1
|
Suzuki Y, Clement P, Dai W, Dolui S, Fernández-Seara M, Lindner T, Mutsaerts HJMM, Petr J, Shao X, Taso M, Thomas DL. ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI). Magn Reson Med 2024; 91:1743-1760. [PMID: 37876299 PMCID: PMC10950547 DOI: 10.1002/mrm.29815] [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: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/13/2023] [Indexed: 10/26/2023]
Abstract
The 2015 consensus statement published by the International Society for Magnetic Resonance in Medicine (ISMRM) Perfusion Study Group and the European Cooperation in Science and Technology ( COST) Action ASL in Dementia aimed to encourage the implementation of robust arterial spin labeling (ASL) perfusion MRI for clinical applications and promote consistency across scanner types, sites, and studies. Subsequently, the recommended 3D pseudo-continuous ASL sequence has been implemented by most major MRI manufacturers. However, ASL remains a rapidly and widely developing field, leading inevitably to further divergence of the technique and its associated terminology, which could cause confusion and hamper research reproducibility. On behalf of the ISMRM Perfusion Study Group, and as part of the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI), the ASL Lexicon Task Force has been working on the development of an ASL Lexicon and Reporting Recommendations for perfusion imaging and analysis, aiming to (1) develop standardized, consensus nomenclature and terminology for the broad range of ASL imaging techniques and parameters, as well as for the physiological constants required for quantitative analysis; and (2) provide a community-endorsed recommendation of the imaging parameters that we encourage authors to include when describing ASL methods in scientific reports/papers. In this paper, the sequences and parameters in (pseudo-)continuous ASL, pulsed ASL, velocity-selective ASL, and multi-timepoint ASL for brain perfusion imaging are included. However, the content of the lexicon is not intended to be limited to these techniques, and this paper provides the foundation for a growing online inventory that will be extended by the community as further methods and improvements are developed and established.
Collapse
Affiliation(s)
- Yuriko Suzuki
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Patricia Clement
- Department of Medical Imaging, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Weiying Dai
- State University of New York at Binghamton, Binghamton, NY, USA
| | - Sudipto Dolui
- Department of Radiology, University of Pennsylvania, Philadelphia, USA
| | - Maria Fernández-Seara
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | | | - Henk JMM Mutsaerts
- Department of Radiology and Nuclear medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, the Netherlands, Amsterdam
| | - Jan Petr
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Xingfeng Shao
- Laboratory of FMRI Technology (LOFT), Mark & Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Manuel Taso
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - David L Thomas
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | | |
Collapse
|
2
|
Li XM, Ma FZ, Quan XY, Zhang XC, Xiao BH, Wáng YXJ. Repeatability and reproducibility comparisons of liver IVIM imaging with free-breathing or respiratory-triggered sequences. NMR Biomed 2024; 37:e5080. [PMID: 38113878 DOI: 10.1002/nbm.5080] [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: 05/10/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023]
Abstract
For liver intravoxel incoherent motion (IVIM) data acquisition, respiratory-triggering (RT) MRI is commonly used, and there are strong motivations to shorten the scan duration. For the same scan duration, more b values or higher numbers of excitations can be allowed for free-breathing (FB) imaging than for RT. We studied whether FB can be used to replace RT when careful IVIM image acquisition and image processing are conducted. MRI data of 22 healthy participants were acquired using a 3.0 T scanner. Diffusion imaging was based on a single-shot spin-echo-type echo-planar sequence and 16 b values of 0, 2, 4, 7, 10, 15, 20, 30, 46, 60, 72, 100, 150, 200, 400, and 600 s/mm2 . Each subject attended two scan sessions with an interval of 10-20 days. For each scan session, a subject was scanned twice, first with RT and then with FB. The mean image acquisition time was 5.4 min for FB and 10.8 min for RT. IVIM parameters were calculated with bi-exponential model segmented fitting with a threshold b value of 60 s/mm2 , and fitting started from b = 2 s/mm2 . There was no statistically significant difference between IVIM parameters measured with FB imaging or RT imaging. Perfusion fraction ICC (intraclass correlation coefficient) for FB imaging and RT imaging in the same scan session was 0.824. For perfusion fraction, wSD (within-subject standard deviation), BA (Bland-Altman) difference, BA 95% limit, and ICC were 0.022, 0.0001, -0.0635~0.0637, and 0.687 for FB and 0.031, 0.0122, -0.0723~0.0967, and 0.611 for RT. For Dslow (×10-3 s/mm2 ), wSD, BA difference, BA 95% limit, and ICC were 0.057, 0.0268, -0.1258~0.1793, and 0.471 for FB and 0.073, -0.0078, -0.2170-0.2014, and <0.4 for RT. The Dfast coefficient of variation was 0.20 for FB imaging and 0.28 for RT imaging. All reproducibility indicators slightly favored FB imaging.
Collapse
Affiliation(s)
- Xin-Ming Li
- Department of Radiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fu-Zhao Ma
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xian-Yue Quan
- Department of Radiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xu-Chang Zhang
- Department of Radiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ben-Heng Xiao
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yì Xiáng J Wáng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
3
|
Hupfeld KE, Zöllner HJ, Hui SCN, Song Y, Murali-Manohar S, Yedavalli V, Oeltzschner G, Prisciandaro JJ, Edden RAE. Impact of acquisition and modeling parameters on the test-retest reproducibility of edited GABA. NMR Biomed 2024; 37:e5076. [PMID: 38091628 PMCID: PMC10947947 DOI: 10.1002/nbm.5076] [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: 02/09/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/26/2023]
Abstract
Literature values vary widely for within-subject test-retest reproducibility of gamma-aminobutyric acid (GABA) measured with edited magnetic resonance spectroscopy (MRS). Reasons for this variation remain unclear. Here, we tested whether three acquisition parameters-(1) sequence complexity (two-experiment MEscher-GArwood Point RESolved Spectroscopy [MEGA-PRESS] vs. four-experiment Hadamard Encoding and Reconstruction of MEGA-Edited Spectroscopy [HERMES]); (2) editing pulse duration (14 vs. 20 ms); and (3) scanner frequency drift (interleaved water referencing [IWR] turned ON vs. OFF)-and two linear combination modeling variations-(1) three different coedited macromolecule models (called "1to1GABA", "1to1GABAsoft", and "3to2MM" in the Osprey software package); and (2) 0.55- versus 0.4-ppm spline baseline knot spacing-affected the within-subject coefficient of variation of GABA + macromolecules (GABA+). We collected edited MRS data from the dorsal anterior cingulate cortex from 20 participants (mean age: 30.8 ± 9.5 years; 10 males). Test and retest scans were separated by removing the participant from the scanner for 5-10 min. Each acquisition consisted of two MEGA-PRESS and two HERMES sequences with editing pulse durations of 14 and 20 ms (referred to here as MEGA-14, MEGA-20, HERMES-14, and HERMES-20; all TE = 80 ms, 224 averages). We identified the best test-retest reproducibility following postprocessing with a composite model of the 0.9- and 3-ppm macromolecules ("3to2MM"); this model performed particularly well for the HERMES data. Furthermore, sparser (0.55- compared with 0.4-ppm) spline baseline knot spacing yielded generally better test-retest reproducibility for GABA+. Replicating our prior results, linear combination modeling in Osprey compared with simple peak fitting in Gannet resulted in substantially better test-retest reproducibility. However, reproducibility did not consistently differ for MEGA-PRESS compared with HERMES, for 14- compared with 20-ms editing pulses, or for IWR-ON versus IWR-OFF. These results highlight the importance of model selection for edited MRS studies of GABA+, particularly for clinical studies that focus on individual patient differences in GABA+ or changes following an intervention.
Collapse
Affiliation(s)
- Kathleen E Hupfeld
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Helge J Zöllner
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Steve C N Hui
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Yulu Song
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Saipavitra Murali-Manohar
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Vivek Yedavalli
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - James J Prisciandaro
- Department of Psychiatry and Behavioral Sciences, Addiction Sciences Division, Center for Biomedical Imaging, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Richard A E Edden
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| |
Collapse
|
4
|
Ye Z, Yao S, Yang T, Li Q, Li Z, Song B. Abdominal Diffusion-Weighted MRI With Simultaneous Multi-Slice Acquisition: Agreement and Reproducibility of Apparent Diffusion Coefficients Measurements. J Magn Reson Imaging 2024; 59:1170-1178. [PMID: 37334872 DOI: 10.1002/jmri.28876] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Simultaneous multi-slice diffusion-weighted imaging (SMS-DWI) can shorten acquisition time in abdominal imaging. PURPOSE To investigate the agreement and reproducibility of apparent diffusion coefficient (ADC) from abdominal SMS-DWI acquired with different vendors and different breathing schemes. STUDY TYPE Prospective. SUBJECTS Twenty volunteers and 10 patients. FIELD STRENGTH/SEQUENCE 3.0 T, SMS-DWI with a diffusion-weighted echo-planar imaging sequence. ASSESSMENT SMS-DWI was acquired using breath-hold and free-breathing techniques in scanners from two vendors, yielding four scans in each participant. Average ADC values were measured in the liver, pancreas, spleen, and both kidneys. Non-normalized ADC and ADCs normalized to the spleen were compared between vendors and breathing schemes. STATISTICAL TESTS Paired t-test or Wilcoxon signed rank test; intraclass correlation coefficient (ICC); Bland-Altman method; coefficient of variation (CV) analysis; significance level: P < 0.05. RESULTS Non-normalized ADCs from the four SMS-DWI scans did not differ significantly in the spleen (P = 0.262, 0.330, 0.166, 0.122), right kidney (P = 0.167, 0.538, 0.957, 0.086), and left kidney (P = 0.182, 0.281, 0.504, 0.405), but there were significant differences in the liver and pancreas. For normalized ADCs, there were no significant differences in the liver (P = 0.315, 0.915, 0.198, 0.799), spleen (P = 0.815, 0.689, 0.347, 0.423), pancreas (P = 0.165, 0.336, 0.304, 0.584), right kidney (P = 0.165, 0.336, 0.304, 0.584), and left kidney (P = 0.496, 0.304, 0.443, 0.371). Inter-reader agreements of non-normalized ADCs were good to excellent (ICCs ranged from 0.861 to 0.983), and agreement and reproducibility were good to excellent depending on anatomic location (CVs ranged from 3.55% to 13.98%). Overall CVs for abdominal ADCs from the four scans were 6.25%, 7.62%, 7.08, and 7.60%. DATA CONCLUSION The normalized ADCs from abdominal SMS-DWI may be comparable between different vendors and breathing schemes, showing good agreement and reproducibility. ADC changes above approximately 8% may potentially be considered as a reliable quantitative biomarker to assess disease or treatment-related changes. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY: Stage 2.
Collapse
Affiliation(s)
- Zheng Ye
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Yao
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Yang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Li
- MR Collaborations, Siemens Healthineers, Shanghai, China
| | - Zhenlin Li
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Bin Song
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
- Department of Radiology, Sanya People's Hospital, Sanya, China
| |
Collapse
|
5
|
Lucchi F, Lloyd B, Nieuwenhuis S. Non-invasive vagus nerve stimulation and the motivation to work for rewards: A replication of Neuser et al. (2020, Nature Communications). Psychophysiology 2024; 61:e14484. [PMID: 37942809 DOI: 10.1111/psyp.14484] [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] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023]
Abstract
The vagus nerve is thought to be involved in the allostatic regulation of motivation and energy metabolism via gut-brain interactions. A recent study by Neuser and colleagues (2020) provided novel evidence for this process in humans, by reporting a positive effect of transcutaneous auricular vagus nerve stimulation (taVNS) on the invigoration of reward-seeking behaviors, especially for food rewards. We conducted an independent direct replication of Neuser et al. (2020), to assess the robustness of their findings. Following the original study, we used a single-blind, sham-controlled, randomized cross-over design. We applied left-sided taVNS in healthy human volunteers (n = 40), while they performed an effort allocation task in which they had to work for monetary and food rewards. The replication study was purely confirmatory in that it strictly followed the analysis plans and scripts used by Neuser et al. Although, in line with Neuser et al., we found strong effects of task variables on effort invigoration and effort maintenance, we failed to replicate their key finding: taVNS did not increase the strength of invigoration (p = .62); the data were five times more likely (BF10 = 0.19) under the null hypothesis. We also found substantial evidence against an effect of taVNS on effort maintenance (p = .50; BF10 = 0.20). Our results provide evidence against the idea that left-sided taVNS boosts the motivational drive to work for rewards. Our study also highlights the need for direct replications of influential taVNS studies.
Collapse
Affiliation(s)
- Federica Lucchi
- Institute of Psychology, Leiden University, Leiden, the Netherlands
| | - Beth Lloyd
- Institute of Psychology, Leiden University, Leiden, the Netherlands
- Leiden Institute for Brain and Cognition, Leiden University, Leiden, the Netherlands
| | - Sander Nieuwenhuis
- Institute of Psychology, Leiden University, Leiden, the Netherlands
- Leiden Institute for Brain and Cognition, Leiden University, Leiden, the Netherlands
| |
Collapse
|
6
|
Xu C, Yin M, Mo W. An independent agreement study of modified Pfirrmann grading system for cervical inter-vertebral disc degeneration in cervical spondylotic myelopathy. Br J Neurosurg 2024; 38:260-264. [PMID: 33332167 DOI: 10.1080/02688697.2020.1861431] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 11/06/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
OBJECTIVE Neck pain, sensory disturbance and motor dysfunction in most patients suffered cervical spondylotic myelopathy (CSM). For CSM surgery, it is necessary to evaluate preoperative inter-vertebral disc degeneration (IDD) which determines whether to adopt fusion strategy, and postoperative IDD which is one of the main reasons for reoperation. Modified Pfirrmann grading system is commonly used to evaluate IDD. The objective of this study is to evaluate its reliability and reproducibility on cervical IDD in CSM patients, and to explore its clinical application value. METHODS All 165 patients with CSM were enrolled. 6 physicians (3 spine surgeons and 3 radiologists) who have certain clinical experience were selected. They graded cervical inter-vertebral disc according to modified Pfirrmann grading system, we used intra-class correlation coefficient (ICC) and weighted kappa (wκ) to assess the inter- and intra-observer agreement. After 12 weeks, we repeated the analysis. RESULTS The inter-observer reliability of modified Pfirrmann grading system was excellent with an ICC value of 0.76 and near perfect with wκ value of 0.82. The intra-observer reproducibility of modified Pfirrmann grading system was excellent with ICC values ranging from 0.80 to 0.91, and near perfect with wκ values ranging from 0.83-0.92. CONCLUSION Modified Pfirrmann grading system has excellent inter-observer reliability and intra-observer reproducibility on cervical IDD in CSM. In addition, it indicates a good appliance among spine surgeons and radiologists, clinical and radiological studies applying it should be deemed accurate. Thus, modified Pfirrmann grading system can be widely used as an appropriate instrument in clinical care.
