8,473 research outputs found

    Single-cell time-series analysis of metabolic rhythms in yeast

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    The yeast metabolic cycle (YMC) is a biological rhythm in budding yeast (Saccharomyces cerevisiae). It entails oscillations in the concentrations and redox states of intracellular metabolites, oscillations in transcript levels, temporal partitioning of biosynthesis, and, in chemostats, oscillations in oxygen consumption. Most studies on the YMC have been based on chemostat experiments, and it is unclear whether YMCs arise from interactions between cells or are generated independently by each cell. This thesis aims at characterising the YMC in single cells and its response to nutrient and genetic perturbations. Specifically, I use microfluidics to trap and separate yeast cells, then record the time-dependent intensity of flavin autofluorescence, which is a component of the YMC. Single-cell microfluidics produces a large amount of time series data. Noisy and short time series produced from biological experiments restrict the computational tools that are useful for analysis. I developed a method to filter time series, a machine learning model to classify whether time series are oscillatory, and an autocorrelation method to examine the periodicity of time series data. My experimental results show that yeast cells show oscillations in the fluorescence of flavins. Specifically, I show that in high glucose conditions, cells generate flavin oscillations asynchronously within a population, and these flavin oscillations couple with the cell division cycle. I show that cells can individually reset the phase of their flavin oscillations in response to abrupt nutrient changes, independently of the cell division cycle. I also show that deletion strains generate flavin oscillations that exhibit different behaviour from dissolved oxygen oscillations from chemostat conditions. Finally, I use flux balance analysis to address whether proteomic constraints in cellular metabolism mean that temporal partitioning of biosynthesis is advantageous for the yeast cell, and whether such partitioning explains the timing of the metabolic cycle. My results show that under proteomic constraints, it is advantageous for the cell to sequentially synthesise biomass components because doing so shortens the timescale of biomass synthesis. However, the degree of advantage of sequential over parallel biosynthesis is lower when both carbon and nitrogen sources are limiting. This thesis thus confirms autonomous generation of flavin oscillations, and suggests a model in which the YMC responds to nutrient conditions and subsequently entrains the cell division cycle. It also emphasises the possibility that subpopulations in the culture explain chemostat-based observations of the YMC. Furthermore, this thesis paves the way for using computational methods to analyse large datasets of oscillatory time series, which is useful for various fields of study beyond the YMC

    Audio-visual multi-modality driven hybrid feature learning model for crowd analysis and classification

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    The high pace emergence in advanced software systems, low-cost hardware and decentralized cloud computing technologies have broadened the horizon for vision-based surveillance, monitoring and control. However, complex and inferior feature learning over visual artefacts or video streams, especially under extreme conditions confine majority of the at-hand vision-based crowd analysis and classification systems. Retrieving event-sensitive or crowd-type sensitive spatio-temporal features for the different crowd types under extreme conditions is a highly complex task. Consequently, it results in lower accuracy and hence low reliability that confines existing methods for real-time crowd analysis. Despite numerous efforts in vision-based approaches, the lack of acoustic cues often creates ambiguity in crowd classification. On the other hand, the strategic amalgamation of audio-visual features can enable accurate and reliable crowd analysis and classification. Considering it as motivation, in this research a novel audio-visual multi-modality driven hybrid feature learning model is developed for crowd analysis and classification. In this work, a hybrid feature extraction model was applied to extract deep spatio-temporal features by using Gray-Level Co-occurrence Metrics (GLCM) and AlexNet transferrable learning model. Once extracting the different GLCM features and AlexNet deep features, horizontal concatenation was done to fuse the different feature sets. Similarly, for acoustic feature extraction, the audio samples (from the input video) were processed for static (fixed size) sampling, pre-emphasis, block framing and Hann windowing, followed by acoustic feature extraction like GTCC, GTCC-Delta, GTCC-Delta-Delta, MFCC, Spectral Entropy, Spectral Flux, Spectral Slope and Harmonics to Noise Ratio (HNR). Finally, the extracted audio-visual features were fused to yield a composite multi-modal feature set, which is processed for classification using the random forest ensemble classifier. The multi-class classification yields a crowd-classification accurac12529y of (98.26%), precision (98.89%), sensitivity (94.82%), specificity (95.57%), and F-Measure of 98.84%. The robustness of the proposed multi-modality-based crowd analysis model confirms its suitability towards real-world crowd detection and classification tasks

    An investigation of entorhinal spatial representations in self-localisation behaviours

