238 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

    Views from a peak:Generalisations and descriptive set theory

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    This dissertation has two major threads, one is mathematical, namely descriptive set theory, the other is philosophical, namely generalisation in mathematics. Descriptive set theory is the study of the behaviour of definable subsets of a given structure such as the real numbers. In the core mathematical chapters, we provide mathematical results connecting descriptive set theory and generalised descriptive set theory. Using these, we give a philosophical account of the motivations for, and the nature of, generalisation in mathematics.In Chapter 3, we stratify set theories based on this descriptive complexity. The axiom of countable choice for reals is one of the most basic fragments of the axiom of choice needed in many parts of mathematics. Descriptive choice principles are a further stratification of this fragment by the descriptive complexity of the sets. We provide a separation technique for descriptive choice principles based on Jensen forcing. Our results generalise a theorem by Kanovei.Chapter 4 gives the essentials of a generalised real analysis, that is a real analysis on generalisations of the real numbers to higher infinities. This builds on work by Galeotti and his coauthors. We generalise classical theorems of real analysis to certain sets of functions, strengthening continuity, and disprove other classical theorems. We also show that a certain cardinal property, the tree property, is equivalent to the Extreme Value Theorem for a set of functions which generalize the continuous functions.The question of Chapter 5 is whether a robust notion of infinite sums can be developed on generalisations of the real numbers to higher infinities. We state some incompatibility results, which suggest not. We analyse several candidate notions of infinite sum, both from the literature and more novel, and show which of the expected properties of a notion of sum they fail.In Chapter 6, we study the descriptive set theory arising from a generalization of topology, Îș-topology, which is used in the previous two chapters. We show that the theory is quite different from that of the standard (full) topology. Differences include a collapsing Borel hierarchy, a lack of universal or complete sets, Lebesgue’s ‘great mistake’ holds (projections do not increase complexity), a strict hierarchy of notions of analyticity, and a failure of Suslin’s theorem.Lastly, in Chapter 7, we give a philosophical account of the nature of generalisation in mathematics, and describe the methodological reasons that mathematicians generalise. In so doing, we distinguish generalisation from other processes of change in mathematics, such as abstraction and domain expansion. We suggest a semantic account of generalisation, where two pieces of mathematics constitute a generalisation if they have a certain relation of content, along with an increased level of generality

    Single-cell analysis of cell competition using quantitative microscopy and machine learning

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    Cell competition is a widely conserved, fundamental biological quality control mechanism. The cell competition assay of MDCK wild-type versus mutant MDCK Scribble-knockdown (ScribKD) relies on a mechanical mechanism of competition, which posits that the emergence of compressing stresses within the tissue at high confluency drive the competitive outcome. According to this mechanism, proliferating wild-type cells out-compete mutant ScribKD cells, resulting in their apoptosis and apical extrusion. Previous studies show that there is an increased division rate of wild-type cells in neighbourhoods with high numbers of ScribKD cells, but what still remains a mystery is whether this is a cause or consequence of increased apoptosis in the “loser” cell population. This project also interrogated the competitive assay of wild-type versus RasV12 , which is hypothesized to operate on a biochemical mechanism and results in the apical extrusion (but not apoptosis) of the loser RasV12 population. For both these mechanisms of competition it is still unknown which population of cells are driving the winner/loser outcome. Is the winner cell proliferation prompting the loser cell demise? Or is an autonomous loser elimination prompting a subsequent winner cell proliferation? In my research, I have employed multi-modal, time-lapse microscopy to image competition assays continuously for several days. These data were then segmented into wild-type or mutant instances using a Convolutional Neural Network (CNN) that can differentiate between the cell types, after which they were tracked across cellular generations using a Bayesian multi-object tracker. A conjugate analysis of fluorescent cell-cycle indicator probes was then utilised to automatically identify key time points of cellular fate commitment using deep-learning image classification. A spatio-temporal analysis was then conducted in order to quantify any correlation between wild-type proliferation and mutant cell demise. For the case of wild-type versus ScribKD , there was no clear evidence for the wild-type cells mitoses directly impacting upon the ScribKD cell apoptotic elimination. Instead, a subsequent analysis found that a more subtle mechanism of pre-emptive, local density increases around the apoptosis site appeared to be determining the eventual ScribKD fate. On the other hand, there was clear evidence of a direct impact of wild-type mitoses on the subsequent apical extrusion and competitive elimination of RasV12 cells. Both of these conclusions agree with the prevailing classification of cell competition types: mechanical interactions are more diffuse and occur over a larger spatio-temporal domain, whereas biochemical interactions are constrained to nearest neighbour cells. The hypothesized density-dependency of ScribKD elimination was further quantified on a single-cell scale by these analyses, as well as a potential new understanding of RasV12 extrusion. Most interestingly, it appears that there is a clear biophysical mechanism to the elimination in the biochemical RasV12 cell competition. This suggests that perhaps a new semantic approach is needed in the field of cell competition in order to accurately classify different mechanisms of elimination

