Applications of CT Perfusion-Based Triaging and Prognostication in Acute Ischemic Stroke

CT Perfusion (CTP) is a minimally invasive imaging technique that aids acute ischemic stroke (AIS) triage and prognostication by determining tissue viability based on hemodynamic parameters. The goals of this research are to determine: 1) CTP thresholds for estimation of infarct and penumbra volume, 2) how CTP scan duration impacts infarct and penumbra volume estimates, and 3) reliability of CTP for predicting functional outcomes following intra-arterial therapy (IAT). Chapter 2 introduced an experimental study for determining ischemia-time dependent thresholds for brain infarction using multimodal imaging in a porcine stroke model that is easier to implement than previous large animal stroke models. CTP determined an absolute cerebral blood flow (CBF) threshold of 12.6±2.8mL∙min-1∙100g-1 for brain infarction after 3h of ischemia, which was close to that derived using hydrogen clearance in a previous study by Jones et al (Journal of Neurosurgery, 1981;54(6):773-782). Chapter 3 retrospectively investigated the impact of CTP scan duration on cerebral blood volume (CBV), CBF, and time-to-maximum (Tmax) and found optimal scan durations that minimized radiation dose while not under- or over-estimating infarct volumes measured using two previously derived CBF thresholds for infarction. We found that CBV and Tmax decreased at shorter scan durations, whereas CBF was independent of scan duration, consequently, infarct volume estimated by both CBF thresholds was independent of scan duration. Chapter 4 compared reperfusion seen on follow-up CTP to reperfusion predicted by post-IAT digital subtraction angiography (DSA) and the ability of the two modalities to predict good 90-day functional outcome in a retrospective study. We found that patients with ‘complete reperfusion’ grades on DSA often had ischemic tissue on follow-up CTP and that follow-up CTP had superior specificity and accuracy for predicting functional outcome compared to DSA. In summary, this research has shown that CBF thresholds can reliably detect infarct in AIS and are independent of scan duration, allowing radiation dose to be minimized by limiting scans to 40s without compromising accuracy of infarct volume estimates. Finally, CTP is a more specific and accurate predictor of functional outcome than the commonly used post-procedural DSA, this could help select patients for neuroprotective therapy

Basic Research Needs for Geosciences: Facilitating 21st Century Energy Systems

Executive Summary Serious challenges must be faced in this century as the world seeks to meet global energy needs and at the same time reduce emissions of greenhouse gases to the atmosphere. Even with a growing energy supply from alternative sources, fossil carbon resources will remain in heavy use and will generate large volumes of carbon dioxide (CO2). To reduce the atmospheric impact of this fossil energy use, it is necessary to capture and sequester a substantial fraction of the produced CO2. Subsurface geologic formations offer a potential location for long-term storage of the requisite large volumes of CO2. Nuclear energy resources could also reduce use of carbon-based fuels and CO2 generation, especially if nuclear energy capacity is greatly increased. Nuclear power generation results in spent nuclear fuel and other radioactive materials that also must be sequestered underground. Hence, regardless of technology choices, there will be major increases in the demand to store materials underground in large quantities, for long times, and with increasing efficiency and safety margins. Rock formations are composed of complex natural materials and were not designed by nature as storage vaults. If new energy technologies are to be developed in a timely fashion while ensuring public safety, fundamental improvements are needed in our understanding of how these rock formations will perform as storage systems. This report describes the scientific challenges associated with geologic sequestration of large volumes of carbon dioxide for hundreds of years, and also addresses the geoscientific aspects of safely storing nuclear waste materials for thousands to hundreds of thousands of years. The fundamental crosscutting challenge is to understand the properties and processes associated with complex and heterogeneous subsurface mineral assemblages comprising porous rock formations, and the equally complex fluids that may reside within and flow through those formations. The relevant physical and chemical interactions occur on spatial scales that range from those of atoms, molecules, and mineral surfaces, up to tens of kilometers, and time scales that range from picoseconds to millennia and longer. To predict with confidence the transport and fate of either CO2 or the various components of stored nuclear materials, we need to learn to better describe fundamental atomic, molecular, and biological processes, and to translate those microscale descriptions into macroscopic properties of materials and fluids. We also need fundamental advances in the ability to simulate multiscale systems as they are perturbed during sequestration activities and for very long times afterward, and to monitor those systems in real time with increasing spatial and temporal resolution. The ultimate objective is to predict accurately the performance of the subsurface fluid-rock storage systems, and to verify enough of the predicted performance with direct observations to build confidence that the systems will meet their design targets as well as environmental protection goals. The report summarizes the results and conclusions of a Workshop on Basic Research Needs for Geosciences held in February 2007. Five panels met, resulting in four Panel Reports, three Grand Challenges, six Priority Research Directions, and three Crosscutting Research Issues. The Grand Challenges differ from the Priority Research Directions in that the former describe broader, long-term objectives while the latter are more focused