Collapse
Affiliation(s)
| | | | - Wen Mo
- Long Hua Hospital, Shanghai, China
| |
Collapse
|
7
|
Gourmelon A, Hubert P, Grignard E, Baumann L, Munn S, Michel C. The benefits of validation of methods for toxicity testing outweigh its costs. ALTEX 2024. [PMID: 38501278 DOI: 10.14573/altex.2403051] [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: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
The 4th Annual Forum on Endocrine Disrupters organized by the European Commission brought together authors of this article around the topic: "From bench to validated test guidelines: (pre)validation of test methods". Validation activities are meant to demonstrate the relevance and reliability of methods and approaches used in regulatory safety testing. These activities are essential to facilitate regulatory use, still they are largely underfunded and unattractive to the scientific community. In the last decade, there has been large amounts of funding invested in European research towards the development of approaches that can be used in regulatory decision-making, including for the identification of endocrine disrupters. There is a vast pool of candidate test methods for potential regulatory applications, but most of them will not be used due to the absence of consideration of their relevance and reliability outside the method developer's laboratory. The article explains the reasons why such a gap exists between the outputs of research projects and the uptake in a regulatory context. In parallel, there are also increasing expectations from the regulatory science community that validation becomes more efficient with respect to time and resources. This article shares some of the lessons learned and proposes paths forward for validation of new methods that are not intended as one-to-one replacements of animal studies. This includes submitting only mature methods for validation that were developed following good practices and good documentation, proposing a greater emphasis on well-documented transferability studies, and adopting a cost-sharing model between those who benefit from validated methods.
Collapse
Affiliation(s)
| | | | | | - Lisa Baumann
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment, Section Environmental Health and Toxicology, Amsterdam, The Netherlands
| | - Sharon Munn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cécile Michel
- REACh-CLP-Endocrine Disrupters Unit, Risk Assessment Department, French Agency for Food, Environmental and Occupational Health Safety (ANSES), Maisons-Alfort, France
| |
Collapse
|
8
|
Paschoal AM, Woods JG, Pinto J, Bron EE, Petr J, Kennedy McConnell FA, Bell L, Dounavi ME, van Praag CG, Mutsaerts HJMM, Taylor AO, Zhao MY, Brumer I, Chan WSM, Toner J, Hu J, Zhang LX, Domingos C, Monteiro SP, Figueiredo P, Harms AGJ, Padrela BE, Tham C, Abdalle A, Croal PL, Anazodo U. Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI)_and the ASL MRI challenge. Magn Reson Med 2024. [PMID: 38502108 DOI: 10.1002/mrm.30081] [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] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
PURPOSE Arterial spin labeling (ASL) is a widely used contrast-free MRI method for assessing cerebral blood flow (CBF). Despite the generally adopted ASL acquisition guidelines, there is still wide variability in ASL analysis. We explored this variability through the ISMRM-OSIPI ASL-MRI Challenge, aiming to establish best practices for more reproducible ASL analysis. METHODS Eight teams analyzed the challenge data, which included a high-resolution T1-weighted anatomical image and 10 pseudo-continuous ASL datasets simulated using a digital reference object to generate ground-truth CBF values in normal and pathological states. We compared the accuracy of CBF quantification from each team's analysis to the ground truth across all voxels and within predefined brain regions. Reproducibility of CBF across analysis pipelines was assessed using the intra-class correlation coefficient (ICC), limits of agreement (LOA), and replicability of generating similar CBF estimates from different processing approaches. RESULTS Absolute errors in CBF estimates compared to ground-truth synthetic data ranged from 18.36 to 48.12 mL/100 g/min. Realistic motion incorporated into three datasets produced the largest absolute error and variability between teams, with the least agreement (ICC and LOA) with ground-truth results. Fifty percent of the submissions were replicated, and one produced three times larger CBF errors (46.59 mL/100 g/min) compared to submitted results. CONCLUSIONS Variability in CBF measurements, influenced by differences in image processing, especially to compensate for motion, highlights the significance of standardizing ASL analysis workflows. We provide a recommendation for ASL processing based on top-performing approaches as a step toward ASL standardization.
Collapse
Affiliation(s)
- Andre M Paschoal
- Institute of Physics, University of Campinas, Campinas, Brazil
- LIM44, Institute of Radiology, Department of Radiology and Oncology of Clinical Hospital, University of Sao Paulo, Sao Paulo, Brazil
| | - Joseph G Woods
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
- Department of Radiology, Center for Functional Magnetic Resonance Imaging, University of California, San Diego, La Jolla, California, USA
| | - Joana Pinto
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Esther E Bron
- Department of Radiology & Nuclear Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jan Petr
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Flora A Kennedy McConnell
- Radiological Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham Biomedical Research Centre, Queens Medical Centre, Nottingham, UK
| | - Laura Bell
- Clinical Imaging Group, Genentech, Inc., South San Francisco, California, USA
| | | | - Cassandra Gould van Praag
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Henk J M M Mutsaerts
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, the Netherlands
| | | | - Moss Y Zhao
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Irène Brumer
- Computer Assisted Clinical Medicine, Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Wei Siang Marcus Chan
- Computer Assisted Clinical Medicine, Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Jack Toner
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK
- Mental Health & Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jian Hu
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK
- Mental Health & Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Logan X Zhang
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Catarina Domingos
- Institute for Systems and Robotics-Lisboa and Department of Bioengineering, Instituto Superior Técnico-Universidade de Lisboa, Lisbon, Portugal
| | - Sara P Monteiro
- Institute for Systems and Robotics-Lisboa and Department of Bioengineering, Instituto Superior Técnico-Universidade de Lisboa, Lisbon, Portugal
| | - Patrícia Figueiredo
- Institute for Systems and Robotics-Lisboa and Department of Bioengineering, Instituto Superior Técnico-Universidade de Lisboa, Lisbon, Portugal
| | - Alexander G J Harms
- Department of Radiology & Nuclear Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Beatriz E Padrela
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, the Netherlands
| | - Channelle Tham
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ahmed Abdalle
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Paula L Croal
- Radiological Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Udunna Anazodo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| |
Collapse
|
9
|
Liu Q, Ning L, Shaik IA, Liao C, Gagoski B, Bilgic B, Grissom W, Nielsen JF, Zaitsev M, Rathi Y. Reduced cross-scanner variability using vendor-agnostic sequences for single-shell diffusion MRI. Magn Reson Med 2024. [PMID: 38469671 DOI: 10.1002/mrm.30062] [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] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 03/13/2024]
Abstract
PURPOSE To reduce the inter-scanner variability of diffusion MRI (dMRI) measures between scanners from different vendors by developing a vendor-neutral dMRI pulse sequence using the open-source vendor-agnostic Pulseq platform. METHODS We implemented a standard EPI based dMRI sequence in Pulseq. We tested it on two clinical scanners from different vendors (Siemens Prisma and GE Premier), systematically evaluating and comparing the within- and inter-scanner variability across the vendors, using both the vendor-provided and Pulseq dMRI sequences. Assessments covered both a diffusion phantom and three human subjects, using standard error (SE) and Lin's concordance correlation to measure the repeatability and reproducibility of standard DTI metrics including fractional anisotropy (FA) and mean diffusivity (MD). RESULTS Identical dMRI sequences were executed on both scanners using Pulseq. On the phantom, the Pulseq sequence showed more than a 2.5× reduction in SE (variability) across Siemens and GE scanners. Furthermore, Pulseq sequences exhibited markedly reduced SE in-vivo, maintaining scan-rescan repeatability while delivering lower variability in FA and MD (more than 50% reduction in cortical/subcortical regions) compared to vendor-provided sequences. CONCLUSION The Pulseq diffusion sequence reduces the cross-scanner variability for both phantom and in-vivo data, which will benefit multi-center neuroimaging studies and improve the reproducibility of neuroimaging studies.
Collapse
Affiliation(s)
- Qiang Liu
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Lipeng Ning
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Imam Ahmed Shaik
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Congyu Liao
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Borjan Gagoski
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Fetal-Neonatal Neuroimaging & Developmental Science Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Berkin Bilgic
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard/MIT Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - William Grissom
- Department of Biomedical Engineering, Case School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jon-Fredrik Nielsen
- Functional MRI Laboratory, Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Maxim Zaitsev
- Division of Medical Physics, Department of Diagnostic and Interventional Radiology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Li Z, Calhoun P, Rickels MR, Gal RL, Beck RW, Jacobs PG, Clements MA, Patton SR, Castle JR, Martin CK, Gillingham MB, Doyle FJ, Riddell MC. Factors Affecting Reproducibility of Change in Glucose During Exercise: Results From the Type 1 Diabetes and EXercise Initiative. J Diabetes Sci Technol 2024:19322968241234687. [PMID: 38456512 DOI: 10.1177/19322968241234687] [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] [Indexed: 03/09/2024]
Abstract
AIMS To evaluate factors affecting within-participant reproducibility in glycemic response to different forms of exercise. METHODS Structured exercise sessions ~30 minutes in length from the Type 1 Diabetes Exercise Initiative (T1DEXI) study were used to assess within-participant glycemic variability during and after exercise. The effect of several pre-exercise factors on the within-participant glycemic variability was evaluated. RESULTS Data from 476 adults with type 1 diabetes were analyzed. A participant's change in glucose during exercise was reproducible within 15 mg/dL of the participant's other exercise sessions only 32% of the time. Participants who exercised with lower and more consistent glucose level, insulin on board (IOB), and carbohydrate intake at exercise start had less variability in glycemic change during exercise. Participants with lower mean glucose (P < .001), lower glucose coefficient of variation (CV) (P < .001), and lower % time <70 mg/dL (P = .005) on sedentary days had less variable 24-hour post-exercise mean glucose. CONCLUSIONS Reproducibility of change in glucose during exercise was low in this cohort of adults with T1D, but more consistency in pre-exercise glucose levels, IOB, and carbohydrates may increase this reproducibility. Mean glucose variability in the 24 hours after exercise is influenced more by the participant's overall glycemic control than other modifiable factors.
Collapse
Affiliation(s)
- Zoey Li
- JAEB Center for Health Research, Tampa, FL, USA
| | | | - Michael R Rickels
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin L Gal
- JAEB Center for Health Research, Tampa, FL, USA
| | - Roy W Beck
- JAEB Center for Health Research, Tampa, FL, USA
| | - Peter G Jacobs
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | | | | | - Jessica R Castle
- Harold Schnitzer Diabetes Health Center, Oregon Health & Science University, Portland, OR, USA
| | - Corby K Martin
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Melanie B Gillingham
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | | |
Collapse
|
11
|
Cunha-Oliveira T, Ioannidis JPA, Oliveira PJ. Best Practices for Data Management and Sharing in Experimental Biomedical Research. Physiol Rev 2024. [PMID: 38451234 DOI: 10.1152/physrev.00043.2023] [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] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building upon results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.
Collapse
Affiliation(s)
| | - John P A Ioannidis
- Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA, United States
| | - Paulo J Oliveira
- Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
| |
Collapse
|
12
|
Kochovska S, Murtagh FE, Agar M, Phillips JL, Dudgeon D, Lujic S, Johnson MJ, Currow DC. Creating more comparable cohorts in observational palliative care studies: A proposed framework to improve applicability and replicability of research. Palliat Med 2024:2692163241234227. [PMID: 38454317 DOI: 10.1177/02692163241234227] [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] [Indexed: 03/09/2024]
Abstract
BACKGROUND Palliative care is characterised by heterogeneous patient and caregiver populations who are provided care in different health systems and a research base including a large proportion of observational, mostly retrospective studies. The inherent diversity of palliative care populations and the often inadequate study descriptions challenge the application of new knowledge into practice and reproducibility for confirmatory studies. Being able to define systematically study populations would significantly increase their generalisability and effective translation into practice. PROPOSAL Based on an informal consensus process by active palliative care researchers challenged by this problem and a review of the current evidence, we propose an approach to creating more comparable cohorts in observational (non-randomised) palliative care studies that relies on defining the study population in relation to a fixed, well-defined event from which analyses are built ('anchoring'). In addition to providing a detailed and complete description of the study population, anchoring is the critical step in creating more comparable cohorts in observational palliative care studies. Anchoring can be done with respect to a single or multiple data points, and can support both prospective and retrospective data collection and analysis. DISCUSSION Anchoring the cohort to reproducible data points will help create more comparable cohorts in palliative care whilst mitigating its inherent heterogeneity. This, in turn, will help optimise the generalisability, applicability and reproducibility of observational palliative care studies to strengthen the evidence base and improve practice.
