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6,266 results on '"Martin, Jonathan"'

3. A Minibatch Alternating Projections Algorithm for Robust and Efficient Magnitude Least-Squares RF Pulse Design in MRI

Author

Martin, Jonathan B., Sappo, Charlotte R., Hardy, Benjamin M., and Grissom, William A.

Subjects
Physics - Medical Physics, Electrical Engineering and Systems Science - Signal Processing
Abstract

A magnitude-least-squares radiofrequency pulse design algorithm is reported which uses interleaved exact and stochastically-generated inexact updates to escape local minima and find low-cost solutions. Inexact updates are performed using a small randomly selected minibatch of the available B1+ measurements to update RF pulse weights, which perturbs the sequence of alternating projections. Applications to RF shimming, parallel transmit spokes RF pulse design, and spectral-spatial RF pulse design are considered. Numerical and simulation studies characterized the optimal minibatch size, which was found to consistently produce lower power and lower RMSE solutions across subjects, coil geometries, B1+ resolutions and orientations. The method was validated in-vivo at 7 Tesla and produced improvements in image quality in a slice-by-slice RF-shimmed imaging sequence. Compared to conventional methods, the pulse design method can more robustly design RF pulses that correct for B1+ inhomogeneities at ultra-high field strengths, and enable pulse designs to be completed with increased computational efficiency, Comment: 14 pages (including initial blank page), 15 figures (including 2 tables)

Published
2024

5. High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage

Author

Lai, Yunjia, Koelmel, Jeremy P, Walker, Douglas I, Price, Elliott J, Papazian, Stefano, Manz, Katherine E, Castilla-Fernández, Delia, Bowden, John A, Nikiforov, Vladimir, David, Arthur, Bessonneau, Vincent, Amer, Bashar, Seethapathy, Suresh, Hu, Xin, Lin, Elizabeth Z, Jbebli, Akrem, McNeil, Brooklynn R, Barupal, Dinesh, Cerasa, Marina, Xie, Hongyu, Kalia, Vrinda, Nandakumar, Renu, Singh, Randolph, Tian, Zhenyu, Gao, Peng, Zhao, Yujia, Froment, Jean, Rostkowski, Pawel, Dubey, Saurabh, Coufalíková, Kateřina, Seličová, Hana, Hecht, Helge, Liu, Sheng, Udhani, Hanisha H, Restituito, Sophie, Tchou-Wong, Kam-Meng, Lu, Kun, Martin, Jonathan W, Warth, Benedikt, Pollitt, Krystal J Godri, Klánová, Jana, Fiehn, Oliver, Metz, Thomas O, Pennell, Kurt D, Jones, Dean P, and Miller, Gary W

Subjects
Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, Bioengineering, 2.5 Research design and methodologies (aetiology), Generic health relevance, Good Health and Well Being, Humans, Mass Spectrometry, Exposome, Metabolomics, Proteomics, Environmental Exposure, exposome, toxicants, high-resolutionmass spectrometry, chromatography, non-targetedanalysis, environmentalexposures, chemical space, metabolomics, environmental exposures, high-resolution mass spectrometry, non-targeted analysis, Environmental Sciences
Abstract

In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.

Published
2024

9. Novel Dynamics in an Additional Food provided Predator-Prey System with mutual interference

Author

Wickramasooriya, Sureni, Martin, Jonathan, Banerjee, Aniket, and Parshad, Rana D.

Subjects
Mathematics - Dynamical Systems
Abstract

The provision of additional food (AF) sources to an introduced predator has been identified as a mechanism to improve pest control. However, AF models with prey dependent functional responses can cause unbounded growth of the predator \cite{S27}. To avoid such dynamics, an AF model with mutual interference effect has been proposed \cite{S02}. The analysis therein reveals that if the quantity of additional food $\xi > h(\epsilon)$, where $\epsilon$ is the mutual interference parameter, then pest eradication is possible, and this is facilitated via a transcritical bifurcation. We revisit this model and show novel dynamical behaviors. In particular, pest eradication is possible for a tighter range of AF $g(\epsilon) < \xi < f(\epsilon) < h(\epsilon)$, and can also occur via a saddle node bifurcation. We observe bi-stability, as well as local bifurcations of Hopf type. We also prove a global bifurcation, of homoclinic type. This bifurcation in turn is shown to create a non-standard dynamic wherein the pest extinction state becomes an ``almost" global attractor. To the best of our knowledge, this is the first proof of existence of such a dynamical structure in AF models. We discuss our analysis in the context of designing novel bio-control strategies.

