6,805 research outputs found

    Is attention all you need in medical image analysis? A review

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    Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated

    Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein

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    The activation of at least 23 different mammalian kinases requires the phosphorylation of their hydrophobic motifs by the kinase PDK1. A linker connects the phosphoinositide-binding PH domain to the catalytic domain, which contains a docking site for substrates called the PIF pocket. Here, we used a chemical biology approach to show that PDK1 existed in equilibrium between at least three distinct conformations with differing substrate specificities. The inositol polyphosphate derivative HYG8 bound to the PH domain and disrupted PDK1 dimerization by stabilizing a monomeric conformation in which the PH domain associated with the catalytic domain and the PIF pocket was accessible. In the absence of lipids, HYG8 potently inhibited the phosphorylation of Akt (also termed PKB) but did not affect the intrinsic activity of PDK1 or the phosphorylation of SGK, which requires docking to the PIF pocket. In contrast, the small molecule valsartan bound to the PIF pocket and stabilized a second distinct monomeric conformation. Our study reveals dynamic conformations of full-length PDK1 in which the location of the linker and the PH domain relative to the catalytic domain determines the selective phosphorylation of PDK1 substrates. The study further suggests new approaches for the design of drugs to selectively modulate signaling downstream of PDK1

    ACOUSTIC SPEECH MARKERS FOR TRACKING CHANGES IN HYPOKINETIC DYSARTHRIA ASSOCIATED WITH PARKINSON’S DISEASE

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    Previous research has identified certain overarching features of hypokinetic dysarthria associated with Parkinson’s Disease and found it manifests differently between individuals. Acoustic analysis has often been used to find correlates of perceptual features for differential diagnosis. However, acoustic parameters that are robust for differential diagnosis may not be sensitive to tracking speech changes. Previous longitudinal studies have had limited sample sizes or variable lengths between data collection. This study focused on using acoustic correlates of perceptual features to identify acoustic markers able to track speech changes in people with Parkinson’s Disease (PwPD) over six months. The thesis presents how this study has addressed limitations of previous studies to make a novel contribution to current knowledge. Speech data was collected from 63 PwPD and 47 control speakers using an online podcast software at two time points, six months apart (T1 and T2). Recordings of a standard reading passage, minimal pairs, sustained phonation, and spontaneous speech were collected. Perceptual severity ratings were given by two speech and language therapists for T1 and T2, and acoustic parameters of voice, articulation and prosody were investigated. Two analyses were conducted: a) to identify which acoustic parameters can track perceptual speech changes over time and b) to identify which acoustic parameters can track changes in speech intelligibility over time. An additional attempt was made to identify if these parameters showed group differences for differential diagnosis between PwPD and control speakers at T1 and T2. Results showed that specific acoustic parameters in voice quality, articulation and prosody could differentiate between PwPD and controls, or detect speech changes between T1 and T2, but not both factors. However, specific acoustic parameters within articulation could detect significant group and speech change differences across T1 and T2. The thesis discusses these results, their implications, and the potential for future studies

    The Future of Work and Digital Skills

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    The theme for the events was "The Future of Work and Digital Skills". The 4IR caused a hollowing out of middle-income jobs (Frey & Osborne, 2017) but COVID-19 exposed the digital gap as survival depended mainly on digital infrastructure and connectivity. Almost overnight, organizations that had not invested in a digital strategy suddenly realized the need for such a strategy and the associated digital skills. The effects have been profound for those who struggled to adapt, while those who stepped up have reaped quite the reward.Therefore, there are no longer certainties about what the world will look like in a few years from now. However, there are certain ways to anticipate the changes that are occurring and plan on how to continually adapt to an increasingly changing world. Certain jobs will soon be lost and will not come back; other new jobs will however be created. Using data science and other predictive sciences, it is possible to anticipate, to the extent possible, the rate at which certain jobs will be replaced and new jobs created in different industries. Accordingly, the collocated events sought to bring together government, international organizations, academia, industry, organized labour and civil society to deliberate on how these changes are occurring in South Africa, how fast they are occurring and what needs to change in order to prepare society for the changes.Deutsche Gesellschaft fĂĽr Internationale Zusammenarbeit (GIZ) British High Commission (BHC)School of Computin

