11 research outputs found

    Decision support continuum paradigm for cardiovascular disease: Towards personalized predictive models

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    Clinical decision making is a ubiquitous and frequent task physicians make in their daily clinical practice. Conventionally, physicians adopt a cognitive predictive modelling process (i.e. knowledge and experience learnt from past lecture, research, literature, patients, etc.) for anticipating or ascertaining clinical problems based on clinical risk factors that they deemed to be most salient. However, with the inundation of health data and the confounding characteristics of diseases, more effective clinical prediction approaches are required to address these challenges. Approximately a few century ago, the first major transformation of medical practice took place as science-based approaches emerged with compelling results. Now, in the 21st century, new advances in science will once again transform healthcare. Data science has been postulated as an important component in this healthcare reform and has received escalating interests for its potential for ‘personalizing’ medicine. The key advantages of having personalized medicine include, but not limited to, (1) more effective methods for disease prevention, management and treatment, (2) improved accuracy for clinical diagnosis and prognosis, (3) provide patient-oriented personal health plan, and (4) cost containment. In view of the paramount importance of personalized predictive models, this thesis proposes 2 novel learning algorithms (i.e. an immune-inspired algorithm called the Evolutionary Data-Conscious Artificial Immune Recognition System, and a neural-inspired algorithm called the Artificial Neural Cell System for classification) and 3 continuum-based paradigms (i.e. biological, time and age continuum) for enhancing clinical prediction. Cardiovascular disease has been selected as the disease under investigation as it is an epidemic and major health concern in today’s world. We believe that our work has a meaningful and significant impact to the development of future healthcare system and we look forward to the wide adoption of advanced medical technologies by all care centres in the near future.Open Acces

    Situating Data

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    Taking up the challenges of the datafication of culture, as well as of the scholarship of cultural inquiry itself, this collection contributes to the critical debate about data and algorithms. How can we understand the quality and significance of current socio-technical transformations that result from datafication and algorithmization? How can we explore the changing conditions and contours for living within such new and changing frameworks? How can, or should we, think and act within, but also in response to these conditions? This collection brings together various perspectives on the datafication and algorithmization of culture from debates and disciplines within the field of cultural inquiry, specifically (new) media studies, game studies, urban studies, screen studies, and gender and postcolonial studies. It proposes conceptual and methodological directions for exploring where, when, and how data and algorithms (re)shape cultural practices, create (in)justice, and (co)produce knowledge

    Characterising the Multi-Scale Properties of Flocculated Sediment by X-ray and Focused Ion Beam Nano-Tomography

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    PhDThe hydrodynamic behaviour of fine suspended aqueous sediments, and stability of the bedforms they create once settled, are governed by the physical properties (e.g., size, shape, porosity and density) of the flocculated particles in suspension (flocs). Consequently, accurate prediction of the transport and fate of sediments and of the nutrients and pollutants they carry depends on our ability to characterise aqueous flocs. Current research primarily focuses on characterising flocs based on their external gross-scale (>1 μm) properties (e.g., gross morphology, size and settling velocity) using in situ techniques such as photography and videography. Whilst these techniques provide valuable information regarding the outward behaviour of flocculated sediment (i.e. transport and settling), difficulties associated with extracting 3D geometries from 2D projections raises concerns regarding their accuracy and key parameters such as density can only be estimated. In addition, they neglect to inform on the internal micro- and nano-scale structure of flocs, responsible for much of their behaviour and development. Transmission electron microscope (TEM) and environmental electron microscope may be used to obtain nano-scale information in, essentially, 2D but there is a large scale gap between this information and the macro-scale of optical techniques. To address this issue this study uses 3D tomographic imaging over a range of spatial scales. Whilst commonly used in materials science and the life sciences, correlative tomography has yet to be applied in the environmental sciences. Threading together 3D Xray micro-computed tomography (X-ray μCT) and focused ion beam nano-tomography (FIBnt) with 2D TEM makes material characterisation from the centimetre to nanometre-scale possible. Here, this correlative imaging strategy is combined with a non-destructive stabilisation procedure and applied to the investigation of flocculated estuarine sediment, enabling the multi length-scale properties of flocs to be accurately described for the first time. This work has demonstrated that delicate aqueous flocs can be successfully stabilised via a resin embedding process and contrasted for both electron microscopy and X-ray tomography imaging. The 3D information obtained can be correlated across all length-scales from nm to mm revealing new information about the structure and morphology of flocs. A new system of characterising floc structure can be defined based on the association of particles and their stability in the structure rather than simply their size. This new model refutes the postulate that floc structures are fractal in nature.Engineering and Physical Sciences Research Council (EPSRC) Queen Mary University London (through the Post Graduate Research Fund) Environment Canad

