The Role of MRI Physics in Brain Segmentation CNNs: Achieving Acquisition Invariance and Instructive Uncertainties

Being able to adequately process and combine data arising from different sites is crucial in neuroimaging, but is difficult, owing to site, sequence and acquisition-parameter dependent biases. It is important therefore to design algorithms that are not only robust to images of differing contrasts, but also be able to generalise well to unseen ones, with a quantifiable measure of uncertainty. In this paper we demonstrate the efficacy of a physics-informed, uncertainty-aware, segmentation network that employs augmentation-time MR simulations and homogeneous batch feature stratification to achieve acquisition invariance. We show that the proposed approach also accurately extrapolates to out-of-distribution sequence samples, providing well calibrated volumetric bounds on these. We demonstrate a significant improvement in terms of coefficients of variation, backed by uncertainty based volumetric validation

Coordinated Emergence of Hippocampal Replay and Theta Sequences during Post-natal Development

Hippocampal place cells encode an animal's current position in space during exploration [1]. During sleep, hippocampal network activity recapitulates patterns observed during recent experience: place cells with overlapping spatial fields show a greater tendency to co-fire ("reactivation") [2], and temporally ordered and compressed sequences of place cell firing observed during wakefulness are reinstated ("replay") [3-5]. Reactivation and replay may underlie memory consolidation [6-10]. Compressed sequences of place cell firing also occur during exploration: during each cycle of the theta oscillation, the set of active place cells shifts from those signaling positions behind to those signaling positions ahead of an animal's current location [11, 12]. These "theta sequences" have been linked to spatial planning [13]. Here, we demonstrate that, before weaning (post-natal day [P]21), offline place cell activity associated with sharp-wave ripples (SWRs) reflects predominantly stationary locations in recently visited environments. By contrast, sequential place cell firing, describing extended trajectories through space during exploration (theta sequences) and subsequent rest (replay), emerge gradually after weaning in a coordinated fashion, possibly due to a progressive decrease in the threshold for experience-driven plasticity. Hippocampus-dependent learning and memory emerge late in altricial mammals [14-17], appearing around weaning in rats and slowly maturing thereafter [14,15]. In contrast, spatially localized firing is observed 1 week earlier (with reduced spatial tuning and stability) [18-21]. By examining the development of hippocampal reactivation, replay, and theta sequences, we show that the coordinated maturation of offline consolidation and online sequence generation parallels the late emergence of hippocampal memory in the rat

Interactive and multimedia contents associated with a system for computer-aided assessment

This paper presents a research study addressing the development, implementation, evaluation and use of Interactive Modules for Online Training (MITO) of mathematics in higher education. This work was carried out in the context of the MITO project, which combined several features of the learning and management system Moodle, the computer-aided assessment for mathematics STACK, the mathematical software GeoGebra, several packages from the type-setting program LaTeX, and tutorial videos. A total of 1962 students participated in this study. Two groups of students taking a Calculus course were selected for a deeper analysis. In regard to usability and functionality, the results indicate that MITO scored well in almost all aspects, which is fundamental for their introduction into formal university courses. The analysis of the data reveals that the use of MITO educational contents by students mainly occurs about one week and a half prior the evaluations. Moreover, there is a strong correlation between the results of online assessments on MITO in a continuous assessment model and the final grade on the course

Leading change beyond your classroom – Capacity building in SoTL and leadership by SaMnet

The issue: The introduction of quality standards can place delegates to the ACSME conference in the forefront of reflection on, and changes to, teaching in their school, faculty, and university. How do you make the transition from being someone who experiments and implements strategies to teach more effectively into someone who leads colleagues in doing so? Furthermore, what support can you gain in that process, both support from within your institution, as you work to help others to satisfy externally imposed standards, as well as outside your university? Approach: Development of the capability of academic staff in science and mathematics to lead change is a chief aim of the ALTC/OLT project developing the Science and Mathematics network of Australian university educators – SaMnet. We have engaged more than 100 university staff (‘SaMnet Scholars’) across 19 institutions in teams of four to pursue action-learning projects. SaMnet are supporting these teams with guidance in the scholarship of teaching and learning and in providing insight into leading organisational change. SaMnet also provides mentoring and contact with other academics who share an interest in the area of a particular project, e.g., standards, inquiry learning, or new ICTs. The effort is meant to change an individual innovation in teaching into a formally recorded experiment. A well documented experiment can not only be published; it can provide data sufficient to convince colleagues, heads of school, deans, and others that the innovation addresses their key performance indicators, such as those that result from national quality standards. This approach builds on an uneven foundation: (1) the growth in SoTL in universities; (2) a history of initiatives to improve teaching in science and mathematics that is recognised has having left little widespread impact; and (3) literature on the nature of change in organisations, in general, and on change in universities, in particular. The first set of SaMnet’s action-learning projects is approaching a mid-point, and the projects have another year to run. The ACSME conference provides an opportune moment to reflect and gain additional perspectives on the strategies being pursued. Progress: Work in progress - initial. Key questions: 1. How might insights into organisational change be relevant to your efforts in your university, particularly in relation to coming standards? 2. What do you feel that you could learn from SaMnet Scholars at this session about tailoring your efforts to gain support from your head of school and dean? 3. What are we missing? What could a national network of science and mathematics academics do for you that we might not have thought of? 4. What aspects of leading change would you like to learn about – steps and transitions in change processes (Kotter and Bridges), aspects of a new idea that spur adoption (Rogers), or surface issues and underlying issues that need to be addressed (Wilber)

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society