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Peters TL, Schow J, Spencer E, Van Leuven JT, Wichman H, Miller C. Directed evolution of bacteriophages: impacts of prolific prophage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601269. [PMID: 38979301 PMCID: PMC11230397 DOI: 10.1101/2024.06.28.601269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Various directed evolution methods exist that seek to procure bacteriophages with expanded host ranges, typically targeting phage-resistant or non-permissive bacterial hosts. The general premise of these methods is to propagate phage on multiple bacterial hosts, pool the lysate, and repeat the propagation process until phage(s) can form plaques on the target host(s). In theory, this propagation process produces a phage lysate that contains input phages and their evolved phage progeny. However, in practice, this phage lysate can also include prophages originating from bacterial hosts. Here we describe our experience implementing one directed evolution method, the Appelmans protocol, to study phage evolution in the Pseudomonas aeruginosa phage-host system, in which we observed rapid host-range expansion of the phage cocktail. Further experimentation and sequencing analysis revealed that this observed host-range expansion was due to a Casadabanvirus prophage that originated from one of the Appelmans hosts. Host-range analysis of the prophage showed that it could infect five of eight bacterial hosts initially used, allowing it to proliferate and persist through the end of the experiment. This prophage was represented in half of the sequenced phage samples isolated from the Appelmans experiment. This work highlights the impact of prophages in directed evolution experiments and the importance of incorporating sequencing data in analyses to verify output phages, particularly for those attempting to procure phages intended for phage therapy applications. This study also notes the usefulness of intraspecies antagonism assays between bacterial host strains to establish a baseline for inhibitory activity and determine presence of prophage. IMPORTANCE Directed evolution is a common strategy for evolving phages to expand host range, often targeting pathogenic strains of bacteria. In this study we investigated phage host-range expansion using directed evolution in the Pseudomonas aeruginosa system. We show that prophage are active players in directed evolution and can contribute to observation of host-range expansion. Since prophage are prevalent in bacterial hosts, particularly pathogenic strains of bacteria, and all directed evolution approaches involve iteratively propagating phage on one or more bacterial hosts, the presence of prophage in phage preparations is a factor that needs to be considered in experimental design and interpretation of results. These results highlight the importance of screening for prophages either genetically or through intraspecies antagonism assays during selection of bacterial strains and will contribute to improving experimental design of future directed evolution studies.
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Robinson MB, Renna M, Otic N, Franceschini MA, Carp SA. Pathlength-selective, interferometric diffuse correlation spectroscopy (PaLS-iDCS). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600096. [PMID: 38979367 PMCID: PMC11230245 DOI: 10.1101/2024.06.21.600096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Diffuse correlation spectroscopy (DCS) is an optical method that offers non-invasive assessment of blood flow in tissue through the analysis of intensity fluctuations in diffusely backscattered coherent light. The non-invasive nature of the technique has enabled several clinical applications for deep tissue blood flow measurements, including cerebral blood flow monitoring as well as tumor blood flow mapping. While a promising technique, in measurement configurations targeting deep tissue hemodynamics, the standard DCS implementations suffer from insufficient signal-to-noise ratio (SNR), depth sensitivity, and sampling rate, limiting their utility. In this work, we present an enhanced DCS method called pathlength-selective, interferometric DCS (PaLS-iDCS), which improves upon both the sensitivity of the measurement to deep tissue hemodynamics and the SNR of the measurement using pathlength-specific coherent gain. Through interferometric detection, PaLS-iDCS can provide time-of-flight (ToF) specific blood flow information without the use of expensive time-tagging electronics and low-jitter detectors. The new technique is compared to time-domain DCS (TD-DCS), another enhanced DCS method able to resolve photon ToF in tissue, through Monte Carlo simulation, phantom experiments, and human subject measurements. PaLS-iDCS consistently demonstrates improvements in SNR (>2x) for similar measurement conditions (same photon ToF), and the SNR improvements allow for measurements at extended photon ToFs, which have increased sensitivity to deep tissue hemodynamics (~50% increase). Further, like TD-DCS, PaLS-iDCS allows direct estimation of tissue optical properties from the sampled ToF distribution without the need for a separate spectroscopic measurement. This method offers a relatively straightforward way to allow DCS systems to make robust measurements of blood flow with greatly enhanced sensitivity to deep tissue hemodynamics, enabling further applications of this non-invasive technology.
