Napoli
- Università di Napoli Federico II, 80126 Napoli
| | - F Metzner
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - H Miyata
- Niigata University, Niigata 950-2181
| | - R Mizuk
- Higher School of Economics (HSE), Moscow 101000
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - G B Mohanty
- Tata Institute of Fundamental Research, Mumbai 400005
| | - T J Moon
- Seoul National University, Seoul 08826
| | - R Mussa
- INFN-Sezione di Torino, 10125 Torino
| | - M Nakao
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - A Natochii
- University of Hawaii, Honolulu, Hawaii 96822
| | - M Nayak
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978
| | - C Niebuhr
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - M Niiyama
- Kyoto Sangyo University, Kyoto 603-8555
| | - N K Nisar
- Brookhaven National Laboratory, Upton, New York 11973
| | - S Nishida
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - K Ogawa
- Niigata University, Niigata 950-2181
| | - S Ogawa
- Toho University, Funabashi 274-8510
| | - H Ono
- Nippon Dental University, Niigata 951-8580
- Niigata University, Niigata 950-2181
| | - Y Onuki
- Department of Physics, University of Tokyo, Tokyo 113-0033
| | - P Pakhlov
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Moscow Physical Engineering Institute, Moscow 115409
| | - G Pakhlova
- Higher School of Economics (HSE), Moscow 101000
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - H Park
- Kyungpook National University, Daegu 41566
| | | | | | | | - L E Piilonen
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - T Podobnik
- J. Stefan Institute, 1000 Ljubljana
- Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana
| | - V Popov
- Higher School of Economics (HSE), Moscow 101000
| | | | - M T Prim
- Institut für Experimentelle Teilchenphysik, Karlsruher Institut für Technologie, 76131 Karlsruhe
| | - P K Resmi
- Indian Institute of Technology Madras, Chennai 600036
| | - M Ritter
- Ludwig Maximilians University, 80539 Munich
| | - A Rostomyan
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - N Rout
- Indian Institute of Technology Madras, Chennai 600036
| | - G Russo
- Università di Napoli Federico II, 80126 Napoli
| | - D Sahoo
- Tata Institute of Fundamental Research, Mumbai 400005
| | - Y Sakai
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - S Sandilya
- University of Cincinnati, Cincinnati, Ohio 45221
| | - A Sangal
- University of Cincinnati, Cincinnati, Ohio 45221
| | - L Santelj
- J. Stefan Institute, 1000 Ljubljana
- Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana
| | - V Savinov
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - O Schneider
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015
| | - G Schnell
- University of the Basque Country UPV/EHU, 48080 Bilbao
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao
| | - J Schueler
- University of Hawaii, Honolulu, Hawaii 96822
| | - C Schwanda
- Institute of High Energy Physics, Vienna 1050
| | - A J Schwartz
- University of Cincinnati, Cincinnati, Ohio 45221
| | - Y Seino
- Niigata University, Niigata 950-2181
| | - K Senyo
- Yamagata University, Yamagata 990-8560
| | - M E Sevior
- School of Physics, University of Melbourne, Victoria 3010
| | - M Shapkin
- Institute for High Energy Physics, Protvino 142281
| | - J-G Shiu
- Department of Physics, National Taiwan University, Taipei 10617
| | - B Shwartz
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - E Solovieva
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - M Starič
- J. Stefan Institute, 1000 Ljubljana
| | - J F Strube
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - T Sumiyoshi
- Tokyo Metropolitan University, Tokyo 192-0397
| | | | - M Takizawa
- J-PARC Branch, KEK Theory Center, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
- Showa Pharmaceutical University, Tokyo 194-8543
| | - U Tamponi
- INFN-Sezione di Torino, 10125 Torino
| | - K Tanida
- Advanced Science Research Center, Japan Atomic Energy Agency, Naka 319-1195
| | - Y Tao
- University of Florida, Gainesville, Florida 32611
| | - F Tenchini
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - K Trabelsi
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay
| | - M Uchida
- Tokyo Institute of Technology, Tokyo 152-8550
| | - T Uglov
- Higher School of Economics (HSE), Moscow 101000