    In silico molecular modelling and design of heme-containing peroxidases for industrial applications

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    It is widely known that the development of modern chemistry and the consequent world industrialization have improved our quality of life to unimaginable levels. However, these advances have come with a high cost, causing environmental, health and societal concerns. As a consequence, during the past two decades a growing need has appeared to update the traditional chemistry industry processes towards greener and efficient alternatives. Along these lines, the use of enzymes has shown to be a suitable alternative to conventional industrial chemical processes. Enzymes are life-essential proteins that catalyze biochemical reaction and show several advantages over conventional chemical catalysts: they work under milder conditions, which decrease the energy requirements and consequently the capital costs of reactions; They show a high degree of selectivity and catalytic efficiency; and in addition, they are inherently non-hazardous, reusable and biodegradable catalysts, making them ideal environmentally friendly reagents. However, the main bottleneck for taking more benefit of enzymes in an industrial context is the lack of biocatalysts with the required selectivity, availability, and compatibility with industrial rigorous process conditions, and because of this, the development of enhanced enzymes by means of enzyme engineering is a main research field nowadays. Along these lines, in silico methodologies have progressively turned into highly valuable tools for the study and design of enzymatic systems, due to their unique potential to offer atomic and electronic-level insights into biocatalysts’ activity. Moreover, the continuous software and hardware improvements, and the cost-effectiveness and rapidness generally associated with these methods, make them very appealing for their application to the real problems that face the industry. Motivated by the advances on computational techniques and by the ease of obtaining valuable experimental data, which has been provided by our collaborators, the main goal of this thesis has been to understand the mechanisms of reaction of the heme-containing peroxidases under study (Auricularia auricula-judae DyP and Agrocybe aegerita UPO). Moreover, the acquired knowledge has been used to evaluate experimentally obtained enzyme variants and to guide the design of new ones towards desired properties. In this way, distinct computational techniques at different levels of accuracy (e.g. PELE, QM/MM or MD calculations) have been used to unravel the atomic and electronic mechanistic details under peroxidases mechanisms (e.g. long range electron transfer pathways, peroxidation and peroxygenation mechanisms) and to rationalize the molecular determinants that guide yield and selectivity in both natural occurring and experimentally designed peroxidases. Furthermore, the better understanding of the molecular principles under enzyme activity, along with the use of in silico semi-rational redesign methods, has enabled us to tailor UPO enzyme towards the enhanced production of high-value chemicals.A causa del desenvolupament de la química moderna i de la consegüent industrialització del món, la nostra qualitat de vida ha millorat a uns nivells que creiem inimaginables. Malauradament, tots aquests avenços han vingut acompanyats de repercussions mediambientals, socials i de salut. Per això, en les dues últimes dècades s'ha percebut una creixent necessitat de reemplaçar els processos químics tradicionals per alternatives més ecològiques i eficients. En aquest sentit, els enzims han demostrat ser una alternativa molt plausible als processos químics convencionals que s'usen avui en dia en la indústria. Els enzims són proteïnes essencials per a la vida que catalitzen reaccions bioquímiques, i l'ús dels quals aporta múltiples avantatges en comparació a les tècniques convencionals: permeten treballar en condicions suaus, fet que disminueix els requisits energètics i conseqüentment els costos de les reaccions a nivells industrials; en general són molt selectius i eficients; i a més a més, són inherentment reutilitzables, segurs i biodegradables, fet que els converteix en reactius respectuosos amb el medi ambient. Tot i això, les seves aplicacions a nivells industrials encara són limitades degut a la baixa tolerància a substrats, la poca disponibilitat d'enzims i a l'escassa resistència a les severes condicions industrials. Per aquesta raó, avui en dia el desenvolupament d'enzims millorats és un camp d'investigació important. Particularment, les tècniques in silico de modelització molecular s'estan convertint cada vegada més en eines clau per a l'estudi i el disseny de biocatalitzadors degut al seu potencial per a obtenir informació, tant a escala electrònica com molecular, sobre els mecanismes d'acció enzimàtics. A més a més, millores en el software i el hardware, i la rapidesa i bona relació cost-qualitat que mostren aquests mètodes, els fan molt atractius per a resoldre els problemes reals de la indústria. Motivada pels avenços en les tècniques computacionals i per la facilitat d'obtenir dades experimentals, que han estat proporcionades pels nostres col·laboradors, l'objectiu principal d'aquesta tesi ha sigut entendre els mecanismes de reacció de les peroxidases (en particular la DyP del fong Auricularia aurícula-judae i la UPO del fong Agrocybe aegerita). D'altra banda, els coneixements adquirits durant aquest procés de racionalització s'han utilitzat per avaluar variants millorats d'enzims obtinguts experimentalment i per guiar el disseny de nous biocatalitzadors cap a les propietats desitjades. Així doncs, s'han utilitzat diferents tècniques computacionals, a diferents nivells de precisió (p. ex. PELE, QM/MM o MD), per tal de comprendre els mecanismes electrònics i moleculars responsables de diferents mecanismes en les peroxidases (p. ex., mecanismes de transferència electrònica de llarg abast, peroxidació o peroxigenació), i racionalitzar els determinants moleculars que guien el rendiment i la selectivitat tant en les peroxidases naturals com en aquelles millorades experimentalment. A banda d'això, la millor comprensió dels principis moleculars responsables de l'activitat enzimàtica, juntament amb l'ús de mètodes computacionals per al disseny d'enzims, ens ha permès adaptar l'enzim UPO cap a la producció de productes químics valuosos