    Effective connectivity reveals distinctive patterns in response to others’ genuine affective experience of disgust

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    Empathy is significantly influenced by the identification of others’ emotions. In a recent study, we have found increased activation in the anterior insular cortex (aIns) that could be attributed to affect sharing rather than perceptual saliency, when seeing another person genuinely experiencing pain as opposed to merely acting to be in pain. In that prior study, effective connectivity between aIns and the right supramarginal gyrus (rSMG) was revealed to represent what another person really feels. In the present study, we used a similar paradigm to investigate the corresponding neural signatures in the domain of empathy for disgust - with participants seeing others genuinely sniffing unpleasant odors as compared to pretending to smell something disgusting (in fact the disgust expressions in both conditions were acted for reasons of experimental control). Consistent with the previous findings on pain, we found stronger activations in aIns associated with affect sharing for genuine disgust (inferred) compared with pretended disgust. However, instead of rSMG we found engagement of the olfactory cortex. Using dynamic causal modeling (DCM), we estimated the neural dynamics of aIns and the olfactory cortex between the genuine and pretended conditions. This revealed an increased excitatory modulatory effect for genuine disgust compared to pretended disgust. For genuine disgust only, brain-to-behavior regression analyses highlighted a link between the observed modulatory effect and a few empathic traits. Altogether, the current findings complement and expand our previous work, by showing that perceptual saliency alone does not explain responses in the insular cortex. Moreover, it reveals that different brain networks are implicated in a modality-specific way when sharing the affective experiences associated with pain vs. disgust

    Fast fluorescence lifetime imaging and sensing via deep learning

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    Error on title page – year of award is 2023.Fluorescence lifetime imaging microscopy (FLIM) has become a valuable tool in diverse disciplines. This thesis presents deep learning (DL) approaches to addressing two major challenges in FLIM: slow and complex data analysis and the high photon budget for precisely quantifying the fluorescence lifetimes. DL's ability to extract high-dimensional features from data has revolutionized optical and biomedical imaging analysis. This thesis contributes several novel DL FLIM algorithms that significantly expand FLIM's scope. Firstly, a hardware-friendly pixel-wise DL algorithm is proposed for fast FLIM data analysis. The algorithm has a simple architecture yet can effectively resolve multi-exponential decay models. The calculation speed and accuracy outperform conventional methods significantly. Secondly, a DL algorithm is proposed to improve FLIM image spatial resolution, obtaining high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images. A computational framework is developed to generate large-scale semi-synthetic FLIM datasets to address the challenge of the lack of sufficient high-quality FLIM datasets. This algorithm offers a practical approach to obtaining HR FLIM images quickly for FLIM systems. Thirdly, a DL algorithm is developed to analyze FLIM images with only a few photons per pixel, named Few-Photon Fluorescence Lifetime Imaging (FPFLI) algorithm. FPFLI uses spatial correlation and intensity information to robustly estimate the fluorescence lifetime images, pushing this photon budget to a record-low level of only a few photons per pixel. Finally, a time-resolved flow cytometry (TRFC) system is developed by integrating an advanced CMOS single-photon avalanche diode (SPAD) array and a DL processor. The SPAD array, using a parallel light detection scheme, shows an excellent photon-counting throughput. A quantized convolutional neural network (QCNN) algorithm is designed and implemented on a field-programmable gate array as an embedded processor. The processor resolves fluorescence lifetimes against disturbing noise, showing unparalleled high accuracy, fast analysis speed, and low power consumption.Fluorescence lifetime imaging microscopy (FLIM) has become a valuable tool in diverse disciplines. This thesis presents deep learning (DL) approaches to addressing two major challenges in FLIM: slow and complex data analysis and the high photon budget for precisely quantifying the fluorescence lifetimes. DL's ability to extract high-dimensional features from data has revolutionized optical and biomedical imaging analysis. This thesis contributes several novel DL FLIM algorithms that significantly expand FLIM's scope. Firstly, a hardware-friendly pixel-wise DL algorithm is proposed for fast FLIM data analysis. The algorithm has a simple architecture yet can effectively resolve multi-exponential decay models. The calculation speed and accuracy outperform conventional methods significantly. Secondly, a DL algorithm is proposed to improve FLIM image spatial resolution, obtaining high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images. A computational framework is developed to generate large-scale semi-synthetic FLIM datasets to address the challenge of the lack of sufficient high-quality FLIM datasets. This algorithm offers a practical approach to obtaining HR FLIM images quickly for FLIM systems. Thirdly, a DL algorithm is developed to analyze FLIM images with only a few photons per pixel, named Few-Photon Fluorescence Lifetime Imaging (FPFLI) algorithm. FPFLI uses spatial correlation and intensity information to robustly estimate the fluorescence lifetime images, pushing this photon budget to a record-low level of only a few photons per pixel. Finally, a time-resolved flow cytometry (TRFC) system is developed by integrating an advanced CMOS single-photon avalanche diode (SPAD) array and a DL processor. The SPAD array, using a parallel light detection scheme, shows an excellent photon-counting throughput. A quantized convolutional neural network (QCNN) algorithm is designed and implemented on a field-programmable gate array as an embedded processor. The processor resolves fluorescence lifetimes against disturbing noise, showing unparalleled high accuracy, fast analysis speed, and low power consumption