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    Spatial-modulated cells of the medial entorhinal cortex (MEC) and neighbouring cortices are thought to provide the neural substrate for self-localisation behaviours. These cells include grid cells of the MEC which are thought to compute path integration operations to update self-location estimates. In order to read this grid code, downstream cells are thought to reconstruct a positional estimate as a simple rate-coded representation of space. Here, I show the coding scheme of grid cell and putative readout cells recorded from mice performing a virtual reality (VR) linear location task which engaged mice in both beaconing and path integration behaviours. I found grid cells can encode two unique coding schemes on the linear track, namely a position code which reflects periodic grid fields anchored to salient features of the track and a distance code which reflects periodic grid fields without this anchoring. Grid cells were found to switch between these coding schemes within sessions. When grid cells were encoding position, mice performed better at trials that required path integration but not on trials that required beaconing. This result provides the first mechanistic evidence linking grid cell activity to path integration-dependent behaviour. Putative readout cells were found in the form of ramp cells which fire proportionally as a function of location in defined regions of the linear track. This ramping activity was found to be primarily explained by track position rather than other kinematic variables like speed and acceleration. These representations were found to be maintained across both trial types and outcomes indicating they likely result from recall of the track structure. Together, these results support the functional importance of grid and ramp cells for self-localisation behaviours. Future investigations will look into the coherence between these two neural populations, which may together form a complete neural system for coding and decoding self-location in the brain

    Novel 129Xe Magnetic Resonance Imaging and Spectroscopy Measurements of Pulmonary Gas-Exchange

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    Gas-exchange is the primary function of the lungs and involves removing carbon dioxide from the body and exchanging it within the alveoli for inhaled oxygen. Several different pulmonary, cardiac and cardiovascular abnormalities have negative effects on pulmonary gas-exchange. Unfortunately, clinical tests do not always pinpoint the problem; sensitive and specific measurements are needed to probe the individual components participating in gas-exchange for a better understanding of pathophysiology, disease progression and response to therapy. In vivo Xenon-129 gas-exchange magnetic resonance imaging (129Xe gas-exchange MRI) has the potential to overcome these challenges. When participants inhale hyperpolarized 129Xe gas, it has different MR spectral properties as a gas, as it diffuses through the alveolar membrane and as it binds to red-blood-cells. 129Xe MR spectroscopy and imaging provides a way to tease out the different anatomic components of gas-exchange simultaneously and provides spatial information about where abnormalities may occur. In this thesis, I developed and applied 129Xe MR spectroscopy and imaging to measure gas-exchange in the lungs alongside other clinical and imaging measurements. I measured 129Xe gas-exchange in asymptomatic congenital heart disease and in prospective, controlled studies of long-COVID. I also developed mathematical tools to model 129Xe MR signals during acquisition and reconstruction. The insights gained from my work underscore the potential for 129Xe gas-exchange MRI biomarkers towards a better understanding of cardiopulmonary disease. My work also provides a way to generate a deeper imaging and physiologic understanding of gas-exchange in vivo in healthy participants and patients with chronic lung and heart disease

    ABC: Adaptive, Biomimetic, Configurable Robots for Smart Farms - From Cereal Phenotyping to Soft Fruit Harvesting

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    Currently, numerous factors, such as demographics, migration patterns, and economics, are leading to the critical labour shortage in low-skilled and physically demanding parts of agriculture. Thus, robotics can be developed for the agricultural sector to address these shortages. This study aims to develop an adaptive, biomimetic, and configurable modular robotics architecture that can be applied to multiple tasks (e.g., phenotyping, cutting, and picking), various crop varieties (e.g., wheat, strawberry, and tomato) and growing conditions. These robotic solutions cover the entire perception–action–decision-making loop targeting the phenotyping of cereals and harvesting fruits in a natural environment. The primary contributions of this thesis are as follows. a) A high-throughput method for imaging field-grown wheat in three dimensions, along with an accompanying unsupervised measuring method for obtaining individual wheat spike data are presented. The unsupervised method analyses the 3D point cloud of each trial plot, containing hundreds of wheat spikes, and calculates the average size of the wheat spike and total spike volume per plot. Experimental results reveal that the proposed algorithm can effectively identify spikes from wheat crops and individual spikes. b) Unlike cereal, soft fruit is typically harvested by manual selection and picking. To enable robotic harvesting, the initial perception system uses conditional generative adversarial networks to identify ripe fruits using synthetic data. To determine whether the strawberry is surrounded by obstacles, a cluster complexity-based perception system is further developed to classify the harvesting complexity of ripe strawberries. c) Once the harvest-ready fruit is localised using point cloud data generated by a stereo camera, the platform’s action system can coordinate the arm to reach/cut the stem using the passive motion paradigm framework, as inspired by studies on neural control of movement in the brain. Results from field trials for strawberry detection, reaching/cutting the stem of the fruit with a mean error of less than 3 mm, and extension to analysing complex canopy structures/bimanual coordination (searching/picking) are presented. Although this thesis focuses on strawberry harvesting, ongoing research is heading toward adapting the architecture to other crops. The agricultural food industry remains a labour-intensive sector with a low margin, and cost- and time-efficiency business model. The concepts presented herein can serve as a reference for future agricultural robots that are adaptive, biomimetic, and configurable

