Functional magnetic resonance imaging : methods and applications

The technique of functional magnetic resonance imaging is rapidly moving from one of technical interest to wide clinical application. However, there are a number of questions regarding the method that need resolution. Some of these are investigated in this thesis. High resolutionf MRI is demonstrated at 3.0 T, using an interleaved echo planar imaging technique to keep image distortion low. The optimum echo time to use in fMRI experiments is investigated using a multiple gradient echo sequence to obtain six images, each with a different echo time, from a single free induction decay. The same data are used to construct T2* maps during functional stimulation. Various techniques for correcting the N/2 ghost are tested for use in fMRI experiments, and a method for removing the image artefact caused by external r. f. interference in a non-linearly sampled matrix is presented. The steps in the analysis of fMRI data are detailed, and two new non-directed analysis techniques, particularly for data from single events, as opposed to epoch based paradigms, are proposed. The theory behind software that has been written for fMRI data analysis is also given. Finally, some of the results from an fMRI study into the initiation of movement are presented, illustrating the power of single event experiments in the separation of cognitive processes

Functional magnetic resonance imaging : methods and applications

The technique of functional magnetic resonance imaging is rapidly moving from one of technical interest to wide clinical application. However, there are a number of questions regarding the method that need resolution. Some of these are investigated in this thesis. High resolutionf MRI is demonstrated at 3.0 T, using an interleaved echo planar imaging technique to keep image distortion low. The optimum echo time to use in fMRI experiments is investigated using a multiple gradient echo sequence to obtain six images, each with a different echo time, from a single free induction decay. The same data are used to construct T2* maps during functional stimulation. Various techniques for correcting the N/2 ghost are tested for use in fMRI experiments, and a method for removing the image artefact caused by external r. f. interference in a non-linearly sampled matrix is presented. The steps in the analysis of fMRI data are detailed, and two new non-directed analysis techniques, particularly for data from single events, as opposed to epoch based paradigms, are proposed. The theory behind software that has been written for fMRI data analysis is also given. Finally, some of the results from an fMRI study into the initiation of movement are presented, illustrating the power of single event experiments in the separation of cognitive processes

Perceptually relevant remapping of human somatotopy in 24 hours

Experience-dependent reorganisation of functional maps in the cerebral cortex is well described in the primary sensory cortices. However, there is relatively little evidence for such cortical reorganisation over the short-term. Using human somatosensory cortex as a model, we investigated the effects of a 24 hr gluing manipulation in which the right index and right middle fingers (digits 2 and 3) were adjoined with surgical glue. Somatotopic representations, assessed with two 7 tesla fMRI protocols, revealed rapid off-target reorganisation in the non-manipulated fingers following gluing, with the representation of the ring finger (digit 4) shifted towards the little finger (digit 5) and away from the middle finger (digit 3). These shifts were also evident in two behavioural tasks conducted in an independent cohort, showing reduced sensitivity for discriminating the temporal order of stimuli to the ring and little fingers, and increased substitution errors across this pair on a speeded reaction time task

Spatial considerations during cryopreservation of a large volume sample

AbstractThere have been relatively few studies on the implications of the physical conditions experienced by cells during large volume (litres) cryopreservation – most studies have focused on the problem of cryopreservation of smaller volumes, typically up to 2 ml.This study explores the effects of ice growth by progressive solidification, generally seen during larger scale cryopreservation, on encapsulated liver hepatocyte spheroids, and it develops a method to reliably sample different regions across the frozen cores of samples experiencing progressive solidification.These issues are examined in the context of a Bioartificial Liver Device which requires cryopreservation of a 2 L volume in a strict cylindrical geometry for optimal clinical delivery. Progressive solidification cannot be avoided in this arrangement. In such a system optimal cryoprotectant concentrations and cooling rates are known. However, applying these parameters to a large volume is challenging due to the thermal mass and subsequent thermal lag. The specific impact of this to the cryopreservation outcome is required.Under conditions of progressive solidification, the spatial location of Encapsulated Liver Spheroids had a strong impact on post-thaw recovery. Cells in areas first and last to solidify demonstrated significantly impaired post-thaw function, whereas areas solidifying through the majority of the process exhibited higher post-thaw outcome. It was also found that samples where the ice thawed more rapidly had greater post-thaw viability 24 h post-thaw (75.7 ± 3.9% and 62.0 ± 7.2% respectively).These findings have implications for the cryopreservation of large volumes with a rigid shape and for the cryopreservation of a Bioartificial Liver Device