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Affiliation(s)
- Mitchell B. Robinson
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marco Renna
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikola Otic
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, Massachusetts, USA
| | - Maria Angela Franceschini
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan A. Carp
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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de Carvalho CC, Porto Genuino W, Vieira Morais MC, de Paiva Oliveira H, Rodrigues AI, El-Boghdadly K. Efficacy and safety of ultrasound-guided versus landmark-guided neuraxial puncture: a systematic review, network meta-analysis and trial sequential analysis of randomized clinical trials. Reg Anesth Pain Med 2024:rapm-2024-105547. [PMID: 38876801 DOI: 10.1136/rapm-2024-105547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Data suggest that preprocedural ultrasound may improve the efficacy of central neuraxial puncture. However, it remains uncertain whether these findings can be extended to various clinical scenarios, including diverse patient populations and the application of real-time ultrasound guidance. Additionally, it is unclear whether ultrasound-guided techniques improve safety and patient-centered outcomes. METHODS We searched six databases for randomized trials of adult patients undergoing neuraxial puncture, comparing real-time ultrasound, preprocedural ultrasound, and landmark palpation for efficacy, safety and patient-centered outcomes. Our primary outcome was a failed first-attempt neuraxial puncture. After two-person screening and data extraction, meta-analyses were conducted and the Grading of Recommendations Assessment, Development and Evaluation approach was applied to assess the certainty of evidence. RESULTS Analysis of 71 studies involving 7153 patients, both real-time ultrasound (OR 0.30; 95% credible interval (CrI) 0.15 to 0.58; low certainty) and preprocedural ultrasound (OR 0.33; 95% CrI 0.24 to 0.44; moderate certainty) showed a significant reduction in the risk of a failed first neuraxial puncture. Real-time ultrasound had the best performance for preventing first-attempt failures (low certainty evidence). Although real-time ultrasound was also the leading method for reducing the risk of complete neuraxial puncture failure, the results did not show a statistically significant difference when compared with landmark palpation. Preprocedural ultrasound, however, significantly reduced the odds of complete puncture failure (OR 0.29; 95% CrI 0.11 to 0.61). These ultrasound-guided approaches also contributed to a reduction in certain complications and increased patient satisfaction without any other significant differences in additional outcomes. Trial sequential analysis confirmed that sufficient information was achieved for our primary outcome. CONCLUSIONS Ultrasound-guided neuraxial puncture improves efficacy, reduces puncture attempts and needle redirections, reduces complication risks, and increases patient satisfaction, with low to moderate certainty of evidence. Despite real-time ultrasound's high ranking, a clear superiority over preprocedural ultrasound is not established. These results could prompt anesthesiologists and other clinicians to reassess their neuraxial puncture techniques.
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Affiliation(s)
- Clístenes Crístian de Carvalho
- Academic Unit of Medicine, Federal University of Campina Grande, Campina Grande, Brazil
- Real Hospital Português, Recife, Pernambuco, Brazil
| | | | | | - Heleno de Paiva Oliveira
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo, Brazil
| | - Adolfo Igor Rodrigues
- Academic Unit of Medicine, Federal University of Campina Grande, Campina Grande, Brazil
| | - Kariem El-Boghdadly
- Department of Anaesthesia and Perioperative Medicine, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Centre for Human and Applied Physiological Sciences, King's College London, London, UK
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Redondo MJ, Morgan NG. Reply to 'Slowly progressive insulin dependent diabetes mellitus in type 1 diabetes endotype 2'. Nat Rev Endocrinol 2024; 20:313. [PMID: 38514818 DOI: 10.1038/s41574-024-00977-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Maria J Redondo
- Pediatric Diabetes & Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA.
| | - Noel G Morgan
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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Kobayashi T, Kadowaki T. Slowly progressive insulin-dependent diabetes mellitus in type 1 diabetes endotype 2. Nat Rev Endocrinol 2024; 20:312. [PMID: 38514816 DOI: 10.1038/s41574-024-00975-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Tetsuro Kobayashi
- Department of Endocrinology and Metabolism, Toranomon Hospital, Tokyo, Japan.