Published
2023

10. A Cryogenic Tune and Match Circuit for Magnetic Resonance Microscopy at 15.2T

Author

Hardy, Benjamin M., Drake, Gary, Chai, Shuyang, Dhakal, Bibek, Martin, Jonathan B., Xu, Junzhong, Does, Mark D., Anderson, Adam W., Yan, Xinqiang, and Gore, John C.

Subjects
Physics - Medical Physics, Physics - Instrumentation and Detectors
Abstract

Signal to noise ratios (SNR) in magnetic resonance microscopy images are limited by acquisition times and the decreasing number of spins in smaller voxels. Significant SNR gains from cooling of the RF receiver are only realized when the Johnson noise generated within the RF hardware is large compared to the electromagnetic noise produced by the sample. Cryogenic cooling of imaging probes is common in high field systems but proves difficult to insulate the sample from extreme temperatures. We designed a chamber to cool only the tune and match circuitry to show it is possible to achieve much of the available SNR gain available for cooled coils. We designed a microcoil circuit to resonate at 650 MHz for imaging on a 15.2 T scanner. Surface loops and solenoids of varying diameters were tested to determine the largest diameter coil that demonstrated significant SNR gains from cooling. A liquid N2 cryochamber was designed to cool the circuitry while leaving the RF coil in ambient air. As the cryochamber was filled with liquid N2, Q-factors were measured on the bench while monitoring the coil's surface temperature. Improvements of SNR on images of solutions were demonstrated via cooling the tune and match circuit in the magnet bore. At 650 MHz, loops and solenoids < 3 mm in diameter showed significant improvements in quality factor on the bench. The resistance of the variable capacitors and the coaxial cable were measured to be 45% and 32% of room temperature values near the Larmor frequency. Images obtained with a 2 turn, 3 mm diameter loop with the matching circuit at room temperature and then cooled with liquid nitrogen demonstrated SNR improvements of a factor of 2. By cooling the tune and match circuit and leaving the surface loop in ambient air, SNR was improved by a factor of 2. The results are significant because it allows for more space to insulate the sample from extreme temperatures., Comment: 33 pages, 10 figures, 1 table, 4 supplemental figures, 1 supplemental table

Published
2023

13. Experimental demonstration of diffusion limitations on resolution and SNR in MR microscopy

Author

Hardy, Benjamin M., Zhu, Yue, Harkins, Kevin D., Dhakal, Bibek, Martin, Jonathan B., Xie, Jingping, Xu, Junzhong, Does, Mark D., Anderson, Adam W., and Gore, John C.

Subjects
Physics - Medical Physics, Physics - Biological Physics
Abstract

Magnetic resonance microscopy images at cellular resolution (< 10 microns) are limited by diffusion. SNR and spatial resolution suffer from the dephasing of transverse magnetization caused by diffusion of spins in strong gradients. Such effects may be reduced by using phase encoding instead of frequency encoding readout gradients. Demonstration of the benefits of phase encoding are lacking, and the conditions in which it is preferred are not clearly established. We quantify when phase encoding outperforms a readout gradient with emphasis on the detrimental effects of diffusion on SNR and resolution. A 15.2T MRI scanner, with 1 T/m gradients, and micro solenoid RF coils < 1 mm in diameter, were used to quantify diffusion effects on resolution and SNR of frequency and phase encoded acquisitions. Frequency and phase encoding resolution and SNR per square root time were calculated and measured for images at the diffusion limited resolution. The point-spread-function was measured for phase and frequency encoding using additional constant time gradients with voxels 3-15 microns. The effect of diffusion during the readout gradient on SNR was experimentally demonstrated. The achieved resolutions of frequency and phase encoded acquisitions were measured via the point-spread-function. SNR per square root time and actual resolution were calculated for a wide range of gradient amplitudes, diffusion coefficients, and relaxation properties. The results provide a practical guide on how to choose between phase and frequency encoding. Images of excised rat spinal cord at 10 x 10 microns in-plane demonstrate benefits of phase encoding in the form of higher measured resolution and SNR vs the same image acquired with a conventional readout. We demonstrate the extent to which phase encoding outperforms readout gradients in SNR and resolution over a wide range of voxel sizes, sample, and hardware properties., Comment: 36 pages, 9 figures, 1 table, and 4 supplemental figures. Submitted to Journal of Magnetic Resonance; cleaned up metadata, fixed heading typo