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease

Background: It is important to identify molecular features that improve prostate cancer (PCa) risk stratification before radical treatment with curative intent. Molecular analysis of historical diagnostic formalin-fixed paraffin-embedded (FFPE) prostate biopsies from cohorts with post-radiotherapy (RT) long-term clinical follow-up has been limited. Utilizing parallel sequencing modalities, we performed a proof-of-principle sequencing analysis of historical diagnostic FFPE prostate biopsies. We compared patients with (i) stable PCa (sPCa) postprimary or salvage RT, (ii) progressing PCa (pPCa) post-RT, and (iii) de novo metastatic PCa (mPCa). Methods: A cohort of 19 patients with diagnostic prostate biopsies (n = 6 sPCa, n = 5 pPCa, n = 8 mPCa) and mean 4 years 10 months follow-up (diagnosed 2009–2016) underwent nucleic acid extraction from demarcated malignancy. Samples underwent 3′RNA sequencing (3′RNAseq) (n = 19), nanoString analysis (n = 12), and Illumina 850k methylation (n = 8) sequencing. Bioinformatic analysis was performed to coherently identify differentially expressed genes and methylated genomic regions (MGRs). Results: Eighteen of 19 samples provided useable 3′RNAseq data. Principal component analysis (PCA) demonstrated similar expression profiles between pPCa and mPCa cases, versus sPCa. Coherently differentially methylated probes between these groups identified ~600 differentially MGRs. The top 50 genes with increased expression in pPCa patients were associated with reduced progression-free survival post-RT (p < 0.0001) in an external cohort. Conclusions: 3′RNAseq, nanoString and 850k-methylation analyses are each achievable from historical FFPE diagnostic pretreatment prostate biopsies, unlocking the potential to utilize large cohorts of historic clinical samples. Profiling similarities between individuals with pPCa and mPCa suggests biological similarities and historical radiological staging limitations, which warrant further investigation

In situ studies of materials for high temperature CO2 capture and storage.

Carbon capture and storage (CCS) offers a possible solution to curb the CO2 emissions from stationary sources in the coming decades, considering the delays in shifting energy generation to carbon neutral sources such as wind, solar and biomass. The most mature technology for post-combustion capture uses a liquid sorbent, amine scrubbing. However, with the existing technology, a large amount of heat is required for the regeneration of the liquid sorbent, which introduces a substantial energy penalty. The use of alternative sorbents for CO2 capture, such as the CaO-CaCO3 system, has been investigated extensively in recent years. However there are significant problems associated with the use of CaO based sorbents, the most challenging one being the deactivation of the sorbent material. When sorbents such as natural limestone are used, the capture capacity of the solid sorbent can fall by as much as 90 mol% after the first 20 carbonation-regeneration cycles. In this study a variety of techniques were employed to understand better the cause of this deterioration from both a structural and morphological standpoint. X-ray and neutron PDF studies were employed to understand better the local surface and interfacial structures formed upon reaction, finding that after carbonation the surface roughness is decreased for CaO. In situ synchrotron X-ray diffraction studies showed that carbonation with added steam leads to a faster and more complete conversion of CaO than under conditions without steam, as evidenced by the phases seen at different depths within the sample. Finally, in situ X-ray tomography experiments were employed to track the morphological changes in the sorbents during carbonation, observing directly the reduction in porosity and increase in tortuosity of the pore network over multiple calcination reactions.M.T. Dunstan acknowledges funding from the Cambridge Commonwealth Trusts and Trinity College, Cambridge. M.T. Dunstan, S.A. Scott, J.S. Dennis and C.P. Grey acknowledge funding from EPSRC Grant No. EP/K030132/1. W. Liu acknowledges funding from NRF, Singapore under its CREATE programme. The authors would like to thank the Science Facilities and Technologies Council, Diamond Light Source and Paul Scherrer Institut for the award of beamtime. The authors would especially like to thank Dr Julie Fife and Dr David Haberthür at TOMCAT, Dr Tristan Youngs and Dr Daniel Bowron at NIMROD, and Dr Philip Chater at I15 for their assistance in collecting and processing the data, and Simon Griggs for assistance with SEM. M.W. Gaultois is grateful for support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 659764.This is the author accepted manuscript. The final version is available from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C6FD00047