    Complexity Science in Human Change

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    This reprint encompasses fourteen contributions that offer avenues towards a better understanding of complex systems in human behavior. The phenomena studied here are generally pattern formation processes that originate in social interaction and psychotherapy. Several accounts are also given of the coordination in body movements and in physiological, neuronal and linguistic processes. A common denominator of such pattern formation is that complexity and entropy of the respective systems become reduced spontaneously, which is the hallmark of self-organization. The various methodological approaches of how to model such processes are presented in some detail. Results from the various methods are systematically compared and discussed. Among these approaches are algorithms for the quantification of synchrony by cross-correlational statistics, surrogate control procedures, recurrence mapping and network models.This volume offers an informative and sophisticated resource for scholars of human change, and as well for students at advanced levels, from graduate to post-doctoral. The reprint is multidisciplinary in nature, binding together the fields of medicine, psychology, physics, and neuroscience

    Economic and Social Consequences of the COVID-19 Pandemic in Energy Sector

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    The purpose of the Special Issue was to collect the results of research and experience on the consequences of the COVID-19 pandemic for the energy sector and the energy market, broadly understood, that were visible after a year. In particular, the impact of COVID-19 on the energy sector in the EU, including Poland, and the US was examined. The topics concerned various issues, e.g., the situation of energy companies, including those listed on the stock exchange, mining companies, and those dealing with renewable energy. The topics related to the development of electromobility, managerial competences, energy expenditure of local government units, sustainable development of energy, and energy poverty during a pandemic were also discussed

    Prompt-Guided Zero-Shot Anomaly Action Recognition using Pretrained Deep Skeleton Features

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    This study investigates unsupervised anomaly action recognition, which identifies video-level abnormal-human-behavior events in an unsupervised manner without abnormal samples, and simultaneously addresses three limitations in the conventional skeleton-based approaches: target domain-dependent DNN training, robustness against skeleton errors, and a lack of normal samples. We present a unified, user prompt-guided zero-shot learning framework using a target domain-independent skeleton feature extractor, which is pretrained on a large-scale action recognition dataset. Particularly, during the training phase using normal samples, the method models the distribution of skeleton features of the normal actions while freezing the weights of the DNNs and estimates the anomaly score using this distribution in the inference phase. Additionally, to increase robustness against skeleton errors, we introduce a DNN architecture inspired by a point cloud deep learning paradigm, which sparsely propagates the features between joints. Furthermore, to prevent the unobserved normal actions from being misidentified as abnormal actions, we incorporate a similarity score between the user prompt embeddings and skeleton features aligned in the common space into the anomaly score, which indirectly supplements normal actions. On two publicly available datasets, we conduct experiments to test the effectiveness of the proposed method with respect to abovementioned limitations.Comment: CVPR 202

    On the role and opportunities in teamwork design for advanced multi-robot search systems

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    Intelligent robotic systems are becoming ever more present in our lives across a multitude of domains such as industry, transportation, agriculture, security, healthcare and even education. Such systems enable humans to focus on the interesting and sophisticated tasks while robots accomplish tasks that are either too tedious, routine or potentially dangerous for humans to do. Recent advances in perception technologies and accompanying hardware, mainly attributed to rapid advancements in the deep-learning ecosystem, enable the deployment of robotic systems equipped with onboard sensors as well as the computational power to perform autonomous reasoning and decision making online. While there has been significant progress in expanding the capabilities of single and multi-robot systems during the last decades across a multitude of domains and applications, there are still many promising areas for research that can advance the state of cooperative searching systems that employ multiple robots. In this article, several prospective avenues of research in teamwork cooperation with considerable potential for advancement of multi-robot search systems will be visited and discussed. In previous works we have shown that multi-agent search tasks can greatly benefit from intelligent cooperation between team members and can achieve performance close to the theoretical optimum. The techniques applied can be used in a variety of domains including planning against adversarial opponents, control of forest fires and coordinating search-and-rescue missions. The state-of-the-art on methods of multi-robot search across several selected domains of application is explained, highlighting the pros and cons of each method, providing an up-to-date view on the current state of the domains and their future challenges