Collapse
Affiliation(s)
- Slavica Kochovska
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Fliss Em Murtagh
- Wolfson Palliative Care Research Centre, Hull York Medical School, University of Hull, Hull, UK
| | - Meera Agar
- IMPACCT, Faculty of Health, University of Technology Sydney, Ultimo, NSW, Australia
| | - Jane L Phillips
- School of Nursing, Faculty of Health, University of Technology Queensland, Brisbane, QLD, Australia
| | - Deborah Dudgeon
- Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Sanja Lujic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, NSW, Australia
| | - Miriam J Johnson
- Wolfson Palliative Care Research Centre, Hull York Medical School, University of Hull, Hull, UK
| | - David C Currow
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| |
Collapse
|
13
|
Wang R, Wang Y, Qiu S, Ma S, Yan F, Yang GZ, Li R, Feng Y. A Comparative Study of Three Systems for Liver Magnetic Resonance Elastography. J Magn Reson Imaging 2024. [PMID: 38449389 DOI: 10.1002/jmri.29335] [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] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Different MR elastography (MRE) systems may produce different stiffness measurements, making direct comparison difficult in multi-center investigations. PURPOSE To assess the repeatability and reproducibility of liver stiffness measured by three typical MRE systems. STUDY TYPE Prospective. POPULATION/PHANTOMS Thirty volunteers without liver disease history (20 males, aged 21-28)/5 gel phantoms. FIELD STRENGTH/SEQUENCE 3.0 T United Imaging Healthcare (UIH), 1.5 T Siemens Healthcare, 3.0 T General Electric Healthcare (GE)/Echo planar imaging-based MRE sequence. ASSESSMENT Wave images of volunteers and phantoms were acquired by three MRE systems. Tissue stiffness was evaluated by two observers, while phantom stiffness was assessed automatically by code. The reproducibility across three MRE systems was quantified based on the mean stiffness of each volunteer and phantom. STATISTICAL TESTS Intraclass correlation coefficients (ICC), coefficients of variation (CV), and Bland-Altman analyses were used to assess the interobserver reproducibility, the interscan repeatability, and the intersystem reproducibility. Paired t-tests were performed to assess the interobserver and interscan variation. Friedman tests with Dunn's multiple comparison correction were performed to assess the intersystem variation. P values less than 0.05 indicated significant difference. RESULTS The reproducibility of stiffness measured by the two observers demonstrated consistency with ICC > 0.92, CV < 4.32%, Mean bias < 2.23%, and P > 0.06. The repeatability of measurements obtained using the electromagnetic system for the liver revealed ICC > 0.96, CV < 3.86%, Mean bias < 0.19%, P > 0.90. When considering the range of reproducibility across the three systems for liver evaluations, results ranged with ICCs from 0.70 to 0.87, CVs from 6.46% to 10.99%, and Mean biases between 1.89% and 6.30%. Phantom studies showed similar results. The values of measured stiffness differed across all three systems significantly. DATA CONCLUSION Liver stiffness values measured from different MRE systems can be different, but the measurements across the three MRE systems produced consistent results with excellent reproducibility. EVIDENCE LEVEL 1 TECHNICAL EFFICACY: Stage 2.
Collapse
Affiliation(s)
- Runke Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, China
| | - Yikun Wang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Medical Imaging Technology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Suhao Qiu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, China
| | - Shengyuan Ma
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Medical Imaging Technology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang-Zhong Yang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, China
| | - Ruokun Li
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Medical Imaging Technology, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Feng
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
14
|
Freire B, Silva LY, Espindola KA, da Rocha JRDO, Michaelsen SM. Motion Analysis of the Mug Transportation Task Through Upper Limb Kinematics. J Mot Behav 2024:1-9. [PMID: 38439504 DOI: 10.1080/00222895.2024.2324903] [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: 10/19/2023] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
The task of transporting objects is a fundamental part of daily living activities. Previous kinematic studies focusing on tasks such as pointing, reach-to-grasp, and drinking have not fully captured the motor behaviors involved in object transportation, including placing a cup on a table or storing items in specific places. Hence, this study aimed to analyze the motor behavior associated with transporting a mug using upper limb kinematic variables. Fifteen healthy adults were instructed to transport an open-handle mug across a table. The kinematic metrics evaluated included object end-error for accuracy, frontal and lateral end-range for precision, movement time, peak velocity, time to peak velocity for control strategy, object path ratio for efficiency, and interjoint coordination. The stability of motor behavior was assessed through a test-retest analysis. The mug transporting task achieved accuracy with a radius <10 mm around the target, a peak velocity of ∼0.4 m/s, a control strategy where acceleration time constituted about 30% of the movement time, and a slightly curved trajectory. The test-retest analysis confirmed stable motor behavior across all kinematic metrics (ICCs > 0.75). Thus, the mug transporting task exhibited unique and stable kinematic characteristics, distinguishing it from non-transport activities and effectively mirroring transporting activities of daily living.
Collapse
Affiliation(s)
- Bruno Freire
- Department of Physical Therapy, Santa Catarina State University, Florianópolis, Brazil
| | - Letícia Yolanda Silva
- Department of Physical Therapy, Santa Catarina State University, Florianópolis, Brazil
| | | | | | | |
Collapse
|
15
|
Wang J, Hill‐Jarrett T, Buto P, Pederson A, Sims KD, Zimmerman SC, DeVost MA, Ferguson E, Lacar B, Yang Y, Choi M, Caunca MR, La Joie R, Chen R, Glymour MM, Ackley SF. Comparison of approaches to control for intracranial volume in research on the association of brain volumes with cognitive outcomes. Hum Brain Mapp 2024; 45:e26633. [PMID: 38433682 PMCID: PMC10910271 DOI: 10.1002/hbm.26633] [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: 08/21/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Most neuroimaging studies linking regional brain volumes with cognition correct for total intracranial volume (ICV), but methods used for this correction differ across studies. It is unknown whether different ICV correction methods yield consistent results. Using a brain-wide association approach in the MRI substudy of UK Biobank (N = 41,964; mean age = 64.5 years), we used regression models to estimate the associations of 58 regional brain volumetric measures with eight cognitive outcomes, comparing no correction and four ICV correction approaches. Approaches evaluated included: no correction; dividing regional volumes by ICV (proportional approach); including ICV as a covariate in the regression (adjustment approach); and regressing the regional volumes against ICV in different normative samples and using calculated residuals to determine associations (residual approach). We used Spearman-rank correlations and two consistency measures to quantify the extent to which associations were inconsistent across ICV correction approaches for each possible brain region and cognitive outcome pair across 2320 regression models. When the association between brain volume and cognitive performance was close to null, all approaches produced similar estimates close to the null. When associations between a regional volume and cognitive test were not null, the adjustment and residual approaches typically produced similar estimates, but these estimates were inconsistent with results from the crude and proportional approaches. For example, when using the crude approach, an increase of 0.114 (95% confidence interval [CI]: 0.103-0.125) in fluid intelligence was associated with each unit increase in hippocampal volume. However, when using the adjustment approach, the increase was 0.055 (95% CI: 0.043-0.068), while the proportional approach showed a decrease of -0.025 (95% CI: -0.035 to -0.014). Different commonly used methods to correct for ICV yielded inconsistent results. The proportional method diverges notably from other methods and results were sometimes biologically implausible. A simple regression adjustment for ICV produced biologically plausible associations.
Collapse
Affiliation(s)
- Jingxuan Wang
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| | | | - Peter Buto
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| | - Annie Pederson
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| | - Kendra D. Sims
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| | - Scott C. Zimmerman
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Michelle A. DeVost
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Erin Ferguson
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Benjamin Lacar
- Bakar Computational Health Sciences InstituteUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Yulin Yang
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Minhyuk Choi
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Michelle R. Caunca
- Memory and Aging Center, Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Renaud La Joie
- Memory and Aging Center, Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Ruijia Chen
- Department of Epidemiology and BiostatisticsUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - M. Maria Glymour
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| | - Sarah F. Ackley
- Department of EpidemiologyBoston UniversityBostonMassachusettsUSA
| |
Collapse
|
16
|
Vidyasagar R, Fazollahi A, Desmond P, Moffat B, Bush AI, Ayton S. Single-session reproducibility of MR spectroscopy measures of glutathione in the mesial temporal lobe with MEGA-PRESS. J Neuroimaging 2024; 34:224-231. [PMID: 38174904 DOI: 10.1111/jon.13179] [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: 05/21/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND AND PURPOSE Magnetic resonance spectroscopy (MRS) measures neurochemicals in vivo. Glutathione (GSH) is a neuroprotective chemical shown to vary significantly in patients with Alzheimer's disease (AD). This work investigates the reproducibility of GSH measures in the mesial temporal lobe (MTL) to identify its potential clinical utility. METHODS MRS data were acquired from eight healthy volunteers (31.1 ± 5.2 years; 4 male/female) using Mescher-Garwood-Point Resolved Spectroscopy (MEGA-PRESS) from the MTL in the left hemisphere across two scan sessions in the same visit. Total N-acetylaspartate (tNAA), choline (tCho), creatine (tCr), and GSH were quantified. Reproducibility of quantifications of these neurochemicals were tested using coefficient of variance (CV) between scan sessions. Reproducibility of voxel placement on the left MTL was calculated by measuring the tissue overlap and percent of hippocampus within that voxel. CV measured across different scan sessions in each individual, with a CV<15% was accepted as "good" reproducibility. Paired t-tests were carried out to establish the significant differences between the two scans across each individual with p<.05 as significant. RESULTS TNAA (%CV = 7.2; p = .5), tCr (%CV = 7.8; p = .6) and tCho (%CV = 9.3; p = .4), and GSH (%CV = 22; p = .1). The dice coefficient that reflects the level of overlap of hippocampal tissue in the voxel was shown to be 0.8 ± 0.1. Voxel tissue composition were: Scan 1 (cerebrospinal fluid [CSF]: 5 ± 1%, white matter [WM]: 52 ± 3%, gray matter [GM]: 43 ± 3%); Scan 2 (CSF: 5 ± 1%, WM: 52 ± 4%, GM: 44 ± 4%). CONCLUSION The data suggest measures of abundant metabolites in the MTL using the MEGA-PRESS sequence has a high reproducibility. Reproducibility of GSH in this area was poorer requiring care when interpreting measures of GSH in the MTL for clinical translational purposes.
Collapse
Affiliation(s)
- Rishma Vidyasagar
- Radiology Department, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Amir Fazollahi
- Radiology Department, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Patricia Desmond
- Radiology Department, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Bradford Moffat
- Melbourne Biomedical Centre Imaging Unit, Department of Radiology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health and University of Melbourne, Melbourne, Victoria, Australia
| | - Scott Ayton
- The Florey Institute of Neuroscience and Mental Health and University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
17
|
Baker C, Piasecki J, Hunt JA, Hough J. The reproducibility of dendritic cell and T cell counts to a 30-min high-intensity cycling protocol as a tool to highlight overtraining. Exp Physiol 2024; 109:380-392. [PMID: 38063067 DOI: 10.1113/ep091326] [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] [Received: 06/01/2023] [Accepted: 11/23/2023] [Indexed: 03/02/2024]
Abstract
Heavy training has been reported to be immunosuppressive in athletes and lead to blunted cortisol responses to exercise. Cortisol elevates the number of dendritic cells (DCs), key antigen-presenting cells that interact with T cells to initiate an immune response. Reproducible cortisol responses to a 30-min cycle test have been identified but were based on percentage of work rate maximum. To ensure physiological consistency, submaximal anchors, that is, ventilatory threshold (VT1 ) should prescribe intensity. This study aims to assess the reproducibility of the DC and T cell responses to an adapted stress test to assess its usefulness in assessing DC dysfunction with intensified training. Twelve males cycled for 1 min at 20% below VT1 and 4 min at 50% between VT1 andV ̇ O 2 max ${\dot{V}}_{{{\mathrm{O}}}_{\mathrm{2}}\max }$ , for 30 min (20/50), with blood samples pre-, post- and 30 min post-exercise. This was repeated twice, 2-7 days apart. Flow cytometry assessed total DCs, plasmacytoid DCs, myeloid DCs, total T cells, T helper cells and T cytotoxic cells. No significant trial or interaction effects were found for any variable. A significant main effect of time for all variables was found; immune cells increased from pre- to post-exercise and decreased to baseline 30 min post-exercise, apart from plasmacytoid DCs, which remained elevated 30 min post-exercise. Intraclass correlation coefficients showed overall good-to-excellent reliability for all immune cells, with smallest real difference and Bland-Altman analysis verifying high reproducibility between trials. These results suggest that the 20/50 exercise test induces reproducible DC and T cell count changes, which, implemented before and after a period of intensified training, may highlight the negative states of overtraining.
Collapse
Affiliation(s)
- Carla Baker
- Department of Sport Science, SHAPE Research Centre, Nottingham Trent University, Nottingham, UK
| | - Jessica Piasecki
- Department of Sport Science, SHAPE Research Centre, Nottingham Trent University, Nottingham, UK
| | - John A Hunt
- Medical Technologies Innovation Facility, Nottingham Trent University, Nottingham, UK
| | - John Hough
- Department of Sport Science, SHAPE Research Centre, Nottingham Trent University, Nottingham, UK
| |
Collapse
|
18
|
Lindsey ML, Usselman CW, Ripplinger CM, Carter JR, DeLeon-Pennell KY. Sex as a biological variable for cardiovascular physiology. Am J Physiol Heart Circ Physiol 2024; 326:H459-H469. [PMID: 38099847 DOI: 10.1152/ajpheart.00727.2023] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 02/03/2024]
Abstract
There have been ongoing efforts by federal agencies and scientific communities since the early 1990s to incorporate sex and/or gender in all aspects of cardiovascular research. Scientific journals provide a critical function as change agents to influence transformation by encouraging submissions for topic areas, and by setting standards and expectations for articles submitted to the journal. As part of ongoing efforts to advance sex and gender in cardiovascular physiology research, the American Journal of Physiology-Heart and Circulatory Physiology recently launched a call for papers on Considering Sex as a Biological Variable. This call was an overwhelming success, resulting in 78 articles published in this collection. This review summarizes the major themes of the collection, including Sex as a Biological Variable Within: Endothelial Cell and Vascular Physiology, Cardiovascular Immunity and Inflammation, Metabolism and Mitochondrial Energy, Extracellular Matrix Turnover and Fibrosis, Neurohormonal Signaling, and Cardiovascular Clinical and Epidemiology Assessments. Several articles also focused on establishing rigor and reproducibility of key physiological measurements involved in cardiovascular health and disease, as well as recommendations and considerations for study design. Combined, these articles summarize our current understanding of sex and gender influences on cardiovascular physiology and pathophysiology and provide insight into future directions needed to further expand our knowledge.