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - Y Unno
- Department of Physics and Institute of Natural Sciences, Hanyang University, Seoul 04763
| | - S Uno
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - Y Ushiroda
- SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193
- High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801
| | - S E Vahsen
- University of Hawaii, Honolulu, Hawaii 96822
| | | | - G Varner
- University of Hawaii, Honolulu, Hawaii 96822
| | - K E Varvell
- School of Physics, University of Sydney, New South Wales 2006
| | - V Vorobyev
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
- Novosibirsk State University, Novosibirsk 630090
| | - C H Wang
- National United University, Miao Li 36003
| | - M-Z Wang
- Department of Physics, National Taiwan University, Taipei 10617
| | - P Wang
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049
| | - X L Wang
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics, Fudan University, Shanghai 200443
| | - E Won
- Korea University, Seoul 02841
| | - X Xu
- Soochow University, Suzhou 215006
| | | | - H Ye
- Deutsches Elektronen-Synchrotron, 22607 Hamburg
| | - J H Yin
- Korea University, Seoul 02841
| | - C Z Yuan
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049
| | - Z P Zhang
- Department of Modern Physics and State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026
| | - V Zhilich
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
| | - V Zhukova
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow 119991
| | - V Zhulanov
- Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090
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Lee JY, Kim BJ, Lee SH, Lee JW, Lee WS. Low quality of life and high HSS-29 scores reflect the risk of loss to follow-up: a study in patients with androgenetic alopecia. J Eur Acad Dermatol Venereol 2021; 35:e457-e459. [PMID: 33657244 DOI: 10.1111/jdv.17212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/24/2021] [Indexed: 11/29/2022]
Affiliation(s)
- J Y Lee
- Department of Dermatology and Institute of Hair and Cosmetic Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - B J Kim
- Department of Dermatology and Institute of Hair and Cosmetic Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - S H Lee
- Department of Dermatology and Institute of Hair and Cosmetic Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - J W Lee
- Department of Dermatology and Institute of Hair and Cosmetic Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - W S Lee
- Department of Dermatology and Institute of Hair and Cosmetic Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
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Hayakawa SH, Agari K, Ahn JK, Akaishi T, Akazawa Y, Ashikaga S, Bassalleck B, Bleser S, Ekawa H, Endo Y, Fujikawa Y, Fujioka N, Fujita M, Goto R, Han Y, Hasegawa S, Hashimoto T, Hayakawa T, Hayata E, Hicks K, Hirose E, Hirose M, Honda R, Hoshino K, Hoshino S, Hosomi K, Hwang SH, Ichikawa Y, Ichikawa M, Imai K, Inaba K, Ishikawa Y, Ito H, Ito K, Jung WS, Kanatsuki S, Kanauchi H, Kasagi A, Kawai T, Kim MH, Kim SH, Kinbara S, Kiuchi R, Kobayashi H, Kobayashi K, Koike T, Koshikawa A, Lee JY, Ma TL, Matsumoto SY, Minakawa M, Miwa K, Moe AT, Moon TJ, Moritsu M, Nagase Y, Nakada Y, Nakagawa M, Nakashima D, Nakazawa K, Nanamura T, Naruki M, Nyaw ANL, Ogura Y, Ohashi M, Oue K, Ozawa S, Pochodzalla J, Ryu SY, Sako H, Sato S, Sato Y, Schupp F, Shirotori K, Soe MM, Soe MK, Sohn JY, Sugimura H, Suzuki KN, Takahashi H, Takahashi T, Takeda T, Tamura H, Tanida K, Theint AMM, Tint KT, Toyama Y, Ukai M, Umezaki E, Watabe T, Watanabe K, Yamamoto TO, Yang SB, Yoon CS, Yoshida J, Yoshimoto M, Zhang DH, Zhang Z. Observation of Coulomb-Assisted Nuclear Bound State of Ξ^{-}-^{14}N System. Phys Rev Lett 2021; 126:062501. [PMID: 33635678 DOI: 10.1103/physrevlett.126.062501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
In an emulsion-counter hybrid experiment performed at J-PARC, a Ξ^{-} absorption event was observed which decayed into twin single-Λ hypernuclei. Kinematic calculations enabled a unique identification of the reaction process as Ξ^{-}+^{14}N→_{Λ}^{10}Be+_{Λ}^{5}He. For the binding energy of the Ξ^{-} hyperon in the Ξ^{-}-^{14}N system a value of 1.27±0.21 MeV was deduced. The energy level of Ξ^{-} is likely a nuclear 1p state which indicates a weak ΞN-ΛΛ coupling.