Ion Dynamics and CO2 Absorption Properties of Nb-, Ta-, and Y-Doped Li2ZrO3 Studied by Solid-State NMR, Thermogravimetry, and First-Principles Calculations

Among the many different processes proposed for large-scale carbon capture and storage (CCS), high temperature CO2 looping has emerged as a favorable candidate due to the low theoretical energy penalties that can be achieved. Many different materials have been proposed for use in such a process, the process requiring fast CO2 absorption reaction kinetics as well as being able to cycle the material for multiple cycles without loss of capacity. Lithium ternary oxide materials, and in particular Li2ZrO3, have displayed promising performance, but further modifications are needed to improve their rate of reaction with CO2. Previous studies have linked rates of lithium ionic conduction-with CO2 absorption in similar materials, and in this work we present work aimed at exploring the effect of aliovalent doping on the efficacy of Li2ZrO3 as a CO2 sorbent. Using a combination of X-ray powder diffraction, theoretical calculations, and solid-state nuclear magnetic resonance, we studied the impact of Nb, Ta, and Y doping on the structure, Li ionic motion, and CO2 absorption properties of Li2ZrO3. These methods allowed us to characterize the theoretical and experimental doping limit into the pure material, suggesting that vacancies formed upon doping are not fully disordered but instead are correlated to the dopant atom positions, limiting the solubility range. Characterization of the lithium motion using variable-temperature solid-state nuclear magnetic resonance confirms that interstitial doping with Y retards the movement of Li ions in the structure, whereas vacancy doping with Nb or Ta results in a similar activation energy as observed for nominally pure Li2ZrO3. However, a marked reduction in the CO2 absorption of the Nb- and Ta-doped samples suggests that doping also leads to a change in the carbonation equilibrium of Li2ZrO3, disfavoring the CO2 absorption at the reaction temperature. This study shows that a complex mixture of structural, kinetic, and dynamic factors can influence the performance of Li-based materials for CCS and underscores the importance of balancing these different factors in order to optimize the process

Improving harmonization and standardization of expanded newborn screening results by optimization of the legacy flow injection analysis tandem mass spectrometry methods and application of a standardized calibration approach

Background Newborn screening (NBS) laboratories in the United Kingdom adhere to common protocols based on single analyte cutoff values (COVs); therefore, interlaboratory harmonization is of paramount importance. Interlaboratory variation for screening analytes in UK NBS laboratories ranges from 17% to 59%. While using common stable isotope internal standards has been shown to significantly reduce interlaboratory variation, instrument set-up, sample extraction, and calibration approach are also key factors. Methods Dried blood spot (DBS) extraction processes, instrument set-up, mobile-phase composition, sample introduction technique, and calibration approach of flow injection analysis–tandem mass spectrometry (FIA-MS/MS) methods were optimized. Inter- and intralaboratory variation of methionine, leucine, phenylalanine, tyrosine, isovaleryl-carnitine, glutaryl-carnitine, octanoyl-carnitine, and decanoyl-carnitine were determined pre- and postoptimization, using 3 different calibration approaches. Results Optimal recovery of analytes from DBS was achieved with a 35-min extraction time and 80% methanol (150 μL). Optimized methodology decreased the mean intralaboratory percentage relative SD (%RSD) for the 8 analytes from 20.7% (range 4.1–46.0) to 5.4% (range 3.0–8.5). The alternative calibration approach reduced the mean interlaboratory %RSD for all analytes from 16.8% (range 4.1–25.0) to 7.1% (range 4.1–11.0). Nuclear magnetic resonance analysis of the calibration material highlighted the need for standardization. The purities of isovaleryl-carnitine and glutaryl-carnitine were 85.13% and 69.94% respectively, below the manufacturer’s stated values of ≥98%. Conclusions For NBS programs provided by multiple laboratories using single analyte COVs, harmonization and standardization of results can be achieved by optimizing legacy FIA-MS/MS methods, adopting a common analytical protocol, and using standardized calibration material rather than internal calibration

Multiple breath washout in bronchiectasis clinical trials:is it feasible?

