Just-in-time deep learning for real-time X-ray computed tomography

Real-time X-ray tomography pipelines, such as implemented by RECAST3D, compute and visualize tomographic reconstructions in milliseconds, and enable the observation of dynamic experiments in synchrotron beamlines and laboratory scanners. For extending real-time reconstruction by image processing and analysis components, Deep Neural Networks (DNNs) are a promising technology, due to their strong performance and much faster run-times compared to conventional algorithms. DNNs may prevent experiment repetition by simplifying real-time steering and optimization of the ongoing experiment. The main challenge of integrating DNNs into real-time tomography pipelines, however, is that they need to learn their task from representative data before the start of the experiment. In scientific environments, such training data may not exist, and other uncertain and variable factors, such as the set-up configuration, reconstruction parameters, or user interaction, cannot easily be anticipated beforehand, either. To overcome these problems, we developed just-in-time learning, an online DNN training strategy that takes advantage of the spatio-temporal continuity of consecutive reconstructions in the tomographic pipeline. This allows training and deploying comparatively small DNNs during the experiment. We provide software implementations, and study the feasibility and challenges of the approach by training the self-supervised Noise2Inverse denoising task with X-ray data replayed from real-world dynamic experiments

X-ray tomography for fully-3D time-resolved reconstruction of bubbling fluidized beds

A new X-ray computed tomography technique for the purpose of imaging fluidized beds is presented. It consists of an experimental set-up with three stationary X-ray source and flat panel detector pairs, a geometric calibration and data processing workflow, and an image reconstruction algorithm. The technique enables sparse-angular tomographic reconstruction in large 3D regions of fluidized beds at framerates up to 200 Hz, and therefore images bubbles along their whole trajectories through the volume. It allows for a unique analysis of bubble dynamics in fluidized beds, including bubble velocities, bubble transformations, i.e., time evolution of the bubble distributions in space, and bubble\xe2\x80\x93bubble interactions. In this article, we first analyze the main limitation of the technique, the sparse angular resolution, through numerical simulations. We then test the experimental set-up through imaging a series of phantoms. Lastly, we demonstrate results from a Geldart B bubbling fluidized bed

Silicon central pattern generators for cardiac diseases

Belgium Herbarium image of Meise Botanic Garden

Silicon central pattern generators for cardiac diseases

Cardiac rhythm management devices provide therapies for both arrhythmias and resynchronisation but not heart failure, which affects millions of patients worldwide. This paper reviews recent advances in biophysics and mathematical engineering that provide a novel technological platform for addressing heart disease and enabling beat-to-beat adaptation of cardiac pacing in response to physiological feedback. The technology consists of silicon hardware central pattern generators (hCPGs) that may be trained to emulate accurately the dynamical response of biological central pattern generators (bCPGs). We discuss the limitations of present CPGs and appraise the advantages of analog over digital circuits for application in bioelectronic medicine. To test the system, we have focused on the cardio-respiratory oscillators in the medulla oblongata that modulate heart rate in phase with respiration to induce respiratory sinus arrhythmia (RSA). We describe here a novel, scalable hCPG comprising physiologically realistic (Hodgkin–Huxley type) neurones and synapses. Our hCPG comprises two neurones that antagonise each other to provide rhythmic motor drive to the vagus nerve to slow the heart. We show how recent advances in modelling allow the motor output to adapt to physiological feedback such as respiration. In rats, we report on the restoration of RSA using an hCPG that receives diaphragmatic electromyography input and use it to stimulate the vagus nerve at specific time points of the respiratory cycle to slow the heart rate. We have validated the adaptation of stimulation to alterations in respiratory rate. We demonstrate that the hCPG is tuneable in terms of the depth and timing of the RSA relative to respiratory phase. These pioneering studies will now permit an analysis of the physiological role of RSA as well as its any potential therapeutic use in cardiac disease

The downward spiral of mental disorders and educational attainment: a systematic review on early school leaving.