Impacts of Feedstock Bark Addition and Centrifugal Filtration on Pyrolysis Oil Properties and Storage Stability

The physicochemical properties of pyrolysis oil have been shown to be dependent on feedstock composition. Accelerated aging tests were performed to understand the effects of feedstock, condensate fraction collected, and filtration on the stability of pyrolysis oil. In this study, pyrolysis oil properties critical for downstream upgrading were measured and compared for different feedstock weight ratios of pine clearwood and pine bark. Post-condensation filtration of pyrolysis oil was evaluated using both lab-scale and pilot plant-scale centrifugal filtration with several operational parameters evaluated. The pilot-plant centrifuge can be used as a three-phase separator [light liquid-heavy liquid-solids] or a two-phase clarifier [liquid-solid]. Since pyrolysis oil is an oil-water micro-emulsion, separation of the heavy and light liquid phases is difficult; therefore, emulsion destabilization studies were performed in concert with centrifugation. Physicochemical properties were monitored to determine the impact of the production and processing parameters on the oil properties critical to biofuel applications

The role of dynamic hydrogen bond networks in protonation coupled dynamics of retinal proteins

Hydrogen bonds (H-bonds) are an essential interaction in membrane proteins. Embedded in complex hydrated lipid bilayers, intramolecular interactions through the means of hydrogen bonding networks are often crucial for the function of the protein. Internal water molecules that occupy stable sites inside the protein, or water molecules that visit transiently from the bulk, can play an important role in shaping local conformational dynamics forming complex networks that bridge regions of the protein via water-mediated hydrogen bonds that can function as wires for the transferring of protons as a part of the protein’s function. For example, the membrane-embedded channelrhodopsins which are found in archaea are proteins that couple light induced isomerization of a retinal chromophore with proton transfer reactions and passive flow of cations through their pore. I contributed to the development of a new algorithm package that features a unique approach to H-bond analyses. I performed analyses of long Molecular Dynamics (MD) trajectories of channelrhodopsin variants embedded in hydrated lipid membranes and large data sets of static structures, to detect and dissect dynamic hydrogen-bond networks. The photocycle of channelrhodopsins begins with absorption and isomerization of the retinal from an all-trans state to a 13-cis state and followed by the deprotonation of the Schiff base. Thus, the retinal is found in the epicenter of the analyses. Through the use of 2-dimensional graphs of the protein H-bond networks I identified protein groups potentially important for the proton transfer activity. Local dynamics are highly affected by point mutations of amino acids important for function. The interior of channelrhodopsin C1C2 hosts extensive networks of protein and H-bonded-water molecules, and a never reported before, network that can bridge transiently the two retinal chromophores in channelrhodopsin dimers. In a recently identified inward proton pump, AntR, I applied centrality measures on MD trajectories of the homology model I generated, to assess the communication of the amino acid residues within the networks. I detected a frequently sampled long water chain that connects the retinal with a candidate proton acceptor, as well as a conserved serine in the vicinity of the retinal chromophore plays a significant role in the connectivity and communication of the H-bond networks upon isomerization. A similar water bridge is sampled in independent simulations of ChR2, where a participant for the proton donor group connects to the 