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Affiliation(s)
- S H Hayakawa
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - K Agari
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - J K Ahn
- Department of Physics, Korea University, Seoul 02841, Korea
| | - T Akaishi
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - Y Akazawa
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - S Ashikaga
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - B Bassalleck
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - S Bleser
- Helmholtz Institute Mainz, 55099 Mainz, Germany
| | - H Ekawa
- High Energy Nuclear Physics Laboratory, RIKEN, Wako 351-0198, Japan
| | - Y Endo
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - Y Fujikawa
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - N Fujioka
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - M Fujita
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - R Goto
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - Y Han
- Institute of Nuclear Energy Safety Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - S Hasegawa
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - T Hashimoto
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - T Hayakawa
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - E Hayata
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - K Hicks
- Department of Physics & Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - E Hirose
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - M Hirose
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - R Honda
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - K Hoshino
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - S Hoshino
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - K Hosomi
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - S H Hwang
- Korea Research Institute of Standards and Science, Daejeon 34113, Korea
| | - Y Ichikawa
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - M Ichikawa
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- Meson Science Laboratory, RIKEN, Wako 351-0198, Japan
| | - K Imai
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - K Inaba
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - Y Ishikawa
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - H Ito
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - K Ito
- Department of Physics, Nagoya University, Nagoya 464-8601, Japan
| | - W S Jung
- Department of Physics, Korea University, Seoul 02841, Korea
| | - S Kanatsuki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - H Kanauchi
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - A Kasagi
- High Energy Nuclear Physics Laboratory, RIKEN, Wako 351-0198, Japan
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - T Kawai
- Center for Advanced Photonics, RIKEN, Wako 351-0198, Japan
| | - M H Kim
- Department of Physics, Korea University, Seoul 02841, Korea
| | - S H Kim
- Department of Physics, Korea University, Seoul 02841, Korea
| | - S Kinbara
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - R Kiuchi
- Institute of High Energy Physics, Beijing 100049, China
| | - H Kobayashi
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - K Kobayashi
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - T Koike
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - A Koshikawa
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - J Y Lee
- Department of Physics, Seoul National University, Seoul 08826, Korea
| | - T L Ma
- Institute of Modern Physics, Shanxi Normal University, Linfen 041004, China
| | - S Y Matsumoto
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- Meson Science Laboratory, RIKEN, Wako 351-0198, Japan
| | - M Minakawa
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - K Miwa
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - A T Moe
- Department of Physics, Lashio University, Lashio 06301, Myanmar
| | - T J Moon
- Department of Physics, Seoul National University, Seoul 08826, Korea
| | - M Moritsu
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - Y Nagase
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - Y Nakada
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - M Nakagawa
- High Energy Nuclear Physics Laboratory, RIKEN, Wako 351-0198, Japan
| | - D Nakashima
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - K Nakazawa
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - T Nanamura
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - M Naruki
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - A N L Nyaw
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Y Ogura
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - M Ohashi
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - K Oue
- Department of Physics, Osaka University, Toyonaka 560-0043, Japan
| | - S Ozawa
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - J Pochodzalla
- Helmholtz Institute Mainz, 55099 Mainz, Germany