Collapse
Affiliation(s)
- Merry L Lindsey
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, United States
- Research Service, Nashville Veterans Affairs Medical Center, Nashville, Tennessee, United States
| | - Charlotte W Usselman
- Cardiovascular Health and Autonomic Regulation Laboratory, Department of Kinesiology and Physical Education, McGill University, Montreal, Quebec, Canada
| | - Crystal M Ripplinger
- Department of Pharmacology, UC Davis School of Medicine, Davis, California, United States
| | - Jason R Carter
- Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, United States
| | - Kristine Y DeLeon-Pennell
- Division of Cardiology, Department of Medicine, School of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- Research Service, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina, United States
| |
Collapse
|
19
|
Keene KR, Bongers J, de Meel RHP, Venhovens J, Verschuuren JJGM, Tannemaat MR. Test-Retest Reliability of Repetitive Ocular Vestibular Evoked Myogenic Potentials in Myasthenia Gravis Patients and Healthy Control Subjects. J Clin Neurophysiol 2024; 41:265-270. [PMID: 36413652 PMCID: PMC10898539 DOI: 10.1097/wnp.0000000000000956] [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: 11/26/2022] Open
Abstract
PURPOSE Repetitive ocular vestibular evoked myogenic potentials (ROVEMP) are a novel diagnostic test to quantify neuromuscular transmission deficits in extraocular muscles in myasthenia gravis. We aimed to investigate the test-retest reliability of the ROVEMP and the effect of amplitude and age. METHODS We performed the ROVEMP test twice in 19 patients with myasthenia gravis (52.7 ± 19.8 years) and in 15 healthy control subjects (46.5 ± 16 years). The Bland-Altman level of agreement was determined. The relationship between test-retest reliability and signal quality, participant age and signal amplitude was studied. RESULTS Limits of agreement were from -179.9 to 139.3 in myasthenia gravis patients and from -56.9 to 89.5 in healthy control subjects. Difference between measurements correlated with signal amplitude ( r = -0.50, P < 0.001). Combining the primary cohort with previously published data from 114 subjects, we found a significant negative correlation between age and reference amplitude ( r = -0.163, P = 0.045). CONCLUSIONS This study shows that in our hands, the test-retest reliability of the ROVEMP is not optimal. Measurements with higher reference amplitude had a better quality, higher reproducibility, and increased diagnostic yield. We caution against the use of ROVEMP measurements of lower amplitude in clinical practice. In addition, given the correlation between age and amplitude, age matching of healthy control subjects and patients is essential in future studies.
Collapse
Affiliation(s)
- Kevin R. Keene
- Department of Neurology and Clinical Neurophysiology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Julia Bongers
- Department of Neurology and Clinical Neurophysiology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Robert H. P. de Meel
- Department of Neurology and Clinical Neurophysiology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Jeroen Venhovens
- Department of Neurology and Clinical Neurophysiology, Albert Schweitzer Hospital, Dordrecht, the Netherlands
| | - Jan J. G. M. Verschuuren
- Department of Neurology and Clinical Neurophysiology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Martijn R. Tannemaat
- Department of Neurology and Clinical Neurophysiology, Leiden University Medical Center, Leiden, the Netherlands; and
| |
Collapse
|
20
|
Kim M, Naish JH, Needleman SH, Tibiletti M, Taylor Y, O'Connor JPB, Parker GJM. Feasibility of dynamic T 2 *-based oxygen-enhanced lung MRI at 3T. Magn Reson Med 2024; 91:972-986. [PMID: 38013206 PMCID: PMC10952203 DOI: 10.1002/mrm.29914] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE To demonstrate proof-of-concept of a T2 *-sensitized oxygen-enhanced MRI (OE-MRI) method at 3T by assessing signal characteristics, repeatability, and reproducibility of dynamic lung OE-MRI metrics in healthy volunteers. METHODS We performed sequence-specific simulations for protocol optimisation and acquired free-breathing OE-MRI data from 16 healthy subjects using a dual-echo RF-spoiled gradient echo approach at 3T across two institutions. Non-linear registration and tissue density correction were applied. Derived metrics included percent signal enhancement (PSE), ∆R2 * and wash-in time normalized for breathing rate (τ-nBR). Inter-scanner reproducibility and intra-scanner repeatability were evaluated using intra-class correlation coefficient (ICC), repeatability coefficient, reproducibility coefficient, and Bland-Altman analysis. RESULTS Simulations and experimental data show negative contrast upon oxygen inhalation, due to substantial dominance of ∆R2 * at TE > 0.2 ms. Density correction improved signal fluctuations. Density-corrected mean PSE values, aligned with simulations, display TE-dependence, and an anterior-to-posterior PSE reduction trend at TE1 . ∆R2 * maps exhibit spatial heterogeneity in oxygen delivery, featuring anterior-to-posterior R2 * increase. Mean T2 * values across 32 scans were 0.68 and 0.62 ms for pre- and post-O2 inhalation, respectively. Excellent or good agreement emerged from all intra-, inter-scanner and inter-rater variability tests for PSE and ∆R2 *. However, ICC values for τ-nBR demonstrated limited agreement between repeated measures. CONCLUSION Our results demonstrate the feasibility of a T2 *-weighted method utilizing a dual-echo RF-spoiled gradient echo approach, simultaneously capturing PSE, ∆R2 * changes, and oxygen wash-in during free-breathing. The excellent or good repeatability and reproducibility on intra- and inter-scanner PSE and ∆R2 * suggest potential utility in multi-center clinical applications.
Collapse
Affiliation(s)
- Mina Kim
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC)University College LondonLondonUK
| | - Josephine H. Naish
- Bioxydyn LimitedManchesterUK
- BHF Manchester Centre for Heart and Lung Magnetic Resonance Research (MCMR)Manchester University NHS Foundation TrustManchesterUK
| | - Sarah H. Needleman
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC)University College LondonLondonUK
| | | | - Yohn Taylor
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC)University College LondonLondonUK
| | - James P. B. O'Connor
- Division of Cancer SciencesUniversity of ManchesterManchesterUK
- Division of Radiotherapy and ImagingInstitute of Cancer ResearchLondonUK
| | - Geoff J. M. Parker
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC)University College LondonLondonUK
- Bioxydyn LimitedManchesterUK
| |
Collapse
|
21
|
Purcell RA, Aurelia LC, Esterbauer R, Allen LF, Bond KA, Williamson DA, Trevillyan JM, Trubiano JA, Juno JJ, Wheatley AK, Davenport MP, Nguyen THO, Kedzierska K, Kent SJ, Selva KJ, Chung AW. Immunoglobulin G genetic variation can confound assessment of antibody levels via altered binding to detection reagents. Clin Transl Immunology 2024; 13:e1494. [PMID: 38433763 PMCID: PMC10902689 DOI: 10.1002/cti2.1494] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Objectives Amino acid variations across more than 30 immunoglobulin (Ig) allotypes may introduce structural changes that influence recognition by anti-Ig detection reagents, consequently confounding interpretation of antibody responses, particularly in genetically diverse cohorts. Here, we assessed a panel of commercial monoclonal anti-IgG1 clones for capacity to universally recognise two dominant IgG1 haplotypes (G1m-1,3 and G1m1,17). Methods Four commercial monoclonal anti-human IgG1 clones were assessed via ELISAs and multiplex bead-based assays for their ability to bind G1m-1,3 and G1m1,17 IgG1 variants. Detection antibodies were validated against monoclonal IgG1 allotype standards and tested for capacity to recognise antigen-specific plasma IgG1 from G1m-1,3 and G1m1,17 homozygous and heterozygous SARS-CoV-2 BNT162b2 vaccinated (n = 28) and COVID-19 convalescent (n = 44) individuals. An Fc-specific pan-IgG detection antibody corroborated differences between hinge- and Fc-specific anti-IgG1 responses. Results Hinge-specific anti-IgG1 clone 4E3 preferentially bound G1m1,17 compared to G1m-1,3 IgG1. Consequently, SARS-CoV-2 Spike-specific IgG1 levels detected in G1m1,17/G1m1,17 BNT162b2 vaccinees appeared 9- to 17-fold higher than in G1m-1,3/G1m-1,3 vaccinees. Fc-specific IgG1 and pan-IgG detection antibodies equivalently bound G1m-1,3 and G1m1,17 IgG1 variants, and detected comparable Spike-specific IgG1 levels between haplotypes. IgG1 responses against other human coronaviruses and influenza were similarly poorly detected by 4E3 anti-IgG1 in G1m-1,3/G1m-1,3 subjects. Conclusion Anti-IgG1 clone 4E3 confounds assessment of antibody responses in clinical cohorts owing to bias towards detection of G1m1,17 IgG1 variants. Validation of anti-Ig clones should include evaluation of binding to relevant antibody variants, particularly as the role of immunogenetics upon humoral immunity is increasingly explored in diverse populations.
Collapse
Affiliation(s)
- Ruth A Purcell
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - L Carissa Aurelia
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Robyn Esterbauer
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Lilith F Allen
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Katherine A Bond
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
- Victorian Infectious Diseases Reference Laboratory (VIDRL)The Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL)The Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Infectious DiseasesThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Janine M Trevillyan
- Department of Infectious DiseasesThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
- Centre for Antibiotic Allergy and Research, Department of Infectious DiseasesAustin HealthHeidelbergVICAustralia
| | - Jason A Trubiano
- Centre for Antibiotic Allergy and Research, Department of Infectious DiseasesAustin HealthHeidelbergVICAustralia
- Department of MedicineUniversity of MelbourneParkvilleVICAustralia
- Department of Infectious DiseasesPeter MacCallum Cancer CentreMelbourneVICAustralia
- National Centre for Infections in CancerPeter MacCallum Cancer CentreMelbourneVICAustralia
| | - Jennifer J Juno
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Adam K Wheatley
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | | | - Thi HO Nguyen
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Katherine Kedzierska
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Stephen J Kent
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Kevin John Selva
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Amy W Chung
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| |
Collapse
|
22
|
Sadeghi SA, Chen W, Wang Q, Wang Q, Fang F, Liu X, Sun L. Pilot Evaluation of the Long-Term Reproducibility of Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics of a Complex Proteome Sample. J Proteome Res 2024. [PMID: 38417052 DOI: 10.1021/acs.jproteome.3c00872] [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: 03/01/2024]
Abstract
Mass spectrometry (MS)-based top-down proteomics (TDP) has revolutionized biological research by measuring intact proteoforms in cells, tissues, and biofluids. Capillary zone electrophoresis-tandem MS (CZE-MS/MS) is a valuable technique for TDP, offering a high peak capacity and sensitivity for proteoform separation and detection. However, the long-term reproducibility of CZE-MS/MS in TDP remains unstudied, which is a crucial aspect for large-scale studies. This work investigated the long-term qualitative and quantitative reproducibility of CZE-MS/MS for TDP for the first time, focusing on a yeast cell lysate. Over 1000 proteoforms were identified per run across 62 runs using one linear polyacrylamide (LPA)-coated separation capillary, highlighting the robustness of the CZE-MS/MS technique. However, substantial decreases in proteoform intensity and identification were observed after some initial runs due to proteoform adsorption onto the capillary inner wall. To address this issue, we developed an efficient capillary cleanup procedure using diluted ammonium hydroxide, achieving high qualitative and quantitative reproducibility for the yeast sample across at least 23 runs. The data underscore the capability of CZE-MS/MS for large-scale quantitative TDP of complex samples, signaling its readiness for deployment in broad biological applications. The MS RAW files were deposited in ProteomeXchange Consortium with the data set identifier of PXD046651.
Collapse
Affiliation(s)
- Seyed Amirhossein Sadeghi
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wenrong Chen
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 535 W Michigan Street, Indianapolis, Indiana 46202, United States
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, Louisiana 70112, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
23
|
Morawietz C, Dumalski N, Wissmann AM, Wecking J, Muehlbauer T. Consistency of spatial ability performance in children, adolescents, and young adults. Front Psychol 2024; 15:1365941. [PMID: 38487665 PMCID: PMC10938598 DOI: 10.3389/fpsyg.2024.1365941] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Background Spatial abilities are essential cognitive skills for many aspects of our everyday life that develop substantially throughout childhood and adolescence. While there are numerous measurement tools to evaluate these abilities, many of them have been designed for specific age groups hampering comparability throughout development. Thus, we determined test-retest-reliability and minimal detectable change for a set of tests that evaluate spatial ability performance in their variety in youth and compared them to young adults. Methods Children (age: 11.4 ± 0.5 years, n = 26), adolescents (age: 12.5 ± 0.7 years, n = 22), and young adults (age: 26.1 ± 4.0 years, n = 26) performed a set of five spatial ability tests twice, 20 min apart: Paper Folding Test (PFT), Mental Rotation Test (MRT), Water Level Task (WLT), Corsi Block Test (CBT), and Numbered Cones Run (NCR). Relative and absolute test-retest reliability was determined by calculating the intraclass correlation coefficient (ICC3,1) and the standard error of measurement (SEM), respectively. Further, the minimal detectable change (MDC95%) was calculated to identify clinically relevant changes between repeated measurements. Results Irrespective of test, reliability was "excellent" (i.e., ICC3,1 ≥ 0.75) in all age cohorts and the SEM values were rather small. The MDC95% values needed to identify relevant changes in repeated measurements of spatial ability performance ranged between 0.8 and 13.9% in children, 1.1 and 24.5% in adolescents, and 0.7 and 20.8% in young adults. Conclusion The determined values indicate that the investigated set of tests is reliable to detect spatial ability performance in healthy children, adolescents, and young adults.