- Division of Immunology and Molecular Medicine, Okinaka Memorial Institute for Medical Research, Tokyo, Japan.
| | - Takashi Kadowaki
- Department of Endocrinology and Metabolism, Toranomon Hospital, Tokyo, Japan
- Division of Endocrinology and Metabolism, Okinaka Memorial Institute for Medical Research, Tokyo, Japan
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Zurita-Salinas C, Tello B, Dueñas-Espín I, Zurita J, Acosta W, León CA, Andrade-Muñoz A, Pareja-Maldonado J. Evaluating low and high vitamin D levels in Ecuadorian cities from 2018 to 2022: interrupted time series and a cross-sectional study. BMJ Open 2024; 14:e079960. [PMID: 38670624 PMCID: PMC11057257 DOI: 10.1136/bmjopen-2023-079960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVES To identify differences in the mean vitamin D concentrations in samples obtained from a private laboratory in Quito and to explore their relationship with the pre-pandemic and pandemic periods spanning from 2018 to 2022. DESIGN A combination of an interrupted time series design and a retrospective cross-sectional approach. SETTING AND PARTICIPANTS The study involved 9285 participants who had their 25-hydroxyvitamin D (25(OH)D) levels tested at a well-known private laboratory in Quito, Ecuador, from 2018 to 2022. PRIMARY AND SECONDARY OUTCOME MEASURES The 25(OH)D levels were analysed and assessed for correlations with age, and the year the measurements were taken. RESULTS The mean 25(OH)D level was 27.53 ng/mL (± 14.11). Approximately 68.8% of participants had serum 25(OH)D levels of less than 30 ng/mL, and 0.6% showed potential harm from excess 25(OH)D, with levels over 100 ng/mL. The analysis indicated a significant monthly increase of 0.133 units in 25(OH)D levels (p=0.006). However, the period after March 2020, compared with before, saw a non-significant decrease of 1.605 units in mean 25(OH)D levels (p=0.477). CONCLUSIONS The study's findings indicate a significant prevalence of 25(OH)D deficiency, underscoring the necessity for preventative measures. However, the increasing trend in high 25(OH)D levels is concerning, emphasising the importance of prudent vitamin D supplement prescriptions and public education against self-medication. For efficient resource allocation and targeting of those with higher risks, it may be advantageous to concentrate vitamin D testing on specific population groups.
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Affiliation(s)
- Camilo Zurita-Salinas
- Biomedical Research Unit, Zurita & Zurita Laboratories, Quito, Ecuador
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Betzabé Tello
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Iván Dueñas-Espín
- Instituto de Salud Pública, Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jeannete Zurita
- Biomedical Research Unit, Zurita & Zurita Laboratories, Quito, Ecuador
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - William Acosta
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Andrés Andrade-Muñoz
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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Howard MK, Hoppe N, Huang XP, Macdonald CB, Mehrota E, Grimes PR, Zahm A, Trinidad DD, English J, Coyote-Maestas W, Manglik A. Molecular basis of proton-sensing by G protein-coupled receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.590000. [PMID: 38659943 PMCID: PMC11042331 DOI: 10.1101/2024.04.17.590000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Three proton-sensing G protein-coupled receptors (GPCRs), GPR4, GPR65, and GPR68, respond to changes in extracellular pH to regulate diverse physiology and are implicated in a wide range of diseases. A central challenge in determining how protons activate these receptors is identifying the set of residues that bind protons. Here, we determine structures of each receptor to understand the spatial arrangement of putative proton sensing residues in the active state. With a newly developed deep mutational scanning approach, we determined the functional importance of every residue in proton activation for GPR68 by generating ~9,500 mutants and measuring effects on signaling and surface expression. This unbiased screen revealed that, unlike other proton-sensitive cell surface channels and receptors, no single site is critical for proton recognition in GPR68. Instead, a network of titratable residues extend from the extracellular surface to the transmembrane region and converge on canonical class A GPCR activation motifs to activate proton-sensing GPCRs. More broadly, our approach integrating structure and unbiased functional interrogation defines a new framework for understanding the rich complexity of GPCR signaling.