- Institut fur Kernphysik, Johannes Gutenberg-Universitat, 55099 Mainz, Germany
| | - S Y Ryu
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047, Japan
| | - H Sako
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - S Sato
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - Y Sato
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - F Schupp
- Helmholtz Institute Mainz, 55099 Mainz, Germany
| | - K Shirotori
- Research Center for Nuclear Physics, Osaka University, Osaka 567-0047, Japan
| | - M M Soe
- Department of Physics, University of Yangon, Yangon 11041, Myanmar
| | - M K Soe
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - J Y Sohn
- Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Korea
| | - H Sugimura
- Accelerator Laboratory, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - K N Suzuki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - H Takahashi
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - T Takahashi
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - T Takeda
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - H Tamura
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - K Tanida
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - A M M Theint
- Graduate School of Engineering, Gifu University, Gifu 501-1193, Japan
| | - K T Tint
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - Y Toyama
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - M Ukai
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - E Umezaki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - T Watabe
- Department of Physics, Nagoya University, Nagoya 464-8601, Japan
| | - K Watanabe
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - T O Yamamoto
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - S B Yang
- Department of Physics, Korea University, Seoul 02841, Korea
| | - C S Yoon
- Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Korea
| | - J Yoshida
- High Energy Nuclear Physics Laboratory, RIKEN, Wako 351-0198, Japan
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - M Yoshimoto
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - D H Zhang
- Institute of Modern Physics, Shanxi Normal University, Linfen 041004, China
| | - Z Zhang
- Institute of Modern Physics, Shanxi Normal University, Linfen 041004, China
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Jeong J, Kang MS, Jeong OM, Lee HJ, Lee JY, Kwon YK, Park JW, Kim JH. Investigation of Genetic Diversity of Pasteurella multocida Isolated from Diseased Poultry in Korea. Braz J Poult Sci 2021. [DOI: 10.1590/1806-9061-2020-1390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J Jeong
- Animal and Plant Quarantine Agency, Republic of Korea
| | - MS Kang
- Animal and Plant Quarantine Agency, Republic of Korea
| | - OM Jeong
- Animal and Plant Quarantine Agency, Republic of Korea
| | - HJ Lee
- Animal and Plant Quarantine Agency, Republic of Korea
| | - JY Lee
- Animal and Plant Quarantine Agency, Republic of Korea
| | - YK Kwon
- Animal and Plant Quarantine Agency, Republic of Korea
| | - JW Park
- Animal and Plant Quarantine Agency, Republic of Korea
| | - JH Kim
- Animal and Plant Quarantine Agency, Republic of Korea
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de Freitas SA, Wong E, Lee JY, Reppas-Rindlisbacher C, Gabor C, Curkovic A, Patterson CJ. The Effect of Multiple Assessments on Delirium Detection: a Pilot Study. Can Geriatr J 2020; 23:277-282. [PMID: 33282047 PMCID: PMC7704074 DOI: 10.5770/cgj.23.433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Delirium is characterized by fluctuating attention or arousal, with high prevalence in the orthopaedic ward. Our aim was to: 1) establish the prevalence of delirium on an orthopaedic ward, and 2) compare delirium prevalence using a single geriatrician assessment vs. multiple 3D-CAM (3-Minute Diagnostic Interview for Confusion Assessment Method) assessments during the day. We hypothesized that multiple assessments would increase the detection rate due to the fluctuating nature of delirium. Methods Comparative study conducted at an academic hospital in Hamilton, Ontario. Participants included patients 65 years and older admitted to the orthopaedic ward (n=55). After a geriatrician made the first assessment of delirium by 3D-CAM on each patient, teams with specialized geriatrics training re-assessed participants up to four times. Delirium rates based on first assessment were compared to cumulative end-of-day rates to determine if detection increased with multiple assessments. Results The prevalence of delirium was 30.9% (17 participants) using multiple assessments. Of these cases, 13 (76.4%) were detected in the initial geriatrician assessment. In patients with hip fractures, 70.6% (12 of 17) were identified as delirious by multiple assessments. Conclusion As symptoms fluctuate, multiple daily CAM assessments may increase the identification of delirium in orthopaedic inpatients.