    In silico molecular modelling and design of heme-containing peroxidases for industrial applications

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    [eng] It is widely known that the development of modern chemistry and the consequent world industrialization have improved our quality of life to unimaginable levels. However, these advances have come with a high cost, causing environmental, health and societal concerns. As a consequence, during the past two decades a growing need has appeared to update the traditional chemistry industry processes towards greener and efficient alternatives. Along these lines, the use of enzymes has shown to be a suitable alternative to conventional industrial chemical processes. Enzymes are life-essential proteins that catalyze biochemical reaction and show several advantages over conventional chemical catalysts: they work under milder conditions, which decrease the energy requirements and consequently the capital costs of reactions; They show a high degree of selectivity and catalytic efficiency; and in addition, they are inherently non-hazardous, reusable and biodegradable catalysts, making them ideal environmentally friendly reagents. However, the main bottleneck for taking more benefit of enzymes in an industrial context is the lack of biocatalysts with the required selectivity, availability, and compatibility with industrial rigorous process conditions, and because of this, the development of enhanced enzymes by means of enzyme engineering is a main research field nowadays. Along these lines, in silico methodologies have progressively turned into highly valuable tools for the study and design of enzymatic systems, due to their unique potential to offer atomic and electronic-level insights into biocatalysts’ activity. Moreover, the continuous software and hardware improvements, and the cost-effectiveness and rapidness generally associated with these methods, make them very appealing for their application to the real problems that face the industry. Motivated by the advances on computational techniques and by the ease of obtaining valuable experimental data, which has been provided by our collaborators, the main goal of this thesis has been to understand the mechanisms of reaction of the heme-containing peroxidases under study (Auricularia auricula-judae DyP and Agrocybe aegerita UPO). Moreover, the acquired knowledge has been used to evaluate experimentally obtained enzyme variants and to guide the design of new ones towards desired properties. In this way, distinct computational techniques at different levels of accuracy (e.g. PELE, QM/MM or MD calculations) have been used to unravel the atomic and electronic mechanistic details under peroxidases mechanisms (e.g. long range electron transfer pathways, peroxidation and peroxygenation mechanisms) and to rationalize the molecular determinants that guide yield and selectivity in both natural occurring and experimentally designed peroxidases. Furthermore, the better understanding of the molecular principles under enzyme activity, along with the use of in silico semi-rational redesign methods, has enabled us to tailor UPO enzyme towards the enhanced production of high-value chemicals.[cat] A causa del desenvolupament de la química moderna i de la consegüent industrialització del món, la nostra qualitat de vida ha millorat a uns nivells que creiem inimaginables. Malauradament, tots aquests avenços han vingut acompanyats de repercussions mediambientals, socials i de salut. Per això, en les dues últimes dècades s'ha percebut una creixent necessitat de reemplaçar els processos químics tradicionals per alternatives més ecològiques i eficients. En aquest sentit, els enzims han demostrat ser una alternativa molt plausible als processos químics convencionals que s'usen avui en dia en la indústria. Els enzims són proteïnes essencials per a la vida que catalitzen reaccions bioquímiques, i l'ús dels quals aporta múltiples avantatges en comparació a les tècniques convencionals: permeten treballar en condicions suaus, fet que disminueix els requisits energètics i conseqüentment els costos de les reaccions a nivells industrials; en general són molt selectius i eficients; i a més a més, són inherentment reutilitzables, segurs i biodegradables, fet que els converteix en reactius respectuosos amb el medi ambient. Tot i això, les seves aplicacions a nivells industrials encara són limitades degut a la baixa tolerància a substrats, la poca disponibilitat d'enzims i a l'escassa resistència a les severes condicions industrials. Per aquesta raó, avui en dia el desenvolupament d'enzims millorats és un camp d'investigació important. Particularment, les tècniques in silico de modelització molecular s'estan convertint cada vegada més en eines clau per a l'estudi i el disseny de biocatalitzadors degut al seu potencial per a obtenir informació, tant a escala electrònica com molecular, sobre els mecanismes d'acció enzimàtics. A més a més, millores en el software i el hardware, i la rapidesa i bona relació cost-qualitat que mostren aquests mètodes, els fan molt atractius per a resoldre els problemes reals de la indústria. Motivada pels avenços en les tècniques computacionals i per la facilitat d'obtenir dades experimentals, que han estat proporcionades pels nostres col·laboradors, l'objectiu principal d'aquesta tesi ha sigut entendre els mecanismes de reacció de les peroxidases (en particular la DyP del fong Auricularia aurícula-judae i la UPO del fong Agrocybe aegerita). D'altra banda, els coneixements adquirits durant aquest procés de racionalització s'han utilitzat per avaluar variants millorats d'enzims obtinguts experimentalment i per guiar el disseny de nous biocatalitzadors cap a les propietats desitjades. Així doncs, s'han utilitzat diferents tècniques computacionals, a diferents nivells de precisió (p. ex. PELE, QM/MM o MD), per tal de comprendre els mecanismes electrònics i moleculars responsables de diferents mecanismes en les peroxidases (p. ex., mecanismes de transferència electrònica de llarg abast, peroxidació o peroxigenació), i racionalitzar els determinants moleculars que guien el rendiment i la selectivitat tant en les peroxidases naturals com en aquelles millorades experimentalment. A banda d'això, la millor comprensió dels principis moleculars responsables de l'activitat enzimàtica, juntament amb l'ús de mètodes computacionals per al disseny d'enzims, ens ha permès adaptar l'enzim UPO cap a la producció de productes químics valuosos