13-cis,15-anti retinal. Proton transfer reactions often take place through certain amino acids, forming patterns. I analyzed H-bond patterns or motifs in large hand-curated datasets of static structures of α-transmembrane helix proteins, organized according to the superfamilies they belong, their function and an alternative classification method. The presence of motifs in TM proteins is tightly related to their families/superfamilies of the host protein and their position along the membrane normal.Wasserstoffbrücken (H-Brücke) sind eine wesentliche Wechselwirkung in Membranproteinen. Eingebettet in komplexe hydratisierte Lipiddoppelschichten sind intramolekulare Wechselwirkungen über Wasserstoffbrückenbindungsnetzwerke oft entscheidend für die Funktion des Proteins. Interne Wassermoleküle, die stabile Stellen im Inneren des Proteins besetzen, oder Wassermoleküle, die vorübergehend aus der Masse zu Besuch kommen, können eine wichtige Rolle bei der Gestaltung der lokalen Konformationsdynamik spielen, indem sie komplexe Netzwerke bilden, die Regionen des Proteins über wasservermittelte Wasserstoffbrückenbindungen überbrücken, die als Drähte für den Transfer von Protonen als Teil der Proteinfunktion funktionieren können. Die in Archaeen vorkommenden, in die Membran eingebetteten Kanalrhodopsine sind beispielsweise Proteine, die die lichtinduzierte Isomerisierung eines Retinachromophors mit Protonentransferreaktionen und dem passiven Fluss von Kationen durch ihre Pore verbinden. Ich habe an der Entwicklung eines neuen Algorithmuspakets mitgewirkt, das einen einzigartigen Ansatz für H-Bindungsanalysen bietet. Ich habe lange Molekulardynamik-Trajektorien von Kanalrhodopsine-Varianten, die in hydratisierte Lipidmembranen eingebettet sind, sowie große Datensätze statischer Strukturen analysiert, um dynamische Wasserstoffbrücken-bindungsnetzwerke zu erkennen und zu zerlegen. Der Photozyklus der Kanalrhodopsine beginnt mit der Absorption und Isomerisierung des Retinals von einem all-trans-Zustand zu einem 13-cis-Zustand, gefolgt von der Deprotonierung der Schiff-Base. Somit steht das Retinal im Mittelpunkt der Analysen. Durch die Verwendung von 2-dimensionalen Graphen der Protein- H-Brückenetzwerke identifizierte ich Proteingruppen, die für die Protonentransferaktivität wichtig sein könnten. Die lokale Dynamik wird durch Punktmutationen der für die Funktion wichtigen Aminosäuren stark beeinflusst. Das Innere von Kanalrhodopsine C1C2 beherbergt ausgedehnte Netzwerke von Protein- und H-Brücke-Wassermolekülen und ein bisher unbekanntes Netzwerk, das die beiden retinalen Chromophore in Kanalrhodopsine-Dimeren vorübergehend überbrücken kann. In einer kürzlich identifizierten Protonenpumpe, AntR, wendete ich Zentralitätsmaße auf MD-Trajektorien des von mir erstellten Homologiemodells an, um die Kommunikation der Aminosäurereste innerhalb der Netzwerke zu bewerten. Ich fand, dass eine häufig gesampelte lange Wasserkette, die das Retinal mit einem Protonenakzeptor verbindet, sowie ein konserviertes Serin in der Nähe des Retinal-Chromophors eine wichtige Rolle bei der Konnektivität und Kommunikation der H-Brückesnetzwerke bei der Isomerisierung spielt. Eine ähnliche Wasserbrücke ist in unabhängigen Simulationen von Kanalrhodopsine-2 zu finden, wo ein Teilnehmer für die Protonendonorgruppe mit dem 13-cis,15-anti-Retinal verbunden ist. Protonenübertragungsreaktionen finden oft über bestimmte Aminosäuren statt und bilden Muster. Ich analysierte H-Brückemuster oder -motive in großen, von Hand kuratierten Datensätzen statischer Strukturen von α-Transmembranhelix-Proteinen, geordnet nach den Superfamilien, zu denen sie gehören, ihrer Funktion und einer alternativen Klassifizierungsmethode. Das Vorhandensein von Motiven in TM-Proteinen steht in engem Zusammenhang mit ihren Familien/Superfamilien des Wirtsproteins und ihrer Position entlang der Membrannormale