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Affiliation(s)
- Matthew K. Howard
- Tetrad graduate program, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
| | - Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics graduate program, University of California, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology and the National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christian B. Macdonald
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
| | - Eshan Mehrota
- Tetrad graduate program, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | | | - Adam Zahm
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donovan D. Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, United States
| | - Justin English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, USA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
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Sanchez JC, Pierpont TM, Argueta-Zamora D, Wilson K, August A, Cerione RA. PTEN loss in glioma cell lines leads to increased extracellular vesicles biogenesis and PD-L1 cargo in a PI3K-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550575. [PMID: 38464280 PMCID: PMC10925116 DOI: 10.1101/2023.07.26.550575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Phosphatase and Tensin Homologue (PTEN) is one of the most frequently lost tumor suppressors in cancer and the predominant negative regulator of the PI3K/AKT signaling axis. A growing body of evidence has highlighted the loss of PTEN with immuno-modulatory functions including the upregulation of the programmed death ligand-1 (PD-L1), an altered tumor derived secretome that drives an immunosuppressive tumor immune microenvironment (TIME), and resistance to certain immunotherapies. Given their roles in immunosuppression and tumor growth, we examined whether the loss of PTEN would impact the biogenesis, cargo, and function of extracellular vesicles (EVs) in the context of the anti-tumor associated cytokine interferon-γ (IFN-γ). Through genetic and pharmacological approaches, we show that PD-L1 expression is regulated by JAK/STAT signaling, not PI3K signaling. Instead, we observe that PTEN loss positively upregulates cell surface levels of PD-L1 and enhances the biogenesis of EVs enriched with PD-L1 in a PI3K-dependent manner. We demonstrate that because of these changes, EVs derived from glioma cells lacking PTEN have a greater ability to suppress T cell receptor (TCR) signaling. Taken together, these findings provide important new insights into how the loss of PTEN can contribute to an immunosuppressive TIME, facilitate immune evasion, and highlight a novel role for PI3K signaling in the regulation of EV biogenesis and the cargo they contain.
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Affiliation(s)
- Julio C Sanchez
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Timothy M Pierpont
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Dariana Argueta-Zamora
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Kristin Wilson
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Richard A Cerione
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
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Mine K, Nagafuchi S, Akazawa S, Abiru N, Mori H, Kurisaki H, Shimoda K, Yoshikai Y, Takahashi H, Anzai K. TYK2 signaling promotes the development of autoreactive CD8 + cytotoxic T lymphocytes and type 1 diabetes. Nat Commun 2024; 15:1337. [PMID: 38351043 PMCID: PMC10864272 DOI: 10.1038/s41467-024-45573-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Tyrosine kinase 2 (TYK2), a member of the JAK family, has attracted attention as a potential therapeutic target for autoimmune diseases. However, the role of TYK2 in CD8+ T cells and autoimmune type 1 diabetes (T1D) is poorly understood. In this study, we generate Tyk2 gene knockout non-obese diabetes (NOD) mice and demonstrate that the loss of Tyk2 inhibits the development of autoreactive CD8+ T-BET+ cytotoxic T lymphocytes (CTLs) by impairing IL-12 signaling in CD8+ T cells and the CD8+ resident dendritic cell-driven cross-priming of CTLs in the pancreatic lymph node (PLN). Tyk2-deficient CTLs display reduced cytotoxicity. Increased inflammatory responses in β-cells with aging are dampened by Tyk2 deficiency. Furthermore, treatment with BMS-986165, a selective TYK2 inhibitor, inhibits the expansion of T-BET+ CTLs, inflammation in β-cells and the onset of autoimmune T1D in NOD mice. Thus, our study reveals the diverse roles of TYK2 in driving the pathogenesis of T1D.
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Affiliation(s)
- Keiichiro Mine
- Division of Metabolism and Endocrinology, Faculty of Medicine, Saga University, Saga, Japan.