    Development of attention to social interactions in naturalistic scenes

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    Exploring the effects of spinal cord stimulation for freezing of gait in parkinsonian patients

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    Dopaminergic replacement therapies (e.g. levodopa) provide limited to no response for axial motor symptoms including gait dysfunction and freezing of gait (FOG) in Parkinson’s disease (PD) and Richardson’s syndrome progressive supranuclear palsy (PSP-RS) patients. Dopaminergic-resistant FOG may be a sensorimotor processing issue that does not involve basal ganglia (nigrostriatal) impairment. Recent studies suggest that spinal cord stimulation (SCS) has positive yet variable effects for dopaminergic-resistant gait and FOG in parkinsonian patients. Further studies investigating the mechanism of SCS, optimal stimulation parameters, and longevity of effects for alleviating FOG are warranted. The hypothesis of the research described in this thesis is that mid-thoracic, dorsal SCS effectively reduces FOG by modulating the sensory processing system in gait and may have a dopaminergic effect in individuals with FOG. The primary objective was to understand the relationship between FOG reduction, improvements in upper limb visual-motor performance, modulation of cortical activity and striatal dopaminergic innervation in 7 PD participants. FOG reduction was associated with changes in upper limb reaction time, speed and accuracy measured using robotic target reaching choice tasks. Modulation of resting-state, sensorimotor cortical activity, recorded using electroencephalography, was significantly associated with FOG reduction while participants were OFF-levodopa. Thus, SCS may alleviate FOG by modulating cortical activity associated with motor planning and sensory perception. Changes to striatal dopaminergic innervation, measured using a dopamine transporter marker, were associated with visual-motor performance improvements. Axial and appendicular motor features may be mediated by non-dopaminergic and dopaminergic pathways, respectively. The secondary objective was to demonstrate the short- and long-term effects of SCS for alleviating dopaminergic-resistant FOG and gait dysfunction in 5 PD and 3 PSP-RS participants without back/leg pain. SCS programming was individualized based on which setting best improved gait and/or FOG responses per participant using objective gait analysis. Significant improvements in stride velocity, step length and reduced FOG frequency were observed in all PD participants with up to 3-years of SCS. Similar gait and FOG improvements were observed in all PSP-RS participants up to 6-months. SCS is a promising therapeutic option for parkinsonian patients with FOG by possibly influencing cortical and subcortical structures involved in locomotion physiology
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