Learning to diagnose cirrhosis from radiological and histological labels with joint self and weakly-supervised pretraining strategies

Identifying cirrhosis is key to correctly assess the health of the liver. However, the gold standard diagnosis of the cirrhosis needs a medical intervention to obtain the histological confirmation, e.g. the METAVIR score, as the radiological presentation can be equivocal. In this work, we propose to leverage transfer learning from large datasets annotated by radiologists, which we consider as a weak annotation, to predict the histological score available on a small annex dataset. To this end, we propose to compare different pretraining methods, namely weakly-supervised and self-supervised ones, to improve the prediction of the cirrhosis. Finally, we introduce a loss function combining both supervised and self-supervised frameworks for pretraining. This method outperforms the baseline classification of the METAVIR score, reaching an AUC of 0.84 and a balanced accuracy of 0.75, compared to 0.77 and 0.72 for a baseline classifier.Comment: Accepted at IEEE ISBI 202

Urban land, planning and governance systems in Nigeria

The narrative of rapid urbanisation in relation to inadequate planning, governance and management regimes in Nigeria is well-rehearsed. The combination of customary and colonial practices, outdated policies and plans and entrenched attitudes is typically regarded as a problem without clear or universal solutions. The aim of this report is to elucidate the urban land administration and planning debate in the country by examining the issues based on literature review and views of key urban sector stakeholders from six cities obtained through interviews.The historical development of land administration, planning and governance regimes in Nigeria is seen to contribute to the failure of the current development system because of an evolution from two distinct paradigms. This leads to confusion and a lack of engagement with formal systems thereby limiting the potential for well-conceived national and state urban development goals from being realised within cities that are not observing the planning frameworks. Colonial segregational policies have been superseded by a succession of policies that increasingly recognise, but cannot enforce, participation, equity, sustainability and climate change adaptation.Simultaneously, massively-scaled urban development continues under a variety of guises to meet the demand for space for urban accommodation, business and services from a diverse population with huge division between the wealthy and the urban poor. There is a growing need to categorise and understand this diversity of development in order to develop policies that adopt the positive aspects of informal development while pursuing national and state development goals and providing healthy and economically viable urban environments for all.It is shown that new development forms such as new towns, developer-built estates and owner built housing are large factors in the foregoing regard as they are in other sub-Saharan African urban areas. In addition, large scale infrastructural development has also led to ribbon and satellite development that takes advantage of the massive investment in national assets. These development forms are far superior to the slum conditions traditionally associated with the term “informal” and they may benefit from some of the “legal” attributes of formal planned developments such as ownership rights and even locally-prepared plans.The advantages of such developments in the vacuum created by the inadequacies of the formal planning system seem self-evident. However, it is apparent that these developments suffer from deficiencies in the provision of infrastructure and services and may also put an intolerable strain on nearby infrastructure and services designed to cope with the much smaller population anticipated by formal planning. Equally, the increasing commodification of lands especially those delivered through the informal system in the face of rapid urbanisation and rising demand are driving land and rental prices to unsustainable levels and out of the reach of essential key workers and the urban poor. This, coupled with the2tendency for the governance arrangements under the informal system to crumble in the face of urbanisation, could potentially displace people that would be considered entitled under the urban land administration and planning system in Nigeria. Furthermore, lack of formal governance and management of housing developments can place people at risk from unhealthy and overcrowded living conditions. This could also empower unscrupulous land owners and developers to prescribe their own governance and management framework, which may result in exploitation of innocent purchasers.The report also examines recent initiatives at national, state and local levels. It concludes that some initiatives have been met with a measure of success and that these are typified by a flexibility that applies global principles at a local level and that canvas the needs and observes the contexts of local populations