- Division of Host Defense, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Seiho Nagafuchi
- Division of Metabolism and Endocrinology, Faculty of Medicine, Saga University, Saga, Japan
| | - Satoru Akazawa
- Department of Endocrinology and Metabolism, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norio Abiru
- Department of Endocrinology and Metabolism, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Midori Clinic, Nagasaki, Japan
| | - Hitoe Mori
- Division of Metabolism and Endocrinology, Faculty of Medicine, Saga University, Saga, Japan
| | - Hironori Kurisaki
- Department of Medical Science and Technology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuya Shimoda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yasunobu Yoshikai
- Division of Host Defense, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hirokazu Takahashi
- Division of Metabolism and Endocrinology, Faculty of Medicine, Saga University, Saga, Japan
- Liver Center, Saga University Hospital, Saga University, Saga, Japan
| | - Keizo Anzai
- Division of Metabolism and Endocrinology, Faculty of Medicine, Saga University, Saga, Japan
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Gurmessa DK, Jimma W. Explainable machine learning for breast cancer diagnosis from mammography and ultrasound images: a systematic review. BMJ Health Care Inform 2024; 31:e100954. [PMID: 38307616 PMCID: PMC10840064 DOI: 10.1136/bmjhci-2023-100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Breast cancer is the most common disease in women. Recently, explainable artificial intelligence (XAI) approaches have been dedicated to investigate breast cancer. An overwhelming study has been done on XAI for breast cancer. Therefore, this study aims to review an XAI for breast cancer diagnosis from mammography and ultrasound (US) images. We investigated how XAI methods for breast cancer diagnosis have been evaluated, the existing ethical challenges, research gaps, the XAI used and the relation between the accuracy and explainability of algorithms. METHODS In this work, Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist and diagram were used. Peer-reviewed articles and conference proceedings from PubMed, IEEE Explore, ScienceDirect, Scopus and Google Scholar databases were searched. There is no stated date limit to filter the papers. The papers were searched on 19 September 2023, using various combinations of the search terms 'breast cancer', 'explainable', 'interpretable', 'machine learning', 'artificial intelligence' and 'XAI'. Rayyan online platform detected duplicates, inclusion and exclusion of papers. RESULTS This study identified 14 primary studies employing XAI for breast cancer diagnosis from mammography and US images. Out of the selected 14 studies, only 1 research evaluated humans' confidence in using the XAI system-additionally, 92.86% of identified papers identified dataset and dataset-related issues as research gaps and future direction. The result showed that further research and evaluation are needed to determine the most effective XAI method for breast cancer. CONCLUSION XAI is not conceded to increase users' and doctors' trust in the system. For the real-world application, effective and systematic evaluation of its trustworthiness in this scenario is lacking. PROSPERO REGISTRATION NUMBER CRD42023458665.
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Affiliation(s)
- Daraje Kaba Gurmessa
- Department of Information Science, Jimma Institute of Technology, Jimma University, Jimma, Oromia, Ethiopia
- Computer Science, Mattu University, Mattu, Oromīya, Ethiopia
| | - Worku Jimma
- Department of Information Science, Jimma Institute of Technology, Jimma University, Jimma, Oromia, Ethiopia
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Bhattacharyya U, John J, Lam M, Fisher J, Sun B, Baird D, Chen CY, Lencz T. Large-Scale Mendelian Randomization Study Reveals Circulating Blood-based Proteomic Biomarkers for Psychopathology and Cognitive Task Performance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301455. [PMID: 38293198 PMCID: PMC10827252 DOI: 10.1101/2024.01.18.24301455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Research on peripheral (e.g., blood-based) biomarkers for psychiatric illness has typically been low-throughput in terms of both the number of subjects and the range of assays performed. Moreover, traditional case-control studies examining blood-based biomarkers are subject to potential confounds of treatment and other exposures common to patients with psychiatric illnesses. Our research addresses these challenges by leveraging large-scale, high-throughput proteomics data and Mendelian Randomization (MR) to examine the causal impact of circulating proteins on psychiatric phenotypes and cognitive task performance. Methods We utilized plasma proteomics data from the UK Biobank (3,072 proteins assayed in 34,557 European-ancestry individuals) and deCODE Genetics (4,719 proteins measured across 35,559 Icelandic individuals). Significant proteomic quantitative trait loci (both cis-pQTLs and trans-pQTLs) served as MR instruments, with the most recent GWAS for schizophrenia, bipolar disorder, major depressive disorder, and cognitive task performance (all excluding overlapping UK Biobank participants) as phenotypic outcomes. Results MR revealed 109 Bonferroni-corrected causal associations (44 novel) involving 88 proteins across the four phenotypes. Several immune-related proteins, including interleukins and complement factors, stood out as pleiotropic across multiple outcome phenotypes. Drug target enrichment analysis identified several novel potential pharmacologic repurposing opportunities, including anti-inflammatory agents for schizophrenia and bipolar disorder and duloxetine for cognitive performance. Conclusions Identification of causal effects for these circulating proteins suggests potential biomarkers for these conditions and offers insights for developing innovative therapeutic strategies. The findings also indicate substantial evidence for the pleiotropic effects of many proteins across different phenotypes, shedding light on the shared etiology among psychiatric conditions and cognitive ability.