Collapse
Affiliation(s)
- Christina Morawietz
- Division of Movement and Training Sciences/Biomechanics of Sport, University of Duisburg-Essen, Essen, Germany
| | | | | | | | | |
Collapse
|
24
|
Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024. [PMID: 38412263 DOI: 10.1021/acs.jproteome.3c00800] [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: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
Collapse
Affiliation(s)
- Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| |
Collapse
|
25
|
Olaisen S, Smistad E, Espeland T, Hu J, Pasdeloup D, Østvik A, Aakhus S, Rösner A, Malm S, Stylidis M, Holte E, Grenne B, Løvstakken L, Dalen H. Automatic measurements of left ventricular volumes and ejection fraction by artificial intelligence: clinical validation in real time and large databases. Eur Heart J Cardiovasc Imaging 2024; 25:383-395. [PMID: 37883712 DOI: 10.1093/ehjci/jead280] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
AIMS Echocardiography is a cornerstone in cardiac imaging, and left ventricular (LV) ejection fraction (EF) is a key parameter for patient management. Recent advances in artificial intelligence (AI) have enabled fully automatic measurements of LV volumes and EF both during scanning and in stored recordings. The aim of this study was to evaluate the impact of implementing AI measurements on acquisition and processing time and test-retest reproducibility compared with standard clinical workflow, as well as to study the agreement with reference in large internal and external databases. METHODS AND RESULTS Fully automatic measurements of LV volumes and EF by a novel AI software were compared with manual measurements in the following clinical scenarios: (i) in real time use during scanning of 50 consecutive patients, (ii) in 40 subjects with repeated echocardiographic examinations and manual measurements by 4 readers, and (iii) in large internal and external research databases of 1881 and 849 subjects, respectively. Real-time AI measurements significantly reduced the total acquisition and processing time by 77% (median 5.3 min, P < 0.001) compared with standard clinical workflow. Test-retest reproducibility of AI measurements was superior in inter-observer scenarios and non-inferior in intra-observer scenarios. AI measurements showed good agreement with reference measurements both in real time and in large research databases. CONCLUSION The software reduced the time taken to perform and volumetrically analyse routine echocardiograms without a decrease in accuracy compared with experts.
Collapse
Affiliation(s)
- Sindre Olaisen
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Erik Smistad
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Medical Image Analysis, Health Research, SINTEF Digital, Trondheim, Norway
| | - Torvald Espeland
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Clinic of Cardiology, St.Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Jieyu Hu
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - David Pasdeloup
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Andreas Østvik
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Medical Image Analysis, Health Research, SINTEF Digital, Trondheim, Norway
| | - Svend Aakhus
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Clinic of Cardiology, St.Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Assami Rösner
- Department of Cardiology, University Hospital of North Norway, Tromsø, Norway
- Institute for Clinical Medicine, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Siri Malm
- Institute for Clinical Medicine, UiT, The Arctic University of Norway, Tromsø, Norway
- Department of Cardiology, University Hospital of North Norway, UNN Harstad, Tromsø, Norway
| | - Michael Stylidis
- Department of Cardiology, University Hospital of North Norway, Tromsø, Norway
- Department of Community Medicine, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Espen Holte
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Clinic of Cardiology, St.Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Bjørnar Grenne
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Clinic of Cardiology, St.Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Lasse Løvstakken
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
| | - Havard Dalen
- Centre for Innovative Ultrasound Solutions, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Clinic of Cardiology, St.Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas Gate 3, 7030 Trondheim, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Kirkegata 2, 7600 Levanger, Norway
| |
Collapse
|
26
|
Chernov G. The Alternative Factors Leading to Replication Crisis: Prediction and Evaluation. Eval Rev 2024:193841X241229106. [PMID: 38379307 DOI: 10.1177/0193841x241229106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Most existing solutions to the current replication crisis in science address only the factors stemming from specific poor research practices. We introduce a novel mechanism that leverages the experts' predictive abilities to analyze the root causes of replication failures. It is backed by the principle that the most accurate predictor is the most qualified expert. This mechanism can be seamlessly integrated into the existing replication prediction market framework with minimal implementation costs. It relies on an objective rather than subjective process and unstructured expert opinions to effectively identify various influences contributing to the replication crisis.
Collapse
Affiliation(s)
- Gregory Chernov
- Department for Computational Neuroscience, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| |
Collapse
|
27
|
Dufour N, Delattre R, Debarbieux L. High-Throughput Bacteriophage Testing with Potency Determination: Validation of an Automated Pipetting and Phage Drop-Off Method. Biomedicines 2024; 12:466. [PMID: 38398068 PMCID: PMC10886619 DOI: 10.3390/biomedicines12020466] [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] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The development of bacteriophages (phages) as active pharmaceutical ingredients for the treatment of patients is on its way and regulatory agencies are calling for reliable methods to assess phage potency. As the number of phage banks is increasing, so is the number of phages that need to be tested to identify therapeutic candidates. Currently, assessment of phage potency on a semi-solid medium to observe plaque-forming units is unavoidable and proves to be labor intensive when considering dozens of phage candidates. Here, we present a method based on automated pipetting and phage drop-off performed by a liquid-handling robot, allowing high-throughput testing and phage potency determination (based on phage titer and efficiency of plaquing). Ten phages were tested, individually and assembled into one cocktail, against 126 Escherichia coli strains. This automated method was compared to the reference one (manual assay) and validated in terms of reproducibility and concordance (ratio of results according to the Bland and Altman method: 0.99; Lin's concordance correlation coefficient: 0.86). We found that coefficients of variation were lower with automated pipetting (mean CV: 13.3% vs. 24.5%). Beyond speeding up the process of phage screening, this method could be used to standardize phage potency evaluation.
Collapse
Affiliation(s)
- Nicolas Dufour
- Réanimation Médico-Chirurgicale, Hôpital NOVO—Site de Pontoise, 95300 Pontoise, France
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- Réanimation, Centre Hospitalier de Digne-les-Bains, 04000 Digne-les-Bains, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
| |
Collapse
|
28
|
Herthum H, Hetzer S. Tensor denoising of quantitative multi-parameter mapping. Magn Reson Med 2024. [PMID: 38368616 DOI: 10.1002/mrm.30050] [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: 10/13/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
PURPOSE Quantitative multi-parameter mapping (MPM) provides maps of physical quantities representing physiologically meaningful tissue characteristics, which allows to investigate microstructure-function relationships reflecting normal or pathologic processes in the brain. However, the achievable spatial resolution and stability of MPM for basic research or clinical applications is severely constrained by SNR limits of the MR acquisition process, resulting in relatively long acquisition times. To increase SNR, we denoise MPM acquisitions using principal component analysis along tensors exploiting the Marchenko-Pastur law (tMPPCA). METHODS tMPPCA denoising was applied to three sets of MPM raw data before the quantification of maps of proton density, magnetization transfer saturation, R1 , and R2 *. The regional SNR gain for high-resolution MPM was investigated as well as reproducibility gains for clinically optimized protocols with moderate and high acceleration factors at different image resolutions. RESULTS Substantial noise reduction in raw data was achieved, resulting in reduced noise for quantitative mapping up to sixfold without introducing bias of mean values (below 1%). Scan-rescan fluctuations were reduced up to threefold. Denoising allowed to decrease the voxel volume fourfold at the same scan time or reduce the scan time twofold at same voxel volume without loss of sensitivity. CONCLUSIONS tMPPCA denoising can (a) improve of fine spatial and temporal patterns, (b) considerably reduce scan time for clinical applications, or (c) increase resolution to potentially push cutting-edge MPM protocols from the upper to the lower limit of the mesoscopic scale.
Collapse
Affiliation(s)
- Helge Herthum
- Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Hetzer
- Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
29
|
Maricot A, Lathouwers E, Verschueren J, De Pauw K, Meeusen R, Roelands B, Tassignon B. Test-retest, intra- and inter-rater reliability of the reactive balance test in patients with chronic ankle instability. Front Neurol 2024; 15:1320043. [PMID: 38434204 PMCID: PMC10906270 DOI: 10.3389/fneur.2024.1320043] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction The Reactive Balance Test (RBT) could be a valuable addition to research on chronic ankle instability (CAI) and clinical practice, but before it can be used in clinical practice it needs to be reliable. It has already been proven reliable in healthy recreational athletes, but not yet in patients with CAI who have shown persistent deficits in dynamic balance. The study aimed to determine the test-retest, intra-, and inter-rater reliability of the RBT in patients with CAI, and the test-retest and inter-rater reliability of the newly developed RBT score sheet. Methods We used a repeated-measures, single-group design to administer the RBT to CAI patients on three occasions, scored by multiple raters. We included 27 participants with CAI. The study used multiple reliability measures, including Pearson r, intra-class correlations (ICC), standard error of measurement (SEM), standard error of prediction (SEP), minimal detectable change (MDC), and Bland-Altman plots, to evaluate the reliability of the RBT's outcome measures (visuomotor response time and accuracy). It also assessed the test-retest and inter-rater reliability of the RBT score sheet using the same measures. Results The ICC measures for test-retest reliability were similar for accuracy (0.609) and VMRT (0.594). Intra-rater reliability had high correlations and ICCs for accuracy (r = 0.816, ICC = 0.815) and VMRT (r = 0.802, ICC = 0.800). Inter-rater reliability had a higher ICC for VMRT (0.868) than for accuracy (0.690). Conclusion Test-retest reliability was moderate, intra-rater reliability was good, and inter-rater reliability showed moderate reliability for accuracy and good reliability for VMRT. Additionally, the RBT shows robust SEM and mean difference measures. The score sheet method also demonstrated moderate test-retest reliability, while inter-rater reliability was good to excellent. This suggests that the RBT can be a valuable tool in assessing and monitoring balance in patients with CAI.
Collapse
Affiliation(s)
- Alexandre Maricot
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elke Lathouwers
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo Verschueren
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kevin De Pauw
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
- Brussels Human Robotics Research Center (BruBotics), Vrije Universiteit Brussel, Brussels, Belgium
| | - Romain Meeusen
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
- Brussels Human Robotics Research Center (BruBotics), Vrije Universiteit Brussel, Brussels, Belgium
- Department of Sports, Recreation, Exercise and Sciences (SRES), Faculty of Community and Health Sciences, University of the Western Cape, Cape Town, South Africa
| | - Bart Roelands
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
- Brussels Human Robotics Research Center (BruBotics), Vrije Universiteit Brussel, Brussels, Belgium
| | - Bruno Tassignon
- Human Physiology and Sports Physiotherapy Research Group, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
30
|
Hankenson FC, Prager EM, Berridge BR. Advocating for Generalizability: Accepting Inherent Variability in Translation of Animal Research Outcomes. Annu Rev Anim Biosci 2024; 12:391-410. [PMID: 38358839 DOI: 10.1146/annurev-animal-021022-043531] [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: 02/17/2024]
Abstract
Advancing scientific discovery requires investigators to embrace research practices that increase transparency and disclosure about materials, methods, and outcomes. Several research advocacy and funding organizations have produced guidelines and recommended practices to enhance reproducibility through detailed and rigorous research approaches; however, confusion around vocabulary terms and a lack of adoption of suggested practices have stymied successful implementation. Although reproducibility of research findings cannot be guaranteed due to extensive inherent variables in attempts at experimental repetition, the scientific community can advocate for generalizability in the application of data outcomes to ensure a broad and effective impact on the comparison of animals to translation within human research. This report reviews suggestions, based upon work with National Institutes of Health advisory groups, for improving rigor and transparency in animal research through aspects of experimental design, statistical assessment, and reporting factors to advocate for generalizability in the application of comparative outcomes between animals and humans.
Collapse
Affiliation(s)
- F C Hankenson
- Division of Laboratory Animal Medicine, Department of Pathobiology, School of Veterinary Medicine and University Laboratory Animal Resources, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - E M Prager
- Research Program Management, Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA;
| | - B R Berridge
- B2 Pathology Solutions LLC, Cary, North Carolina, USA;
| |
Collapse
|
31
|
Noriega N, Shekhirev M, Shuck CE, Salvage J, VahidMohammadi A, Dymond MK, Lacey J, Sandeman S, Gogotsi Y, Patel BA. Pristine Ti 3C 2T x MXene Enables Flexible and Transparent Electrochemical Sensors. ACS Appl Mater Interfaces 2024; 16:6569-6578. [PMID: 38261552 DOI: 10.1021/acsami.3c14842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
In the era of the internet of things, there exists a pressing need for technologies that meet the stringent demands of wearable, self-powered, and seamlessly integrated devices. Current approaches to developing MXene-based electrochemical sensors involve either rigid or opaque components, limiting their use in niche applications. This study investigates the potential of pristine Ti3C2Tx electrodes for flexible and transparent electrochemical sensing, achieved through an exploration of how material characteristics (flake size, flake orientation, film geometry, and uniformity) impact the electrochemical activity of the outer sphere redox probe ruthenium hexamine using cyclic voltammetry. The optimized electrode made of stacked large Ti3C2Tx flakes demonstrated excellent reproducibility and resistance to bending conditions, suggesting their use for reliable, robust, and flexible sensors. Reducing electrode thickness resulted in an amplified faradaic-to-capacitance signal, which is advantageous for this application. This led to the deposition of transparent thin Ti3C2Tx films, which maintained their best performance up to 73% transparency. These findings underscore its promise for high-performance, tailored sensors, marking a significant stride in advancing MXene utilization in next-generation electrochemical sensing technologies. The results encourage the analytical electrochemistry field to take advantage of the unique properties that pristine Ti3C2Tx electrodes can provide in sensing through more parametric studies.