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Affiliation(s)
- S A de Freitas
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton.,Joseph Brant Hospital Corporation, Burlington.,Hamilton Health Sciences Corporation, Hamilton
| | - Ekc Wong
- Department of Medicine, Faculty of Medicine, University of Toronto, Toronto.,Geriatric Education and Research in Aging Sciences (GERAS) Centre, Hamilton Health Sciences/McMaster University, Hamilton, ON
| | - J Y Lee
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton.,Geriatric Education and Research in Aging Sciences (GERAS) Centre, Hamilton Health Sciences/McMaster University, Hamilton, ON
| | | | - C Gabor
- Hamilton Health Sciences Corporation, Hamilton
| | - A Curkovic
- Hamilton Health Sciences Corporation, Hamilton
| | - C J Patterson
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton.,Hamilton Health Sciences Corporation, Hamilton.,Geriatric Education and Research in Aging Sciences (GERAS) Centre, Hamilton Health Sciences/McMaster University, Hamilton, ON
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Leal-Neto OB, Santos FAS, Lee JY, Albuquerque JO, Souza WV. Prioritizing COVID-19 tests based on participatory surveillance and spatial scanning. Int J Med Inform 2020; 143:104263. [PMID: 32877853 PMCID: PMC7449898 DOI: 10.1016/j.ijmedinf.2020.104263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This study aimed to identify, describe and analyze priority areas for COVID-19 testing combining participatory surveillance and traditional surveillance. DESIGN It was carried out a descriptive transversal study in the city of Caruaru, Pernambuco state, Brazil, within the period of 20/02/2020 to 05/05/2020. Data included all official reports for influenza-like illness notified by the municipality health department and the self-reports collected through the participatory surveillance platform Brasil Sem Corona. METHODS We used linear regression and loess regression to verify a correlation between Participatory Surveillance (PS) and Traditional Surveillance (TS). Also a spatial scanning approach was deployed in order to identify risk clusters for COVID-19. RESULTS In Caruaru, the PS had 861 active users, presenting an average of 1.2 reports per user per week. The platform Brasil Sem Corona started on March 20th and since then, has been officially used by the Caruaru health authority to improve the quality of information from the traditional surveillance system. Regarding the respiratory syndrome cases from TS, 1588 individuals were positive for this clinical outcome. The spatial scanning analysis detected 18 clusters and 6 of them presented statistical significance (p-value < 0.1). Clusters 3 and 4 presented an overlapping area that was chosen by the local authority to deploy the COVID-19 serology, where 50 individuals were tested. From there, 32 % (n = 16) presented reagent results for antibodies related to COVID-19. CONCLUSION Participatory surveillance is an effective epidemiological method to complement the traditional surveillance system in response to the COVID-19 pandemic by adding real-time spatial data to detect priority areas for COVID-19 testing.
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Affiliation(s)
- O B Leal-Neto
- Department of Economics, University of Zurich, Zurich, Switzerland; Epitrack, Recife, Brazil.