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Affiliation(s)
- Upasana Bhattacharyya
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jibin John
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Max Lam
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jonah Fisher
- Biogen Inc., Cambridge, MA
- Harvard T.H. Chan School of Public Health, Cambridge, MA
| | | | | | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
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Shakiba S, Haddadi NS, Afshari K, Lubov JE, Raef HS, Li R, Yildiz-Altay Ü, Daga M, Refat MA, Kim E, de Laflin JG, Akabane A, Sherman S, MacDonald E, Strassner JP, Zhang L, Leon M, Baer CE, Dresser K, Liang Y, Whitley JB, Skopelja-Gardner S, Harris JE, Deng A, Vesely MD, Rashighi M, Richmond J. Spatial characterization of interface dermatitis in cutaneous lupus reveals novel chemokine ligand-receptor pairs that drive disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574422. [PMID: 38260617 PMCID: PMC10802382 DOI: 10.1101/2024.01.05.574422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Chemokines play critical roles in the recruitment and activation of immune cells in both homeostatic and pathologic conditions. Here, we examined chemokine ligand-receptor pairs to better understand the immunopathogenesis of cutaneous lupus erythematosus (CLE), a complex autoimmune connective tissue disorder. We used suction blister biopsies to measure cellular infiltrates with spectral flow cytometry in the interface dermatitis reaction, as well as 184 protein analytes in interstitial skin fluid using Olink targeted proteomics. Flow and Olink data concordantly demonstrated significant increases in T cells and antigen presenting cells (APCs). We also performed spatial transcriptomics and spatial proteomics of punch biopsies using digital spatial profiling (DSP) technology on CLE skin and healthy margin controls to examine discreet locations within the tissue. Spatial and Olink data confirmed elevation of interferon (IFN) and IFN-inducible CXCR3 chemokine ligands. Comparing involved versus uninvolved keratinocytes in CLE samples revealed upregulation of essential inflammatory response genes in areas near interface dermatitis, including AIM2. Our Olink data confirmed upregulation of Caspase 8, IL-18 which is the final product of AIM2 activation, and induced chemokines including CCL8 and CXCL6 in CLE lesional samples. Chemotaxis assays using PBMCs from healthy and CLE donors revealed that T cells are equally poised to respond to CXCR3 ligands, whereas CD14+CD16+ APC populations are more sensitive to CXCL6 via CXCR1 and CD14+ are more sensitive to CCL8 via CCR2. Taken together, our data map a pathway from keratinocyte injury to lymphocyte recruitment in CLE via AIM2-Casp8-IL-18-CXCL6/CXCR1 and CCL8/CCR2, and IFNG/IFNL1-CXCL9/CXCL11-CXCR3.