Searching for Imaging Biomarkers of Psychotic Dysconnectivity

Background: Progress in precision psychiatry is predicated on identifying reliable individual-level diagnostic biomarkers. For psychosis, measures of structural and functional connectivity could be promising biomarkers given consistent reports of dysconnectivity across psychotic disorders using magnetic resonance imaging. Methods: We leveraged data from four independent cohorts of patients with psychosis and control subjects with observations from approximately 800 individuals. We used group-level analyses and two supervised machine learning algorithms (support vector machines and ridge regression) to test within-, between-, and across-sample classification performance of white matter and resting-state connectivity metrics. Results: Although we replicated group-level differences in brain connectivity, individual-level classification was suboptimal. Classification performance within samples was variable across folds (highest area under the curve [AUC] range = 0.30) and across datasets (average support vector machine AUC range = 0.50; average ridge regression AUC range = 0.18). Classification performance between samples was similarly variable or resulted in AUC values of approximately 0.65, indicating a lack of model generalizability. Furthermore, collapsing across samples (resting-state functional magnetic resonance imaging, N = 888; diffusion tensor imaging, N = 860) did not improve model performance (maximal AUC = 0.67). Ridge regression models generally outperformed support vector machine models, although classification performance was still suboptimal in terms of clinical relevance. Adjusting for demographic covariates did not greatly affect results. Conclusions: Connectivity measures were not suitable as diagnostic biomarkers for psychosis as assessed in this study. Our results do not negate that other approaches may be more successful, although it is clear that a systematic approach to individual-level classification with large independent validation samples is necessary to properly vet neuroimaging features as diagnostic biomarkers

Imaging local genetic influences on cortical folding

Recent progress in deciphering mechanisms of human brain cortical folding leave unexplained whether spatially patterned genetic influences contribute to this folding. High-resolution in vivo brain MRI can be used to estimate genetic correlations (covariability due to shared genetic factors) in interregional cortical thickness, and biomechanical studies predict an influence of cortical thickness on folding patterns. However, progress has been hampered because shared genetic influences related to folding patterns likely operate at a scale that is much more local (cm) than that addressed in prior imaging studies. Here, we develop methodological approaches to examine local genetic influences on cortical thickness and apply these methods to two large, independent samples. We find that such influences are markedly heterogeneous in strength, and in some cortical areas are notably stronger in specific orientations relative to gyri or sulci. The overall, phenotypic local correlation has a significant basis in shared genetic factors and is highly symmetric between left and right cortical hemispheres. Furthermore, the degree of local cortical folding relates systematically with the strength of local correlations, which tends to be higher in gyral crests and lower in sulcal fundi. The relationship between folding and local correlations is stronger in primary sensorimotor areas and weaker in association areas such as prefrontal cortex, consistent with reduced genetic constraints on the structural topology of association cortex. Collectively, our results suggest that patterned genetic influences on cortical thickness, measurable at the scale of in vivo MRI, may be a causal factor in the development of cortical folding

Seeking safety beyond refuge : the impact of immigration and citizenship policy upon refugees in the UK

Western states are concerned about maintaining and securing national borders. Across Europe, one response has been to implement restrictive asylum regimes that prevent ‘bogus’ applicants and grant refuge only to the ‘deserving’. Alongside these concerns, states are eager to encourage socially cohesive communities. One recent tool adopted by the UK government has been citizenship policy, including English language/life in the UK tests and citizenship ceremonies. By drawing upon in-depth interviews with refugees in Scotland (UK), this paper explores the impact of the current asylum regime and citizenship policies from the perspective of individual voices that are often absent from wider debates. It explores how temporary refugee status impacts upon individuals’ everyday lives including employment and education, and impacts upon children. The data also question the reasons for refugees deciding to become British citizens (or not) and highlight instrumental reasons alongside less tangible factors such as gaining a sense of security. Taking the discussion forward, the study explores some unintended consequences of immigration and citizenship policies in the UK. The research suggests that not only do restrictive asylum policies negatively impact upon refugees and their integration but also serve to elevate fear and uncertainty, which can unintentionally spur individuals to seek naturalisation