| | - F A S Santos
- Agreste Academic Center, Federal University of Pernambuco, Caruaru, Brazil
| | | | - J O Albuquerque
- Epitrack, Recife, Brazil; Immunopathology Laboratory Keizo Asami, Federal University of Pernambuco, Recife, Brazil
| | - W V Souza
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Recife, Brazil
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Song HS, Stegen JC, Graham EB, Lee JY, Garayburu-Caruso VA, Nelson WC, Chen X, Moulton JD, Scheibe TD. Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling. Front Microbiol 2020; 11:531756. [PMID: 33193121 PMCID: PMC7644784 DOI: 10.3389/fmicb.2020.531756] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation into biogeochemical models is often prohibited due to an over-simplified description of reaction networks. To fill this gap, we proposed a new concept of biogeochemical modeling-termed substrate-explicit modeling-that enables parameterizing OM-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools. Based on previous developments in the literature, we characterized the resulting kinetic models by only two parameters regardless of the complexity of OM profiles, which can greatly facilitate the integration with reactive transport models for ecosystem simulations by alleviating the difficulty in parameter identification. The two parameters include maximal growth rate (μmax) and harvest volume (Vh) (i.e., the volume that a microbe can access for harvesting energy). For every detected organic molecule in a given sample, our approach provides a systematic way to formulate reaction kinetics from chemical formula, which enables the evaluation of the impact of OM character on biogeochemical processes across conditions. In a case study of two sites with distinct OM thermodynamics using ultra high-resolution metabolomics datasets derived from Fourier transform ion cyclotron resonance mass spectrometry analyses, our method predicted how oxidative degradation is primarily driven by thermodynamic efficiency of OM consistent with experimental rate measurements (as shown by correlation coefficients of up to 0.61), and how biogeochemical reactions can vary in response to carbon and/or oxygen limitations. Lastly, we showed that incorporation of enzymatic regulations into substrate-explicit models is critical for more reasonable predictions. This result led us to present integrative biogeochemical modeling as a unifying framework that can ideally describe the dynamic interplay among microbes, enzymes, and substrates to address advanced questions and hypotheses in future studies. Altogether, the new modeling concept we propose in this work provides a foundational platform for unprecedented predictions of biogeochemical and ecosystem dynamics through enhanced integration with diverse experimental data and extant modeling approaches.
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Affiliation(s)
- Hyun-Seob Song
- Pacific Northwest National Laboratory, Richland, WA, United States
- Departments of Biological Systems Engineering and Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - James C. Stegen
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | | | - Xingyuan Chen
- Pacific Northwest National Laboratory, Richland, WA, United States
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Lee HJ, Lee JY, Lee MJ, Kim HK, Kim N, Kim GU, Lee JS, Park HW, Chang HS, Yang DH, Choe J, Byeon JS. Association of low skeletal muscle mass with the presence of advanced colorectal neoplasm: integrative analysis using three skeletal muscle mass indices. Colorectal Dis 2020; 22:1293-1303. [PMID: 32363686 DOI: 10.1111/codi.15103] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/14/2020] [Indexed: 02/08/2023]
Abstract
AIM This study aimed to evaluate an association between colorectal neoplasm (CRN) and skeletal muscle mass using three widely accepted skeletal muscle mass indices (SMIs) in a large population at average risk. METHOD We performed a cross-sectional study using a screening colonoscopy database of 33 958 asymptomatic subjects aged 40-75 years. Appendicular skeletal muscle mass (ASM) was measured using a bioelectrical impedance analyser. ASM adjusted for height squared (ASM/ht2 ), weight (ASM/wt) and body mass index (ASM/BMI) were used as indices for muscle mass. Logistic regression models were used to evaluate the association between SMIs and CRN. RESULTS In a multivariable-adjusted model, the risk of an advanced CRN increased linearly with decreasing quartiles for all three SMIs. The adjusted odds ratios (ORs) for advanced CRN in quartiles 1, 2 and 3 of ASM/wt compared with that in quartile 4 were 1.279, 1.196 and 1.179, respectively (Ptrend = 0.017); for ASM/BMI, ORs were 1.307, 1.144 and 1.091, respectively (Ptrend = 0.002); and for ASM/ht2 , ORs were 1.342, 1.169 and 1.062, respectively (Ptrend = 0.002). The risk of distally located advanced CRN was higher in quartile 1 than in quartile 4 for all three SMIs (ASM/wt, OR = 1.356; ASM/BMI, OR = 1.383; ASM/ht2 , OR = 1.430). CONCLUSION Our study demonstrated that low skeletal muscle mass was consistently associated with the presence of advanced CRN in a population at average risk regardless of the operational definition of the SMI, and it was particularly associated with distal advanced CRN.
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Affiliation(s)
- H J Lee
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J Y Lee
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - M J Lee
- Division of Endocrinology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - H-K Kim
- Division of Endocrinology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - N Kim
- Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - G-U Kim
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-S Lee
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - H W Park
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - H-S Chang
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - D-H Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J Choe
- Division of Gastroenterology, Health Screening and Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-S Byeon
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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