Published
2023
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17. In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures

Author

Abrahamsson, Dimitri, Siddharth, Adi, Young, Thomas M, Sirota, Marina, Park, June-Soo, Martin, Jonathan W, and Woodruff, Tracey J

Subjects
Humans, Isomerism, Molecular Structure, Solvents, Water, Analytical Chemistry, Medicinal and Biomolecular Chemistry, Physical Chemistry (incl. Structural)
Abstract

While important advances have been made in high-resolution mass spectrometry (HRMS) and its applications in non-targeted analysis (NTA), the number of identified compounds in biological and environmental samples often does not exceed 5% of the detected chemical features. Our aim was to develop a computational pipeline that leverages data from HRMS but also incorporates physicochemical properties (equilibrium partition ratios between organic solvents and water; Ksolvent-water) and can propose molecular structures for detected chemical features. As these physicochemical properties are often sufficiently different across isomers, when put together, they can form a unique profile for each isomer, which we describe as the "physicochemical fingerprint". In our study, we used a comprehensive database of compounds that have been previously reported in human blood and collected their Ksolvent-water values for 129 partitioning systems. We used RDKit to calculate the number of RDKit fragments and the number of RDKit bits per molecule. We then developed and trained an artificial neural network, which used as an input the physicochemical fingerprint of a chemical feature and predicted the number and types of RDKit fragments and RDKit bits present in that structure. These were then used to search the database and propose chemical structures. The average success rate of predicting the right chemical structure ranged from 60 to 86% for the training set and from 48 to 81% for the testing set. These observations suggest that physicochemical fingerprints can assist in the identification of compounds with NTA and substantially improve the number of identified compounds.

Published
2022

18. Maternal pre-pregnancy BMI influences the associations between bisphenol and phthalate exposures and maternal weight changes and fat accumulation

Author

Kaplan, B.J., Field, C.J., Bell, R.C., Bernier, F.P., Cantell, M., Casey, L.M., Eliasziw, M., Farmer, A., Gagnon, L., Giesbrecht, G.F., Goonewardene, L., Johnston, D., Kooistra, L., Letourneau, N., Manca, D.P., Martin, J.W., McCargar, L.J., O'Beirne, M., Pop, V.J., Deane, A.J., Singhal, N., Letourneau (current Pi), N., Dewey, D., Forbes, L., Giesbrecht, G., Lebel, C., Leung, B., McMorris, C., Ross, K., Irvine, Nathalie, Bell, Rhonda C., Subhan, Fatheema B., Field, Catherine J., Liu, Jiaying, MacDonald, Amy M., Kinniburgh, David W., Martin, Jonathan W., Dewey, Deborah, and England-Mason, Gillian

Published
2024
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29. An ethnographic study of digital humanists : combining virtual and traditional ethnography in the Electronic Textual Cultures Laboratory

Author

Martin, Jonathan, Hedges, Mark Charles, and Lavagnino, John David

Abstract

This is an ethnographic study of digital humanists. As of writing, this remains the only long-term participant ethnographic study of a Digital Humanities centre. It draws upon traditional fieldwork methodologies, as well as virtual ethnographic techniques, in order to construct a complex portrait of the work and relations of a DH centre (the University of Victoria's Electronic Textual Cultures Laboratory). With respect to traditional fieldwork, I became a member of the ETCL from 2017-2019. In this, I was embedded with the Lab's technical staff, and was able to observe its relationships in this capacity. With respect to virtual ethnography, I have gathered extensive data from Twitter - examining conference networks and other engagements in which the Lab's members feature - and have used this data to augment the analysis of research and administrative practices in the Lab. While such engagement with social media is now common in other disciplines, it remains particularly meaningful to the DH community, where many conferences will host pre-conference sessions to introduce Twitter to newcomers and others still will appoint "Twitter chairs" to ensure that there is a bridge between virtual discussions and conference panels. In light of this, and as part of creating a comprehensive understanding of a given DH community, it is essential, in the Age of the Internet, to consider where a community locates itself - be that in virtual or material space. As anthropologists Heather Horst and Daniel Miller (2012) observe: "... the digital, as all material culture, is more than a substrate; it is becoming a constitutive part of what makes us human". In this thesis, I explore not only the ETCL, but the virtual communities that have arisen on Twitter around the Lab-organised Digital Humanities Summer Institute. I have endeavoured to use both my physical and virtual observations to provide rich context for an exploration of the social, cultural, and academic forces at work at the ETCL. Beyond this, I have worked to relate these findings to other ethnographic work in DH, in order to discuss the forces that are influencing the field by shaping the spaces where its work is carried out. Finally, this thesis pays considerable attention to the long tail of the "hack vs. yack" debate that has been common in the Digital Humanities over the last decade. This debate, and the negotiations that many labs and practitioners have made in light of it, is particularly important to forming an understanding of research labs like the ETCL. It is hoped that this work will further the understanding of a young, dynamic field that has attracted considerable attention in recent years.