    An Artificial DNA for Self-Descripting and Self-Building Embedded Real-Time Systems

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    Situating Data: Inquiries in Algorithmic Culture

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    Taking up the challenges of the datafication of culture, as well as of the scholarship of cultural inquiry itself, this collection contributes to the critical debate about data and algorithms. How can we understand the quality and significance of current socio-technical transformations that result from datafication and algorithmization? How can we explore the changing conditions and contours for living within such new and changing frameworks? How can, or should we, think and act within, but also in response to these conditions? This collection brings together various perspectives on the datafication and algorithmization of culture from debates and disciplines within the field of cultural inquiry, specifically (new) media studies, game studies, urban studies, screen studies, and gender and postcolonial studies. It proposes conceptual and methodological directions for exploring where, when, and how data and algorithms (re)shape cultural practices, create (in)justice, and (co)produce knowledge

    Photonic application of proteins

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    The currently faced biggest challenge in integrated optics (IO) is finding or developing materials that can be used as active components for optical circuits. In order for a material to be considered for IO applications, it has to possess optimal non-linear optical (NLO) properties, such as a large light-induced refractive index change, but also mechanical stability. In my thesis, I investigated the photoactive yellow protein (PYP) with various experimental methods to assess the protein’s IO applicability. During the measurements, a glycerol-doped (GL) PYP film was used to maintain high mechanical stability and optical homogeneity of the investigated PYP-films. First, the kinetics of certain photocycle intermediates of PYP were monitored with absorption kinetics measurements to find the optimal environment to use the protein films in. This was followed by measuring the linear and non-linear refractive index of GL-PYP films. The NLO refractive index was investigated with the Z-scan technique as a function of excitation laser pulse parameters, i.e., average and peak intensities, and repetition rate of the pulses. For investigating the potential miniaturization and the possibility of creating homogeneous protein monolayers for further IO applications, PYP films were monitored with vibrational sum-frequency spectroscopy (VSFG). Finally, IO switching was demonstrated utilizing different photocycle intermediates. Mach- Zehnder interferometer was used for slow, while transient grating spectroscopy was applied to perform sub-ps optical switching. Based on the results, GL-PYP films are viable alternatives as IO active materials
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