Soluble Guanylate Cyclase α1–Deficient Mice: A Novel Murine Model for Primary Open Angle Glaucoma

Primary open angle glaucoma (POAG) is a leading cause of blindness worldwide. The molecular signaling involved in the pathogenesis of POAG remains unknown. Here, we report that mice lacking the $α_1$ subunit of the nitric oxide receptor soluble guanylate cyclase represent a novel and translatable animal model of POAG, characterized by thinning of the retinal nerve fiber layer and loss of optic nerve axons in the context of an open iridocorneal angle. The optic neuropathy associated with soluble guanylate cyclase $α_1$–deficiency was accompanied by modestly increased intraocular pressure and retinal vascular dysfunction. Moreover, data from a candidate gene association study suggests that a variant in the locus containing the genes encoding for the $α_1$ and $β_1$ subunits of soluble guanylate cyclase is associated with POAG in patients presenting with initial paracentral vision loss, a disease subtype thought to be associated with vascular dysregulation. These findings provide new insights into the pathogenesis and genetics of POAG and suggest new therapeutic strategies for POAG

A qualitative investigation of lived experiences of long-term health condition management with people who are food insecure.

Background: As more people are living with one or more chronic health conditions, supporting patients to become activated, self-managers of their conditions has become a key health policy focus both in the UK and internationally. There is also growing evidence in the UK that those with long term health conditions have an increased risk of being food insecure. While international evidence indicates that food insecurity adversely affects individual's health condition management capability, little is known about how those so affected manage their condition(s) in this context. An investigation of lived experience of health condition management was undertaken with food insecure people living in north east Scotland. The study aimed to explore the challenges facing food insecure people in terms of, i. their self-care condition management practices, and ii. disclosing and discussing the experience of managing their condition with a health care professional, and iii. Notions of the support they might wish to receive from them. Methods: Twenty in-depth interviews were conducted with individuals attending a food bank and food pantry in north east Scotland. Interview audio recordings were fully transcribed and thematically analysed. Results: Individuals reporting multiple physical and mental health conditions, took part in the study. Four main themes were identified i.e.: 1. food practices, trade-offs and compromises, that relate to economic constraints and lack of choice; 2. illness experiences and food as they relate to physical and mental ill-health; 3. (in) visibility of participants' economic vulnerability within health care consultations; and 4. perceptions and expectations of the health care system. Conclusions: This study, the first of its kind in the UK, indicated that participants' health condition management aspirations were undermined by the experience of food insecurity, and that their health care consultations in were, on the whole, devoid of discussions of those challenges. As such, the study indicated practical and ethical implications for health care policy, practice and research associated with the risk of intervention-generated health inequalities that were suggested by this study. Better understanding is needed about the impact of household food insecurity on existing ill health, wellbeing and health care use across the UK

The ABC130 barrel module prototyping programme for the ATLAS strip tracker

For the Phase-II Upgrade of the ATLAS Detector, its Inner Detector, consisting of silicon pixel, silicon strip and transition radiation sub-detectors, will be replaced with an all new 100 % silicon tracker, composed of a pixel tracker at inner radii and a strip tracker at outer radii. The future ATLAS strip tracker will include 11,000 silicon sensor modules in the central region (barrel) and 7,000 modules in the forward region (end-caps), which are foreseen to be constructed over a period of 3.5 years. The construction of each module consists of a series of assembly and quality control steps, which were engineered to be identical for all production sites. In order to develop the tooling and procedures for assembly and testing of these modules, two series of major prototyping programs were conducted: an early program using readout chips designed using a 250 nm fabrication process (ABCN-25) and a subsequent program using a follow-up chip set made using 130 nm processing (ABC130 and HCC130 chips). This second generation of readout chips was used for an extensive prototyping program that produced around 100 barrel-type modules and contributed significantly to the development of the final module layout. This paper gives an overview of the components used in ABC130 barrel modules, their assembly procedure and findings resulting from their tests.Comment: 82 pages, 66 figure