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Affiliation(s)
- Saeed Shakiba
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | | | | | - Janet E. Lubov
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | - Haya S. Raef
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | - Robert Li
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | | | - Mridushi Daga
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | | | - Evangeline Kim
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | | | - Andressa Akabane
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | - Shany Sherman
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | | | | | | | | | - Christina E. Baer
- UMass Chan Medical School, Sanderson Center for Optical Experimentation, Dept of Microbiology and Physiological Systems, Worcester, MA, USA
| | - Karen Dresser
- UMass Chan Medical School, Dept of Pathology, Worcester, MA, USA
| | - Yan Liang
- NanoString Technologies, Seattle, WA, USA
| | - James B Whitley
- Dartmouth Hitchcock Medical Center, Dept of Medicine, Lebanon, NH, USA
| | | | - John E Harris
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | - April Deng
- UMass Chan Medical School, Dept of Pathology, Worcester, MA, USA
| | - Matthew D. Vesely
- Yale University School of Medicine, Dept of Dermatology, New Haven, CT, USA
| | - Mehdi Rashighi
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
| | - Jillian Richmond
- UMass Chan Medical School, Dept of Dermatology, Worcester, MA, USA
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13
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Su C, Kent CL, Pierpoint M, Floyd W, Luo L, Wiliams NT, Ma Y, Peng B, Lazarides AL, Subramanian A, Himes JE, Perez VM, Hernansaiz-Ballesteros RD, Roche KE, Modliszewski JL, Selitsky SR, Mari Shinohara, Wisdom AJ, Moding EJ, Mowery YM, Kirsch DG. Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573968. [PMID: 38260522 PMCID: PMC10802286 DOI: 10.1101/2024.01.03.573968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Radiation therapy is frequently used to treat cancers including soft tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to radiation therapy (RT) in transplanted tumors, but the mechanism(s) remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft tissue sarcomas with high tumor mutation burden. Treatment with a single fraction of 20 Gy RT and two doses of CpG significantly enhanced tumor response, which was abrogated by genetic or immunodepletion of CD8+ T cells. To characterize the immune response to RT + CpG, we performed bulk RNA-seq, single-cell RNA-seq, and mass cytometry. Sarcomas treated with 20 Gy and CpG demonstrated increased CD8 T cells expressing markers associated with activation and proliferation, such as Granzyme B, Ki-67, and interferon-γ. CpG + RT also upregulated antigen presentation pathways on myeloid cells. Furthermore, in sarcomas treated with CpG + RT, TCR clonality analysis suggests an increase in clonal T-cell dominance. Collectively, these findings demonstrate that RT + CpG significantly delays tumor growth in a CD8 T cell-dependent manner. These results provide a strong rationale for clinical trials evaluating CpG or other TLR9 agonists with RT in patients with soft tissue sarcoma.
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Affiliation(s)
- Chang Su
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Collin L. Kent
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Matthew Pierpoint
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Nerissa T. Wiliams
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Brian Peng
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Jonathan E. Himes
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | | - Mari Shinohara
- Department of Immunology, Duke University, Durham, NC, USA
| | - Amy J. Wisdom
- Department of Radiation Oncology, Harvard University, Cambridge, MA, USA
| | - Everett J. Moding
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - David G. Kirsch
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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14
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Lemos JRN, Hirani K, von Herrath M. Immunological and virological triggers of type 1 diabetes: insights and implications. Front Immunol 2024; 14:1326711. [PMID: 38239343 PMCID: PMC10794398 DOI: 10.3389/fimmu.2023.1326711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Type 1 diabetes (T1D) is caused by an autoimmune process which culminates in the destruction of insulin-producing beta cells in the pancreas. It is widely believed that a complex and multifactorial interplay between genetic and environmental factors, such as viruses, play a crucial role in the development of the disease. Research over the past few decades has shown that there is not one single viral culprit, nor one single genetic pathway, causing the disease. Rather, viral infections, most notably enteroviruses (EV), appear to accelerate the autoimmune process leading to T1D and are often seen as a precipitator of clinical diagnosis. In support of this hypothesis, the use of anti-viral drugs has recently shown efficacy in preserving beta cell function after onset of diabetes. In this review, we will discuss the various pathways that viral infections utilize to accelerate the development of T1D. There are three key mechanisms linking viral infections to beta-cell death: One is modulated by the direct infection of islets by viruses, resulting in their impaired function, another occurs in a more indirect fashion, by modulating the immune system, and the third is caused by heightened stress on the beta-cell by interferon-mediated increase of insulin resistance. The first two aspects are surprisingly difficult to study, in the case of the former, because there are still many questions about how viruses might persist for longer time periods. In the latter, indirect/immune case, viruses might impact immunity as a hit-and-run scenario, meaning that many or all direct viral footprints quickly vanish, while changes imprinted upon the immune system and the anti-islet autoimmune response persist. Given the fact that viruses are often associated with the precipitation of clinical autoimmunity, there are concerns regarding the impact of the recent global coronavirus-2019 (COVID-19) pandemic on the development of autoimmune disease. The long-term effects of COVID-19 infection on T1D will therefore be discussed, including the increased development of new cases of T1D. Understanding the interplay between viral infections and autoimmunity is crucial for advancing our knowledge in this field and developing targeted therapeutic interventions. In this review we will examine the intricate relationship between viral infections and autoimmunity and discuss potential considerations for prevention and treatment strategies.