Published
2022

33. A multicentre randomised controlled trial of a guided self-help cognitive behavioural therapy to MANage the impact of hot flushes and night sweats in patients with prostate CANcer undergoing androgen deprivation therapy (MANCAN2)

Author

Crabb, Simon, Morgan, Alannah, Hunter, Myra S., Stefanopoulou, Evgenia, Griffiths, Gareth, Richardson, Alison, Fenlon, Deborah, Fleure, Louisa, Raftery, James, Boxall, Cherish, Wilding, Sam, Nuttall, Jacqueline, Eminton, Zina, Tilt, Emma, O’Neill, Alice, Bacon, Roger, and Martin, Jonathan

Published
2023
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39. The Safety of Robotic Pneumonectomy

Author

Mack, Shale J., Collins, Micaela L., Till, Brian M., Whitehorn, Greg L., Martin, Jonathan, Rshaidat, Hamza, Grenda, Tyler, Evans, Nathaniel R., and Okusanya, Olugbenga T.

Published
2024
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43. Defining the Scope of Exposome Studies and Research Needs from a Multidisciplinary Perspective

Author

Zhang, Pei, Carlsten, Christopher, Chaleckis, Romanas, Hanhineva, Kati, Huang, Mengna, Isobe, Tomohiko, Koistinen, Ville M, Meister, Isabel, Papazian, Stefano, Sdougkou, Kalliroi, Xie, Hongyu, Martin, Jonathan W, Rappaport, Stephen M, Tsugawa, Hiroshi, Walker, Douglas I, Woodruff, Tracey J, Wright, Robert O, and Wheelock, Craig E

Subjects
Chemical Engineering, Engineering, Environmental Sciences, Pollution and Contamination, Generic health relevance, Good Health and Well Being, Environmental Science and Management, Environmental Engineering, Environmental Biotechnology, Chemical engineering, Pollution and contamination
Abstract

The concept of the exposome was introduced over 15 years ago to reflect the important role that the environment exerts on health and disease. While originally viewed as a call-to-arms to develop more comprehensive exposure assessment methods applicable at the individual level and throughout the life course, the scope of the exposome has now expanded to include the associated biological response. In order to explore these concepts, a workshop was hosted by the Gunma University Initiative for Advanced Research (GIAR, Japan) to discuss the scope of exposomics from an international and multidisciplinary perspective. This Global Perspective is a summary of the discussions with emphasis on (1) top-down, bottom-up, and functional approaches to exposomics, (2) the need for integration and standardization of LC- and GC-based high-resolution mass spectrometry methods for untargeted exposome analyses, (3) the design of an exposomics study, (4) the requirement for open science workflows including mass spectral libraries and public databases, (5) the necessity for large investments in mass spectrometry infrastructure in order to sequence the exposome, and (6) the role of the exposome in precision medicine and nutrition to create personalized environmental exposure profiles. Recommendations are made on key issues to encourage continued advancement and cooperation in exposomics.

Published
2021

44. Air quality impacts of a large waste fire in Stockholm, Sweden

Author

Elihn, Karine, Dalmijn, Joost, Froment, Jean, Håland, Alexander, Johansson, Jana H., Karlsson, Hanna L., Martin, Jonathan W., Mikoviny, Tomas, Norman, Michael, Piel, Felix, Sadiktsis, Ioannis, Schlesinger, Daniel, Silvergren, Sanna, Srikanth Vallabani, N.V., Wisthaler, Armin, and Steimer, Sarah S.

Published
2023
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