Collapse
Affiliation(s)
- Natalia Noriega
- School of Applied Sciences, University of Brighton, Brighton BN2 4GJ, U.K
- Department of Materials Science and Engineering and A. J. Drexel Nanomaterials Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Mikhail Shekhirev
- Department of Materials Science and Engineering and A. J. Drexel Nanomaterials Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Christopher E Shuck
- Department of Materials Science and Engineering and A. J. Drexel Nanomaterials Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Jonathan Salvage
- School of Applied Sciences, University of Brighton, Brighton BN2 4GJ, U.K
| | - Armin VahidMohammadi
- Department of Materials Science and Engineering and A. J. Drexel Nanomaterials Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Marcus K Dymond
- School of Applied Sciences, University of Brighton, Brighton BN2 4GJ, U.K
| | - Joseph Lacey
- Rayner Intraocular Lenses Limited, The Ridley Innovation Centre, Worthing BN14 8AQ, U.K
| | - Susan Sandeman
- School of Applied Sciences, University of Brighton, Brighton BN2 4GJ, U.K
| | - Yury Gogotsi
- Department of Materials Science and Engineering and A. J. Drexel Nanomaterials Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Bhavik Anil Patel
- School of Applied Sciences, University of Brighton, Brighton BN2 4GJ, U.K
| |
Collapse
|
32
|
Kim S, Oh J, Park J, Lee B, Mai TLH, Sun Z, Jeong S, Cho Y, Kim W, Yang C. High-Precision Tailored Polymer Molecular Weights for Specific Photovoltaic Applications through Ultrasound-Induced Simultaneous Physical and Chemical Events. Angew Chem Int Ed Engl 2024:e202401097. [PMID: 38308505 DOI: 10.1002/anie.202401097] [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] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/04/2024]
Abstract
It is highly challenging to reproducibly prepare semiconducting polymers with targeted molecular weight tailored for next-generation photovoltaic applications. Once such an easily accessible methodology is established, which can not only contribute to overcome the current limitation of the statistically determined nature of semiconducting polymers, but also facilitate rapid incorporation into the broad synthetic chemists' toolbox. Here, we describe a simple yet robust ultrasonication-assisted Stille polymerization for accessing semiconducting polymers with high-precision tailored molecular weights (from low to ultrahigh molecular weight ranges) while mitigating their interbatch variations. We propose that ultrasound-induced simultaneous physical and chemical events enable precise control of the semiconducting polymers' molecular weights with high reproducibility to satisfy all the optical/electrical and morphological demands of diverse types of high-performance semiconducting polymer-based devices; as demonstrated in in-depth experimental screenings in applications of both organic and perovskite photovoltaics. We believe that this methodology provides a fast development of new and existing semiconducting polymers with the highest-level performances possible on various photovoltaic devices.
Collapse
Affiliation(s)
- Seoyoung Kim
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Jiyeon Oh
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Jeewon Park
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Byongkyu Lee
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Thi Le Huyen Mai
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Zhe Sun
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Seonghun Jeong
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Yongjoon Cho
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Wonjun Kim
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| | - Changduk Yang
- School of Energy and Chemical Engineering, Perovtronics Research Center, Low Dimensional Carbon Materials Center, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, South Korea
| |
Collapse
|
33
|
Vignola S, Donadono V, Cavalli C, Azzaretto V, Casagrandi D, Pandya P, Napolitano R. Use of focus point for plane acquisition to improve reproducibility in fetal biometry. Ultrasound Obstet Gynecol 2024; 63:237-242. [PMID: 37519218 DOI: 10.1002/uog.27436] [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: 01/05/2023] [Revised: 06/24/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVE To assess the reproducibility of ultrasound measurements of fetal biometry using a 'focus point' to assist the acquisition of the relevant plane. METHODS This was a study of 80 women with a singleton non-anomalous pregnancy who attended University College London Hospital, London, UK, between 18 and 37 weeks' gestation. Planes to measure head circumference (HC), abdominal circumference (AC) and femur length (FL) were obtained four times by two different sonographers with different levels of experience, who were blinded to one another; the first set of images was obtained with reference to a standard image, and the second set of images was obtained using the focus point technique. The focus point was defined as a unique fetal anatomical landmark in each plane (cavum septi pellucidi for HC, two-thirds of the umbilical vein for AC and one of the two extremities of the diaphysis for FL). Once identified, the focus point was maintained in view while the sonographer rotated the probe along three axes (x, y, z) to acquire the relevant plane. Sonographers were either in training or had > 3000 scans worth of experience. Intra- and interobserver reproducibility were assessed using Bland-Altman plots, and absolute values and percentages for mean difference and 95% limits of agreement (LoA) were reported. RESULTS Overall reproducibility was good, with all 95% LoA < 8%. Reproducibility was improved by use of the focus point compared with the standard technique for both intraobserver comparison (95% LoA, < 4% vs < 6%) and interobserver comparison (95% LoA, < 7% vs < 8%). These findings were independent of sonographer seniority and plane acquired. CONCLUSIONS Reproducibility of fetal biometry assessment is improved with use of the focus point for plane acquisition, regardless of sonographer experience. We propose that this method should be implemented in clinical practice and training programs in fetal biometry. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- S Vignola
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - V Donadono
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - C Cavalli
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
- ASTT Spedali Civili, Brescia, Italy
| | - V Azzaretto
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
- ASTT Spedali Civili, Brescia, Italy
| | - D Casagrandi
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - P Pandya
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - R Napolitano
- Fetal Medicine Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| |
Collapse
|
34
|
Xiao Y, Lanz B, Lim SI, Tkáč I, Xin L. Improved reproducibility of γ-aminobutyric acid measurement from short-echo-time proton MR spectroscopy by linewidth-matched basis sets in LCModel. NMR Biomed 2024; 37:e5056. [PMID: 37839823 DOI: 10.1002/nbm.5056] [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: 03/01/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
γ-Aminobutyric acid (GABA), as the primary inhibitory neurotransmitter, is extremely important for maintaining healthy brain function, and deviations from GABA homeostasis are related to various brain diseases. Short-echo-time (short-TE) proton MR spectroscopy (1 H-MRS) has been employed to measure GABA concentration from various human brain regions at high magnetic fields. The aim of this study was to investigate the effect of spectral linewidth on GABA quantification and explore the application of an optimized basis-set preparation approach using a spectral-linewidth-matched (LM) basis set in LCModel to improve the reproducibility of GABA quantification from short-TE 1 H-MRS. In contrast to the fixed-linewidth basis-set approach, the LM basis-set preparation approach, where all metabolite basis spectra were simulated with a linewidth 4 Hz narrower than that of water, showed a smaller standard deviation of estimated GABA concentration from synthetic spectra with varying linewidths and lineshapes. The test-retest reproducibility was assessed by the mean within-subject coefficient of variation, which improved from 19.2% to 12.0% in the thalamus, from 27.9% to 14.9% in the motor cortex, and from 9.7% to 2.8% in the medial prefrontal cortex using LM basis sets at 7 T. We conclude that spectral linewidth has a large effect on GABA quantification from short-TE 1 H-MRS data and that using LM basis sets in LCModel can improve the reproducibility of GABA quantification.
Collapse
Affiliation(s)
- Ying Xiao
- Center for Biomedical Imaging (CIBM), Lausanne, Switzerland
- Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bernard Lanz
- Center for Biomedical Imaging (CIBM), Lausanne, Switzerland
- Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Song-I Lim
- Center for Biomedical Imaging (CIBM), Lausanne, Switzerland
- Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ivan Tkáč
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lijing Xin
- Center for Biomedical Imaging (CIBM), Lausanne, Switzerland
- Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
35
|
Ladthavorlaphatt K, Surti FB, Beishon LC, Robinson TG, Panerai RB. Depression of dynamic cerebral autoregulation during neural activation: The role of responders and non-responders. J Cereb Blood Flow Metab 2024:271678X241229908. [PMID: 38301726 DOI: 10.1177/0271678x241229908] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Neurovascular coupling (NVC) interaction with dynamic cerebral autoregulation (dCA) remains unclear. We investigated the effect of task complexity and duration on the interaction with dCA. Sixteen healthy participants (31.6 ± 11.6 years) performed verbal fluency (naming-words (NW)) and serial subtraction (SS) paradigms, of varying complexity, at durations of 05, 30 and 60 s. The autoregulation index (ARI), was estimated from the bilateral middle cerebral artery blood velocity (MCAv) step response, calculated by transfer function analysis (TFA), for each paradigm during unstimulated (2 min) and neuroactivated (1 min) segments. Intraclass correlation (ICC) and coefficient of variation (CV) determined reproducibility for two visits and objective criteria were applied to classify responders (R) and non-responders (NoR) to task-induced MCAv increase. ICC values demonstrated fair reproducibility in all tasks. ARI decreased in right (RH) and left (LH) hemispheres, irrespective of paradigm complexity and duration (p < 0.0001). Bilateral ARI estimates were significantly decreased during NW for the R group only (p < 0.0001) but were reduced in both R (p < 0.0001) and NoR (p = 0.03) groups for SS tasks compared with baseline. The reproducible attenuation of dCA efficiency due to paradigm-induced NVC response, its interaction, and different behaviour in R and NoR, warrant further research in different physiological and clinical conditions.
Collapse
Affiliation(s)
- Kannaphob Ladthavorlaphatt
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Medical Diagnostics Unit, Thammasat University Hospital, Thammasat University, Pathum Thani, Thailand
- Thammasat University Centre of Excellence in Computational Mechanics and Medical Engineering, Thammasat University, Pathum Thani, Thailand
| | - Farhaana Bs Surti
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Lucy C Beishon
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| | - Thompson G Robinson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| | - Ronney B Panerai
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| |
Collapse
|
36
|
Wang Y, Greer JS, Zhou L, Lin SQ, Hulsey KM, Udayakumar D, Madhuranthakam AJ. A 3D-printed phantom for quality-controlled reproducibility measurements of arterial spin labeled perfusion. Magn Reson Med 2024; 91:819-827. [PMID: 37815014 PMCID: PMC10841664 DOI: 10.1002/mrm.29886] [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: 04/06/2023] [Revised: 08/29/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE To develop a portable MR perfusion phantom for quality-controlled assessment and reproducibility of arterial spin labeled (ASL) perfusion measurement. METHODS A 3D-printed perfusion phantom was developed that mimics the branching of arterial vessels, capillaries, and a chamber containing cellulose sponge representing tissue characteristics. A peristaltic pump circulated distilled water through the phantom, and was first evaluated at 300, 400, and 500 mL/min. Longitudinal reproducibility of perfusion was performed using 2D pseudo-continuous ASL at 20 post-label delays (PLDs, ranging between 0.2 and 7.8 s at 0.4-s intervals) over a period of 16 weeks, with three repetitions each week. Multi-PLD data were fitted into a general kinetic model for perfusion quantification (f) and arterial transit time (ATT). Intraclass correlation coefficient was used to assess intersession reproducibility. RESULTS MR perfusion signals acquired in the 3D-printed perfusion phantom agreed well with the experimental conditions, with progressively increasing signal intensities and decreasing ATT for pump flow rates from 300 to 500 mL/min. The perfusion signal at 400 mL/min and the general kinetic model-derived f and ATT maps were similar across all PLDs for both intrasession and intersession reproducibility. Across all 48 experimental time points, the average f was 75.55 ± 3.83 × 10-3 mL/mL/s, the corresponding ATT was 2.10 ± 0.20 s, and the T1 was 1.84 ± 0.102 s. Intraclass correlation coefficient was 0.92 (95% confidence interval 0.83-0.97) for f, 0.96 (0.91-0.99) for ATT, and 0.94 (0.88-0.98) for T1 , demonstrating excellent reproducibility. CONCLUSION A simple, portable 3D-printed perfusion phantom with excellent reproducibility of 2D pseudo-continuous ASL measurements was demonstrated that can serve for quality-controlled and reliable measurements of ASL perfusion.
Collapse
Affiliation(s)
- Yiming Wang
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Philips Healthcare, Shanghai, China
| | - Joshua S Greer
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Philips Healthcare, Cincinnati, Ohio, USA
| | - Limin Zhou
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sheng-Qing Lin
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Keith M Hulsey
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Durga Udayakumar
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ananth J Madhuranthakam
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
37
|
Strunk M, Heo GS, Hess A, Luehmann H, Ross TL, Gropler RJ, Bengel FM, Liu Y, Thackeray JT. Toward Quantitative Multisite Preclinical Imaging Studies in Acute Myocardial Infarction: Evaluation of the Immune-Fibrosis Axis. J Nucl Med 2024; 65:287-293. [PMID: 38176717 DOI: 10.2967/jnumed.123.266526] [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] [Received: 08/10/2023] [Revised: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
The immune-fibrosis axis plays a critical role in cardiac remodeling after acute myocardial infarction. Imaging approaches to monitor temporal inflammation and fibroblast activation in mice have seen wide application in recent years. However, the repeatability of quantitative measurements remains challenging, particularly across multiple imaging centers. We aimed to determine reproducibility of quantitative inflammation and fibroblast activation images acquired at 2 facilities after myocardial infarction in mice. Methods: Mice underwent coronary artery ligation and sequential imaging with 68Ga-DOTA-ECL1i to assess chemokine receptor type 2 expression at 3 d after myocardial infarction and 68Ga-FAPI-46 to assess fibroblast activation protein expression at 7 d after myocardial infarction. Images were acquired at 1 center using either a local or a consensus protocol developed with the second center; the protocols differed in the duration of isoflurane anesthesia and the injected tracer dose. A second group of animals were scanned at the second site using the consensus protocol. Image analyses performed by each site and just by 1 site were also compared. Results: The uptake of 68Ga-DOTA-ECL1i in the infarct territory tended to be higher when the consensus protocol was used (P = 0.03). No difference was observed between protocol acquisitions for 68Ga-FAPI-46. Compared with the local protocol, the consensus protocol decreased variability between individual animals. When a matched consensus protocol was used, the 68Ga-DOTA-ECL1i infarct territory percentage injected dose per gram of tissue was higher on images acquired at site B than on those acquired at site A (P = 0.006). When normalized to body weight as SUV, this difference was mitigated. Both the percentage injected dose per gram of tissue and the SUV were comparable between sites for 68Ga-FAPI-46. Image analyses at the sites differed significantly, but this difference was mitigated when all images were analyzed at site A. Conclusion: The application of a standardized acquisition protocol may lower variability within datasets and facilitate comparison of molecular radiotracer distribution between preclinical imaging centers. Like clinical studies, multicenter preclinical studies should use centralized core-based image analysis to maximize reproducibility across sites.