Investigating left ventricular infarct extension after myocardial infarction using cardiac imaging and patient-specific modelling

Acute myocardial infarction (MI) is one of the leading causes of death worldwide that commonly affects the left ventricle (LV). Following MI, the LV mechanical loading is altered and may undergo a maladaptive compensatory mechanism that progressively leads to adverse LV remodelling and then heart failure. One of the remodelling processes is the infarct extension which involves necrosis of healthy myocardium in the border zone (BZ), progressively enlarging the infarct zone (IZ) and recruiting the remote zone (RZ) into the BZ. The mechanisms underlying infarct extension remain unclear, but myocyte stretching has been suggested as the most likely cause. A recent personalized LV modelling work found that infarct extension was correlated to inadequate diastolic fibre stretch and higher infarct stiffness. However, other possible factors of infarct extension may not have been elucidated in this work due to the limited number of myocardial locations analysed at the subendocardium only. Using human patient-specific left- ventricular (LV) models established from cardiac magnetic resonance imaging (MRI) of 6 MI patients, the correlation between infarct extension and regional mechanics impairment was studied. Prior to the modelling, a 2D-4D registration-cum-segmentation framework for the delineation of LV in late gadolinium enhanced (LGE) MRI was first developed, which is a pre-requisite for infarct scar quantification and localization in patient-specific 3D LV models. This framework automatically corrects for motion artifacts in multimodal MRI scans, resolving the issue of inaccurate infarct mapping and geometry reconstruction which is typically done manually in most patient-specific modelling work. The registration framework was evaluated against cardiac MRI data from 27 MI patients and showed high accuracy and robustness in delineating LV in LGE MRI of various quality and different myocardial features. This framework allows the integration of LV data from both LGE and cine scans and to facilitate the reconstruction of accurate 3D LV and infarct geometries for subsequent computational study. In the patient-specific LV mechanical modelling, the LV mechanics were formulated using a quasi-static and nearly incompressible hyperelastic material law with transversely isotropic behaviour. The patient-specific models were incorporated with realistic fibre orientation and excitable contracting myocardium. Optimisation of passive and active material parameters were done by minimizing the myocardial wall distance between the reference and end-diastole/end-systole LV geometries. Full cardiac cycle of the LV models was then simulated and stress/strain data were extracted to determine the correlation between regional mechanics abnormality and infarct extension. The fibre stress-strain loops (FSSLs) were analysed and its abnormality was characterized using the directional regional external work (DREW) index, which measures FSSL area and loop direction. Sensitivity studies were also performed to investigate the effect of infarct stiffness on regional myocardial mechanics and potential for infarct extension. It was found that infarct extension was correlated to severely abnormal FSSL in the form of counter-clockwise loop, as indicated by negative DREW values. In regions demonstrating negative DREW values, substantial isovolumic relaxation (IVR) fibre stretching was observed. Further analysis revealed that the occurrence of severely abnormal FSSL near the RZ-BZ boundary was due to a large amount of surrounding infarcted tissue that worsen with excessively stiff IZ

Syndecan-4 regulates cell-surface trafficking and biological activity of transglutaminase-2

Transglutaminase-2 (TG2) is a Ca2+-dependent crosslinking enzyme involved in the post-translational modification of proteins via the formation of Nε(γ-glutamyl)lysine isodipeptides. TG2 is externalised in the extracellular matrix (ECM) through an unconventional and not fully understood pathway. Under normal conditions, TG2 modulates cell adhesion, proliferation and tissue repair. Under continuous cell insult higher expression and elevated extracellular trafficking of TG2 contribute to the pathogenesis of tissue scarring. TG2 is known to have affinity for heparin, and in a previous study cell-surface heparan sulphate (HS) has been implicated in extracellular TG2 mediated RGD-independent cell adhesion, a non-enzymatic process independent from the α5β1 integrin-binding to the RGD domain on FN (Verderio et al., 2003). Hence HS proteoglycan (HSPG) could act as cell surface co-receptor for FNbound TG2 or contribute to the regulation of extracellular TG2 activity in cell adhesion and tissue repair