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Affiliation(s)
- Joana R. N. Lemos
- Diabetes Research Institute (DRI), University of Miami Miller School of Medicine, Miami, FL, United States
| | - Khemraj Hirani
- Diabetes Research Institute (DRI), University of Miami Miller School of Medicine, Miami, FL, United States
- Division of Endocrine, Diabetes, and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Matthias von Herrath
- Diabetes Research Institute (DRI), University of Miami Miller School of Medicine, Miami, FL, United States
- Division of Endocrine, Diabetes, and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
- Global Chief Medical Office, Novo Nordisk A/S, Søborg, Denmark
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Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. MPRAbase: A Massively Parallel Reporter Assay Database. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567742. [PMID: 38045264 PMCID: PMC10690217 DOI: 10.1101/2023.11.19.567742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of these experiments. To address this, we developed MPRAbase, a manually curated database that currently harbors 129 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface ( http://www.mprabase.com ) serves as a centralized user-friendly repository to download existing MPRA data for independent analysis and is designed with the ability to allow researchers to share their published data for rapid dissemination to the community.
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Liu LP, Pua R, Rosario-Berrios DN, Sandvold OF, Perkins AE, Cormode DP, Shapira N, Soulen MC, Noël PB. Reproducible spectral CT thermometry with liver-mimicking phantoms for image-guided thermal ablation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.04.23296423. [PMID: 37873236 PMCID: PMC10593007 DOI: 10.1101/2023.10.04.23296423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Objectives Evaluate the reproducibility, temperature sensitivity, and radiation dose requirements of spectral CT thermometry in tissue-mimicking phantoms to establish its utility for non-invasive temperature monitoring of thermal ablations. Materials and Methods Three liver mimicking phantoms embedded with temperature sensors were individually scanned with a dual-layer spectral CT at different radiation dose levels during heating and cooling (35 to 80 °C). Physical density maps were reconstructed from spectral results using a range of reconstruction parameters. Thermal volumetric expansion was then measured at each temperature sensor every 5°C in order to establish a correlation between physical density and temperature. Linear regressions were applied based on thermal volumetric expansion for each phantom, and coefficient of variation for fit parameters was calculated to characterize reproducibility of spectral CT thermometry. Additionally, temperature sensitivity was determined to evaluate the effect of acquisition parameters, reconstruction parameters, and image denoising. The resulting minimum radiation dose to meet the clinical temperature sensitivity requirement was determined for each slice thickness, both with and without additional denoising. Results Thermal volumetric expansion was robustly replicated in all three phantoms, with a correlation coefficient variation of only 0.43%. Similarly, the coefficient of variation for the slope and intercept were 9.6% and 0.08%, respectively, indicating reproducibility of the spectral CT thermometry. Temperature sensitivity ranged from 2 to 23 °C, decreasing with increased radiation dose, slice thickness, and iterative reconstruction level. To meet the clinical requirement for temperature sensitivity, the minimum required radiation dose ranged from 20, 30, and 57 mGy for slice thickness of 2, 3, and 5 mm, respectively, but was reduced to 2 mGy with additional denoising. Conclusions Spectral CT thermometry demonstrated reproducibility across three liver-mimicking phantoms and illustrated the clinical requirement for temperature sensitivity can be met for different slice thicknesses. Moreover, additional denoising enables the use of more clinically relevant radiation doses, facilitating the clinical translation of spectral CT thermometry. The reproducibility and temperature accuracy of spectral CT thermometry enable its clinical application for non-invasive temperature monitoring of thermal ablation.
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