Background: Evaluation of Multiple Breath Washout (MBW) set-up including staff training, certification and central “over-reading” for data quality control is essential to determine the feasibility of MBW in future bronchiectasis studies. Aims: To assess the outcomes of a MBW training, certification and central over-reading programme. Methods: MBW training and certification was conducted in European sites collecting LCI data in the BronchUK clinimetrics and/or i-BEST-1 studies. The blended training programme included the use of an eLearning tool and a 1-day face-to-face session. Sites submitted MBW data to trained central over-readers who determined validity and quality. Results: Thirteen training days were delivered to 56 participants from 22 sites. 18/22 (82%) were MBW naïve. Participant knowledge and confidence increased significantly (p<0.001). By the end of the study recruitment, 15/22 sites (68%) had completed certification with a mean (range) time since training of 6.2 (3-14) months. In the BronchUK clinimetrics study, 468/589 (79%) tests met45 the quality criteria following central over-reading, compared with 137/236 (58%) tests in the i-BEST-1 study. Conclusions: LCI is feasible in a bronchiectasis multicentre clinical trial setting however, consideration of site experience in terms of training as well as assessment of skill drift and the need for re-training may be important to reduce time to certification and optimise data quality. Longer times to certification, a higher percentage of naive sites and patients with worse lung function may have contributed to the lower success rate in the i-BEST-1 study

Study protocol for a randomised placebo-controlled trial of pramipexole in addition to mood stabilisers for patients with treatment resistant bipolar depression (the PAX-BD study)

Abstract Background Treatment Resistant Bipolar Depression (TRBD) is a major contributor to the burden of disease associated with Bipolar Disorder (BD). Treatment options for people experiencing bipolar depression are limited to three interventions listed by National Institute for Health and Care: lamotrigine, quetiapine and olanzapine, of which the latter two are often not well tolerated. The majority of depressed people with BD are therefore prescribed antidepressants despite limited efficacy. This demonstrates an unmet need for additional interventions. Pramipexole has been shown to improve mood symptoms in animal models of depression, in people with Parkinson’s Disease and two proof of principle trials of pramipexole for people with BD who are currently depressed. Methods The PAX-BD study, funded by the United Kingdom (UK) National Institute for Health Research, aims to extend previous findings by assessing the efficacy, safety and health economic impact of pramipexole in addition to mood stabilisers for patients with TRBD. A randomised, double-blind, placebo controlled design is conducted in a naturalistic UK National Health Service setting. An internal pilot study to examine feasibility and acceptability of the study design is included. Participants with TRBD are screened from National Health Service secondary care services in up to 40 mental health trusts in the UK, with the aim of recruiting approximately 414 participants into a pre-randomisation phase to achieve a target of 290 randomised participants. Primary safety and efficacy measures are at 12 weeks following randomisation, with follow up of participants to 52 weeks. The primary outcome is depressive symptoms as measured by Quick Inventory for Depressive Symptomatology – Self Report. Secondary outcomes include changes in anxiety, manic symptoms, tolerability, acceptability, quality of life and cost-effectiveness. Outcome measures are collected remotely using self-report tools implemented online, and observer-rated assessments conducted via telephone. ANCOVA will be used to examine the difference in rating scale scores between treatment arms, and dependent on compliance in completion of weekly self-report measures. A mixed effects linear regression model may also be used to account for repeated measures. Trial registration ISRCTN72151939. Registered on 28 August 2019, http://www.isrctn.com/ISRCTN72151939 Protocol Version: 04-FEB-2021, Version 9.0