Characterising population variability in brain structure through models of whole-brain structural connectivity

Models of whole-brain connectivity are valuable for understanding neurological function. This thesis seeks to develop an optimal framework for extracting models of whole-brain connectivity from clinically acquired diffusion data. We propose new approaches for studying these models. The aim is to develop techniques which can take models of brain connectivity and use them to identify biomarkers or phenotypes of disease. The models of connectivity are extracted using a standard probabilistic tractography algorithm, modified to assess the structural integrity of tracts, through estimates of white matter anisotropy. Connections are traced between 77 regions of interest, automatically extracted by label propagation from multiple brain atlases followed by classifier fusion. The estimates of tissue integrity for each tract are input as indices in 77x77 ”connectivity” matrices, extracted for large populations of clinical data. These are compared in subsequent studies. To date, most whole-brain connectivity studies have characterised population differences using graph theory techniques. However these can be limited in their ability to pinpoint the locations of differences in the underlying neural anatomy. Therefore, this thesis proposes new techniques. These include a spectral clustering approach for comparing population differences in the clustering properties of weighted brain networks. In addition, machine learning approaches are suggested for the first time. These are particularly advantageous as they allow classification of subjects and extraction of features which best represent the differences between groups. One limitation of the proposed approach is that errors propagate from segmentation and registration steps prior to tractography. This can cumulate in the assignment of false positive connections, where the contribution of these factors may vary across populations, causing the appearance of population differences where there are none. The final contribution of this thesis is therefore to develop a common co-ordinate space approach. This combines probabilistic models of voxel-wise diffusion for each subject into a single probabilistic model of diffusion for the population. This allows tractography to be performed only once, ensuring that there is one model of connectivity. Cross-subject differences can then be identified by mapping individual subjects’ anisotropy data to this model. The approach is used to compare populations separated by age and gender

Understanding the power of the "solo"

Solitude is a fundamental aspect of wilderness experiences and solo experiences, lasting 5 hours or more, have a strong 'survival' element and are a beneficial component to outdoor therapy programmes, sometimes marking life transitions for people. A shift has been made, however, towards solo experiences that centre on the natural environment rather than 'survival'. Shorter experiences of solitude in wilderness, e.g. quiet time or mini-solos, can offer the most "powerful" form of private reflection and can be self-initiated or prescribed. These 'shorter' solos have not, however, been extensively researched and neither have they been investigated in local green or semi-natural areas. This paper discusses a study that qualitatively explored people's experience, meaning-making and human-environment interaction during a mini-solo in a local green space and identified the impact of the experience on participants' sense of well-being. The mini-solo involved participants spending time in nature without distraction from technology or books and, if possible, people, lasting from 20 minutes to 1 hour. 12 older adults (55-74 years; 8 females and 4 males) recruited from walking groups and six younger adults (19-22 years; 4 females and 2 males) undertook a mini-solo. Pre- and post-experience interviews and journal writing (before, during and after the mini-solo) were analysed using thematic analysis. Four themes were created: ' Exerting Control', 'Aspects of Distraction' and 'Receptivity to Solo Experience'. Findings will be explained in relation to theory, literature and policy and may have implications for 'green prescriptions' as a short-term nature-based solution for well-being. Future directions for research are discussed. Keywords: mini-solo experience, wellbeing

Familiarity-based stimulus generalization of conditioned suppression

We report that stimulus novelty/familiarity is able to modulate stimulus generalization and discuss the theoretical implications of novelty/familiarity coding. Rats in Skinner boxes received clicker → shock pairings before generalization testing to a tone. Before clicker training, different groups of rats received preexposure treatments designed to systematically modulate the clicker and the tone's novelty and familiarity. Rats whose preexposure matched novelty/familiarity (i.e., either both or neither clicker and tone were pre-exposed) showed enhanced suppression to the tone relative to rats whose preexposure mixed novelty/familiarity (i.e., only clicker or tone was pre-exposed). This was not the result of sensory preconditioning to clicker and tone