    WearPut : Designing Dexterous Wearable Input based on the Characteristics of Human Finger Motions

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    Department of Biomedical Engineering (Human Factors Engineering)Powerful microchips for computing and networking allow a wide range of wearable devices to be miniaturized with high fidelity and availability. In particular, the commercially successful smartwatches placed on the wrist drive market growth by sharing the role of smartphones and health management. The emerging Head Mounted Displays (HMDs) for Augmented Reality (AR) and Virtual Reality (VR) also impact various application areas in video games, education, simulation, and productivity tools. However, these powerful wearables have challenges in interaction with the inevitably limited space for input and output due to the specialized form factors for fitting the body parts. To complement the constrained interaction experience, many wearable devices still rely on other large form factor devices (e.g., smartphones or hand-held controllers). Despite their usefulness, the additional devices for interaction can constrain the viability of wearable devices in many usage scenarios by tethering users' hands to the physical devices. This thesis argues that developing novel Human-Computer interaction techniques for the specialized wearable form factors is vital for wearables to be reliable standalone products. This thesis seeks to address the issue of constrained interaction experience with novel interaction techniques by exploring finger motions during input for the specialized form factors of wearable devices. The several characteristics of the finger input motions are promising to enable increases in the expressiveness of input on the physically limited input space of wearable devices. First, the input techniques with fingers are prevalent on many large form factor devices (e.g., touchscreen or physical keyboard) due to fast and accurate performance and high familiarity. Second, many commercial wearable products provide built-in sensors (e.g., touchscreen or hand tracking system) to detect finger motions. This enables the implementation of novel interaction systems without any additional sensors or devices. Third, the specialized form factors of wearable devices can create unique input contexts while the fingers approach their locations, shapes, and components. Finally, the dexterity of fingers with a distinctive appearance, high degrees of freedom, and high sensitivity of joint angle perception have the potential to widen the range of input available with various movement features on the surface and in the air. Accordingly, the general claim of this thesis is that understanding how users move their fingers during input will enable increases in the expressiveness of the interaction techniques we can create for resource-limited wearable devices. This thesis demonstrates the general claim by providing evidence in various wearable scenarios with smartwatches and HMDs. First, this thesis explored the comfort range of static and dynamic touch input with angles on the touchscreen of smartwatches. The results showed the specific comfort ranges on variations in fingers, finger regions, and poses due to the unique input context that the touching hand approaches a small and fixed touchscreen with a limited range of angles. Then, finger region-aware systems that recognize the flat and side of the finger were constructed based on the contact areas on the touchscreen to enhance the expressiveness of angle-based touch input. In the second scenario, this thesis revealed distinctive touch profiles of different fingers caused by the unique input context for the touchscreen of smartwatches. The results led to the implementation of finger identification systems for distinguishing two or three fingers. Two virtual keyboards with 12 and 16 keys showed the feasibility of touch-based finger identification that enables increases in the expressiveness of touch input techniques. In addition, this thesis supports the general claim with a range of wearable scenarios by exploring the finger input motions in the air. In the third scenario, this thesis investigated the motions of in-air finger stroking during unconstrained in-air typing for HMDs. The results of the observation study revealed details of in-air finger motions during fast sequential input, such as strategies, kinematics, correlated movements, inter-fingerstroke relationship, and individual in-air keys. The in-depth analysis led to a practical guideline for developing robust in-air typing systems with finger stroking. Lastly, this thesis examined the viable locations of in-air thumb touch input to the virtual targets above the palm. It was confirmed that fast and accurate sequential thumb touch can be achieved at a total of 8 key locations with the built-in hand tracking system in a commercial HMD. Final typing studies with a novel in-air thumb typing system verified increases in the expressiveness of virtual target selection on HMDs. This thesis argues that the objective and subjective results and novel interaction techniques in various wearable scenarios support the general claim that understanding how users move their fingers during input will enable increases in the expressiveness of the interaction techniques we can create for resource-limited wearable devices. Finally, this thesis concludes with thesis contributions, design considerations, and the scope of future research works, for future researchers and developers to implement robust finger-based interaction systems on various types of wearable devices.ope
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