Collapse
Affiliation(s)
- Maja Strunk
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany; and
| | - Gyu Seong Heo
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Annika Hess
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany; and
| | - Hannah Luehmann
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Tobias L Ross
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany; and
| | - Robert J Gropler
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Frank M Bengel
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany; and
| | - Yongjian Liu
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - James T Thackeray
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany; and
| |
Collapse
|
38
|
Nickerson JL, Gagnon H, Wentzell PD, Doucette AA. Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics. Proteomics 2024:e2300339. [PMID: 38299459 DOI: 10.1002/pmic.202300339] [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] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024]
Abstract
Detergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation strategy incorporating cartridge-based protein precipitation with organic solvent to deplete SDS. The variance of data-independent acquisition (SWATH-MS) data was isolated from sample preparation error by modelling the variance as a function of peptide signal intensity. Our SDS-assisted cartridge workflow yield a coefficient of variance (CV) of 13%-14%. By comparison, conventional (detergent-free) in-solution digestion increased the CV to 50%; in-gel digestion provided lower CVs between 14% and 20%. By filtering peptides predicting to display lower precision, we further enhance the validity of data in global comparative proteomics. These results demonstrate the detergent-based precipitation workflow is a reliable approach for in depth, label-free quantitative proteome analysis.
Collapse
Affiliation(s)
| | - Hugo Gagnon
- PhenoSwitch Bioscience Inc., Sherbrooke, Quebec, Canada
| | - Peter D Wentzell
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
39
|
Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon‐Perez JM, Fu Q, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Colombo F, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic‐Talisman T, Kruh‐Garcia NA, Ku'ulei‐Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens‐Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter‐Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ, MISEV Consortium, Théry C, Witwer KW. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles 2024; 13:e12404. [PMID: 38326288 PMCID: PMC10850029 DOI: 10.1002/jev2.12404] [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: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024] Open
Abstract
Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.
Collapse
Affiliation(s)
- Joshua A. Welsh
- Translational Nanobiology Section, Laboratory of PathologyNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Deborah C. I. Goberdhan
- Nuffield Department of Women's and Reproductive HealthUniversity of Oxford, Women's Centre, John Radcliffe HospitalOxfordUK
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical SciencesTrinity College DublinDublinIreland
- Trinity Biomedical Sciences InstituteTrinity College DublinDublinIreland
- Trinity St. James's Cancer InstituteTrinity College DublinDublinIreland
| | - Edit I. Buzas
- Department of Genetics, Cell‐ and ImmunobiologySemmelweis UniversityBudapestHungary
- HCEMM‐SU Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
- HUN‐REN‐SU Translational Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
| | - Cherie Blenkiron
- Faculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Tom A. P. Driedonks
- Department CDL ResearchUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Uta Erdbrügger
- University of Virginia Health SystemCharlottesvilleVirginiaUSA
| | - Juan M. Falcon‐Perez
- Exosomes Laboratory, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Metabolomics Platform, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | - Qing‐Ling Fu
- Otorhinolaryngology Hospital, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Extracellular Vesicle Research and Clinical Translational CenterThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneAustralia
| | - Metka Lenassi
- Faculty of MedicineUniversity of LjubljanaLjubljanaSlovenia
| | - Sai Kiang Lim
- Institute of Molecular and Cell Biology (IMCB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Paracrine Therapeutics Pte. Ltd.SingaporeSingapore
- Department of Surgery, YLL School of MedicineNational University SingaporeSingaporeSingapore
| | - Mỹ G. Mahoney
- Thomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Sujata Mohanty
- Stem Cell FacilityAll India Institute of Medical SciencesNew DelhiIndia
| | - Andreas Möller
- Chinese University of Hong KongHong KongHong Kong S.A.R.
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Susmita Sahoo
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ana C. Torrecilhas
- Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP) Campus DiademaDiademaBrazil
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Andries Zijlstra
- Department of PathologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- GenentechSouth San FranciscoCaliforniaUSA
| | - Sarah Abuelreich
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Reem Bagabas
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Paolo Bergese
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
- National Center for Gene Therapy and Drugs based on RNA TechnologyPaduaItaly
| | - Esther M. Bridges
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Marco Brucale
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Dylan Burger
- Kidney Research CentreOttawa Hopsital Research InstituteOttawaCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaCanada
- School of Pharmaceutical SciencesUniversity of OttawaOttawaCanada
| | - Randy P. Carney
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Federico Colombo
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Rossella Crescitelli
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
- Wallenberg Centre for Molecular and Translational Medicine, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Edveena Hanser
- Department of BiomedicineUniversity Hospital BaselBaselSwitzerland
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | | | - Norman J. Haughey
- Departments of Neurology and PsychiatryJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Tijana Jovanovic‐Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Nicole A. Kruh‐Garcia
- Bio‐pharmaceutical Manufacturing and Academic Resource Center (BioMARC)Infectious Disease Research Center, Colorado State UniversityFort CollinsColoradoUSA
| | - Vroniqa Ku'ulei‐Lyn Faustino
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Diego Kyburz
- Department of BiomedicineUniversity of BaselBaselSwitzerland
- Department of RheumatologyUniversity Hospital BaselBaselSwitzerland
| | - Cecilia Lässer
- Krefting Research Centre, Department of Internal Medicine and Clinical NutritionInstitute of Medicine at Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine at Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Adam L. Maddox
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Elena S. Martens‐Uzunova
- Erasmus MC Cancer InstituteUniversity Medical Center Rotterdam, Department of UrologyRotterdamThe Netherlands
| | - Rachel R. Mizenko
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Lauren A. Newman
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andrea Ridolfi
- Department of Physics and Astronomy, and LaserLaB AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eva Rohde
- Department of Transfusion Medicine, University HospitalSalzburger Landeskliniken GmbH of Paracelsus Medical UniversitySalzburgAustria
- GMP Unit, Paracelsus Medical UniversitySalzburgAustria
- Transfer Centre for Extracellular Vesicle Theralytic Technologies, EV‐TTSalzburgAustria
| | - Tatu Rojalin
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
- Expansion Therapeutics, Structural Biology and BiophysicsJupiterFloridaUSA
| | - Andrew Rowland
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andras Saftics
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Ursula S. Sandau
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Celer DiagnosticsTorontoCanada
| | - Simon Swift
- Waipapa Taumata Rau University of AucklandAucklandNew Zealand
| | - Dmitry Ter‐Ovanesyan
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMassachusettsUSA
| | - Juan P. Tosar
- Universidad de la RepúblicaMontevideoUruguay
- Institut Pasteur de MontevideoMontevideoUruguay
| | - Zivile Useckaite
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Zoltan Varga
- Biological Nanochemistry Research GroupInstitute of Materials and Environmental Chemistry, Research Centre for Natural SciencesBudapestHungary
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
| | - Edwin van der Pol
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Biomedical Engineering and Physics, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Martijn J. C. van Herwijnen
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Marca H. M. Wauben
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | | | | | - Andrea Zendrini
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
| | - Alan J. Zimmerman
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | | | - Clotilde Théry
- Institut Curie, INSERM U932PSL UniversityParisFrance
- CurieCoreTech Extracellular Vesicles, Institut CurieParisFrance
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- EV Core Facility “EXCEL”, Institute for Basic Biomedical SciencesJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's DiseaseJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| |
Collapse
|
40
|
Axfors C, Malički M, Goodman SN. Research rigor and reproducibility in research education: A CTSA institutional survey. J Clin Transl Sci 2024; 8:e45. [PMID: 38476247 PMCID: PMC10928701 DOI: 10.1017/cts.2024.10] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
We assessed the rigor and reproducibility (R&R) activities of institutions funded by the National Center for Advancing Translational Sciences (NCTSA) through a survey and website search (N = 61). Of 50 institutional responses, 84% reported incorporating some form of R&R training, 68% reported devoted R&R training, 30% monitored R&R practices, and 10% incentivized them. Website searches revealed 9 (15%) freely available training curricula, and 7 (11%) institutional programs specifically created to enhance R&R. NCATS should formally integrate R&R principles into its translational science models and institutional requirements.
Collapse
Affiliation(s)
- Cathrine Axfors
- Stanford University School of Medicine,
Stanford Program on Research Rigor & Reproducibility (SPORR), Stanford,
CA, USA
- Meta-Research Innovation Center at Stanford (METRICS),
Stanford University, Stanford, CA,
USA
| | - Mario Malički
- Stanford University School of Medicine,
Stanford Program on Research Rigor & Reproducibility (SPORR), Stanford,
CA, USA
- Meta-Research Innovation Center at Stanford (METRICS),
Stanford University, Stanford, CA,
USA
- Department of Epidemiology and Population Health, Stanford
University School of Medicine, Stanford, CA,
USA
| | - Steven N. Goodman
- Stanford University School of Medicine,
Stanford Program on Research Rigor & Reproducibility (SPORR), Stanford,
CA, USA
- Meta-Research Innovation Center at Stanford (METRICS),
Stanford University, Stanford, CA,
USA
- Department of Epidemiology and Population Health, Stanford
University School of Medicine, Stanford, CA,
USA
- Department of Medicine, Stanford University School of
Medicine, Stanford, CA, USA
| |
Collapse
|
41
|
Li Y, Hu YJ, Satten GA. MERIT: Controlling Monte-Carlo error rate in large-scale Monte-Carlo hypothesis testing. Stat Med 2024; 43:279-295. [PMID: 38124426 PMCID: PMC10909586 DOI: 10.1002/sim.9959] [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: 09/01/2022] [Revised: 09/13/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
The use of Monte-Carlo (MC)p $$ p $$ -values when testing the significance of a large number of hypotheses is now commonplace. In large-scale hypothesis testing, we will typically encounter at least somep $$ p $$ -values near the threshold of significance, which require a larger number of MC replicates thanp $$ p $$ -values that are far from the threshold. As a result, some incorrect conclusions can be reached due to MC error alone; for hypotheses near the threshold, even a very large number (eg,1 0 6 $$ 1{0}^6 $$ ) of MC replicates may not be enough to guarantee conclusions reached using MCp $$ p $$ -values. Gandy and Hahn (GH)6-8 have developed the only method that directly addresses this problem. They defined a Monte-Carlo error rate (MCER) to be the probability that any decisions on accepting or rejecting a hypothesis based on MCp $$ p $$ -values are different from decisions based on idealp $$ p $$ -values; their method then makes decisions by controlling the MCER. Unfortunately, the GH method is frequently very conservative, often making no rejections at all and leaving a large number of hypotheses "undecided". In this article, we propose MERIT, a method for large-scale MC hypothesis testing that also controls the MCER but is more statistically efficient than the GH method. Through extensive simulation studies, we demonstrate that MERIT controls the MCER while making more decisions that agree with the idealp $$ p $$ -values than GH does. We also illustrate our method by an analysis of gene expression data from a prostate cancer study.
Collapse
Affiliation(s)
- Yunxiao Li
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Glen A. Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
42
|
Cho H, She J, De Marchi D, El-Zaatari H, Barnes EL, Kahkoska AR, Kosorok MR, Virkud AV. Machine Learning and Health Science Research: Tutorial. J Med Internet Res 2024; 26:e50890. [PMID: 38289657 PMCID: PMC10865203 DOI: 10.2196/50890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Machine learning (ML) has seen impressive growth in health science research due to its capacity for handling complex data to perform a range of tasks, including unsupervised learning, supervised learning, and reinforcement learning. To aid health science researchers in understanding the strengths and limitations of ML and to facilitate its integration into their studies, we present here a guideline for integrating ML into an analysis through a structured framework, covering steps from framing a research question to study design and analysis techniques for specialized data types.
Collapse
Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jane She
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Daniel De Marchi
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Helal El-Zaatari
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Edward L Barnes
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Gastrointestinal Biology and Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Anna R Kahkoska
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Endocrinology and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Aging and Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michael R Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Arti V Virkud
- Kidney Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
43
|
Xiao J, Sun C, Chen R, Zhao Z, Wang G, Wu D. Reproducibility of Diffusion MRI-Based Tractography in the Fetal Brain. J Magn Reson Imaging 2024. [PMID: 38284561 DOI: 10.1002/jmri.29253] [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] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Tractography based on diffusion MRI (dMRI) is a useful tool to study white matter of the developing brain. However, its application in fetal brains is limited due to motion artifacts and low resolution of in utero dMRI, leading to reduced reliability, which was scarcely investigated in previous studies. PURPOSE To identify reliably traceable fibers in fetal brains and assess whether reproducibility varies with gestational age (GA) and varies between brain regions. STUDY TYPE Prospective cohort study. SUBJECTS A total of 44 healthy fetuses with GAs between 25 and 37 (31 ± 6). FIELD STRENGTH/SEQUENCE 3-T, diffusion-weighted echo-planar imaging sequence (2-5 repeated dMRI scans within the same session per subject). ASSESSMENT We fitted dMRI with constrained spherical deconvolution model and conducted tractography on eight fibers. We extracted volume, fractional anisotropy, and fiber count for each fiber and assessed the reproducibility of these metrics between repeated scans within each subject. Data were divided into two age-based subgroups (≤30 weeks, N = 28, and >30 weeks, N = 16) for further tests. STATISTICAL TESTS The reproducibility were compared between fibers by analysis of variance and two-sample t tests. Multiple comparisons were corrected by the false discovery rate (5% was accepted). RESULTS The reproducibility of the anterior thalamic radiation, inferior longitudinal fasciculus (ILF), genu of the corpus callosum (GCC), and body of the corpus callosum (BCC) significantly decreased with advancing GA (correlation coefficient = 0.525-0.823), as confirmed by group comparisons between fetuses in early GA (≤30 weeks) and late GA (>30 weeks) groups. Corticospinal tract, inferior fronto-occipital fasciculus, and GCC showed high reproducibility for fiber count (weighted dice average = 0.846 vs. 0.814), while BCC and ILF exhibited the lowest reproducibility in both age groups. DATA CONCLUSION The study indicates that the reliability of fetal brain tractography depends on GA and varies among different fibers. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY: Stage 2.