BACKGROUND: Most psychiatric disorders present symptom patterns that cause severe impairment on the emotional, cognitive and social level. Thus, adolescents who suffer from a mental disorder risk finding themselves in a downward spiral caused by the reciprocal association of psychological symptoms and negative school experiences that may culminate in early school leaving. In addition to previous collective work that mainly focused on school refusing behaviour among children and was presented as an expert's opinion, the following systematic review fills the knowledge gap by providing a structured overview of the bidirectional association between mental health and secondary school dropout based on a sound methodology and with a particular focus on mediating factors. METHODS: Four electronic databases were searched from January 1990 until June 2014. Selected references were assessed for study details, main results, mediating factors and methodological limitations. Standardized risk of bias assessment was conducted. RESULTS: Mood and anxiety disorders seemed to have a less consequential direct effect on early school leaving than substance use and disruptive behaviour disorders. The association between externalizing disorders and educational attainment was even stronger when the disorder occurred early in life. On the other hand, internalizing disorders were reported to develop as a consequence of school dropout. Only few studies had addressed gender differences, with discrepant results. Socio-economic background, academic achievement and family support were identified as significant mediating factors of the association between mental disorders and subsequent educational attainment. CONCLUSIONS: Findings suggested a strong association between mental health and education, in both directions. However, most studies focused on mediating factors that could not be targeted by intervention programs

Stakeholder enhanced environmental flow assessment: The Rufiji Basin case study in Tanzania

Environmental flows (E flows) are now a standard part of sustainable water management globally but are only rarely implemented. One reason may be insufficient engagement of stakeholders and their priority outcomes in the E flow-setting process. A recent environmental flow assessment (EFA) in the Kilombero basin of the Rufiji River in Tanzania concentrated on a broad-based investigation of stakeholders’ use and perceptions of the ecosystem services provided by the river. The EFA process generally followed the Building Block Methodology but with an enhanced engagement of stakeholders. Engagement began with the involvement of institutional stakeholders to explain the purpose of the EFA and to elicit their priority outcomes. Extensive interactions with direct-use stakeholders followed to investigate their uses of and priorities for the rivers. Results were used by the EFA specialist team in choosing flow indicators and defining measurable environmental objectives. The specialists then met to reach a consensus of the flow requirements. The EFA results were lastly reported back to stakeholders. During the Kilombero EFA we learned that stakeholders at all levels have a good awareness of the natural services provided by a healthy river and can contribute to the setting of environmental objectives for the rivers and floodplain. These can be factored into the biophysical assessments of river flows required to maintain habitats, processes, water quality and biodiversity. It is therefore important to allocate significant resources to stakeholder engagement. It now remains to be seen if enhanced stakeholder engagement, including the increased understanding and capacity built among all stakeholders, will increase support for the implementation of the recommended flows

Environmental flow case studies: Southern and Eastern Africa

SLIDES: Environmental Flow Case Studies: Southern and Eastern AfricaTanzania National Water Policy 2002 Water Resources Management Act (WRMA) No. 11 of 2009 “water for basic human needs will receive highest priority, water for the environment to protect the ecosystems that underpin our water resources will attain second priority and will be reserved” “take into account and give effect to the requirements of the reserve” Kenya Water Resources Management Rules 2007 “establish the reserve based on water resource records and reserve water demand or ecological vulnerability, human vulnerability, local observations of historic drought flows, maintenance of perennial flows and consultations with WUAs” The Water Bill 2014 "reserve, in relation to a water resource, means that quantity and quality of water required (a) to satisfy basic human needs for all people who are or may be supplied from the water resource; and (b) to protect aquatic ecosystems in order to secure ecologically sustainable development and use of the water resource

Environmental flow case studies: Southern and Eastern Africa

SLIDES: Environmental Flow Case Studies: Southern and Eastern AfricaTanzania National Water Policy 2002 Water Resources Management Act (WRMA) No. 11 of 2009 “water for basic human needs will receive highest priority, water for the environment to protect the ecosystems that underpin our water resources will attain second priority and will be reserved” “take into account and give effect to the requirements of the reserve” Kenya Water Resources Management Rules 2007 “establish the reserve based on water resource records and reserve water demand or ecological vulnerability, human vulnerability, local observations of historic drought flows, maintenance of perennial flows and consultations with WUAs” The Water Bill 2014 "reserve, in relation to a water resource, means that quantity and quality of water required (a) to satisfy basic human needs for all people who are or may be supplied from the water resource; and (b) to protect aquatic ecosystems in order to secure ecologically sustainable development and use of the water resource