    General Course Catalog [2022/23 academic year]

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    General Course Catalog, 2022/23 academic yearhttps://repository.stcloudstate.edu/undergencat/1134/thumbnail.jp

    Machine learning of molecular motifs in soft supramolecular systems

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    L'abstract è presente nell'allegato / the abstract is in the attachmen

    WiFi-Based Human Activity Recognition Using Attention-Based BiLSTM

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    Recently, significant efforts have been made to explore human activity recognition (HAR) techniques that use information gathered by existing indoor wireless infrastructures through WiFi signals without demanding the monitored subject to carry a dedicated device. The key intuition is that different activities introduce different multi-paths in WiFi signals and generate different patterns in the time series of channel state information (CSI). In this paper, we propose and evaluate a full pipeline for a CSI-based human activity recognition framework for 12 activities in three different spatial environments using two deep learning models: ABiLSTM and CNN-ABiLSTM. Evaluation experiments have demonstrated that the proposed models outperform state-of-the-art models. Also, the experiments show that the proposed models can be applied to other environments with different configurations, albeit with some caveats. The proposed ABiLSTM model achieves an overall accuracy of 94.03%, 91.96%, and 92.59% across the 3 target environments. While the proposed CNN-ABiLSTM model reaches an accuracy of 98.54%, 94.25% and 95.09% across those same environments

    Teaching informatics to novices: big ideas and the necessity of optimal guidance

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    This thesis reports on the two main areas of our research: introductory programming as the traditional way of accessing informatics and cultural teaching informatics through unconventional pathways. The research on introductory programming aims to overcome challenges in traditional programming education, thus increasing participation in informatics. Improving access to informatics enables individuals to pursue more and better professional opportunities and contribute to informatics advancements. We aimed to balance active, student-centered activities and provide optimal support to novices at their level. Inspired by Productive Failure and exploring the concept of notional machine, our work focused on developing Necessity Learning Design, a design to help novices tackle new programming concepts. Using this design, we implemented a learning sequence to introduce arrays and evaluated it in a real high-school context. The subsequent chapters discuss our experiences teaching CS1 in a remote-only scenario during the COVID-19 pandemic and our collaborative effort with primary school teachers to develop a learning module for teaching iteration using a visual programming environment. The research on teaching informatics principles through unconventional pathways, such as cryptography, aims to introduce informatics to a broader audience, particularly younger individuals that are less technical and professional-oriented. It emphasizes the importance of understanding informatics's cultural and scientific aspects to focus on the informatics societal value and its principles for active citizenship. After reflecting on computational thinking and inspired by the big ideas of science and informatics, we describe our hands-on approach to teaching cryptography in high school, which leverages its key scientific elements to emphasize its social aspects. Additionally, we present an activity for teaching public-key cryptography using graphs to explore fundamental concepts and methods in informatics and mathematics and their interdisciplinarity. In broadening the understanding of informatics, these research initiatives also aim to foster motivation and prime for more professional learning of informatics

    Connected Coordinated Motion Planning with Bounded Stretch

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    We consider the problem of connected coordinated motion planning for a large collective of simple, identical robots: From a given start grid configuration of robots, we need to reach a desired target configuration via a sequence of parallel, collision-free robot motions, such that the set of robots induces a connected grid graph at all integer times. The objective is to minimize the makespan of the motion schedule, i.e., to reach the new configuration in a minimum amount of time. We show that this problem is NP-complete, even for deciding whether a makespan of 2 can be achieved, while it is possible to check in polynomial time whether a makespan of 1 can be achieved. On the algorithmic side, we establish simultaneous constant-factor approximation for two fundamental parameters, by achieving constant stretch for constant scale. Scaled shapes (which arise by increasing all dimensions of a given object by the same multiplicative factor) have been considered in previous seminal work on self-assembly, often with unbounded or logarithmic scale factors; we provide methods for a generalized scale factor, bounded by a constant. Moreover, our algorithm achieves a constant stretch factor: If mapping the start configuration to the target configuration requires a maximum Manhattan distance of dd, then the total duration of our overall schedule is O(d)\mathcal{O}(d), which is optimal up to constant factors.Comment: 28 pages, 18 figures, full version of an extended abstract that appeared in the proceedings of the 32nd International Symposium on Algorithms and Computation (ISAAC 2021); revised version (more details added, and typing errors corrected
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