Collapse
Affiliation(s)
- Jiaxin Xiao
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Cong Sun
- Department of Radiology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruike Chen
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Zhiyong Zhao
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Guangbin Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
44
|
Lin CW, Chen LY, Huang YC, Kumar P, Guo YZ, Wu CH, Wang LM, Chen KL. Improving Sensitivity and Reproducibility of Surface-Enhanced Raman Scattering Biochips Utilizing Magnetoplasmonic Nanoparticles and Statistical Methods. ACS Sens 2024; 9:305-314. [PMID: 38221769 DOI: 10.1021/acssensors.3c02007] [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: 01/16/2024]
Abstract
Surface-enhanced Raman scattering (SERS) technology has been widely recognized for its remarkable sensitivity in biochip development. This study presents a novel sandwich immunoassay that synergizes SERS with magnetoplasmonic nanoparticles (MPNs) to improve sensitivity. By taking advantage of the unique magnetism of these nanoparticles, we further enhance the detection sensitivity of SERS biochips through the applied magnetic field. Despite the high sensitivity, practical applications of SERS biochips are often limited by the issues of stability and reproducibility. In this study, we introduced a straightforward statistical method known as "Gaussian binning", which involves initially binning the two-dimensional Raman mapping data and subsequently applying Gaussian fitting. This approach enables a more consistent and reliable interpretation of data by reducing the variability inherent in Raman signal measurements. Based on our method, the biochip, targeting for C-reactive protein (CRP), achieves an impressive detection limit of 5.96 fg/mL, and with the application of a 3700 G magnetic field, it further enhances the detection limit by 5.7 times, reaching 1.05 fg/mL. Furthermore, this highly sensitive and magnetically tunable SERS biochip is easily designed for versatile adaptability, enabling the detection of other proteins. We believe that this innovation holds promise in enhancing the clinical applicability of SERS biochips.
Collapse
Affiliation(s)
- Chin-Wei Lin
- Department of Physics, National Taiwan University, Taipei 106, Taiwan
| | - Li-Yu Chen
- Department of Physics, National Chung Hsing University, Taichung 402, Taiwan
| | - Yu-Ching Huang
- Biochemical Technology R&D Center, Ming Chi University of Technology, New Taipei City 243, Taiwan
| | - Pradeep Kumar
- Department of Physics, National Chung Hsing University, Taichung 402, Taiwan
| | - Yu-Zhi Guo
- Department of Physics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chiu-Hsien Wu
- Department of Physics, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Nanoscience, National Chung Hsing University, Taichung 402, Taiwan
| | - Li-Min Wang
- Department of Physics, National Taiwan University, Taipei 106, Taiwan
| | - Kuen-Lin Chen
- Department of Physics, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Nanoscience, National Chung Hsing University, Taichung 402, Taiwan
| |
Collapse
|
45
|
Petrović V, Šlaj M, Buljan M, Čivljak T, Zulijani A, Perić B. Comparison of Tooth Size Measurements in Orthodontics Using Conventional and 3D Digital Study Models. J Clin Med 2024; 13:730. [PMID: 38337424 PMCID: PMC10856778 DOI: 10.3390/jcm13030730] [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: 12/28/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
(1) Background: The objective of this study was to assess which digitization method produces the biggest deviation in the 3D images of tooth size from plaster models made using alginate impressions, which are considered the gold standard in orthodontics. (2) Methods: The sample used in this study included 30 subjects (10 males and 20 females). Measurements were made on four types of models: (1) digital models obtained through intraoral scanning and digitized models of plaster cast made from (2) alginate impressions, (3) silicone impressions, and (4) conventional plaster models. Mesio-distal (MD) and buccal/labial-lingual/palatal (BL) dimensions were measured on the reference teeth of the right side of the jaw (central incisor, canine, first premolar, and first molar). Comparisons of tooth size between the methods were conducted using a repeated measurement analysis of variance and the Friedman test, while the intraclass correlation coefficient was used to determine agreement between the different methods. (3) Results: The results showed a similar level of agreement between the conventional and digital models in both jaws and the anterior, middle, and posterior segments. Better agreement was found for the MD measurements (r = 0.337-0.798; p ≤ 0.05) compared to the BL measurements (r = 0.016-0.542), with a smaller mean difference for MD (0.001-0.50 mm) compared to BL (0.02-1.48 mm) and a smaller measurement error for MD (0.20-0.39) compared to BL (0.38-0.89). There was more frequently a better level of agreement between 3D images than measurements made using a digital caliper on the plaster models with 3D images. (4) Conclusions: The differences in measurements between the digital models and conventional plaster models were small and clinically acceptable.
Collapse
Affiliation(s)
| | - Martina Šlaj
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.Š.); (B.P.)
| | - Mia Buljan
- General Hospital ‘Dr Josip Benčević’, 35000 Slavonski Brod, Croatia;
| | | | - Ana Zulijani
- Department of Oral Surgery, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
- Department of Dental Medicine, Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Berislav Perić
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.Š.); (B.P.)
- Department of Oral and Maxillofacial Surgery, University Hospital Dubrava, 10000 Zagreb, Croatia
| |
Collapse
|
46
|
Obeid JS, Tsalatsanis A, Chaphalkar C, Robinson S, Klein S, Cool S, Szwast E, Bunnell BE. A Reproducible Model Based on Clinical Text for Predicting Suicidal Behavior. Stud Health Technol Inform 2024; 310:1486-1487. [PMID: 38269709 DOI: 10.3233/shti231257] [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: 01/26/2024]
Abstract
Suicide risk models are critical for prioritizing patients for intervention. We demonstrate a reproducible approach for training text classifiers to identify patients at risk. The models were effective in phenotyping suicidal behavior (F1=.94) and moderately effective in predicting future events (F1=.63).
Collapse
Affiliation(s)
- Jihad S Obeid
- Medical University of South Carolina, Charleston, SC, USA
| | | | | | | | | | - Sarah Cool
- University of South Florida, Tampa, FL, USA
| | | | | |
Collapse
|
47
|
Patrick HM, Kildea J. More than one way to skin a dose volume: the impact of dose-surface map calculation approach on study reproducibility. Phys Med Biol 2024; 69:025025. [PMID: 38168029 DOI: 10.1088/1361-6560/ad19ef] [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] [Received: 09/11/2023] [Accepted: 01/02/2024] [Indexed: 01/05/2024]
Abstract
Objective.Dose-surface maps (DSMs) provide spatial representations of the radiation dose to organ surfaces during radiotherapy and are a valuable tool for identifying dose deposition patterns that are predictive of radiation toxicities. Over the years, many different DSM calculation approaches have been introduced and used in dose-outcome studies. However, little consideration has been given to how these calculation approaches may be impacting the reproducibility of studies in the field. Therefore, we conducted an investigation to determine the level of equivalence of DSMs calculated with different approaches and their subsequent impact on study results.Approach.Rectum and bladder DSMs were calculated for 20 prostate radiotherapy patients using combinations of the most common slice orientation and spacing styles in the literature. Equivalence of differently calculated DSMs was evaluated using pixel-wise comparisons and DSM features (rectum only). Finally, mock cohort comparison studies were conducted with DSMs calculated using each approach to determine the level of dosimetric study reproducibility between calculation approaches.Main results.We found that rectum DSMs calculated using the planar and non-coplanar orientation styles were non-equivalent in the posterior rectal region and that equivalence of DSMs calculated with different slice spacing styles was conditional on the choice of inter-slice distance used. DSM features were highly sensitive to choice of slice orientation style and DSM sampling resolution. Finally, while general result trends were consistent between the comparison studies performed using different DSMs, statisitically significant subregions and features could vary greatly in position and magnitude.Significance.We have determined that DSMs calculated with different calculation approaches are frequently non-equivalent and can lead to differing conclusions between studies performed using the same dataset. We recommend that the DSM research community work to establish consensus calculation approaches to ensure reproducibility within the field.
Collapse
Affiliation(s)
- Haley M Patrick
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
| | - John Kildea
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
| |
Collapse
|
48
|
Gutzen R, De Bonis G, De Luca C, Pastorelli E, Capone C, Allegra Mascaro AL, Resta F, Manasanch A, Pavone FS, Sanchez-Vives MV, Mattia M, Grün S, Paolucci PS, Denker M. A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets. Cell Rep Methods 2024; 4:100681. [PMID: 38183979 PMCID: PMC10831958 DOI: 10.1016/j.crmeth.2023.100681] [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: 04/07/2023] [Revised: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Neuroscience is moving toward a more integrative discipline where understanding brain function requires consolidating the accumulated evidence seen across experiments, species, and measurement techniques. A remaining challenge on that path is integrating such heterogeneous data into analysis workflows such that consistent and comparable conclusions can be distilled as an experimental basis for models and theories. Here, we propose a solution in the context of slow-wave activity (<1 Hz), which occurs during unconscious brain states like sleep and general anesthesia and is observed across diverse experimental approaches. We address the issue of integrating and comparing heterogeneous data by conceptualizing a general pipeline design that is adaptable to a variety of inputs and applications. Furthermore, we present the Collaborative Brain Wave Analysis Pipeline (Cobrawap) as a concrete, reusable software implementation to perform broad, detailed, and rigorous comparisons of slow-wave characteristics across multiple, openly available electrocorticography (ECoG) and calcium imaging datasets.
Collapse
Affiliation(s)
- Robin Gutzen
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany.
| | - Giulia De Bonis
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Chiara De Luca
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Elena Pastorelli
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Cristiano Capone
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Anna Letizia Allegra Mascaro
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy
| | - Francesco Resta
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Arnau Manasanch
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, Italy
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maurizio Mattia
- National Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Sonja Grün
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany
| | | | - Michael Denker
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany
| |
Collapse
|
49
|
Cronin AE, Liebig P, Detombe SA, Duggal N, Bartha R. Reproducibility of 3D pH-weighted chemical exchange saturation transfer contrast in the healthy cervical spinal cord. NMR Biomed 2024. [PMID: 38243648 DOI: 10.1002/nbm.5103] [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: 08/07/2023] [Revised: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Spinal cord ischemia and hypoxia can be caused by compression, injury, and vascular alterations. Measuring ischemia and hypoxia directly in the spinal cord noninvasively remains challenging. Ischemia and hypoxia alter tissue pH, providing a physiologic parameter that may be more directly related to tissue viability. Chemical exchange saturation transfer (CEST) is an MRI contrast mechanism that can be made sensitive to pH. More specifically, amine/amide concentration independent detection (AACID) is a recently developed endogenous CEST contrast that has demonstrated sensitivity to intracellular pH at 9.4 T. The goal of this study was to evaluate the reproducibility of AACID CEST measurements at different levels of the healthy cervical spinal cord at 3.0 T incorporating B1 correction. Using a 3.0 T MRI scanner, two 3D CEST scans (saturation pulse train followed by a 3D snapshot gradient-echo readout) were performed on 12 healthy subjects approximately 10 days apart, with the CEST volume centered at the C4 level for all subjects. Scan-rescan reproducibility was evaluated by examining between and within-subject coefficients of variation (CVs) and absolute AACID value differences. The C4 level of the spinal cord demonstrated the lowest within-subject CVs (4.1%-4.3%), between-subject CVs (5.6%-6.3%), and absolute AACID percent difference (5.8-6.1%). The B1 correction scheme significantly improved reproducibility (adjusted p-value = 0.002) compared with the noncorrected data, suggesting that implementing B1 corrections in the spinal cord is beneficial. It was concluded that pH-weighted AACID measurements, incorporating B1 -inhomogeneity correction, were reproducible within subjects along the healthy cervical spinal cord and that optimal image quality was achieved at the center of the 3D CEST volume.
Collapse
Affiliation(s)
- Alicia E Cronin
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | - Sarah A Detombe
- Department of Clinical Neurological Sciences, London Health Sciences Centre, London, Ontario, Canada
| | - Neil Duggal
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Clinical Neurological Sciences, London Health Sciences Centre, London, Ontario, Canada
| | - Robert Bartha
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| |
Collapse
|
50
|
Aramendía-Vidaurreta V, Solís-Barquero SM, Vidorreta M, Ezponda A, Echeverria-Chasco R, Bastarrika G, Fernández-Seara MA. Comparison of Myocardial Blood Flow Quantification Models for Double ECG Gating Arterial Spin Labeling MRI: Reproducibility Assessment. J Magn Reson Imaging 2024. [PMID: 38206090 DOI: 10.1002/jmri.29220] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Arterial spin labeling (ASL) allows non-invasive quantification of myocardial blood flow (MBF). Double-ECG gating (DG) ASL is more robust to heart rate variability than single-ECG gating (SG), but its reproducibility requires further investigation. Moreover, the existence of multiple quantification models hinders its application. Frequency-offset-corrected-inversion (FOCI) pulses provide sharper edge profiles than hyperbolic-secant (HS), which could benefit myocardial ASL. PURPOSE To assess the performance of MBF quantification models for DG compared to SG ASL, to evaluate their reproducibility and to compare the effects of HS and FOCI pulses. STUDY TYPE Prospective. SUBJECTS Sixteen subjects (27 ± 8 years). FIELD STRENGTH/SEQUENCE 1.5 T/DG and SG flow-sensitive alternating inversion recovery ASL. ASSESSMENT Three models for DG MBF quantification were compared using Monte Carlo simulations and in vivo experiments. Two models used a fitting approach (one using only a single label and control image pair per fit, the other using all available image pairs), while the third model used a T1 correction approach. Slice profile simulations were conducted for HS and FOCI pulses with varying B0 and B1. Temporal signal-to-noise ratio (tSNR) was computed for different acquisition/quantification strategies and inversion pulses. The number of images that minimized MBF error was investigated in the model with highest tSNR. Intra and intersession reproducibility were assessed in 10 subjects. STATISTICAL TESTS Within-subject coefficient of variation, analysis of variance. P-value <0.05 was considered significant. RESULTS MBF was not different across acquisition/quantification strategies (P = 0.27) nor pulses (P = 0.9). DG MBF quantification models exhibited significantly higher tSNR and superior reproducibility, particularly for the fitting model using multiple images (tSNR was 3.46 ± 2.18 in vivo and 3.32 ± 1.16 in simulations, respectively; wsCV = 16%). Reducing the number of ASL pairs to 13/15 did not increase MBF error (minimum = 0.22 mL/g/min). DATA CONCLUSION Reproducibility of MBF was better for DG than SG acquisitions, especially when employing a fitting model. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY: Stage 1.
Collapse
Affiliation(s)
- Verónica Aramendía-Vidaurreta
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Sergio M Solís-Barquero
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | | | - Ana Ezponda
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Rebeca Echeverria-Chasco
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Gorka Bastarrika
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - María A Fernández-Seara
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| |
Collapse
|