Prospects for Stochastic Background Searches Using Virgo and LSC Interferometers

We consider the question of cross-correlation measurements using Virgo and the LSC Interferometers (LIGO Livingston, LIGO Hanford, and GEO600) to search for a stochastic gravitational-wave background. We find that inclusion of Virgo into the network will substantially improve the sensitivity to correlations above 200 Hz if all detectors are operating at their design sensitivity. This is illustrated using a simulated isotropic stochastic background signal, generated with an astrophysically-motivated spectrum, injected into 24 hours of simulated noise for the LIGO and Virgo interferometers.Comment: 11 pages, uses IOP style files, submitted to CQG for GWDAW11 proceedings; revised in response to referee comment

Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future experiments to accurately address the question of whether T cell responses contribute to SVR upon antiviral therapy. This pipeline represents a novel technique to analyze T cell dynamics in situations where conventional antigen-dependent methods are limited due to suppression of T cell functions and highly diverse antigenic sequences

Testing self-report time-use diaries against objective instruments in real time

This study provides a new test of time-use diary methodology, comparing diaries with a pair of objective criterion measures: wearable cameras and accelerometers. A volunteer sample of respondents (n = 148) completed conventional self-report paper time-use diaries using the standard UK Harmonised European Time Use Study (HETUS) instrument. On the diary day, respondents wore a camera that continuously recorded images of their activities during waking hours (approximately 1,500–2,000 images/day) and also an accelerometer that tracked their physical activity continuously throughout the 24-hour period covered by the diary. Of the initial 148 participants recruited, 131 returned usable diary and camera records, of whom 124 also provided a usable whole-day accelerometer record. The comparison of the diary data with the camera and accelerometer records strongly supports the use of diary methodology at both the aggregate (sample) and individual levels. It provides evidence that time-use data could be used to complement physical activity questionnaires for providing population-level estimates of physical activity. It also implies new opportunities for investigating techniques for calibrating metabolic equivalent of task (MET) attributions to daily activities using large-scale, population-representative time-use diary studies

Reducing the stress of drug administration:implications for the 3Rs

Restraint in animals is known to cause stress but is used during almost all scientific procedures in rodents, representing a major welfare and scientific issue. Administration of substances, a key part of most scientific procedures, almost always involves physical restraint of the animal. In this study, we developed a method to inject substances to rats using a non-restrained technique. We then compared the physiological, behavioral and emotional impacts of restrained versus non-restrained injection procedures. Our results highlight the negative welfare implications associated with physical restraint and demonstrate a method which can be used to avoid this. Our work shows how adopting strategies that avoid restraint can minimize a widespread source of stress in laboratory animals and improve welfare through refinement

Conformational Change of Mitochondrial Complex I Increases ROS Sensitivity During Ischemia

Aims: Myocardial ischemia/reperfusion (I/R) is associated with mitochondrial dysfunction and subsequent cardiomyocyte death. The generation of excessive quantities of reactive oxygen species (ROS) and resultant damage to mitochondrial enzymes is considered an important mechanism underlying reperfusion injury. Mitochondrial complex I can exist in two interconvertible states: active (A) and deactive or dormant (D). We have studied the active/deactive (A/D) equilibrium in several tissues under ischemic conditions in vivo and investigated the sensitivity of both forms of the heart enzyme to ROS. Results: We found that in the heart, t(½) of complex I deactivation during ischemia was 10 min, and that reperfusion resulted in the return of A/D equilibrium to its initial level. The rate of superoxide generation by complex I was higher in ischemic samples where content of the D-form was higher. Only the D-form was susceptible to inhibition by H(2)O(2) or superoxide, whereas turnover-dependent activation of the enzyme resulted in formation of the A-form, which was much less sensitive to ROS. The mitochondrial-encoded subunit ND3, most likely responsible for the sensitivity of the D-form to ROS, was identified by redox difference gel electrophoresis. Innovation: A combined in vivo and biochemical approach suggests that sensitivity of the mitochondrial system to ROS during myocardial I/R can be significantly affected by the conformational state of complex I, which may therefore represent a new therapeutic target in this setting. Conclusion: The presented data suggest that transition of complex I into the D-form in the absence of oxygen may represent a key event in promoting cardiac injury during I/R. Antioxid. Redox Signal. 19, 1459–1468